title: CINC-2 and miR-199a-5p in EVs secreted by transplanted Thy1+ cells activate hepatocytic progenitor cell growth in rat liver regeneration

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

institute: Sapporo Medical University School of Medicine

summary:
Thy1 + cells isolated from male F344 rats with Dgalactosamine-induced liver injury were cultured for one week. Bone marrow mesenchymal cells isolated from from the femurs and tibias of a 5-week old male F344 rat. Small hepatocytes (SH) and mature hepatocytes (MH) were isolated from normal livers of 7-week old male F344 rat,
Extracellular vesicles (EVs) were separedt from culture media by ultracentrifugation.

overall_design: MicroRNAs (miRNAs) were extracted from EVs using the Qiazol lysis reagent and miRNeasy mini kit (Qiagen). A comprehensive analysis of miRNA expression was performed using a 3D-Gene miRNA Labeling kit and a 3DGene miRNA Oligo Chip (Toray Industries, Inc. Tokyo, Japan), which was designed to detect 727 miRNA sequences registered in miRBase release 20.

first: Toshihiro

last: Mitaka


title: Genome wide DNA methylation analysis of liver cancer cell lines

status: Public on Apr 05 2023

city: Newcastle

first: Gordon

last: Strathdee

address: Paul O'Gorman Building, Framlington Place

country: United Kingdom

institute: Newcastle University

type: Methylation profiling by genome tiling array

summary: DNA methylation was analysed in liver cancer cell lines and one normal heapatocyte cell line using Illumina Infinium MethylationEPIC arrays.

overall_design: Five liver cancer cell lines and one normal hepatocyte cell line were analysed


title: Influence of two bacterial effectors on the transcriptional landscape of the host cell

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

type: Expression profiling by high throughput sequencing

summary: To investigate the role of two secreted bacterial proteins (LphD and RomA) of Legionella pneumophila we infected THP-1 monocytes with GFP-producing bacteria. After 7 hours of infection, the cells were sorted (to enrich infected cells based on GFP-signal) and RNAseq was performed on the infected and sorted cells.

overall_design: THP-1 monocytes were infected with either L. pneumophila wild type, ∆lphD, ∆romA, or ∆lphD∆romA. Non-infected cells were used as control and the resuls of the different knockout mutants were compared to wild type infected cells. All samples were analyzed in triplicate.

first: Daniel

last: Schator

first: Monica

last: Rolando


title: Gene expression and intron retention analysis of 15.5K-knockdown human cells

status: Public on Apr 10 2023

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

summary: 15.5K is a RNA binding protein involved in the Minor Spliceosome. Here, we used shRNAs to knock down 15.5K in HEK293T cells to analysis the function of 15.5K in gene expression and intron retention.

overall_design: We analysed RNA from negative control HEK293T (shNC) cells and two 15.5K-knockdown  (sh15.5K-1 and sh15.5K-2) cells. For each condition, mRNA-seq analysis was conducted in triplicate from three independent expriments. We compare 15.5K-knockdown cells vs WT cells.

first: Bin

last: Li

first: Shurong

last: Liu

first: Wujian

last: Zheng

first: Peng

last: Yu

first: Anrui

first: Di

last: Wu

first: Jie

last: Zhou

first: Ping

last: Zhang

first: Chang

first: Qiao

last: Lin

first: Xiaoqin

first: Qiaojuan

last: Huang

first: Hui

first: Lianghu

last: Qu

first: Jianhua


title: Transcriptomic differences underlying the Activin-A induced large osteoclast formation in both healthy control and Fibrodysplasia Ossificans Progressiva osteoclasts

status: Public on Apr 07 2023

city: Amsterdam

first: Ton

last: Schoenmaker

state: SELECT

address: GUSTAV MAHLERLAAN 3004, Room 11N-07

department: Periodontology

country: Netherlands

institute: ACTA

summary: Activin-A has been identified as the driver for heterotopic ossification in FOP. It's effect on osteoclast formation is not extensively studied in control or FOP samples.

overall_design: Osteoclasts were generated from CD14+ cells, in the absence or presence of Activin-A, from healthy controls and FOP patients. RNA was isolated after 14 days and RNAsequencing was performed.

first: T

first: R

last: Volckmann

middle: J

last: de Vries

first: E

middle: M

last: Eekhoff


title: Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars [RNA-seq]

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

country: USA

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

summary: Although oncogene-induced senescence (OIS) is a potent tumor-suppressor mechanism, recent studies revealed that cells can escape from OIS with features of transformed cells. However, the mechanisms that promote OIS escape remain unclear, and evidence of post-senescent cells in human cancers is missing. Here, we unravel the regulatory mechanisms underlying OIS escape using dynamic multidimensional profiling. We demonstrate a critical role for AP1 and POU2F2 transcription factors for escape from OIS and identify ‘senescence-associated chromatin scars (SACS)’ as an epigenetic memory of OIS, detectable during colorectal cancer progression. POU2F2 levels are elevated already in precancerous lesions and as cells escape from OIS, and its expression and binding activity to cis-regulatory elements are associated with decreased patient survival. Our results support a model in which POU2F2 exploits a precoded enhancer landscape to promote senescence escape and reveal POU2F2 gene signatures and SACS as valuable biomarkers with diagnostic and prognostic potential.

overall_design: RNA-seq of GM21 human skin fibroblasts at days 14 and 27 after overexpression of H-RAS-G12V expressing control (non-targeting pLKO) or POU2F2-targeting (shPOU2F2 #324 and #325) shRNAs

middle: I

last: Zamudio

first: Alketa

last: Stefa

first: José

middle: A

last: Nabuco

first: Themistoklis

last: Vasilopoulos

first: Mark

last: Simpson

first: Gregory

last: Doré

first: Pierre-François

last: Roux

last: Galan

first: Ravi

last: Chokshi

first: Oliver

last: Bischof

first: Utz

last: Herbig


title: Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Timeseries Assay for transposase accessible chromatin followed by sequencing (ATAC-seq) in GM21 human skin fibroblasts entering and exiting RAS-induced oncogene-induced senescence

last: Freitas


title: Gene expression and intron retention analysis of ZCRB1-knockdown human cells

first: Jian-Hua

last: Yang

summary: ZCRB1 is a RNA binding protein involved in the Minor Spliceosome. Here, we used shRNAs to knock down ZCRB1 in HCT116 cells to analysis the function of ZCRB1 in gene expression and intron retention.

overall_design: We analysed RNA from negative control HCT116 (shNC) cells and two ZCRB1-knockdown  (shZCRB1-1 and shZCRB1-2) cells. For each condition, mRNA-seq analysis was conducted in triplicate from three independent expriments. We compare ZCRB1-knockdown cells vs WT cells.

first: Bin

last: Li

first: Shurong

last: Liu

first: Wujian

last: Zheng

first: Peng

last: Yu

first: Anrui

first: Di

last: Wu

first: Jie

last: Zhou

first: Ping

last: Zhang

first: Chang

first: Qiao

last: Lin

first: Xiaoqin

first: Qiaojuan

last: Huang

first: Hui

last: Qu


title: Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars

first: Ricardo

last: Martínez Zamudio

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

overall_design: Refer to individual Series


title: Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars [Expression]

overall_design: RNA from each time-point (days 0, 8, 13 , 14, 18, 19, 21, 22, 23 , 25, 32, 45, 46, 50, 56)  from GM21 fibroblasts undergoing escape from RAS-induced senescence was purified using the Macherey-Nagel Nucleospin RNA Plus XS kit according to the manufacturer’s instructions. 100 ng RNA per sample was analyzed using Affymetrix Human Transcriptome Arrays 2.0

last: Zamudio

first: Alketa

last: Stefa

first: José

last: Nabuco

first: Themistoklis

last: Vasilopoulos

first: Mark

last: Simpson

first: Gregory

last: Doré

first: Pierre-François

last: Roux

last: Galan

first: Ravi

first: Oliver


title: Aldose reductase inhibition decelerates optic nerve degeneration by suppressing retinal microglia activation

city: Pittsburgh

first: Kun-Che

last: Chang

state: PA

address: 1622 Locust St

department: Department of Ophthalmology

institute: University of Pittsburgh School of Medicine

summary: To investigate the role of aldose reductase (AR) inhibition using Sorbinil on retinal microglia (RMG) activation, retinal ganglion cell (RGC) survival, and axon regeneration after optic nerve trauma. We observed that AR inhibition using Sorbinil attenuates RMG activation and subsequently promotes RGC survival and delays axon degeneration one week after optic nerve crush.

overall_design: We performed RNA-seq on injured retina samples treated with DMSO or Sorbinil seven days after optic nerve crush. We wanted to to identify the regulatory mechanism that contributes to the delay of axonal degeneration after Sorbinil-dependent microglial inactivation.

first: Mishal

last: Rao


title: Antigen-specific CD8 T cells against SARS-CoV-2

status: Public on Apr 09 2023

city: Rijeka

first: Felix

middle: Martinus

last: Wensveen

address: Braće Branchetta 20

department: Histology & Embryology

country: Croatia

institute: University of Rijeka faculty of medicine

summary: In this project, we characterized the antigen-specific CD8 T cells of people from five groups. We used HLA:A2 tetramers loaded with the GILGFVFTL (Influenza) or YLQPRTFLL (Sars-CoV-2) peptides to label cells. Cells were sorted based on CD3+CD8+TTM+. We distinguished between four groups: 1. SARS2-TTM+ cells 6 months after infection, 2. SARS2-TTM+ cells 1 motnhs after 2nd vaccination with the Pfizer vaccine, 3. SARS2-TTM+ cells of people that were both infected and vaccinated and 4. FLU-TTM+ cells. Cells were sorted and analyzed by bulk RNA sequencing.

overall_design: We characterized the antigen-specific CD8 T cells of people from five groups. We used HLA:A2 tetramers loaded with the GILGFVFTL (Influenza) or YLQPRTFLL (Sars-CoV-2) peptides to label cells. Cells were sorted based on CD3+CD8+TTM+. We distinguished between four groups: 1. SARS2-TTM+ cells 6 months after infection, 2. SARS2-TTM+ cells 1 motnhs after 2nd vaccination with the Pfizer vaccine, 3. SARS2-TTM+ cells of people that were both infected and vaccinated and 4. FLU-TTM+ cells. Cells were sorted and analyzed by bulk RNA sequencing.

first: Inga

last: Kavazović


title: Widespread multi-targeted therapy resistance via drug-induced secretome fucosylation

city: Daejeon

first: Yoosik

last: Kim

state: Daejeon

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Chemical and biomolecular engineering

country: South Korea

institute: KAIST

summary: Cancer secretome is a reservoir for aberrant glycosylation. How therapies alter this post59 translational cancer hallmark and the consequences thereof remain elusive. Here we show that an elevated secretome fucosylation is a pan-cancer signature of both response and resistance to multiple targeted therapies. Large-scale pharmacogenomics revealed that fucosylation genes display widespread association with resistance to these therapies. In both cancer cell cultures and patients, targeted kinase inhibitors distinctively induced core fucosylation of secreted proteins less than 60 kDa. Label-free proteomics of N-glycomes revealed that fucosylation of the antioxidant PON1 is a critical component of the therapy66 induced secretome. Core fucosylation in the Golgi impacts PON1 stability and folding prior to secretion, promoting a more degradation-resistant PON1. Non-specific and PON1-specific secretome deglycosylation both limited the expansion of resistant clones in a tumor regression model. Our findings demonstrate that core fucosylation is a common modification indirectly induced by targeted therapies that paradoxically promotes resistance.

