title: Profiling pig microglia gene expression

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

institute: Lancaster University

summary: Microglia are thought to play a key role in brain in both homeostasis and diseases. The pig has been seen as an attractive, physiologically-relevant model for studying human neurological and mental disorders, as well as being an important agricultural species. Here we sought to characterise microglia markers genes for pigs.

overall_design: Compared the gene expression in FACs sorted macrophages (n=3), cerebellum microglia (n=8), frontal cortex microglia (n=8), hippocampal microglia (n=8) and hippocampal tissue (n=4).

first: Sarah

last: Brown

first: Alistair

last: Lawrence


title: ChIPseq for NB4 cell line with either no treatment or LDB1 overexpression

status: Public on Sep 22 2022

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

country: China

institute: Children’s Hospital of Soochow University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore ChIPseq results for LDB1 in NB4 cell line.

overall_design: 1 NB4 sample with no treatment and 1 NB4 sample with LDB1 overexpression

first: Pan

last: Jian

first: Lu

last: Lihui


title: VPRBP, a novel androgen receptor and OGT target is an essential mediator of cellular transformation in prostate cancer

city: Oxford

first: Ninu

last: Poulose

state: Oxfordshire

address: Headley Way

department: Nuffield Department of Surgical Sciences

country: United Kingdom

institute: University of Oxford

summary: Androgen receptor (AR) plays a central role in the development of prostate cancer. Increased expression of O-GlcNAc transferase (OGT) and O-GlcNAcylation are also implicated in metastatic prostate caner. We have identified VPRBP as a novel androgen-regulated gene and the stability of the encoded protein is regulated by OGT.VPRBP downregulation led to significant decrease in cell proliferation and p53 stabilization in LNCaPs. In this study, we employed chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) to identify changes in p53 binding to the genome in VPRBP knockdown LNCaPs compared to scrambled siRNA transfected control cells. Stabilization of p53 was associated increased p53 recruitment to the chromatin.

overall_design: ChIP-seq studies were carried out in nutlin-3a treated LNCaPs, and scrambled siRNA vs VPRBP siRNA 1 and VPRBP siRNA 2 transfected LNCaPs using antibody against p53  (Santa Cruz Biotechnology, sc-126)

last: Maguire

first: Ian

middle: G

last: Mills


title: Targeted Escalation of Tyrosine Kinase Super-Enhancer Network Engineered by Acetylated HOXB13  Spurs Prostate Tumor Autonomy

city: St. Louis

first: Kiran

last: Mahajan

state: Missouri

address: CB 8242 600 South Euclid Ave

department: Surgery

country: USA

institute: Washington University

type: Expression profiling by high throughput sequencing

summary: While tissue and lineage-specific super-enhancers (SEs) regulate cell fate decision during development, the nature of Castration Resistant Prostate Cancer (CRPC)-specific SEs (CSEs) is unknown. Herein we report the lysine 13 (K13) acetylation of HOXB13 mediated by the histone acetyltransferase CBP/p300 regulates prostate tumor autonomy. The acK13-HOXB13 shadows H3K27ac at lineage specific SEs and surpasses it at CSEs. In contrast, mutation of  HOXB13 at K13  sensitizes CRPCs to Enzalutamide, disables spheroid and xenograft tumor formation. Mechanistically, the acK13-HOXB13 interacts with chromatin remodeling bromodomain proteins to regulate tumor-specific CSE selection.   These CSEs sprout at critical lineage genes NKX3-1, Androgen receptor (AR), AR regulator  ACK1 tyrosine kinase and tyrosine kinase ligands regulating angiogenesis. Single-cell transcriptomic analysis of human prostate tumor organoids reveal ACK1 expression underlies sensitivity to the small molecule  inhibitor (R)-9b over AR-targeted agents. Collectively, our studies reveal acK13-HOXB13 regulated epigenome as a key cog in prostate cancer cell autonomy.

overall_design: Human prostate organoids were grown as described above. Single cell suspension was processed for library preparation as described in the 10X Genomics single cell suspension protocol. All samples were quantitated  twice on the bioanalyzer and checked to ensure integrity.  10x Single Cell/Nuclei RNAseq  Library and Sequencing Targeting 25K read pairs/cell.  The samples amplified well for adequate libraries set up as per the 10X Genomics protocol.  25k depth per cell  sequencing was performed  using the NovaSeq S4. The Cell Ranger software was used to align the reads to the reference genome. Cloupe browser analysis was performed to generate the t-SNE plot and UMAP clustering analysis.

first: Paul

last: Cliften


title: A miRNA signature for early non-invasive diagnosis of pre-eclampsia

status: Public on Sep 21 2022

city: Wenzhou

first: Meng

last: Zhou

address: 270 Xueyuan Xi Road

institute: Wenzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Preeclampsia (PE) is a multi-systemic maternal syndrome with substantial maternal and fetal morbidity and mortality. Currently, there is no clinically viable non-invasive biomarker assay for early detection, thus limiting the effective prevention and therapeutic strategies for PE.
Methods: We conducted a discovery-training-validation three-phase retrospective and prospective study with cross-platform and multicenter cohorts. The initial biomarkers were discovered and verified in tissue specimens by small RNA sequencing and qRT-PCR. A miRNA signature (miR2PE-score) was developed using the Firth’s bias-reduced logistic regression analysis, and subsequently validated in two independent multinational retrospective cohorts and two prospective plasma cohorts.
Results: We initially identified five PE-associated differentially expressed miRNAs from miRNA sequencing data and subsequently validated two miRNAs (miR-196b-5p and miR-584-5p) as robust biomarkers by association analysis with clinical characteristics and qRT-PCR in tissue specimens in the discovery phase. Using the Firth’s bias-reduced logistic regression analysis, we developed the miR2PE-score for the early detection of PE. The miR2PE-score showed a high diagnostic performance with an area under the receiver operating characteristic curve (AUROC) of 0.920, 0.848, 0.864 and 0.812 in training, internal and two external validation cross-platform and multicenter cohorts, respectively. Finally, we demonstrated the non-invasive diagnostic performance of the miR2PE-score in two prospective plasma cohorts with AUROC of 0.933 and 0.787. Furthermore, the miR2PE-score revealed superior performance in non-invasive diagnosis compared with previously published miRNA biomarkers.
Conclusions: We developed and validated a novel and robust blood-based miRNA signature, which may serve as a promising clinically applicable non-invasive tool for the early detection of PE.

overall_design: Isolated total RNA from placental tissue samples of 10 women (5 normotensive women, denoted with a NC, and 5 preeclamptic women, denoted with a PE) and used it for miRNA-sequencing on the Nova6000 platform (Illumina). Sequences were aligned to the sequences of human mature microRNAs downloaded from the miRbase database. Aligned sequences were then used to quantify the miRNAs and perform differential expression analysis.

first: Siqi

last: Bao

first: Tong

first: Congcong

last: Yan

first: Jiale

first: Fan

last: Yang

first: Shan

last: Chao

first: Zhangye

last: Xu


title: Transcriptome and DNA Methylome Analyses Reveal Underlying Mechanisms for the Racial Disparity in Uterine Fibroids [EPIC Human Methylation Array]

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of normal myometrial and fibroid samples.
Uterine fibroids (leiomyomas) affect Black women disproportionately in terms of prevalence, incidence, and severity of symptoms.  The causes of this racial disparity are essentially unknown. We hypothesized that myometria of Black women are more susceptible to developing fibroids and examined the transcriptomic and DNA methylation profiles of myometria and fibroids from Black and White women for comparison. Myometrial samples cluster by race in both their transcriptome and DNA methylation profiles, whereas fibroid samples only cluster by race in the latter. More differentially expressed genes (DEGs) were detected in the Black and White myometrial comparison than in the fibroid comparison. Leiomyoma gene set expression analysis showed four different clusters of DEGs, including a cluster with highest expression in Black myometrial samples and elevated in all fibroids.  One of the DEGs in this group, VWF, was significantly hypomethylated at two CpG probes near a putative enhancer site in Black myometrial and in all fibroid samples compared with White myometrial samples, suggesting that VWF expression is responsive to DNA hypomethylation, a known stress response.  These results suggest that the molecular basis for the disparity in fibroid disease between Black and White women could be found in the myometria before fibroid development and not in the fibroids themselves.

overall_design: DNA from myometrial (n=32) and fibroid (n=41) samples were hybridized to the Illumina Infinium EPIC Human Methylation Array


title: Redox Imbalance in COVID-19 Pathophysiology

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: The pathophysiologic significance of redox imbalance is unquestionable as numerous reports and topic reviews indicate alterations in redox parameters during corona virus disease 2019 (COVID-19). However, a more comprehensive understanding of redox-related parameters in the context of COVID-19-mediated inflammation and pathophysiology is required.  COVID-19 subjects (n=64) and control subjects (n=19) were enrolled, and blood was drawn within 72 hours of diagnosis. Serum multiplex assay and buffy coat cell mRNA sequencing was performed. Oxidant/free radical (electron paramagnetic resonance (EPR) spectroscopy, nitrite-nitrate assay) and antioxidant (ferrous reducing ability of serum assay and high-performance liquid chromatography) were performed. Multivariate analyses were performed to evaluate potential of indicated parameters to predict clinical outcome. Significantly greater levels of multiple inflammatory and vascular markers were quantified in the subjects admitted to the ICU compared to non-ICU subjects. Gene set enrichment analyses indicated significant enhancement of oxidant related pathways and biochemical assays confirmed a significant increase in free radical production and uric acid reduction in COVID-19 subjects. Multivariate analyses confirmed a positive association between serum levels of VCAM-1, ICAM-1 and a negative association between the abundance of one electron oxidants (detected by ascorbate radical formation) and mortality in COVID subjects while IL-17c and TSLP levels predicted need for intensive care in COVID-19 subjects.

overall_design: Experiment was designed to compare the expression of differentially expressed transcripts between the blood samples fromNON-COVID subjects and COVID-19 PCR positive subjects. Samples were collected with in 72 hours of the positive PCR test.

first: Nairrita

last: Majumder

first: Vishal

last: Deepak

first: Sarah

last: Hadique

first: Drake

last: Aesoph

first: Murugesan

last: Velayutham

first: Qing

last: Ye

first: Md

middle: H

last: Mazumder

first: Sara

middle: E

last: Lewis

first: Vamsi

last: Kodali

first: Anthony

last: Roohollahi

first: Nancy

last: LGuo

first: Valery

middle: V

last: Khramtsov

first: Richard

middle: J

last: Johnson

first: Sijin

last: Wen

first: Eric

last: Kelley

first: Salik

last: Hussain


title: Targeted Escalation of an Acetylated HOXB13-dependent Tyrosine Kinase Super-Enhancer Network Promotes Prostate Tumor Autonomy

first: Kiran

last: Mahajan

summary: While tissue and lineage-specific super-enhancers (SEs) regulate cell fate decision during development, the nature of Castration Resistant Prostate Cancer (CRPC)-specific SEs (CSEs) that drive resistance to AR-targeted therapies is unknown. Herein we report the lysine 13 (K13)-acetylation of Homeodomain transcription factor HOXB13 as a critical feature underlying CSE exclusivity. The histone acetyltransferase (HAT) CBP/p300 specifically acetylates HOXB13 (acK13-HOXB13) in prostate cancer cells. The acK13-HOXB13 enriched CSEs sprout at critical lineage genes such as the NKX3-1, Androgen receptor (AR), AR regulator ACK1/TNK2 a tyrosine-kinase and tyrosine kinase ligands associated with angiogenesis, including VEGFA and ANGPT2/ANGPTL3 to expedite prostate tumor autonomy.

