title: Role of CASZ1 in keratinocyte differentiation

city: Beer Sheva

first: Idan

last: Cohen

address: David Ben Gurion Blvd 1

department: Microbiology, Immunology and Genetics

country: Israel

institute: Ben-Gurion University


title: Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence

status: Public on Apr 16 2024

city: Beijing

first: Xue

last: Han

address: Zhongguancun North Street

department: School of Medicine

country: China

institute: Tsinghua University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence.

overall_design:
To explore the systems-level function of RNA metabolism, we investigated the effects of depleting the RNA exosome over time in mouse embryonic stem cells using an auxin-inducible system. We established AID-FBEXOSC2 ESCs to deplete the essential exosome component, EXOSC2. Addition of the auxin analog indole-3-acetic acid (IAA) induced rapid degradation of EXOSC2 protein.
To investigate the impact of EXOSC2 on nuclear functions, we performed profiling of RNA subcellular localization, nascent transcription, gene expression, epigenetic landscape and chromatin organization in AID-FBEXOSC2 ESCs treated with IAA for a period of 20 hours.
All experiments were designed to reveal the differences between control and EXOSC2-depleted ESCs.

first: Linqing

last: Xing

first: Xiaohua

last: Shen


title: The role of MEIOC at the transition from mitosis to meiosis during mammalian spermatogenesis [bulkRNAseq]

city: Cincinnati

first: Maria

middle: M.

last: Mikedis

state: OH

address: 240 Albert Sabin Way

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary:
We investigated how MEIOC affects testicular germ cells at the transition from mitosis to meiosis.
We performed gene expression profiling analysis using data obtained from RNA-seq of preleptotene-enriched testes from wild-type and Meioc KO pups.

overall_design: Gene expression profiling of preleptotene-enriched testes from wild-type and Meioc KO pups undergoing meiotic initiation by RNA-seq

middle: M


title: IRAK4 is an immunological checkpoint in neuropsychiatric systemic lupus erythematosus

city: Farmington

first: Anthony

last: Vella

state: Connecticut

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

summary: Here were provide RNA-seq from MRL, MRL-IRAK4-KinaseDead(KD), IRAK4-KD, and C57BL6/J mouse hippocampi of 10 month old mice

overall_design: 4 groups - MRL, MRL-IRAK4-KD, IRAK4-KD, C56BL6/J

first: Timofey

last: Karginov

first: Antoine

last: Menoret


title: Epigenomic profiling by ATAC-seq and  ChIL-seq in B cells and plasma cells

status: Public on Apr 17 2024

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

summary: We performed ATAC-seq and H3.3 ChIL-seq to underdatand dynamic change of chromatin accessibility and H3.3 deposition into genome during B cell differentiation.

overall_design: ChIL-seq for H3.3 on naive B cells, activated B cells and PCs after LPS stimulation was conducted. ATAC-seq was perfomed in naïve B cells and LPS-induced  plamsa cells. We also used B cells expressing GFP-H3.3  or control vector for ATAC-seq and  ChiL-seq for anti-H3.3 or GFP antibodies.

first: Y

last: Saito

first: A

last: Harada

last: Baba


title: Aging-regulated PNUTS maintains endothelial barrier function via SEMA3B suppression [PNUTS]

status: Public on Apr 15 2024

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

summary: Age-related diseases pose great challenges to health care systems worldwide. During aging, endothelial senescence increases the risk for cardiovascular disease. Recently, it was described that Phosphatase 1 Nuclear Targeting Subunit (PNUTS) has a central role in cardiomyocyte aging and homeostasis. Here, we determined the role of PNUTS in endothelial cell aging. We confirmed that PNUTS is repressed in senescent endothelial cells (ECs). Moreover, PNUTS silencing elicits several of the hallmarks of endothelial aging: senescence, reduced angiogenesis and loss of barrier function. To validate our findings in vivo, we generated an endothelial-specific inducible PNUTS-deficient mouse line (Cdh5-CreERT2;PNUTSfl/fl), termed PNUTSEC-KO. Two weeks after PNUTS deletion, PNUTSEC-KO mice presented severe multiorgan failure and vascular leakage. Transcriptomic analysis of PNUTS-silenced HUVECs and lungs of PNUTSEC-KO mice revealed that the PNUTS-PP1 axis tightly regulates the expression of semaphorin 3B (SEMA3B). Indeed, silencing of SEMA3B completely restored barrier function after PNUTS loss-of-function. These results reveal a pivotal role for PNUTS in endothelial homeostasis through a SEMA3B downstream pathway that provides a potential target against the effects of aging in ECs.

overall_design: 3 mice in which Pnuts (Ppp1r10) was deleted in endothelial cells only (Cdh5-CreERT2; Pnuts fl/fl) by injection of Tamoxifen 12 days prior to termination of the experiment and 3 control mice that did receive tamoxifen but lacked the CreERT2 (Pnuts fl/fl) and therefore have a functional Pnuts (Ppp1r10) gene were used for this experiment. Mice were terminated and lungs were isolated. Then, RNA was isolated from total lung tissue.

middle: A

first: Noelia

last: Lozano Vidal


title: Defining Mesenchymal Stem/Stromal Cell-Induced Myeloid-Derived Suppressor Cells Using Single-Cell Transcriptomics

city: Seoul

first: Joo Youn

last: Oh

state: Korea, Republic of

address: 103 Daehakro, Jongrogu, Yeongondong

department: Ophthalmology

country: South Korea

institute: Seoul National University College of Medicine

summary: Mesenchymal stem/stromal cells (MSCs) modulate the immune response through interactions with innate immune cells. We previously demonstrated that MSCs alleviate ocular autoimmune inflammation by directing BM cell differentiation from pro-inflammatory CD11bhiLy6ChiLy6Glo cells into immunosuppressive CD11bmidLy6CmidLy6Glo cells. Herein, we analyzed MSC-induced CD11bmidLy6Cmid cells using single-cell RNA sequencing and compared them with CD11bhiLy6Chi cells. Our investigation revealed 7 distinct immune cell types including myeloid-derived suppressor cells (MDSCs) in the CD11bmidLy6Cmid cells, while CD11bhiLy6Chi cells included mostly monocytes/macrophages with a small cluster of neutrophils. These MSC-induced MDSCs highly expressed Retnlg, Cxcl3, Cxcl2, Mmp8, Cd14 and Csf1r as well as Arg1. Comparative analyses of CSF-1RhiCD11bmidLy6Cmid and CSF-1RloCD11bmidLy6Cmid cells demonstrated that the former had a homogeneous monocyte morphology and produced elevated levels of IL-10. Functionally, these CSF-1RhiCD11bmidLy6Cmid cells, compared with the CSF-1RloCD11bmidLy6Cmid cells, inhibited CD4+ T cell proliferation and promoted CD4+CD25+Foxp3+ Treg expansion in culture and in a mouse model of experimental autoimmune uveoretinitis. RELM-γ encoded by Retnlg, one of the highly-upregulated genes in MSC-induced MDSCs, had no direct effects on T cell proliferation, Treg expansion or splenocyte activation. Together, our study revealed a distinct transcriptional profile of MSC-induced MDSCs and identified CSF-1R as a key cell-surface marker for detection and therapeutic enrichment of MDSCs.

overall_design: We purified CD11bmidLy6Cmid cells from BM cells cocultured with MSCs as well as CD11bhiLy6Chi cells from BM cells without MSC coculture by fluorescence-activated cell sorting (FACS), and subjected these two FACS-sorted live cell populations to scRNA-seq using the 10x Genomics Chromium platform.

first: Hyun Ju

last: Lee


title: IL-12 drives the diferentiation of human T follicular regulatory cells [CUT&RUN]

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: T follicular regulatory (Tfr) cells can counteract the B cell-helper activity of T follicular helper (Tfh) cells and hinder the production of antibodies against self-antigens or allergens. A mechanistic understanding of the cues initiating the differentiation of T regulatory (Treg) cells into Tfr cells, which is instrumental for the therapeutic manipulation of diseases associated with a Tfr cell imbalance, is still missing. Despite their opposed roles, Tfr and Tfh cell differentiation appears to be controlled by partially overlapping signals, including TCR stimulation and costimulatory molecules. However, it is still unknown if cytokines that have been shown to control the biology of human Tfh cells, including IL-12 and activin A, can influence the differentiation of Tfr cells. To address this question, we evaluated the impact of these two cytokines on the in vitro differentiation of Tfr cells. Herein, we report a role for IL-12 and down stream Stat4 chromatin binding in driving, on activated Treg cells, the induction of molecules that belong to the Tfr cell program, including CXCR5, PD-1, BCL6 and ICOS meanwhile preserving Tfr regulatory function.

overall_design: CUT&RUN for Stat4 in cord or peripheral blood derived Treg and Tnaive cells treated with or without IL-12

first: Roberto

last: Bonasio

first: Michela

last: Locci

first: Diana

last: Castano

first: Segovia

last: Atencio-Garcia


title: Identification of mesenchymal cell populations during neonatal lung development

city: St. Louis

first: David

last: Ornitz

state: MO

address: 660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University in St. Louis

summary: Alveologenesis is the final stage of lung development in which the internal surface area of the lung is increased to facilitate efficient gas exchange in the mature organism. The first phase of alveologenesis involves the formation of septal ridges (secondary septae) which are covered by alveolar type 1 (AT1) and alveolar type 2 (AT2) cells and contain mesenchymal cells, capillaries, and an elastin rich extracellular matrix (ECM). The second phase involves thinning of the alveolar septa. Mesenchymal cells include a transient population of alveolar myofibroblasts (MyoFB) and a stable but poorly described population of lipid rich cells that have been referred to as lipofibroblasts or matrix fibroblasts (MatFB). Using a unique Fgf18CreER lineage trace mouse line, cell sorting, single cell RNA sequencing, and primary cell culture, we have identified multiple subtypes of mesenchymal cells in the neonatal lung, including an immature progenitor cell that gives rise to mature MyoFB. We also show that the endogenous and targeted ROSA26 locus serves as a sensitive reporter for MyoFB maturation. These studies increase the known repertoire of mesenchymal cell types in the neonatal lung, identify potential intercellular signals, and provide a neonatal time point for comparison with embryonic and adult lung mesenchymal cell subtypes.

overall_design: Fgf18CreERT2/+; ROSATDTomato/+; PdgfrαEGFP/+ pups were injected with tamoxifen from P2-P5 and lung cells isolated at P7. Three populations (GFP-lowTdt-neg (C1), GFP-hi Tdt-neg (C2), GFP-hi Tdt-hi (C3)) were obtained by FACS and separately submitted for scRNASeq analysis.

first: Yongjun

last: Yin

first: Jeffrey

middle: R

last: Koenitzer

first: Debabrata

last: Patra

first: Sabine

last: Dietmann


title: Replication-competent HIV-1 gRNA Constructs for CRISPR/Cas9-based Discovery of Antiviral Factors