overall_design: Total RNA-sequencing was performed in drug resistance clones at 48 h after co-culture with altered secretome conditions in vitro. Two replicates were used for each sample.

middle: D

last: Aldonza

first: Jayoung

last: Ku


title: Comparative transcriptomes reveal pro-survival and cytotoxic programs of mucosal-associated invariant T cells upon Bacillus Calmette–Guérin stimulation

status: Public on Apr 04 2023

city: Cincinnati

first: Shouxiong

last: Huang

state: OH

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati College of Medicine

summary: To comprehensively characterize MAIT activation programs responding to different bacteria, we stimulated MAIT cells with E. coli to compare with Bacillus Calmette-Guérin (BCG), which remains the only licensed vaccine and a feasible tool for investigating anti-mycobacterial immunity in humans. Upon sequencing mRNA from the activated and inactivated CD8+ MAIT cells, results demonstrated the altered MAIT cell gene profiles by each bacterium with upregulated expression of activation markers, transcription factors, cytokines, and cytolytic mediators crucial in anti-mycobacterial responses.

overall_design: Human blood mononuclear cells were magnetically sorted to enrich MAIT cells, which were stimulated with E. coli-, M. bovis, or Listeria-incubated MR1-expressing cells . After incubation, MAIT cells were further sorted into CD69+CD26++ and CD69-CD26+/- subsets from the Va7.2+CD161+CD4-CD8+ -gated population.

first: Manju

last: Sharma

first: Liang

last: Niu

first: Xiang

last: Zhang


title: 10 Inflammatory Factors in Cerebrospinal Fluid and Serum of Parkinson's Disease Rats

status: Public on Apr 03 2023

city: Xinxiang

first: Han

last: Li

address: 601 Jinsui Road, Hongqi District, Xinxiang City, Henan Province

institute: Xinxiang Medical University

summary: A protein microarray kit (QAR-INF-1-2, RayBiotech Life Inc., Norcross, GA, USA) was used to detect 10 kinds of inflammatory factors in the CSF and serum (nN=5 per group), including IFN-γ,  IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-10, IL-13, MCP-1, and TNF-α.

overall_design: We randomly divided the Parkinson's rat model into Sham group, PD+PBS treatment group, and PD+MenSCs group using a lot drawing method. A protein microarray kit (QAR-INF-1-2, RayBiotech Life Inc., Norcross, GA, USA) was used to detect 10 kinds of inflammatory factors in the CSF and serum of rats (N=5 per group), including IFN-γ,  IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-10, IL-13, MCP-1, and TNF-α.

first: H

first: J

last: Lin


title: Targeting advanced prostate cancer with STEAP1 chimeric antigen receptor T cell and tumor-localized IL-12 immunotherapy [TCR-seq]

city: Seattle

first: John

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: Six transmembrane epithelial antigen of the prostate 1 (STEAP1) is a compelling tumor-associated cell surface antigen for therapeutic targeting in solid tumors. Here, we identified broad expression of STEAP1 relative to the established theranostic target prostate-specific membrane antigen (PSMA) in a series of lethal metastatic prostate cancers which prompted the development of a STEAP1-directed chimeric antigen receptor (CAR) T cell therapy. STEAP1 CAR T cells demonstrated reactivity in low antigen density, antitumor activity across multiple metastatic human and mouse prostate cancer models, and preliminary safety in a human STEAP1 knock-in mouse model. In human-in-mouse and mouse-in-mouse studies, STEAP1 CAR T cell therapy yielded effective tumor responses, but antigen escape was appreciated as a recurrent mechanism of treatment resistance and STEAP1 antigen loss was associated with diminished tumor antigen processing and presentation. The application of tumor-localized interleukin-12 (IL-12) therapy in the form of a collagen binding domain (CBD)-IL-12 fusion protein as an adjunct to STEAP1 CAR T cell therapy enhanced antitumor efficacy by remodeling the immunologically cold tumor microenvironment of prostate cancer and combating STEAP1 antigen escape through the engagement of host immunity and epitope spreading. In summary, we describe the extent of STEAP1 expression in treatment-refractory metastatic prostate cancer, characterize a STEAP1 CAR T cell therapy with preclinical evidence of potency and safety, and nominate a combinatorial immunotherapy strategy to overcome barriers to the efficacy of CAR T cell therapy in advanced prostate cancer.

overall_design:
T cell receptor Beta sequencing (TCRB-Seq) was performed on tumor inflitrating T cells collected from lung metastases of mice treated with  untransduced T cells or STEAP1-mBBz CAR T cells with or without CBD-IL-12.
***Please note that the data  are from Adaptive Biotech ImmunoSeq, which does not make its raw data files available****

first: Vipul

last: Bhatia

first: Nikhil

middle: V

last: Kamat

first: Tiffany

middle: E

last: Pariva

first: Li-Ting

last: Wu

first: Annabelle

last: Tsao

first: Koichi

last: Sasaki

first: Huiyun

last: Sun

first: Gerardo

last: Javier

first: Ilsa

last: Coleman

first: Lauren

middle: T

last: Wiest

first: Ailin

first: Dmytro

last: Rudoy

first: Roman

last: Gulati

first: Radhika

last: Patel

first: Martine

middle: P

last: Roudier

first: Lawrence

last: True

first: Michael

middle: C

last: Haffner

first: Peter

middle: S

last: Nelson

first: Saul

last: Priceman

first: Jun

last: Ishihara


title: Mouse transcriptome changes by Adrb1 mutation in PS19 mice

city: San Francisco

first: Qing

last: Dong

state: CA

institute: UCSF

summary: To investigate effects of the FNSS mutation Adrb1-A187V on the gene expression profile in a mouse model of tauopathy.

overall_design: We collected the mouse cortex from both the experimental and control groups at 8 months old of age. 4 mice of each group.

first: Ying-Hui

last: Fu


title: Targeting the NF-κB pathway enhances responsiveness of mammary tumors to JAK inhibitors

city: Minneapolis

first: Kaylee

last: Schwertfeger

state: MN

address: 420 Delaware St. SE MMC 609

department: Lab Medicine and Pathology

institute: University of Minnesota

summary: Interactions between tumor cells and the tumor microenvironment are critical for tumor growth, progression, and response to therapy. Effective targeting of oncogenic signaling pathways in tumors requires an understanding of how these therapies impact both tumor cells and cells within the tumor microenvironment. One such pathway is the janus kinase (JAK)/signal transducer and activator or transcription (STAT) pathway, which is activated in both breast cancer cells and in tumor associated macrophages. This study demonstrates that exposure of macrophages to JAK inhibitors leads to activation of NF-κB signaling, which results in increased expression of genes known to be associated with therapeutic resistance. Furthermore, inhibition of the NF-κB pathway improves the ability of ruxolitinib to reduce mammary tumor growth in vivo. Thus, the impact of the tumor microenvironment is an important consideration in studying breast cancer and understanding such mechanisms of resistance is critical to development of effective targeted therapies.

overall_design: Bone marrow mRNA profiles of 8-week old WT Balb/c mice treated with DMEM, 4T1 tumor conditioned media, ruxolitinib and IKK-16

first: Kathryn

middle: L

first: Aditi

last: Bapat

first: Christine

middle: H

last: O'Connor


title: Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena [RNA-seq]

city: Toronto

first: Jeffrey

last: Fillingham

address: 350 Victoria Steet

country: Canada

institute: Toronto Metropolitan University

summary: Through epigenetic modifications and selective incorporation of histone variants into chromatin, eukaryotic cells can adjust their transcriptional profile in response to molecular needs. We used the nuclear dimorphic ciliate protozoan, Tetrahymena thermophila, as a model system to investigate the dynamics of H3 variant function. H3.3 is the ancestral H3 variant with key roles in regulating chromatin states and transcription. Functional proteomics and immunofluorescence analyses of H3.1 and H3.3 revealed a conserved role for Nrp1 and Asf1 histone chaperones in nuclear influx of histones. Cac2 and Hir1 have distinct localization patterns during different stages of the Tetrahymena life cycle and suggests that both Cac2 and Hir1 might be dispensable for the replication-dependent and -independent deposition of H3.1 and H3.3, respectively. ChIP-seq experiments in growing Tetrahymena show H3.3 enrichment over promoters, genes bodies, and transcription termination sites of highly transcribed genes. H3.3 knockout followed by RNA-seq reveals large-scale transcriptional alterations in functionally important genes. Our results provide an evolutionary perspective on H3.3’s conserved role in maintaining the transcriptional landscape of cells and on the emergence of specialized chromatin assembly pathways.

overall_design: RNA-seq analysis of H3.3 knockout Tetrahymena cells during vegetative growth. Experiment was conducted in 2 biological replicates in parallel with 2 control replicates using parental Tetrahymena strains.

first: Syed

last: Nabeel-Shah

first: Jyoti

last: Garg

first: Kanwal

last: Ashraf

first: Renu

last: Jeyapala

first: Hyunmin

last: Lee

first: Alexandra

last: Petrova

first: James

last: Burns

first: Shuye

last: Pu

first: Zhaolei

last: Zhang

first: Jack

middle: F

last: Greenblatt

first: Ronald

last: Pearlman

first: Jean-Philippe

last: Lambert


title: Activation-induced cell death of ILC2s via TIGIT suppresses chronic airway allergy

city: Akita City

first: Takashi

last: Ebihara

address: 1-1-1 Hondo

department: Department of Medical Biology

country: Japan

institute: Akita University Graduate School of Medicine

summary: Chronic allergy induces TIGIT+ ILC2s at the sites of severe inflammation. To clearly isolate and follow the TIGIT+ ILC2s, we generated Tigit-Cre-ERT2: Rosa26-loxp-stop-loxp-tdTomato mice. tdTomato expression was induced in the TIGIT+ ILC2 of the mice by repeated intranasal administration of papain and oral tamoxifen treatment for 19 days. The tdTomato- and + ILC2s were sorted for RNA-seq and ATAC-seq analysis. We then performed gene expression profiling analysis using data obtained from RNA-seq of tdTomaoto- and + ILC2s. To call peaks, ATAC-seq data were aggregated by each unique cell type, and peak summits were called using HOMER.

overall_design: Comparative gene expression profiling analysis of RNA-seq data between tdTomato-TIGIT- ILC2s and tdTomao+TIGIT+ILC2s. Peak call from ATAC-seq data of tdTomato-TIGIT- ILC2s and tdTomao+TIGIT+ILC2s.

