title: A human blood-derived microRNA facilitates flavivirus infection in fed mosquitoes [miRNA-seq]

summary: We report the human small RNA expression levels  in mosquitoes following a blood meal

overall_design: To address the roles of snRNAs in cross-species interactions between humans and mosquitoes, we allowed A. aegypti mosquitoes to feed on fresh human blood from 4 donors. The engorged mosquitoes were reared for snRNA sequencing at 1 hr and 6 days following a blood meal


title: ZFP423 Controls EBF2 Co-activator Recruitment and PPARgamma Occupancy to Determine the Thermogenic Plasticity of Adipocytes_ChIP-seq

status: Public on May 01 2022

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

country: USA

institute: Duke University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Energy-storing white adipocytes maintain their identity by suppressing the gene program defining energy-burning thermogenic brown/beige adipocytes. Here, we reveal that the protein-protein interaction between the transcriptional co-regulator ZFP423 and brown/beige cell determination factor, EBF2, is essential for restraining the thermogenic phenotype of white adipose tissue (WAT). Disruption of the ZFP423-EBF2 protein interaction through CRISPR-Cas9 gene editing triggers widespread “browning” of WAT in adult mice. Mechanistically, adipocyte Zfp423 deficiency induces an EBF2 NuRD-to-BAF co-regulator switch and a shift in PPARgamma occupancy to thermogenic genes. This shift in PPARgamma occupancy increases the anti-diabetic efficacy of the PPARgamma agonist rosiglitazone in obesity while diminishing the unwanted weight-gaining effect of the drug. These data indicate that ZFP423 controls EBF2 co-activator recruitment and PPARgamma occupancy to determine the thermogenic plasticity of adipocytes and raise the concept of targeting transcriptional brakes in adipocyte gene expression as a therapeutic strategy to induce thermogenic adipocyte biogenesis in obesity.

overall_design: ChIP-seq experiment to analyze EBF2, PPARgamma, BRG1, CHD4 DNA binding sites and H3K27ac modification levels in Control (wild-type) and Zfp423-iAKO (Zfp423 inactivation) differentiated adipocytes.

first: Mengle

last: Shao


title: Single-cell transcriptomics of mouse alveolar type 2 cells after bleomycin treatment

city: Beijing

first: Zheng

last: Wang

address: 7 Science Park Road ZGC Life Science Park, Beijing

country: China

institute: National Institute of Biological Sciences, Beijing

type: Expression profiling by high throughput sequencing

summary: Aging-related impairment in alveolar regeneration has been identified in a variety of acute and chronic lung diseases. As the aging population increases, understanding the mechanisms involved in age-dependent deterioration in alveolar stem cell function can support the development of new therapies for lung diseases. In this study, we investigated the cellular and molecular mechanisms underlying AT2 cell differentiation and how aging affected post-injury alveolar regeneration. We discovered that the process of AT2 cells differentiating into AT1 cells is an energetically costly process. During the differentiation of AT2 cells, activated AMPK-PFKFB2 signaling up-regulates glycolysis, which is essential to enhance cellular ATP production and to support the intracellular energy expenditure that is required for cell shape change and cytoskeletal remodeling during AT2 cells differentiating into AT1 cells.  AT2 cells in aging lungs show reduced AMPK-PFKFB2 signaling and decreased ATP production, resulting in impaired AT2 cell differentiation. Activating AMPK-PFKFB2 signaling in aged AT2 cells can rescue defects in alveolar regeneration. Thus, beyond demonstrating that the activation of AMPK-PFKFB2 signaling facilitates the great energy demands of AT2 cells during alveolar regeneration, our study suggests that modulating these pathways could promote the alveolar repair in aged lungs.

overall_design: Lineage labeled alveolar epithelial type 2 (GFP+ AT2) cells of 3-month old and 12-month old mice were harvested by FACS. AT2 cells isolated from three replicates of each group were identically mixed and then processed to sc-RNA seq following the 10X Genomics protocol. Four single-cell RNA sequencing datasets were generated named as "3-mo day0","3-mo day30","12-mo day0", and "12-mo day30". The "3-mo day0" and "12-mo day0" datasets were sequenced for AT2s of PBS-treated 3-month old or 12-month old Sftpc-creER;Rosa26-mTmG mice. The "3-mo day30" and "12-mo day30" datasets were sequenced for AT2s of 3-month old or 12-month old Sftpc-creER;Rosa26-mTmG mice on post-bleomycin day30.

first: Ennan

last: Bin

last: Tang


title: A human blood-derived microRNA facilitates flavivirus infection in fed mosquitoes

first: Yibin

last: Zhu

address: Tsinghua, Beijing, China

institute: Tsinghua University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single Cell RNAseq of CD8 positive Lymphocyte T

city: Paris

first: Sebastien

last: Mella

state: IDF

address: 28 rue du Dr Roux

department: CBUTechs

country: France

institute: Pasteur Institut

summary:
Purpose: Analysis at the single cell level of the CD8+ Lymphocytes T extracted from Kidney Tumor in Human patients.
Methods: Single Cell RNAseq performed using the 10X genomics platform
Results: We present a list of differentially expressed genes between two populations of interest : TCD8_CD27negative cells vs TCD8_CD27 positive cells

overall_design: Lymphocytes T CD8+ mRNA profiles of Kidney Tumor from Human donor

first: Milena

last: Hasan

first: Bernd

last: Jagla

first: Valentina

last: Libri

first: Nadège

last: Gruel


title: Neuronal Activity Increases Translocator Protein (TSPO) Levels in the Adult Mouse Brain

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary:
Background: The mitochondrial protein, translocator protein (TSPO), is a widely used biomarker of neuroinflammation, but its non-selective cellular expression pattern implies roles beyond inflammatory processes. The present study investigated whether neuronal activity modifies TSPO expression in the adult central nervous system.
Methods: Single-cell RNA sequencing was performed to generate a cellular landscape of basal TSPO gene expression in the hippocampus of adult (12 weeks old) C57BL6/N mice, whereas confocal laser scanning microscopy was used to verify TSPO protein in neuronal and non-neuronal cell populations. TSPO RNA and protein were quantified after stimulating neuronal activity with distinct stimuli, including designer receptors exclusively activated by designer drugs (DREADDs), exposure to a novel environment and acute treatment with the psychostimulant drug, amphetamine.
Results: Single-cell RNA sequencing demonstrated a non-selective and multi-cellular gene expression pattern of TSPO at basal conditions in the adult mouse hippocampus. Confocal laser scanning microscopy confirmed that TSPO protein is expressed in neuronal and non-neuronal (astrocytes, microglia, vascular endothelial cells) cells of cortical (medial prefrontal cortex) and subcortical (hippocampus) brain regions. Stimulating neuronal activity through chemogenetic (DREADDs), physiological (novel environment exposure) or psychopharmacological (amphetamine treatment) approaches led to consistent increases in TSPO gene and protein levels in neurons but not in microglia or astrocytes.
Conclusions: Neuronal activity has the potential to modify TSPO expression in the adult central nervous system. These findings challenge the general assumption that altered TSPO levels unequivocally mirrors ongoing neuroinflammation and emphasize the need to consider non-inflammatory interpretations in some physiological or pathological contexts.

first: Tina

last: Notter

first: Sina

middle: M

last: Schalbetter

first: Nicholas

middle: E

last: Clifton

first: Daniele

last: Mattei

first: Juliet

last: Richetto

first: Urs

last: Meyer

first: Jeremy

last: Hall


title: Study of cellular architecture and immune cell characters in human lung GGNs through scRNA-seq

city: Shanghai

first: Pengfei

last: Ma

address: Dongchuan Road 800

department: Renji Hospital

institute: School of Medicine, Shanghai Jiao Tong University

summary: We apply scRNA-seq to dissect the multicellular ecosystem of human lung GGNs, investigate cell-cell interactions and explore the correlations between tumor response and specific clinical factors.

overall_design: scRNA-seq of 12 human lung GGNs

first: Guanglei

last: Zhuang

first: Meichun

last: Cai

first: Yujie

last: Fu


title: Chromatin Accessibility Analysis Reveals Distinct Functions for HDAC and EZH2 Activities in Early Regeneration

city: Seattle

first: Anneke

middle: Dixie

last: Kakebeen

state: WA

address: 5611 9th Ave NW

department: Biochemistry

institute: University of Washington

summary: Xenopus tropicalis tadpoles have the capability to scarlessly regenerate appendages including the limb and tail. Following injury, complex genetic processes must be activated and inactivated with high spatial and temporal resolution to result in a properly patterned appendage. Functional studies have established that histone modifying enzymes that act to close chromatin are required for regeneration, but the genomic regions sensitive to these activities are not established. Here we show that early inhibition of HDAC or Ezh2 activity results in incomplete regeneration. To identify the impact that each of these perturbations has on chromatin accessibility, we applied an assay for transposase accessible chromatin (ATAC-seq) to HDAC or Ezh2 inhibited regenerating tadpoles. We find that neither perturbation results in a global increase in chromatin accessibility, but that both inhibitors have targeted effects on chromatin accessibility and gene expression. Upon HDAC inhibition, promoter regions and regulatory regions neighboring genes associated with neuronal regeneration are precociously accessible, whereas following EZH2 inhibition we find gene bodies and regulatory regions associated with regulation of the immune response and apoptosis are preferentially accessible. Together this suggests distinct roles for EZH2 activity and HDAC activity in appendage regeneration.

overall_design: ATAC-seq timecourse analysis of chromatin dynamics of HDAC inhibited or EZH2 inhibited regenerated tadpole tails and their vehicle controls. Samples in duplicate.

first: Hannah

last: Arbach

first: M

last: Harland-Dunaway

first: C

last: Braden

first: A

middle: D

last: Chitsazan

first: E

last: Pickering

first: J

middle: H

last: Patel

last: Wills


title: Dietary intervention improves health metrics and life expectancy of the genetically obese Titan mouse

city: Berlin

first: Anuroop

middle: Venkateswaran

last: Venkatasubramani

state: Berlin

address: Robert-Rössle-Straße 10

country: Germany

institute: MDC-Berlin

summary: Suitable animal models are essential for translational research, especially in the case of complex, multifactorial conditions, such as obesity. The non-inbred mouse (Mus musculus) line Titan, also known as DU6, is one of the world’s longest selection experiments for high body mass and was previously described as a model for metabolic healthy (benign) obesity. The present study further characterizes the geno- and phenotypes of this non-inbred mouse line and testes its suitability as an interventional obesity model. In contrast to previous findings, our data suggest that Titan mice are metabolically unhealthy obese and short-lived. Line-specific patterns of genetic invariability are in accordance with observed phenotypic traits. Titan mice also show modifications in the liver transcriptome, proteome, and epigenome linked to metabolic (dys)regulations. Importantly, dietary intervention partially reversed the metabolic phenotype in Titan mice and significantly extended their life expectancy. Therefore, the Titan mouse line is a valuable resource for translational and interventional obesity research.

