title: Characterization of porcine induced pluripotent stem cells derived from Sertoli cells with activation of Wnt signaling pathway

city: Yangling

first: Shuai

last: YU

address: No.22 Xinong Road,

institute: Northwest A&F University

summary: Studies on porcine induced pluripotent stem (iPS) cells served as a great reference for human clinical research due to the similarity in organ size, physiology, anatomy, and heredity between pig and human. However, the reprogramming efficiency of iPS cells was currently poor. In this study, we reported the induction of iPS cells from porcine Sertoli cells (SCs) via infecting with four separate lentiviral vectors expressing pig OCT4, SOX2, KLF4 and c-MYC. Typical embryonic stem-like cells began to form on day 3 after infection, and alkaline phosphatase (AP)-positive colonies were picked up on 7 days. The porcine iPS cells derived from SCs, termed SC-iPS cells, strongly expressed pluripotent markers, showed a normal karyotype, and had differentiation characteristics to the three germ layers and primordial germ cell-like cells via an incipient mesoderm-like cell state. Further results showed that OCT4 was the core factor for AP-positive colonies formation, and the OCT4 and c-MYC were the minimum combination group to achieve the SCs reprogramming process. RNA-seq results showed that SCs could express BMP4 and activate the Wnt signaling pathway, which promoted reprogramming process. In conclusion, our findings demonstrated that the SCs could efficiently serve as a better cell source for reprogramming than porcine embryonic fibroblasts and lay a foundation of achieving the trans-differentiation capacity from SCs to germ cells.

overall_design: RNA-seq in SCs, SCs-piPSCs (iPS cells derived from Sertoli Cells), PEF-piPSCs (iPS cells derived from embryonic fibroblasts).

last: Yu

first: Jinlian

last: Hua


title: CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions [scRNA-Seq]

status: Public on Jul 12 2024

city: San Francisco

first: Emmy

last: Li

email: emmyli0306@gmail.com, emmy.li@ucsf.edu

state: CA

address: 675 Nelson Rising Lane

country: USA

institute: UCSF

type: Expression profiling by high throughput sequencing

summary: The sheer complexity of the brain has complicated our ability to understand its cellular mechanisms in health and disease. Genome-wide association studies have uncovered genetic variants associated with specific neurological phenotypes and diseases. In addition, single-cell transcriptomics have provided molecular descriptions of specific brain cell types and the changes they undergo during disease. Although these approaches provide a giant leap forward towards understanding how genetic variation can lead to functional changes in the brain, they do not establish molecular mechanisms. To address this need, we developed a 3D co-culture system termed iAssembloids (induced multi-lineage assembloids) that enables the rapid generation of homogenous neuron-glia spheroids. We characterize these iAssembloids with immunohistochemistry and single-cell transcriptomics and combine them with large-scale CRISPRi-based screens. In our first application, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response in the presence of reactive oxygen species elicited by high neuronal activity, which was not previously found in 2D monoculture neuron screens. We also apply the platform to investigate the role of APOE-𝜀4, a risk variant for Alzheimer’s Disease, in its effect on neuronal survival. We find that APOE-𝜀4 expressing astrocytes may promote more neuronal activity as compared to APOE-𝜀3 expressing astrocytes.  This platform expands the toolbox for the unbiased identification of mechanisms of cell-cell interactions in brain health and disease.

overall_design: Examination of cellular differention and composition in 3D neuron-astrocyte-microglia co-culture models (iAssembloids)

first: Li

last: Emmy


title: Temporal profiling of the phosphate starvation response in Arabidopsis root hair cells reveals that induction of polycomb target genes does not depend on removal of H3K27me3 or H2A.Z V

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Altered nutrient conditions can trigger massive transcriptional reprogramming in plants, leading to the activation and silencing of thousands of genes. To gain a deeper understanding of the phosphate starvation response and the relationships between transcriptional and epigenetic changes that occur during this reprogramming, we conducted a time-resolved analysis of transcriptome and chromatin alterations in root hair cells of Arabidopsis thaliana during phosphate (P) starvation and subsequent resupply. We found that 96 hours of P starvation causes induction or repression of thousands of transcripts, and most of these recover to pre-starvation levels within 4 hours of P resupply. Among the phosphate starvation-induced genes are many polycomb targets with high levels of H3K27me3 and histone variant H2A.Z. When induced, these genes show increased H3K4me3 consistent with active transcription, but surprisingly minimal loss of H3K27me3 or H2A.Z. These results indicate that the removal of silencing marks is not a prerequisite for activation of these genes. Our data provide a cell type- and time-resolved resource for studying the dynamics of a systemic nutrient stress and recovery and suggest that our current understanding of the switch between silent and active transcriptional states is incomplete.

overall_design: CUT&Tag-seq profilng of H3K27me3 in root hair cell chromatin extracted from plants subject to 10 days of phosphate rich growth (0h_Pi) followed by 96h of Pi starvation (96h_noPi), then 30m, 1h, or 4h of Pi resupply (30m_rePi, 1h_rePi, 4h_rePi). Nuclei extracted from 100mg of root tissue in triplicate via INTACT (100k nuclei per rep).

first: Dylan

middle: H

last: Holder


title: Temporal profiling of the phosphate starvation response in Arabidopsis root hair cells reveals that induction of polycomb target genes does not depend on removal of H3K27me3 or H2A.Z III

overall_design: RNA-seq profilng of  root hair cell nuclear mRNA extracted from plants subject to 10 days of phosphate rich growth (0h_Pi) followed by 96h of Pi starvation (96h_noPi), then 30m, 1h, or 4h of Pi resupply (30m_rePi, 1h_rePi, 4h_rePi). Nuclei extracted from 100mg of root tissue in triplicate via INTACT.


title: Temporal profiling of the phosphate starvation response in Arabidopsis root hair cells reveals that induction of polycomb target genes does not depend on removal of H3K27me3 or H2A.Z I


title: Seasonal influenza A virus lineages exhibit divergent abilities to antagonize interferon induction and signaling

city: urbana

first: christopher

last: brooke

state: IL

address: B103 CLSL, MC-110, 601 South Goodwin Avenue

institute: University of Illinois at Urbana-Champaign

summary: The circulation of seasonal influenza A viruses (IAVs) in humans relies on effective evasion and subversion of the host immune response. While the evolution of seasonal H1N1 and H3N2 viruses to avoid humoral immunity is well characterized, relatively little is known about the evolution of innate immune antagonism phenotypes in these viruses. Numerous studies have established that only a small subset of infected cells are responsible for initiating the type I and type III interferon (IFN) response during IAV infection, emphasizing the importance of single cell studies to accurately characterize the IFN response during infection. We developed a flow cytometry-based method to examine transcriptional changes in IFN and interferon stimulated gene (ISG) expression at the single cell level. We observed that NS segments derived from seasonal H3N2 viruses are more efficient at antagonizing IFN signaling but less effective at suppressing IFN induction, compared to the pdm2009 H1N1 lineage. We compared a collection of NS segments spanning the natural history of the current seasonal IAV lineages, and demonstrate long periods of stability in IFN antagonism potential, punctuated by occasional phenotypic shifts. Altogether, our data reveal significant differences in how seasonal and pandemic H1N1 and H3N2 viruses antagonize the human IFN response at the single cell level.

overall_design: Comparison of host gene expression in human alveolar epithelial cells infected with either Cal07 (H1N1) or Perth09 (H3N2) and collected at different timepoints post infection.

first: Joel

last: Rivera-Cardona

first: Neeha

last: Kakuturu

first: Elizabeth

middle: F

last: Rowland

first: Qi

middle: W

last: Teo

middle: A

last: Thayer

first: Timothy

middle: C

last: Tan

first: Jiayi

last: Sun

first: Collin

last: Kieffer

first: Nicholas

last: Wu

first: Christopher

last: Brooke


title: Temporal profiling of the phosphate starvation response in Arabidopsis root hair cells reveals that induction of polycomb target genes does not depend on removal of H3K27me3 or H2A.Z II

overall_design: CUT&Tag-seq profilng of H2A.Z in root hair cell chromatin extracted from plants subject to 10 days of phosphate rich growth (0h_Pi) followed by 96h of Pi starvation (96h_noPi), then 30m, 1h, or 4h of Pi resupply (30m_rePi, 1h_rePi, 4h_rePi). Nuclei extracted from 100mg of root tissue in triplicate via INTACT (100k nuclei per rep).


title: Anti-tumor Efficacy of HRS-4642 and Its Potential Combination with Proteasome Inhibition in KRAS G12D-mutant Cancer

city: Shanghai

first: Chongyang

address: 131 Dong 'an Road, Xuhui District

country: China

institute: Fudan University

summary: KRAS G12D is the most frequently mutated oncogenic KRAS subtype in solid tumors and remains undruggable in clinical settings. Here, we developed a high affinity, selective, long-acting, and non-covalent KRAS G12D inhibitor, HRS-4642, with an affinity constant of 0.083 nM. HRS-4642 demonstrats robust efficacy against KRAS G12D-mutant cancers both in vitro and in vivo. Importantly, in a phase 1 clinical trial, HRS-4642 exhibits promising anti-tumor activity in the escalating dosing cohorts. Furthermore, the sensitization and resistance spectrum for HRS-4642 was deciphered through genome-wide CRISPR/Cas9 screening, which unveiled the proteasome as a synergistic target. We further observed that the proteasome inhibitor, carfilzomib, prominently improved the anti-tumor efficacy of HRS-4642. Additionally, HRS-4642, especially when combined with carfilzomib, significantly reshapes the tumor microenvironment towards an immune permissive one. In summary, this study provides potential therapies for patients with KRAS G12D-mutant cancers, for whom effective treatments are currently lacking.

overall_design: All conditions are in triplicate and analyzed after treatment for 48hrs. Control KP-1 cells were treated only with 0.04% DMSO (DM). Experiment groups were treated with 200nM HRS-4642 (HR), 200nM Carfilzomib (Car), or 200nM HRS-4642 plus 200nM Carfilzomib (HR_Car) respectively. RNA-seq was performed on mRNA isolated from KP-1 cells. Libraries were prepared using Illumina TruseqTM RNA sample prep kit, and sequenced on Illumina NovaSeq X Plus platform, to generate 150-bp paired end reads. Raw fastq files were pseudo-aligned against mm10 using Kallisto 0.50.1 to generate count tables for each gene. R 4.3.2 and Bioconductor packages limma 3.58.1 and EdgeR 4.0.3 were used to perform data quality control and differential gene analysis. GSEA analysis were performed using MSigDB GSEA software v4.3.2.