first: Megumi

last: Tatematsu

first: Shunsuke

last: Takasuga

first: Toshiki

last: Yamada


title: Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena [ChIP-seq]

first: Jeffrey

last: Fillingham

overall_design: Examination of two ChIP-seq biological replicates for H3.3-GFP during Tetrahymena vegetative growth


title: Long-term proliferation of immature hypoxia-dependent JMML cells supported by a 3D in vitro system

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary:
Juvenile myelomonocytic leukemia (JMML) is a rare stem cell disorder occurring in early childhood and characterized by RAS pathway hyperactivation in 95% of patients. JMML is identified by a hyperproliferation of granulocyte and monocyte, and little is known about the heterogeneous nature of leukemia initiating cells as well as the cellular hierarchy of the JMML bone marrow (BM). In this study, we reported the generation and characterization of a novel patient-derived 3D in vitro JMML model (pd-JAO) sustaining long-term proliferation of JMML cells with stem cell features and patient specific hallmarks. JMML cells brewed in the 3D model under different microenvironmental conditions acquired a proliferative and survival advantage when placed at low oxygen tensions. Transcriptomic and microscopic analysis revealed the activation of specific metabolic energy pathways and the inactivation of processes leading to cell death. Furthermore, we demonstrated pd-JAO derived cells’ migratory, propagation and self-renewal capacities both in in vitro and in vivo mouse model. Our study contributed to the development of a robust JMML 3D in vitro model to study and comprehend the impact of microenvironment stimuli on JMML disease and the molecular mechanisms regulating JMML initiating and propagating cells. Pd-JAO may become a promising model for compound tests focusing on new therapeutic intervention aiming to eradicate JMML progenitors and control JMML disease.
We defined a 3D in vitro model that under hypoxic conditions is able to sustain long-term propagation of JMML-patients cells with specific hallmarks. Different  oxygen level enviroment drive specific metabolic switch that prompts JMML cells to self-renewal.

overall_design: Gene expression was measured using Affymetrix platform in pairs of primary JMML pd-JAO derived cells maintained both in hypoxia and normoxia conditions

first: Silvia

last: Bresolin


title: Adaptive and Innate Immune Responses in Multiple Sclerosis with  2 Anti-CD20 Therapy: Gene Expression and Protein Profiles

city: Chicago

first: Anthony

last: Reder

state: IL

address: 5841 S Maryland Ave

department: Neurology

institute: University of Chicago Medicine

summary:
Transcriptome analysis of RNA samples from human PBMCs of anti-CD20 therapy in multiple sclerosis patients.
Anti-CD20 is a highly effective therapy for multiple sclerosis (MS), a disease with multiple abnormalities in function of B and T cells and innate immune cells. Anti-CD20 therapy depletes B cells, which alters antibody production and has diverse effects on B cell immunity. These changes potentially affect immunity beyond B cells in MS. We determined if anti-CD20 therapy effects non-B-cell, as well as B-cell, gene expression and serum protein levels. We found anti-CD20 therapy reduced expression of 413 total genes and 185 B-cell-regulated genes at 2 weeks vs. pre-therapy. Expression of 19 (15%) of these B cell genes returned towards baseline by 6 months, including genes for the B cell activation protein, CD79A, and for immunoglobulin A, D, and G heavy chains. Expression pathways for Th17 and CD4 regulatory T cell (Treg) development, differentiation, and proliferation also quieted. In contrast, expression increased in Th1 and myeloid cell antiviral, pro-inflammatory, and toll-like receptor (TLR) gene pathways.

overall_design: Samples were collected from 10 healthy controls and from clinically stable relapsing-remitting MS - 10 untreated, 9 interferon-β-treated, and 15 ocrelizumab-treated patients were studied before, and 2 weeks and 6 months after, the first anti-CD20 infusion. Peripheral blood mononuclear cells (PBMC) were analyzed with sensitive, 135,000-transcript RNA expression microarrays, using stringent criteria. Gene expression was compared to 43 MS-relevant serum immune and neurotrophic proteins, using multiplex protein assays.

first: Chloe

last: Fong

first: Julian

last: Spencer

first: Quentin

last: Howlett-Prieto

first: Xuan

last: Feng


title: Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars [ChIP-seq]

first: Ricardo

last: Martínez Zamudio

overall_design: Timeseries chromatin Immunoprecipitation DNA sequencing (ChIP-seq) of histone modifications H3K4me1 and H3K27ac in GM21 human skin fibroblasts entering and exiting RAS-induced oncogene-induced senescence

last: Zamudio

first: Alketa

last: Stefa

first: José

last: Nabuco

first: Themistoklis

last: Vasilopoulos

first: Mark

last: Simpson

first: Gregory

last: Doré

first: Pierre-François

last: Roux

last: Galan

first: Ravi

middle: J

last: Chokshi

first: Oliver

last: Bischof

first: Utz

last: Herbig


title: Effect of endothelial specific inhibition of Brg1 on gene expression during zebrafish heart regeneration [RNA-seq]

city: Beijing

first: Jing-Wei

last: Xiong

address: Peking University, No.5 Yiheyuan Road Haidian District

institute: Institute of Molecular Medicine, Peking University

summary: To decipher the molecular action of endothelial Brg1 in the regulation of zebrafish heart regeneration, we applied Tg(kdrl:eGFP) to label cardiac endothelial cells including the endocardium, and achieved endothelium-specific over-expression of DN-xBrg1 by using the compound zebrafish line consisting of Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1; kdrl:CreER; kdrl:eGFP) (defined as DNK), while we used Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1; kdrl-eGFP) as control (CtrlK) in the presence of 4-HT starting at 3 days before ventricular resection. The kdrl:eGFP endothelial cells, which were sorted by FACS (fluorescence-activated cell sorting) from CtrlK and DNK hearts at 7 dpa, were subjected to RNA-seq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CtrlK group and DNK group. There were two biological replicates for each group.

first: Wanqiu

last: Ding

first: Junjie

last: Hou

first: Chenglu

last: Xiao

first: Jingwei


title: Effect of endothelial specific inhibition of Brg1 on histone marker H3K4me3 in the zebrafish genome [ChIP-seq]

summary: To decipher the effect of endothelial specific inhibition of Brg1 on histone marker H3K4me3 in the zebrafish genome during zebrafish heart regeneration, we achieved endothelium-specific over-expression of DN-xBrg1 by using the compound zebrafish line consisting of Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1; kdrl:CreER) (defined as DN), while we used Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1) as control (Ctrl) in the presence of 4-HT starting at 3 days before ventricular resection. The whole ventricles from CtrlK and DNK hearts at 7 dpa were subjected to ChIP-seq analysis using H3K4me3 antibody.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me3 in Ctrl and DN amputated ventricles at 7dpa.


title: Skeletal muscle transcriptomics dissects the pathogenesis of Friedreich's Ataxia

status: Public on Apr 01 2023

city: Innsbruck

first: Alexander

last: Kirchmair

address: Innrain 80-82

country: Austria

institute: Medical University of Innsbruck

summary: RNA sequencing of skeletal muscle biopsies from healthy controls and Friedreich's Ataxia (FRDA) patients before and after treatment with recombinant human erythropoietin (rhuEPO) to dissect the mechanisms of disease.

overall_design: Comparison of seven healthy controls and seven FRDA patients before and after rhuEPO treatment.

first: Elisabetta

last: Indelicato

first: Anne

last: Krogsdam

first: Matthias

last: Amprosi


title: Effect of endothelial specific inhibition of Brg1

overall_design: Refer to individual Series


title: Senescence-Induced Immune Remodeling Facilitates Metastatic Adrenal Cancer in a Sex-Dimorphic Manner [bulk RNA-seq]

city: Salt Lake City

first: Kaitlin

last: Basham

state: UT

address: 2000 Circle of Hope Dr.

department: Oncological Sciences

institute: Huntsman Cancer Institute, University of Utah

summary: Using the adrenal gland as a model, we investigated the interplay between genetic Znrf3 inactivation and the aging microenvironment. We hypothesized that SF1-Cre-driven Znrf3 cKO mice would progress from adrenal hyperplasia to carcinoma with age. Unexpectedly, after an initial phase of hyperplasia, we found that Znrf3 cKO adrenals steadily regress over time. We demonstrate this phenotypic switch from hyperplasia to regression is driven by activation of cellular senescence and a subsequent senescence-associated secretory phenotype (SASP).

overall_design: To identify potential mechanisms that mediate the switch from hyperplasia to regression, we compared transcriptome changes in adrenal glands isolated from Znrf3 cKO mice and littermate controls in females (6-, 9-, and 12-weeks of age) and males (4-, 6-, and 9-weeks of age). Each group contains samples obtained from 4 independent mice.

first: Kate

middle: M

last: Warde

first: Chris

last: Stubben


title: Multi-omics analyses reveal ClpP activators disrupt essential mitochondrial pathways in triple-negative breast cancer

city: Chapel Hill

first: Lee

last: Graves

state: NC

address: 120 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: ClpP activators ONC201 and related small molecules (TR compounds, Madera Therapeutics), have demonstrated significant anti-cancer potential in an array of in vitro and in vivo studies, including clinical trials for refractory solid tumors. Though progress has been made in identifying specific phenotypic outcomes following ClpP activation, the exact mechanism by which ClpP activation leads to broad anti-cancer activity has yet to be fully elucidated. In this study, we utilized a multi-omics approach to identify the ClpP-dependent proteomic, transcriptomic, and metabolomic changes resulting from ONC201 or the TR compound TR-57 in triple-negative breast cancer cells. Applying mass spectrometry- based methods of proteomics and metabolomics, we identified ~8000 proteins and 588 metabolites, respectively. From proteomics data, approximately 3400 (ONC201) and 3000 (TR-57) proteins increased and ~4600 (ONC201) and ~4800 (TR-57) proteins decreased in this study. Gene ontological (GO) analysis revealed strong similarities between proteins up- or downregulated by ONC201 or TR-57 treatment. Notably, this included the downregulation of many mitochondrial processes and proteins, including mitochondrial translation and mitochondrial matrix proteins. We performed a large-scale transcriptomic analysis of WT SUM159 cells, identifying ~7700 transcripts (~3600 and 3800 increasing, ~4000 and 3900 decreasing in ONC201 and TR-57 treated cells, respectively). Less than 21% of these genes were affected by these compounds in ClpP null cells. GO analysis of these data demonstrated additional similarity of response to ONC201 and TR-57, including a decrease in transcripts related to the mitochondrial inner membrane and matrix, cell cycle, and nucleus, and increases in other nuclear transcripts and transcripts related to metal-ion binding. Comparison of response between both compounds demonstrated a highly similar response in all -omics datasets. Analysis of metabolites also revealed significant similarities between ONC201 and TR-57 with increases in α-ketoglutarate and 2-hydroxyglutaric acid and decreased ureidosuccinic acid, L-ascorbic acid, L-serine, and cytidine observed following ClpP activation in TNBC cells. Further analysis identified multiple pathways that were specifically impacted by ClpP activation, including ATF4 activation, heme biosynthesis, and the citrulline/urea cycle. In summary the results of our studies demonstrate that ONC201 and TR-57 induce highly similar and broad effects against multiple mitochondrial processes required for cell proliferation.