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

country: Germany

institute: Ulm University Medical Center

summary: Innate cellular defense mechanisms and viral countermeasures govern the outcome of pathogen exposure but the complex virus-host interplay remains poorly understood. Here, we developed a virus-guided technology platform where the pathogen itself reveals its cellular opponents. To accomplish this, we engineered replication-competent HIV-1 expressing single guide RNAs (sgRNAs) targeting potential antiviral genes in Cas9 expressing CD4+ T cells. Screening of HIV-1 constructs targeting >500 potential antiviral genes revealed that sgRNAs against GRN, CIITA, EHMT2, CEACAM3, CC2D1B, RHOA and HMOX1 provide significant advantages for viral replication. We verified that GRN and CIITA inhibit HIV-1 in primary CD4+ T cells by reducing viral transcription. Lack of the accessory nef gene increased selection for sgRNAs targeting SERINC5 and IFI16. Functional analyses demonstrated that Nef counteracts the inhibitory effects of IFI16. Altogether, we established a highly versatile, effective and robust approach that forces HIV-1 to reveal its cellular opponents.

overall_design: RNA from virus was reverse transcribed and a cassette containing a sgRNA was amplified to sequence the sgRNA

first: Caterina

middle: P

last: Bozzo

first: Alexandre

last: Laliberté

first: Stefan

last: Krebs

first: Alexander

last: Graf

first: Helmut

last: Blum

first: Frank

last: Kirchhoff


title: Fibroblasts as an in vitro model of circadian genetic and genomic studies: A temporal analysis

city: Los Angeles

first: Marcelo

last: Francia

state: CA

address: 1771 Beloit Avenue, Unit 204

department: Neuroscience

institute: University of California, Los Angeles

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

overall_design: Refer to individual Series


title: EWSR1::FLI1 fusion oncoproteins’ regulation of ETS1 (RNA-seq)

city: Bethesda

first: Natasha

middle: J

last: Caplen

state: Maryland

address: 37 Convent Drive, Bldg. 37, Rm 6128

department: National Cancer Institute

institute: National Institutes of Health

summary: Ewing sarcomas harbor few mutations beyond the chromosomal translocation that initiates disease and the mechanistic basis for the metastasis of these tumors remains poorly understood. The epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the repressive activities of the EWSR1::FLI1/ERG fusion oncoproteins. Focusing on one of the repressed EWSR1::FLI1/ERG target genes, ETS1, we detected EWSR1::FLI1 binding and a H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1’s binding of promoter regions, and we show ETS1 regulates the expression of multiple proteins that function in extracellular matrix organization including TENSIN3 (TSN3). Interestingly, TSN3 expression in EWS tumors significantly correlates with that of ETS1 (0.85, FDR <0.01). TNS3 is a focal adhesion protein that contributes to tumor cell migration by connecting the cytoplasmic tail of integrins to the actin cytoskeleton. EWS cell lines, in which we activated ETS1 expression (CRISPRa) exhibited increased TNS3 expression and a migratory phenotype. Critically, the activated ETS1 EWS cell lines show TNS3 accumulation at leading cell edges, with F-actin cytoskeletal reorganization, a phenotype associated with cell migration.

overall_design: Ewing sarcoma cell lines (TC-32) were analyzed by RNA-seq. To interrogate ETS1 regulation of gene expression in the presence of EWSR1::FLI1, we ectopically expressed ETS1 in TC-32 cells, generating single cell clones that expressed ETS1 at levels comparable to EWSR1::FLI1-depleted cells (TC-32-ETS1-High) and cells expressing lower levels of ETS1 (TC-32-ETS-Low).

first: Vernon

last: Ebegboni


title: Insulin and leptin oscillations license food-entrained browning and metabolic flexibility

city: New York

first: Prashant

last: Rajbhandari

state: New York

address: 1468 Madison Ave, Annenberg 18-10

institute: Icahn School of Medicine at Mount Sinai

summary: Timed-feeding leads to adipose browning, although the integrative mechanisms for the same remain unclear. Here we show that twice-a-nocturnal (TAN) feeding causes biphasic oscillations of circulating insulin and leptin, representing their entrainment by timed-feeding. Insulin and leptin surges lead to marked cellular, functional and metabolic remodeling of sWAT resulting in increased energy expenditure. Single-cell RNAseq analyses and flow cytometry reveal a role for insulin and leptin surges in ILC2 recruitment and sWAT browning, since depleting leptin or blocking insulin receptor signaling or ILC2 cell recruitment, each dampens TAN feeding-induced sWAT remodeling and energy expenditure. Consistently, recreating insulin and leptin oscillations via once-a-day co-injections is sufficient to favorably remodel innervated sWAT. Indeed, innervation is necessary for sWAT remodeling since denervation of sWAT, but not BAT, blocks TAN-induced sWAT remodeling and resolution of inflammation. In sum, timed feeding reorganizes nutrient-sensitive pathways to remodel sWAT, which drives the metabolic benefits of timed-feeding.

overall_design: 10X Genomics single cell sequencing was performed on the SVF fourth inguinal white adipose tissue (iWAT) depot  from 8-week old mice exposed to Ad-Lib or twice-a-night (TAN) feeding.

first: P


title: EWSR1::FLI1 fusion oncoproteins’ regulation of ETS1 (CUT&RUN)

overall_design: We assessed EWSR1::FLI1’s associations with distinct epigenetic states. Using samples generated from TC-32 cells, we employed CUT&RUN to determine EWSR1::FLI1 binding sites and mapped histone modifications associated with transcriptional activation, H3K27ac, and repression, H3K9me3 and H3K27me3


title: Enhanced Osteogenesis of Mesenchymal Stem Cells Encapsulated in Injectable Microporous Hydrogel

city: Durham

first: Seth

last: Edwards

state: NH

address: 105 Main St

department: Chemical Engineering

institute: University of New Hampshire

summary: Delivery of therapeutic stem cells to treat bone tissue damage is a promising strategy that faces many hurdles to clinical translation. Among them is the design of a delivery vehicle which promotes desired cell behavior for new bone formation. In this work, we describe the use of an injectable microporous hydrogel, made of crosslinked gelatin microgels, for the encapsulation and delivery of human mesenchymal stem cells (MSCs) and compared it to a traditional nonporous injectable hydrogel. MSCs encapsulated in the microporous hydrogel showed rapid cell spreading with direct cell-cell connections whereas the MSCs in the nonporous hydrogel were entrapped by the surrounding polymer mesh and isolated from each other. Microporous hydrogel induced more robust osteogenic differentiation of MSCs and calcium mineral deposition than the nonporous hydrogel confirmed by alkaline phosphatase (ALP) assay and calcium assay. RNA-seq confirmed the upregulation of the genes and pathways that are associated with cell spreading and cell-cell connections, as well as the osteogenesis in the microporous hydrogel. These results demonstrate that the microgel-based injectable hydrogels can be useful tools for therapeutic cell delivery for bone tissue repair.

overall_design: Gene expression data of human mesenchymal stem cells comparing 3D hydrogel culture conditions at 3 and 14 days after introdution of osteogenic differentiation media.

first: Kyung

last: Jeong


title: SOD1 is a synthetic lethal target in PPM1D-mutant leukemia cells

city: HOUSTON

first: Margaret

last: Goodell

state: TX

address: 1 Baylor Plz, Rm N1030

institute: Baylor College of Medicine

summary: Using CRISPR/Cas9 dropout screening, we identified superoxide dismutase-1 (SOD1) as a genetic dependency specific to PPM1D-mutant leukemia cells. We found that the mutant cells exhibited a compromised response to oxidative stress that can be rescued with SOD1 inhibitors. PPM1D-mutant fcells also exhibit significant genomic instability, highlighting the essential role of SOD1 in safeguarding against oxidative stress and DNA damage.

overall_design: Transcriptomic profiling of RNA-seq data for WT and PPM1D-mutant Cas9-OCI-AML2 cells with or without SOD1-knockout.

first: Linda

last: Zhang

first: Chun-Wei

last: Chen


title: miRNA Expression Profiles in Isolated Ventricular Cardiomyocytes: Insights into Doxorubicin-Induced Cardiotoxicity

city: Bogota DC

first: Yohana

last: Dominguez

state: Bogota

address: El Dorado avenue 51-20

department: Sub-Direction of Scientific and Technological Research

country: Colombia

institute: National Institute of Health

summary: Doxorubicin (DOX) is a first-line chemotherapeutic agent widely used in the treatment of various cancers, but its clinical efficacy is limited by its early and late cardiotoxic effects. Prior to the visible morphological manifestation of lesions in cardiomyocytes after exposure to DOX, they can detect damage and initiate a complex cascade of responses, including the modulation of gene expression, including the regulation of microRNAs (miRNAs).In this study, we used small RNA sequencing to evaluate miRNA expression levels in cardiomyocytes exposed to DOX at a concentration of 10 μM for periods of 1 and 22 hours, compared to unexposed cells. By analyzing the normalized data and using DESeq2, we identified significant changes in the expression of certain miRNAs in DOX-treated cells. These miRNAs emerge as promising biomarker candidates that, if further investigated, could provide a valuable early detection tool for DOX sensitivity and guide the timely administration of cardioprotective agents.

overall_design: Ventricular cardiomyocytes were isolated from adult female Hartley guinea pigs using the Langendorff retrograde perfusion system and enzymatic dissociation. These cardiomyocytes were exposed to 10 μM DOX and incubated at room temperature for 1 and 22 hours. Total RNA was extracted with Trizol reagent and quantified by spectrophotometry. Small RNA sequencing was performed using Illumina technology, and RNA quality was assessed using the RNA integrity parameter (RIN). A library of small RNAs was constructed using the TruSeq kit and sequenced on a HiSeq 2500. Reads were aligned to the Homo sapiens reference genome and miRNAs were identified from the sequencing data using miRDeep.