overall_design: Genome-wide binding site analysis of lysine 13 acetylated HOXB13 in chromatin extracts prepared from prostate cancer cell lines.

first: Will

last: Yang


title: Synthetic mimetics assigned a major role to IFNAR2 in type I Interferon signaling

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

summary: Type I Interferons (IFNs) are potent inhibitors of viral replication. Here, we reformatted the natural murine and human type I Interferon-α/β receptors IFNAR1 and IFNAR2 into fully synthetic biological switches. The transmembrane and intracellular domains of natural IFNAR1 and IFNAR2 were conserved, whereas the extracellular domains were exchanged by nanobodies directed against the fluorescent proteins Green fluorescent protein (GFP) and mCherry. Using this approach, multimeric single-binding GFP-mCherry ligands induced synthetic IFNAR1/IFNAR2 receptor complexes and initiated STAT1/2 mediated signal transduction via Jak1 and Tyk2. Homodimeric GFP and mCherry ligands showed that IFNAR2 but not IFNAR1 homodimers were sufficient to induce sustained STAT1/2 signaling. Transcriptome analysis revealed that synthetic murine type I IFN signaling was highly comparable to IFNα4 signaling and resulted in efficient elimination of vesicular stomatitis virus (VSV) in a cell culture based viral infection model using MC57 cells stimulated with synthetic type IFN ligands. Using intracellular deletion variants and point mutations, Y510 and Y335 in murine IFNAR2 were verified as unique phosphorylation sites for STAT1/2 activation, whereas the other tyrosine residues in IFNAR1 and IFNAR2 were not involved in STAT1/2 phosphorylation. Comparative analysis of synthetic human IFNARs supporting this finding. In summary, our data showed that synthetic type I IFN signal transduction is originating from IFNAR2 rather than IFNAR1.

overall_design: We used microarrays to detail the overall influence of the constructs to confirm background free action of the  receptor constructs.

first: Nele

last: Zoellner

first: Doreen

last: Floss

first: Jürgen

last: Scheller


title: Whole-genome CRISPR screening identifies N-glycosylation as an essential pathway and a potential novel therapeutic target in CALR-mutant MPN (Pooled CRISPR Screen).

city: Madrid

first: María José

last: Jiménez

state: Madrid

address: C. de Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: Spanish National Cancer Research Centre

summary: Calreticulin (CALR) mutations are frequent, disease-initiating events in myeloproliferative neoplasms (MPN). Although the biological mechanism by which CALR mutations cause MPN has been elucidated, there currently are no clonally selective therapies for CALR-mutant MPN. To identify unique genetic dependencies in CALR-mutant MPN, we performed a whole-genome CRISPR knockout depletion screen in mutant CALR-transformed hematopoietic cells. We found that genes in the N-glycosylation pathway (amongst others) were differentially depleted in mutant CALR-transformed cells as compared with control cells. Using a focused pharmacological screen targeting unique vulnerabilities uncovered in the CRISPR screen, we found that chemical inhibition of N-glycosylation impaired the growth of mutant CALR-transformed cells in vitro. We treated Calr-mutant knockin mice with the N-glycosylation inhibitor, 2-deoxy-glucose (2-DG), and found a preferential sensitivity of Calr-mutant cells to 2-DG as compared to wild-type cells, and a normalization of key MPN disease features. These findings advance the development of clonally selective treatments for CALR-mutant MPN.

overall_design: CRISPR pooled screen, BA/F3-MPL cells, n=4 biological replicates per condition, empty vector cells and CALR DEL52-expressing cells, grown in the presence or absence of interleukin 3 (IL3). Genes of special interest included genes related to N-glycosylation, protein secretion, unfolded protein response, protein arginine methylation and top hits from our whole-genome screen. 1 positive control (EV#2 -_Day 21_without IL3) was included in order to corroborate that most of BA/F3-MPL cells are unviable without IL3.

first: Jonas

middle: S

last: Jutzi

first: Anna

last: Marneth

first: Ann

last: Mullally


title: Whole-genome CRISPR screening identifies N-glycosylation as an essential pathway and a potential novel therapeutic target in CALR-mutant MPN

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

overall_design: Refer to individual Series


title: Transcriptome and DNA Methylome Analyses Reveal Underlying Mechanisms for the Racial Disparity in Uterine Fibroids [RNA-seq]

first: Jose

last: Teixeira

summary: Uterine fibroids (leiomyomas) affect Black women disproportionately in terms of prevalence, incidence, and severity of symptoms.  The causes of this racial disparity are essentially unknown. We hypothesized that myometria of Black women are more susceptible to developing fibroids and examined the transcriptomic and DNA methylation profiles of myometria and fibroids from Black and White women for comparison. Myometrial samples cluster by race in both their transcriptome and DNA methylation profiles, whereas fibroid samples only cluster by race in the latter. More differentially expressed genes (DEGs) were detected in the Black and White myometrial comparison than in the fibroid comparison. Leiomyoma gene set expression analysis showed four different clusters of DEGs, including a cluster with highest expression in Black myometrial samples and elevated in all fibroids.  One of the DEGs in this group, VWF, was significantly hypomethylated at two CpG probes near a putative enhancer site in Black myometrial and in all fibroid samples compared with White myometrial samples, suggesting that VWF expression is responsive to DNA hypomethylation, a known stress response.  These results suggest that the molecular basis for the disparity in fibroid disease between Black and White women could be found in the myometria before fibroid development and not in the fibroids themselves.

overall_design: RNA-seq results for 20 fibroid samples and 15 myometrial samples from Black and White patients

first: Emmanuel

middle: N

last: Paul

first: Joshua

middle: A

last: Grey

first: Tyler

last: Carpenter

first: Zachary

middle: B

last: Madaj

first: Kin

last: Lau

first: Scott

last: Givan

first: Gregory

middle: W

last: Burns

first: Ronald

middle: L

last: Chandler

first: Ganesa

middle: R

last: Wegienka

first: Hui

last: Shen


title: Transcriptome analysis after ALKBH3 knockdown in ocular melanoma cells

city: Shanghai

first: Xiang

last: Gu

address: Zhizaoju Road

institute: shanghai ninth people hospital

summary: To study the mechanism of ALKBH3 in ocular melanoma, we performed  RNA-seq of  wide type cells and ALKBH3-deficient cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 92.1 cells and its KD derivatives (shALKBH3).

first: X

first: P

last: Chai


title: Genome-wide maps of 5hmC in control and Tet3 inactivated lung smooth muscle cells.

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

type: Methylation profiling by high throughput sequencing

summary: To examine the influences for 5hmC enrichment on genome wide after Tet3 inactivation, we determined the enrichment profiles of 5hmC, the direct demethylated target of Tet3, by Nano-hmC-seq with genomic DNA from control and Tet3 inactivated lung smooth muscle cells

overall_design: Examination of 5hmC genomic distribution of control and Tet3 inactivated lung smooth muscle cells.

first: Fan

last: Wu

first: Stefan

last: Guenther

first: Thomas

last: Braun


title: Whole-genome CRISPR screening identifies N-glycosylation as an essential pathway and a potential novel therapeutic target in CALR-mutant MPN (RNA-Seq).

first: María José

last: Jiménez

summary: RNA-sequencing of megakaryocyte-erythroid progenitors of CALRdel52/+ MxCre mice treated with either vehicle or 2-deoxy-D-glucose for 21 days.

overall_design: FACS sort of in vivo treated megakaryocyte-erythroid progenitors using the following markers: CD3- CD5- B220- Gr-1- CD11b- Ter119- Sca-1- c-Kit+ CD34low FcgRlow.

first: Jonas

last: Jutzi

first: Anna

last: Marneth

first: Ann

last: Mullally


title: HOXB13 epigenome in castration-resistant prostate cancer

first: Kiran

last: Mahajan

summary: Treatment induced-resistance of CRPC is an imminent undesirable outcome in patients. Tissue and lineage-specific super-enhancers (SEs) determine cell fate and plasticity during development and disease respectively. However, the identity and function of CRPC-specific SEs (CSEs) regulated genes is unknown. Herein we report the lysine 13 acetylation of the prostate-enriched transcription factor HOXB13 (acK13-HOXB13) mediated by the histone acetyl transferase (HAT) CBP/p300 as a critical mechanism of CSE establishment. Mechanistically, acK13-HOXB13 establishes the CRPC enhanceosome comprising chromatin remodeling bromo-domain proteins SMARCA2/BAZ2B and the HAT p300/CBP which enable histone and non-histone protein acetylation at CSEs. Such CSEs sprout at tyrosine kinase genes encoding ACK1/TNK2, VEGFA, and ANGPT2/ANGPTL3 to increase pathogenic output in primary human tumors. These tyrosine kinase mediated signaling cascades establish robust networks to conduce growth, survival and androgen-bypass. Consistently, the loss of function acK13-HOXB13 mutants show significant reduction of proliferation, spheroid formation, and xenograft tumor growth that correlates with the high sensitivity to the AR-antagonist Enzalutamide. Targeting HOXB13 acetylation mediated CRPC-SE establishment at critical tyrosine kinase genes could therefore have significant clinical implications in preventing PC recurrence.

overall_design: Genome-wide binding site analysis of HOXB13 in chromatin extracts prepared from prostate cancer cell lines.


title: Whole-genome CRISPR screening identifies N-glycosylation as an essential pathway and a potential novel therapeutic target in CALR-mutant MPN (Whole Genome CRISPR Screen).

overall_design: Whole-genome CRISPR screen, n=2 biological replicates per cell line, BA/F3-MPL cells expressing an empty vector or CALR 52 bp deletion (DEL52), grown in the presence or absence of interleukin 3 (IL3).


title: Transcriptomic profiles of myometrial PGR deficient and control mouse uteri at gestation day 13

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: Progesterone signaling is crucial for pregnancy. To investigate the role of myometrial progesterone receptor in support of pregnancy, genome-wide gene expression profiles of pregnant uterine tissues from myometrial PGR knockout and control mice were profiled by RNAseq. The transcriptomic alterations in response to PGR loss permit identification of the underlying molecular mechanisms by which progesterone and PGR control myometrial homeostasis for pregnancy.

overall_design: Mouse uterine tissues surrounding the embryo implantation sites at gestation day 13 were subject to RNA-seq analysis.