overall_design:
Comparison of effects of ClpP agonists ONC201 and TR-57 on gene expression in WT and ClpP-KO SUM159 cells
Novogene Co (contributor)

first: Emily

last: Fennell

first: Megan

last: Partridge


title: Characterisation of the functional and transcriptomic effects of pro-inflammatory cytokines on human EndoC-βH5 beta cells

city: Herlev

first: Joachim

last: Størling

address: Borgmester Ib Juuls Vej 83,

country: Denmark

institute: Steno Diabetes Center Copenhagen

summary: EndoC-βH5 is a newly established human beta-cell model which may be superior to previous models of native human beta cells. Exposure of beta cells to proinflammatory cytokines is a widely used in vitro model of immune-mediated beta-cell failure in type 1 diabetes and we therefore performed an in-depth characterisation of the effects of cytokines on EndoC-βH5 cells. Global gene expression was characterised by stranded RNA sequencing.

overall_design: Human EndoC-βH5 cells were left untreated or exposed to proinflammatory cytokines (IL-1β+IFN-γ+TNFα) for 48 h (n=4, in each condition).

first: Caroline

last: Frørup

first: Simranjeet

last: Kaur


title: Protein Amount in Conditioned Medium of MenSCs

first: Han

last: Li

summary: Protein microarray containing 1000  factors was used to detect protein components in the conditioned media of MenSCs. Select the protein with high expression content, and the enrichment result shows that it is related to inflammatory response, negative regulation of apoptotic process, microglial cell activation, negative regulation of TNF-α production, and innate immune response. These biological processes may partly explain the therapeutic functions of MenSCs on promoting the survival of DAergic neurons and anti-inflammation by regulating microglia polarization.

overall_design: Protein array kit (GSH-CAA-X00-1, RayBiotech Life Inc., Norcross, GA, USA) was used to detect the amount of 1000 kinds of factors in the conditioned medium of MenSCs (MenSCs-CM).Two samples were included. The preparation method of MenSCs is as follows. When MenSCs were 70%–80% sub-confluent,  the growth medium was replaced with 20 mL serum-free DMEM-HG medium (containing 100 m/mL penicillin, 100 mg/mL streptomycin). Culture medium was collected  after  48 h incubation, centrifuged at 600 g for 5 min and passed through a 0.22 mm filter, which was termed  as MenSCs-CM. Signals were scanned by InnoScan 300 Microarray Scanner. Select the protein with high expression content, and the enrichment result shows that it is related to inflammatory response, negative regulation of apoptotic process, microglial cell activation, negative regulation of TNF-α production, and innate immune response. These biological processes may partly explain the therapeutic functions of MenSCs on promoting the survival of DAergic neurons and anti-inflammation by regulating microglia polarization.

first: H

first: J

last: Lin


title: ChIP-seq for Col-0, atchz1ab, and arp6-1 using H2A.Z and H3 antibodies

city: Shanghai

first: Jiachen

last: Wang

state: Shanghai

address: No. 2005, Songhu Road

department: Institute of Plant Biology

institute: Fudan University

summary:
To investigate the influence of  the AtChz1A/B  and ARP6 in H2A.Z incorporation, we analysed genome-wide H2A.Z density in the mutant and wild-type by ChIP-seq.
We then performed H2A.Z occupancy analysis using data obtained from ChIP-seq of 3 different plants including mutants and wild-type.

overall_design: Comparative H2A.Z occupancy analysis of ChIP-seq data for Col-0, atchz1ab, and arp6-1.

first: Aiwu

last: Dong

first: Wen-Hui

last: Shen

first: Jiabing

last: Wu


title: ChIP-seq for HA-HTR5/Col-0 and Col-0 using HA antibody

summary:
To investigate the deposition of HTR5 in Arabidopsis, we analysed genome-wide HTR5 density in the wild-type Col-0 by ChIP-seq.
We then performed HTR5 occupancy analysis using data obtained from ChIP-seq of 3 different plants including HA-HTR5/Col-0 and Col-0. Col-0 acted as negative control.

overall_design: Analysis of HTR5 occupancy of ChIP-seq data for HA-HTR5/Col-0 and Col-0.


title: Transcriptome analysis reveals differences in cell cycle, growth and migration related genes that distinguish fibroblasts derived from pre-invasive and invasive breast cancer.

status: Public on Mar 31 2023

city: Kansas City

first: Nikki

last: Cheng

state: Kansas

address: 3901 Rainbow Blvd Mailstop 3045

institute: KUMC

summary: As the most common form of pre-invasive breast cancer, ductal carcinoma in situ (DCIS) affects over 50,000 women in the US annually. Despite standardized treatment involving lumpectomy and radiation therapy, up to 25 % of patients with DCIS experience disease recurrence often with invasive ductal carcinoma (IDC), indicating that a subset of patients may be under-treated. As most DCIS cases will not progress to invasion, many patients may experience over-treatment. By understanding the underlying processes associated with DCIS to IDC progression, we can identify new biomarkers to determine which DCIS cases may become invasive and improve treatment for patients. Accumulation of fibroblasts in IDC is associated with disease progression and reduced survival. While fibroblasts have been detected in DCIS, little is understood about their role in DCIS progression.We sought to determine whether DCIS fibroblasts were similar or distinct from normal and IDC fibroblasts at the transcriptome level, fibroblasts underwent transcriptome profilingthrough bulk RNA seq and pathway analysis.  DCIS fibroblasts are phenotypically distinct from normal breast and IDC fibroblasts, and play an important role in breast cancer growth, invasion, and recruitment of myeloid cells. These studies provide novel insight into the role of DCIS fibroblasts in breast cancer progression and identify some key biomarkers associated with DCIS progression to IDC, with important clinical implications.

overall_design: Fibroblasts were isolated from normal breast, DCIS and IDC tissues and were subject to bulk RNA seq. Differential gene expression analysis was conducted on DCIS fibroblast vs. normal fibroblast, DCIS fibroblast vs. IDC fibroblast and IDC fibroblast vs. normal fibroblast. Genes were validated by RT-PCR. Data were subject to pathway enrichment analysis and network analysis.

first: Wei

middle: B

last: Fang

first: Jennier

middle: R

last: Knapp

first: Janelle

last: Noel-Macdonnell

first: Clark

last: Bloomer


title: RNA-sequencing comparing activation of wild-type transcription factor KLF1 with mutant KLF1 (KLF1-325K) in iPSC-derived macrophages.

city: Edinburgh

first: Alisha

last: May

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

summary: Congenital dyserythropoietic anaemia (CDA) type IV has been associated with an amino acid substitution, Glu325Lys (E325K), in the transcription factor KLF1. Patients with CDA type IV present with a range of symptoms, including the persistence of nucleated red blood cells (RBCs) in the peripheral blood which reflects the known role for KLF1 within the erythroid cell lineage. The final stages of RBCs maturation and enucleation take place within the erythroblastic island (EBI) niche in close association with EBI macrophages. It is not known whether the detrimental effects of the E325K mutation in KLF1 are restricted to the erythroid lineage or whether deficiencies in macrophages associated with their niche also contribute to the disease pathology. To address this question, we generated iPSC lines genetically modified to express a KLF1-E325K-ERT2 protein that could be activated with 4OH-tamoxifen. We performed bulk RNA-sequencing on macrophages generated from these iPSCs, macrophages generated from one KLF1-E325K-ERT2 iPSC line (iCDA4.1) was compared to macrophages generated from one inducible KLF1-WT-ERT2 (K2) iPSC line which was derived from the same parental iPSCs (SFCi55) as the KLF1-E325K-ERT2 line.

overall_design: Bulk RNA-sequencing was performed on macrophages generated from the parental (SFCi55), inducible KLF1-WT activation iPSC line (K2), and the inducible KLF1-E325K activation iPSC line. Macrophages were either untreated or treated with 100 nM of 4OH-tamoxifen (5 replicates of each for a total of 30 samples).

first: Telma

last: Ventura

first: Helen

middle: A

last: Taylor

first: Antonella

last: Fidanza

first: Lesley

last: Forrester


title: STIL/AURKA axis promotes cell proliferation by influencing primary cilia formation in bladder cancer

city: Tianjin

first: Jingxian

address: Pingjiang Road 23#, Hexi District, Tianjin

institute: Tianjin institute of urology

summary: Our research showed that primary cilia was reduced in human bladder cancer (BLCA) cells, and PC deficiency promote cell proliferation. However, the concrete mechanisms remain unknown. SCL/TAL1 interrupting locus (STIL), a PC-related protein, was screened in our previous study and could influence the cell cycle by regulating PC in tumor cells. To elucidate the function of STIL for PC to explore the underlying mechanism of PC in BLCA, we establisded siNC and siSTIL EJ cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EJ-siNC and EJ-siSTIL cells.

first: Yuanjiong

last: Qi

first: Zhihong

last: Zhang

first: E

last: Du


title: HAPLN1 potentiates peritoneal metastasis in pancreatic cancer

city: Heidelberg

first: Lena

last: Wiedmann

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary: Pancreatic ductal adenocarcinoma (PDAC) frequently metastasizes into the peritoneum, which contributes to poor prognosis. Metastatic spreading is promoted by cancer cell plasticity, yet its regulation by the microenvironment is incompletely understood. Here, we show that the presence of hyaluronan and proteoglycan link protein-1 (HAPLN1) in the extracellular matrix enhances tumor cell plasticity and PDAC metastasis. Bioinformatic analysis showed that HAPLN1 expression is enriched in the basal PDAC subtype and associated with worse overall patient survival. In a mouse model for peritoneal carcinomatosis, HAPLN1-induced immunomodulation favored a more permissive microenvironment, which accelerated the peritoneal spread of tumor cells. Mechanistically, HAPLN1, via upregulation of tumor necrosis factor receptor 2 (TNFR2), promoted TNF-mediated upregulation of Hyaluronan (HA) production, facilitating EMT, stemness, invasion and immunomodulation. Extracellular HAPLN1 modified cancer cells and fibroblasts, rendering them more immunomodulatory. As such, we identified HAPLN1 as a prognostic marker and as a driver for peritoneal metastasis in PDAC.

overall_design: 15 samples in total, 3x tumor cells from solid KPC tumors, 3x tumor cells from solid KPC HAPLN1 tumors, 3x tumor cells from ascites of KPC HAPLN1, 3x fibroblasts from KPC tumors, 3x fibroblasts from KPC HAPLN1 tumors.