first: Luis

last: A. Gomez

first: Gladis

last: Montoya


title: GATAD2B containing NuRD complex drives R-loop dependent chromatin boundary formation at double strand breaks

city: Oxford

first: Kamal

last: Ajit

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology

summary: To understand how components of NuRD could be recruited to DNA double-stranded break sites, we generate site-specific DNA double strand breaks through an inducible endonuclease AsiSI-ER system by adding 4-OHT, we applied antibodies against GATAD2B and HDAC1, both of which are components of NuRD complex, to pero ChIP in either DMSO or 4OHT treatment condition.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HDAC1 and GATAD2B in human U2OS AsiSI-ER cell lines upon DMSO  and 4OHT treatment

first: Zhichao

last: Liu

first: Monika

last: Gullerova


title: EWSR1::FLI1 fusion oncoproteins’ regulation of ETS1 (ChIP-seq)

summary: Ewing sarcomas harbor few mutations beyond the chromosomal translocation that initiates disease and the mechanistic basis for the metastasis of these tumors remains poorly understood. The epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the repressive activities of the EWSR1::FLI1/ERG fusion oncoproteins. Focusing on one of the repressed EWSR1::FLI1/ERG target genes, ETS1, we detected EWSR1::FLI1 binding and a H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1’s binding of promoter regions, and we show ETS1 regulates the expression of multiple proteins that function in extracellular matrix organization including TENSIN3 (TNS3). Interestingly, TNS3 expression in EWS tumors significantly correlates with that of ETS1 (0.85, FDR <0.01). TNS3 is a focal adhesion protein that contributes to tumor cell migration by connecting the cytoplasmic tail of integrins to the actin cytoskeleton. EWS cell lines, in which we activated ETS1 expression (CRISPRa) exhibited increased TNS3 expression and a migratory phenotype. Critically, the activated ETS1 EWS cell lines show TNS3 accumulation at leading cell edges, with F-actin cytoskeletal reorganization, a phenotype associated with cell migration.

overall_design: Ewing sarcoma cell line (TC-32) was analyzed by ChIP-seq. EWSR1::FLI1 was depleted by transfection with siRNA (siFLI1 and siNeg control).


title: Osteopontin drives neuroinflammation and cell loss in MAPT-N279K frontotemporal dementia patient neurons

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

summary: Frontotemporal dementia (FTD) is an incurable group of early-onset dementias that can be caused by deposition of hyperphosphorylated tau in patient brains. However, the mechanisms leading to neurodegeneration remain largely unknown. Here, we combined single-cell analyses of FTD patient brains with a stem cell culture and transplantation model of FTD. We identified disease phenotypes in FTD neurons carrying the MAPT-N279K mutation, which were related to oxidative stress, oxidative phosphorylation and neuroinflammation with an upregulation of the inflammation-associated protein osteopontin (OPN). Human FTD neurons survived less and elicited an increased microglial response after transplantation into the mouse forebrain, that we further characterized by single nucleus RNA-sequencing of microdissected grafts. Notably, downregulation of OPN in engrafted FTD neurons resulted in improved engraftment and reduced microglial infiltration, indicating an immune-modulatory role of OPN in patient neurons, which may represent a potential therapeutic target in FTD.

overall_design: Samples from both control and FTD samples were generated using either post mortem human brain samples or iPSC derived neurons

last: Al-Dalahmah

first: Matti

last: Lam

first: Julie

last: McInvale

first: Wenhui

last: Qu

first: Trang

last: Nguyen

first: Jeongyeon

last: Mun

first: Sam

last: Kwon

first: Nkechime

last: Ifediora

first: Aayushi

last: Mahajan

first: Nelson

last: Humala

first: Tristan

last: Winters

first: Ellen

last: Angeles

first: Kelly

last: Jakubiak

first: Rebekka

last: Kühn

first: Yoon

last: Kim

first: Maria

middle: C

last: De Rosa

first: Claudia

last: Doege

first: Fahad

last: Paryani

first: Xena

last: Flowers

first: Athanassios

last: Dovas

first: Angeliki

last: Mela

first: Hong

last: Lu

first: Michael

last: DeTure

first: Jean

last: Vonsattel

first: Zbigniew

middle: K

last: Wszolek

first: Dennis

middle: W

last: Dickson

first: Tanja

last: Kuhlmann

first: Holm

last: Zaehres

first: Hans

last: Schöler

first: Andrew

last: Sproul

first: Markus

middle: D

last: Siegelin

first: Philip

middle: L

last: De Jager

first: James

middle: E

last: Goldman

first: Vilas

last: Menon

first: Peter

last: Canoll

first: Gunnar

last: Hargus


title: The ureters of Col17a1-KO mice at 4 days after unilateral ureteral obsruction

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

institute: Hokkaido University

summary: Collagen 17A1 (COL17A1) is induced in urothelium under disease conditions of urinary system organs, such as chronic nephritis and urinary obstruction. Thus, the ureters of Col17a1-knock out (KO) mice were injured by unilateral ureteral obsruction (UUO), and the gene expression was compared with those of wild-tyoe (WT).

overall_design: The ureters were collected from 2-month-old Col17a1-KO mice (C57BL/6N background) at 4 days after UUO.  And then, RNA was collected and gene expression was analyzed.

first: Takashi

last: Namba


first: Osama

last: Al Dalahmah

overall_design: Analysis of post-mortem human iPSC neurons

last: Al-Dalahmah

first: Matti

last: Lam

first: Julie

last: McInvale

first: Wenhui

last: Qu

first: Trang

last: Nguyen

first: Jeongyeon

last: Mun

first: Sam

last: Kwon

first: Nkechime

last: Ifediora

first: Aayushi

last: Mahajan

first: Nelson

last: Humala

first: Tristan

last: Winters

first: Ellen

last: Angeles

first: Kelly

last: Jakubiak

first: Rebekka

last: Kühn

first: Yoon

last: Kim

first: Maria

last: De Rosa

first: Claudia

last: Doege

first: Fahad

last: Paryani

first: Xena

last: Flowers

first: Athanassios

last: Dovas

first: Angeliki

last: Mela

first: Hong

last: Lu


title: Transcriptional profile of human monocyte-derived macrophages stimulated with Interleukin 27

city: Medellin

first: Yordi

middle: Sebastián

last: Tamayo Molina

state: Antioquia

institute: University of Antioquia

summary: Interleukin 27 (IL-27) is a member of the IL-6 and/or IL-12 family that elicits both pro- and anti-inflammatory responses. Interferons (IFNs) are a family of cytokines that activate the JAK-STAT signaling pathway to induce an antiviral state in cells. Recent studies have reported that IL-27 also induces a robust antiviral response against diverse viruses, both in vitro and in vivo, suggest that IFNs and IL-27 share many similarities at the functional level. However, it is still unknown how similar or different IFN- and IL-27-dependent signaling pathways are. We reported that IFNs and IL-27 activate JAK-STAT signaling and induce shared pro-inflammatory and antiviral pathways in monocyte-derived macrophages (MDMs), leading to the common and unique expression of inflammatory factors and IFN-stimulated genes (ISGs). Importantly, the ability of IL-27 to induce those responses is independent of IFN induction and cellular lineage. Additionally, functional analysis demonstrated that like IFNs, IL-27-mediated response reduced chikungunya and dengue viruses replication in MDMs. In summary, IL-27 exhibits properties similar to those of all three types of human IFN, including the ability to stimulate a protective antiviral response.

overall_design: Human primary FBS-MDMs cultures (n= 3) were either stimulated or not with 25 ng/mL recombinant-human IL27 for 18 hours and mRNA sequencing was then performed using bulk RNA-seq


title: Linc-ADAIN, A Human Adipose LincRNA Regulates Adipogenesis by Modulating KLF5 and IL-8 mRNA stability

first: Chenyi

last: Xue

institute: Columbia University

summary: Adipose tissue remodeling and dysfunction, characterized by increased inflammation and insulin resistance, play a central role in obesity-related development of type 2 diabetes (T2DM) and cardiovascular diseases. Long intergenic non-coding RNAs (lincRNAs) are important regulators of cellular functions. Here we describe the functions of linc-ADAIN (ADipose Anti-INflammatory), an adipose lincRNA that is downregulated in white adipose tissue of obese humans. We demonstrate that linc-ADAIN knockdown (KD) increases KLF5 and IL-8 mRNA stability and translation, by interacting with IGF2BP2. Upregulation of KLF5 and IL-8, via linc-ADAIN KD, led to an enhanced adipogenic program and adipose tissue inflammation, mirroring the obese state, in vitro and in vivo, KD of linc-ADAIN in human ASC hTERT adipocytes implanted into mice, increased adipocyte size and macrophage infiltration compared to implanted control adipocytes, mimicking hallmark features of obesity-induced adipose tissue remodeling. Linc-ADAIN is an anti-inflammatory lincRNA that limits adipose tissue expansion and lipid storage.

overall_design: Confluent primary ASC52telo hTERTs were transfected with Scramble shRNA or linc-ADAIN shRNA. Then after 2 days adipocyte differentiation media was added for 7 days, then maintenance media for 7 days (Day 14). On Day 14, LPS (100 ng/mL) was added for 4 hours. 3 replicates were used for each combination of Scramble/linc-ADAIN shRNA and +/- LPS. RNA was extracted and submitted to sequencing.

first: Marcella

last: O'Reilly

first: Eunyoung


first: Osama

last: Al Dalahmah

overall_design: Analysis of post-mortem human brain samples and iPSC neurons genomic information

last: Al-Dalahmah

first: Matti

last: Lam

first: Julie

last: McInvale

first: Wenhui

last: Qu

first: Trang

last: Nguyen

first: Jeongyeon

last: Mun

first: Sam

last: Kwon

first: Nkechime

last: Ifediora

first: Aayushi

last: Mahajan

first: Nelson

first: Michael

last: DeTure

first: Jean

last: Vonsattel

first: Zbigniew

last: Wszolek

first: Dennis

last: Dickson

first: Tanja

last: Kuhlmann

first: Holm

last: Zaehres

first: Hans

last: Schöler

first: Andrew

last: Sproul

first: Markus

last: Siegelin

first: Philip

last: De Jager

first: James

last: Goldman

first: Vilas

last: Menon

first: Peter

last: Canoll

first: Gunnar

last: Hargus


title: Maintenance of beta cell function in adolescent T1D subjects treated with a single dose of polyclonal expanded Treg is linked to lower ex vivo Treg expansion

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Adoptive transfer of CD4+CD25hiCD127low FOXP3+ regulatory T cells (Treg) improves outcome as an adjunct treatment in transplantation to maintain tolerance. Phase I clinical trials have shown safety in adults, however, adoptive Treg tolerance is poorly understood in autoimmunity. Here, we explore factors contributing to efficacy in an autologous polyclonal expanded Treg (expTregs) Phase 2 clinical trial in 107 adolescents with recent-onset T1D (Sanford/Lisata Therapeutics Trex Phase 2 clinical trial) randomized 1:1:1 high and low treatment to placebo. A single dose of expTreg therapy (1-24x106cells/kg) did not prevent the decline in the residual beta cell function over two years compared to placebo (p=0.39), regardless of age, baseline c-peptide, or dose of expTreg (p=0.27). expTregs were a highly activated, pure, and suppressive Treg population as determined using flow cytometry and bulk RNA-seq prior to adoptive transfer. A transient increase of activated memory Tregs was detectable by flow cytometry and single-cell RNA-seq one week after infusion in the high dose cohort (p=0.003), suggesting effective transfer of expTreg. However, lower in vitro fold expansion and its linked gene signature associated with better outcome regardless of Treg dose. Together, these results suggest that expTregs quantity alone does not alter outcome; instead, expTreg quality, likely influenced by endogenous Treg features, may be important factors contributing to the efficacy of this treatment in preventing T1D progression.