first: Caicun

last: Zhou

first: Libo

last: Luo

first: Xin

first: Keyi

last: Jia

first: Ning

last: He

first: Shiqi

last: Mao

first: Wanying

last: Wang

first: Chuchu

last: Shao

first: Xinyu

last: Liu

first: Kan

last: Huang

first: Yaxin

last: Yu

first: Xinlei

last: Cai

first: Yingxue

last: Chen

first: Zican

last: Dai

first: Wei

first: Jia

first: Jiayu

first: Feng

last: Shen

first: Zaiyong

first: Xing

first: Rongfu

last: Shi

first: Jun

last: Zhang

first: Tao

last: Jiang

first: Zhe

first: Fei

first: Shengxiang

last: Ren


title: Anti-tumor Efficacy of HRS-4642 and Its Potential Combination with Proteasome Inhibition in KRAS G12D-mutant Cancer [CRISPR]

first: Chongyang

last: Li

overall_design: genome-wide CRISPR screen in mouse  lung cancer and pancreatic cancer cells

first: Caicun

last: Zhou

first: Libo

last: Luo

first: Xin

first: Keyi

first: Ning

first: Shiqi

first: Wanying

first: Chuchu

first: Xinyu

first: Kan

last: Sun


title: Temporal profiling of the phosphate starvation response in Arabidopsis root hair cells reveals that induction of polycomb target genes does not depend on removal of H3K27me3 or H2A.Z IV

first: Roger

last: Deal

overall_design: ATAC-seq profilng of root hair cell chromatin extracted from plants subject to 10 days of phosphate rich growth (0h_Pi) followed by 96h of Pi starvation (96h_noPi), then 30m, 1h, or 4h of Pi resupply (30m_rePi, 1h_rePi, 4h_rePi). Nuclei extracted from 100mg of root tissue in duplicate via INTACT (20k nuclei per rep).

first: Dylan

last: Holder


title: ST36 acupuncture ameliorates immune cell proliferation and polarization by inhibiting sympathetic activity in rheumatoid arthritis

city: Tianjin

first: Yue

address: Poyang Lake Road

institute: Tianjin University of Traditional Chinese Medicine

summary: To investigate the upstream mechanism of anti-inflammatory effects of ST36 acupuncture, including regulatory mechanism on T cell proliferation and polarization in peripheral immune organs, and whether peripheral sympathetic innervation in immune organs mediates the autoimmune response modulation by acupuncture.

overall_design: We analyzed the molecular mechanisms of AA and acupuncture stimulation by RNA sequencing.

first: Yinan

last: Gong

first: Yi

last: Guo

first: Zhifang

last: XU


title: Inflammation of the Nasal Mucosa is Associated with Susceptibility to Experimental Pneumococcal Challenge in Older Adults

city: Oxford

first: Andre

last: Goncalves

address: Old Road Campus, Roosevelt Dr, Headington

department: Department of Paediatrics

country: United Kingdom

institute: University of Oxford

summary: Streptococcus pneumoniae colonization in the upper respiratory tract is linked to pneumococcal disease development, predominantly affecting young children and older adults. As the global population ages and comorbidities increase, there is a heightened concern about this infection. We investigated the immunological responses of older adults to pneumococcal controlled human infection by analysing the cellular composition and gene expression in the nasal mucosa. Our comparative analysis with data from a concurrent study in younger adults revealed distinct gene expression patterns in older individuals susceptible to colonization, highlighted by neutrophil activation and elevated levels of CXCL9 and CXCL10. Unlike younger adults challenged with pneumococcus, older adults did not show recruitment of monocytes into the nasal mucosa following nasal colonization. However, older adults who were protected from colonization showed increased degranulation of CD8+ T cells, both before and after pneumococcal challenge. These findings suggest age-associated cellular changes, in particular enhanced mucosal inflammation, that may predispose older adults to pneumococcal colonization.

overall_design:
Healthy adults aged 50-84 were inoculated with an estimated 80,000 CFU per nostril of Streptococcus pneumoniae serotype 6B (strain BHN418, GenBank accession number ASHP00000000.1). Key eligibility criteria included capacity to give informed consent, no immunocompromised state or contact with susceptible individuals or children, no pneumococcal or influenza vaccine or infection in the last 2 years and not having taken part in EHPC studies in the past 3 years. All volunteers gave written informed consent, and research was conducted in compliance with all relevant ethical regulations. Participants who carried non-experimental pneumococcal strains at baseline (day -5) or had a viral infection were excluded from all analyses. Ethical approval was provided by the East Liverpool National Health Service Research and Ethics Committee (reference numbers 15/NW/0146 and 14/NW/1460) and Human Tissue Authority licensing number 12548. RNA sequencing: Nasal cells were collected in RLT (QIAGEN) and stored at -80°C until extraction. RNA extraction (RNeasy; QIAGEN), sample integrity assessment (Bioanalyzer; Agilent 2100), library preparation and RNA sequencing (BGISEQ-500RS) were performed at the Beijing Genome Institute. Quality control of raw sequencing data was done using FastQC tool. Mapping to a human reference genome assembly (GRCh38) was done using STAR 2.5.0a. Read counts from the resulting binary alignment map (BAM) files were obtained with featureCounts using a general transfer format (GTF) gene annotation from the Ensembl database. The R/Bioconductor package DESeq2 (version 1.34.0) was used to identify differentially expressed genes among the samples after removing absent features (zero counts in more than 75% of samples). Genes with a p-value of < 0.05 and an absolute fold-change of > 2.0 were identified as differentially expressed.
***Submitters state that raw data have been lost and therefore are not provided.

first: Goncalves

last: Andre

first: Urban

last: Britta

first: Ferreira

last: Daniela


title: Bulk Omni-ATAC-seq in young (2 months) and aged (22-24 months) mice across 23 cell-types

status: Public on Jul 15 2024

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

summary: To understand how age rewires the chromatin accessibility landscape, we molecularly profiled 23 purified cell types from 11 tissues and organs by assessing the cumulative signature of 15-25 young and aged mice for robust difference detection.

overall_design: We performed Omni-ATAC-seq for young (2 months) and aged (22-24 months) mice for FACS sorted cell-types. For sequencing of libraries derived from primary cell samples the DNBSEQ-G400 instrument (Bejing Genomics Institute) was used for ATAC-seq libraries (100 bp paired end mode).

first: Marina

last: Naval-Sanchez

first: Ralph

last: Patrick

first: Nikita

last: Depanhe


title: Gene expression profile of human monocyte-derived macrophage stimulated with AGP, anti-CD74 antibody, CRP, and mycobacterium avium infaction.

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

summary: Macrophages are immune cells inctributing to several kinds of diseases, and activation status of macrophages are considered to be regulated by several stimulations. To test the gene expression change in activated macrophages, human monocyte-derived macrophages were stimulated with alpha1-acid glycoprotein (AGP), anti-CD74 blocking antobody, anti-CD74-agonistic antibody. Macrophages infected with Micobacterium avium were also tested. The mRNA expression in control, stimulated, infected macrophages were analysed.

overall_design: Macrophages (200000 cells/well in 6-well plate) were stimulated with AGP(ORM1) and anti-CD74 antibodies. Macrophages were infected with mycobacterium avium for 3 days and 7days. Based culture madium was DMEM/HamF12 medium supplemented with 10% FBS.


title: Gene expression profile of human monocyte-derived macrophage stimulated with anti-CD74 antibody(10mg/mL).

summary: Macrophages are immune cells inctributing to several kinds of diseases, and activation status of macrophages are considered to be regulated by several stimulations.

overall_design: To test the gene expression change in activated macrophages, human monocyte-derived macrophages were stimulated with anti-CD74  antobodies (clone LN2 and CDLA74-1). The mRNA expression in control, stimulated, infected macrophages were analysed. Macrophages (200000 cells/well in 6-well plate) were stimulated with anti-CD74 antibodies. Based culture madium was DMEM/HamF12 medium supplemented with 10% FBS.


title: Embryo implantation failure with defective luteinization and aberrant activated CD8+T cells in interferon-γ-induced hypophysitis

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: We report an increase in activated CD8+T cells in the ovaries of a mouse model with chronic elevated IFN-γ. We demonstrate that these mice experience hypophysitis with defective luteinization and embryo implantation failure.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 3mice / 3 genotypes.

first: Bafor

last: Enitome E.

first: Ewin-Cohen

last: Rebecca

first: Martin

last: Toni

first: Baker

last: Clayton

first: Feimore

last: John

first: Kimmel

last: Adrienne E.

first: Ramba

last: Meredith

first: Hess

last: Megan A.

first: Sanford

last: Michael

first: Lazarevic

last: Vanja

first: Benayoun

last: Berenice A.

first: Young

last: Howard A.

first: Valencia

last: Julio C.


title: IFN-γ activates an immune-like regulatory network in the cardiac vascular endothelium

city: La Jolla

first: Timothy

middle: D

last: Arthur

address: 9500 Gilman Drive #0761

department: Pediatrics

institute: UCSD

summary: The regulatory mechanisms underlying the response to pro-inflammatory cytokines during myocarditis are poorly understood. Here, we use iPSC-derived cardiovascular progenitor cells (CVPCs) to model the response to interferon gamma (IFN-γ) during myocarditis. We generate RNA-seq and ATAC-seq for four CVPCs that were treated with IFN-γ and compare them with paired untreated controls. Transcriptional differences after treatment show that IFN-γ initiates an innate immune cell-like response in the vascular cardiac endothelium. IFN-γ treatment also shifts the CVPC transcriptome towards the adult coronary artery and aorta-like profile and expands the relative endothelial cell population in all four CVPC lines. Analysis of the accessible chromatin shows that IFN-γ is a potent chromatin remodeler and establishes an IRF-STAT immune-cell like regulatory network.  Our findings reveal insights into the endothelial-specific protective mechanisms during myocarditis.

overall_design: RNA-seq and ATAC-seq was generated for four iPSC-derived cardiovascular progenitor cells (CVPCs) stimulated with 100nM IFNg. Both stimulated and paired control CVPCs have molecular data resulting in 16 FASTQ files.

first: Arthur

last: Timothy D

first: Frazer

last: Kelly A

first: D'Antonio

last: Matteo


title: Nr5a2 is dispensable for ZGA but essential for morula development [ATAC-seq]

city: Paris

first: Nicola

last: Festuccia

address: 25-28 Rue du Docteur Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

summary: Early embryogenesis is driven by transcription factors (TFs) that first activate the zygotic genome and then specify the lineages constituting the blastocyst. While the TFs specifying the blastocyst’s lineages are well characterised, those playing earlier roles are ill-defined. Using mouse models of the TF Nr5a2, we show that Nr5a2-/- embryos arrest at the early morula stage and exhibit overt phenotypical problems such as altered lineage specification, frequent mitotic failure and substantial chromosome segregation defects. We further show that whilst NR5A2 plays a minor but measurable role during zygotic genome activation, it predominantly acts as a master regulator at the 8-cells stage, controlling expression of lineage-specifying TFs and genes involved in mitosis, telomere maintenance and DNA repair. We conclude that NR5A2 coordinates proliferation, genome stability and lineage specification to ensure proper morula development.