first: Francesca

last: De Angelis Rigotti

first: Nuria

last: Vaquero-Siguero

first: Elisa

last: Donato

last: Espinet

first: Iris

last: Moll

first: Elisenda

last: Alsina-Sanchis

first: Hanibal

last: Bohnenberger

first: Elena

last: Fernandez-Florido

first: Ronja

last: Mülfarth

first: Margherita

last: Vacca

first: Jennifer

last: Gerwing

first: Lena-Christin

last: Conradi

first: Philipp

last: Ströbel

first: Andreas

last: Trumpp

first: Carolin

last: Mogler

last: Fischer

first: Juan

last: Rodriguez-Vita


title: Comparative transcriptomic analysis in patients with Behçet syndrome

city: Ankara

first: Ali

middle: Kemal

last: Oguz

address: Baskent Universitesi Ankara Hastanesi, Maresal Fevzi Cakmak Caddesi No: 45

department: Internal Medicine

country: Turkey

institute: Baskent University School of Medicine

summary: Behçet syndrome (BS) is a chronic, multisystemic inflammatory condition with unanswered questions regarding its pathogenesis, classification, and rational therapeutics. A microarray-based comparative genome-wide expression analysis was performed to elucidate the molecular mechanisms of BS and identify any potential therapeutic targets. Twenty-nine BS patients (B) and 15 age and sex-matched control subjects (C) were recruited. Patients with BS were grouped as mucocutaneous (M), ocular (O), and vascular (V) according to their clinical phenotypes. GeneChip Human Genome U133 Plus 2.0 arrays were used for gene expression profiling on peripheral blood samples of the patients and the control subjects. Following the documentation of the differentially expressed gene (DEG) sets, the data were further evaluated with bioinformatics analysis/visualization and enrichment tools. Validation of the microarray data were performed using real-time qRT-PCR. When p<0.05 and fold change >2.0 were chosen, the following numbers of DEGs were obtained; B vs. C: 28, M vs. C: 20, O vs. C: 8, V vs. C: 555, M vs. O: 6, M vs. V: 324, O vs. V: 142. Venn diagram analysis indicated only two genes, CLEC12A and IFI27, in the intersection of M vs. C ∩ O vs. C ∩ V vs. C. Another noteworthy gene appeared as CLC in the DEG sets. Cluster analyses successfully clustered distinct clinical phenotypes of BS. While innate immunity-related biological processes were enriched in the M group, adaptive immunity-specific biological processes were significantly enriched in the O and V groups. Distinct clinical phenotypes of BS patients displayed distinct expression profiles. In Turkish patients with BS, expression differences regarding the genes CLEC12A, IFI27, and CLC seemed to be operative in BS pathogenesis. Based on these findings, future research should consider the immunogenetic heterogeneity of BS clinical phenotypes. Two anti-inflammatory genes, namely CLEC12A and CLC, may be valuable as therapeutic targets and may also help design an experimental model in BS.

overall_design: 29 Behçet syndrome patients (B, n=29) and 15 age and sex-matched control subjects (C, n=15) were recruited. Patients with Behçet syndrome were grouped as mucocutaneous (M, n=8), ocular (O, n=5), and vascular (V, n=9) according to their clinical phenotypes. 7 Behçet syndrome patients (D, n=7) were excluded from further analyses, based on their complex clinical phenotypes and significantly low counts. Class comparison analyses were performed among Behçet syndrome subgroups, as well as Behçet syndrome subgroups and the control group.

first: Cagdas

last: Oygur

first: Seda

last: Tasır

first: Askın

last: Ates

first: Aysel

last: Gurler

first: Hilal

middle: O

last: Sevgili

first: Nejat

last: Akar


title: Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena.

first: Jeffrey

last: Fillingham

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


title: Phenotypic and transcriptomic impact of expressing mammalian TET2 in the Drosophila melanogaster model

city: Beirut

first: Margret

last: Shirinian

address: Bliss street

country: Lebanon

institute: American University of Beirut

summary:
To examine the Ten-Eleven Translocation (TET) proteins and their role in tumorigenesis in hemocytes and heads in Drosophila melanogaster.
To identify the transcriptomic profile of wild type mTET2 versus mTET2 mutants (catalytic versus non-catalytic) to investigate TET2 role in normal central nervous system (CNS) function and innate immunity.

overall_design: • For RNA-Seq experiment, the following four Drosophila Melanogaster groups were used: mTET2-Wt (flies expressing wild type mammalian TET2), mTet2-R1261C (flies expressing mammalian TET2 with an Arginine to Cysteine mutation; R1261C), mTET2-R43G (flies expressing mammalian TET2 with an Arginine to Glycine mutation; R43G), and W1118 (wild type flies; control). 12 RNA samples from heads of these 4 groups of flies (3 biological replicates for each group) were used for RNA-Seq analysis.

first: Joy

middle: N

last: Ismail

first: Sarah

last: Mantash

first: Mohammad

last: Hallal

first: Nada

last: Jabado

first: Pierre

last: Khoueiry


title: Genomic BRD8-binding sites in human colorectal cancer cells

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

institute: The University of Tokyo

summary: Although BRD8 has been considered to act as a coactivator of the NuA4/TIP60-histone acetyltransferase complex, the role of BRD8 in colorectal cancer cells remains to be elucidated. We explored genomic BRD8-binding sites in human colorectal cancer cells.

overall_design: Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) for BRD8 in HCT116 and SW480 cells.

first: Yoichi

last: Furukawa


title: The effect of depletion of BRD8 or TIP60 on gene expression in colorectal cancer cells

summary: Although BRD8 has been considered to act as a coactivator of the NuA4/TIP60-histone acetyltransferase complex, the role of BRD8 in colorectal cancer cells remains to be elucidated. We performed transcriptome analysis to identify BRD8- and TIP60-regulated genes in colorectal cancer cells.

overall_design: Gene expression analysis of RNA-seq data using HCT116 and SW480 cells transfected with control, BRD8, or TIP60 siRNAs.


title: Senescence-Induced Immune Remodeling Facilitates Metastatic Adrenal Cancer in a Sex-Dimorphic Manner [scRNA-seq]

first: Kaitlin

last: Basham

summary: Using single-cell RNA-sequencing (scRNA-seq), we characterize diverse immune cell infiltrates that remodel the tissue microenvironment following senescence activation in female Znrf3 cKO mice.

overall_design: We performed scRNA-seq to provide an unbiased profile of the immune microenvironment following senescence activation. We specifically focused on the initial switch from hyperplasia (6-weeks) to regression (9-weeks) where we expected to identify the most proximal senescence-driven immune response. Adrenal glands were isolated from female SF1-Cre+;Znrf3-Fx/Fx mice at 6-weeks (n=2 adrenals) or 9-weeks (n=3 adrenals).

first: Kate

last: Warde

first: Brian

last: Lohman

first: Chris

last: Stubben


title: Senescence-Induced Immune Remodeling Facilitates Metastatic Adrenal Cancer in a Sex-Dimorphic Manner


title: Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states [plateseq]

city: New York

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

summary: Glioblastoma is an aggressive diffusely infiltrating neoplasm that spreads beyond surgical resection margins, where it intermingles with non-neoplastic brain cells. This complex microenvironment harbouring infiltrating glioma and non-neoplastic brain cells is the origin of tumor recurrence. Thus, understanding the cellular and molecular features of the glioma microenvironment is therapeutically and prognostically important. Here, we used single-nucleus RNA sequencing (snRNAseq) of primary and recurrent glioma to define three compositional ‘tissue-states’ rooted in cohabitation of cell-types and transcriptional states. These comprise a state featuring A) minimally infiltrated-brain, B) reactive inflamed infiltrated tissue, and C) cellular tumor. Spatial transcriptomics confirmed that the cell-types and transcriptomics states which compositionally cohabitate indeed do colocalize in space. Tissue states are clinically significant because they correlate with radiographic, histopathologic, and prognostic features. We found that in addition to enrichment of tissue state B signature, enrichment of both neoplastic and non-neoplastic cell-type gene signatures in tissue state B correlated with decreased survival. Importantly, we found that our compositionally defined tissue states are enriched in distinct metabolic pathways. One such pathway is fatty acid biosynthesis, which was enriched in tissue state B – a state enriched in recurrent glioblastoma and composed of astrocyte-like/mesenchymal glioma cells, reactive astrocytes resembling those seen in neurodegeneration, and monocyte-like myeloid cells. We discovered that targeting fatty acid synthesis was sufficient to deplete the transcriptional signature of tissue state B. Our findings define a novel compositional approach to the glioma infiltrated tissue which allows us to discover prognostic and targetable features, paving the way to new mechanistic and therapeutic discoveries.

overall_design: Comparative gene expression and molecular analysis on GBM tissue that are primary glioma versus a recurrent glioma.

last: Al-Dalahmah

first: Michael

last: Argenziano

first: Aayushi

last: Mahajan

first: Julia

last: Furnari

first: Fahad

last: Paryani

first: Deborah

last: Boyett

first: Akshay

last: Save

first: Fatima

last: Khan

first: Juncheng

last: Li

first: Hong

last: Lu

first: Yu

last: Sun

first: John

last: Tuddenham

first: Alexander

last: Goldberg

first: Athanassios

last: Dovas

first: Matei

last: Banu

first: Tejaswi

last: Sudhakar

first: Erin

last: Bush

first: Andrew

last: Lassman

last: Bruce

first: Peter

last: A Sims

first: Vilas

last: Menon

last: Canoll

first: Adithya

last: Kannan

first: Nelson

last: Humala

first: Guy

last: McKhann

last: A Gill

first: Brett

last: Youngerman

last: Sisti


title: Single cell RNA-sequence reveals the effect of neoadjuvant chemotherapy on immune cells in human esophageal squamous cell carcinoma.

city: Higashiku

first: Sho

last: Okuda

state: Fukuoka

address: Maidashi 3-1-1

department: Surgery and Oncology

institute: Kyushu University

summary: In this study, we comprehensively investigated the impact of neoadjuvant chemotherapy (NAC) on immune cells in the tumor microenvironment (TME) of esophageal squamous cell carcinoma (ESCC) using single cell RNA sequence. CD8+ T cells, CD4+ T cells, dendritic cells, and macrophages in TME of ESCC all showed higher levels of anti-tumor immune response in the NAC(+) group than in the NAC(-) group. Furthermore, the immune cells in the TME of the NAC(+) group interacted with each other to enhance the anti-tumor immune response. Our results suggest that NAC potentially enhance the anti-tumor immune response of immune cells in the TME.

overall_design: 18 human ESCC tissues and 12 human normal esophageal tissues with squamous cell mucosa from surgically resected specimens or biopsied specimens under gastroscopy

first: Kenoki

last: Ohuchida


title: Nucleolus assembly impairment leads to two-cell transcriptional repression via NPM1-mediated PRC2 recruitment

city: Hefei

first: Ding

middle: feng

last: Li

address: Huang shan road 443

institute: USTC

summary: We report the high-throughput sequencing of RNA expression in control embryos ,LoNA KO embryos, control 2c like mESC and LoNA KD 2c like mESC

overall_design:
Examination of RNA expression pattern in control embryos ,LoNA KO embryos, control 2c like mESC and LoNA KD 2c like mESC
Examination of H3K27ac histone modifications and AcNPM1 pattern in control embryos ,LoNA KO embryos, LoNA KO embryos with P300 inhibitor treatment

first: Qiang

last: Liu

first: Juan

last: Zhang

first: Dingfeng


title: LXR signaling controls homeostatic dendritic cell maturation

status: Public on Mar 30 2023

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

overall_design: Refer to individual Series


title: Large scale production of melanocyte derived from pluripotent stem cells for biotherapeutic approaches to treat skin pigmentation disorders