overall_design: These data contain 10x Gene Expression and Feature Barcode (CITE-seq) data from Bronchial Alveolar Lavage samples from twelve samples taken from eight intubated patients at two timepoints. Each bam file corresponds to a single sample from a single patient at a timepoints (denoted v1 or v2 for time). Four patients were suffering from Acute Respiratory Distress Syndrom (ARDS) at time of first sample (SLK3, SLK7, SLK22, SLK23).

first: Christine

last: Bender

first: Alice

last: Wiedeman

first: Alex

last: Hu

first: Alyssa

last: Ylescupidez

first: Stephen

last: Gitelman

first: William

last: Sietsema

first: Kurt

last: Griffen

first: S

last: Long


first: Natasha

last: Caplen

overall_design: Ewing sarcoma cell lines (TC-32, TC-71, A673 and ES-5838) were analyzed by RNA-seq. EWSR1::FLI1 was depleted by transfection with siRNA (siFLI1 or siERG and siNeg control).

first: Vernon

last: Ebegboni


title: Response to Treg therapy is linked to rate of ex vivo Treg expansion

summary: Background: CD4+CD25hiCD127lo/-FOXP3+ regulatory T cells (Tregs) play a key role in preventing autoimmunity. In type 1 diabetes, adoptive transfer of autologous polyclonal Tregs has been shown to be safe in adults in Phase I clinical trials.  Methods: We explore factors contributing to efficacy in autologous polyclonal expanded Tregs (expTregs) Phase 2 clinical trial in 111 children and adolescents with new-onset type 1 diabetes (Sanford/Lisata Therapeutics Trex Phase 2 clinical trial) randomized 1:1:1 high and low treatment to placebo. Cytometry, bulk and single cell RNA-seq were perfomed on selected expTregs and PBMC samples from subjects. Results: A single dose of expTreg therapy (1-24x106cells/kg) was safe but did not prevent the decline in residual beta cell function over one year compared to placebo (p=0.39), regardless of age, baseline C-peptide, or dose of expTregs. ExpTregs were highly activated and suppressive, and a transient increase of activated memory Tregs was detectable one week after infusion in the high dose cohort, suggesting effective transfer of expTregs. However, in vitro fold expansion on expTregs varied across subjects even when accounting for age. Lower fold expansion and its’ associated gene signature was linked with better outcome, regardless of Treg dose.  Conclusion: These results suggest that expTregs quantity alone does not alter outcome; instead, expTreg quality may be an important factor contributing to the efficacy of adoptive Treg therapy to prevent type 1 diabetes progression.

overall_design: Children and adolescents with recent-onset T1D aged 8 to <18 years (mean 13.66 ±2.52 SD) were enrolled in this study. Tregs sorted from PBMC samples from 14 placebo and 19 Treg-treated patients were taken for bulk RNA-Sequencing at 6 time points (or fewer, depending on sample availability) before and after treatment. 17 of 19 of those treated with Tregs also had samples containing sorted expanded Tregs generated for infusion. C-peptide response and Treg fold-expansion were also measured for these patients.


title: STAT5 Gain-of-Function Mutations Promote Precursor T-Cell Receptor Activation to Drive Immature T-Lymphoblastic Leukemia or Lymphoma

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive immature T-cell cancer.  Hotspot mutations in JAK-STAT pathway members IL7R, JAK1 and JAK3 were analyzed in  depth, but the role of STAT5A or STAT5B in T-cell development or T-ALL transformation is  unclear. Importantly, the driver mutation STAT5BN642H encodes the most frequent activating  STAT5 variant in T-ALL and it correlated with disease relapse upon chemotherapy. Here, we  show that STAT5BN642H promotes T-ALL-like cancer in mice and transcriptionally upregulates  a collection of genes that are involved in T-cell receptor signaling (TCR), even in the absence  of surface TCR. Importantly, these genes were also overexpressed in human T-ALL patients.  Moreover, T-ALL cells were sensitive to pharmacologic inhibition of STAT3/5 or ZAP70  activity. Collectively, we discovered how hyperactive STAT5 induces and accelerates T-ALL  and we suggest therapeutic targeting using selective ZAP70 or STAT5 activity inhibitors in a  subgroup of T-ALL patients with prominent IL-7R-JAK1/3-STAT5 activity.

overall_design: STAT5B ChIP-seq data from human T-ALL cell lines with high or low STAT5 activation

first: Tobias

last: Suske

first: Helena

last: Sorger

first: Frank

last: Ruge

first: Nicole

last: Prutsch

first: Mark

last: Zimmerman

first: Barbara

last: Maurer

first: Christina

last: Wagner

first: Susann

last: Schönefeldt

first: Katrin

last: Spirk

first: Alexander

last: Pichler

first: Tea

last: Pemovska

first: Carmen

last: Schweicker

first: Daniel

last: Pölöske

first: Dennis

last: Jungherz

first: Tony

last: Müller

first: Myint

last: Aung

first: Ha

middle: T

last: Pham

first: Kerstin

last: Zimmel

last: Krausgruber

first: Christoph

last: Bock

first: Mathias

first: Maik

last: Dahlhoff

first: Auke

last: Boersma

last: Rülicke

first: Roman

last: Fleck

first: Patrick

last: Gunning

first: Tero

last: Aittokallio

first: Satu

last: Mustjoki

first: Takaomi

last: Sanda

first: Sylvia

last: Hartmann

first: Florian

last: Grebien

first: Gregor

last: Hoermann

first: Torsten

last: Haferlach

first: Philipp

middle: B

last: Staber

first: Heidi

last: Neubauer

first: Alfred

last: Look

first: Marco

last: Herling

first: Richard

last: Moriggl


title: Brainstem Dbh+ Neurons Control Chronic Allergen-Induced Airway Hyperreactivity

city: San Diego

first: Xin

last: Sun

address: 9500 Gilman Dr., CMME, Room 1055

department: Department of Pediatrics, Department of Biological Sciences

institute: UNIVERSITY OF CALIFORNIA AT SAN DIEGO

summary: Exaggerated airway constriction triggered by exposure to irritants such as allergen, also called hyperreactivity, is a hallmark of asthma and can be life-threatening. Aside from immune cells, vagal sensory neurons are important for airway hyperreactivity 1-4. However, the identity and signature of the downstream nodes of this adaptive circuit remains poorly understood. Here we show that Dbh+ neurons in the nucleus of the solitary tract (nTS) of the brainstem, and downstream neurons in the nucleus ambiguus (NA), are both necessary and sufficient for chronic allergen-induced airway hyperreactivity. We found that repeated exposures of mice to inhaled allergen activates nTS neurons in a mast cell-, interleukin 4 (IL-4)- and vagal nerve-dependent manner. Single-nucleus RNA-seq followed by RNAscope quantification of the nTS at baseline and following allergen challenges reveals that a Dbh+ population is preferentially activated. Ablation or chemogenetic inactivation of Dbh+ nTS neurons blunted, while chemogenetic activation promoted hyperreactivity. Viral tracing indicates that Dbh+ nTS neurons, capable of producing norepinephrine, project to the NA, and NA neurons are necessary and sufficient to relay allergen signals to postganglionic neurons that then directly drive airway constriction. Focusing on transmitters, delivery of norepinephrine antagonists to the NA blunted allergen-induced hyperreactivity. Together, these findings provide molecular, anatomical and functional definitions of key nodes of a canonical allergen response circuit. The knowledge opens the possibility of targeting neural modulation as an approach to control allergen-induced airway constriction.

overall_design: Mice were euthanized using CO2 inhalation. For nTS, brainstems were acutely harvested from either four groups of adult wild-type naïve mice (N=4 biological repeats, 2 males in each group); from mice at 1.5 hours after the 4th saline treatment (N=1, 2 males); and from mice at 1.5 hours after the 4th HDM challenge (N=1, 2 males). nTS was visualized by microscopy and harvested based on anatomical landmarks.

first: Yujuan

last: Su

first: Ji

last: Chin

first: Le

last: Xu

first: Ziai

last: Zhu


title: An IFNg-dependent immune-endocrine circuit lowers blood glucose to potentiate the innate anti-viral immune response (Lung)

status: Public on Apr 14 2024

city: Rijeka

first: Felix

middle: Martinus

last: Wensveen

address: Braće Branchetta 20

department: Histology & Embryology

country: Croatia

institute: University of Rijeka faculty of medicine

summary: Viral infection makes us feel sick. The extent of these changes to our metabolism are relative to the severity of disease. Whether blood glucose levels are subject to infection-induced modulation is largely unknown. Here we show that strong, non-lethal infection restricts systemic glucose availability which promotes the antiviral IFN-I response. Following systemic viral infection of mice, we find that IFNγ produced by γδ T cells directly stimulates pancreatic β-cells to increase glucose-induced insulin release. Subsequently, hyperinsulinemia lessens endogenous glucose output by the liver. Glucose restriction enhances type-I interferon production by curtailing lactate-mediated inhibition of IRF3 and NF-κB signaling. Induced hyperglycemia constrained IFN-I production and increased mortality upon infection. Our findings identify glucose restriction as a physiological mechanism to bring the body into a heightened state of responsiveness to viral pathogens. This immune-endocrine circuit is disrupted in hyperglycemia, which explains why patients with metabolic disease are more susceptible to viral infection.

overall_design:
Mice were infected with LCMV and fasted for 3 days in presence or absence of glucose in drinking water. Next, lungs were isolated and total RNA was isolated of lung homogenates.
We then performed gene expression analysis using data obtained from RNA-seq of 3 biological replicates under two different conditions
Comparative gene expression profiling analysis of RNA-seq data for lung tissue isolated from LCMV-infected mice fasted for 3 days with drinking water containing nothing (LCMV) or glucose (LCMV+glucose)

first: Marko

last: Šestan

first: Christoforos

last: Dimitropoulos


title: MYH7 G256E hiPSC-CM (Day 30)

city: Suwon-si

first: Soah

last: Lee

state: Geonggi-do

address: 2066 Seobu-ro, Jangan-gu, 530502

department: Pharmacy

institute: Sungkyunkwan University

summary: MYH7 G256E hiPSC-CM (Day 30)

overall_design: Examine any transcriptomic alterations in day 30 human iPSC-derived cardiomyocytes bearing MYH7 G256E mutation in comparison to the isogenic control. Feature barcoding technology was used to multiplex samples for scRNAseq. Please refer to each scRNAseq batch information for de-multiplexing samples used for this study. In the raw data, the FB files contain feature barcode sequencing information for sample multiplexing, while the GE files contain gene expression sequencing information.


title: High Expression of SRSF1 Facilitates Osteosarcoma Progression and Unveilsits Potential Mechanisms

city: GuangZhou

first: Shuqi

last: Li

state: GuangDong

address: #58, Zhongshan Road II, Guangzhou, China.