overall_design: ATAC-seq reactions were performed ex-vivo on 8-cell stage embryos for maternal and zygotic Nr5a2 KO samples. Instead, embryos from Inducible NrKO samples (iNrko) were dissected at the early 2C stage (30h post hCG), and kept in culture for additional 45h (until they reached the 8C stage) before processing, treating or not with 750nM 4-hydroxytamoxifen for the first 24h.

first: Pablo

last: Navarro


title: In vivo CRISPR base editing for treatment of Huntington’s disease

city: Urbana

last: Perez-Pinera

state: Illinois

address: 1406 W Green Street

institute: University of Illinois, Urbana-Champaign

summary: Huntington's disease (HD) is an inherited and ultimately fatal neurodegenerative disorder caused by an expanded polyglutamine-encoding CAG repeat within exon 1 of the huntingtin (HTT) gene, which produces a mutant protein that destroys striatal and cortical neurons.Importantly, a critical event in the pathogenesis of HD is the proteolytic cleavage of the mutant HTT protein by caspase-6, which generates fragments of the N-terminal domain of the protein that form highly toxic aggregates. Given the role that proteolysis of the mutant HTT protein plays in HD, strategies forpreventing this process hold potential for treating the disorder.By screening 141 CRISPR base editor variants targeting splice elements in the HTT gene, we identified platforms capable of producing HTT protein isoforms resistant to caspase-6-mediated proteolysis via editing of the splice acceptor sequence for exon 13. When delivered to the striatum of a rodent HD model, these base editors induced efficient exon skipping and decreased the formation of the N-terminal fragments, which in turn reduced HTT protein aggregation and attenuatedstriatal and cortical atrophy.Collectively, these results illustrate the potential for CRISPR base editing to decrease the toxicity of the mutant HTT protein for HD.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mammalian cell transfections with CRISPR base editors to modify DNA bases in HTT exon and influence RNA splicing to investigate its impact on caspase-6 induced proteolysis. Stereotaxic injections using AAV delivery into mice brains to study DNA editing and exon skipping using base editing tools

first: Shraddha

last: Shirguppe

first: Michael

last: Gapinske

first: Devyani

last: Swami

first: Nicholas

last: Gosstola

first: Pankaj

last: Acharya

first: Angelo

last: Miskalis

first: Dana

last: Joulani

first: Maddie

middle: G

last: Szkwarek

first: Abhishek

last: Bhattacharjee

first: Gianna

last: Elias

first: Michelle

last: Stilger

first: Jackson

last: Winter

first: Wendy

middle: S

last: Woods

first: Daphine

last: Anand

first: Colin

middle: K

last: Lim

first: Thomas

last: Gaj


title: Increased viral tolerance mediates by antiviral RNA interference in bat cells

first: Yang

last: Li

address: 2005 Songhu Rd, Yangpu district

institute: Fudan university

type: Non-coding RNA profiling by high throughput sequencing

summary: Bats harbor highly virulent viruses that can infect other mammals, including humans, posing questions about their immune tolerance mechanisms. Bat cells employ multiple strategies to limit virus replication and virus-induced immunopathology, but the coexistence of bats and fatal viruses remains poorly understood. Here, we investigated the antiviral RNA interference (RNAi) pathway in bat cells and discovered that they have an enhanced antiviral RNAi response, producing canonical viral small interfering RNAs (vsiRNAs) upon Sindbis virus (SINV) infection that were missing in human cells. Disruption of Dicer function resulted in increased viral load for three different RNA viruses in bat cells, indicating an interferon-independent antiviral pathway. Furthermore, our findings reveal the simultaneous engagement of Dicer and pattern-recognition receptors (PRRs), such as retinoic acid-inducible gene I (RIG-I), with double-stranded RNA, suggesting that Dicer attenuates the interferon response initiation in bat cells. These insights advance our comprehension of the distinctive strategies bats employ to coexist with viruses.

sample_organism:
Pteropus alecto
Tadarida brasiliensis
Homo sapiens

overall_design: We performed small RNA-seq in virus-infected PaKi cells and human cells including HeLa and A549, we analyzed distribution of virus-derived small RNAs and mature microRNAs

first: Yunpeng

last: Dai

first: Binbin

last: Wang

first: Jiaxin

last: wang


title: Nr5a2 is dispensable for ZGA but essential for morula development

first: Nicola

last: Festuccia

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

overall_design: Refer to individual Series


title: Real time quantitative PCR analysis of mouse biliary epithelial cells

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

summary: Biliary complications are disabling conditions that arise in up to 25% of liver transplanted patients, resulting in additional surgical procedures, re-transplantation or, in the absence of a suitable regraft, death. Here, we investigate the role of the primary cilia, a highly-specialised sensory organelle, in biliary injury leading to biliary complications. Human biopsies were used to study the structure and function of primary cilia in liver transplant recipients that develop biliary complications (N=7), compared to successful transplants (N=12). To study the biological effects of the primary cilia during transplantation, we used murine models that recapitulate liver procurement and cold storage conditions, and the K19CreERT Kif3a flox/flox mouse model to conditionally eliminate primary cilia in cholangiocytes. Microarray and RNA-seq analysis were used to study these biological effects at the transcriptional level. To explore the molecular mechanisms responsible for the observed phenotypes, we used in vitro models of ischemia, cellular senescence and primary cilia ablation. Pharmacological and genetic approaches were used to target cellular senescence and the primary cilia, in mouse models and human donor livers. Prolonged ischemic periods pre-transplantation result in ciliary shortening and cellular senescence. Primary cilia damage results in biliary injury and a loss of regenerative potential. Initiation of senescence negatively primary cilia structure, establishing a negative feedback loop that further impairs regeneration. We conclude that primary cilia play an essential role in biliary regeneration; we demonstrate that senolytics and cilia-stabilising treatments provide a potential therapeutic opportunity to reduce the rate of biliary complications and improve the outcome of the liver transplanted patient.

overall_design: RT-PCR gene expression profiling

first: Hannah

last: Esser

first: Sofia

last: Ferreira-Gonzalez

first: Alastair

middle: M

last: Kilpatrick

first: Tak

middle: Y

last: Man

first: Rhona

middle: E

last: Aird

first: Daniel

last: Rodrigo-Torres

first: Luke

last: Boulter

first: Gabriel

last: Oniscu

first: Stefan

last: Schneeberger

middle: J


title: Real time quantitative PCR analysis of human biliary epithelial cells


title: Primary cilia as a targetable node between biliary injury, senescence and regeneration


title: Primary cilia as a targetable node between biliary injury, senescence and regeneration [RNA-seq]

overall_design: Differential expression between primary cilia competent and primary cilia depleted biliary epithelial cells


title: Romidepsin and afatinib combination treatment induce synergistic anti-lymphoma effect in CTCL

city: New York

first: Bobby

last: Shih

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

summary: Cutaneous T-cell lymphomas (CTCL) are an aggressive group of T-cell lymphomas that present in the skin and are associated with dismal prognosis. Romidepsin is a histone deacetylase (HDAC) inhibitor that is an FDA approved systemic therapeutic indicated for the treatment of CTCL in patients who have received at least one prior systemic therapy. Romidepsin demonstrates promising single agent activity in patients with advanced stages of CTCL, however response is typically low and not durable. One method of overcoming resistance to romidepsin and improving response is through combination therapies. Here, we demonstrate that romidepsin in combination with the epidermal growth factor receptor (EGFR) inhibitor afatinib and afatinib dimaleate produce strongly synergistic anti-tumor effects in CTCL cell lines and an in vivo model of CTCL. Gene expression and western blot analysis further identifies the decreased activation of the JAK-STAT signalling pathway as a key driver of synergy in this combination. These results suggest a potential indication for FDA-approved EGFR inhibitors previously unrecognized in CTCLs as a combination therapeutic with HDAC inhibitors that can be rapidly adopted in the clinic.

overall_design: To investigate mechanisms of synergy between romidepsin and afatinib dimaleate in CTCL, we treated MYLA cell line with DMSO, romidepsin, afatinib dimaleate, or romidepsin + afatinib dimaleate in triplicate and performed bulk RNA-seq.

first: Teresa

last: Palomero


title: Spatial transcriptomic analysis of a pre-clinical NF1 pseudarthrosis fracture model

city: Dallas

first: Jonathan

last: Rios

state: TX

address: 2222 Welborn Street

institute: Scottish Rite for Children

summary: Patients with Neurofibromatosis Type 1 (NF1) present with fracture pseudarthroses, though the exact mechanism underlying this abnormal healing remains unknown. Here, we performed spatial transcriptomics to spatially-define the molecular signatures across endochondral healing following fracture. Integrating single-cell sequencing of patient fracture-derived primary cells, our results provide a dynamic cellular context to the molecular dysregulation associated with somatic fracture healing defects in NF1.

overall_design: 8-week old control and Postn-cre;Nf1[flox/-] mice underwent distal tibia fracture surgery. Fractures were stabilized with an intramedullary pin. Ten days post-fracture, calluses were harvested, fixed in formallin for 24h, decalcified in 14% EDTA for 3 days prior to embedding in paraffin. Both fracture calluses were embedded together, and two sections through the fracture callus were analyzed using the 10X Genomics Visium spatial transcriptome platform following manufacturer's recommendations. Following sequencing, bioinformatic analyses were conduced using Partek Flow.

first: J

first: R

last: Tower


title: NTF3 as a biomarker for prediction allergic diseases in children postnatal or adolescence [mouse RRBS]

city: Chiayi County

first: Mita

last: Tran

address: 168 University Road

department: Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation alteration marks phthlate mediated transgenerational inheritance in murine allergic diseases.

overall_design: cDC samples were collected from C57BL/6 mice model with F0 mice treated DEHP

middle: T

first: Michael

last: Chan

first: Jau-Ling

last: Suen

first: Ming-Tsang

last: Wu

first: Pearlly

last: Yan


title: Nr5a2 is dispensable for ZGA but essential for morula development [RNA-seq]

first: Nicola

last: Festuccia

summary: Early embryogenesis is driven by transcription factors (TFs) that first activate the zygotic genome and then specify the lineages constituting the blastocyst. While the TFs specifying the blastocyst’s lineages are well characterised, those playing earlier roles are ill-defined. Using mouse models of the TF Nr5a2, we show that Nr5a2-/- embryos arrest at the early morula stage and exhibit overt phenotypical problems such as altered lineage specification, frequent mitotic failure and substantial chromosome segregation defects. Transcriptomic profiling shows that Nr5a2 is a master regulator required for appropriate expression of thousands of genes at the 8-cells stage, including lineage-specifying TFs and genes involved in mitosis, telomere maintenance and DNA repair. We conclude that Nr5a2 coordinates proliferation, genome stability and lineage specification to ensure proper morula development.

overall_design: RNA-seq in mouse embryos at the 2C, 4C and 8C stage, after the maternal and zygotic knockout of Esrrb or Nr5a2, or the zygotic knockout of Nr5a2. Reads are divided into two groups: one containing unique molecular identifiers (UMI) originating from the 5’ of poly-A transcripts, and another including NON-UMI reads, covering the full length of poly-A transcripts.