overall_design: RNA Seq experiment of wild-type (non-selected) and Titan (selected for 45 years based on size and weight) in 5 biological replicates

middle: V

first: Shahaf

last: Peleg


title: ChIP-seq analyses with eHAP cells

city: Kanazawa

first: Yusuke

last: Miyanari

address: Kakuma

department: NanoLSI

country: Japan

institute: Kanazawa University

summary: ChIP-seq analyses with eHAP cells for TFDP1 and histone modifications

first: Satoko

last: Ishii


title: MNase-seq analyses with TFDP1 knockout eHAP cells

summary: A genome-wide screening identified effector genes of chromatin accessibility. To investigate the functional consequences of the loss of each effector gene, we conducted Mnase-seq with eHAP cells knocked out for TFDP1.

overall_design: MNase-seq with spike-in control


title: ATAC-seq analyses by using Tn5 transposome assembled with IEOE19 adaptor DNAs

summary: To investigate the specificity of the Tn5 transposome with short adaptor DNAs under the non-crosslinked condition, we conducted ATAC-seq using alternative 19 bp adaptor DNAs (IE and OE) harboring 7 nucleotide differences between them (Maggie.JMB.1998), which allowed for specific PCR amplification without losing the superior enzymatic activity.

overall_design: ATAC-seq analyses by using Tn5 transposome assembled with different adaptor DNAs


title: Endometriosis: normal and ectopic endometrium

city: hefei

first: xuxu

last: zhao

address: 81 Meishan Road

institute: Anhui Medical University

summary: To explore the difference between ectopic and normal endometrium and find out the characteristics and critical changes in ectopic endometrium, we analyzed transcripts of stromal cells from two groups of patients. The ectopic endometrium and normal endometrium had similar tissue structures and compositions, unlike normal ovaries. The similarity of gene expression profile between the two groups is as high as 97.2%, only 2.8% is significantly different. The differentially expressed genes in the ectopic endometrium are mainly enriched in the adhesion process and the adhesion pathway, which has the adhesion characteristics. Among these differentially expressed genes, CNTN1 is the most variable and participates in multiple pathogenic pathways, which is considered as the core gene to enhance stromal cell adhesion. The up-regulated expression of CNTN1 in all stages of ectopic endometrium is confirmed.

overall_design: The tissues of four ovarian ectopic endometrial patients at different stages of the disease from the secretory phase were mixed into one, compared to the normal endometrium, also from the secretory phase.

first: Qingping

last: Zhang

first: Bingqing

last: Zeng

first: Yanwei

last: Pei

first: Jingrou

last: Chen

first: Feifei

last: Li


title: Genome-wide CRISPR screening combined with ATAC-see assay

summary: Cas9 expressing eHAP cells were transduced with human sgRNA lentivirus library (Doench, 2016 Nature biotech, Addgene, #73178). The cells were selected with 1 µg/ml of puromycin for 2 days, and then used for ATAC-see at 5 and 7 days post-transduction, respectively. Cells in the G2 phase were specifically gated to sort th 5% of the cells with the highest and lowest ATAC-see signal intensity(“high” or “low” population) . The sgRNA enrichment in each population was analysed by high-throughput sequencing and computationally compared by using the MAGeCK program (Li et al., Genome Biology 2014).

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: CRISPR-seq with ATAC-see


title: Combined CDK inhibition overcomes MEK inhibitor resistance in plexiform neurofibroma of neurofibromatosis type I

first: Zhichao

last: Wang

address: 639 Zhizaoju Road, Shanghai 200011, P.R. China

department: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

institute: Department of Plastic and Reconstructive Surgery

summary: MEK1/2 inhibitors (MEKi) have recently achieved surprising success in treating unresectable plexiform neurofibromas (PNFs). However, few studies have investigated the mechanisms of MEKi resistance in PNF patients. We determined the efficacy of 6 different MEKi for treating PNFs, explored drug resistance mechanisms and identified potential combination therapies to overcome resistance. By screening drug efficacy among 6 MEKi in human NF1-deficient PNF cell lines, TAK-733 was found reduce PNF cell viability the most. We then cultured the TAK-733 resistant cells and explored potential targets for further treatment. Both high-throughput drug screening and RNA sequencing analyses of MEKi-resistant PNF cells identified cyclin-dependent kinase inhibitors (CDKi) as potential agents for PNFs. Dinaciclib, a CDKi, showed synergistic effects on MEKi-resistant cells. Coadministration of dinaciclib and TAK-733 significantly reduced cell viability, inhibited sphere formation and colony formation. Dinaciclib did not affect MEK signaling but decreased the expression of several prosurvival proteins, including survivin and CDK1, to induce apoptosis and inhibit mitosis. TAK-733/dinaciclib combination therapy induced tumor reduction in PNF patient-derived xenografts mouse models. Therefore, the combination of MEKi and CDKi may be promising for treating inoperable PNFs, especially when drug resistance exists. Our findings provide evidence for future clinical trials with MEKi-resistant PNF patients.

overall_design: The mRNA profiles of resistant and non-resistant PNF cell lines were generated by deep sequencing, in triplicate.

first: Wei

first: Yihui

last: Gu

first: Xiwei

last: Cui


title: Tsc1 and Vhl loss cooperates to drive renal cell carcinoma through augmenting HIF1 and NRF2 signaling pathways

city: New York

first: Jianing

last: Xu

state: NY

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Besides the truncal VHL mutations, ccRCC is characterized by upregulated MTOR signals from both preclinical and clinical studies. To understand how upregulated MTOR signals cooperate with VHL loss in promoting kidney tumorigenesis, we generated kidney-specific deletion of Vhl and Tsc1 (Vhl;Tsc1 cDKO) in mice. The mice showed decreased life span with maximal age of 11 weeks, bilateral polycystic kidney diseases from ~3 weeks and multifocal solid renal cell carcinoma with eosinophilic cytoplasm and grade 2-3 from 7 weeks old. The mouse tumors resemble histology of the human kidney tumors with VHL and TSC1 mutations. To understand the mechanism of how Tsc1 loss cooperates with Vhl loss in promoting tumorigenesis, we performed transcriptomic, metabolomic and immunohistochemical profilings of renal cortices from age-matched wild-type, Vhl  or Tsc1  single knockout, and Vhl;Tsc1 cDKO mice. Tsc1 loss cooperates with Vhl loss by augmenting the HIF1 transcriptional output, as well as altering the glutamine/glutamate metabolism, urea cycle, glycogen metabolism, and activating NRF2 signaling pathways which reprogram the cells to counteract the high oxidative stress associated with the proliferation. Our study reports a ccRCC mouse model recapitulating human ccRCC with same genetic background, provides mechanistic insights concerning cooperation between upregulated mTORC1 signals and VHL loss, generates in vivo reagents for studying ccRCC, and implicates potential clinical values.

overall_design: Kidney Cortices mRNA profiles of 4-week-old wild type (WT), Vhl cKO, Pbrm1 cKO, Tsc1 cKO, Vhl;Pbrm1 cDKO, and Vhl;Tsc1 cDKO mice were generated by deep sequencing, in quadruplicates, using HiSeq 4000.

first: Xu

last: Jianing

first: Hsieh

last: James


title: RNA-seq analyses with TFDP1 knockout eHAP cells

summary: Cas9 expressing eHAP cells were transfected with sgRNA against TFDP1. 5 days after the transfection, polyA RNA was analyzed by RNA-seq

overall_design: RNA-seq with spike-in control


title: Transcriptome profiling of the rat retina following ischemia-reperfusion injury

city: NanChang

first: Lei

last: Shang

state: JiangXi

address: Donghu District Bayi Road #463

department: Affiliated Eye Hospital of Nanchang University

institute: NanChang University

summary: Transcriptomics has played valuable roles in deciphering differences between normal and diseased conditions at the molecular level. Herein is presented a transcriptome profile of ischemia-reperfusion (I/R) injury in adult Sprague-Dawley rat model and control group. Following acute I/R induction, a pool of the rats’ retinas at 12hr post I/R was made. RNA sequencing was performed on both the model and the control groups, followed by their transcriptomic analyses. Sample validation and quality control were done in accordance with standard protocols. Comparison of the sequenced data revealed significant variations in genes expression between the I/R model and their sham counterparts.  These differentially expressed genes may provide valuable information to understanding the molecular mechanisms underlying retinal cell dysfunction, cell death and structure collapse in adult rats, and may help characterize or develop therapeutic interventions for visual impairment.

first: Xiang

first: Xiaodong

first: Dekang

last: Lv


title: Microarray analysis of knockdown of nicotinamide N-methyltransferase (NNMT) in human cancer-associated fibroblasts

city: Chicago

first: Mark

middle: Adam

last: Eckert

state: IL

address: 929 East 57th St, W107

department: OB/GYN

institute: University of Chicago

summary: Analysis of gene expression in human CAFs with control (shCtrl) or shRNA against NNMT (shNNMT) expression. Cells were infected with lentivirus to express the indicated shRNA construct. Hypothesis is that knockdown of NNMT will affect expression of genes via regulation of histone methylation status.

overall_design: Total RNA was collected from human cancer associated fibroblasts expressing the indicated shControl or shNNMT constructs and expression analyzed with Illumina microarray.

middle: A


title: Temporal Regulation of Head-on Transcription at Replication Initiation Sites

status: Public on Apr 30 2022

city: Los Angeles

first: MICHAEL

last: KRONENBERG

state: CA

address: 615 Charles E Young Drive S

department: Biological Chemistry

institute: UCLA

summary: Head-on collisions between the DNA replication machinery and RNA polymerase are potent genotoxic events leading to replication fork stalling, R-loop formation, and DNA breaks. Current models suggest that head-on collisions are avoided through replication initiation site (RIS) placement upstream of active genes, thus ensuring co-orientation of replication fork movement and genic transcription. However, this model does not account for pervasive transcription units, or intragenic replication initiation events. Through mining phased GRO-seq data, and developing a rigorous informatic strategy to identify RIS, we demonstrate that head-on transcription occurs frequently in a breast cancer cell line, and that this transcription is significantly downregulated during S-phase, particularly in regions susceptible to R-loop formation. Collectively, our analysis suggests the existence of a temporally tuned transcriptional regulation mechanism that functions to maintain genome stability.

overall_design: ChIP-seq for the INO80 complex subunit ACTR5 in MCF-7 cells.

first: Michael

last: Kronenberg

middle: F

last: Carey


title: Transient expansion and myofibroblast conversion of marrow adipogenic lineage precursors (MALPs) mediate bone marrow repair after radiation

