title: Single nucleus RNA-seq of brain regions showing high-low Abeta plaque pathology in a mouse model of Alzheimer’s disease

summary: Alzheimer’s Disease (AD) pathology and amyloid-beta plaque deposition progress slowly in the cerebellum compared to other regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in mouse model (App KI) of preclinical AD, we show that within the cerebellum, the deep cerebellar nuclei (DCN) show particularly low Aβ plaque accumulation. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all celltypes in the DCN and EC of wild-type and App KI male mice at age 7 months.

overall_design: EC and DCN from N=2 wild-type and AppNL-G-F knock-in mice were dissected. Single nuclei were then isolated by sucrose cushion centrifugation and sequenced using the 10X droplet-based method.

first: Alaric

last: Yip


title: Saturation genome editing of 11 codons and exon 13 of BRCA2 determines pathogenicity of variants

status: Public on Aug 30 2023

city: Frederick

first: Shyam

last: Sharan

state: MD

address: Building 560, Room 32-33

country: USA

institute: Mouse Cancer Genetics Program

summary: The pathogenicity of majority of variants identified in cancer-causing genes is unknown due to limited epidemiological data, hence they are considered to be variant of uncertain significance (VUS). To date, Breast Cancer gene-2 (BRCA2) has the highest number of VUSs, which has necessitated the development of several robust functional assays to determine their functional significance. Here we report the use of a humanized-mouse embryonic stem cell (mESC) line expressing a single copy of the human BRCA2 for a CRISPR-Cas9-based high-throughput functional assay.  As a proof-of-principle, we have saturated 11 codons encoded by BRCA2 exons 3, 18, 19 and all possible single-nucleotide variants in exon 13 and multiplexed these variants for their functional categorization. Specifically, we used a pool of 180-mer single-stranded donor DNA to generate all possible combination of variants. Using a high throughput sequencing-based approach, we show a significant drop in the frequency of non-functional variants, whereas functional variants are enriched in the pool of the cells. We further demonstrate that variants with partial loss of BRCA2 function are sensitive to the DNA-damaging agents, cisplatin and olaparib, allowing us to discriminate between functional and intermediate variants. We have categorized 599 BRCA2 variants including 93-single nucleotide variants (SNVs) across the 11 codons, of which 28 are reported in ClinVar. We also functionally categorized 252 SNVs from exon 13 into 188 functional, 60 non-functional and 4 intermediate variants, demonstrating that saturation genome editing (SGE) coupled with drug sensitivity assays can enhance functional annotation of BRCA2 VUS.

overall_design: Saturation genome editing (SGE) coupled with drug sensitivity assays of BRCA2

first: Sahu

last: Sounak

first: Sharan

last: Shyam


title: Topical glucocorticosteroids inhibit allergic skin inflammation but are ineffective in impeding the formation and expansion of resident memory T cells

status: Public on Aug 31 2023

city: Lyon

first: Marc

last: Vocanson

address: 21 avenue Tony Garnier

country: France

institute: INSERM

type: Expression profiling by high throughput sequencing

summary: Tissue-resident memory T (TRM) cells are detrimental in numerous chronic inflammatory diseases, including allergic contact dermatitis (ACD), in which they contribute to the chronicity and severity of the disease. We assessed the impact of a standard glucocorticosteroid treatment, triamcinolone acetonide (TA), on the formation, maintenance and reactivation of epidermal TRM cells in ACD.

overall_design: We used an experimental model of ACD to 2,4-dinitrofluorobenzene, that is mediated by allergen-specific CD8+ T cells. TA 0.01% was applied at different time points of CHS response and we monitored skin inflammation and tracked CD8+CD69+CD103 TRM by flow cytometry and RNA sequencing

first: Emi

last: Ono

first: Marine

last: Lefevre


title: The Bone marrow stroma in human myelodysplastic syndrome reveals alterations that regulate disease progression [Human and Mouse]