first: Almira

last: Chervova

first: Pablo

last: Navarro


title: Single nucleus RNA-sequencing integrated into risk variant colocalization discovers 17 cell-type-specific abdominal obesity genes for metabolic dysfunction-associated steatotic liver disease [ATAC-seq]

status: Public on Jul 11 2024

city: Los Angeles

first: Seung Hyuk

middle: T.

last: Lee

address: 695 Charles E. Young Drive South

institute: UCLA

summary: Abdominal obesity increases the risk for non-alcoholic fatty liver disease (NAFLD), now known as metabolic dysfunction-associated steatotic liver disease (MASLD). To elucidate the directional cell-type level biological mechanisms underlying the association between abdominal obesity and MASLD, we integrated adipose and liver single nucleus RNA-sequencing and bulk cis-expression quantitative trait locus (eQTL) data with the UK Biobank genome-wide association study (GWAS) data using colocalization. Then we used colocalized cis-eQTL variants as instrumental variables in Mendelian randomization (MR) analyses, followed by functional validation experiments on the target genes of the cis-eQTL variants. We identified 17 colocalized abdominal obesity GWAS variants, regulating 17 adipose cell-type marker genes. Incorporating these 17 variants into MR discovers a putative tissue-of-origin, cell-type-aware causal effect of abdominal obesity on MASLD consistently with multiple MR methods without significant evidence for pleiotropy or heterogeneity. Single cell data confirm the adipocyte-enriched mean expression of the 17 genes. Our cellular experiments across human adipogenesis identify risk variant -specific epigenetic and transcriptional mechanisms. Knocking down two of the 17 genes, PPP2R5A and SH3PXD2B, shows a marked decrease in adipocyte lipidation and significantly alters adipocyte function and adipogenesis regulator genes, including DGAT2, LPL, ADIPOQ, PPARG, and SREBF1. Furthermore, the 17 genes capture a characteristic MASLD expression signature in subcutaneous adipose tissue. Overall, we discover a significant cell-type level effect of abdominal obesity on MASLD and trace its biological effect to adipogenesis (Lee et. al, eBioMedicine 2024).

overall_design: We initiated a 14 day differentiation in primary human preadipocytes and collected ATAC-seq data at 6 different timepoints.

first: Kristina

last: Garske

first: Päivi

last: Pajukanta


title: Gene expression profile of the major phenotypic subsets of tissue-resident and tissue disease-associated macrophages from healthy and nephritic NZB/W lupus prone mice respectively in comparison to disease-monocyte transcriptional profile

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

summary: We employed bulk RNA-sequencing to compare gene expression between the two major phenotypic subsets of disease-associated macrophages based on MHCII protein expression as well as tissue-resident macrophages and disease-monocytes.

overall_design: Different clusters of kidney macrophages and monocytes were isolated by Fluorescence-activated cell sorting (FACS) and depended  and analyzed using bulk-RNAseq.

first: Stylianos

middle: I

last: Georgallis

first: Tom

last: Ashman

first: Katerina

last: Stergioula

first: Frauke

last: Schreiber

first: Vajiheh

last: Jafari

first: Anna

last: Taranko

first: Tejal

last: Karmalkar

first: Ana

last: Kasapi

first: Tihana

middle: L

last: Rovis

first: Vedrana

last: Jelencic

first: David

last: Bejarano

first: Lea

last: Fabry

first: Irene

last: Mattiola

first: Martina

last: Molgora

first: Jinchao

last: Hou

first: Karolin

last: Hublitz

first: Gabriela

last: Guerra

first: Pawel

last: Durek

first: Giannino

last: Patone

first: Eric

last: Lindberg

first: Henrike

last: Maatz

first: Oliver

last: Hölsken

first: Gerhard

last: Krönke

first: Arthur

last: Mortha

first: Reinhard

last: Voll

first: Alexander

last: Clarke

first: Anja

last: Hauser

first: Marco

last: Colonna

first: Kevin

last: Thurley

first: Andreas

last: Schlitzer

first: Christoph

last: Schneider

first: Efstathios

last: Stamatiades

first: Mir-Farzin

last: Mashreghi

first: Stipan

last: Jonjic

first: Norbert

last: Hübner

last: Diefenbach

first: Masatoshi

last: Kanda

first: Antigoni

last: Triantafyllopoulou


title: Gene expression profile at single cell level of tissue- associated kidney NKp46+NK1.1+ or NK1.1+ ILC from untreated and poly (I:C) treated  RORgt-FM mice

first: Frederik

last: Heinrich

summary: We next asked whether RORgt-FM+ ILC are transcriptionally similar to the Tnfrsf9+ tILC that we identified in lupus-prone mice. To explore this, we isolated tissue RORgt-FM+ and RORgt-FM- NKp46+ ILC from RORgt-FM mice, some of which were treated with poly(I:C) and analyzed them by scRNA-seq

overall_design: Kidney NKp46+ ILC were isolated by Fluorescence-activated cell sorting (FACS) and depended  and analyzed using scRNAseq.

first: Stylianos

last: Georgallis

first: Tom

last: Ashman

first: Katerina

last: Stergioula

first: Frauke

last: Schreiber

first: Vajiheh

last: Jafari

first: Anna

last: Taranko

first: Tejal

last: Karmalkar

first: Ana

last: Kasapi

first: Tihana

last: Rovis

first: Vedrana

last: Jelencic

first: David

last: Bejarano

first: Lea

last: Fabry

first: Irene

last: Mattiola

first: Martina

last: Molgora

first: Jinchao

last: Hou

first: Karolin

middle: W

last: Hublitz

first: Gabriela

last: Guerra

first: Pawel

last: Durek

first: Giannino

last: Patone

first: Eric

last: Lindberg

first: Henrike

last: Maatz

last: Hölsken


title: Gene expression profile at single cell level of kidney CD45 cells including vessel-associated (CD45.2iv.+) NK cells in nephritic and NKp46 blocking antibody treated NZB/W mice

first: Frederik

last: Heinrich

summary: We explored the effects of treatment with NKp46 blocking antibodies in the transcriptome of kidney CD45+ cells

first: Stylianos

last: Georgallis

first: Tom

last: Ashman

first: Katerina

last: Stergioula

first: Frauke

last: Schreiber

first: Vajiheh

last: Jafari

last: Taranko

first: Oliver

first: Gerhard

last: Krönke

first: Arthur

last: Mortha

first: Reinhard

last: Voll

first: Alexander

last: Clarke

first: Anja

last: Hauser

first: Marco

last: Colonna

first: Kevin

last: Thurley

first: Andreas

last: Schlitzer

first: Christoph

last: Schneider

first: Efstathios

last: Stamatiades

first: Mir-Farzin

last: Mashreghi

first: Stipan

last: Jonjic

first: Norbert

last: Hübner

last: Diefenbach

first: Masatoshi

last: Kanda

first: Antigoni

last: Triantafyllopoulou


title: RNAi-dependent expression of sperm genes in ADL chemosensory neurons is required for olfactory responses in Caenorhabditis elegans

city: Syracuse

first: Maria

middle: C.

last: Ow

address: 107 College Dr, LSC117

institute: Syracuse University

summary: Environmental conditions experienced early in the life of an animal can result in gene expression changes later in its life history. We have previously shown that C. elegans animals that experienced the developmentally arrested and stress resistant dauer stage (postdauers) retain a cellular memory of early-life stress that manifests during adulthood as genome-wide changes in gene expression, chromatin states, and altered life history traits. One consequence of developmental reprogramming in C. elegans postdauer adults is the downregulation of osm-9 TRPV channel gene expression in the ADL chemosensory neurons resulting in reduced avoidance to a pheromone component, ascr#3. This altered response to ascr#3 requires the principal effector of the somatic nuclear RNAi pathway, the Argonaute (AGO) NRDE-3. To investigate the role of the somatic nuclear RNAi pathway in regulating the developmental reprogramming of ADL due to early-life stress, we profiled the mRNA transcriptome of control and postdauer ADL in wild-type and nrde-3 mutant adults. We found 711 differentially expressed (DE) genes between control and postdauer ADL neurons, 90% of which are dependent upon NRDE-3. Additionally, we identified a conserved sequence that is enriched in the upstream regulatory sequences of the NRDE-3-dependent DE genes. Surprisingly, 214 of the ADL DE genes are considered “germline-expressed”, including 21 genes encoding the Major Sperm Proteins and two genes encoding the sperm-specific PP1 phosphatases, GSP-3 and GSP-4. Loss of function mutations in gsp-3 resulted in both aberrant avoidance and attraction behaviors. We also show that an AGO pseudogene, Y49F6A.1 (wago-11), is expressed in ADL and is required for ascr#3 avoidance. Overall, our results suggest that small RNAs and reproductive genes program the ADL mRNA transcriptome during their developmental history and highlight a nexus between neuronal and reproductive networks in calibrating animal neuroplasticity.

first: Sarah

last: Hall


title: Hepatitis C Virus-induced Differential Transcriptional Traits in Host Cells After Persistent Infection Elimination by Direct-Acting Antivirals In Cell Culture

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Chronic hepatitis C virus infection (HCV) causes liver inflammation and fibrosis, leading to development of severe liver disease, such as cirrhosis or hepatocellular carcinoma (HCC). Approval of direct acting antiviral (DAA) drug combinations has revolutionized chronic HCV therapy, with virus eradication in >98% of the treated patients. The efficacy of these treatments is such that it is formally possible for cured patients to carry formerly infected cells that display irreversible transcriptional alterations directly caused by chronic HCV Infection. Combining differential transcriptomes from two different persistent infection models, we observed a major reversion of infection-related transcripts after complete infection elimination. However, a small number of transcripts were abnormally expressed in formerly infected cells. Comparison of the results obtained in proliferating and growth-arrested cell culture models suggest that permanent transcriptional alterations may be established by several mechanisms. Interestingly, some of these alterations were also observed in the liver biopsies of virologically cured patients. Overall, our data suggest a direct and permanent impact of persistent HCV infection on the host cell transcriptome even after virus elimination, possibly contributing to development of HCC.

overall_design: To determine the impact of direct-acting antiviral (DAA) treatment on the reversal of persistent hepatitis C virus (HCV) infection-induced host cell transcriptional alterations, human hepatoma cells were persisitently infected in cell culture with recombinant HCV viruses. Persistent infection was maintained for weeks before infection elimination by DAA treatment. Experiments were performed in two experimental models: one in proliferating cell cultures and a second model in quiescent, partially-differentiated human hepatoma cells. Four biological replicates from mock, infected and the corresponding DAA-treated samples were analyzed by RNAseq in the proliferating cell culture model (Huh7pro). Three biological replicates  from mock, infected and the corresponding DAA-treated samples were analyzed by RNAseq in the partially-differentiated cell culture model (Huh7DMSO).