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

summary: Radiation causes a collapse of bone marrow cells and elimination of microvasculature. Bone marrow has a limited regenerative ability and the mechanism governing such recovery is largely unknown. Mesenchymal lineage cells provide supportive microenvironment for hematopoiesis and angiogenesis in bone. We recently discovered a non-proliferative mesenchymal subpopulation, marrow adipogenic lineage precursors (MALPs), that express most adipogenic markers with no lipid accumulation. To investigate the acute radiation effects, we performed single cell RNA-sequencing (scRNA-seq) on bone marrow mesenchymal lineage cells at day 3 after focal radiation. Interestingly, computational analysis revealed that MALPs become highly proliferative and acquire myofibroblast features after radiation. Using an adipocyte-specific Adipoq-Cre to label MALPs in vivo, we found that radiation indeed rapidly and transiently expands MALPs. MALPs have a cell body with multiple cell processes that form a 3D network inside bone marrow. Shortly after radiation, MALPs lost most of cell processes, became more elongated, and highly expressed myofibroblast-related genes, coinciding with marrow vessel dilation and diminished bone marrow cellularity. Later when vessels and hematopoietic cells recovered, MALPs returned to the baseline number and a normal reticular shape. Ablation of MALPs completely blocked the recovery of bone marrow vasculature and cellularity, including hematopoietic stem and progenitors. MALPs highly express several hematopoietic and angiogenic factors. Depleting one of them, VEGFa, specifically in MALPs, delayed bone marrow recovery after radiation. Taken together, our research demonstrates a critical role of MALPs in mediating the marrow repair after radiation injury and sheds light on a new cellular target for treating marrow suppression after radiotherapy.

overall_design: Single-cell RNA-seq of Col2/Td+ cells from mouse bone marrow at day 3 post radiation.

first: Leilei

last: Zhong

first: Ling

last: Qin


title: Expression profiling of human aortic endothelial cells vs human dermal endothelial cells

first: Joshua

last: Sasine

address: 8700 Beverly Blvd., AHSP, #8110B

institute: Cedars-Sinai Medical Center

summary: Multiple myeloma cells display a reciprocal relationship with neighboring niche cells in the bone marrow, particularly vascular endothelial cells. This relationship drives disease initiation, progression, and therapy resistance, but the mechanisms underlying this interaction remain incompletely understood. We performed transcriptomic analysis of endothelial cells from multiple human tissues and analyzed their capacity to promote MM growth in order to discover novel regulators of MM pathogenesis.

overall_design: 6 replicates of human aortic endothelial cells and 6 replicates of human dermal endothelial cells

middle: P

first: Jennifer

last: Dukov

first: Dana

last: Tran

first: Heather

last: Himburg

first: Michelle

first: Jenny

last: Kan

first: Mary

last: Sehl

first: Gary

middle: J

last: Schiller

first: Christina

last: Termini

first: Elena

middle: B

last: Pasquale

first: John

last: Chute


title: Genome-wide maps of chromatin state in refed mouse liver.

city: Berkeley

first: Jose

last: Viscarra

state: Ca

address: 220 Morgan Hall

department: NST

institute: UC Berkeley

summary: Using high throughput sequencing we report H3K9 methylation status in mouse liver upon refeeding a high carb diet.  We find accumulation of H3K9me2 in genes that are typically repressed upon refeeding, confirming that H3K9me2 methylation works to repress transcription.

overall_design: Examination of H3K9me2 methylation in mouse liver

first: Hei

middle: S

last: Sul


title: GATA-3 is a proto-oncogene in T-cell lymphoproliferative neoplasms [ChIP-seq]

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

summary: In order to identify GATA-3 target genes in T-cell lymphoproliferative neoplasms, we performed GATA-3 ChIP-seq on 3 cutaneous T-cell lymphoma (CTCL) and 4 T-cell acute lymphoblastic leukemia (T-ALL). We have also established cell lines in which GATA-3 was knocked down by shRNA.

overall_design: Chromatin immunoprecipitation DNA-sequencing for GATA-3 in three CTCL and four T-ALL cell lines.

first: Xiangrong

last: Geng

first: Ryan

last: Wilcox


title: Effect of NK1.1+ cell depletion on vaginal neutrophil gene expression during HSV-1 infection

city: St. Louis

first: Haina

last: Shin

state: MO

address: 660 South Euclid Ave

department: Internal Medicine

institute: Washington University School of Medicine

summary: Depletion of NK1.1+ cells from mice prior to intravaginal HSV-1 infection results in severely increased genital disease and mucosal tissue damage. We determined that this loss of host protection in the absence of NK1.1+ cells was dependent on neutrophils, suggesting that NK1.1+ cells may be modulating neutrophil behavior during infection. To obtain an unbiased view of the transcriptional changes occuring in neutrophils that might explain this difference in disease outcomes, we performed sequencing of total RNA from neutrophils isolated from vaginas of intact or NK1.1 depleted mice 5 days after HSV-1 infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for neutrophils sorted from vaginas of control or anti-NK1.1 treated mice 5 days after intravaginal HSV-1 infection.

first: Aisha

last: Lee


title: Dissecting genetic components associated with eye disease using integrative genomic analysis [ChIP-seq]

city: San Francisco

first: Kirsty

last: Jamieson

address: 400 Parnassus Ave

institute: University of California

summary: GWAS studies have revealed thousands of variants strongly associated with AMD, yet connecting these variants to their cognate genes has not been explored. In this study we fine-mapped AMD risk loci and examined long-range cis chromatin interactions at essential genes of RPE function and disease-associated variants in iPSC-induced retinal pigmented epithelium (RPE) and primary RPE.

overall_design: ChIP-seq and input from iPSC-induced RPE (2 replicates).

first: Yin

last: Shen


title: Dissecting genetic components associated with eye disease using integrative genomic analysis [RNA-seq]

overall_design: RNA-seq from iPSCs (2 replicates), iPSC-induced RPE (3 replicates) and primary RPE (3 replicates)


title: Dissecting genetic components associated with eye disease using integrative genomic analysis [ATAC-seq]

overall_design: ATAC-seq from iPSCs (2 replicates), iPSC-induced RPE (3 replicates) and primary RPE (3 replicates)


title: Whole-genome bisulfite sequencing (WGBS) of Medicago truncatula developmental and mature embryos at four seed developmental stages produced at optimal (20°C) or  heat stress conditions (26°C).

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

institute: INRAE / IRHS

type: Methylation profiling by high throughput sequencing

summary: We analysed the methylated cytocines in gDNA sequence of Medicago (A17) embryos during seed maturation concerning Heat Stress. Embryos were harvested at four developemental stages (called S1 to S4): 17, 26, 36 and 44 days after polination (DAP) at 20°C and 14, 17, 22 and 28 days after polination (DAP) at 26°C.

overall_design: Three replicates of embryos at four seed developemental stages produced at 20 and 26 degrees

first: Zhijuan

last: Chen


title: Brg1 controls stemness and metastasis of pancreatic cancer through regulating hypoxia pathway (ChIP-seq)

city: Kyoto

first: Osamu

last: Araki

state: Kyoto

address: 54 Shogoin-Kawahara-cho, Sakyo-ku

department: Gastroenterology and Hepatology

institute: Kyoto University Graduate School of Medicine

summary: Brg1 is a subunit of SWI/SNF chromatin remodeling complex. To clarify the role of Brg1 for the progression and metastasis of pancreatic ductal adenocarcinoma (PDAC), we generated a PDAC mouse model with a dual recombinase system (Brg1 lox/lox; Pdx1-Flp; Kras FSF-G12D; Trp53 frt/frt; Rosa26 FSF-CreERT2) which enabled to ablate Brg1 in established PDAC with tamoxifen treatment. We established cancer cell lines derived from PDAC tumors developed in those mice and investigated the effect of Brg1 ablation on PDAC cell proliferation and metastasis. In order to determine the genes that Brg1 directly regulates, we conducted a chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) analysis for Brg1 and histone modifications (H3K27ac and H3K27me3) using Brg1 wild type and Brg1-deleted mouse PDAC cells.

overall_design: ChIP analysis for BRG1, IgG (negative control), H3K27ac, and H3K27me3 was performed using Brg1 wild type and Brg1 deleted PDAC cells which were treated with methanol and 4-hydroxytamoxifen for four days, respectively.

first: Akihisa

last: Fukuda


title: The impact of inflammation-induced tumor plasticity during myeloid transformation [mononcytes]

first: Anna

last: Yeaton

state: New York

address: 550 1st ave

department: Pathology

institute: NYU Langone

summary:
RNA-seq analysis of mouse bone marrow monnocytes isolated from Tet2 mutant and Tet2 Wildtype mice
RNA-seq of mononcytes from mice.

overall_design: Anna, Yeaton

first: Geraldine

last: Cayanan

first: Iannis

last: Aifantis

first: Maria

last: Guillamot-Ruano


title: PI3Kδ Inhibition Modulates the Innate Inflammatory Response in Pancreatic Ductal Adenocarcinoma and Normalizes Aberrant Metabolism Associated with Cachexia

city: London

first: Jun

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

summary: PDAC is an inflammatory disease in urgent need of effective therapeutic intervention. The PI3K p110δ isform inhibition resulted in sustained survival rarely seen in KPC mouse model of pancreatic cancer. The single agent therapy significantly decreased tumor burden, differentially regulated tumour inflammatory and metabolic transcirptome profile and normalized muscle metabolic response associated with cachexia.

overall_design: Tumour bearing KPC mice were treated with either vehicle or PI3K p110δ inhibitor for 2 weeks. Whole tumour was then harvested and RNA sequencing was perfomred on total RNA. For immature myeloid RNA seq, cells were sorted from the spleen of tumor bearing mice treated with vehicle or drug for 14 days. Total RNA was then isolated and sequenced on an NGS platform.

first: Michael

middle: O

last: Ports

first: Maryam

last: Jangani

first: Essam

last: Ghazaly

first: Juliana

last: Candido

first: Thorsten

last: Hagemann


title: Role of Neuropilin-1 in regulatory T cell stability and function

city: Ithaca

first: Weishan

last: Huang

address: C5 121, Cornell U.

department: Microbiology & Immunology

institute: Cornell University

summary:
To investigate the function of Neuropilin-1 (NRP-1) in Foxp3+ regulatory T (Treg) cell stability and function, we cultured naïve CD4+ T cells under induced Treg cell (iTreg)-differentiating condition.
We then flow sorted NRP-1+ and NRP-1- iTreg cells and performed gene expression profiling analysis.

overall_design: Differential gene expression analysis of RNA-seq data for NRP-1+ and NRP-1- iTreg cells.

first: Avery

last: August


title: Dissecting genetic components associated with eye disease using integrative genomic analysis

first: Kirsty

last: Jamieson

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

overall_design: Refer to individual Series


title: Linc1557 is critical for the differentiation initiation of embryonic stem cells by directly targeting LIF/STAT3 signaling pathway

city: Shanghai

first: Chenqi

last: Lu

address: Handan Road 220

department: school of lifescience

institute: Fudan University

summary: This paper not only elucidated the critical function of linc1557 in mouse ESC differentiation initiation, but also clarified its specific mechanism by directly affecting the mRNA stability of Stat3.

overall_design: The transcriptome of lncRNA knockdown and control mESCs were generarted by deep sequencing.

first: Yuanyuan

last: Lan

first: Jiuhong

last: Kang

first: Guiying

last: Wang


title: Epigenetic application of ATAC-seq based on Tn5 transposase purification technology