city: Boston

first: Youmna

last: Kfoury

state: MA

address: 185 Cambridge street

department: Harvard stem cell institute

institute: Harvard University

summary: Myelodysplastic syndromes (MDS) are a heterogenous group of diseases affecting the hematopoietic stem cell that are curable only by stem cell transplantation. Both hematopoietic cell intrinsic changes and extrinsic signals from the bone marrow niche seem to ultimately lead to MDS. Animal models of MDS indicate that alterations in specific mesenchymal progenitor subsets in the bone marrow microenvironment can induce or select for abnormal hematopoietic cells. Here we identify a subset of human bone marrow (BM) mesenchymal cells marked by the expression of CD271, CD146 and CD106. This subset of human mesenchymal cells is equivalent to those in mice that, when perturbed, results in an MDS-like syndrome. Transcriptional analysis identified epithelial to mesenchymal transition as the most enriched gene set and Osteopontin (SPP1) as the most overexpressed gene. The loss of expression of Spp1 in the microenvironment resulted in an accelerated progression of the transplanted Vav-driven Nup98-HoxD13 MDS model as demonstrated by increased chimerism, increased contribution of mutant cells to the myeloid lineage and a more pronounced anemia when compared to animals with a wild type microenvironment. These data indicate that molecular perturbations can occur in specific bone marrow mesenchymal subsets of MDS patients. However, the niche adaptations to dysplastic clones include Spp1 overexpression that can constrain disease progression. Therefore, niche changes with malignant disease can also serve to protect the host.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Human: Sorted mesenchymal subsets from bone marrow and digested spicules from filter bags of transplant procedure. Dead, hematopoieitc, erythroid and endothelaial cells were removed by gating on 7AAD-, CD45-, CD235ab-, CD31- and CD34- cells. Five subsets were sorted as follows: DP (CD271+CD146+CD106+), DN (CD271+, CD146+, CD106-), SP (CD271+, CD146-, CD106+), SN (CD271+CD146-, CD106-), N (CD271-, CD146-). In addition, non-hematopoietic non-endothelial CD51+ cells and CD45+ cells were sorted as controls
Mouse: Sorted GFP+ osteoblasts and osteoprogenitors from digested bones of Ocn-GFP and Osx-GFP:Cre reporter mice respectively. Dead, hematopoietic, erythroid and endothelial cells were removed by gating on 7AAD-, CD45-, Ter119-, CD31- cells. In addition, non-hematopoietic non endothelial CD51+ and CD45+ cells (from bone marrow) were sorted as controls

middle: S

first: Fei

last: Ji

first: Esha

last: Jain

first: Giulia

last: Schiroli

first: Ani

last: Papazian

first: Francois

last: Mercier

first: David

middle: b

last: Sykes

first: Mark

last: randolph

first: Omar

last: Abdel-Wahab

first: Ruslan

middle: I

last: Sadreyev

middle: T

last: Scadden


title: The Bone marrow stroma in human myelodysplastic syndrome reveals alterations that regulate disease progression [Mesenchymal subsets]

overall_design: Sorted bone marrow mesenchymal subsets from patients with myelodysplastic syndromes or age and gender matched controls from patients undergoing hip replacement surgery. Dead, hematopoieitc, erythroid and endothelaial cells were removed by gating on 7AAD-, CD45-, CD235ab-, CD31- and CD34- cells. Four subsets were sorted as follows: DP (CD271+CD146+CD106+), DN (CD271+, CD146+, CD106-), S (CD271+, CD146-), N (CD271-, CD146-)


title: A Single Cell Genomics Atlas of the Drosophila Larval Eye Reveals Distinct Developmental Timelines and Novel Markers for All Photoreceptor Subtypes

city: Houston

first: Komal Kumar

last: Bollepogu Raja

state: TX

address: One Baylor plaza

department: Pathology and Immunology

institute: baylor college of medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Drosophila eye is a powerful model system to study the dynamics of cell differentiation, cell state transitions, cell maturation, and pattern formation. However, a high-resolution single cell genomics resource that accurately profiles all major cell types of the larval eye disc and their spatiotemporal relationships is lacking. Here, we report transcriptomic and chromatin accessibility data for all known cell types in the developing eye. Photoreceptors appear as strands of cells that represent dynamic developmental timelines. Photoreceptor subtypes are transcriptionally distinct when they begin to differentiate, but then appear to assume a common transcriptome as they mature. We identify novel cell type maturation genes, enhancers, and potential regulators, as well as genes with distinct R3 or R4 photoreceptor specific expression. Finally, we observe that photoreceptor chromatin accessibility is more permissive than non-neuronal lens-secreting cone cells, which show a more restrictive chromatin profile. These single cell genomics atlases will greatly enhance the power of the Drosophila eye as a model system.