first: San-Pin

first: Francesco

last: DeMayo

first: Tianyuan

last: Wang

first: Lecong

last: Zhou


title: Selective targeting of GARP-LTGFb axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell anti-tumor immunity

city: Columbus

first: Yuzhou

last: chang

state: OH

address: 1800 Cannon Drive, Lincoln Tower ,

institute: ohio state univeristy

summary: Immune checkpoint blockade (ICB) has revolutionized cancer immunotherapy. However, the majority of cancer patients fail to respond clinically. One potential reason is the accumulation of transforming growth factor-beta (TGFb) in the tumor microenvironment (TME). TGFb drives cancer immune evasion in part by inducing regulatory T cells (Tregs) and limiting CD8+ T cell function. Glycoprotein-A repetitions predominant (GARP) is a cell surface docking receptor for activating latent TGF1, TGFb2 and TGFb3, with its expression restricted in effector Tregs, cancer cells as well as platelets. Herein we demonstrate that GARP overexpression in human cancers correlates with unfavorable TME and poor clinical response to ICB, raising a possibility of GARP blockade to improve cancer immunotherapy. However, it is unclear if targeting GARP in the TME is feasible without affecting platelets. We report an anti-human GARP antibody (named PIIO-1) specific for its ligand-interacting domain, effectively blocking activation of latent TGFb1. PIIO-1 lacks recognition of GARP-TGF complex on platelets. Using human GARP knock-in mice, we demonstrate that PIIO-1 does not cause thrombocytopenia, and is preferentially distributed in the TME and effective for treating both GARP+ and GARP- cancers, alone or in combination with anti-PD-1 antibody. PIIO-1 treatment reduces canonical TGFb signaling in tumor-infiltrating immune cells, prevents T cell exhaustion, and enhances CD8+ T cell migration into the TME in a CXCR3-dependent manner. Collectively, we conclude that GARP contributes to multiple aspects of immune resistance in cancer; anti-GARP antibody PIIO-1 is an efficacious and safe strategy to overcome ICB resistance, therefore warranting clinical development.

overall_design: 1x10^5 MB-49 Bladder Cancer cells were injected s.c. on the right flank of hLrrc32KI mice. PIIO-1 (200 ug/mouse, i.p.) were delivered on day 6 and 9 for 2 doses. Tumors were collected on day 10. Single cell suspension and RNA isolation were prepared, and then subjected to bulk RNA sequencing.

first: Anqi

last: Li


title: Exploring transcriptional regulation of Mycobacterium avium subsp. paratuberculosis after human THP-1 cell infection via dual RNA-seq analysis

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

summary: Host-pathogen interactions of Mycobacterium avium subsp. paratuberculosis infection at transcriptomic level were investigated in an in vitro macrophage infection model by dual RNA-seq analysis.

sample_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: Human THP-1 cells differentiated by PMA were infected with Mycobacterium avium subsp. paratuberculosis for 3 hrs. Total RNA of infected cells were subjected to dual RNA-seq.

first: Sang-Mok

last: Lee

first: Donghyuk

last: Kim

first: Han

last: Yoo


title: Mouse uteri at gestation day 13

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus


title: Chromatin conformation of the genome of pregnant mouse uteri

summary: To gain insight on the epigenomic environment of the pegnant uterus tissues, the Hi-C assay was emloyed to comprehensively document the chromatin conformation of the genome at gestation 13.

overall_design: Pooled uterine tissues from C57BL/6J mice at gestation day 13 were subject to the Hi-C library preparation by the Arima Genomics, followed by NextGen sequencing and data analysis.

last: Wu


title: DNA methylation profiling of umbilical cord blood cells from Trypanosoma cruzi infected and uninfected mothers

city: New Orleans

first: Eric

last: Dumonteil

state: LA

address: 1440 Canal st.

department: Tropical Medicine

institute: Tulane University

summary: Genome wide DNA methylation profiling of umbilical cord blood DNA samples using the Illumina Infinium MethylationEPIC array (approximately 850,000 CpGs). Samples included cord blood samples from infants born to women with (exposed) and without (control) infection with Trypanosoma cruzi parasites, to test for a potential epigenetic effect of in utero exposure to maternal infection.

overall_design: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip

first: Hans

last: Desale

first: Pierre

last: Buekens

first: Jackeline

last: Alger

first: Maria

last: Cafferata

first: Emily

last: Harville

first: Claudia

last: Herrera

first: Carine

last: Truyens


title: PGR genome occupancy and the H3K27ac histone mark profile in mouse uteri at gestation day 13

first: Franco

last: Demayo

summary: PGR genome occupancy and H3K27ac histone mark profiles in pregnant mouse uterine specimens were documented by ChIP-seq to investigate downstream targets of the progesterone receptor and candidate partner transcription regulators.

overall_design: Uterine tissues surrounding the embryo implantation sites from gestation day 13 wild type mice were subject to the ChIP-seq assay. ChIP-seq was performed by the Active Motif.

first: San-Pin

first: Francesco

last: DeMayo

last: Wang


title: Using single-worm RNA sequencing to study C. elegans responses to pathogen infection

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

summary: We have developed a single-worm RNA-seq method to effectively profile gene expression in individual C. elegans and applied this method to study C. elegans responses to pathogen infection.

overall_design: Five replicates of two groups of samples (five worms with or without exposure to P. aeruginosa for 24 hours) were collected and subjected to mechanical worm lysis, RNA isolation, cDNA synthesis, library preparation, sequencing, and sequence data analysis. At each step, the results of the single-worm RNA-seq were compared to those of standard RNA-seq. The sequence data (FASTQ files) of standard RNA-seq were generated in the study of Sellegounder et al. (Science Advances 2019; 5(11):eaaw4717) and were retrieved from the NCBI’s SRA database through the GEO using the accession number GSE122544. These sequence data (from N2_OP50 and N2_PA14 samples) were re-analyzed in the current study in the same way as in the single-worm RNA-seq.

first: Archer

first: Blake

last: Geppert


title: Cystatin M/E prevents osteolytic bone disease by inhibiting cathepsin-dependent stages of osteoclastogenesis

city: little rock

first: Dongzheng

last: Gai

state: AR

address: 4301 W Markham St

institute: UAMS

summary: To further determine how CST6 regulates osteoclast differentiation.

overall_design: RNA sequencing were performed on in vitro osteoclastogenesis on control macrophages (without RANKL sitimulation), RANKL treatment for 48h, RANKL plus CST6 treatment for 48h.

first: Fenghuang

last: Zhan


title: CD47 regulates the immunodynamics of CD8+ T cells

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: CD47 is a transmembrane glycoprotein that is ubiquitously expressed in different organs and tissues (Barclay and Van den Berg 2014; Liu, et al. 2017). In the human immune system, CD47 interacts with some integrins, two counter-receptor signal regulator protein (SIRP) family members, and the secreted thrombospondin-1 (TSP1) (Barclay and Van den Berg 2014; Gao, et al. 2016; Kaur, et al. 2013; Oldenborg, et al. 2000). CD47 has two established roles in the immune system. The CD47-SIRPα interaction was identified as a critical innate immune checkpoint, which delivers an antiphagocytic signal to macrophages and inhibits neutrophil cytotoxicity (Martínez- Sanz, et al. 2021). Its interaction with inhibitory SIRPα is a physiological anti-phagocytic “don’t eat me” signal on circulating red blood cells that is co-opted by cancer cells (Matlung, et al. 2017). Many malignant cells overexpress CD47 (Betancur, et al. 2017; Chao, et al. 2011; Jaiswal, et al. 2009; Majeti, et al. 2009; Oronsky, et al. 2020; Petrova, et al. 2017). CD47/SIRPα-targeted therapeutics have been developed to overcome this immune checkpoint for cancer treatment (Kaur, et al. 2020; Matlung, et al. 2017). Secondly, engagement of CD47 on T cells by TSP1 regulates their differentiation and survival (Grimbert, et al. 2006; Lamy, et al. 2007) and inhibits T cell receptor signaling and antigen presentation by dendritic cells (DCs) (Kaur, et al. 2014; Li, et al. 2002; Liu, et al. 2015; Miller, et al. 2013; Soto-Pantoja, et al. 2014; Weng, et al. 2014). TSP1/CD47 signaling has similar inhibitory functions to limit NK cell activation (Kim, et al. 2008; Nath, et al. 2018; Nath, et al. 2019; Schwartz, et al. 2019) and IL1β production by macrophages (Stein, et al. 2016). CD47 is therefore a checkpoint that regulates both innate and adaptive immunity. The recent understanding of CD47 antagonism associated with increased antigen presentation by DCs (Liu, et al. 2016) and natural killer cell cytotoxicity (Nath, et al. 2019) contributes to the heightened interest in CD47 as a therapeutic target (Kaur, et al. 2020).

overall_design: 16 total samples in 4 Groups: 4 WT Untreated, 4 CD47KO Untreated, 4 WT CD3+CD28 Activated, and 4 CD47KO CD3+CD28 Activated.

first: Pulak

last: Nath

first: Dipasmita

last: Pal-Nath

first: Sukhbir

last: Kaur

first: Arunkumar

last: Gangaplara

first: Margaret

middle: C

last: Cam

first: David

middle: D

last: Roberts


title: Experimental mouse model of chronic kidney disease reveals altered cardiac oxidative stress responses in CKD

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: Uremic cardiomyopathy is a clinically highly relevant cause of cardiovascular events in patients with chronic kidney disease (CKD). This study aimed at a comprehensive analysis of cardiac function and cardiac pathological characteristics in adenine-induced CKD in 129/Sv mice. This included the analysis of kidney function and morphology, heart function as well as cardiac hypertrophy, fibrosis and calcification. Also, cardiac RNA-sequencing was performed. Although overall, no cardiac dysfunction, hypertrophy or fibrosis could be observed, prolonged moderate CKD in this mouse model enhanced cardiac oxidative stress markers. In line, cardiac RNA-sequencing revealed an increase in oxidative stress-inducing signaling in CKD as well as anti-inflammatory feedback responses. This suggests a maladaptive preconditioning of the heart in CKD, which could increase the risk of enhanced cardiovascular damage upon additional cardiovascular risk factors and/or events.