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

summary: We report a set of rapid, efficient and low-cost methods for ATAC-seq library construction and data analysis, realized large-scale and rapid sequencing. These methods can provide a reference for the study of epigenetic regulation of gene expression.

overall_design: We propose reliable approaches for purifying the hyperactive Tn5 transposase by Chitin Magnetic bead sorting. Double-stranded DNA of J76 cells and 293T cells were digested and subjected to tagmentation as test samples with Tn5 transposase, and libraries were established and sequenced. Sequencing data was then analyzed for peak calling, GO enrichment and motif analysis.

first: Lijuan

last: Gao


title: Brg1 controls stemness and metastasis of pancreatic cancer through regulating hypoxia pathway

first: Osamu

last: Araki

summary: Brg1 is a subunit of SWI/SNF chromatin remodeling complex. To clarify the role of Brg1 for the progression and metastasis of pancreatic ductal adenocarcinoma (PDAC), we generated a PDAC mouse model with a dual recombinase system (Brg1 lox/lox; Pdx1-Flp; Kras FSF-G12D; Trp53 frt/frt; Rosa26 FSF-CreERT2) which enabled to ablate Brg1 in established PDAC with tamoxifen treatment. We established cancer cell lines derived from PDAC tumors developed in those mice and investigated the effect of Brg1 ablation on PDAC cell proliferation and metastasis. In order to determine the genes expression in Brg1-deleted mouse PDAC cells, we conducted a transcriptomic analysis using microarray using Brg1 wild type and Brg1-deleted mouse PDAC cells.

overall_design: Microarray analysis was performed using Brg1 wild type and Brg1 deleted mouse PDAC cells which were treated with methanol and 4-hydroxytamoxifen for four days, respectively.

first: Akihisa

last: Fukuda


title: MicroRNA and mRNA profiling of cerebral cortex in a transgenic mouse model of Alzheimer’s disease by RNA sequencing

city: Beijing

first: li

last: zeng

state: Beijing

address: Institute of Medical Biotechnology, Tiantan Xili, Dongcheng District, Beijing

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: In this study, we investigated the abnormal expression of miRNA and mRNA and the pathogenesis of AD at the epigenetic level. To this aim, we performed RNA sequencing and an integrative analysis of the cerebral cortex of the widely  used amyloid precursor protein and presenilin-1 double transgenic mouse model of AD. Overall, 129 mRNAs and 68 miRNAs were aberrantly expressed. Among these, eight down-regulated miRNAs and seven up-regulated miRNAs appeared as promising noninvasive biomarkers and therapeutic targets. The main enriched signaling pathways involved mitogen-activated kinase protein, phosphatidylinositol 3-kinase-protein kinase B, mechanistic target of rapamycin kinase, forkhead box O, and autophagy. An miRNA-mRNA network between dysregulated miRNAs and corresponding target genes connected with AD progression was also constructed. These miRNAs and mRNAs are potential biomarkers and therapeutic targets for new treatment strategies, early diagnosis, and prevention of AD. The present results provide a novel perspective on the role of miRNAs and mRNAs in AD.

overall_design: Twelve APP/PS1 mice were grouped by age (1 month, 3 months, 6 months, and 9 months), and the same grouping was applied to the twelve corresponding WT control mice. Each age group included three mice (two female and one male).

first: Li

last: Zeng

first: Hai-Lun

last: Jiang

first: Zhuo-Rong

last: Li

first: Rui

last: Liu


title: Epigenetic regulation of the DNMT1/MT1G/KLF4/CA9 axis synergizes the anticancer effects of sorafenib in hepatocellular carcinoma

city: Shenzhen

first: Hao

address: No. 1098, Xueyuan Road

institute: Shenzhen University

summary: Sorafenib, a multiple-kinase inhibitor, has been widely used as a first-line anticancer drug for advanced hepatocellular carcinoma (HCC). However, the development of drug resistance to sorafenib is frequently observed in clinical applications. Potential non-kinase targets of sorafenib have not been well documented and may provide insights into reversing drug resistance. Herein, we report that sorafenib exerted its anticancer effects by activating metallothionein 1G (MT1G) expression. MT1G served as a novel marker in HCC and correlated well with patient survival. MT1G overexpression suppressed the cellular proliferation, migration, invasion, and tumor formation of HCC, and sensitized cells to sorafenib treatment. However, the disruption of MT1G attenuated sorafenib’s anticancer effects. Mechanistically, sorafenib upregulated MT1G expression via hypomethylation of its promoter region by binding and inhibiting DNA methyltransferase 1 (DNMT1) and increasing its promoter accessibility in HCC cells. The activation of MT1G also inhibited CA9 transcription through the degradation of HIF1a as mediated by KLF4. Our collective data revealed that sorafenib exerted its anticancer effects through epigenetic regulation of the DNMT1/MT1G/KLF4/CA9 axis in HCC, and that the activation of MT1G might constitute a strategy for reversing sorafenib resistance.

overall_design:
6 mRNA profiles of Huh7 cell lines, including 3 samples treated by DMSO, 3 samples treated by Sorafenib
6 mRNA profiles of Huh7 cell lines, including 3 MT1G over expression sampels, 3 empty vector samples
2 ATAC-seq samples, including  2 samples treated by DMSO, 2 samples treated by Sorafenib

first: Tianzi

last: Wei


title: Identification of biomarkers of response to preoperative talazoparib monotherapy   in treatment naïve gBRCA+ breast cancers

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Germline mutations in BRCA1 or BRCA2 exist in approximately 7% of patients diagnosed with breast cancer and are associated with defects in homologous recombination repair, which has led to the approval of PARP inhibitors for treatment of these cancers in the advanced setting.  We have previously reported a phase II neoadjuvant trial of single agent talazoparib for patients with germline BRCA pathogenic variants with a pathologic complete response (pCR) rate of 53%.  However, nearly half of the patients treated did not have pCR, thus better strategies are needed to overcome treatment resistance, as well as to identify tumors likely to respond to therapy.  To this end, we conducted multi-omic analysis of 13 treatment naïve breast cancer tumors from patients that went on to receive single-agent neoadjuvant talazoparib.  We looked for biomarkers that were predictive of response (assessed by residual cancer burden) after 6 months of therapy.  We found that all resistant tumors exhibited either the loss of SHLD2, expression of a hypoxia signature, or expression of a stem cell signature.  These results indicate that the underlying biology of pre-treatment tumors contain activities that are predictive of response to talazoparib and potentially other PARP inhibitors, and provides a framework that will allow for the better selection of patients for treatment, as well as a roadmap for the development of novel therapies to overcome resistance.

overall_design:
Treatment naïve tumors from early breast cancer patients with germline mutations in BRCA1 or BRCA2 were subjected to RNA-Seq profiling.  Response to single agent talazoparib was assessed after six months of treatment.
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Submitter states the following:
Due to IRB requirements, we are not allowed to upload the raw data, except to a controlled access database.  We will be submitting the raw data to a controlled access database.  However, we would like to make the processed data available here without controlled access to maximize data accessibility.

first: Xuan

first: Zhongqi

last: Ge

first: Fei

last: Yang

first: Alejandro

last: Contreras

first: Sanghoon

last: Lee

first: Jason

last: White

first: Yiling

first: Marilyne

last: Labrie

first: Banu

last: Arun

first: Stacy

middle: L

last: Moulder

first: Gordon

last: Mills

first: Helen

last: Piwnica-Worms

first: Jennifer

last: Litton

middle: T


title: Transcriptomic profiling of iAT2s

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University


title: Divergent roles of KLF4 and TFCP2L1 in ground-state naive pluripotency and human primordial germ cell development

city: Haining

first: Wanlu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: During development, human primordial germ cells (hPGCs) transition through a transcriptional and epigenetic state similar to pre-implantation epiblast cells called naive ground-state pluripotency. Diagnostic transcription factors that define this state include TFAP2C, KLF4, and TFCP2L1, with TFAP2C necessary for both establishment of the naive-like state in hPGC-like cells (hPGCLCs) as well as establishment and self-renewal of naive human embryonic stem cells (hESCs). Here, we show that KLF4 and TFCP2L1 are not required for hPGC specification or establishment of the naive-like state in hPGCLCs.  Instead, KLF4 and TFCP2L1 are each required for reversion of primed hESCs to the self-renewing naive ground state. Additionally, TFCP2L1 but not KLF4 function after hPGC specification in the proliferation of the hPGCLC population.

overall_design: H1_hESC_WT_derived_hPGCLCs and H1_hESC_KLF4KO_derived_hPGCLCs at passage numbers 65 and 68

first: Grace

last: Hancock


title: Dual functions of NEIL3 in DNA repair and the epithelial-mesenchymal transition

city: Tainan

first: Wenya

last: Huang

address: No.1, University Road

country: Taiwan

institute: NCKU

summary: Twelve pairs of tumorous and peritumorous liver tissues (6 HBV- and 6 HCV-related HCC) that were obtained during the surgical liver resection of HCC patients were subjected to cDNA microarray analysis (Agilent Human Gene Expression v2 4x44K Microarray Kit) to screen the genes with expression levels that were different in the tumor than they were in the peritumorous tissue.

overall_design: The patients were regularly followed up at clinic visits every 1-3 months after hepatic resection. All the patients provided signed informed consent to use their surgical specimens for this research. All of the protocols for this study were reviewed and approved by the NCKUH Institutional Review Board (IRB No.: ER-100-058 [04/25/2011]). A total of 162 HCC cases were recruited: samples from 12 patients, 6 with HBV-related and 6 with HCV-related HCC, were analyzed with a cDNA microarray assay

first: Hui-Huang

last: Lai


title: Single cell transcriptomic profiling of pluripotent stem cell-derived alveolar type 2 cells expressing SFTPC-tdTomato cultured in 3D spheres, 2D submerged culture, and air-liquid interface culture with and without cigarette smoke exposure

summary: We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using previously described distal lung directed differentiation protocol to generate alveolar type 2 cells (iAT2s). We used the SPC2-ST-B2 (“SPC2”) line containing a SFTPC-tdTomato knock in reporter. iAT2s were cultured as 3D spheres (3D), on Transwells in 2D submerged conditions (2D), or at ALI for a total of 10 days post passaging. iAT2s in ALI culture were exposed to cigarette smoke 12 hours prior to cell collection (Smoke) or air (ALI). On day 10, and at 12 hours post cigarette smoke exposure, cultures were dissociated to single cells and live cells were sorted on calcein blue on a Mo-Flo Astrios Cell Sorter.  Capture and library preparation was performed using a 10X Chromium system. Libraries were sequenced using a NextSeq 500. We find that ALI culture promotes maturation of iAT2s compared to 3D, and that iAT2s mount an inflammatory and xenobiotic metabolism response to cigarette smoke exposure at ALI.