overall_design: The Drosophila larval eye disc was dissected and dissociated into single cells using collagensae and dispase.

first: Komal

middle: K

last: Raja

first: Kelvin

last: Yeung

first: Yoon-Kyung

last: Shim

first: Yumei

last: Li

first: Rui

last: Chen

first: Graeme

last: Mardon


title: The Bone marrow stroma in human myelodysplastic syndrome reveals alterations that regulate disease progression [CD34+CD38-_MDS]

first: Youmna

last: Kfoury

overall_design: Sorted bone marrow CD34+CD38- from MDS patients or age and gender matched controls from patients undergoing hip replacement surgery

last: Ji


title: The Bone marrow stroma in human myelodysplastic syndrome reveals alterations that regulate disease progression

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

overall_design: Refer to individual Series


title: Severity of lung function impairment drives transcriptional phenotypes of COPD and relates to immune and metabolic processes

city: New Lambton Heights

first: Katherine

last: Baines

state: NSW

address: Hunter Medical Research Institute, Level 2 East, Lot 1, Kookaburra Cct

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

summary: Gene expression profiles were generated from induced sputum samples in COPD and healthy controls. The study identified transcriptional phenotypes of COPD.

overall_design: This study used unsupervised hierarchical clustering of induced sputum gene expression profiles of 72 stable COPD patients and 15 healthy controls to identify distinct and clinically relevant transcriptional COPD phenotypes.

first: Netsanet

middle: A

last: Negewo

first: Peter

middle: G

last: Gibson

first: Jodie

middle: L

last: Simpson

first: Vanessa

middle: M

last: McDonald

middle: J


title: XPO1 enables adaptive regulation of mRNA export required for genotoxic stress tolerance in cancer cells

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

summary:
To determine how exposure to CHOP, Selinexor or their combination affects gene expression in DLBCL, we first established a patient-derived xenograft model of DLBCL.
Next, mice were randomized to receive either vehicle, CHOP, Selinexor or their combination. Tumors were harvested at the end of treatment and gene expression profile analyzed by RNA-sequencing.

overall_design: Three replicates per treatment arm (vehicle, CHOP, Selinexor, CHOP + selinexor) were sequenced.

first: Rossella

last: Marullo

middle: V

first: Leandro

last: Cerchietti


title: Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress [ChIP-seq]

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Activated Notch signaling is highly prevalent in T-cell acute lymphoblastic leukemia (T-ALL). But in clinical trials, pan-Notch inhibitors caused excessive toxicity. To find alternative ways to target Notch signals, we investigated Cell division cycle 73 (Cdc73), which is a component of the RNA polymerase-associated transcriptional machinery and has been previously described as a Notch cofactor. Emerging evidence also suggests that transcriptional machinery might be an attractive vulnerability in T-ALL. In this setting, we show that CDC73 co-binds a subset of Notch-occupied regulatory elements in an ETS1-dependent context. In mouse models, Cdc73 is important for Notch-induced T-cell development and maintenance of Notch-induced T-ALL. Mechanistically, Cdc73, Ets1, and Notch activate genes that promote DNA repair and oxidative phosphorylation. Cdc73 induces these pathways through canonical functions in mRNA synthesis rather than non-canonical functions in enhancer activation. Our study suggests that Cdc73 acts through context-dependent mechanisms to promote a gene expression program that mitigates the genotoxic and metabolic stress of supraphysiological Notch signaling. We also provide mechanistic support for testing inhibitors of DNA repair, oxidative phosphorylation, and transcriptional machinery as anti-leukemic therapy while highlighting strategies that disable pathways that intersect with Notch at chromatin to target Notch signals without directly targeting the Notch complex.