first: Victoria

last: Castro

first: Gema

last: Calvo

middle: C

first: Sofía

last: Pérez-del-Pulgar

first: Pablo

last: Gastaminza


title: Single nucleus RNA-sequencing integrated into risk variant colocalization discovers 17 cell-type-specific abdominal obesity genes for metabolic dysfunction-associated steatotic liver disease [scRNA-seq]

first: Seung Hyuk

last: Lee

overall_design:
We performed single-nucleus RNA-sequecing on subcutaneous adipose tissue biopsies from 8 individuals from the KOBS cohort.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Uma

last: Thanigai Arasu

first: Jussi

last: Pihlajamäki

first: Minna

middle: U

last: Kaikkonen

first: Päivi

last: Pajukanta


title: FLASH proton radiotherapy mitigates inflammatory and fibrotic pathways and preserves cardiac function in a preclinical mouse model of radiation-induced heart disease

city: Philadelphia

first: Ioannis

last: Verginadis

state: PA

address: 3400 Civic Center Blvd, Perelman School of Medicine, TRC 8-155

department: Radiation Oncology

institute: University of Pennsylvania

summary:
Purpose: Studies during the past 9 years suggest that delivering radiation at dose rates exceeding 40 Gy/s, known as “FLASH” radiotherapy, enhances the therapeutic index of radiation therapy (RT) by decreasing normal tissue damage while maintaining tumor response compared to conventional (or standard) RT. This study demonstrates the cardioprotective benefits of FLASH proton RT (F-PRT) compared to standard (conventional) proton RT (S-PRT), as evidenced by reduced acute and chronic cardiac toxicities.
Methods and Materials: Mice were imaged using cone beam computed tomography to precisely determine the heart’s apex as the beam isocenter. Irradiation was conducted utilizing a shoot-through technique with a 5mm collimator. Bulk RNA-sequencing was performed on non-irradiated (NR) samples, as well as apexes treated with F-PRT or S-PRT, at 2 weeks following a single 40 Gy dose. Inflammatory responses were assessed through multiplex cytokine/chemokine microbead assay and immunofluorescence analyses. Levels of perivascular fibrosis were quantified using Masson’s Trichrome and Picrosirius red staining. Additionally, cardiac tissue functionality was evaluated by 2D echocardiograms at 8 and 30 weeks post-PRT.
Results: Radiation damage was specifically localized in the heart’s apex. RNA profiling of cardiac tissues treated with PRT revealed that S-PRT induced unique pathways associated with DNA damage response, induction of tumor necrosis factor superfamily and inflammatory response, while F-PRT primarily affected cytoplasmic translation, mitochondrion organization and ATP synthesis. Notably, F-PRT led to a milder inflammatory response, accompanied by significantly attenuated changes in TGF-1 and SMA levels. Critically, F-PRT decreased collagen deposition, and better preserved cardiac functionality compared to S-PRT.
Conclusions: This study demonstrated that F-PRT reduces the induction of an inflammatory environment with lower expression of inflammatory cytokines and profibrotic factors. Importantly, the results indicate that F-PRT better preserves cardiac functionality, as confirmed by echocardiography analysis, while also mitigating the development of long-term fibrosis.

overall_design:
To gain a better understanding of the effects of each treatment modality on cardiac tissue, we performed bulk RNA-sequencing on non-irradiated (NR) samples, as well as apexes treated with F-PRT(FLASH proton RT) or S-PRT (Standard proton RT), at 2 weeks following a single dose of 40 Gy
Bulk RNA-seq on 4 NR, 4 S-PRT and 3 F-PRT samples

first: Giorgos

last: Skoufos


title: Polymerization of BTB transcription factors regulates chromatin occupancy [ChIP-Seq]

city: Boston

first: Jared

last: Brown

state: MA

address: Mailtop CLS11007, 450 Brookline Ave

department: Data Science

institute: Dana Farber Cancer Institute

summary: The broad-complex, tramtrack and bric-à-brac (BTB) family of transcription factors (TFs) serve as important regulators of hematopoietic development. The BTB domains of these TFs mediate co-repressor recruitment and dimerization, but their propensity to self-assemble into higher-order structures has not been established. Here, we survey 189 human BTB proteins and identify 18 BTB TFs that form punctate nuclear foci. We demonstrate that these foci-forming BTB TFs polymerize into filaments and present the cryo-EM structures of ZBTB5BTB and ZBTB9BTB filaments. Finally, we find that polymerization in BTB TFs enhances chromatin occupancy within regions containing homotypic clusters of TF binding sites. This increased chromatin occupancy in turn leads to the repression of target genes. Taken together, our results reveal a novel mechanism to regulate BTB TFs, and suggest an underappreciated role for polymerization in regulating TF function.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was performed for ZBTB3 and ZBTB9 in HEK 293T cells modified to knock out endogenous ZBTB3 and ZBTB9 respectively. In each case, sequencing was performed across both doxycycline inducable over expression of wild-type (WT) ZBTB3/9 and non-polymerizing mutant (K166A for ZBTB3, W128A for ZBTB9) ZBTB3/ZBTB9. Samples were prepared in duplicate across 0.01, 0.1, and 1.0 ug/mL dosages of doxycycline. Fractions of each sample were sequenced absent precipitation as matched input datasets.

first: Paul

last: Park

first: Jiho

first: Moritz

last: Hunkeler

first: Shourya

last: Roy Burman

first: Katherine

middle: A

last: Donovan

first: Ryan

last: Lumpkin

first: Hojong

last: Yoon

first: Radosław

middle: P

last: Nowak

first: Mikołaj

last: Słabicki

first: Benjamin

last: Ebert

first: Eric

last: Fischer


title: Polymerization of BTB transcription factors regulates chromatin occupancy


title: Temporal profiling of the phosphate starvation response in Arabidopsis root hair cells reveals that induction of polycomb target genes does not depend on removal of H3K27me3 or H2A.Z

city: Atlanta

first: Roger

middle: B

last: Deal

address: 1510 Clifton Rd NE

institute: Emory University


title: Polymerization of BTB transcription factors regulates chromatin occupancy [RNA-Seq]

overall_design: RNA sequencing (RNA-seq) was performed for ZBTB3 and ZBTB9 in HEK 293T cells modified to knock out endogenous ZBTB3 and ZBTB9 respectively. In each case, sequencing was performed across each of otherwise-unaltered-cells treated with doxycycline/DMSO (control) and cells with a doxycycline inducable over expression of wild-type (WT) ZBTB3/9 and non-polymerizing mutant (K166A for ZBTB3, W128A for ZBTB9). Among cells with the doxycycline system, treatment ranged across DMSO 24h/48h (control), dosage of 0.01, 0.1, and 1 ug/mL doxycycline for 24h and one treatment group of 1 ug/mL doxycycline for 48h. Each condition was prepared and sequenced in triplicate.

middle: M

middle: S


title: Global alteration of transcript decay rates upon ZNF598 knockdown

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

summary: We calculated half-life of transcripts in HEK293T cells expressing control or ZNF598-targeting shRNA.

overall_design: BRIC-Seq of HEK293T cells

first: Kota

last: Ishibashi

first: Yuichi

last: Shichino

first: Yuichiro

last: Mishima


title: KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [RNA-seq]

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

summary: Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tomato M82 wild type and KRYPTONITE(Kyp) mutant. 3 biological replicates for each condition.

first: Rim

last: Brik Chaouche

first: David

last: Latrasse

first: Qingyi

last: Wang

first: Moussa

last: Benhamed


title: KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [Hi-C]

overall_design: Comparative analysis of genome conformation changes for tomato M82 wild type and KRYPTONITE(Kyp) mutant


title: KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-seq]

overall_design: Comparative analysis of twenty-six histone modifications and Pol II  ChIP-seq data for tomato M82 wild type

first: Ying

last: Huang


title: KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ATAC-Seq]

overall_design: Comparative analysis of twenty-six histone modifications and Pol II  ChIP-seq data for tomato M82 wild type, HiC and Comparative analysis of ChIP-seq, ATACseq, RNAseq for tomato M82 wild type and Kyp mutant

last: Chaouche


title: Gene expression profile at single cell level of tissue- associated kidney NKp46+NK1.1+ or NK1.1+ ILC from healthy, nephritic and NKp46 blocking antibody treated NZB/W lupus prone mice

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Kidney NKp46+ ILC have never been characterized at single cell level before. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of kidney NKp46+ ILC in the kidney

first: Stylianos

last: Biniaris Georgallis

first: Tom

last: Ashman

first: Katerina

last: Stergioula

first: Frauke

last: Schreiber

first: Vajiheh

last: Jafari

first: Anna

last: Taranko

first: Tejal

last: Karmalkar

first: Ana

last: Kasapi

first: Tihana

last: Rovis

first: Vedrana

last: Jelencic

last: Bejarano

first: Lea

last: Fabry

first: Irene

last: Mattiola

first: Martina

last: Molgora

first: Jinchao

last: Hou

first: Karolin

last: Hublitz

first: Frederik

last: Heinrich

first: Gabriela

last: Guerra

first: Giannino

last: Patone

first: Eric Lars-Helge

last: Lindberg

first: Henrike

last: Maatz

first: Oliver

last: Hölsken

first: Gerhard

last: Krönke

first: Arthur

last: Mortha

first: Reinhard

last: Voll

first: Alexander

last: Clarke

first: Anja

middle: E

last: Hauser

first: Marco

last: Colonna

first: Kevin

last: Thurley

first: Andreas

last: Schlitzer

first: Christoph

last: Schneider

first: Efstathios

last: Stamatiades

first: Mir-Farzin

last: Mashreghi

first: Stipan

last: Jonjic

first: Norbert

last: Hübner

last: Diefenbach

first: Masatoshi

last: Kanda

first: Antigoni

last: Triantafyllopoulou


title: Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed –1 ribosomal frameshifting

city: New Haven

first: Lian-Huan

last: Wei

state: CT

address: 295 Congress Ave BCMM141

department: Department of Neuroscience

institute: Yale University

summary: Many positive-strand RNA viruses, including all known coronaviruses, employ programmed –1 ribosomal frameshifting (–1 PRF) to regulate the translation of polycistronic viral RNAs. However, only a few host factors have been shown to regulate –1 PRF. Through a reporter-based genome-wide CRISPR/Cas9 knockout screen, we identified several host factors that either suppressed or enhanced –1 PRF of SARS-CoV-2. One of these factors is eukaryotic translation initiation factor 2A (eIF2A), which specifically and directly enhanced –1 PRF in vitro and in cells. Consistent with the crucial role of efficient –1 PRF in transcriptase/replicase expression, loss of eIF2A reduced SARS-CoV-2 replication in cells.  Transcriptome-wide analysis of eIF2A-interacting RNAs showed that eIF2A primarily interacted with 18S ribosomal RNA near the contacts between the SARS-CoV-2 frameshift-stimulatory element (FSE) and the ribosome. Thus, our results revealed an unexpected role for eIF2A in modulating the translation of specific RNAs independent of its previously described role during initiation.