first: Kristy

last: Abo

first: Carlos

last: Villacorta-Martin

first: Andrew

last: Wilson


title: The Role of Quiescent Cells in the Maintenance of the Thyroid Gland

status: Public on Apr 29 2022

city: Groningen

first: Rob

last: Coppes

address: Ant. Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

summary: The regenerative capacities of an organ rely on the presence of (adult) tissue-specific stem cells. With regards to the thyroid gland, the existence of adult stem cells remains a topic of controversy. Previously, evidence has already suggested the presence of a population of thyroid cells with self-renewal capacity, capable of long-term culturing in vitro. However, the mechanisms that govern these proliferative abilities remain poorly understood. In addition, the slow turnover rate of the tissue-specific cells complicates the search for a distinct marker to identify these cells. Here, we employ a murine label retention assay based on the doxycycline-inducible expression of an H2B-GFP fusion protein which facilitates the observation of these slow cycling cells over time. Induction of the label during embryogenesis followed by a chasing period from birth up to nine months of age allowed for analysis of the GFP label retention at specific time points. Immunofluorescent imaging of the thyroid tissue immediately after birth, and after three, six, and nine months indicated the loss of GFP over time. Moreover, fluorescence-activated cell sorting of the GFP negative (GFP-) population versus the GFP positive (GFP+) population followed by in vitro culturing of the two subgroups into organoids demonstrated a predominant difference in the proliferative capacities of these populations. While GFP+ cells were able to form organoids and establish a long-term culture system at all aforementioned time points, this was not the case for the GFP- subgroup. These data provide the first in-depth examination of thyroid stem/progenitor cell dynamics over time, and suggest the presence of a quiescent thyroid stem cell population which harbours proliferative capacities regardless of age.

overall_design: RNA-seq


title: RNA sequencing of murine bone marrow dendritic cells and monocytes following TLR1/2 stimulation

city: Saint Louis

first: Christopher

last: Miller

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St Louis

summary: Treatment with a TLR1/2 agonist induces expression of interleukin-1beta that regulates hematopoietic stem cell number and function

overall_design: Wildtype mice were treated with a single dose of the TLR1/2 agonist PAM3CSK4 and then dendritic cells and monocytes were purified from the bone marrow for RNA sequencing

first: Juo-Chin

last: Yao

first: Sidan

last: Liu

first: Joseph

last: Krambs

first: Daniel

middle: C

last: Link


title: single cell RNA sequencing of sham and 3 dpi spinal cords in mice

city: hangzhou

first: linlin

last: wang

state: zhejiang

address: Yuhangtang Road No.866

institute: zhejiang university

summary: We report the application of single cell RNA sequencing technology for high-throughput profiling of sham and 3 dpi spinal cords in mice. By obtaining a total of 16051 cells from sham and 14295 cells from 3 dpi tissue, we identified 26 distinct cell clusters and 11 major cell types expressing known markers. These clusters comprised oligodendrocytes (Mbp, Mobp, Mog, Plp1), microglia (Gpr84, Cx3cr1, Csf1r), astrocytes (Gpr37l1, Bcan, Gfap), neutrophils (S100a9, Mmp9, S100a8), fibroblasts (Col1a1, Col1a2, Dcn), pericytes (Pdgfrb, Rgs5), endothelial cells (Flt1, Pecam1, Egfl7), macrophages (Ms4a7), monocytes (Ccr2, Cxcl3), b cells (CD19) and t cells (CD3e). neurons were not included because they were not expected to fit the sequencing protocol. We found that the most abundant cell type in the sham group was oligodendrocytes, accounting for 46.12%, while it decreased to 15.9% in the 3 dpi group. The second was microglia, accounting for 22.41%, which increased in number in the 3 dpi group, making it the most abundant cell in the SCI 3 dpi tissue (26.65%). The number of astrocytes also increased to 9.24% after SCI. Foreign immune cells such as neutrophils, macrophages, and monocytes accounted for 11.15%, 17.74%, and 9.41% of all cells after SCI, respectively. Among these, the percentage of pericytes decreased from 8.64% in the sham group to 1.28% in the 3 dpi group. The number of fibroblasts varied dramatically, rising rapidly from 0.33% in the sham group to 5.65% in the SCI 3 dpi group (Figure 2B). This study provides a framework for the application of single cell sequencing towards characterization of diverse cell populations in the sham and 3 dpi spinal cord.

overall_design: Single cell mRNA profiles of sham and 3dpi spinal cords (five male and five female C57/BL6 mice aged 8w in each group)

first: gerong

last: shen

first: ning

last: he


title: Expression data from cultured WT and NCK1/2 knockout mouse podocyte cells

city: Guelph

first: Nina

last: Jones

state: ON

address: 50 Stone Rd E

department: Molecular and Cellular Biology

country: Canada

institute: University of Guelph

summary:
Background: Maintenance of the kidney filtration barrier requires coordinated interactions between podocytes and the underlying glomerular basement membrane (GBM). GBM ligands bind podocyte integrins to trigger actin-based signaling events critical for adhesion. Nck1/2 adaptors have emerged as essential regulators of podocyte cytoskeletal dynamics. However, the precise signaling mechanisms mediated by Nck1/2 in podocytes remain to be fully elucidated.
Methods: We generated podocytes deficient in Nck1 and Nck2, and used transcriptomic approaches to profile expression differences. We further applied proteomic techniques to identify specific binding partners for Nck1 and Nck2 in podocytes. We used cultured podocytes and mice deficient in Nck1 and/or Nck2 along with podocyte injury models to comprehensively verify our findings.
Results: Compound loss of Nck1/2 resulted in altered expression of genes involved in actin binding, cell adhesion and extracellular matrix composition. Accordingly, Nck1/2-deficient podocytes showed defects in actin organization and cell adhesion in vitro, with podocyte detachment and altered GBM morphology present in vivo. We identified distinct interactomes for Nck1 and Nck2, and uncovered a mechanism by which Nck1 and Nck2 cooperate to regulate actin bundling and integrin activation at focal adhesions via α-actinin-4. Furthermore, we found that loss of either Nck1 or Nck2 resulted in increased matrix deposition in vivo, with more prominent defects in Nck2 deficient mice, consistent with enhanced susceptibility to podocyte injury.
Conclusion: These findings highlight distinct yet complementary roles for Nck proteins in regulating podocyte adhesion, controlling GBM composition and sustaining filtration barrier integrity.

overall_design: We generated conditionally immortalized Widtype and NCK1/2 knockout mouse podocyte cell lines. Podocytes were differentiated for 10 days, after which RNA was isolated for hybridization on Affymetrix microarrays. There were three independent replicates for each line.

first: Claire

first: Noah

last: Phippen

first: Ava

last: Keyvani Chahi

first: Manali

last: Tilak

first: Sara

last: Banerjee

first: Peihua

last: Lu

first: Laura

last: New

first: Casey

middle: R

last: Williamson

first: Matthew

last: Platt

first: Jeremy

last: Simpson

first: Mira

last: Krendel

first: Nicholas

last: Bisson

first: Anne-Claude

last: Gingras


title: Transcriptomic Response to High Light in the Charophyte Klebsormidium nitens

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

summary: During the evolution of life on Earth, the conquest of land by plants played a pivotal role producing a boost in land biomass, a substantial drop in atmospheric CO2, an increase in oxygen and the emergence of new terrestrial habitats facilitating land colonization by animals. Therefore, the characterization of the molecular mechanisms that allowed plant terrestralization is a cornerstone in evolutionary studies. Viridiplantae or the green lineage is divided into two clades Chlorophyta or green microalgae and Streptophyta that in turn splits into Embryophyta or land plants and Charophyta. The latest are mainly considered aquatic algae although some facultative terrestrial species has been identified. Charophyta are generally accepted as the extant algal species most closely related to current land plants and, therefore, they are used in evolutionary studies on plant terrestralization. High light irradiance was one of the major stressors that ancestral charophytic algae needed to overcome during the transition from aquatic to terrestrial environments. In this study, we have chosen the facultative terrestrial early charophytic alga Klebsormidium nitens to perform an integrative transcriptomic and metabolomic analysis under high light in order to unveil key mechanisms involved in the early steps of plants terrestralization. We found a fast chloroplast retrograde signaling possibly mediated by reactive oxygen species and the inositol polyphosphate 1-phosphatase (SAL1) and 3′-phosphoadenosine-5′-phosphate (PAP) pathways inducing gene expression and accumulation of specific metabolites. Systems used by both Chlorophyta and Embryophyta were activated such as the xanthophyll cycle with an accumulation of zeaxanthin and protein folding and repair mechanisms constituted by NADPH-dependent thioredoxin reductases, thioredoxin-disulfide reductases and peroxiredoxins. Similarly, cyclic electron flow, specifically the pathway dependent on Proton Gradient Regulation 5, was strongly activated under high light. We detected a simultaneous co-activation of the non-photochemical quenching mechanisms based on LHC-like Stress Related protein and the photosystem II subunit S that are specific to Chlorophyta and Embryophyta respectively. Exclusive Embryophyta systems for the synthesis, sensing and response to the phytohormone auxin were also activated under high light in Klebsormidium leading to an increase in auxin content with the concomitant accumulation of amino acids such as tryptophan, histidine and phenylalanine.

overall_design: Klebsormidium nitens (strain NIES-2285) was obtained from the National Institute for Environmental Studies (Japan). Cells were grown photoautotrophically in Bold’s Basal Medium  using photobioreactors containing 0.8 L of cell suspension and bubbled with air supplemented with 1% (v/v) CO2 as carbon source. Photobioreactors were continuously illuminated with white light lamps at 50 μE m-2 s-1 and maintained at 20ºC. Defoamer (Antifoam 204) was added to avoid the contamination of the aeration systems. Cultures at exponential phase with 45 μg/ml chlorophyll content were used in our experiments. Control cultures were kept under a control light irradiance of 50 μE m-2 s-1 whereas high light cultures were illuminated for three hours with an irradiance of 1500 μE m-2 s-1. Cells were collected by centrifugation at 3500xg for 5min at 4ºC. Cell pellets were washed with PBS, flash frozen with liquid Nitrogen and stored at -80ºC. Two independent biological replicates were considered for control low light and experimental high light conditions.

last: Romero Campero

first: Mercedes

last: García González

first: Ana

last: Romero Losada

first: Emma

last: Serrano-Pérez


title: Gene expression profiles analysis ofradiation-damaged mice brain and bonemarrow  after anti-radiation drugs intervention

status: Public on Apr 28 2022

first: Zhang

middle: Xiao

last: Chang

address: Taiping 27 Road

institute: Beijing Institute of Radiation Medicine

summary:
Mice were pretreated with  anti-radiation drugs before irradiation，including amifostine, bacterial flagellin, recombinant human thrombopoietin , nilestriol tablets. Comparing the gene expression profile of the mice in the drug pretreatment group and the radiation control group, the gene with the opposite expression was screened out.
The down-regulated gene phospholipase C gmma 1 (Plcg1) was screened out after the action of anti-radiation drugs.