overall_design: 4 control samples and 4 treatment samples were analysed with no replicates

first: Heidi

last: Noels

first: Janina

last: Frisch

first: Corinna

last: Schulte

first: Julia

last: Wollenhaupt


title: Circulating tumor cell-derived N-cadherin induces NK cell exhaustion and contributes to tumor self-seeding via the KLRG1 receptor

first: Chao

last: Lou

address: No. 639 Zhizaoju Road

institute: Shanghai Jiaotong University

summary: Circulating tumor cells (CTCs) can survive in the circulation and return to primary tumors through a self-seeding process. However, the mechanisms underlying CTC escape from natural killer (NK) cell-mediated immune surveillance remain unclear. In the present study, self-seeded tumor cells were isolated and characterized by applying a modified mouse model. The harvested self-seeded cells displayed resistance to NK cell-mediated lysis and a higher tumor seeding ability than their parental cells. Elevated expression levels of the CDH2 gene and its protein product, N-cadherin were found in self-seeded cell lines. We revealed an unrecognized role for soluble N-cadherin in inhibiting NK cell antitumor immunity. NK cells secreted cytokines, and fluid shear stress facilitated N-cadherin release from tumor cells by enhancing the activity of A disintegrin and metalloprotease 10 (ADAM10). Soluble N-cadherin triggered NK cell functional exhaustion by interacting with the killer cell lectin-like receptor subfamily G member 1 (KLRG1) receptor and therefore protected tumor cells from NK cell killing. Elevated N-cadherin expression was observed in recurrent oral cancer samples compared to matched primary tumors. Our findings illustrated an unknown mechanism by which CTCs evaded NK cell-mediated immune surveillance, which may contribute to tumor self-seeding and recurrence.

overall_design: Examination of differentially expressed mRNAs between SCC9-seeded and SCC9-parental cells.

first: Jianbo

last: Shi

first: Zhenlin

last: Dai

first: Qin

last: Xu


title: ChIP-seq of a transcriptional regulator AtSDR4L

city: Vancouver

first: Liang

last: Song

state: British Columbia

address: 2231-6270 University Boulevard

department: Botany

country: Canada

institute: University of British Columbia

summary: Repression of embryonic traits during the seed-to-seedling phase transition requires the inactivation of master transcription factors associated with embryogenesis. How the timing of such inactivation is controlled is unclear. Here, we report on a novel transcriptional co-repressor, Arabidopsis thaliana SDR4L, that forms a feedback inhibition loop with the master transcription factors LEC1 and ABI3 to repress post-germinative embryonic traits. LEC1 and ABI3 regulate their own expression by inducing AtSDR4L during mid- to late embryogenesis. AtSDR4L directly binds to the promoter of LEC1. Atsdr4l mutant seedlings phenocopy the LEC1 overexpressors, and their embryonic traits could be partially rescued by impairing LEC1 or ABI3. The penetrance and expressivity of the Atsdr4l phenotypes depend on both developmental and external cues, demonstrating the broad regulatory potential offered by AtSDR4L during the seed-to-seedling phase transition.

overall_design: ChIP was carried out using two biological replicates of β-Estradiol induced AtSDR4-HA seedlings. A control ChIP was carried out using uninduced AtSDR4-HA seedlings.  β-Estradiol induced treament samples and  uninduced control sample were harvested at 4 days after imbibition. Libraries were sequenced on Illumina NextSeq2000. Peaks were called by MACS2 (v2.2.7.1) between the treatment and control samples using demultiplexed and adatper-trimmed pair-end reads.

first: Bailan

last: Lu

first: Milad

last: Alizadeh

first: Ryan

last: Hoy


title: RNA-sequencing in medial prefrontal cortex of early socially isolated mice

summary: To explore the molecular mechanism underlying social isolation and resocialization, we performed RNA-seq on mPFC samples from the ~7-week-old control and social isolation mice. We identified 1265 differentially expressed genes (DEGs) that were enriched in 4 pathways: cognitive behavior, myelin development, synaptic development, and ion channels.

overall_design: 7-week-old Control and Social isolation mice


title: Transcriptome and DNA Methylome Analyses Reveal Underlying Mechanisms for the Racial Disparity in Uterine Fibroids

first: Jose

last: Teixeira

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

overall_design: Refer to individual Series


title: Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine


title: Comparison of WT and CHD2 haploinsufficent human interneuron progenitor (hMGE) and interneuron (hcIN) models, to define differences in RNA expression, genomic accessibility and histone 3 lysine 27 acetylation

summary:
Background: Mutations in the chromatin remodeller CHD2 have been strongly associated with multiple neurodevelopmental disorders. However the precise function of CHD2 through neuronal development remains largely uncharacterized.
Methods: We have used our protocol for generating cortical interneurons from human embryonic stem cells to study the role of CHD2 in cortical interneuron development, by comparing wild type hMGE and hcINs with a model with CHD2 haploinsufficency
Results: This work found that CHD2 controls the expresson of genes with rolls in cell-cell interaction in neuronal precursors and directly influences the exprssion of genes necessary for the production of post-mitotic cortical interneurons
Conclusions: As CHD2 plays distinct roles in several aspects of interneuron development, pathogenic CHD2 mutations have high potential to disrupt one or more of these events, contributing to neurodevelopmental disorders

overall_design: For each time point, genotype and data set there are 2-4 biological replicates generated from parrellel differentiation from clonal hESC lines.

first: Emily

last: Lewis

first: Gareth

last: Chapman

first: Paul

last: Gontarz

first: Bo

last: Zhang


title: Comparative RNAseq of human WT and PARP3-/- LN229 cells

city: Illkirch

first: Françoise

last: DANTZER

address: 300 boulevard S. Brant

country: France

institute: CNRS

summary: To identify the biological pathways regulated by PARP3, RNAseq of the WT and PARP3-/- LN229 human glioblastoma cells were performed. Samples were collected from subconfluent cells for total RNA isolation and RNA sequencing

overall_design: Three biological replicates of PARP3WT_LN229 and PARP3KO_LN229 cells were collected. PARP3KO_LN229 were engineered using the Crispr/Cas9 technology (disruption exon2-exon9).

first: Francoise

last: Dantzer


title: Characterization of CHD2 binding, H3K27ac, H3K27me3 and H3K4me3 in hESC, hMGE and hcIN

summary:
Background: Mutations in the chromatin remodelling protein CHD2 have been strongly associated with multiple neurodevelopmental disorders. However the precise function of CHD2 through neuronal development remains largely uncharacterized.
Methods: We have used our protocol for generating cortical interneurons from human embryonic stem cells to study the role of CHD2 in brain development
Results: This work found that CHD2 binding is largely associated with open and active chromatin
Conclusions: As CHD2 plays distinct roles in several aspects of interneuron development, pathogenic CHD2 mutations have high potential to disrupt one or more of these events, contributing to NDDs.

overall_design: For each time point and data set, 3-4 biological replicates were generated from parallel differentiation from H9 hESCs.


title: shCDK9 or shDHODH sensitizes cells to gilteritinib treatment by altering transcriptomes of AML cells

first: Pu

address: 1258 Bunkerhill Blvd, AptB

institute: Ohio State University

summary: Acquisition of an internal tandem duplication of the juxtamembrane region of FLT3 (FLT3-ITD) is a common event in Acute myeloid leukemia (AML) patients and is associated with poor outcomes at high allelic frequency.  Although targeted therapies against FLT3-ITD exist, narrow therapeutic index as monotherapies and failure to achieve complete remission limits their clinical application. Using a genome-wide CRISPR knockout screen, we identified cyclin-dependent kinase (CDK9), protein arginine methyltransferase (PRMT5) and dihydroorotate dehydrogenase (DHODH) as novel synthetic lethal partners with gilteritinib treatment. We demonstrated that genetic or pharmacologic inhibition of these targets in combination with gilteritinib synergistically kill AML cells. The presence of FLT3-ITD was shown to cause a significant increase in aerobic glycolysis, rending the leukemia cells highly sensitive to pharmacological inhibition of glycolytic activity. Supportive of this, our screen shows that sgRNAs targeting ~28 genes in the glycolysis pathway are enriched in cells treated with gilteritinib, suggesting that switching to oxidative phosphorylation from aerobic glycolysis may represent a metabolic adaption of the leukemic cells to resistance to FLT3-targeted therapy. Interestingly, the knockdown of CDK9, PRMT5 or DHODH in presence of gilteritinib cooperatively shuts down oxidative phosphorylation and associated purine biosynthesis and mevalonate pathway, implying inhibition of these genes along with proteins involved in the mitochondria respiratory chain complexes and energy metabolism may represent an attractive strategy to resensitize leukemic cells to gilteritinib treatment. Overall, these findings provide the basis for maximizing therapeutic impact of FLT3-ITD inhibitors and provide a rationale for a clinical trial of these novel combinatorial therapies.

overall_design:
shCDK9 or shDHODH -stable MOLM13 cells were treated with sublethal doses of gilteritinib before being subject to RNA-seq analysis
shCDK9, shDHODH or scrambled shRNA-stable MOLM13 were treated with DMSO or 8nM gilteritinib for 48 or 96 hrs in triplicates before RNA was extracted.

first: P

first: R

last: Lapalombella

last: Yan


title: Single-Cell Analysis of Transcriptome and TCR Sequencing Reveals Functional Heterogeneity of T Cell in Murine Heart Transplantation

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

summary: To illustrate the functional heterogeneity of T cells in the heart allograft rejection，we established the murine heterotopic heart transplantation model and  isolated   CD45  positive cells from cardiac grafts and spleens for single cell transcriptome and TCR sequencing.

overall_design: 8-10 weeks male C57BL/6 (H-2b) and BALB/c(H-2d) were purchased from Charles River (Beijing, China). All mice experiments were performed in a specific pathogen-free facility according to the guidelines of the animal care and use committee of Huazhong University of Science and Technology. We established the murine heterotopic heart transplantation model as previously described . Allograft group: BALB/c (H2d) hearts were transplanted into fully MHC-mismatched C57BL/6 (H2b) recipients. Isograft group: C57BL/6 (H2b) hearts were transplanted into MHC-matched C57BL/6 (H2b) recipients. Cardiac allografts normally arrest at day 7 after transplantation because of acute transplantation rejection. Therefore, we harvested spleens and cardiac allografts of allograft group recipients at day 6 before cardiac allografts arrest. At the same time, spleens and cardiac isografts of isograft group recipients were harvested. CD45+ cells were respectively isolated from cardiac allografts, allograft group recipients’ spleen, cardiac isografts and isograft group recipients’ spleen after digestion, centrifugation and flow sorting. In brief, cardiac grafts were cut into pieces and digested with 1 mg/mL of collagenase B (Roche 11088815001) in HEPES buffer for 45 min at 37°C. After digestion, cell suspensions were collected and filtered with 70-μm cell strainers (BIOFIL), Percoll (Beijing Solarbio Science & Technology Co., Ltd.) was used to purify mononuclear cells through density centrifugation with 600g 25min RT not-brake. Splenocytes were prepared through grinding, erythrocyte lysis, washing and centrifugation (600g, 3min). CD45+ live cells were then sorted by FACSAria flow cytometer after Cardiac graft infiltrating cells and splenocytes stained with CD45-APC (Biolegend 103112) and Zombie GreenTM Fixable Viability Kit (Biolegend 423112).

first: Zhang

last: Chen

first: Heng


title: Transcriptomic profiles of myometrial PGR deficient and control mouse uteri at pseudopregnancy day 6

first: Franco

last: Demayo

summary: Progesterone signaling is crucial for pregnancy. To investigate the role of myometrial progesterone receptor in support of pregnancy, genome-wide gene expression profiles of pregnant uterine tissues from myometrial PGR knockout and control mice were profiled by RNAseq. The transcriptomic alterations in response to PGR loss permit identification of the underlying molecular mechanisms by which progesterone and PGR control myometrial homeostasis for pregnancy.