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: SRSF1, a member of Serine/Arginine-Rich Splicing Factors (SRSFs), has been observed to significantly influence cancer progression. However, the precise role of SRSF1 in osteosarcoma (OS) remains unclear. In this study, we aimed to investigate the functions of SRSF1 and its underlying mechanism in OS.SRSF1 expression level in OS was obtained from the TCGA dataset, TAGET-OS database. qRT-PCR and Western blotting were employed to assess SRSF1 expression in human OS cell lines and human bone marrow mesenchymal stem cells (BMSC), as well as the interfered ectopic expression states. The effect of SRSF1 on cell migration, invasion, proliferation, and apoptosis of OS cells were measured by transwell assay and flow cytometry. RNA sequence and bioinformatic analyses were conducted to elucidate the relevant biological pathways regulated by SRSF1. Subsequently, Alternative Splicing (AS) events mediated by SRSF1 were identified through RNA-seq and summarized briefly.Our results highlight the oncogenic role of high SRSF1 expression in promoting OS progression, and further explore the potential mechanisms of action. The significant involvement of SRSF1 in OS development suggests its potential utility as a therapeutic target in OS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U2OS cells and its derivatives（siSRSF1-2,siSRSF1-3 and LINC01134 upregulated）

first: Li

last: Shuqi

first: Cao

last: Qinghua


title: A single-cell atlas of chromatin accessibility in mouse organogenesis

city: beijing

first: Keyong

address: Hai Dian street

institute: tsinghua university

summary: Recent surveys of mouse organogenesis cell atlas (MOCA) with single cell transcriptomics have uncovered hundreds of cell types, but the cell-type-specific transcriptional regulatory programs responsible for the unique identity and function of each cell type have yet to be elucidated. We  applied a four-level combinatorial indexing assay, SPATAC-seq, to profile the chromatin accessibility in >350,000 cells derived from 13 embryos staged between embryonic day (E) 10.5 and 13.5 in a single experiment. The resulting map revealed the status of open chromatin for 844,817 candidate cis-regulatory elements (cCREs) in 33 main cell types and 296 subtypes. By integrating this accessible chromatin atlas with scRNA data of MOCA, we characterized the gene regulatory sequences and transcription factors associated with cell fate commitment, such as unreported role of Nr5a2 and Gata6 in gastrointestinal tract. Finaly, we integrated this atlas with previous scATAC-seq data from mouse embryos at E8.25 and 13 adult mouse tissues to dissect life stage specific gene regulatory programs across different cell types. This rich resource and comprerhensive analysis provide a foundation for  expolring  gene regulators in mammalian cell differentiation.

overall_design: Nuclei from different mice embryos at embryonic day (E) 10.5, E11.5, E12.5 and E13.5 were extracted by previously described methods (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Then extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment.

first: Xun

last: Lan


title: Transcriptome changes in a rat model of progressive heart failure

city: Giessen

first: Axel

last: Weber

state: Hesse

address: Schubertstrasse 81

department: Rudolf Buchheim Institute of Pharmakology

institute: Justus-Liebig-University Giessen

summary:
Heart failure is among the leading causes of death globally. Ventricular failure progresses through a hypertrophic compensatory phase followed by failure of the ventricle function through rapid decompensation. In order to unravel right heart specific mechanisms of disease, rat animal models were established that (i) reflect the slowly progressive mode of compensation / decompensation and (ii) allow comparative analyses of left versus right heart failure in the same experimental set up.
Differential gene expression analysis was performed for all three treatment groups (sham, AOB, PAB), at both time points (compensation, decompensation) and for both ventricles as well as the septum

overall_design: From both phases of AOB and PAB, as well as from matching sham-operated animals, whole heart  tissues were isolated and total RNA was extracted from the left ventricle, from the right  ventricle and from the septum area. Then, polyA mRNAseq was performed.  A total of 33 animals were included in this study.

first: Kracht

last: Michael

first: Weber

last: Axel

first: Werner

last: Sebastian

first: Jurida

last: Liane


first: Yujuan

last: Su

state: CALIFORNIA

address: 9500 Gilman Dr. MC0766 CMME, Room 1087

institute: UCSD

summary: Exaggerated airway constriction triggered by exposure to irritants such as allergen, also called hyperreactivity, is a hallmark of asthma and can be life-threatening. Aside from immune cells, vagal sensory neurons are important for airway hyperreactivity 1-4. However, the identity and signature of the downstream nodes of this adaptive circuit remains poorly understood. Here we show that Dbh+ neurons in the nucleus of the solitary tract (nTS) of the brainstem, and downstream neurons in the nucleus ambiguus (NA), are both necessary and sufficient for chronic allergen-induced airway hyperreactivity. We found that repeated exposures of mice to inhaled allergen activates nTS neurons in a mast cell-, interleukin 4 (IL-4)- and vagal nerve-dependent manner. Single-nucleus RNA-seq followed by RNAscope quantification of the nTS at baseline and following allergen challenges reveals that a Dbh+ population is preferentially activated. Ablation or chemogenetic inactivation of Dbh+ nTS neurons blunted, while chemogenetic activation promoted hyperreactivity. Viral tracing indicates that Dbh+ nTS neurons, capable of producing norepinephrine, project to the NA, and NA neurons are necessary and sufficient to relay allergen signals to postganglionic neurons that then directly drive airway constriction. Focusing on transmitters, delivery of norepinephrine antagonists to the NA blunted allergen-induced hyperreactivity. Together, these findings provide molecular, anatomical and functional definitions of key nodes of a canonical allergen response circuit. The knowledge opens the possibility of targeting neural modulation as an approach to control refractory allergen-induced airway constriction.

overall_design: We dissected the GFP+ NA region from 7 Chat-cre; CAG-Sun1/sfGFP mice brainstem under the fluorescence microscope. Mice were euthanized using CO2 inhalation. Brains were acutely harvested. Dissected NA were put in liquid N2 immediately and stored at -80°C or proceeded directly to nuclei isolation. NA nuclei were processed into cDNA libraries using Chromium Single Cell 3' v3 kit (10XGenomics). Sequencing was carried out on NovaSeq (Illumina) platform. CellRanger package (version 3.0.2) was used to align the raw reads onto the mouse reference genome (GRCm38) and generate the feature-barcode matrix. R package Seurat (version 4.0) was used to perform data quality control, normalization, principal components analysis and uniform manifold approximation and projection (UMAP method).

first: Chin

last: Ji

first: Haoze

last: Yu


title: The role of corticosterone in nevirapine-induced idiosyncratic drug-induced liver injury

city: Toronto

first: Jack

last: Uetrecht

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

summary: Nevirapine, an antiretroviral used in the treatment of HIV, is associated with idiosyncratic drug-induced liver injury (IDILI), a potentially life-threatening adverse drug reaction. Its usage has decreased due to this concern, but it is still widely used in lower-resource settings. In general, the mechanisms underlying idiosyncratic drug reactions (IDRs) are poorly understood, but evidence indicates that most are immune-mediated. There is very limited understanding of the early immune response following administration of drugs associated with IDRs, which likely occurs due to reactive metabolite formation. In this work, we aimed to characterize the links between covalent binding of nevirapine, the development of an early immune response, and the subsequent liver injury using a mouse model. We describe initial attempts to characterize an early immune response to nevirapine followed by the discovery that nevirapine induced the release of corticosterone. Corticosterone release was partially associated with the degree of drug covalent binding in the liver, but was also likely mediated by additional mechanisms at higher drug doses. Transcriptomic analysis confirmed metabolic activation, glucocorticoid signaling, and decreased immune activation; GDF-15 also warrants further investigation as part of the immune response to nevirapine. Finally, glucocorticoid blockade preceding the first dose of nevirapine attenuated nevirapine-induced liver injury at 3 weeks, suggesting that acute glucocorticoid signaling is harmful in the context of nevirapine-induced liver injury. This work demonstrates that nevirapine induces acute corticosterone release, which contributes to delayed-onset liver injury. It also has implications for screening drug candidates for IDILI risk and preventing nevirapine-induced IDILI.

overall_design: Primary liver samples from C57BL/6NCrl male mice treated with vehicle or nevirapine (n = 3/group) were used for RNA sequencing

first: Jee

last: Alison

first: Sernoskie

last: Samantha Christine

first: Uetrecht

last: Jack


title: Transcriptome changes in cardiomyocytes isolated from a rat model of progressive heart failure

summary:
Heart failure is among the leading causes of death globally. Ventricular failure progresses through a hypertrophic compensatory phase followed by failure of the ventricle function through rapid decompensation. In order to unravel right heart specific mechanisms of disease, rat animal models were established that (i) reflect the slowly progressive mode of compensation / decompensation and (ii) allow comparative analyses of left versus right heart failure in the same experimental set up.
Non-restrictive clips around the pulmonary artery (pulmonary artery banding, PAB) or the aorta (aortic banding, AOB) were surgically implanted into weanling rats. Upon animal growth the clips become increasingly constrictive, leading to a compensatory, hypertrophic state at around 6 weeks and heart failure at 21 (PAB) or 24 weeks (AOB). Disease progression was monitored functionally and by sonography.
Differential gene expression analysis was performed for all three treatment groups (sham, AOB, PAB), at both time points (compensation, decompensation) and for both ventricles.

overall_design: From both phases of AOB and PAB, as well as from matching sham-operated animals, cardiomyocytes (CM) were isolated from the left ventricle and from the right  ventricle and total RNA was extracted . Then, total RNAseq was performed after depletion of ribosomal RNAs. A total of 41 animals were included in this study.


title: An IFNg-dependent immune-endocrine circuit lowers blood glucose to potentiate the innate anti-viral immune response

first: Felix

last: Wensveen

overall_design:
To investigater the impact of cytokines on gene transcription in pancreatc beta cells, we FACS-purified these cells, after which we stimulated them with glucose in presence or absence of IFNg and IL-1b.
We then performed gene expression analysis using data obtained from RNA-seq of 4 biolgical replicates under two different conditions
Comparative gene expression profiling analysis of RNA-seq data for pancreatic beta cells stimulated with glucose in the presence (IFNg/IL1b) or absence (control) of IFNg and IL1b

first: Marko

last: Šestan

first: Christoforos

last: Dimitropoulos


title: Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli

city: Martinsired

first: Kilian

last: Schumacher

address: Großhaderner Straße 2-4

institute: LMU Munich

summary: Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g. in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e. they are induced under mild acid stress but not under severe acid stress. However, it was not known to what extent fine-tuned expression of motility genes is related to fitness and the ability to survive periods of acid shock. In this study, we demonstrate that the expression of FlhDC, the master regulator of flagellation, is inversely correlated with acid shock survival of E. coli. We encountered this phenomenon when analyzing mutants from the Keio collection in which the expression of flhDC was altered by an IS element. These results suggest a fitness trade-off between acid tolerance and motility.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Comparison of genome-wide mRNA levels in E. coli MG1655 WT and dmhpR, as well as BW25113 and BW25113 mhpR::km (Keio collection) at pH 4.4 in LB medium.