overall_design: Matlab/Perl was utilized to analyze genome-wide expression profiling.  First, we tried to find genes whose expression level had significant variations at 6 hours 7 days or 14 days post radiation. All the three different time points have their own corresponding normal control. Since no normal control was prepared before radiation, the identical genes from the three normal controls of different time points were used as time 0 control. Our data revealed that radiation affected the genome expression profiling of bone marrow more severely than brain. 551 genes were identified in bone marrow, while 32 genes were found in brain, with only one identical in both the tissues.

first: Lei

last: Ren


title: Single-cell RNAseq analysis of H1N1-induced lung injury

city: Chicago

first: Jalees

last: Rehman

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

summary: The lungs of mice inoculated with H1N1 were harvested at day 7. The DAPI- lung cells were loaded into a 10x Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium controller using v3 kit according to the manufacturer's instructions.

overall_design: Isolated mouse lung cells from H1N1-inoculated lung at Day 7.

first: Lianghui

last: Zhang

first: Shang

last: Gao


title: The conserved histone chaperone Spt6 facilitates DNA replication and mediates genome instability [S1-DRIP-seq]

first: Catherine

middle: LW

last: Miller

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard

summary: Histone chaperones are an important class of factors that regulate chromatin accessibility for DNA-templated processes. Spt6 is a conserved histone chaperone and key regulator of transcription and chromatin structure. However, its functions outside of these roles have been little explored. In this work, we demonstrate a role for Spt6 in DNA replication and more broadly as a regulator of genome stability. Spt6 binds the replication machinery and mutations or loss of Spt6 impair DNA replication in vivo. Additionally, spt6 mutants are sensitive to DNA replication stress inducing agents, with increased sensitivity when combined with loss of DNA replication associated factors. Furthermore, spt6 mutants have elevated levels of DNA double strand breaks and are hyper-recombinogenic. R-loops do not appear to be elevated in spt6 mutants. In total, we identify Spt6 as a regulator of genome stability, at least in part through a role for Spt6 in DNA replication.

overall_design: S1-nuclease DNA-RNA hybrid IP (S1-DRIP-sq) in WT and spt6-YW samples. A RNaseH treated negative control is included for each sample. Samples were prepared in biological duplicate.

first: Fred

last: Winston


title: The conserved histone chaperone Spt6 facilitates DNA replication and mediates genome instability [BrdU-IP-seq]

overall_design: BrdU-IP in WT, spt6-YW, and spt6-50 strains in biological duplicate. S-phase samples were harvested with HU treatment (0.2M for 1 hour) or without (untreated, 30 min)


title: A Faithful In Vivo Model Of Human Macrophages In Metastatic Melanoma

city: Cape Town

first: Valentin

last: Voillet

state: Western Cape

address: First Floor Wembley Square, 3 McKenzie St, Gardens

country: South Africa

institute: cape town hvtn immunology laboratory

summary: Despite recent therapeutic progress, advanced melanoma remains lethal for many patients. The composition of the immune tumor microenvironment (TME) has decisive impacts on disease outcome and therapy response. High dimensional analyses of patient samples provide insight on the composition and heterogeneity of the immune TME. Macrophages are known for their cancer-supportive role, but the underlying mechanisms are incompletely understood, and experimental in vivo systems are needed to test the functional properties of these cells. We characterize a humanized mouse model, reconstituted with a human immune system and a human melanoma, in which: (1) human macrophages support metastatic spread of the tumor; and (2) tumor-infiltrating macrophages have a specific transcriptional signature that faithfully represents the transcriptome of macrophages from patient melanoma samples and is associated with shorter survival. This model complements patient sample analyses, enabling the elucidation of fundamental principles in melanoma biology, and the development and evaluation of candidate therapies.

overall_design: Immunodeficient "MISTRG" mice were repopulated with human CD34+ hematopoietic stem and progenitor cells. A human melanoma cell line (Me275) was implanted in the flank of the mice. Human CD45+ cells were isolated from tissues of 5 mice (repopulated with CD34+ cells from 2 donors) and pooled for scRNAseq analysis.

first: Anthony

last: Rongvaux


title: RNA immunoprecipitation sequencing (RIP-seq) of human Dicer-bound miRNAs in HIV-1 Gag replicating cells.

city: Montreal

first: Anne

last: Gatignol

state: Quebec

address: Lady Davis Institute, Jewish General Hospital

department: Medicine

institute: McGill University

summary: Micro (mi)RNAs are critical regulators of gene expression in human cells, whose functions can be affected during viral replication. We showed that the Human Immunodeficiency Virus type 1 (HIV-1) Gag protein interacts with the human miRNA processor Dicer and modifies its retention of specific miRNAs without affecting the enzyme’s pre-miRNA processing activity. This sequencing experiment was performed to elucidate whether the presence of Gag in human cells has an effect on the distribution of miRNAs loaded onto Dicer.

overall_design: Profile of short RNAs immunoprecipitated with Dicer in cells expressing or not expressing HIV-1 Gag

first: Owen

last: Dunkley

first: Sergio

last: Alpuche-Lazcano


title: Tet2 deficiency drives pathobiont translocation triggering Tc1 cell autoimmune hepatitis

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

summary: The triggers that drive interferon-g (IFNg)-producing CD8 T cell (Tc1 cell)-mediated autoimmune hepatitis (AIH) remain obscure. Here we show that lack of hematopoietic Tet methylcytosine dioxygenase 2 (Tet2), an epigenetic regulator associated with autoimmunity, results in the development of microbiota-dependent AIH-like pathology, accompanied by hepatic enrichment of aryl hydrocarbon receptor (AhR) ligand-producing pathobionts and rampant Tc1 cell immunity. We report that AIH-like disease development is dependent on both IFNg and AhR signaling, as blocking either reverts ongoing AIH-like pathology. Illustrating the critical role of AhR ligand-producing pathobionts in this condition, hepatic translocation of the AhR ligand indole-3-aldehyde (I3A)-releasing Lactobacillus reuteri is sufficient to trigger AIH-like pathology. Finally, we demonstrate that I3A is required for L. reuteri-induced Tc1 cell differentiation in vitro and AIH-like pathology in vivo, both of which are restrained by Tet2 within CD8 T cells. This AIH-disease model may contribute to the development of therapeutics to alleviate AIH.

overall_design: A piece of the left liver lobe (~3x3mm) was incubated in RNAlaterTM (Qiagen) at 4 °C for 48 h and stored at -80 °C until further analysis. For RNA extraction a Tissue-Tearor Homogenizer (Biospec) was used. RNA was extracted using the RNeasy Mini Kit (Qiagen).

first: Surya

last: Pandey

first: Mackenzie

last: Bender

first: Alex

last: McPherson

middle: M

last: Phelps

first: Luzmariel

last: Medina Sanchez

first: Mohit

last: Rana

first: Lee

last: Hedden

first: Kishan

last: Sangani

first: Li

last: Chen

first: Jake

middle: H

last: Shapira

first: Magdalena

last: Siller

first: Chhavi

last: Goel

first: Elena

last: Verdú

first: Bana

last: Jabri

first: Steven

last: Mullett

first: Stacy

middle: G

last: Wendell

first: Aatur

middle: D

last: Singhi

first: Jeremy

last: Tilstra

first: Joseph

last: Pierre

first: Gavin

middle: E

last: Arteel

first: Reinhard

last: Hinterleitner

first: Marlies

last: Meisel


title: Dynamic profiles of the Yak mammary transcriptome during lactation

city: Chengdu

first: Yu

last: Wang

state: Sichuan

address: #16, South Section, 1st Ring Road

institute: Southwest Minzu University

summary: Dynamic transcriptome profiles in yak mammary gland were evaluated by sampling mammary tissue at -30, -15, 1, 15, 30, 60, 120, 180 and 240 d relative to parturition and using a bovine commercial microarray platform. Several bioinformatics tools were used to analyze the data, both as expression relative to -30 d and as expression relative to the previous time point. There were >6,000 differentially expressed transcript (DEG; FDR＜0.05; P＜0.05) throughout lactation with larger DEG observed at the onset (1 vs. -15d) and at the end of lactation (240 vs. 180d). Bioinformatics analysis allowed to identify lactation-related genes on yak chromosomes which laid the foundation for determination of QTL location. Among most-impacted bovine chromosomes (BTA), BTA6, BTA9 and BTA28 were induced while BTA3, BTA4 and BTA14 were inhibited throughout lactation. Functional analysis underlined an overall induction of lipid metabolism, suggesting increases in triglycerides synthesis likely regulated by PPAR signaling. Data suggested induction of amino acid metabolism while increasing secretion or protein, but decreasing proteasome, indicating a major role of amino acid handling and reduced protein degradation in the synthesis and secretion of milk proteins. Glycan biosynthesis, both for N-glycan and O-glycan, was induced suggesting increased glycan content in milk. Cell cycle and immune response, especially antigen processing and presentation, were strongly inhibited during lactation suggesting morphological changes were minimized while the mammary gland prevents immune hyper responses during lactation. Transcripts associated with response to radiation and low oxygen were enriched in the down-regulated DEG affected by stage of lactation. Except for the latter, functions affected by the transcriptomic adaptation to lactation in mammary tissue of yak were very similar to the ones observed in dairy cows.

overall_design: Transcriptome of Yak mammary gland at -30, -15, +1, +15, +30, +60, +120, +180, +240 days relative to parturitio were analyzed by the Agilent Bovine (V2) Gene Expression Microarray. The array data were analyzed  by using the GeneSpring software V12 (Agilent). The expression data were analyzed using JMP genomics (v7; SAS) using the default ANOVA model with time as main effect and yak as random with all comparison possible. The Dynamic Impact Approach (DIA) was used for bioinformatics analysis of DEG at all time points vs. -30 d, and between each subsequent time point. Enrichment analysis of DEG was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8 and Ingenuity Pathway Analysis (IPA). Validation of microarray data was performed by comparing prior RTqPCR data published from the same tissues   with the Microarray data.

first: Mingfeng

last: Jiang

first: Massimo

last: Bionaz

first: Wei

last: Xia

first: Yili

last: Liu

first: Juan

last: Loor


title: Transcriptional changes associated with functioning and non-functioning Pituitary adenomas.

city: Milwaukee

first: Stephanie

last: Olivier Van-Stichelen

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: The reasons why some pituitary adenomas are fucntioning(secreting hormones) or not is not well understood. This analysis dig into the transcriptomes of secreting and non-secreting corticotropic adenomas as well as  non-fucntioning gonadotropic adenomas.

overall_design: Human pituitary adenomas were banked following surgical resection (MCW brain tumor bank). Classification of the pituitary adenomas was done on clinical presentation, complemented by pathology analysis.mRNA was extarcted and RNA-sequencing was performed.

last: Olivier-Van Stichelen

first: Nathan

last: Zwagerman

first: Logan

last: Massman


title: Time-course of host cell transcription during the HTLV-1 transcriptional burst

city: London

first: Charles

middle: R. M.

last: Bangham

address: Norfolk Place

department: Infectious Disease

institute: Imperial College London

summary: We report the host cell transcription during the phases of the HTLV-1 plus-strand burst.