overall_design: Mouse uterine tissues surrounding the embryo implantation sites at pseudopregnancy day 6 (PPD6) were subject to RNA-seq analysis.

first: San-Pin

first: Francesco

last: DeMayo

first: Tianyuan

last: Wang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and EedcKO Forebrain Transcriptomes

city: Beijing

last: shuangfeng

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: The histone methyltransferase complex PRC2 is a crucial chromatin modifier and controls key steps in developmental transitions and cell fate choices. Mutations in PRC2 core subunits are found in Weaver syndrome with craniofacial defects, intellectual disabilities, and often macrocephaly, but its pathogenicity and molecular mechanism are unknown. Here, we examined the role of PRC2/Eed in neural stem/progenitor cells (NSPCs) during cortical neurogenesis We found that Eed is highly expressed in embryonic cerebral cortex and specific deletion of Eed in forebrain reduced the number of upper layer neurons but not deeper layer neurons and ultimately contributed to abnormal cortical development. In addition, our results revealed that PRC2/Eed regulated Hedgehog signaling pathway through activation of Gli3 not dependent on H3K27me3 but H3K27ac. What?s more, Increased Gli3 in NSPCs could reduce Gli1 expression and contribute to the defects of cortical neurogenesis caused by Eed deletion. Finally, Hedgehog signaling activation with small molecule SAG or genetic inactivation of Ptch1 could partially rescue the cortical neurogenesis defects in vivo after Eed depletion. In general, we identified a novel PRC2/Eed-Gli3-Gli1 regulatory axis that is critical for normal cortical neurogenesis. Our findings define a critical function for PRC2/Eed in cortical development and shed light on the genetic basis of intellectual disabilities of neural developmental disorders caused by PRC2/Eed mutation.

overall_design:
We report the forebrain RNA-seq data of wild type and EedcKO littermate mice at E12.5. We mapped about 30 million sequence reads per sample to the mouse genome (build mm10). By comparing the sequencing data of mice in the wild time group and the EedcKO group, the transcriptome map of Eed deletion can be obtained. These data are useful for the study of Eed in early neurodevelopment.
Examination of 2 different group in E12.5 forbrain tissues..

first: Shuang-Feng

first: Shang-Kun

last: Dai

first: Hong-Zheng

last: Du

first: Hui

first: Chang-Mei

last: Liu


title: Genome-wide maps of chromatin state in E12.5 forebrain tissues

overall_design:
We report the combined application of X-ChIP and CUT&Tag sequencing technology for high-throughput profiling of transcription factor and histone modifications in mammalian cells. By obtaining enough bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of E12.5 wild type and EedcKO forebrains. We find that Eed, histone 3 lysine 27 trimethylation, histone 3 lysine 27 acetylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. These data help us better understand the intrinsic regulatory mechanism of Eed in neurodevelopment.
Examination of 2 different groups in E12.5 forbrain tissues..


title: PRC2/Eed Downregulates Hedgehog Signaling through Activation of Gli3 Expression in Cortical Neurogenesis


title: Effect of DDX5/DDX17 on genome-wide RNA Polymerase II distribution in SH-SY5Y cells

city: Lyon

first: Cyril

middle: F

last: Bourgeois

address: 46 Allée d'Italie

department: LBMC

institute: ENS de Lyon

summary: This project includes ChIP of total RNA pol II in human SH-SY5Y neuroblastoma cells following the joint depletion of RNA helicases DDX5 and DDX17 to determine the genome-wide effect of DDX5/DDX17 on RNA Pol II distribution.

overall_design: Cells were treated with a control siRNA or with a siRNA targeting DDX5/DDX17, chromatin was extracted and total RNA Pol II was immunoprecipitated using the F12 antibody. All biological conditions were prepared in triplicates.

first: Jessica

last: Valat


title: Gene expression of mouse oral cancer cell lines

city: Miaoli County

first: Ya-Wen

address: 35, Keyan Rd, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary:
We established two murine OSCC cell lines, named M1-2 and M2-3, from a mouse tumor induced by 4-nitroquinoline 1-oxide (4-NQO)/arecoline.
After in vitro selection using sphere culture, NHRI-HN1 and NHRI-HN2 were derived from M1-2 and M2-3 cells, respectively. Only NHRI-HN1 cells are capable of generating orthotopic tumors in syngeneic mice.

overall_design: Total RNA was extracted using Trizol reagent and purified using RNeasy mini kit. Genome-wide gene expression analysis was performed using the Affymetrix Mouse Clariom S Assay. Microarray analysis were conducted as followed the standard Affymetrix procedures. Hybridized slides were scanned by Affymetrix Gene Chip scanner 3000 7G system. Raw data were generated using Partek Genomics Suite version 7 software.

first: Yu-Lin


title: Effect of gene expression changes after LJ4827, 5-iodotubercidin treatment on HeLa cells

status: Public on Sep 20 2022

first: Eun-Ji

last: Kwon

summary: Analysis of compound (LJ4827, 5ITU) induced gene expression on HeLa cell. We investigated the mode of action of the LJ4827 and enriched gene signatures by treatment induced transcriptome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HeLa cells and its treated cells.

first: Hyuk-Jin

last: Cha


title: RNA-seq of microglia from 3-dpf siblings, mafba and mafbb single mutant and DMut zebrafish

city: Hong Kong

first: LIANG

last: LOU

address: HKUST

department: LIFS

institute: HKUST

summary: In order to search for the downstream target genes of Mafba and Mafbb, we isolated microglia (3 cells per sample) from 3-dpf zebrafish brain of siblings, mafba and mafbb single mutants and DMut under Tg(mpeg1:DsRedx) transgenic background (3 samples per genotype), respectively, and then performed RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of microglia from 3-dpf siblings, mafba and mafbb single mutants and DMut

first: Liang

last: Lou

first: Tao

last: Yu

first: Yimei

first: Shizheng

last: Zhao

first: Shachuan

last: Feng

first: Jin

last: Xu

first: Zilong

last: Wen


title: Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development

city: Stanford

first: Ragni

last: Phansalkar

address: 318 Campus Drive

institute: Stanford University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development (Human)

summary: Most cell fate trajectories during development follow a diverging, tree-like branching pattern, but the opposite can occur when distinct progenitors contribute to the same cell type. During this convergent differentiation, it is unknown if cells ‘remember’ their origins transcription- ally or whether this influences cell behavior. Most coronary blood vessels of the heart develop from two different progenitor sources- the endocardium (Endo) and sinus venosus (SV)—but whether transcriptional or functional differences related to origin are retained is unknown. We addressed this by combining lineage tracing with single-cell RNA sequencing (scRNAseq) in embryonic and adult mouse hearts. Shortly after coronary development begins, capillary endothelial cells (ECs) transcriptionally segregated into two states that retained progenitor-specific gene expression. Later in development, when the coronary vasculature is well established but still remodeling, capillary ECs again segregated into two populations, but transcriptional differences were primarily related to tissue localization rather than lineage. Specifically, ECs in the heart septum expressed genes indic- ative of increased local hypoxia and decreased blood flow. Adult capillary ECs were more homoge- neous with respect to both lineage and location. In agreement, SV- and Endo-derived ECs in adult hearts displayed similar responses to injury. Finally, scRNAseq of developing human coronary vessels indicated that the human heart followed similar principles. Thus, over the course of development, transcriptional heterogeneity in coronary ECs is first influenced by lineage, then by location, until heterogeneity declines in the homeostatic adult heart. These results highlight the plasticity of ECs during development, and the validity of the mouse as a model for human coronary development.

overall_design:
Single cell RNA-sequencing of endothelial cells from lineage-traced embryonic and adult mouse hearts, and from human fetal hearts at 3 gestational ages.
--------------------------------------
Authors state "We are not uploading the raw human data due to privacy concerns."

first: Ragini

first: Josephine

last: Krieger

first: Mingming

first: Sai

last: Kolluru

first: Robert

last: Jones

first: Stephen

last: Quake

first: Irving

last: Weissman

first: Daniel

last: Bernstein

first: Virginia

last: Winn

first: Gaetano

last: D'Amato

first: Kristy

last: Red-Horse


title: Murine liver: Sperm vs. seminal plasma influences

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary:
Transcriptional profiling of adult mouse liver tissue comparing offspring derived from sperm and seminal plasma of normal protein diet fed males (controls, NN), sperm and seminal plasma from males fed a low protein diet fed males (LL), sperm from normal protein fed males and seminal plasma from low protein fed males (NL) or sperm from low protein diet fed males and seminal plasma from normal protein diet males (NL). The first letter denotes the diet of the sperm donor and the second letter the diet of the seminal plasma donor.
Three-condition experiment: NN vs. LL, NN vs. NL, NN vs. LN. Adult offspring liver tissue. Biological replicates: 7 control (NN), 9 LL, 7 NL and 7 LN. One replicate per array chip.

overall_design: Offspring were generated using sperm and seminal plasma from males fed different diets. At 16 weeks of age, offspring were culled and liver samples collected from males and females from across all litters generated to ensure biological variation was standardised across all groups.

first: Adam

last: Watkins


title: Global hypermethylation of intestinal epithelial cells is a hallmark feature of neonatal surgical necrotizing enterocolitis [lcm_colon_ileum]

city: Pittsburgh

first: David

last: Peters

state: PA

address: 204 Craft Avenue

institute: Magee-Womens Research Institute

summary: Necrotizing enterocolitis (NEC) remains one of the overall leading causes of dealth in premature infants, and the pathogenesis is unpredictable and not well characterized. The aim of our study was to determine the molecular phenotype of NEC via transcriptomic and epithelial cell-specific epigenomic analysis, with a specific focus on DNA methylation.

overall_design: Using laser capture microdissection, epithelial cell-specific methylation signatures were characterized by whole-genome bisulfite sequencing of ileal and colonic samples at the time of surgery for NEC and after NEC had healed at reanastomosis (n=40). RNA sequencing was also preformed to determine the transcriptomic profile of these samples, and a comparison was made to the methylome data.

first: Misty

last: Good

first: Tianjiao

last: Chu

first: Patricia

last: Shaw

first: Lora

last: McClain

first: Austin

last: Chamberlain

first: Carlos

last: Castro

first: Jamie

last: Rimer

first: Belgacem

last: Mihi

first: Qingqing

last: Gong

first: Lila

last: Nolan

first: Krista

last: Cooksey

first: Laura

last: Linneman

first: Pranjal

last: Agrawal

last: Finegold


title: Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development (Mouse)

first: Ragni

last: Phansalkar

overall_design: Single cell RNA-sequencing of endothelial cells from lineage-traced embryonic and adult mouse hearts, and from human fetal hearts at 3 gestational ages.