first: Djanna

last: Braun

first: Karin

last: Kleigrewe

first: Kirsten

last: Jung


title: SPATAC-seq: split-pool ligation-based single cell ATAC-seq method

first: Keyong

last: Sun

department: School of Medicine

summary: To establish an ultra-high-throughput single cell chromatin accessibility profiling method that is cost-effective and widely accessible, we built on sci-ATAC-seq (Cusanovich, D. A. et al. Science. 2015; Amini, S. et al. Nature Genetics. 2014) and SPLIT-seq (Rosenberg, A. B. et al. Science. 2018) to design SPATAC-seq, which in situ label chromatin fragment in the same single cell through combinatorial barcoding. Briefly, in SPATAC-seq, (1) fixed nuclei are transposed in 48 different wells by 48 unique Tn5 transposase, which containing barcoded adaptors and 5'-phosphorylation; (2) the nuclei from all wells are collected and redistributed into second and third 48-well plate in turn, where the next two rounds of indexing are achieved through into either end of the custom transposome, which result in the generation of more than 110,000 (48^3) unique barcode combinations. (3) the nuclei are pooled, split into sublibraries and lysed, and the DNA was amplified by polymerase chain reaction (PCR), which introduce illumina sequencing barcodes and complete libraries construction. (4) After sequencing, fastq files were demultiplexed according to the same four-barcode combinations. For profiling more cells in one sublibrary, we can increase the number of barcode combinations by increase the number of indexing of each round to 96, which can produce about 1 million combinations. To assess the fidelity of SPATAC-seq, we performed a species-mixing experiment with cultured human (K562) and mouse (Hepa) cells.  Here, we tagged mixed permeabilized nuclei with only 8 barcoded transposome. In round 4, we generated eight sublibraries with different cell-recovery targets, which can be used to evaluating the stability of this method and the correlation between real doublet rates and theoretical value.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We firstly assembled 48 indexed Tn5 transposome complexes, and then performed a species-mixing experiment with cultured human (K562) and mouse (Hepa) cells to prove the feasibility of SPATAC-seq.  Here, we tagged mixed permeabilized nuclei with only 8 barcoded transposome, and generated eight sublibraries with different cell-recovery targets.

first: Xun

last: Lan


title: Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation [Trim33 RNA-Seq]

status: Public on Apr 12 2024

city: New York

first: Ioanna

last: Tiniakou

address: 435 E 30th St

institute: NYU Langone

summary: The development of all dendritic cells (DCs) including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs) is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected this common Flt3L-driven pathway of DCs differentiation using CRISPR/Cas9-based dropout screening in a Flt3L dependent progenitor cell line. Genome-wide screening identified multiple regulators of DC differentiation including the glycosylphosphatidylinositol transamidase complex and arginine methyltransferase Carm1, whose role was confirmed in vivo. It also showed that negative regulators of mTOR signaling, including the subunits of TSC and GATOR1 complexes, restricted progenitor growth but enabled DC differentiation, demonstrating that a TSC- and GATOR1-mediated shutdown of mTOR is required for the process. An orthogonal screen focused on transcriptional regulators showed that Trim33 (TIF-1g) is required for DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, inducible deletion of Trim33 caused a rapid loss of all DC progenitors, pDCs and the cross-presenting cDC1 subset. The loss of Trim33 from DC progenitors caused spontaneous interferon and inflammatory response, aberrant induction of macrophage-specific genes, and failure to induce DC differentiation program. Collectively, these data elucidate common mechanisms that control Flt3L-driven differentiation of the entire DC lineage, and identify Trim33 as its essential regulator.

overall_design: Expression profiling of dendritic cell progenitor cultures, derived from sorted mouse bone marrow total progenitors, by high throughput sequencing.

first: Boris

last: Reizis


title: ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3

city: Bethesda

first: Natasha

last: Caplen

address: 37 Convent Drive, Bldg. 37, Rm 6128

institute: National Institutes of Health

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

overall_design: Refer to individual Series


title: A brain-enriched circular RNA controls excitatory neurotransmission and restricts sensitivity to aversive stimuli

status: Public on Apr 13 2024

city: CABA

first: Damian

last: Refojo

state: CABA

address: Godoy Cruz 2390

country: Argentina

institute: Biomedicine Research Institute of Buenos Aires (IBioBA)

summary: Circular RNAs are a large class of non-coding RNAs present in all eukaryotic taxa. Despite the identification of thousands of circular transcripts, the biological significance of most of them remains largely unexplored, partly due to the lack of effective methods for generating loss-of-function animal models. In this study, we focused on circTulp4, a highly abundant circRNA that is enriched in the brain and synaptic compartments. By creating a circTulp4-deficient mouse model, in which we mutated the splice acceptor site responsible for generating circTulp4 without affecting the corresponding linear mRNA or protein levels, we were able to conduct a comprehensive phenotypic analysis. Our results demonstrate that circTulp4 is critical in regulating neuronal and brain physiology, modulating the strength of excitatory neurotransmission and sensitivity to aversive stimuli. This study provides compelling evidence that circRNAs can regulate biologically relevant functions in neurons, with modulatory effects at multiple levels of the phenotype, establishing a proof-of-principle for the regulatory role of circRNAs in neural processes.

overall_design: We experimentally assessed the potential impact of circTulp4 downregulation in the brain by performing a comparative transcriptomic analysis of three brain regions between wild-type and a circTulp4-deficient (CD) mouse model mice: hippocampus, cortex, and cerebellum (n hippocampus= 2 wt, 3 CD; n cortex= 3 wt, 3 CD; n cerebellum= 3 wt, 2 CD).

first: Sebastian

last: Giusti

first: Jeronimo

last: Lukin

first: Ines

last: Patop

last: Kadener


title: DUSP6 inhibition overcomes Neuregulin/HER3-driven therapy resistance in HER2+ breast cancer [BT474]

city: Turku

first: Teemu

middle: Daniel

last: Laajala

address: Turun yliopisto

department: Department of Mathematics and Statistics

country: Finland

institute: University of Turku

summary:
To investigate transcriptomic changes during development of resistance to lapatinib in a HER2+ breast cancer cell line
We performed gene expression profiling analysis using data obtained from RNA-seq of 4 different stage of development of lapatinib resistance in a HER2+ breast cancer cell line

overall_design: Comparative gene expression profiling analysis of RNA-seq data in parental drug sensitive, drug tolerant persister, drug tolerant expanding persister and longtem resistant cells

first: Majid

last: Momeny

first: Jukka

last: Westermarck


title: Aging-regulated PNUTS maintains endothelial barrier function via SEMA3B suppression

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

institute: Amsterdam UMC

summary: Age-related diseases pose great challenges to health care systems worldwide. During aging, endothelial senescence increases the risk for cardiovascular disease. Recently, it was described that Phosphatase 1 Nuclear Targeting Subunit (PNUTS) has a central role in cardiomyocyte aging and homeostasis. Here, we determined the role of PNUTS in endothelial cell aging. We confirmed that PNUTS is repressed in senescent endothelial cells (ECs). Moreover, PNUTS silencing elicits several of the hallmarks of endothelial aging: senescence, reduced angiogenesis and loss of barrier function. To validate our findings in vivo, we generated an endothelial-specific inducible PNUTS-deficient mouse line (Cdh5-CreERT2;PNUTSfl/fl), termed PNUTSEC-KO. Two weeks after PNUTS deletion, PNUTSEC-KO mice presented severe multiorgan failure and vascular leakage. Transcriptomic analysis of PNUTS-silenced HUVECs and lungs of PNUTSEC-KO mice revealed that the PNUTS-PP1 axis tightly regulates the expression of semaphorin 3B (SEMA3B). Indeed, silencing of SEMA3B completely restored barrier function after PNUTS loss-of-function. These results reveal a pivotal role for PNUTS in endothelial homeostasis through a SEMA3B downstream pathway that provides a potential target against the effects of aging in ECs.

overall_design: 3 replicates human umbilical vein endothelial cells were transfected with control siRNAs and, in parallel, 3 replicates human umbilical vein endothelial cells were transfected with siRNAs targeting lncRNA PNUTS (PPP1R10)

first: Noelia

last: Lozano Vidal


title: Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8KO]

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

summary: To identify target genes of the histone demethylase Phf8 in oligodendroglial cells in a genome-wide and unbiased approach, RNA-sequencing studies were performed on wildtype CG4 cells and CRISPR/Cas9-edited Phf8 knockout cell lines. We compared three wildtype and one CRISPR/Cas9-treated clone without genome editing with four CRISPR/Cas9 Phf8-knockout clones. Among others we detected substantial changes in the expression of genes associated with cell cycle and replication of DNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CG4 wildtype cells and CRISPR/Cas9 edited Phf8-knockout cell lines.

first: Kremp

last: Marco

first: Wegner

last: Michael


title: DUSP6 inhibition overcomes Neuregulin/HER3-driven therapy resistance in HER2+ breast cancer [MDA]

summary:
To investigate transcriptomic changes regulated by DUSP6 in a HER2+ breast cancer cell line
We performed gene expression profiling analysis using data obtained from RNA-seq of SCR vs DUSP6 KD MDA-MB-453 cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCR controls vs. DUSP6 KD model


title: In vitro stimulation of mouse spleen cells by mouse urine

city: Sapporo

first: Osamu

last: Ichii

address: Kita 18-Nishi 9

institute: Hokkaido University

summary: Urinary tract-associated lymphoid structures (UTLASs), tertiary lymphoid tissues, are formed in renal pelvis (RP) of humans and mice with chronic kidney disease. We found that UTALS development was accelerated by urine leakage from RP lumen to the parenchyma following dysfunction of transitional epithelium covering UTLASs. Thus, UTALS-forming cells were stimulated by urine including urinary bio active substances.

overall_design: The spleens were isolated from MRL/MpJ at 6-month-old, minced, washed, resuspended, and cultured. These cultured cells were stimulated with urine supernatant derived from MRL/MpJ or MRL/MpJ-Faslpr/lpr mice or with PBS for 3 hours. And then, RNA was collected and gene expression was analyzed.