overall_design: sgRNA were quantified by high-throughput sequencing in CRISPR screens for samples with high and low GFP/mCherry ratios. eCLIP was used to identify RNAs bound to eIF2A in HEK293T cells with GFP as a control

first: Yu

last: Sun

first: Junjie

last: Guo


title: Reconstitution of the Multiple Myeloma Microenvironment Following Lymphodepletion with BCMA CAR-T Therapy

status: Public on Jul 10 2024

city: Beijing

first: Sen

last: Qin

address: 38, Xueyuan Road

institute: Peking University

summary: Despite the acknowledged effectiveness of BCMA chimeric antigen receptor T (CAR-T) cells in killing multiple myeloma (MM) cells, predicting treatment responsivity to BCMA CAR-T therapy remains a challenge. In this study, we demonstrated that the best overall responses (BORs) of patients over the 15-month follow-up are positively correlated with the abundance and targeted cytotoxic activity of CD8+ effector CAR-T cells on day 28 after CAR-T cell infusion. Additionally, favorable responses are associated with attenuated immunosuppression mediated by regulatory T cells (Tregs), enhanced CD8+ effector T cell cytotoxic activity, and elevated type 1 conventional dendritic cell (cDC1) antigen presentation ability. Our study sheds light on MM microenvironment dynamics after BCMA CAR-T therapy, offering clues for predicting treatment responsivity.

overall_design: The collected paired bone marrow (BM) specimens from MM patients before and after BCMA CAR-T therapy were isolated into single cell suspensions, and 3'-scRNA-seq (Chromium Single Cell 3' v3 Libraries) analysis was performed on each sample.

first: Luyang

first: Hui

last: Liu

first: Yazi

last: Yang


title: Telomerase reverse transcriptase promotes stem cell competition through MYC

city: Stanford

first: Kazuteru

last: Hasegawa

address: Lorry Lokey Stem Cell Research Building (SIM1), G2165 265 Campus Drive

institute: Stanford University

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

overall_design: Refer to individual Series


title: Changes in global open chromatin structure caused by acute deletion of TERT in spermatogonial stem cells

summary: To understand the catalytic activity-independent functions of TERT in global chromatin structure, we acutely deleted TERT in spermatogonial stem cell (SSC) populations in the testis, and performed ATAC-seq. We find significant global loss of open chromatin structure in TERT-deleted SSC populations.

overall_design: TERT was acutely deleted by tamoxifen-dependent Cre-LoxP system, and ATAC-seq libraries were prepared from testicular cells purified by FACS.

first: Yang

last: Zhao

first: Ryan

last: Corces

first: Yuning

first: Howard

last: Chang

first: Steven

last: Artandi


title: Effect of dopamine on gene expression in SK-N-SH cells

city: Shanghai

last: Yaqi

address: No.1678 Dongfang Road, Pudong, Shanghai, China

institute: Shanghai Children Medical Centre

summary: Dopaminylation, the covalent attachment of dopamine to the side chain of glutamine (Gln, Q) in proteins, has been identified as a class of posttranslational modification. Due to the limited number of substrates, the functions and underlying molecular mechanisms of dopaminylation are not fully characterized. Utilizing an alkyne-functionalized dopamine probe, we have developed a method to selectively enrich dopaminylated proteins in the whole-cell context. We identified 4133 proteins potentially modified with dopamine and validated the modification of histone H4 glutamine 27 by dopamine (H4Q27dop). H4Q27dop can inhibit cell proliferation through downregulating cyclin D1 gene CCND1 transcription, a classical well-known proliferation promoter. Our study provides a valuable resource of putative substrate proteins modified with dopamine and reveals a novel mechanism of dopamine regulating cell growth in a neuroblastoma cancer model.

overall_design: Comparative ChIP-Seq analysis of H4Q27dop in SK-N-SH cells under control conditions and with dopamine treatment.

first: Yinfeng

last: Zhang

first: Yaqi

first: Wenyan

last: Wu

first: Wenting

last: Song


title: Multi-omics Analysis Revealing the Impact of Excessive Maternal Folate Supplementation on Offspring Brain Development [single nuclei multiome]

city: Blacksburg

first: Timothy

last: Jarome

address: Mail Stop: 0306,ANIMAL SCIENCES  MC0306,LITTON REEVES   STE 3490

institute: Virginia Tech

summary: Folate is crucial for diverse biological processes including neurogenesis. While folate supplementation during pregnancy is standard for preventing neural tube defects (NTDs), concerns are growing over the potential risks of excessive maternal intake. In this study, we employed spatial transcriptomics and single-nucleus multi-omics techniques to investigate the impact of increased maternal folate intake on offspring brain development. Elevated folate intake broadly affected gene pathways linked to neurogenesis and neuronal axon myelination across multiple brain regions. Furthermore, specific gene expression alterations related to learning and memory processes emerged in thalamic and ventricular regions.  Single-nucleus multi-omics analysis revealed that maturing excitatory neurons in dentate gyrus are particularly vulnerable to suboptimal maternal folate intake. Aberrant gene expression and chromatin accessibility changes were primarily centered on pathways governing ribosomal biogenesis, which is critical for synaptic formation. Altogether, our findings provide novel insights into how excessive maternal folate supplementation affects offspring brain development, notably by influencing gene expression and chromatin accessibility.

overall_design: Adult female mice (8 weeks old) were randomly assigned to either a control folic acid (FA) diet (2mg/kg) or an excessive FA diet (20mg/kg) for two weeks before mating with males. These diets were maintained throughout pregnancy and lactation. Pups were harvested on postnatal day 21 (P21). To profile spatial transcriptome, the mouse brains were freshly isolated to prepare FFPE tissue blocks, then coronally sectioned and placed onto the Visium slides for Visium Spatial Gene Expression library preparation. To simultaneously profile the transcriptome and chromatin accessibility at single cell resolution, hippocampus tissues were micro-dissected from the freshly isolated mouse brain tissues for single nuclei suspension preparation and subsequently loaded onto the Chromium iX using the single nucleus multiome kit from 10x genomics. Single nucleus RNA-seq (snRNA-seq) and single nucleus ATAC-seq (snATAC-seq) libraries were simultaneously constructed from the same nucleus following the manufactures' instructions.

first: Xiguang

last: Xu

last: Lin

first: Hehuang

last: Xie


title: Multi-omics Analysis Revealing the Impact of Excessive Maternal Folate Supplementation on Offspring Brain Development [spatial transcriptome]

overall_design: Adult female mice (8-12 weeks old) were randomly assigned to either a control folic acid (FA) diet (2mg/kg) or an excessive FA diet (20mg/kg) for two weeks before mating with males. These diets were maintained throughout pregnancy and lactation. Pups were harvested on postnatal day 21 (P21). To profile spatial transcriptome, the mouse brains were freshly isolated to prepare FFPE tissue blocks, then coronally sectioned and placed onto the Visium slides for Visium Spatial Gene Expression library preparation. To simultaneously profile the transcriptome and chromatin accessibility at single cell resolution, hippocampus tissues were micro-dissected from the freshly isolated mouse brain tissues for single nuclei suspension preparation and subsequently loaded onto the Chromium iX using the single nucleus multiome kit from 10x genomics. Single nucleus RNA-seq (snRNA-seq) and single nucleus ATAC-seq (snATAC-seq) libraries were simultaneously constructed from the same nucleus following the manufactures' instructions.

first: Yu


title: Semaphorin 3C (Sema3C) reshapes stromal microenvironment to promote hepatocellular carcinoma progression

city: Nanjing

first: Hao

last: Peng

state: State...

address: Dingjiaqiao

institute: Southeast University

summary: More than 90% of hepatocellular carcinoma (HCC) cases develop in the presence of fibrosis or cirrhosis, making the tumor microenvironment (TME) of HCC distinctive due to the intricate interplay between cancer-associated fibroblasts (CAFs) and cancer stem cells (CSCs), which collectively regulate HCC progression. However, the mechanisms through which CSCs orchestrate the dynamics of the tumor stroma during HCC development remain elusive. Our study unveils a significant upregulation of Sema3C in fibrotic liver, HCC tissues, peripheral blood of HCC patients, as well as sorafenib-resistant tissues and cells, with its overexpression correlating with the acquisition of stemness properties in HCC. We further identify NRP1 and ITGB1 as pivotal functional receptors of Sema3C, activating downstream AKT/Gli1/c-Myc signaling pathways to bolster HCC self-renewal and tumor initiation. Additionally, HCC cells-derived Sema3C facilitated extracellular matrix (ECM) contraction and collagen deposition in vivo, while also promoting the proliferation and activation of hepatic stellate cells (HSCs). Mechanistically, Sema3C interacted with NRP1 and ITGB1 in HSCs, activating downstream NF-kB signaling, thereby stimulating the release of IL-6 and upregulating HMGCR expression, consequently enhancing cholesterol synthesis in HSCs. Furthermore, CAF-secreted TGF-β1 activates AP1 signaling to augment Sema3C expression in HCC cells, establishing a positive feedback loop that accelerates HCC progression. Notably, blockade of Sema3C effectively inhibits tumor growth and sensitizes HCC cells to sorafenib in vivo. In sum, our findings spotlight Sema3C as a novel biomarker facilitating the crosstalk between CSCs and stroma during hepatocarcinogenesis, thereby offering a promising avenue for enhancing treatment efficacy and overcoming drug resistance in HCC.

overall_design: To investigate the regulatory effects of Sema3C on hepatic stellate cells, we stimulated LX-2 cells in vitro with recombinant human Sema3C (rhSema3C) or PBS for 48 hours. We then performed gene expression profiling of data obtained from RNA-seq of LX-2 cells in two different treatments. Comparative gene expression profiling analysis of  RNA-seq data for LX-2 cells treated with rhSema3C and  PBS.

first: Meng

first: Kun

last: Feng

first: Qingpeng

last: Lv

first: Yewei


title: Aged vascular niche hinders osteogenesis of mesenchymal stem cells through  paracrine repression of Wnt-axis

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary: Age-induced decline in osteogenic potential of bone marrow mesenchymal stem cells (BMSCs) potentiates osteoporosis and increases risk for bone fractures. Despite epidemiology studies reporting concurrent development of vascular- and bone diseases in the elderly, the underlying mechanisms for the vascular-bone cross-talk in aging are largely unknown. In this study, we show that accelerated endothelial aging deteriorates bone tissue through paracrine repression of Wnt-driven-axis in BMSCs. Here, we utilize physiologically aged mice in conjunction with our transgenic endothelial progeria mouse model (Hutchinson-Gilford progeria syndrome; HGPS) that displays hallmarks of an aged bone marrow vascular niche. We find bone defects associated with diminished BMSC osteogenic differentiation that implicate the existence of angiocrine factors with long-term inhibitory effects. microRNA-transcriptomics of HGPS-patient plasma combined with aged-vascular niche analyses in progeria mice reveal abundant secretion of Wnt-repressive microRNA-31-5p. Moreover, we show that inhibition of microRNA-31-5p as well as selective Wnt-activator CHIR99021 boost the osteogenic potential of BMSCs through de-repression and activation of the Wnt-signalling, respectively. Our results demonstrate that the vascular niche significantly contributes to osteogenesis defects in aging and pave ground for microRNA-based therapies of bone loss in elderly.