overall_design: We used two naturally HTLV-1-infected clones isolated from patient blood, which were transduced with a Tax-responsive Timer construct reporter, that allowed the separation of proviral plus-strand burst into silent (DN – double negative), early (Blue), mid (DP – double positive), late phases (Red). The cells were sorted into these populations based on the Timer fluorescence and submitted to RNA sequencing. Each timepoint had two replicates.

first: Saumya

last: Ramanayake

first: Helen

last: Kiik


title: OTUD3 interacts with various transcriptional factors [ChIP-Seq]

city: Jinan

first: Junjun

address: 18877 Jingshi road

institute: Shandong First Medical University

summary: The ovarian tumor domain-containing deubiquitinases (OTUDs) reverse ubiquitin-dependent protein degradation and are involved in diverse signaling pathways.

overall_design: OTUD3 stabilizes various regulators involved in glucose and lipid metabolism and oxidative phosphorylation

last: Zhou

first: Hailong

last: Qi

first: Yongfeng

last: Song

first: Yuxin

last: Yin


title: BiCCA: Bi-order multiomics integration of single-cell data

city: Houston

first: Katy

last: Rezvani

address: Zayed Building, 5th floor 6565 MD Anderson Blvd. Unit 1061 Houston, TX 77030

department: Stem Cell Transplantation & Cellular Therapy department

institute: MD Anderson Cancer Center

summary: Chimeric antigen receptor (CAR) engineering of NK cells is an active area of research with early-phase clinical studies showing an excellent safety profile with encouraging clinical responses. However, the transcriptional signatures that control the fate of CAR-NK cell after infusion and their association with tumor control remain poorly understood. Here, we performed single-cell RNA sequencing (scRNA-seq) to depict the evolution of various engineered CAR-NK cells Single cell RNA sequencing (scRNA) has revolutionized high-thoughout systems-based analysis of cellular and functional heterogeneity,  The goals of this work are to compare transcriptome profiling (RNA-seq).

overall_design: The objective of this study was to investigate the kinetics of function and evolution of adoptively-transferred CAR-NK cells in the context of lymphoma treatment. Of particular interest to us was to determine the impact of IL-15 on the function and persistence of CAR-NK cell and to assess the contribution of IL-15 to NK-mediated anti-tumor activity. To accomplish this, we applied a multi-modal omics approach to characterize pre-infusion NK products and describe the evolution of NK cells post-infusion.

first: Li

last: Li

first: Katayoun


title: Microarray profiling of mRNA in Chlamydia trachomatis-infected recurrent spontaneous aborters

city: New Delhi

first: Ankita

last: Ray

state: Delhi

address: Safdarjung hospital campus

country: India

institute: ICMR-National Institute of Pathology

summary: The present study aimed to investigate the profile of serum-circulating mRNAs and their target genes and elucidate their role in infected and non-infected C. trachomatis RSA patients by microarray

overall_design: Non-heparanized blood was collected from women with history of RSA. Urine sample was also collected to test for presence of C.trachomatisby conventional PCR assay. Samples positive and negative for C. trachomatiswere studied for mRNA microarray analysis

first: Sangita

last: Rastogi


title: Global Analysis of Translational Reprogramming during Flagellar Regeneration Reveals the Role of Sphingolipid Metabolism in Ciliogenesis and Ciliopathies

city: Beijing

first: Jingying

last: Huang

address: Haidian  District

department: School of Life Sciences

institute: Tsinghua University

summary: Protein synthesis is essential for cilium assembly, but little is known about translational reprogramming that occurs during ciliogenesis. Using ribosome footprinting, we perform global translatome profiling on Chlamydomonas during flagellar regeneration.

sample_organism:
Chlamydomonas reinhardtii
Caenorhabditis elegans

overall_design: Chlamydomonas reinhardtii (strain CC-125) that were grown for 15, 30, 60, and 90 min after deflagellation to generate libraries for ribosome footprint sequencing (Ribo-seq) and RNA sequencing (RNA-seq) . A reference sample was collected from the same culture before deflagellation (Non-Treated). We also performed RNA sequencing for C.elegans mutants : sptl-1/sptl-2/sptl-3. Each strain was analyzed in biological duplicate.

first: Dou

last: Wu


title: OTUD3 regulates energy metabolism

last: Liu

summary: OTUD3 KO affect various regulators involved in glucose and lipid metabolism and oxidative phosphorylation

overall_design: We compared the expression profiles between WAT of WT and Otud3 KO mice


title: Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer

status: Public on Apr 27 2022

city: San Francisco

first: Arjun

middle: Arkal

last: Rao

state: CA

address: 505 Parnassus Ave, S-447

department: CoLabs

institute: University of California, San Francisco

summary: The tumor immune microenvironment (TIME) is commonly infiltrated by diverse collections of myeloid cells. Yet, the complexity of myeloid cell identity and plasticity has challenged efforts to define bona fidepopulations and determine their connections to T cell functionand their relation to patient outcome. Here we leverage single-cell RNA-sequencing (scRNA-seq) analysis of several mouse and human tumors and find that monocyte-macrophage diversity is characterized by a combination of conserved lineage states as well as transcriptional programs accessed along the differentiation trajectory. Using mouse models, we also find that tumor monocyte-to-macrophage progression is profoundly tied to regulatory T cell (Treg) abundance. Importantly, in human kidney cancer, heterogeneity in macrophage accumulation and myeloid composition corresponded to variancein, not only Tregdensity, but also the quality of infiltrating CD8+T cells.In this way, holistic analysis of monocyte-to-macrophage differentiation creates a framework for critically different immune states

overall_design: 3 samples (blood and tumor from control mice injected with B16-F10, and tumor from a Treg-depleted mouse injected with B16-F10)

first: Adriana

last: Mujal

first: Alexis

middle: J

last: Combes

middle: A

first: Mikhail

last: Binnewies

first: Bushra

last: Samad

first: Jessica

last: Tsui

first: Alexandre

last: Boissonnas

first: Joshua

last: Pollack

first: Rafael

last: Argüello

first: Megan

middle: K

last: Ruhland

first: Kevin

last: Barry

first: Vincent

last: Chan

first: Matthew

middle: F

last: Krummel


title: De novo variants of CSNK2B cause a new intellectual disability-craniodigital syndrome by disrupting the canonical Wnt signaling pathway

city: Cologne

first: Muhammad Sajid

last: Hussain

address: Weyertal 115b

department: Cologne Center for Genomics

institute: University of Cologne

summary: Main purpose of the project is to investigate the consequences of de novo CSNK2B variant on transcriptome profiling of the patient compared to control. In this data, we seen differential expression of genes involved in the Wnt signaling pathway and transcription regulator.

overall_design: We propose that the investigated variant disturb the canonical Wnt signaling pathway.

first: Maria

last: Asif

first: Prerana

last: Wagle

first: Peter

last: Nürnberg

first: Muhammad

middle: S


title: Neuronal apoptosis drives remodeling states of microglia and shifts in survival pathway dependence

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

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

overall_design: Refer to individual Series


title: Neuronal apoptosis drives remodeling states of microglia and shifts in survival pathway dependence [scRNA-seq]

summary: Microglia serve critical remodeling roles that shape the developing nervous system, responding to the changing neural environment with phagocytosis or soluble factor secretion. Recent single-cell sequencing (scRNAseq) studies have revealed the context-dependent diversity in microglial properties and gene expression, but the cues promoting this diversity are not well defined. Here, we ask how interactions with apoptotic neurons shape microglial state, including lysosomal and lipid metabolism gene expression and dependence on Colony-stimulating factor 1 receptor (CSF1R) for survival. Using early postnatal mouse retina, a CNS region undergoing significant developmental remodeling, we performed scRNAseq on microglia from mice that are wild-type, lack neuronal apoptosis (Bax KO), or are treated with CSF1R inhibitor (PLX3397). We find that interactions with apoptotic neurons drives multiple microglial remodeling states, subsets of which are resistant to CSF1R inhibition. We find that TAM receptor Mer and complement receptor 3 are required for clearance of apoptotic neurons, but that Mer does not drive expression of remodeling genes. We show TAM receptor Axl is negligible for phagocytosis or remodeling gene expression but is consequential for microglial survival in the absence of CSF1R signaling. Thus, interactions with apoptotic neurons shift microglia towards distinct remodeling states and through Axl, alter microglial dependence on survival pathway, CSF1R.

overall_design: Single cell gene expression comparison of postnatal retinal microglia in Bax KO, PLX-treatment, and control.

first: Sarah

middle: R

last: Anderson

first: Jacqueline

last: Roberts

first: Nathaniel

last: Ghena

first: Emmalyn

last: Irvin

first: Joon

last: Schwakopf

first: Isabelle

middle: B

last: Cooperstein

first: Alejandra

last: Bosco

middle: L


title: Neuronal apoptosis drives remodeling states of microglia and shifts in survival pathway dependence [RNA-Seq]

overall_design: bulk RNA sequencing of postnatal retinal microglia from MerTK knockout, Axl knockout, double knockout, and control animals.


title: Validate whether the targeting of crRNAs affected the host cell gene expression

city: Stanford

first: Augustine

last: Chemparathy

address: 290 Jane Stanford Way

department: Bioengineering

institute: Stanford University

summary: We explored whether the targeting of crRNAs affected the host cell gene expression. To do this, we used a type LNP, termed a lipitoid, to transiently transfect human A549 lung carcinoma cells with the Cas13d mRNA and in vitro synthesized crRNA(s). At 48 hpi, we isolated cellular RNA and performed whole-cell RNA sequencing (RNA-seq). We observed high reproducibility between biological replicates. We examined the off-target effects of viral-targeting crRNA for SARS-CoV-2 or 229E as well as the NT crRNA by comparing their transcriptome profiles to that of cells expressing Cas13d alone, and we saw highly similar gene expression profiles. Furthermore, co-delivery of Cas13d and two targeting crRNAs showed a very similar transcriptome profile to that of the Cas13d alone. These data suggest that Cas13d and antiviral crRNAs are highly specific, with a minimal impact on host cell transcriptomes.

overall_design: mRNA profile of A549 cells after two days Cas13d mRNA and related crRNAs transfection

first: Yanxia

last: Liu

first: Xueqiu

last: Lin


title: Inheritance of Repressed Chromatin Domains during S-phase Requires the Histone Chaperone NPM1

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

summary: The epigenetic process safeguards cell identity during cell division through the inheritance of appropriate gene expression profiles. We demonstrated previously that parental nucleosomes are inherited by the same chromatin domains during DNA replication only in the case of repressed chromatin. We now show that this specificity is conveyed by NPM1, a histone H3/H4 chaperone. Proteomic analyses of late S-phase chromatin revealed NPM1 in association with both H3K27me3, an integral component of facultative heterochromatin and MCM2, an integral component of the DNA replication machinery; moreover NPM1 interacts directly with PRC2 and with MCM2. Given that NPM1 is essential, the inheritance of repressed chromatin domains was examined anew using mESCs expressing an auxin-degradable version of endogenous NPM1. Upon NPM1 degradation, cells accumulated in S-phase of the cell-cycle and parental nucleosome inheritance from repressed chromatin domains was markedly compromised. Appropriate inheritance required the NPM1 acidic patches that function in chaperone activity, pointing to NPM1 being integral to the epigenetic process.