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary: In this study, we successfully defined a highly efficient standardize method to derive hPSCs into a pure population of functional melanocytes. These cells can be maintain for more than 20 passages without observed any senescence. Transcriptomic anlaysis revealed a differentiation process with a logic gene expression profile following the kinetic of melanocyte embryonic development as previously described in mice. Our findings represent a fruitful ground that can serve as a database tool to decipher molecular signatures in normal and pathological conditions

overall_design: Kinetic of a differentiation process from D0 to D30, comparaison of P0 and P4 stages to established a maturation phase and caracterisation of mature Mel-hESC in comparaison with hESC and HEM.

first: Manoubia

last: Saidani

first: Annabelle

last: Darle

first: Jennifer

last: Allouche

first: Margot

last: Jarrige

first: Christine

last: Baldeschi


title: Comparison of Vdelta1 and Vdelta2 cells

status: Public on Mar 29 2023

city: Washington

first: Natalia

last: Soriano-Sarabia

state: DC

address: 2300 I St. NW

department: Microbiology Immunology and tropical Medicine

institute: George Washington University

summary:
Gene expression analysis comparison of ex vivo isolated GD T cell subpopulations
Under non-pathological conditions, human gd T cells represent a small fraction of CD3+ T cells in peripheral blood (1-10%). They constitute a unique subset of T lymphocytes that recognize stress ligands or non-peptide antigens through MHC-independent presentation. Major human gd T cell subsets, Vd1 and Vd2, expand in response to microbial infection or malignancy, but possess distinct tissue localization, antigen recognition, and effector responses. We hypothesized that differences at the gene, phenotypic, and functional level would provide evidence that gd T cell subpopulations belong to distinct lineages. Comparisons between each subset and the identification of the molecular determinants that underpin their differences has been hampered by experimental challenges in obtaining sufficient numbers of purified cells. By utilizing a stringent FACS-based isolation method, we compared highly purified human Vd1 and Vd2 cells in terms of phenotype, gene expression profile, and functional responses. We found distinct genetic and phenotypic signatures that define functional differences in gd T cell populations. Differences in TCR components, repertoire, and responses to calcium-dependent pathways suggest that Vd1 and Vd2 T cells are different lineages. These findings will facilitate further investigation into the ligand specificity and unique role of Vd1 and Vd2 cells in early immune responses.

overall_design: Ex vivo isolated GD populations from peripheral blood of healthy donor volunteers were FACS sorted to high purity and whole genome microarray performed

first: Holger

last: Hackstein

first: Miltenyi

last: Biotec


title: RNA sequencing of paVICs exposed to LPC and dantrolene

city: Houston

first: K.

middle: Jane

last: Grande-Allen

state: TX

address: 6500 Main St

department: Bioengineering

institute: Rice University

summary:
To investigate the gene expression changes due to LPC-induced calcific nodule formation in porcine aortic valve interstitial cells (paVICs).
We then examined differential gene expression due to treatment with dantrolene, which inhibits calcific nodule formation, with and without LPC after 24 hours of exposure.

overall_design: Comparative gene expression profiling analyis of RNA-seq data for primary paVICs.

first: Christopher

last: Sylvester

first: Angelina

last: Bortoletto

last: Connell

first: K


title: RNAseq analysis of PS+ vs. PS- effector CD8 T cells sorted from spleen of LCMV-Armstrong infected mice

city: Planegg-Martinsried

first: Jan

last: Kranich

address: Großhaderner Straße 9

department: Biomedical Center, Institute for Immunology

institute: Ludwig-Maximilians-Universität Munich

summary: We report the transcriptional profile of phosphatidylserine (PS) positive and PS negative CD44+CD62L- effector CD8+ T cells from LCMV-Armstrong infected mice sorted from spleens on day5 amd day10 after infection. PS was stained in vivo by injection of MFG-E8-eGFP. PS+ cells acquire PS through binding of extracellular vesicles (EVs). Binding of EVs by effector CD8+ T cells is strongly enhanced during LCMV infection and peaks between day5 and day10 post infection. Effector T cell gene signature is increased in EV+ CD8+ T cells compared to their EV- counterparts.

overall_design: Mice were infected ip with 2x10^5 pfu LCMV Armstrong. On day 5 and day10 of infection, 100µg MFG-E8-eGFP were administered iv to stain phosphatidylserine positive cells (mainly apoptotic cells and cells associated with EVs). 1h after MFG-E8-eGFP administration mice were sacrificed and CD44+CD62L- CD8+ T cells sorted from the spleen using a FACS AriaIII. Cells were lysed in Trizol and subjected to RNAseq analysis.

first: Thomas

last: Brocker

first: Lisa

last: Rausch


title: Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states

first: Osama

last: Al Dalahmah


title: IMP1-interactive lncRNA regulates human endoderm differentiation via stabilizing WNT targets

city: WuHan

first: Jie

last: Yang

state: Hubei Province

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: WuHan university

summary: Long noncoding RNAs (lncRNAs) have been shown to play important roles in diverse biological process, including embryonic development and cell differentiation. Extensive studies have revealed the function and mechanism of those lncRNAs adjacent to protein-coding genes (PCGs), but there are relatively fewer reports about the lncRNAs within gene desert, particularly in human early germ layer differentiation. Here based on transcriptome analysis during human definitive endoderm (DE) differentiation, we identified a “desert” lncRNA named CTD-2501M5.1, a cytoplasm-located transcript with no protein-coding gene nearby within the 50 kb genomic region, highly expressed in human definitive endoderm. Depletion of CTD-2501M5.1 by either shRNA or promoter deletion could cause the deficiency of DE differentiation from human pluripotent stem cells (PSCs). The biochemical analysis showed that CTD-2501M5.1 functionally interacted with insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1, also named IMP1), which is necessary for endoderm differentiation demonstrated by loss-of-function assay. We further found depletion of CTD-2501M5.1 could result in reduced WNT signaling activities. More importantly, manipulating WNT activity by chemicals could rescue the phenotype of DE deficiency due to the depletion of CTD-2501M5.1 or IMP1. Mechanistically, CTD-2501M5.1 facilitated the interaction between IMP1 and FZD5 mRNA, stabilizing FZD5 which is required for WNT signaling activation and DE differentiation. Ultimately, our study not only revealed the biological function of a novel desert lncRNA CTD-2501M5.1 in human DE differentiation, but also underlined lncRNA-mediated mRNA stability regulation via IMP1.

overall_design: We performed RNA-seq using hESC-derived wildtype, lncRNA CTD-2501M5.1-KO and IMP1-KO definitive endoderm cells. IMP1 RIPseq was performed in wildtype and CTD-2501M5.1-KO definitive endoderm cell.

first: Pei

last: Lu

first: Wei

last: Jiang


title: LXR signaling controls homeostatic dendritic cell maturation [BulkRNAseq]

first: Sophie

last: Janssens

summary: Depending on how an antigen is perceived, dendritic cells (DCs) mature in an immunogenic or tolerogenic manner, safeguarding the balance between immunity and tolerance. Whereas the pathways driving immunogenic maturation in response to infectious insults are well characterized, the signals driving tolerogenic maturation in homeostasis are still poorly understood. Here we demonstrate that engulfment of apoptotic cells triggers homeostatic maturation of conventional cDC1s in the spleen. This process can be modeled by engulfment of empty, non-adjuvanted lipid nanoparticles (LNPs), is marked by intracellular accumulation of cholesterol, and highly unique to type 1 DCs. Engulfment of apoptotic cells or cholesterol-rich LNPs leads to activation of the LXR pathway driving cellular cholesterol efflux and repression of immunogenic genes. In contrast, simultaneous engagement of TLR3 to mimic viral infection via administration of poly(I:C)-adjuvanted LNPs represses the LXR pathway, thus delaying cellular cholesterol efflux and inducing genes that promote T cell immunity. These data demonstrate how DCs exploit the conserved cellular cholesterol efflux pathway to regulate induction of tolerance or immunity and reveal that administration of non-adjuvanted cholesterol-rich LNPs is a powerful platform for inducing tolerogenic DC maturation.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for immature and homeostatic mature splenic WT cDC1s.
(The cDC1s come from Xbp1fl and Xbp1flIre1fl mice which are both functionally WT mice. Those genes have been floxed, but are not knocked out in these mice.)

first: Victor

last: Bosteels

first: Sandra

last: Maréchal

first: Clint

last: De Nolf


title: mRNA Transcriptome analysis reveals key mRNAs and pathways on aorta of diabetic mouse

city: Beijing

first: yanru

last: duan

state: Beijing

address: Beijing, Chaoyang

institute: Capital Medical University

summary: Our research is helpful to understand the physiological and pathological level changes of aorta caused by diabetes

overall_design: In this study, the control group and the model  group subjected to mRNA sequencing.

first: Duan

last: Yanru


title: BCAA insufficiencies lead to premature ovarian insufficiency via ceramide induced elevation of ROS

status: Public on Mar 28 2023

city: Shanghai

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

summary: Premature ovarian insufficiency (POI) is a disease featured by early menopause before 40 years of age, accompanied by an elevation of follicle-stimulating hormone (FSH). Though POI affects many aspects of women’s health, its major causes remain unknown. Many clinical studies have shown that POI patients are generally underweight, indicating a potential correlation between POI and metabolic disorders. To understand the pathogenesis of POI, we performed metabolomics analysis on serum and identified branch chain amino acid (BCAA) insufficiency related metabolic disorders in two independent cohorts from two clinics. A low BCAA diet phenotypically reproduced the metabolic, endocrine, ovarian, and reproductive changes of POI in young C57 B6 mice. A mechanism study revealed that the BCAA insufficiency induced POI is associated with abnormal activation of the ceramide-ROS axis and consequent impairment of ovarian granulosa cell function. Significantly, dietary supplement of BCAA prevented the development of ROS-induced POI in female mice. The results of this pathogenic study will lead to the development of specific therapies for POI.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