first: Ragini

first: Josephine

last: Krieger

first: Mingming

last: Zhao

first: Sai

last: Kolluru

first: Robert

last: Jones

first: Stephen

last: Quake

first: Irving

last: Weissman

first: Daniel

last: Bernstein

first: Virginia

last: Winn

first: Gaetano

last: D'Amato

first: Kristy

last: Red-Horse


title: Effect of PJ-34, 5-aza-dC, TSA on HCT116 & RKO cells

city: Nagasaki

first: Mitsuko

last: Masutani

state: Nagasaki

address: 1-12-4 Sakamoto

department: Department of Molecular and Genomic Biomedicine

country: Japan

institute: Nagasaki University

summary: In microarray analysis, combinational treatment with PJ-34 and 5-aza-dC caused dissimilar broad changes in gene expression profiles compared with their single treatments in both HCT116 and RKO cells. Profiles of reactivation of silenced genes were also different in combination of PJ-34 and 5-aza-dC and their single treatments. The results suggest that combinational use of 5-aza-dC and PARP inhibitor may be useful by causing distinct transcriptional profile changes.

overall_design: HCT116 & RKO cells were treated with control, single and combinational treatment with PJ-34, 5-aza-dC, TSA and microarray analysis was carried out to examine transcriptional profiles.

first: Hideki

last: Ogino

first: Miho

last: Maeda

first: Kensuke

last: Hamda

first: Tomonori

last: Araki


title: Monoamine oxidase-dependent pro-survival signaling in diabetic hearts is mediated by miRNAs

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: Diabetes leads to cardiomyopathy and heart failure, the leading cause of death for diabetic patients. Monoamine oxidase (MAO)-dependent reactive oxygen species (ROS) formation contributes to the development of diabetic cardiomyopathy by inducing mitochondrial and cardiomyocyte dysfunction. Yet, it is unclear whether, in addition to the direct effects exerted by MAO-dependent ROS on mitochondria, MAO activity is able to post-transcriptionally regulate cardiomyocyte function and survival in diabetes. To this aim, we performed gene and miRNA expression profiling in cardiac tissue from a mouse model of type 1 diabetes (T1D) with or without pharmacological MAO inhibition. We found that MAO-dependent ROS generation in T1D hearts leads to profound transcriptomic changes, affecting autophagy and pro-survival pathways activation. MAO activity in T1D hearts affected expression levels of miR-133a-3p, -193a-3p, and -27a-3p that target insulin-like growth factor receptor 1 (Igf1r), growth factor receptor bound protein 10 and inositol polyphosphate 4 phosphatase type 1A, respectively, all components of the Igf1r/PI3K/Akt signaling pathway. Indeed, Akt activation was significantly downregulated in T1D hearts, whereas MAO inhibition restored the activation of this pro-survival pathway. The present study provides an important link between MAO activity, transcriptomic changes, and activation of pro-survival signaling and autophagy in diabetic cardiomyopathy.

overall_design: Heart samples were collected from three different mice per group. Groups were: 1) control mice (healthy no treated), 2) controls treated with pargyline to inhibit MAO (monoammine oxidase), 3) diabetic mice, and 4) diabetic mice trated with pargyline. For a complete description of the experiment see the section treatment protocol.

first: Stefano

last: Cagnin

first: Caterina

last: Millino

first: Beniamina

last: Pacchioni

first: Marco

last: Brugnaro

first: Moises

last: Di Sante

first: Carmen

last: Troiano

first: Nina

last: Kaludercic


title: Monoamine oxidase-dependent pro-survival signaling in diabetic hearts [total RNA]


title: Monoamine oxidase-dependent pro-survival signaling in diabetic hearts

type:
Non-coding RNA profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: A New Model Organism to Investigate Extraocular Photoreception: Opsin and Retinal Gene Expression in the Sea Urchin Paracentrotus lividus

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

institute: Stazione Zoologica Anton Dohrn

summary: Sea urchins lack proper eye organs but are photosensitive. In this study, we investigate an extraocular photoreceptor cell (PRC) system in developmental stages of the sea urchin Paracentrotus lividus.

overall_design: Generation and analysis of single cell RNA-seq data of mature Paracentrotus lividus rudiment.

first: Periklis

last: Paganos

first: Esther

last: Ullrich-Lüter

first: Filomena

last: Caccavale

first: Danila

last: Voronov

first: Inés

last: Fournon Berodia

first: Maria

middle: I


title: Metastasis-repressive CircRNA MASCOT Regulates Distribution of the Splicing Factor hnRNP M

city: chengdu

first: PAN

last: YiTong

address: Wangjiang Street

institute: Sichuan University

summary: Alternative splicing (AS) diversifies the transcriptome complexity and is usually hijacked by cancer cells. Here, we identified heterogeneous nuclear ribonucleoprotein M (hnRNP M) as an indispensable contributor to EMT-related AS reprogramming, whose sub-nuclear distribution of hnRNP M is altered in metastatic tumors. Upon TGFβ stimulation, hnRNP M trends to disassociate with a circRNA called MASCOT (hnRNP M-ASsociated Circular RNA Of TGFβ) that demonstrated an impressive inhibitory effect on EMT process and tumor metastasis. Mechanistically, the anti-metastatic effect of MASCOT is attributed to not only its competition with U2 RNA splicing factors to recruit hnRNP M in the nucleoplasm, but also the anchorage of hnRNP M with nucleolin into the nucleolus to cause a temporospatial separation of hnRNP M from spliceosome. Moreover, the correlation between MASCOT expression and hnRNP M sub-nuclear localization was validated in clinical specimens. Our study deciphers the regulatory codes controlling AS networks and highlights MASCOT as a promising therapeutic to treat metastasis.

overall_design: A549 cells overexpressing the flag-hnRNP M or the empty flag plasmids were stressed by TGFβ and cell lysates were precipitated with anti-flag agarose to caputure hnRNP M-associating factors. Next, the RNA components were extracted from agarose and generate RIP-seq library.

first: Jiawei

last: Guo

first: Ke

last: Li

first: Yue

last: Ming

first: Yitong

last: Pan

first: Wenrong

last: Liu


title: RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2

city: Baltimore

first: Venu

last: Raman

address: 720 Rutland Ave, Traylor 338

department: Radiology

institute: Johns Hopkins University

summary: SARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and vaccine efficacy towards them is waning. As a result, SARS-CoV-2 will continue to have a deadly impact on public health into the foreseeable future. One strategy to bypass the continuing problem of newer variants is to target host proteins required for viral replication. We have used this host-targeted antiviral (HTA) strategy that targets DDX3, a host DEAD-box RNA helicase that is usurped by SARS-CoV-2 for virus production. We demonstrated that targeting DDX3 with RK-33, a small molecule inhibitor, reduced the viral load in four isolates of SARS-CoV-2 (Lineage A, and Lineage B Alpha, Beta, and Delta variants) by one to three log orders in Calu-3 cells. Furthermore, proteomics and RNA-seq analyses indicated that most SARS-CoV-2 genes were downregulated by RK-33 treatment. Also, we show that the use of RK-33 decreases TMPRSS2 expression, which may be due to DDX3s ability to unwind G-quadraplex structures present in the TMPRSS2 promoter. The data presented supports the use of RK-33 as an HTA strategy to control SARS-CoV-2 infection, irrespective of its mutational status, in humans.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Calu-3 cells infected with SARS-CoV-2 virus and treated with RK-33 in biological replicates of four. Controls are uninfected cells and DMSO.

first: Farhad

last: Vesuna


title: Organotypic stromal cells impact endothelial cell transcriptome in 3D microvessel networks

city: Davis

first: Matthew

last: Curtis

address: One Shields Dr.

institute: University of California, Davis

summary: ECFC-ECs are considered to be a plastic and naive endothelial cell.  We combined ECFC-ECs with different stromal cells to see the resultant change of endothelial cell transcriptome due to different stromal cells.

overall_design: ECFC-ECs and a variety of organotypic stromal cells (Bone marrow, heart, skin, lung, pancreatic cancer, normal pancreas) were combined in 3D in vitro fibrin hydrogels and allowed to grow for 7 days into microvessel networks.

first: Natalie

last: Kelly

first: Christopher

last: Hughes

first: Steven

last: George


title: Myeloid cell-expressed heme oxygenase-1 mitigates liver injury and fibrosis via the ligand of numb-protein X1 (LNX1)-Notch1 pathway

city: Boston

first: Sean

last: Lawler

state: MA

address: 75 Francis St

institute: Brigham and Women's Hospital

summary: Activation of resident macrophages (Mf) and hepatic stellate cells in the perisinusoidal space is a key event in chronic liver injury. Under these circumstances, dysregulated innate immunity and inflammatory processes drive progressive accumulation of collagen, resulting in scarring and eventually, cirrhosis with life-threatening complications. In summary, by using RiboTag-based sequencing, we identified a novel regulatory LNX1/Notch1 pathway downstream of HO-1 that drives a protective form of M2 polarization of Mf and inhibits expansion of reactive cholangiocytes and liver fibrosis.

overall_design: To investigate the role of HO-1+ Mf in liver fibrosis progression we subjected Hmox1flfl and LysM-Cre:Hmox1flfl mice to BDL surgery. To understand the mechanisms behind the protective role of M-expressed HO-1 in the BDL model, we employed the RiboTag technology to specifically analyze the gene expression profile of HO-1-deficient M. This approach allows efficient isolation of ribosome-associated mRNAs from specific cell types based on Cre-driven expression that drives tissue-specific HA-tagging of ribosomes (Sanz et al., 2009). We bred LysM-Cre:RiboTag mice to Hmox1flfl mice and obtained animals with conditional deletion of HO-1 in myeloid cells and concomitant myeloid-specific ribosome epitope-tagging (LysM-Cre:Hmox1flfl:RiboTag mice)

first: Barbara

last: Wegiel


title: ERN2/IRE1b regulates microbiota-induced goblet cell development in the mouse colon

first: Michael

last: Grey

address: 300 Longwood Avenue, Enders 606

department: Gastroenterology, Hepatology, and Nutrition

institute: Boston Children's Hospital

summary: The purpose of this study was to understand how the epithelial specific ER stress sensor ERN2/IRE1b contributes to goblet cell development in reseponse to gut microbes.

overall_design: Comparative gene expression analysis of RNAseq data for colon crypt epithelial cells isolated from conventinally raised, germ free, and microbially colonized germ free WT and Ern2-/- mice

first: Wayne

last: Lencer


title: Identification of Src Family Kinases as potential therapeutic targets for chemotherapy-resistant triple negative breast cancer