overall_design: NPM1 degradable mESC (NPM1AID) were synchronized to G1 phase and then released for 12h with or without the addition of several chemical: Auxin, PRC2i. Cells were then harvested for ChIP-Seq and CUT&RUN against H3K27me3 as well as for RNA-Seq.

first: Thelma

last: Escobar

first: Jia-Ray

last: Yu

first: Sanxiong

first: Danny

last: Reinberg


title: Transfection experiments with several innate-immune stimulators and pathogens in human cells

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: The innate immune system represents the first line of defense against invading organisms. Among several key innate-immune signaling pathways, the cGAS-STING signaling has emerged as a pivotal component of innate immunity for both foreign- and self-DNA detection. Here, we conducted both computional and experimental assays to identify and characterize novel and key innate immune protein-coding genes and long noncoding RNAs

overall_design: Total RNA after transfecting with innate-immune stimulators and pathogens  were isolated and sequenced by deep sequencing using Illumina HiSeq 4000

first: Chenhui

last: Li

first: Lele

last: Zhang

first: Mingju

last: Lyu


title: Predicting Relapse in Patients With Medulloblastoma by Integrating Evidence From Clinical and Genomic Feature

city: San Diego

first: Jill

middle: P

last: Mesirov

address: 9500 Gilman Drive

institute: University of California, San Diego

type:
Expression profiling by array
Third-party reanalysis

summary:
Despite significant progress in the molecular understanding of medulloblastoma, stratification of risk in patients remains a challenge. Focus has shifted from clinical parameters to molecular markers, such as expression of specific genes and selected genomic abnormalities, to improve accuracy of treatment outcome prediction. Here, we show how integration of high-level clinical and genomic features or risk factors, including disease subtype, can yield more comprehensive, accurate, and biologically interpretable prediction models for relapse versus no-relapse classification. We also introduce a novel Bayesian nomogram indicating the amount of evidence that each feature contributes on a patient-by-patient basis.

The training set consisted of 96 samples for which relapse status at 30 months post-treatment was known. Matched normal blood samples were collected through the COG Tumor Bank (protocol ACNS02B3) and from Children's Hospital Boston under institutional review board approval. The test set included 78 samples: 47 samples from our original study6 not used for training, 16 samples from Kool et al,33 and 15 samples from the COG Tumor Bank. All training and test samples correspond to patients at least 3 years old treated with conventional chemotherapy, surgical resection, and craniospinal irradiation. In the test set, 15 samples (Children's Oncology Group Tumor Bank) were processed as described above. Of those 15, a total of six have DNA copy number data. Another set of 47 samples was taken from the data set from Pomeroy et al. (Affymetrix Hu6800; Affymetrix). None of those samples had DNA copy number data. The remaining 16 samples, all with DNA copy number data, came from Kool et al. (Affymetrix U133; Affymetrix).

overall_design:
A Bayesian cumulative log-odds model of outcome was developed from a training cohort of 96 children treated for medulloblastoma, starting with the evidence provided by clinical features of metastasis and histology (model A) and incrementally adding the evidence from gene-expression-derived features representing disease subtype-independent (model B) and disease subtype-dependent (model C) pathways, and finally high-level copy-number genomic abnormalities (model D). The models were validated on an independent test cohort (n = 78).

Information on Kool et al. samples (GSM) used: In total 62 medulloblastoma samples were selected for Affymetrix gene expression profiling. The set included 60 primary tumors and 2 local relapses. All samples were snap frozen in the institutional pathology departments immediately upon arrival. All samples were reviewed by experienced neuropathologists and examined for tumor content. Samples were excluded from analysis when less than 70% of the sample contained tumor cells. RNA and DNA was isolated using Trizol (Invitrogen, Carlsbad, CA). RNA purification was performed using the RNeasy mini kit (Qiagen, Germantown, USA). DNA and RNA quantity and quality was determined by spectrophotometry (Nanodrop, Wilmington, USA) and microfluidics-based electrophoresis (Agilent 2100 Bioanalyzer, Agilent, Palo Alto, USA). Four µg total RNA was used for hybridization of Affymetrix HG-U133 plus 2.0 Genechips according to the manufacturer's instructions (Affymetrix Inc. Santa Barbara, USA). Quality of the arrays was ensured by inspection of the beta-actin and GAPDH 5′-3′ ratio's as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc. Santa Barbara, USA). For clustering and gene expression analyses data were normalized using the gcRMA algorithm in the Bioconductor package (http://www.bioconductor.org) of the R statistical environment (http://www.r-project.org/). Present call information from the MAS5.0 algorithm was added to the gcRMA gene expression measures. Expression data have been deposited in NCBI's Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE10237

Information on Pomeroy et al. samples (Brain_MD) used: Patients included 60 children with medulloblastomas, 10 young adults with malignant gliomas (WHO grades III and IV), 5 children with AT/RTs, 5 with renal/extrarenal rhabdoid tumours, and 8 children with supratentorial PNETs (see Supplementary Information I). Medulloblastoma patients were treated with craniospinal irradiation to 2,400–3,600 centiGray (cGy) with a tumour dose of 5,300–7,200 cGy. All patients with medulloblastoma were treated with chemotherapy consisting of cisplatin and vincristine, plus combinations of carboplatin, etoposide, cyclophosphamide or lumustine (1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea, CCNU) (details in Supplementary Information II). Samples were snap frozen in liquid nitrogen and stored at -80 °C. Studies were done with approval of the Committee for Clinical Investigation of Boston Children's Hospital. The data were organized into three sets: data set A (42 samples containing 10 medulloblastomas, 10 malignant gliomas, 10 AT/RTs, 8 PNETs and 4 normal cerebella); data set B (34 samples containing 9 desmoplastic medulloblastomas and 25 classic medulloblastomas); and data set C (60 samples containing 39 medulloblastoma survivors and 21 treatment failures). The clinical attributes of each of the patients in the study are available in Supplementary Information II. Tissues were homogenized in guanidinium isothiocyanate and RNA was isolated by centrifugation over a CsCl gradient. RNA integrity was assessed either by northern blotting or by gel electrophoresis. Ten–twelve micrograms total RNA was used to generate biotinlylated antisense RNAs, which were hybridized overnight to HuGeneFL arrays containing 5,920 known genes and 897 expressed sequence tags, as described previously6. Arrays were scanned on Affymetrix scanners and the expression value for each gene was calculated using GENECHIP software (Affymetrix, Santa Clara, California). Minor differences in microarray intensity were corrected using a linear scaling method as detailed in Supplementary Information I. Scans were rejected if the scaling factor exceeded 3, fewer than 1,000 genes received ‘present’ calls, or microarray artefacts were visible.

Please note that processed data is provided in the *.gct files as indicated in each sample description field.

first: Pablo

last: Tamayo

first: Yoon-Jae

last: Cho

first: Aviad

last: Tsherniak

first: Heidi

last: Greulich

first: Lauren

last: Ambrogio

first: Netteke

last: Schouten-van Meeteren

first: Tianni

last: Zhou

first: Allen

last: Buxton

first: Marcel

last: Kool

first: Matthew

last: Meyerson

first: Scott

last: Pomeroy


title: miR-196b-5p and miR-107 expression differentiates ocular sebaceous carcinoma from squamous cell carcinoma of the comjunctiva

status: Public on Apr 26 2022

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

institute: Erasmus University Medical Center

summary:
Ocular Sebaceous Carcinoma (OSC) is a rare malignant tumor for which initial clinical and pathological diagnosis is often incorrect. OSC can mimic Squamous Cell Carcinoma of the Conjunctiva (SCCC). Aim of this study was to find microRNA biomarkers to distinguish OSC and SCCC from normal tissue and from each other.
Clinical OSC and SCCC case files and corresponding histopathological slides were collected and reviewed. Microdissected formalin-fixed paraffin-embedded tumor and control tissue were sub-jected to semi-high throughput microRNA profiling.
MicroRNA expression distinguishes OSC and SCCC from corresponding control tissues. Selected differentially expressed miRNAs were validated using single RT-PCR assays. No prognostic miRNAs could be identified that reliable predict SCCC metastasis or OSC recurrence. A com-parison between OSC (n=14) and SCCC (n=18) revealed 38 differentially expressed microRNAs (p<0.05). Differentially expressed miRNAs were selected for validation in the discovery cohort and an independent validation cohort (OSC, n=11; SCCC, n=12). At least two miRNAs miR-196b-5p (p ≤ 0.05) and miR-107 (p ≤ 0.001) displayed a statistically significant differential expression between OSC and SCCC with miR-196b-5p upregulated in SCCC and miR-107 up-regulated in OSC. In the validation cohort microRNA miR-493-3p also showed significant up-regulation in SCCC when compared to OSC (p ≤ 0.05).  ROC analyses indicated that the com-bined miR-196b-5p and miR-107 expression levels predicted OSC with 90.0% sensitivity and 83.3% specificity.
In conclusion, combined testing of miR-196b-5p and miR-107, can be of additional use in routine diagnostics to discriminate OSC from SCCC.

overall_design: MicroRNA expression profiles were determined from archival formalin-fixed paraffin-embedded (FFPE) tumor samples of ocular sebaceous carcinoma (OSC, n=14); squamous cell carcinoma of the conjunctiva (SCCC, n=18) and control tissues Meibomian gland tissue (n=6, control to OSC); conjunctival squamous epithelium of the eyelid (n=6; control to SCCC). TaqMan® Low Density Array (TLDA) Human MicroRNA Cards (A card v2.0, Applied Biosystems/Thermo Fisher Scientific) were used. The microRNA expression profiling data was used for a comparison between OSC and corresponding control tissue, between SCCC and corresponding control tissue, between OSC and SCCC, between primary OSC that eventually exhibit recurrence or no recurrence and between SCCC that eventually exhibit metastasis or no metastasis.

first: Ronald

middle: O

last: de Keizer

first: Anne

last: Vriends

first: Gijsbert

last: Hötte

first: Dion

last: Paridaens

first: Robert

middle: M

last: Verdijk


title: Elucidation of differential TF binding and epigenome in response to MYCi975.

city: Chicago

first: Debu

last: Chakravarti

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: We report the differential ChIP-, RNA- and ATAC-seq results in cultrered cells following MYCi975 treatment. From chromatin immunopercipitated DNA of MYCi975 treated cells we determine MYCi975 selectively alters MYC chromatin binding and target gene expression. In addition, largescale epigenomic changes in MYCi975 treated cells inform of MYC regulated TFs with alterations in expression, chromatin binding and histone H3K27 acetylation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In a time-depedent manner, we examine the effects of MYCi975 treatment on largescale differential TF binding and the epigenomic landscape.

first: Austin

last: Holmes