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

first: Xiao

last: Guo

first: Lu

first: Yiwen

last: Qi

first: Yuemeng

last: Zhu


title: Assessment of transcriptional reprogramming of lettuce roots in response to chitin soil amendment

city: Waedenswil

first: Moritz

last: Kaufmann

state: Zurich

address: Einsiedlerstrasse 29

department: Institute of Natural Resource Sciences

country: Switzerland

institute: ZHAW

summary: Chitin soil amendment is known to improve soil quality, plant growth and plant stress resilience, but the underlying mechanisms are not well understood. In this study, we monitored chitin’s effect on lettuce physiology every two weeks through an eight-week growth period, analyzed the early transcriptional reprogramming and related metabolomic changes of lettuce, in response to crab chitin treatment in peat-based potting soil. In commercial growth conditions, chitin amendment still promoted lettuce growth, increased chlorophyll content, the number of leaves and crop head weight from week six. The flavonoid content in lettuce leaves was altered as well, showing an increase at week two but a decrease from week six. Transcriptomic analysis showed that over 300 genes in lettuce root were significant differentially expressed after chitin soil treatment. Gene Ontology-term (GO) enrichment analysis revealed statistical overrepresentation of GO terms linked to photosynthesis, pigment metabolic process and phenylpropanoid metabolic process. Further analysis of the differentially expressed genes (DEGs) showed that the flavonoid pathway is mostly upregulated whereas the bifurcation of upstream phenylpropanoid pathway towards lignin biosynthesis is mostly downregulated. Metabolomic analysis revealed the upregulation of salicylic acid, chlorogenic acid, ferulic acid, and p-coumaric acid in chitin treated lettuce seedlings. These phenolic compounds mainly influence the phenylpropanoid biosynthesis pathway and may play important roles in plant defense reactions. Our results suggest that chitin soil amendments might activate induced resistance by priming lettuce plants and promote lettuce growth via transcriptional changes.

overall_design: In this experiment the gene expression of lettuce roots of two treatment groups was analyzed. The first group was lettuce grown in potting soil and the second group was lettuce grown in chitin amended potting soil ( 2g/L). The samples were taken after transplanting 3 to 4 leave stage lettuce plants to either treatment group. For each group five replicas were analyzed. Each replica was a pool of five plants.

first: Leilei

last: Li

first: Moffat

last: Mackechemu

first: Christof

last: Van Poucke

first: Ellen

last: De Keyser

first: Mieke

last: Uyttendaele

first: Cyril

last: Zipfel

first: Bart

last: Cottyn

first: Joël

last: Pothier


title: The role of Fgf9 in mouse pancreas development [scRNA-seq]

city: San Francisco

first: Julie

last: Sneddon

state: California

address: 500 Parnassus Ave.

institute: UCSF

summary: Temporally and spatially coordinated epithelial–mesenchymal interactions are central to the development of the primitive gut tube endoderm and are necessary to form functional organs of the gastrointestinal tract, including the pancreas. Here, we examined the functional role of the secreted factor Fgf9 in murine pancreatic development. Single-cell RNA-sequencing was performed on embryonic day (E) 14.5 mouse pancreas from both wildtype and Fgf9 knockout embryos. Our data reveal shifts in cellular populations upon loss of Fgf9. In addition, we have identified specific transcriptional programs and signaling pathways perturbed in the context of loss of Fgf9 during pancreatic development.

overall_design: We profiled embryonic pancreas from Fgf9-LacZ mice (3 pancreata from 3 litters pooled into a single Null sample), in which a LacZ cassette has been inserted into the Fgf9 locus, rendering it a functional knockout. Fgf9 replete littermates (8 pancreata from 3 litters pooled into a single Control sample) served as corresponding control.

first: Sophie

last: Patzek

first: Zhe

first: Sean

last: de la O


title: Loss of FGF9 in mice leads to pancreatic hypoplasia and asplenia

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


title: SARS-CoV-2 Omicron boosting induces de novo B cell response in humans

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: SARS-CoV-2 booster immunizations in humans induce robust germinal centre B cell responses and can generate de novo B cell responses targeting variant-specific epitopes.

overall_design: Examination of 39 single-cell RNA-seq samples from PBMCs and from fine need aspirations of lymph nodes taken at multiple time points post-vaccination across multiple participants.

first: Wafaa

last: Alsoussi

first: Sameer

middle: K

last: Malladi

middle: Q

first: Zhuoming

first: Baoling

last: Ying

first: Wooseob

last: Kim

first: Aaron

last: Schmitz

first: Tingting

last: Lei

first: Stephen

last: Horvath

first: Alexandria

last: Sturtz

first: Katherine

last: McIntire

first: Birk

last: Evavold

first: Fangjie

last: Han

first: Suzanne

last: Scheaffer

first: Isabella

last: Fox

first: Senaa

last: Mirza

first: Luis

last: Parra-Rodriguez

first: Raffael

last: Nachbagauer

first: Biliana

last: Nestorova

first: Spyros

last: Chalkias

first: Christopher

middle: W

last: Farnsworth

first: Michael

last: Klebert

first: Iskra

last: Pusic

first: Benjamin

last: Strnad

first: William

middle: D

last: Middleton

first: Sharlene

last: Teefey

last: Whelan

last: Diamond

first: Robert

last: Paris

first: Jane

last: O'Halloran

first: Rachel

last: Presti

first: Jackson

last: Turner

first: Ali

last: Ellebedy


title: Single-cell Transcriptomics of Endometrial Cells from Patients with Minimal/mild Endometriosis.

city: Chengdu

first: Xin

last: Huang

address: Chenglongdadao

institute: West China Second University Hospital

summary: We profiled the transcriptomes of 128, 243 endometrial cells from 6 infertile minimal/mild endometriosis patients and 4 controls. Our results provide new insight of pathogenesis and impaired endometrial receptivity of endometriosis.

overall_design: Single-cell RNA sequence of 138, 057 endometrial cells from 6 endometriosis patients (3 samples from proliferative phase and 3 samples from secretory phase) and 7 control (3 samples from proliferative phase and 4 samples from secretory phase).

first: Huili

last: Zhu

first: Wei

first: Tianjiao

last: Pei

first: Lukanxuan

last: Wu


title: The role of Fgf9 in mouse pancreas development [bulk RNA-seq]

first: Julie

last: Sneddon

summary: Temporally and spatially coordinated epithelial–mesenchymal interactions are central to the development of the primitive gut tube endoderm and are necessary to form functional organs of the gastrointestinal tract, including the pancreas. Here, we examined the functional role of the secreted factor Fgf9 in murine pancreatic development. Bulk RNA-sequencing was performed on embryonic day (E) 13.5 and 14.5 mouse pancreas from both wildtype and Fgf9 knockout embryos. Our data have identified specific transcriptional programs and signaling pathways perturbed in the context of loss of Fgf9 during pancreatic development.

overall_design: We profiled embryonic pancreas from E13.5 and E14.5 Fgf9-LacZ mice, in which a LacZ cassette has been inserted into the Fgf9 locus, rendering it a functional knockout. Fgf9 replete littermates served as corresponding control.

first: Sophie

last: Patzek

first: Zhe

last: Liu

first: Sean

last: de la O


title: Identification of a Broadly Fibrogenic Macrophage Subset Induced by Type 3 Inflammation

status: Public on Mar 27 2023

city: Cambridge

first: Ken

last: Dower

state: MA

address: 1 Portland St.

department: Inflammation and Immunology Research Unit

institute: Pfizer, Inc.

summary: Cross-sectional single cell RNA sequencing (scRNAseq) of hepatic cells enzymatically isolated from murine models of toxin- (CCl4) or diet-induced (Gubra Amlyn Nash or GAN) liver fibrosis to identify macrophage populations associated with fibrosis.

overall_design: Cells were enzymatically isolated from murine livers at the peak of fibrosis (see paper for details), FACS sorted to remove dead cells and fixed in methanol before analysis using 10x Genomics scRNAseq platform. For samples labeled MMPNeg or MMPPos, cells were additionally FACS sorted based on signal from the MMPsense dye which distinguishes active intracellular matrix metalloproteases (MMPs).

first: Alexander

last: Barron

first: Stephen

last: Christensen

first: Marc

last: Wadsworth II

first: Xiao

last: Chen

first: Chang

last: Wang

first: Kellie

last: Kravarik

first: Thomas

last: Wynn


title: MORC proteins regulate transcription factor binding through mediating chromatin compaction at active chromatin regions

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary:
The Microrchidia (MORC) family proteins are evolutionarily conserved GHKL type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylation (RdDM) pathway where they act as molecular tethers to ensure the efficient establishment of RdDM and de novo gene silencing.  However, they also have RdDM independent functions in which the underlying mechanism is unknown.
In this study, we examined MORC binding regions that are devoid of RdDM to shed light on MORCs RdDM independent functions. We found that MORC proteins can compact chromatin, exclude the accessibility of DNA to transcription factors (TFs) and thereby repress gene expression. We also found that MORC-mediated repression is particularly important under stress conditions. In addition, we showed that MORC proteins may regulate TFs through direct or indirect interactions. These TFs in turn regulate their own transcription, indicating a feedforward loop.
Our findings provide insights into the molecular mechanisms of MORC-mediated chromatin compaction and transcription regulation.

overall_design: This dataset includes ChIP-seq, RNA-seq, and ATAC-seq to understand the molecular mechanism of Arabidopsis MORC proteins.

first: Zhong

last: Zhenhui

first: Xue

last: Yan


title: Stay or Go: Sulfolobales Biofilm Dispersal is Dependent on a Bifunctional VapB Antitoxin

city: Raleigh

first: Robert

last: Kelly

state: North Carolina

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: A Type II VapB14 Antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius, not only through traditional Toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC Toxins are ribonucleases that are neutralized by their proteinaceous cognate Type II VapB Antitoxin. VapB Antitoxins have a flexible tail at their C-terminus that covers the Toxin’s active site neutralizing its activity. VapB Antitoxins also have a DNA binding domain at their N-terminus that allows them to not only auto-repress their own promoters but also distal targets. VapB14 Antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate Toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for Type II Antitoxins that are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both up-regulated in biofilm cells, supporting the role of the Antitoxin in biofilm regulation. The findings here suggest that a stand-alone VapB-type Antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior.

overall_design: Data is comparing gene expression of pooled triplicate samples of biofilm and planktonic cultures of Sulfolobus acidocaldarius MW001 parent strain and a Sulfolobus acidocaldarius Saci_1223 mutant.

first: April

last: Lewis

first: Daniel

last: Willard

first: Mohammad

last: Manesh

first: Shamphavi

last: Sivabalasarma

first: Sonja-Verena

last: Albers

first: Alvaro

last: Orell

first: Arpan

last: Mukherjee


title: The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Prolonged cell cycle arrests occur naturally in differentiated cells and in response to various stresses  such as nutrient deprivation or treatment with chemotherapeutic agents. Whether and how cells survive  prolonged cell cycle arrests is not clear. Here, we used S. cerevisiae to compare physiological cell  cycle arrests and genetically induced arrests in G1-, meta- and anaphase. Prolonged cell cycle arrest  led to growth attenuation in all studied conditions, coincided with activation of the Environmental  Stress Response (ESR) and with a reduced ribosome content as determined by whole ribosome purification  and TMT mass spectrometry. Suppression of the ESR through hyperactivation of the Ras/PKA pathway reduced  cell viability during prolonged arrests, demonstrating a cytoprotective role of the ESR. Attenuation of  cell growth and activation of stress induced signaling pathways also occur in arrested human cell lines,  raising the possibility that the response to prolonged cell cycle arrest is conserved.

overall_design: Quantification of the ESR in a variety of cell cycle-arrested S. cerevisae cells.