overall_design: Conditional Cdc73 knockout murine Notch-induced T-ALL cell lines (969 and 970) and a control murine Notch-induced T-ALL cell line (708)  were  treated  with ethanol (EtOH) vehicle or tamoxifen (OHT) and assayed by ChIP-seq. ChIP-quality antibodies targeted the following: H3K27Ac (23 libraries: 3 replicates per condition per cell line, except for 708 + EtOH, which only had 2 replicates);  H2K120Ub1 (12 libraries; 3 replicates per condition in 969 and 970 cells), and Ets1 (2 libraries: untreated 969 and 970 cells, unreplicated). One input library was sequenced for each of the three cell lines (untreated).  Human THP6 cells were transduced with control or one of two CDC73-targeting shRNAs followed by ChIP-seq targeting ETS1 (6 libraries: 2 replicates per condition).

first: Elizabeth

last: Choe

first: Mark

last: Chiang

first: Russell

last: Ryan


title: Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress [Bru-seq and BruUV-seq]

overall_design: Conditional Cdc73 knockout murine Notch-induced T-ALL cell lines (969 and 970) and a control murine Notch-induced T-ALL cell line (708) were treated with EtOH vehicle or OHT.  Three biological replicates were prepared per condition and subject to both metabolic labeling with bromouridine and sequencing (Bru-seq) and Bru-seq with ultraviolet irradiation (BruUV-seq).  36 libraries were produced for Bru-seq and BruUV-seq (18 each).

first: Ashley

last: Melnick


title: Maternal Circulating miRNAs Contribute to Negative Pregnancy Outcomes by Altering Placental Transcriptome and Fetal Vascular Dynamics

status: Public on Aug 29 2023

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

summary: We performed RNA sequencing on the fetal portion of murine placentas isolated at gestational day (GD) 18, 8 days after dams are exposed to a single intravascular administration of either pooled murine-conserved HEamiRNAs (50 μg of pooled equimolar quantities of mmu-miR-222-5p, mmu-miR-187-5p, mmu-mir-299a, mmu-miR-491-3p, miR-760-3p, mmu-miR-671-3p, mmu-miR-449a-5p and mmu-miR-204-5p mimics) or control scrambled miRNAs.

overall_design: Pregnant C57Bl6/J mice served as controls or were exposed to HEamiRNAs by intravascular administration on gestational day (GD) 10. On GD18, the fetal portion of murine placentas, excluding the decidual portion (maternal), was micro-dissected. A total of 19 samples (10 male and 9 female samples), originating from 11 pregnant dams, 6 HEamiRNAs -treated and 5 control.

first: Marisa

middle: R

last: Pinson

first: Alexander

last: Tseng

first: Amy

last: Adams

first: Tenley

middle: E

last: Lehman

first: Karen

last: Chung

first: Jessica

last: Gutierrez

first: Kirill

last: Larin

first: Christina

last: Chambers

middle: C


title: Single cell gene expression data of CD45 high to intermediate immune cells from T cell replete and deficient mice harboring EO771 breast cancer metastases.

status: Public on Aug 28 2023

city: Irvine

first: Aaron

last: Longworth

state: California

address: Sprague Hall, 839 Health Sciences Rd

department: Physiology & Biophysics

institute: University of California, Irvine

summary: Resident and infiltrating myeloid cells are frequently reported to be tumor-promoting upon incidence of BCBM, but these cells are often poorly discriminated. We utilized scRNAseq to transcriptionally discriminate key immune cell populations and identify that microglia are predominantly pro-inflammatory upon BCBM initiation, and driven to an antigen presenting phenotype by infiltrating T cells.

overall_design: Myelinated cells were removed from whole brain homogenates of C57BL/6 and RAG1-KO mice by density gradient and sorted for CD45hi-int cells by FACS.

first: Jacob

last: Insua-Rodriguez

first: Katrina

last: Evans

first: Kerrigan

last: Blake

first: Devon

last: Lawson


title: Transcriptomic profiling of human induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs) and cardiac progentiors (hiPSC-CPs) from tetralogy of Fallot (TOF) patients with DiGeorge Syndrome (DG) and without DiGeorge Syndrome (ND)

city: Hong Kong

first: Chun Ho

last: Chan

address: 5 Sassoon Road Pokfulam

country: Hong Kong

institute: The University of Hong Kong

summary: DG accounts for most of the identifiable cases of TOF. Exploring and comparing the transcriptome of hiPSC-CMs and hiPSC-CPs from TOF-DG and TOF-ND could provide a bettering understanding on TOF.