overall_design:
To screen for microRNAs that are physiologically relevant for HGPS patients and possibly aging population, we obtained plasma samples from HGPS patients and corresponding unaffected controls that were kindly provided by Progeria Research Foundation (PRF). Selma Osmanagic-Myers harbors PRF approved “Material Transfer Agreement” and Application and Agreement for Cells, DNA or Tissue HGPS and control plasma samples (11/12/2019). PRF harbors ethical approval for human research from Rhode Island Hospital's Institutional Review Board, for which all donors have given consent.
We then performed gene expression profiling analysis of HGPS plasma samples and those from unaffected controls.
Comparative gene expression profiling analysis of RNA-Seq data for HGPS plasma samples (194p, 230, 204) and unaffected (612, 648p, 555)

first: Selma

last: Osmanagic-Myers

first: Roland

last: Foisner

first: Matthias

last: Hackl

first: Viviane

last: Fleischhacker


title: Changes in global gene expression patterns caused by acute deletion of TERT in spermatogonial stem cells

first: Kazuteru

last: Hasegawa

summary: To understand the catalytic activity-independent functions of TERT in global gene expression, we acutely deleted TERT in spermatogonial stem cells in the testis, and performed RNA-seq. We find significant down-regulation of MYC pathway genes in TERT-deleted SSCs.

overall_design: TERT was acutely deleted by tamoxifen-dependent Cre-LoxP system, and RNA-seq libraries were prepared from SSCs purified by FACS.

first: Alina

last: Garbuzov

first: Steven

last: Artandi


title: Gene expression profile at a single cell level of differentiating J1  mouse embryonic stem cells cocultured with OP9 cells

first: Kyuwon

last: Cho

address: 201 Dowman Dr

summary: The OP9 coculture system is widely used to differentiate pluripotent  stem cells into mesodermal lineages. We used single cell RNA sequencing to analyze differentiation trajectories and heterogeniety of differentiating pluripotent stem cells using the OP9 coculture system.

overall_design: J1 mouse embryonic stem cells were cocultured with mitomycin-treated OP9 cells for 5 days. Undifferentiated J1 mouse embryonic stem cells were used as a control group.

first: Young-sup

last: Yoon


title: The effect of exposure to neighborhood violence on GR signaling in lung tumors [Spatial Transcriptomics]

city: Urbana

first: Zeynep

last: Madak Erdogan

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary: Despite lower rates and intensity of smoking, Black men experience a higher incidence of lung cancer compared to White men. The racial disparity in lung cancer is particularly pronounced in Chicago, a highly segregated urban city. Neighborhood conditions, particularly social stress, may play a role in lung tumorigenesis. Preliminary studies indicate that Black men residing in neighborhoods with higher rates of violent crime have significantly higher levels of hair cortisol, an indicator of stress response. To examine the relationship between social stress exposure and gene expression in lung tumors, we investigated glucocorticoid receptor (GR) binding in lung tumor samples in relation to GR target gene expression levels and zip code level residential neighborhood violence. Spatial transcriptomics and a version of ChIP-sequencing known as CUT & RUN were used. GR recruitment to chromatin was correlated with neighborhood violent crime rate and overall GR binding increased with increasing neighborhood violent crime rates. Among patients residing in high-violence neighborhoods, tumor samples, compared to normal neighboring lung tissue, had fewer GR binding sites. The opposite was seen in patients residing in low-violence neighborhoods, with tumor samples having more GR binding sites when compared to normal lung tissue. Tumor samples from patients living in high-violence neighborhoods exhibited increased GR recruitment to genes associated with greater tumor aggressiveness. Our findings suggest that exposure to neighborhood violence may influence tumor biology via reprogramming GR recruitment. Prioritizing lung cancer screening in neighborhoods with increased social stress, such as high violence, may reduce racial disparities in lung cancer.

overall_design: Fifteen lung tumor samples from lung adenocarcinoma patient were analyzed using spatial transcriptomics and ChIP-seq (CUT&RUN)

first: Hannah

last: Heath

first: JinYoung

last: Yoo

first: Sabrina

last: Akter

first: Atharv

last: Jain

first: Vani

last: Sharma

last: McGee

first: Aiman

last: Soliman

first: Abeer

last: Mohamed

first: Alicia

middle: K

last: Matthews

first: Robert

last: Winn

last: Madak-Erdogan

first: Kim

middle: J

last: Sage


title: Transcriptomics reveal a unique phago-mixotrophic response to low nutrient concentrations in the prasinophyte Pterosperma cristatum

city: Selinsgrove

first: Sophie

last: Charvet

address: 514 University Avenue

institute: Susquehanna University

summary:
To investigate the transcriptional dynamics behind changes in bacterivorous behavior in prasinophycean green algae we measured feeding frequency under decreasing nutrient concentrations and collected RNA when significant differences were observed.
We then performed differential expression analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pterosperma cristatum grown in nutrient replete (RR), nutrient reduced (NR) and nutrient depleted (ND) conditions.

first: Nicolas

last: Bock

first: Eunsoo

last: Kim

first: Solange

last: Duhamel


title: Dissection of transcriptional events in incompatible reactions of ‘Bearss’ lemon (Citrus limon) and ‘Valencia’ sweet orange (C. sinensis) on a novel citrandarin (C. reticulata × Poncirus trifoliata) rootstock

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Citrus and most other fruit crops are commercially propagated via grafting, which ensures trees have consistent fruit traits combined with favorable traits from the rootstock such as soil adaptability, vigor, and resistance to soil pathogens. Breeding new rootstocks requires careful agronomic evaluations, and widespread use of new rootstocks and scions requires graft compatibility with commercially important scions and rootstocks. Graft incompatibility can occur when the scion and rootstock are not able to form a permanent, healthy union. Understanding and preventing graft incompatibility is therefore of paramount importance in the breeding of new fruit cultivars and in the choice of scion and rootstock by growers. The rootstock US-1283 is a citrandarin generated from a cross of ‘Ninkat’ mandarin (Citrus reticulata) and ‘Gotha Road’ #6 trifoliate orange (Poncirus trifoliata). It was released in 2014 after years of field evaluation because of its superior productivity and good fruit quality on ‘Hamlin’ sweet orange (C. sinensis) under Florida’s growing conditions. Subsequently, it was observed that trees of ‘Bearss’ lemon (C. limon) and ‘Valencia’ sweet orange (C. sinensis) grafted onto US-1283 exhibited apparent incompatible and unhealthy growth near the graft union. The incompatibility manifested as stem grooving and necrosis underneath the bark on the rootstock side of the graft. A genetically similar citrandarin rootstock, US-812 (C. reticulata ‘Sunki’ × P. trifoliata ‘Benecke’), is fully graft compatible with the same scions. Transcriptome analysis was performed on the vascular tissues above and below the graft union of compatible US-812 and incompatible US-1283 graft combinations with ‘Bearss’ and ‘Valencia’ to identify expression networks associated with incompatibility and help understand the processes and potential causes of incompatibility in citrus. Transcriptional reprogramming was stronger in the incompatible rootstock than in the grafted scions. Functional analysis of the transcriptional events below the graft unions of US-1283 incompatible combinations revealed differentially expression genes (DEGs) associated with oxidative stress and plant defense, among other pathways, similar to a pathogen-induced immune response localized to the rootstock, although no known pathogens were detected in the assayed plants. These changes were not observed above the graft unions.Differentially expressed genes (DEGs) in US-1283, but not the scions, were associated with oxidative stress and plant defense, among others, similar to a pathogen-induced immune response localized to the rootstock. No pathogen infection was detected. It is hypothesized this response could have been triggered by signaling miscommunications between rootstock and scion either through 1) unknown molecules from the scion that were perceived as danger signals by the rootstock, 2) missing signals from the scion or missing receptors in the rootstock necessary for the formation of a healthy graft union, 3) the overall perception of the scion by the rootstock as non-self, or 4) a combination of the above.

overall_design: Our objective was to identify pathways, expression networks, and molecular mechanisms associated with incompatibility by analyzing transcriptome changes in rootstocks with similar genetic backgrounds but different responses to grafting. Given the increased numbers of novel scions and rootstocks developed by citrus breeders and the importance of grafting for propagation, there is an urgent need to develop effective and fast tools to understand and diagnose graft incompatibility and prevent consequent unexpected tree loss in the nursery and the field

first: Vicente

last: Febres

first: Anas

last: Fadli

first: Bo

last: Meyering

first: Fahong

last: Yu

last: Bowman

first: Jose-Xavier

last: Chaparro

first: Ute

last: Albrecht


title: Gene expression data from a xenograft derived from the bladder cancer cell line HT1367

city: Bangor

first: Tim

last: Smith

address: Dean Street

department: School of Computer Science and Engineering

institute: University of Bangor

summary:
A mouse bearing a xenograft derived from the bladder cancer cell line HT1376 was administered the hypoxia-targeted compound pimodidazole.
Gene expression data was derived from samples microdissected from 3 regions of  pimonidazole enriched staining and 3 regions with low pimonidazole staining.

overall_design: Full transcriptome analysis on Clariom S microarray platform.

first: Kaye

last: Williams

first: Muhammad

last: Bubar

first: Ben

last: Dickie

first: Brian

last: Telfer

first: Mark

last: Reardon

first: Rekaya

last: Shabbir

first: Ananya

last: Choudhury

first: Catharine

last: West


title: RNA-seq analysis of human healthy and osteoarthritis meniscus reveals autophagy-related mRNAs and long noncoding RNAs

city: Wuhan

first: Jun

last: Zhang

state: hubei

address: No. 169, Donghu Road

institute: wuhan university

summary: Aim To identify transcript level differences between healthy and osteoarthritis meniscus  in human keen joint using RNA-seq.Methods human menisci were isolated from non-OA patients and OA patients during arthroscopic surgery (N=5). Based on the RNA sequencing, differentially expressed lncRNAs (DELs) and mRNAs (DEMs) were screened.Expression level of selected autophagy-related lncRNAs and mRNAs was validated by real-time qPCR.Results we identified 310 DELs and 320 DEMs, and found five upregulated and one downregulated autophagy-related DEMs. After reverse prediction of miRNA, paired miRNA–lncRNA interactions and verification by RT-qPCR, the ceRNA regulatory networks were constructed consisting of two lncRNAs (PCAT19, CLIP1-ASA) and two mRNAs (BAG3 and HSP90AB1). Finally, GSEA indicated that the increased expressions of autophagy-related mRNAs inhibited the glycosaminoglycan biosynthesis in the degenerative meniscus.Conclusions for the first time ,we constructed an autophagy-related lncRNA-miRNA-mRNA regulatory ceRNA network based on RNA sequencing and experimental validation, which might provide new mechanistic insights and potential therapeutic targets for meniscal degeneration.