title: Osteopontin drives neuroinflammation and cell loss in MAPT-N279K frontotemporal dementia patient neurons

first: Osama

last: Al Dalahmah

address: 622 West 168th Street

institute: Columbia University Irving Medical Center


title: The transcriptional regulation of a putative hemicellulose gene, PtrPARVUS2 in poplar

city: Syracuse

first: Dan

last: Wang

address: 107 College Place

department: Biology

institute: Syracuse University

summary: The plant cell wall serves as a critical interface between the plant and its environment, offering protection against various stresses and contributing to biomass production. Hemicellulose is one of the major components of the cell wall, and understanding the transcriptional regulation of its production is essential to fully understanding cell wall formation. This study explores the regulatory mechanisms underlying one of the genes involved in hemicellulose biosynthesis, PtrPARVUS2. Six transcription factors (TFs) were identified from a xylem-biased library to negatively regulate PtrPARVUS2 expression. These TFs, belonging to diverse TF families, were confirmed to bind to specific cis-elements in the PtrPARVUS2 promoter region, as validated by Yeast One-Hybrid (Y1H) assays, transient expression analysis, and Chromatin Immunoprecipitation sequencing (ChIP-seq) assays. Furthermore, motif analysis identified putative cis-regulatory elements bound by these TFs, shedding light on the transcriptional regulation of SCW biosynthesis genes. Notably, several TFs targeted genes encoding uridine diphosphate glycosyltransferases (UGTs), crucial enzymes involved in hemicellulose glycosylation. Phylogenetic analysis of UGTs regulated by these TFs highlighted their diverse roles in modulating hemicellulose synthesis. Overall, this study identifies a set of TFs that regulate Parvus2 in poplar, providing insights into the intricate coordination of TFs and PtrPARVUS2 in SCW formation. Understanding these regulatory mechanisms enhances our ability to engineer plant biomass for tailored applications, including biofuel production and bioproduct development.

overall_design: Chromatin Immunoprecipitation DNA sequencing for PtrC2H2ZF2, PtrC2H2ZF2, PtrARF5a, PtrBLH, PtrNAC127 and PtrCORONA in Populus tremula × alba

first: Wang

last: Dan

first: Coleman

last: Heather D


title: Insulin and leptin oscillations license food-entrained browning and metabolic flexibility [RNA-seq]

first: Prashant

last: Rajbhandari

address: 1468 Madison Ave, Annenberg 18-10

institute: Icahn School of Medicine at Mount Sinai

summary: Timed-feeding leads to adipose browning, although the integrative mechanisms for the same remain unclear. Here we show that twice-a-nocturnal (TAN) feeding causes biphasic oscillations of circulating insulin and leptin, representing their entrainment by timed-feeding. Insulin and leptin surges lead to marked cellular, functional and metabolic remodeling of sWAT resulting in increased energy expenditure. Single-cell RNAseq analyses and flow cytometry reveal a role for insulin and leptin surges in ILC2 recruitment and sWAT browning, since depleting leptin or blocking insulin receptor signaling or ILC2 cell recruitment, each dampens TAN feeding-induced sWAT remodeling and energy expenditure. Consistently, recreating insulin and leptin oscillations via once-a-day co-injections is sufficient to favorably remodel innervated sWAT. Indeed, innervation is necessary for sWAT remodeling since denervation of sWAT, but not BAT, blocks TAN-induced sWAT remodeling and resolution of inflammation. In sum, timed feeding reorganizes nutrient-sensitive pathways to remodel sWAT, which drives the metabolic benefits of timed-feeding.

overall_design: RNA-seq was performed on the SVF fourth inguinal white adipose tissue (iWAT) depot  from 8 month old mice exposed to Ad-Lib or twice-a-night (TAN) feeding.

first: P


title: The PML1-WDR5 axis regulates H3K4me3 marks and promotes stemness of estrogen receptor-positive breast cancer

city: Cleveland

first: Hung-Ying

last: Kao

state: OH

address: 10900 Euclid Avenue

department: Biochemistry

institute: Case Western Reserve University

summary: The alternative splicing of PML precursor mRNA gives rise to various PML isoforms, yet their expression profile in breast cancer cells remains uncharted. We discovered that PML1 is the most abundant isoform in all breast cancer subtypes, and its expression is associated with unfavorable prognosis in estrogen receptor-positive (ER+) breast cancers. PML depletion reduces cell proliferation, invasion, and stemness, while heterologous PML1 expression augments these processes and fuels tumor growth and resistance to fulvestrant, an FDA-approved drug for ER+ breast cancer, in a mouse model. Moreover, PML1, rather than the well-known tumor suppressor isoform PML4, rescues the proliferation of PML knockdown cells. ChIP-seq analysis reveals significant overlap between PML-, ER-, and Myc-bound promoters, suggesting their coordinated regulation of target gene expression, including genes involved in breast cancer stem cells (BCSCs), such as JAG1, KLF4, YAP1, SNAI1, and MYC. Loss of PML reduces BCSC-related gene expression, and exogenous PML1 expression elevates their expression. Consistently, PML1 restores the association of PML with these promoters in PML-depleted cells. We identified a novel association between PML1 and WDR5, a key component of H3K4 methyltransferase (HMTs) complexes that catalyze H3K4me1 and H3K4me3. ChIP-seq analyses showed that the loss of PML1 reduces H3K4me3 in numerous loci, including BCSC-associated gene promoters. Additionally, PML1, not PML4, re-establishes the H3K4me3 mark on these promoters in PML-depleted cells. Significantly, PML1 is essential for recruiting WDR5, MLL1, and MLL2 to these gene promoters. Inactivating WDR5 by knockdown or inhibitors phenocopies the effects of PML1 loss, reducing BCSC-related gene expression and tumorsphere formation and enhancing fulvestrant’s anticancer activity. Our findings challenge the conventional understanding of PML as a tumor suppressor, redefine its role as a promoter of tumor growth in breast cancer and offer new insights into the unique roles of PML isoforms in breast cancer.

overall_design: ChIP-seq was conducted on H3K4me3 in control and PML knockdown MCF-7 and ZR-75-1 cells, along with PML ChIP-seq in ZR-75-1 cells.


title: Genome-wide identification of the translation ability of the RNC-SRP complex [RIBO-seq]

city: Seoul

first: Min-kyung

last: Shin

address: Anam-ro

institute: Korea University

summary: Ribosome profiling (Ribo-seq) analysis to identify number of ribosome-protected reads from CBC-associated mRNAs or eIF4E-associated mRNAs encoding either a signal sequence or transmembrane domain (TMD)

overall_design: Ribo-seqs and mRNA-seqs experiments were performed in HEK293T cell either undepleted or depleted of endogenous SRα. In HEK293T cells, mRNAs bound to either CBP80 or eIF4E were immunoprecipitated (IPed) and then subjected to ribo-seq.

first: Jae-Sung

last: Woo

first: Yoon

last: Kim


title: Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation [Hoxb8-FL TF sgRNA-Seq]

first: Ioanna

last: Tiniakou

type:
Other
Third-party reanalysis

overall_design:
sgRNA-Seq of Hoxb8-FL cells transduced with mouse transcription factor (TF) CRISPR library.
Please note that, as a baseline we used the plasmid DNA GSM4886995 (SAMN16686430/SRR12998828/SRX9450250) which was sequenced as part of the Series GSE160963 (PRJNA675005).

first: Boris

last: Reizis


title: Biological Effects of Intraoperative Radiation Therapy (IORT): Histopathological Changes and Immunomodulation in Breast Cancer Patients

city: Santa Monica

first: Javier

last: Orozco

state: CA

address: 2200 Santa Monica Blvd

institute: Saint John's Cancer Institute

summary: Intraoperative radiation therapy (IORT) delivers a single accelerated radiation dose directly to the breast tumor bed. The synergistic effects of simultaneous surgery and radiation are poorly understood. We here explored the cellular and molecular changes induced by IORT in the tumor bed compared to no-IORT exposed breast tissues. Squamous metaplasia (SM) was identified in both cohorts; however, squamous metaplasia with atypia (SMwA) was only seen in IORT specimens (63.6%, p=0.004). SMwA mimicked DCIS on histology, requiring confirmatory stains (i.e., estrogen receptor and p63) for diagnosis. Neither SM nor SMwA were found in the initial BCS specimen. We identified 1,662 differentially expressed genes (875 upregulated and 787 downregulated) between IORT and non-IORT samples. Gene ontology analyses showed that IORT was associated with the enrichment of several immune response pathways, such as inflammatory response, granulocyte activation, and T-cell activation (p<0.001). Notably, when only considering normal tissue from both cohorts, IORT was associated with intrinsic apoptotic signaling (p<0.001). Finally, we inferred a higher abundance of gamma delta T-cells, dendritic cells, and monocytes in the IORT samples compared to non-IORT samples. In conclusion, IORT induces histological changes, including squamous metaplasia with atypia, and elicits molecular alterations associated with intrinsic apoptotic signaling and immune response pathways. The higher abundance of immune-related components in breast tissue exposed to IORT suggests a potential shift towards active immunogenicity in traditionally considered immune-desert tumors such as HR-positive/HER2-negative breast cancer.

overall_design: We selected a cohort of patients with hormone receptor (HR)-positive/HER2-negative, ductal carcinoma in situ (DCIS), or early-stage invasive breast carcinoma who underwent breast-conserving surgery requiring margin re-excision. Histopathological evaluation and RNA-sequencing were performed from regions containing normal breast tissue, squamous metaplasia (SM), and squamous metaplasia with atypia (SMwA) in the re-excision specimens and compared between patients with IORT (n=11) vs. non-IORT (n=11).

middle: I

first: Betsy

last: Valdez

first: Chikako

last: Matsuba

first: Miquel

last: Ensenyat-Mendez

first: Yuki

last: Takasumi

first: Janie

middle: G

last: Grumley


title: Genome-wide identification of the translation ability of the RNC-SRP complex


title: Genome-wide identification of target genes for the histone demethylase Phf8 in the oligodendroglial cell line CG4 [Phf8OE]

first: Michael

last: Wegner

summary: To identify target genes of the histone demethylase Phf8 in oligodendroglial cells in a genome-wide and unbiased approach,  RNA-sequencing studies were performed on CG4 cells transduced with control or Phf8-overexpressing retroviruses. Transduced, GFP-expressing cells underwent fluorescence-activated cell-sorting, were expanded and then differentiated for three days. Two biological replicates were used for each condition. Gene expression analysis revealed an increase in oligodendrocyte progenitor proliferation and a general decrease in cell differentiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CG4 wildtype cells that were transduced with either CAG-IRES-GFP-containing (ctrl) or CAG-Phf8-IRES-GFP-containing (Phf8oe) retroviruses.