overall_design: Day 7,8 and 11 hiPSC-CPs undergoing in vitro cardiac differentiation derived from 2 control-, 1 TOF-DG- and 1 TOF-ND-hiPSC lines. Day22 hiPSC-CMs (fabricated into cardiac anisotropic sheets, CAS) derived from 2 control-, 2 TOF-DG- and 2 TOF-ND-hiPSC lines.

first: Yin

middle: Y

last: Lam

first: Chun

middle: H

first: Wendy

last: Keung

first: Yiu

middle: F

last: Cheung


title: SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes [RNA-seq-nos-Gal4]

status: Public on Aug 26 2023

city: Pasadena

first: Baira

last: Godneeva

state: CA

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

summary: The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members, Drosophila only encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonus’s repressive activity. SUMOylation influences Bonus’s subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.

overall_design: Gene expression and genome occupancy profiling by high throughput sequencing

first: Maria

last: Ninova

first: Katalin

last: Toth

first: Alexei

last: Aravin


title: An ex vivo model of Toxoplasma recrudescence reveals the developmental plasticity of the bradyzoite stage

city: Riverside

first: Edward

last: Vizcarra

address: 900 University Ave

institute: UC Riverside

summary: Reactivation of toxoplasmosis poses a significant health risk to chronically infected people especially those with compromised immune systems.  Molecular studies of reactivation have been difficult due to the lack of accurate models of bradyzoite recrudescence, which initiates disease reactivation.  Here, we performed single cell RNA-sequencing (scRNA-seq) on parasite populations that form after bradyzoite infection of two host-cell types: primary mouse astrocytes and human foreskin fibroblasts.  The study revealed that metabolic gene signatures characterized distinct parasite populations and differences in the non-adapted bradyzoite population which uncovered significant developmental pluripotency. Our data revealed previously unknown complexity in the clinically important stages that form during reactivation of the bradyzoite tissue cyst.

overall_design: We sequenced >45,000 parasites at 1 billion reads per sample: recrudescent populations from infected mouse astrocytes at Day-2 (6,382), Day-5 (6,542), and Day-7 (26,931) post-bradyzoite infection; recrudescent populations from infected human fibroblasts at Day-2 (844), Day-5 (4,827), and Day-7 (1,206) post-bradyzoite infection.

first: Arzu

last: Ulu

first: Karine

last: Le Roch

first: Emma

last: Wilson

first: Michael

middle: W

last: White


title: SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes [RNA-seq-MT-Gal4]


title: SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes [ChIP-seq]


title: SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes.


title: XRE Transcription Factors in Caulobacter and φCbK Modulate Adhesion and Phage Viability

status: Public on Aug 25 2023

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University


title: XRE Transcription Factors in Caulobacter and φCbK Modulate Adhesion and Phage Viability [RNA-seq]

summary: During infection, transcriptional changes in both the phage and its host bacterium influence the outcome of infection. The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and phages, regulate diverse aspects of bacterial cell physiology and can impact phage infection dynamics. Through a pangenome analysis of Caulobacter species isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of an XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation in C. crescentus. We further discovered related XRE TFs across the class Alphaproteobacteria and its phages, including the φCbK Caulophage, suggesting that members of this gene cluster impact host-phage interactions. Here we show that that a closely related group of XRE proteins, encoded by both C. crescentus and φCbK, can interact to form heteromeric associations and control the transcription of a common gene set, influencing processes such as adhesin development and the progression of φCbK infection. The φCbK XRE paralog, tgrL, is highly expressed at the earliest stages of infection and can directly repress transcription of hfiA, a potent adhesion factor, and gafYZ, a transcriptional activator of prophage-like gene transfer agents (GTAs) encoded on the C. crescentus chromosome. A group of C. crescentus XRE proteins also directly repress gafYZ transcription, revealing a functionally redundant set of host regulators that may protect against spurious production of GTA particles and inadvertent cell lysis. Deleting host XRE transcription factors reduced φCbK burst size, while overexpressing these genes or φCbK tgrL rescued this burst defect. We conclude that a large XRE TF gene cluster, shared by C. crescentus and φCbK, plays an important role in adhesion regulation under phage-free conditions, and influences host-phage dynamics during infection.