first: Xinyu

last: Zou

first: Yiming

last: Liu

first: Bin

last: Li


title: RNA sequencing analysis of SW480 cells treated with Amuc_0904

city: 天津市

first: Liu

last: yang

state: 天津市

address: qixiangtai Road

institute: Tianjin medical university

summary: We performed RNA sequencing analysis in SW480 cells treated with Amuc_0904  to study the molecular mechanisms through which Amuc_0904 regulates goblet cell signature.

overall_design: Gene expression profiles of SW480 cells received treatment with Amuc_0904 or buffer were generated by deep sequencing, using Illumina NovaSeq 6000.To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM)method. RSEM was used to quantify gene abundances.

first: Zhi

last: Yao

first: Quan

last: Wang

first: Jianming

last: Yang


title: The effect of exposure to neighborhood violence on GR signaling in lung tumors [CUT&Run]

first: Zeynep

last: Madak Erdogan

first: Hannah

last: Heath

first: JinYoung

last: Yoo

first: Sabrina

last: Akter

first: Atharv

last: Jain

first: Vani

last: Sharma

last: McGee

first: Aiman

last: Soliman

first: Abeer

last: Mohamed

first: Alicia

last: Matthews

first: Robert

last: Winn

last: Madak-Erdogan

first: Kim

last: Sage


title: Transcriptomic analysis of pulmonary vein under pathological pulmonary vein stenosis

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

summary: We reported the RNAseq analyses of pulmonary vein tissues at the age of postnatal day 21 (P21) on SD rats with or without pulmonary vein stenosis. Pulmonary vein stenosis was induced by performing pulmonary vein banding surgery within 24 hours postnatally. RNAseq analyses of the pulmonary vein tissues was generated at P21 from 3 sham-operated rats and 3 pulmonary vein banding rats. The results revealed that there were 1124 differentially expressed genes between PAB and sham group at P7, among which 714 were upregulated and 410 were downregulated.

overall_design: RNAseq analyses of the pulmonary vein tissues in PAB and sham-operated neonatal rats.

first: Peisen

last: Ruan

first: Chun

last: Shen

first: Lincai

last: Ye


title: Identification of Chromatin proteins involved in gene repression in lamina-associated domains

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

country: Italy

institute: University of Milan


title: IFNγ mediates the resistance of tumor cells to distinct NK cell subsets.

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

institute: DKFZ

summary: Tumor resistance to immune cells remains a major obstacle for successful treatment. NK cells are emerging tools for cancer therapy. However, due to differential and subset-specific expression of inhibitory NK cell receptors, often only subsets of NK cells exert reactivity against particular cancer types. Using a genome-wide CRISPR/Cas9 knockout (KO) screen in melanoma, we revealed resistance factors against NK cell attack and evaluated their differential impact on NK cell subpopulations. We show that melanoma cells deficient in antigen-presenting machinery or the IFNγ signaling pathway displayed enhanced sensitivity to NK cell killing. Treatment with IFNγ induced melanoma cell resistance that depended on B2M required for both classical and non-classical MHC-I expression. HLA-E mediated melanoma cell resistance to NKG2A+ KIR-, and partially to NKG2A+ KIR+ NK cells. Treatment of NK cells with the NKG2A blocking monalizumab resulted in enhanced NK cell reactivity to similar extent as deletion of HLA-E in melanoma cells. The combination of monalizumab with lirilumab, blocking KIR2 receptors, together with DX9, an anti-KIR3DL1 mAb, was required to restore the response of all NK cells against IFNγ-pretreated tumor cells of different origins. Our data reveal insights into NK cell subset reactivity and strategies how to leverage their full anti-tumor potential.

overall_design: To investigate genetic changes crucial to the NK cells’ effector function during encounters with melanoma cells, a CRISPR mediated genetic screen was carried out on A375 melanoma cell line using a genome-wide CRISPR sgRNA library. The pool of edited A375 cells were treated with different amounts of NK cells to reach medium or high killing efficiency during 24 hours. Important modulators in the NK cell- melanoma interaction can be inferred from the abundance of each of the remaining sgRNA in the pool of the 3 samples. The medium-killing and high-killing samples were collapsed as replicates in the analysis.

first: Tomáš

last: Hofman

first: Siu

last: Ng

first: Irene

middle: G

last: Lázaro

first: Florian

last: Heigwer

first: Michael

last: Boutros

first: Adelheid

last: Cerwenka


title: Identification of Chromatin proteins involved in gene repression in lamina-associated domains (pA-DamID)

summary: Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here we performed a full-genome genetic screen in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few lamina proteins, but revealed roles for dozens of known chromatin regulators. Among these are the negative elongation factor (NELF) complex and interacting factors, suggesting that regulation of RNA polymerase pausing can be a mechanism to repress transcription in LADs. Furthermore, the chromatin remodeler complex BAF and the activation complex Mediator can work both as activators and repressors in LADs, depending on the local context and possibly rewiring of heterochromatin. Our data suggest that fundamental regulatory steps of the transcription process and chromatin remodeling, rather than interaction with NL proteins, have a major role in the regulation of transcription in LADs.

overall_design:
pA-DamID experiment were performed on a clonal HAP1 cell line genetically modified to express dCAs9-KRAB domain and transduced with a lentiguide against ADAM22 (negative control in RNAseq as not expressed in HAP1). Lamina association  were probed using anti-LaminB2 (LB2) (Abcam, ab8983)
pA-DamID experiment were performed on a HCT116 cells (TOP2A-mAID, from Vassilis Roukos) and HeLa cells. Lamina association  were probed using anti-LaminB2 (LB2) (Abcam, ab8983)

first: Abdelghani

last: Mazouzi

first: Christ

last: Leemans

first: Tom

last: van Schaik

first: Nadia

last: Neyazi

first: Marjon

last: van Ruiten

first: Benjamin

middle: D

last: Rowland

first: Thijn

last: Brummelkamp

first: Bas

last: van Steensel


title: Shtn1, a retinal ganglion cell (RGC) specific gene, regulates RGC neurite development: Insights from an RGC direct somatic cell reprogramming model

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

summary: Retinal ganglion cells (RGCs) are the projection neurons of the retina. Proper development of the axon and dendrite of RGCs is the basis for these cells to function as projection neurons to deliver visual information to the brain. The purpose of this study was to investigate the function of a newly identified RGC-specific gene, Shtn1, in neurite development in RGCs. Using IF, we demonstrated that SHTN1 is distinctively expressed in RGCs during the period in which RGCs actively develop and adjust the connections of their neurites with upstream and downstream neurons. Using the iRGC system, we demonstrated that Shtn1 promotes the growth and complexity of neurites, and thus the electrophysiological maturation, of iRGCs. RNA-Seq analyses showed that Shtn1 may also regulate gene expression and neurogenesis in iRGCs. These findings improve our understanding of the molecular machinery governing RGC neurite development, and may help to optimize future RGC regeneration methods.

overall_design: MEFs was infected with lentiviruses overexpressing Ascl1+Brn3b+Islet1 to generate RGC-like neurons (iRGCs),  shRNAs were used to knock down Shtn1. Cells were collected 5 days after exogenous gene induciton, and processed for RNA-Seq sequencing.

first: Shuyi

last: Chen


title: The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

institute: Murdoch University

summary: Osteosarcoma is a form of bone cancer that predominantly impacts osteoblasts, the cells responsible for creating fresh bone tissue. Typical indications include bone pain, inflammation, sensitivity, mobility constraints, and fractures. Utilizing imaging techniques such as X-rays, MRI scans, and CT scans can provide insights into the size and location of the tumor. Additionally, a biopsy is employed to confirm the diagnosis. Analyzing genes with distinct expression patterns unique to osteosarcoma can be valuable for early detection and the development of effective treatment approaches. In this research, we conducted a comprehensive examination of the entire transcriptome and pinpointed genes with altered expression profiles specific to osteosarcoma.The study mainly aimed to identify the molecular fingerprint of osteosarcoma. In this study, we processed a total of 90 FFPE samples from PathWest of which 45 were OS and equal number of healthy tissues. RNA was extracted from Paraffin-embedded tissue; RNA was sequenced, the sequencing data was analysed and gene expression was compared to healthy of the same patients. Differentially expressed genes in osteosarcoma derived samples were identified and the functions of those genes were explored. This result was combined to perform meta-analysis with our previous studies based on FFPE and fresh samples. We identified 1,500 identical differentially expressed genes in PathWest osteosarcoma samples when compared with normal tissue sample of the same patients. Meta-analysis with combined fresh issue samples identified 504 differentially expressed genes. IFITM5, MMP13, PANX3, MAGEA6 were some of the most overexpressed genes in osteosarcoma samples while SLC4A1, HBA1, HBB, AQP7 genes were some of the top downregulated genes. Through the metanalysis, 504 differentially expressed genes were identified to be identical among FFPE (105 FFPE samples) and 36 fresh bone samples. These 504 differentially expressed genes can be taken as a molecular fingerprint of osteosarcoma.

overall_design: We performed whole transcriptome analysis on 90 FFPE osteosarcoma samples, 50 tumours and 40 controls.

first: Bal

middle: H

last: Poudel


title: Tumor suppressor FRMD3 Controls Mammary Epithelial Cells Fate Decision via Notch signaling pathway

first: Qianchen

last: Li

address: Beijing

institute: PKU

summary: Luminal to basal transition in mammary gland is accompanied by the changes of epithelial cell lineage plasticity, however, the underlying mechanism remains elusive. Here, we demonstrated that loss of the scaffold protein FRMD3 in breast cancer predicts poor outcomes. Knockout of Frmd3 inhibits mammary gland lineage development and induces mammary epithelium cells (MECs) stemness, and later on emerge of TNBC. Loss of Frmd3 in PyMT mice results in luminal to basal phenotype transition. Single- MEC mRNA sequencing analysis indicated that knockout of Frmd3 corresponds to inhibition of Notch signaling pathway. Mechanistically, FRMD3 assists Dishevelled-2 degradation via enhancing its interaction with the deubiquitinase USP9x. FRMD3 also interrupts the interaction of Dishevelled-2 with CK1, FOXK1, FOXK2 and NICD, causing a decrease in Dishevelled-2 phosphorylation, entry into the nucleus and impairing the Notch-dependent luminal epithelial lineage plasticity in MECs respectively. Taken together, FRMD3 is a tumor suppressor and an endogenous activator of the Notch signaling pathway that regulates mammary epithelial cell lineage plasticity.

overall_design: FIve mice mammary tissues  from the Frmd3 knockout and wild type mice  were harvested and analyzed using 10x Genomics.Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) , according to the manufacturer’s instructions.

first: Ji

last: Ma

first: Yuqing

last: Gong

first: Hongquan

last: Zhang

first: Jun

last: Zhan