first: Kremp

last: Marco

first: Wegner

last: Michael


title: SRRM2 splicing factor modulates cell fate in early development

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrueck Center for Molecular Medicine


title: DUSP6 inhibition overcomes neuregulin/HER3-driven therapy tolerance in HER2+ breast cancer

first: Teemu

last: Laajala


title: Increased AID Results in Mutations at the CRLF2 Locus Implicated in Latin American ALL Health Disparities

city: Stanford

first: Richard

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

summary: Activation-induced cytidine deaminase (AID) is a B cell-specific base editor required during class switch recombination and somatic hypermutation for B cell maturation and antibody diversification. However, it has also been implicated as a factor in the etiology of several B cell malignancies. Evaluating the AID-induced mutation load in patients at-risk for certain types of blood cancers is critical in assessing disease severity and treatment options. Here, we have developed a digital PCR (dPCR) assay that allows us to track the mutational landscape resulting from AID modification or DNA double-strand break (DSB) formation and repair at sites known to be prone to DSBs. Implementation of this new assay showed that increased AID levels in immature B cells increases genome instability at loci linked to translocation formation. This included the CRLF2 locus that is often involved in chromosomal translocations associated with a subtype of acute lymphoblastic leukemia (ALL) that disproportionately affects Latin Americans (LAs). To support this LA-specific identification of AID mutation signatures, we characterized DNA from immature B cells isolated from the bone marrow of ALL patients. Our ability to detect and quantify these mutation signatures will potentiate future risk identification, early detection of cancers, and reduction of associated cancer health disparities.

overall_design: We employed Cas9:IGHM1 and Cas9:IGHM6 gRNA bait DNA double strand break to map translocation and rejoining outcomes in the presence or absence of an additional gRNA targeting cancer gene loci implicated in LatinX populations.

first: Valeria

last: Rangel

first: Jason

middle: N

last: Sterrenberg

first: Nicholas

middle: R

last: Pannunzio


title: Single cell RNA-sequencing of stromal vascular fraction cells from subcutanous adipose tissue

city: Dallas

first: Philipp

last: Scherer

address: 5323 Harry Hines Boulevard

department: Touchstone Diabetes Center, Internal Medicine

institute: UT Southwestern Medical Center

summary: Gene expression at single cell level of CD45- stromal vascular fraction cells from subcutaneous white adipose tissues from adult WT and Paqr4-transgenic mice.

overall_design: Adipose stem progenitor cells are heterogenous, we performed scRNA-seq to examine how PAQR4 impacts the progenitor pool. We pooled CD45- cells from subcutaneous fat from three mice, which isolated by flow cytometry, and performed library preparation using the 10X Genomics Single Cell 3 v2 according to the manufacturer’s instructions.

first: Qingzhang

last: Zhu


title: The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation

city: Chapel Hill

first: Courtney

middle: M

last: Clark-Hachtel

state: NC

address: 120 South Rd

institute: UNC Chapel Hill


title: The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation [IR_RNA-seq]

summary: Tardigrades can survive remarkable doses of ionizing radiation, up to about 1000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but damage is repaired. We show that this tardigrade has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme, making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important for tardigrade radiation tolerance. We hypothesize that tardigrades’ ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.

overall_design:
To identify genes that are enriched following ionizing radiation (IR) exposure, Hypsibius exemplaris were exposed to 0, 100, 500, or 2,180 Gy of IR.
We then performed gene expression profiling analysis from data obtained from 3 replicates of each dose of IR and compared to the 0 Gy (not irradiated) samples

first: Jonathan

last: Hibshman

first: Tristan

last: De Buysscher

first: Evan

last: Stair

first: Leslie

last: Hicks

first: Bob

last: Goldstein


title: The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation [Bleo_RNA-seq]

summary: Tardigrades can survive remarkable doses of ionizing radiation, up to about 1000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but damage is repaired. We show that tardigrades have a specific and robust response to ionizing radiation: irradiation induces a rapid and dramatic upregulation of many DNA repair genes. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is necessary for tardigrade radiation tolerance. Tardigrades’ ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.

overall_design:
To identify genes that are enriched following Bleomycin exposure, Hypsibius exemplaris were exposed to 0 mg/mL (untreated), 10 µg/mL, 100 µg/mL, or 1 mg/mL Bleomycin for 24 hours.
We then performed gene expression profiling analysis from data obtained from 3 replicates of each dose of Bleomycin and compared to the 0 mg/mL (untreated) samples.


title: Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation

first: Ioanna

last: Tiniakou

address: 435 E 30th St

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

sample_organism:
Mus musculus
unidentified plasmid

platform_organism:
Mus musculus
unidentified plasmid

overall_design: Refer to individual Series


title: Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation [Hoxb8-FL RNA-Seq]

summary: The development of all dendritic cells (DCs) including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs) is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected this common Flt3L-driven pathway of DCs differentiation using CRISPR/Cas9-based dropout screening in a Flt3L-dependent progenitor cell line. Genome-wide screening identified multiple regulators of DC differentiation including the glycosylphosphatidylinositol transamidase complex and arginine methyltransferase Carm1, whose role was confirmed in vivo. It also showed that negative regulators of mTOR signaling, including the subunits of TSC and GATOR1 complexes, restricted progenitor growth but enabled DC differentiation, demonstrating that a TSC- and GATOR1-mediated shutdown of mTOR is required for the process. An orthogonal screen focused on transcriptional regulators showed that Trim33 (TIF-1g) is required for DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, inducible deletion of Trim33 caused a rapid loss of all DC progenitors, pDCs and the cross-presenting cDC1 subset. The loss of Trim33 from DC progenitors caused spontaneous interferon and inflammatory response, aberrant induction of macrophage-specific genes, and failure to induce DC differentiation program. Collectively, these data elucidate common mechanisms that control Flt3L-driven differentiation of the entire DC lineage, and identify Trim33 as its essential regulator.

overall_design: Expression profiling of Hoxb8-FL cells at different stages of differentiation by high throughput sequencing

first: Boris

last: Reizis


title: Exosomes targeting Myc reverse the proneural-mesenchymal transition and extend the survival of end-stage glioblastoma mice [DroNc-seq ]

status: Public on Apr 11 2024

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: Exosomes generated from human bone marrow Mesenchymal Stem cells (MSC) and engineered to encapsulate different anti-Myc siRNAs (iExo-Myc) and scramble-siRNAs (iExo-Scr) were administered via retro-orbital injection to mice harboring late stage intracranial U87 tumor xenografts. Tumor growth and survival were monitored, and tumor xenografts were collected and transcriptionally profiled.

overall_design:
Next, we performed gene expression profiling analysis using data obtained from single nuclei RNA-seq of U87 tumor xenografts collected at the endpoint of the survival study from 2 iExo-Myc#1 treated mice and 2 iExo-Scr#1 treated mice
We implanted luciferase expressing U87 cells orthotopically in nude mice. At Day 28 post tumour implantation, mice were allocated into 2 treatment groups that received, via retro-orbital venous sinus injection, iExo-Scr #1 or iExo-Myc #1, every other day at a dose of 1x10E9 exosomes in 100 μl. When mice reached euthanisa conditions, tumors were collected and  total RNA was extracted and cleaned up from iExo-Scr #1 (N=4) and iExo-Myc #1 (N=3) treated mice. RNA concentration was measured  and RNA quality was assessed and an equal amount of RNA was submitted for Illumnia Next Seq 500 sequencing

first: Wafa

last: Hassen

first: Bingui

last: Li

first: Valerie

middle: S

last: LeBleu

first: Raghu

last: Kalluri


title: Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

institute: Nagoya University

summary: Two molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) have been proposed: the “Classical” and “Basal-like” subtypes. However, the “molecular” classification has not been applied in real-world clinical practice. This study aimed to establish patient-derived organoids (PDOs) for PDAC and evaluate their application in subtype classification and clinical outcome prediction. We constructed a PDO library for morphologic and RNA-seq analyses and drug response assays in vitro. PDOs of PDAC were established at a high efficiency (> 70%) with at least 100,000 live cells. Morphologically, PDOs were classified as gland-like structures (GL type) or densely proliferating inside (DP type). RNA-seq analysis revealed that the “morphological” subtype (GL vs. DP) roughly corresponded to the “molecular” subtype (“Classical” vs. “Basal-like”). The proposed “morphological” classification predicted clinical treatment response and prognosis; the median overall survival of patients with GL type were significantly longer than that of those with DP type (P < 0.005). The GL type showed a better response to gemcitabine than the DP type in vitro, whereas the drug response of the DP type was improved by the combination of ERK and autophagy inhibition. PDAC PDOs facilitated subtype determination and clinical outcome prediction, thereby advancing precision medicine for PDAC.

overall_design: Transcriptome analysis of two types of patient-derived PDAC organoids

first: Kazuhide

last: Matsumoto

first: Nao

last: Fujimori

first: Yoshihiro

last: Ogawa


title: Exosomes targeting Myc reverse the proneural-mesenchymal transition and extend the survival of end-stage glioblastoma mice

summary:
Exosomes generated from human bone marrow Mesenchymal Stem cells (MSC) and engineered to encapsulate different anti-Myc siRNAs (iExo-Myc) and scramble-siRNAs (iExo-Scr) were administered via retro-orbital injection to mice harboring late stage intracranial U87 tumor xenografts. Tumor growth and survival were monitored, and tumor xenografts were collected and transcriptionally profiled.
Next, we performed gene expression profiling analysis using data obtained from RNA-seq of U87 tumor xenografts collected at the endpoint of the survival study from 3 iExo-Myc#1 treated mice and 4 iExo-Scr#1 treated mice

overall_design: We implanted luciferase expressing U87 cells orthotopically in nude mice. At Day 28 post tumour implantation, mice were allocated into 2 treatment groups that received, via retro-orbital venous sinus injection, iExo-Scr #1 or iExo-Myc #1, every other day at a dose of 1x10E9 exosomes in 100 μl. When mice reached euthanisa conditions, tumors were collected and  total RNA was extracted and cleaned up from iExo-Scr #1 (N=4) and iExo-Myc #1 (N=3) treated mice. RNA concentration was measured  and RNA quality was assessed and an equal amount of RNA was submitted for Illumnia Next Seq 500 sequencing


title: Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation [Hoxb8-FL ATAC-Seq]

city: New York

institute: NYU Langone

overall_design: Genome binding/occupancy profiling of Hoxb8-FL cells at different stages of differentiation by high throughput sequencing


title: Transcriptomic profiling of high-density neutrophils in human thyroid cancer.

city: DAEJEON

first: SEONG EUN

last: LEE

address: 282 MUNHWA-RO

institute: CHUNGNAM NATIONAL UNIVERSITY

summary: We performed transcriptomics analysis on the high-density neutrophils from whole blood of thyroid cancer patients.

overall_design: We the performed gene expression profiling analysis using data obtained from RNA-seq of isolated-high-density neutrophils of 11 thyroid cancer patients whole blood.

first: SeongEun

last: Lee

first: DaHyun

last: Kang

first: YeaEun