overall_design: RNA sequencing (RNA-seq) during phiCbK infection and CbK_tgrL overexpression in Caulobacter crescentus CB15

first: McLaughlin

last: Maeve

first: Fiebig

last: Aretha

first: Crosson

last: Sean


title: Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells [ATAC-Seq]

status: Public on Aug 24 2023

city: London

first: Anne

last: OGarra

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

summary:
CD4+ Th1 cells producing IFN-g are required to eradicate intracellular pathogens, however if uncontrolled these cells can mediate immunopathology. The cytokine IL-10 is produced by multiple immune cells including Th1 cells during infection and regulates the immune response to minimise collateral host damage. In this study we aimed to elucidate the transcriptional network of genes controlling the expression of Il10 and proinflammatory cytokines, including Ifng in Th1 cells.

We show that the transcription factors Blimp-1 and c-Maf each have unique and common effects on cytokine gene regulation and not only co-operate to induce Il10 gene expression in IL-12 plus IL-27 differentiated Th1 cells, but additionally directly negatively regulate key proinflammatory cytokines including Ifng, thus providing mechanisms for reinforcement of regulated Th1 cell responses.

overall_design: We have applied computational analysis of gene regulation derived from temporal profiling of gene expression clusters obtained from bulk RNA sequencing (RNA-Seq) of flow cytometry sorted CD4+ Th1 effector cells differentiated in vitro with IL-12 and IL-27 to produce Ifng and Il10, compared to control dirven-CD4+ T cells. Data was integrated with analysis of active genomic regions from these Th1 cells using ATAC-seq, integrated with literature derived-ChIP-seq data and the RNA-seq data, to elucidate the transcriptional network of genes controlling expression of Il10 and pro-inflammatory effector genes in Th1 cells. The co-dominant role for the transcription factors, Prdm1 (encoding Blimp-1) and Maf (encoding c-Maf), in cytokine gene regulation in Th1 cells, was confirmed using T cells obtained from mice with T-cell specific deletion of these transcription factors.

first: Luke

middle: S

last: Cox

first: Marisol

last: Alvarez-Martinez

first: Xuemei

last: Wu

first: Leona

last: Gabryšová

first: Raphaëlle

last: Luisier

first: James

last: Briscoe

first: Nicholas

last: Luscombe

last: O’Garra


title: Influence of the downregulation of the ARES lncRNA (AT4G14548) on gene regulation in Arabidopsis thaliana

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

institute: CNRS

summary: We analyze the effect of the downexpression of the ARES lncRNA (AT4G14548) on the transcriptome of Arabidopsis roots. 12 DAS roots were harvested and total RNA extracted for RNA sequencing.

overall_design: RNA-seq experiments (polyA+ RNA) in quadriplicate for each genotype (Col-0 and RNAI-ARES-6,2 lines).

first: María

last: Legascue

first: Aurélie

last: Christ

first: Federico

last: Ariel


title: Short-term depletion in Drosophila enteroendocrine cells

status: Public on Aug 23 2023

city: South San Francisco

first: Nadja

middle: Sandra

last: Katheder

address: 1 DNA

department: Regenerative Medicine

institute: Genentech


title: XRE Transcription Factors in Caulobacter and φCbK Modulate Adhesion and Phage Viability [ChIP-seq]

first: Sean

last: Crosson

overall_design: Chromatin Immunoprecipitation sequencing (ChIP-seq) for 3xFLAG-tagged XRE transcription factors in Caulobacter crescentus CB15

first: Maeve

last: McLaughlin

first: Aretha

last: Fiebig


title: Patterns of metastasis and recurrence in urothelial cancer molecular subtypes

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

type:
Expression profiling by array
Third-party reanalysis

summary:
This series contains the gene expression data from urothelial bladder cancer samples from Swedish patients that were used to analyze metastatic sites. Included patients have a recurrence or distant metastasis before or after treatment with chemotherapy. Patients with only lymph-node metastases are not included. A previous series (GSE169455) contains data from all patients that recieved two or more cycles of neoadjuvant chemotherapy with curative intent. Patients in that series that developed distant recurrence are re-analyzed here. A few samples from a previous cystectomy series (GSE83586) are also included as re-analysis. In addition, the current series contains data from patients treated with palliative first-line chemotherapy, curative adjuvant chemotherapy, or < 2 cycles of neoadjuvant chemotherapy.
Raw data should be adjusted in data processing for batch variables: Labeling batch and Labeling kit.