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Neoadjuvant chemotherapy (NAC) remains the cornerstone of treatment for triple negative breast cancer (TNBC) with the goal of complete eradication of disease.  However, for patients with residual disease after NAC, recurrence and mortality rates are high and identification of novel therapeutic targets are urgently needed. Here we quantified tyrosine phosphorylation (pTyr) mediated signaling networks in chemotherapy sensitive (CS) and resistant (CR) TNBC patient derived xenografts (PDX) to gain novel therapeutic insights. We identified Src Family Kinases (SFKs) as potential therapeutic targets in CR TNBC PDXs. Treatment with dasatinib, an FDA approved SFK inhibitor, led to inhibition of tumor growth in vivo. Further analysis of post-treatment PDXs revealed multiple mechanisms of actions of the drug confirming the multi-target inhibition of dasatinib. Direct analysis of pTyr in tumor specimens from TNBC patients suggest a low prevalence of SFK driven tumors in the clinic which may explain why clinical trials evaluating dasatinib failed in unselected breast cancer patients. Taken together, these results underscore the importance of pTyr characterization of tumors in identifying new targets as well as stratifying patients based on their activated signaling networks for therapeutic options. Our data also suggest that treatment with an SFK inhibitor may benefit a subset of TNBC patients with CR disease.

overall_design: Three to five replicates each of PDXs derived from 4 different PDX lines of triple negative breast cancer were treated with vehicle, paclitaxel, dasatinib or dasatinib+paclitaxel for 21 days. Mice were euthanized when met the euthanization criteria. Tumors were resected and flash frozen. RNA was isolated from the tumor tissues and subjected to RNAseq analysis.

first: Ishwar

last: Kohale

first: Jia

last: Yu

first: Yongxian

last: Zhuang

first: Xiaoyang

last: Fan

first: Judy

last: Boughey

first: Jodi

middle: M

last: Carter

middle: P

last: Goetz

first: Liewei

last: Wang

first: Forest

last: White


title: Role of ERN2/IRE1b in mediating unfolded protein response to ER stress

summary: The purpose of this study was to understand how expression of the ER stress sensor ERN2/IRE1b affects the unfolded protein response to ER stress

overall_design: Comparative gene expression analysis of RNAseq data for HEK293 cell line with inducible expression of FLAG-ERN2 transgene under control conditions (no stress) and stress stimulation


title: Abnormal Transcriptome-wide of DNA demethylation in Folate deficiency caused neural tube defects [hMeDIP]

city: beijing

first: shan

last: wang

address: 2yabao road

institute: Capital Institute of Pediatrics

summary: To investigate the associated with abnormal DNA demethylation and neural tube defects (NTDs) with folate deficiency, we etablished  mouse embryonic stem cells (mESCs) Sv/129 in folate-deficiency-treated.

overall_design:
We then performed 5hmC profiling analysis using data obtained from hMeDIP-seq of the cell model.
Comparative 5hmC profiling analysis of RNA-seq data for sv129 cells as control group and its folate-deficiency-treated as experimental group.

first: Shan

first: Yubing

last: Zeng

first: Pei

last: Pei

first: Ting

last: Zhang


title: Abnormal Transcriptome-wide of DNA demethylation in Folate deficiency caused neural tube defects [MeDIP]

overall_design:
We then performed 5mC profiling analysis using data obtained from MeDIP-seq of the cell model.
Comparative 5mC profiling analysis of RNA-seq data for sv129 cells as control group and its folate-deficiency-treated as experimental group.


title: Abnormal Transcriptome-wide of DNA demethylation in Folate deficiency caused neural tube defects [ChIP-seq]

summary: To investigate the associated with DNA demethylation and neural tube defects (NTDs) with folate deficiency, we etablished  mouse embryonic stem cells (mESCs) Sv/129 in folate-deficiency-treated.

overall_design:
We then performed the enrichment of H3K27ac analysis using data obtained from H3K27ac ChIP-seq in the cell model.
Comparative the enrichment of H3K27ac analysis of ChIP-seq data for sv129 cells as control group and its folate-deficiency-treated as experimental group.


title: Effects of age and sex on gene expression in the mouse heart

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

summary: To compare the effects of biological sex (female/male) and age (4 mo./20 mo.) on C57BL/6J mouse hearts, we performed mRNA sequencing.

overall_design: Comparative gene expression analysis in male, female mouse hearts from 4 mo. and 20 mo. C57BL/6J mouse hearts (n=3 per group) using short-read Illumina polyA+ mRNA sequencing on a NovaSeq 6000 platform

first: Yu

last: Han

first: Maggie

last: Lam


title: The osteogenic capacity and lncRNA/mRNA expression profile of periosteal-derived mesenchymal stem cells of congenital pseudarthrosis of the tibia

city: Hunan

first: Yang

last: Ge

address: No. 86, Ziyuan Road, Changsha City, Hunan Province

institute: Hunan Children’s Hospital, Hunan

summary:
Purpose: Congenital pseudarthrosis of the tibia (CPT) is an uncommon disease. The biological properties, molecular patterns, and regulatory mechanisms of periosteal-derived mesenchymal stromal cells (PDMSCs) remain unclear.
Methods: PDMSCs were separated from patients with either CPT or control donors. The purity of stem cells was determined by flow cytometry. Using osteogenic induction culture and Co-culture THP1-derived macrophage and PDMSCs, the osteogenic and osteoclastic activities were determined by histological examination and western blot analysis. The differential expression of lncRNA/mRNA was analyzed through RNA-Seq.
Results: The proportion of CD31 and CD34 positive cells were less than 1.5%, while CD44 and CD90 positive cells were higher than 95% in PDMSCs. After osteogenic differentiation induction, the calcium nodule formation and osteogenic protein indicators levels were lower in CPT-PDMSCs.  Co-culture THP1-derived macrophage and PDMSCs, after osteoclast differentiation induction, dissolved hydroxyapatite plate activity, osteoclastic protein indicators levels of co-culture with CPT PDMSCs were shown to be higher than control. RNA-seq results revealed 822 differentially expressed mRNAs and 194 differentially expressed lncRNAs, respectively. Functional analysis showed that differentially expressed lncRNAs involved in tryptophan metabolism, steroid biosynthesis, and so on. Based on differential mRNAs and lncRNAs, we conducted correlation analysis of their cis regulation, and the results showed that 27 mRNAs were cis regulated with 24 lncRNAs, a total of 30 cis-regulated combinations.
Conclusion: CPT-PDMSCs has weak osteogenesis ability, but stronger ability to promotes osteoclast differentiation, we found that certain lncRNAs and mRNAs were differentially expressed in CPT-PDMSCs which have important roles in regulated osteogenesis and osteoclast differentiation.

first: Ge

last: Yang

first: Yiyong

last: Huang

first: Haibo

last: Mei

first: Guanghui

last: Zhu

first: Yaoxi

last: Liu

first: Hui

first: Qian

last: Tan


title: Abnormal Transcriptome-wide of DNA demethylation in Folate deficiency caused neural tube defects [RNA-seq]

summary:
To investigate the associated with the levels of DNA demethylation and neural tube defects (NTDs) with folate deficiency, we etablished  mouse embryonic stem cells (mESCs) Sv/129 in folate-deficiency-treated.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the cell model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sv129 cells as control group and its folate-deficiency-treated as experimental group.


title: The Transcription Factor Zfp503 Promotes the D1 MSN Identity and Represses the D2 MSN Identity

city: shanghai

first: song

last: xingrui

address: Dong An Road

department: institute of brain science

institute: fudan university

summary: The striatum is primarily composed of two types of medium spiny neurons (MSNs) expressing either D1- or D2-type dopamine receptors. However, the fate determination of these two types of neurons is not fully understood. Here, we found that D1 MSNs undergo fate switching to D2 MSNs in the absence of Zfp503. Furthermore, scRNA-seq revealed that the transcription factor Zfp503 affects the differentiation of these progenitor cells in the lateral ganglionic eminence (LGE). More importantly, we found that the transcription factors Sp8/9, which are required for the differentiation of D2 MSNs, are repressed by Zfp503.

overall_design: Purpose: To assess changes in gene expression profiles of single cell from the E14.5 LGE of striatum of Dlx2-Cre;Zfp503-CKO mice.

first: Zicong

last: Shang

first: Lin

first: Ziwu

last: Tian

first: Yanjing

last: Gao

first: Zihao

last: Su

first: Rongliang

last: Guo

first: Weiwei

last: Li

first: Guoping

first: Xiaosu

first: Zhengang

first: Zhenmeiyu

first: Zhuangzhi


title: Abnormal Transcriptome-wide of DNA demethylation in Folate deficiency caused neural tube defects

first: shan

last: wang


title: Expression data from PD-1+/- Th cells

city: Guangzhou

first: Haixia

last: Wei

address: #1, Xinzao Road

department: Department of Pathogen Biology and Immunology

institute: Guangzhou Medical University

summary:
PD-1+/- Th cells were sorted by flow cytometry
C57BL/6 mice were infected with P. yoelii. The differentially expressed genes of PD-1+/- Th cells from the spleen of the infected mice were acquired by microarray

overall_design: PD-1+/- Th cells from P. yoelii infected mice were sorted for RNA extraction and hybridization on Affymetrix microarrays.

first: Jun


title: An experimental model for ovarian cancer: Propagation of ovarian cancer initiating cells and generation of ovarian cancer organoids

city: Taipei

first: YuAn

last: Chen

address: No.1, Sec. 1, Jen Ai Rd., Taipei Taiwan

institute: College of Medicine, National Taiwan University

summary:
To establish an iOCIC model, an high-grade serous ovarian cancer (HGSOC) cell line, OVCAR-3 was reprogrammed  by transducing Yamanaka four factors OCT4, SOX2, KLF4 and MYC (OSKM)
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data.


title: Long term high glucose exposure in retinal endothelial cells

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

institute: Hospital San Raffaele

summary: RNA-seq was performed on 4-week high glucose (25mM D-glucose) treated human retinal microvascular endothelial cells (HRMECs) and control (5mM D-glucose) passage-matched cells.

overall_design: Total RNA was extracted from three biological replicates of HRMECs cultured in vitro and treated with 25mM or 5mM D-glucose for 4 weeks, as the high glucose or control experimental groups, respectively.

first: Pietro

last: Bertelli

first: Jasenka

last: Guduric-Fuchs

first: Reinhold

last: Medina


title: RNA-seq of ITPR3 and RELB knockout in SW480 under normoxia and hypoxia

city: New York

first: Ryan

last: Moy

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Here we compare the transcriptional profiles of SW480 cells with ITPR3 or RELB knockout with control cells under normoxia and hypoxia.

overall_design: 100K cells were plated in 6 well in duplicate. 24H later cells were either kept at normoxia or transferred to hypoxia chamber 0.5% O2. Cells were harvested at 72 H for RNAseq analysis.

middle: H


title: Single-cell RNA-sequencing analysis reveals the molecular mechanism of subchondral bone cell heterogeneity in the development of osteoarthritis

city: Shanghai

first: Yan

last: Hu

address: 99th Shangda Rd

institute: Shanghai University

summary: The composition of subchondral bone cell types in patients with osteoarthritis (OA) and the underlying spatiotemporal transformation processes remain unknown. Here, we identified various subchondral bone cell subsets and investigated the mechanism of subchondral bone microstructure alteration using single-cell RNA sequencing (scRNA-seq).