first: Allegra

last: Terhorst

first: Arzu

last: Sandikci

first: Tamás

last: Szórádi

first: Liam

last: Holt

first: Gabriel

middle: E

last: Neurohr

first: Angelika

last: Amon


title: Identification and Validation of Hub Genes in Drug Induced Acute Kidney Injury Basing on Integrated Transcriptomic Analysis

city: Changsha

first: Kun

last: Liu

address: Tongzipo road 138.

department: Pharmacy

institute: The Third Xiangya Hospital, Central South University

summary: In this study, RNA-seq was used to detect mRNA changes in DI-AKI cell models induced by three drugs (Iohexol, cisplatin and vancomycin), and was analyzed and validated to screen key hub genes and specific biomarkers for DI-AKI.

overall_design: This study was divided into four groups of samples with three replicates in each group. The first group was the control group, and water was the control lysozyme. The second group was iohexol induced-AKI. Iohexol (75 mg I/mL) was used to intervene HK-2 cells for 48h. The third group was the cisplatin induced-AKI group. The HK-2 cells were treated with cisplatin (5 μM) for 48h. The fourth group was vancomycin induced-AKI.Vancomycin (4 mM) was used to intervene HK-2 cells for 48h.

first: Xiaocong

last: Zuo

first: Yixuan

last: Deng


title: LXR signaling controls homeostatic dendritic cell maturation [scRNAseq]

first: Sophie

last: Janssens

institute: VIB/UGhent

overall_design: We performed CITE-seq to decipher tolerogenic maturation of wild-type cDC1s within the spleen. Combining the measurement of the transcriptome and the surface epitopes of cDC1s facilitated a detailed analysis of the various stages cDC1s go through during this maturation process.

first: Victor

last: Bosteels

first: Sandra

last: Maréchal

first: Clint

last: De Nolf


title: Phosphorylation and stabilization of EZH2 by VprBP trigger aberrant gene silencing in colon cancer

first: Nikhil

middle: Baban

last: Ghate

state: CA

address: 1450 Biggy st, Norris Research Tower

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: Our recent work has shown that VprBP is overexpressed in colon cancer and phosphorylates histone H2AT120 to drive epigenetic gene inactivation and oncogenic transformation. We have extended these observations by investigating whether VprBP also phosphorylates non-histone proteins as an additional mechanism linking its kinase activity to colon cancer development. We now demonstrate that VprBP directly phosphorylates EZH2 at T367 to augment its nuclear stabilization and enzymatic activity in colon cancer cells. Consistent with this mechanistic role, VprBP-mediated EZH2 phosphorylation leads to elevated levels of H3K27me3 and altered expression of growth regulatory genes in cancer cells. Furthermore, our preclinical studies using organoid and xenograft models revealed that EZH2 requires phosphorylation for its oncogenic function, which may have therapeutic implications for gene reactivation in colon cancer cells. Together, our data define a new mechanism underlying VprBP-driven colonic tumorigenesis by linking VprBP-mediated EZH2 phosphorylation to EZH2 stability that is crucial for establishing H3K27me3 and gene silencing program.

overall_design: mRNA-seq of EZH2-knocked down (n=3) in colon cancer cell line (SW620)

first: Suhn

last: Rhie

first: Woojin

last: An


title: Transcriptomic atlas and interaction networks of brain cells in mouse CNS demyelination and remyelination [Trem2KO]

city: Saint Louis

first: Yingyue

last: Zhou

state: Missouri

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology

department: Pathology and Immunology

summary: Demyelination is a hallmark of multiple sclerosis, leukoencephalopathies, cerebral vasculopathies and several neurodegenerative diseases. The cuprizone mouse model is widely used to simulate demyelination occurring in these diseases. Here, we present a high-resolution snRNA-seq analysis of gene expression changes across all brain cells in this model. We define signatures of prototypic responses to demyelination and remyelination for each cell type, including anti-stress, anti-oxidant-, metabolic-, hypoxia-, IFN-, and IL-33-driven responses, and validate them at the protein level and in IL-33R-deficient mice. We identify related transcription regulators underpinning these pathways, including STAT3, NF-κB, OLIG1 and MAFB. Furthermore, snRNA- seq data provide novel insights into how various brain cell types connect and interact, defining complex circuitries previously unknown to impact demyelination and remyelination. As an explicative example, perturbation of microglia caused by TREM2 deficiency impacts the oligodendrocyte responses to demyelination. Altogether, this study provides a rich resource for future studies investigating mechanisms underlying demyelination and remyelination.

overall_design: Single nucleus RNA-seq analysis of cortex and corpus callosum from WT and TREM2 knockout  mice treated with or without cuprizone. Three experimental groups were set up in each genotype: a) demyelination (5-week CPZ treatment); b) remyelination (5-week CPZ treatment, followed by 2-week regular chow); c) control (regular chow throughout the time course)

first: Jinchao

last: Hou

first: Amanda

last: Swain

first: Prabhakar

middle: S

last: Andhey


title: Transcriptomic atlas and interaction networks of brain cells in mouse CNS demyelination and remyelination [B6]

overall_design: Single nucleus RNA-seq analysis of cortex and corpus callosum from B6 mice treated with or without cuprizone. Three experimental groups were set up: a) demyelination (5-week CPZ treatment); b) remyelination (5-week CPZ treatment, followed by 2-week regular chow); c) control (regular chow throughout the time course)


title: Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis

city: Irvine

first: Ken

last: Cho

address: University of California, Irvine

institute: University of California, Irvine

summary: Histone acetylation is a pivotal epigenetic modification that controls chromatin structures and regulates gene expression. It plays an essential role in modulating zygotic transcription and cell lineage specification of developing embryos. While the outcomes of many inductive signals have been described to require enzymatic activities of histone acetyltransferases and deacetylases (HDACs), the mechanisms by which HDACs confines the utilization of the zygotic genome are not well-characterized. Here, we show that histone deacetylase 1 (Hdac1) progressively binds to the zygotic genome from early blastula and onward. The recruitment of Hdac1 to the genome at the blastula stage is instructed maternally. Cis-regulatory modules (CRMs) bound by Hdac1 possess distinctive epigenetic signatures. We highlight a dual functional model of Hdac1 where Hdac1 not only sustains a histone hypoacetylation state on inactive chromatin but also participates in dynamic histone acetylation cycles on active chromatin. As a result, Hdac1 maintains differential histone acetylation states of bound CRMs between different germ layers and reinforces the transcriptional program underlying cell lineage identities both in time and space. Taken together, our study reveals a comprehensive role of Hdac1 during early vertebrate embryogenesis.

overall_design: Examination of Hdac1, Hdac2, Sox3, H3K18ac, pan-H3Kac bindings in Xenopus tropicalis early embryos; Examination of gene expression changes due to HDAC inhibition by TSA, VPA in Xenopus tropicalis gastrulae

first: Jeff

middle: J


title: RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia

status: Public on Mar 26 2023

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology & Immunology

institute: University of British Columbia

summary: Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including MYC, DTX1, HES4, IL7R, and NOTCH3. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.

overall_design: Examination of the epigenetic and transcriptomic changes in T-ALL cell lines following NOTCH1 inhibition and RUNX1 knockdown.

first: Rashedul

last: Islam

first: Catherine

last: Jenkins

first: Qi

last: Cao

first: Jasper

last: Wong

first: Misha

last: Bilenky

first: Annaick

last: Carles

first: Michelle

last: Moksa

first: Andrew

middle: P

last: Weng


title: DNA methylation changes in SHRSP rat offspring due to maternal protein restriction are reprogrammed by postnatal nutritional environments

city: Yayoi, Bunkyo-ku

first: Chika

last: Ando

state: Tokyo

institute: University of Tokyo

summary: We previously demonstrated that maternal protein restriction during pregnancy increased salt sensitivity in their offspring during adulthood, involving alterations in renal DNA methylation status. In this study, we used DNA methylation arrays to comprehensively analyze the DNA methylation status of the renal promoter regions and the effects of postnatal protein intake on DNA methylation. We fed SHRSP dams a normal diet or a low-protein diet during pregnancy, and their 4-week-old offspring were fed a normal diet or a high-/low-protein diet for two weeks. We found that the methylation status of 2,395 differentially methylated DNA regions was reprogrammed, and 34 genes were reset by different levels of postnatal protein intake. Among these genes, Adora2b, Trpc5, Ar, Xrcc2, and Atp1b1 are involved in renal disease and blood pressure regulation. Our findings indicate that postnatal nutritional interventions can potentially reprogram epigenetic changes and provide novel therapeutic and preventive epigenetic targets for salt-sensitive hypertension.

overall_design: In the study presented here, 12 samples were analyzed. Methylation of DNA in rat kidneys was analyzed.  CN, 20%-Casein diet; LP, 9%-Casein diet, HP, 40%-Casein diet. * AIN-76 prescription (Oriental Yeast Co., Ltd., Tokyo, Japan).

first: Moe

last: Miyoshi

first: Kyohei

last: Furukawa

first: Xuguang

last: Li

first: Huijuan

last: Jia

first: Hisanori

last: Kato


title: Single cell RNA sequecning of sorted human lung mast cells

status: Public on Mar 25 2023

city: Solna

first: Elin

last: Rönnberg Höckerlind

address: NKs Bioclinicum J7:30, Visionsgatan 4

department: Medicine (Solna)

country: Sweden

institute: Karolinska Institutet

summary: Single cell RNA sequencing was performed on sorted human lung mast cells to analyze the heterogeniety.

overall_design:
Human lung tissue were obtained from 4 patients undergoing lobectomies due to lung cancer. Single cell suspention was obtained by enzymatic and mecanical disruption. The human lung mast cells were FACS sorted and single cell RNA sequencing was performed using the SmartSeq2 protocol.
NOTE FROM SUBMITTER: The data is generated from human samples and due to GDPR and swedish legislation we are not allowed to release the raw data.

first: Avinash

last: Ravindran

first: Luca

last: Mazzurana

first: Yitao

last: Gong

first: Julie

last: Lorent

first: Olga

last: Dethlefsen

first: Joakim

last: Dahlin

first: Jenny

last: Mjösberg

first: Gunnar

last: Nilsson


title: Identifying signatures of EV secretion in metastatic breast cancer through functional single-cell profiling

city: Houston

first: Navin

last: Varadarajan

address: 4722 Calhoun Rd

institute: University of Houston

summary: Extracellular vesicles (EVs) regulate the tumor microenvironment by facilitating transport of biomolecular cargo including RNA, protein, and metabolites. We developed an integrated method to identify individual cells with differences in EV secretion and linked single-cell RNA-sequencing on cloned single cells from MDAMB231 cell line. Additionally, We profiled parental MDAMB231, MCF7 and HCC70 cell lines.

overall_design: Single-cell RNA sequencing of two monoclonal cell lines (MDAMB231-S with high and MDAMB231-NS with low EV secretion), parental MDAMB231, MCF7, and HCC70 cell lines.

first: Mohsen

last: Fathi

first: Melisa

last: Martinez-Paniagua

first: Ali

last: Rezvan

last: Montalvo

first: Vakul

last: Mohanty

first: Ken

last: Chen

first: Sendurai

last: Mani