overall_design: Retrospective cohort study aiming to study metastatic sites and  chemotherapy response in muscle-invasive bladder cancer.

last: Sjödahl

first: Pontus

last: Eriksson

first: Johan

last: Abrahamsson

first: Karin

last: Holmsten

first: Carina

last: Bernardo

first: Mattias

last: Höglund

first: Anders

last: Ullén

first: Fredrik

last: Liedberg


title: Short-term depletion of acetylcholine synthesis in Drosophila enteroendocrine cells

summary: Bulk RNAseq from whole adult Drosophila melanogaster guts expressing either mCherry-RNAi (control) or RNAi against ChAT (Choline acteyltransferase) under control of a enteroendocrine-specific driver to assess the role of epithelial acetylcholine production in intestinal barrier function.

overall_design: UAS-GFP, tubGal80ts, propero-Gal4 was used as a driver to induce mCherry (Bloomington line BL 35785) or ChAT (VDRC line v20183) RNAi-mediated knockdown in enteroendocrine cells. Knockdown was induced for 3 days by shifting adult mated female flies (5 days old) to the permissive temperature (29ºC). 4 replicates were included for each genotype, consisting of 25 dissected whole midguts guts each (crop, malpighian tubules and hindgut were removed).

first: Luz

last: Orozco

first: David

last: Garfield

first: Yuxin

last: Liang

first: Heinrich

last: Jasper


title: Ex vivo drug sensitivity screening predicts response to temozolomide in glioblastoma patients and identifies candidate biomarkers

city: Rotterdam

first: Martine

last: Lamfers

state: Zuid Holland

address: Wytemaweg 80

department: Neurosurgery

country: Netherlands

institute: Erasmus MC

summary: To investigate in situ-in vitro molecular correspondence and the relationship between in vitro and patient response to temozolomide (TMZ)

overall_design: Gene expression profiling analysis using data obtained from RNA-seq of 24 different GBM cell cultures

first: Ioannis

last: Ntafoulis

first: Anne

last: Kleijn

first: Jie

last: Ju

first: Kevin

last: Jimenez-Cowell

first: Federica

last: Fabro

first: Michelle

last: Klein

first: Romain

middle: T

last: Chi Yen

first: Rutger

middle: K

last: Balvers

first: Yunlei

last: Li

first: Andrew

middle: P

last: Stubbs

first: Trisha

last: Kers

first: Andreas

last: Kremer

first: Annette

last: Byrne

first: Alice

last: O’Farrell

first: Diether

last: Lambrechts

first: Gonca

last: Dilcan

first: Francesca

last: Lodi

first: Ingrid

last: Arijs

first: Clemens

last: Dirven

first: Sieger

last: Leenstra


title: Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture

status: Public on Aug 22 2023

city: Kunming

first: Mq

last: Peng

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

country: China

institute: Kunming University of Science and Technology

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells [in vitro]

first: Anne

last: OGarra

summary: CD4+ Th1 cells producing IFN-g are required to eradicate intracellular pathogens, however if uncontrolled these cells can mediate immunopathology. The cytokine IL-10 is produced by multiple immune cells including Th1 cells during infection and regulates the immune response to minimise collateral host damage. In this study we aimed to elucidate the transcriptional network of genes controlling the expression of Il10 and proinflammatory cytokines, including Ifng in Th1 cells.

overall_design: RNA-seq analysis (in 2-4 biological replicates) of flow cytometry sorted naïve CD4+ T cells activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3

first: Luke

last: Cox

first: Marisol

last: Alvarez-Martinez

first: Xuemei

last: Wu

first: Leona

last: Gabryšová

first: Raphaëlle

last: Luisier

first: James

last: Briscoe

first: Nicholas

last: Luscombe

last: O’Garra


title: Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells


title: Single-nuclei RNA-seq (snRNA-seq) of postnatal hypothalamus of CRH-IRESCre (CRH-Cre) mice using a retrograde Connect-seq approach

status: Public on Aug 19 2023

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

country: South Korea

institute: Ajou University School of Medicine

summary: We generated a single nuclei RNA-seq (snRNA-seq) dataset derived from the postnatal hypothalamus of CRH-IRESCre (CRH-Cre) mice using a retrograde Connect-seq approach.