overall_design: Four samples from two OA patients

first: Jiacan


title: Gene network downstream plant stress response modulated by peroxisomal H2O2

city: Granada

first: Laura

middle: Carmen

last: Terron Camero

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

department: Bioinformática

institute: IPBLN

summary:
Study of the effect of cadmium on KO and overexpressor mutants of glycolate oxidase-GOX2, which is one of the main sources of H202 from peroxisomes.
Reactive oxygen species (ROS) act as secondary messengers that can be sensed by specific redox sensitive proteins responsible for the activation of signal transduction culminating in altered gene expression. ROS, which are involved in different activities, elicit a wide range of protein modifications, which might elicit different gene expressions. The subcellular site, in which modifications in ROS/oxidation state occur, can also act as a specific cellular redox network signal. The chemical identity of ROS and their subcellular origin actually is a specific imprint on the transcriptome response. In recent years, a number of transcriptomic studies related to altered ROS metabolism in plant peroxisomes have been carried out. In this study, we made a meta-analysis of these transcriptomic findings to identify common transcriptional footprints for plant peroxisomal-dependent signaling at early and later time points. These footprints highlight the regulation of various metabolic pathways and gene families, which are also found in plant responses to several abiotic stresses. Major peroxisomal-dependent genes are associated with protein and endoplasmic reticulum (ER) protection at later stages of stress while, at earlier stages, these genes are related to hormone biosynthesis and signaling regulation. Further, in silico analyses allowed us to assign human orthologs to some of the peroxisomal-dependent genes, which are mainly associated with different cancer types pathologies. Peroxisomal footprints provide a valuable resource for assessing and supporting key peroxisomal functions in cellular metabolism under control and stress conditions across species.

overall_design: Three independent biological replicates, each composed of leaves pooled from at least five different plants, were used per experimental condition

last: Terrón-Camero

first: M

last: Peláez-Vico

first: A

last: Rodríguez-González

first: Coral

last: del Val

first: Luisa

last: Sandalio

first: María

last: Romero-Puertas


title: Gene expression profiling study by RNA-seq for identifying genes associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors.

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Treatment with ALK tyrosine kinase inhibitors often elicits profound initial antitumor responses in ALK fusion-positive patients with lung adenocarcinoma. However, patients invariably develop acquired resistance to ALK inhibitors. In this study, we aimed to identify molecular events that limit the response to ALK inhibition using genetic and epigenetic approaches. To identify novel mechanisms of acquired resistance to ALK inhibitors, we established in vitro models of acquired resistance to ceritinib using H3122 cell. For in vitro model, H3122 parental cells, ceritinib-treated resistant cells, and non-resistant cells that combinely treated with certinib and panobinostat were used for RNA-seq based gene expression profiling.

overall_design: Single cell RNA-seq data of 2 samples, H3122 parental cells and one ceritinib-treated resistant cells, were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using NextSeq 500 platform (Illumina).

first: Haejeong

last: Heo

first: Jong-Hwan

first: Jeong-Hwan

first: Eun

middle: K

last: Choi

first: Dong-Uk

first: Yong

middle: S

first: Byoung

last: Cho

first: Seon-Young

first: Mirang


title: Analysis of Expression Profile of Over-expressed Brassinolide Synthase DET2 in Poplar

city: Hangzhou

first: Yao

last: Wang

address: 866 Yu Hang tang Road

institute: Zhejiang University

summary: We overexpressed the brassinolide synthase DET2 in 84K poplar and obtained an overexpression material.It was found that the brassinolide content of the overexpression material increased significantly.And it was found that the plant height, diameter, and number of internodes of the overexpression material increased significantly.However,the mechanism of this phenotype is unknown.We collected two-month-old DET2 overexpression material and 84K wild-type material in three parts, apex,cambium,and xylem,and conducted high-throughput sequencing.The sequencing results were mined, and the difference genes that were significantly changed in the DET2 overexpression material and the 84K wild-type material were found.Find out how the increase in brassinolide content promotes the development of wood.

overall_design: The differentially expressed genes between two-month-old DET2-OE and wild type were detected.

first: Juan

last: Du

first: Huixia

last: Shou


title: Differential gene expression of Candida albicans under no stress conditions or fluconazole stress

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: QUANT-seq approach was utilized to determine the gene expression in the transcriptome of C. albicans treated with the solvent control DMSO or the antifungal drug fluconazole (FLC). Biological triplicates of C. albicans grown in YPD medium treated with either DMSO or 3 µg/ml fluconazole for 30 minutes at 37˚C were harvested and total RNA was isolated using standard procedures (hot phenol method).

overall_design: Analysis of gene expession in C. albicans

first: Ana

last: Traven

first: Ka

last: Yau

first: Harshini

last: Weerasinghe

first: Michael

last: See

first: Paul

last: Harrison


title: Protein Kinase A (PKAc alpha ) regulates gastric homeostasis and preneoplastic lesions

city: Tuskegee

first: Pawan

last: Puri

state: Alabama

address: 1200 W Montgomery Road

department: Biomedical Sciences

institute: Tuskegee University

summary: We generated a novel Six2-Cre+/-PKAcaRfl/wt (CA-PKA) CA-PKA mouse in which expression of constitutive-active PKAcaR was induced in gastric mesenchyme progenitors. CA-PKA mice showed disruption of gastric homeostasis characterized by aberrant mucosal development and epithelial hyperproliferation; ultimately developing multiple features of gastric corpus preneoplasia including decreased parietal cells, mucous cell hyperplasia, spasmolytic peptide expressing metaplasia (SPEM) with intestinal characteristics and dysplastic and invasive cystic glands. Our results show that  constitutively active PKAcaR in the stomach mesenchyme nonautonomously disrupts gastric homeostasis characterized by increased epithelial proliferation and aberrant epithelial maldevelopment, ultimately leading to gastric preneoplasia.

overall_design: To identify differentially expressed genes mRNA sequencing was performed on samples isolated from the corpus region of control and mutant mice. Four biological replicates were analyzed from control and mutant mice.

first: Garfield

last: Grimmett

first: Bradley

last: Yoder

first: Rawah

last: Faraj

first: Ebony

last: Gilbreath

first: Laurielle

last: Gibson


title: An immunological signature to predict outcome in patients with triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

institute: University of Bordeaux

summary: When triple-negative breast cancer (TNBC) patients have residual disease after neoadjuvant chemotherapy (NACT), they have a high risk of metastatic relapse. With immune infiltrate in TNBC being prognostic and predictive of response to treatment, our aim was to develop an immunologic transcriptomic signature using post NACT samples to predict relapse.

overall_design: We identified 115 samples of residual tumors from post-NACT TNBC patients. We profiled the expression of 770 genes related to cancer microenvironment using the Nanostring PanCancer IO360 panel to develop a prognostic transcriptomic signature, and we describe the immune microenvironments of the residual tumors.

first: Céline

last: Blaye

first: Claire

last: Larmonier

first: Elodie

first: Gaëtan

last: ManGrogan


title: Translational activation of ATF4 through mitochondrial anaplerotic metabolic pathways is required for DLBCL growth and survival

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: Cancer cells frequently hijack adaptive stress response signals/pathways to protect themselves from metabolic or genetic vulnerabilities, pointing to candidate therapeutic targets. Among these SIRT3 was recently identified as a non-oncogene addiction mechanism in DLBCL through its role in glutamine metabolism. Here, we investigated downstream signaling pathways linked to SIRT3 function in lymphoma.  We performed RNA-seq in DLBCL cells after SIRT3 knockdown and observed that ATF4 target genes were significantly downregulated in SIRT3 deficient cells. ATF4, a master regulator of cellular stress, was required to maintain proliferation and survival of DLBCL cells and its target genes were overexpressed in DLBCL patients as compared to normal germinal center B cells. Translation of ATF4 mRNA was inhibited in SIRT3 knockdown cells and expression of exogenous ATF4 partially rescued cell proliferation and viability inhibited by SIRT3 deficiency.  Accordingly, ATF4 protein was expressed at relatively lower levels SIRT3 deficient murine lymphomas, whereas its higher expression was associated with more severe disease.  We characterized mechanisms through which SIRT3 maintains ATF4 expression, downstream of its effects on glutamine entry into the TCA cycle and suppression of autophagy.  Specifically, loss of SIRT3 disrupted amino acid metabolism in DLBCL cells, with subsequent impairment of ATF4 response to metabolic stressors such as glutamine depletion. Collectively, the data suggest a key SIRT3-ATF4 axis maintains survival of DLBCL cells enabling them to optimize amino acid metabolism and cope with metabolic vulnerabilities possibly associated with their high proliferative rate.

overall_design: RNAseq following shRNA knockdown of SIRT3 in DLBCL cell lines

first: Meng

last: Li

first: Ari

last: Melnick


title: Inhibition of Karyopherin β1-mediated nuclear import of lineage-defining TFs in small cell lung cancer

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Extensive genomic studies support the classification of small cell lung cancer (SCLC) into subtypes based on expression of lineage-defining transcription factors including ASCL1 and NEUROD1, which together account for ~80% of this disease. ASCL1 and NEUROD1 activate SCLC oncogene expression and drive distinct transcriptional programs. ASCL1 is also required for tumorigenesis in SCLC mouse models, and both ASCL1 and NEUROD1 maintain the in vitro growth and oncogenic properties of ASCL1+ or NEUROD1+ SCLC cell lines. Strategies to inhibit ASCL1 and NEUROD1 may therefore represent an attractive, targeted SCLC therapy and provide a tool to investigate the underlying plasticity of the predominant SCLC subtypes. However, ASCL1 and NEUROD1 have long been considered “undruggable” vulnerabilities. Here, we use a proteomic approach to identify Karyopherin β1 (KPNB1) as a nuclear import receptor for ASCL1 and NEUROD1 in SCLC, and demonstrate that the inhibition of KPNB1 using a variety of genetic or pharmacological approaches leads to impaired ASCL1 and NEUROD1 nuclear accumulation and transcriptional activity. Pharmacological targeting of KPNB1 preferentially disrupts ASCL1/NEUROD1+ SCLC cell line growth in vitro and ASCL1+ tumor growth in an in vivo patient derived xenograft (PDX) model of SCLC.

overall_design: Bulk mRNA profiles of SCLC-A subtype NCI-H2107 cell lines (Empty Vector n=2 for CRISPRi ASCL1 experiment and CRISPRi KPNB1 experiment, CRISPRi ASCL1 n=2, CRISPRi KPNB1 n=2), SCLC-A subtype JHU-LX44 PDX samples (Vehicle n=2, INI-43-treated n=3), SCLC-N subtype JHU-LX22 PDX samples (Vehicle n=3, INI-43-treated n=3), and RPM GEMM tumor samples (Control n=6, INI-43 treated n=7). "Control" = Vehicle treated or untreated.

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