overall_design:
A snRNA-seq dataset of 1,533 cells were generated from the postnatal hypothalamus and the bed nucleus of CRH-IRESCre (CRH-Cre) mice with ages ranging from 6 to 14 weeks. The Connect-seq method combines the use of conditional neurotropic viruses that cross synapses with transcriptome analysis of single upstream neurons infected with the virus in order to identify the molecular identities in postnatal hypothalamic brain regions.
<<<Submitter states that raw data are not available>>>

first: Muhammad

last: Junaid

first: SuBin

first: EunJeong

last: Lee


title: Microglial senescence contributes to female-biased neuroinflammation in the aging mouse hippocampus: implications for Alzheimer’s disease

status: Public on Aug 18 2023

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Microglia, the brain’s principal immune cells, have been implicated in the pathogenesis of Alzheimer’s disease (AD), a condition shown to affect more females than males. Although sex differences in microglial function and transcriptomic programming have been described across development and in disease models of AD, no studies have comprehensively identified the sex divergences that emerge in the aging mouse hippocampus. Further, existing models of AD generally develop pathology (amyloid plaques and tau tangles) early in life and fail to recapitulate the aged brain environment associated with late-onset AD. Here, we examined and compared the transcriptomic and translatomic sex effects in young and old murine hippocampal microglia. Hippocampal tissue from C57BL6/N and microglial NuTRAP mice of both sexes were collected at young (5-6 month-old [mo]) and old (22-25 mo) ages. Cell sorting and affinity purification techniques were used to isolate the microglial transcriptome and translatome for RNA-sequencing and differential expression analyses. Flow cytometry, qPCR, and imaging approaches were used to confirm the transcriptomic findings.  There were marginal sex differences identified in the young hippocampal microglia, with most differentially expressed genes (DEGs) restricted to the sex chromosomes. Both sex chromosomally- and autosomally-encoded sex differences emerged with aging. These sex DEGs identified at old age were primarily female-biased and enriched in senescent and disease-associated microglial signatures. Pathway analyses identified upstream regulators induced to a greater extent in females than in males, including inflammatory mediators IFNG, TNF, and IL1B, as well as AD-risk genes TREM2 and APP. These data suggest that female microglia adopt disease-associated and senescent phenotypes in the aging mouse hippocampus, even in the absence of disease pathology, to a greater extent than males. This sexually divergent microglial phenotype may explain the difference in susceptibility and disease progression in the case of AD pathology. Future studies will need to explore sex differences in microglial heterogeneity in response to AD pathology and determine how sex-specific regulators (i.e., sex chromosomal or hormonal) elicit these sex effects.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for transcriptome (CD11b-MACS) and translatome (Cx3cr1-TRAP) from hippocampal microglia isolated from young and old mice

first: Sarah

last: Ocañas

first: Kevin

middle: D

last: Pham

first: Jillian

first: Alex

last: Keck

first: Sunghwan

last: Ko

first: Felix

middle: A

last: Ampadu

first: Hunter

middle: L

last: Porter

first: Victor

last: Ansere

first: Adam

last: Kulpa

first: Collyn

last: Kellogg

first: Adeline

last: Machalinski

first: Ana

last: Chucair-Elliott

first: Willard

last: Freeman


title: Quiescent Müller glia heterogeneity influences regenerative response following photoreceptor ablation in the zebrafish retina

status: Public on Aug 21 2023

city: SHANGHAI

first: Shuguang

last: Yu

address: 320 Yueyang Road

institute: Institute of Neuroscience, Chinese Academy of Sciences

summary: Loss of neurons in the neural retina is a leading cause of vision loss. Retinal regeneration in zebrafish is attributed to Müller glia, which are activated, adopt a stem cell-like state, proliferate, and generate new neurons. Despite the same endogenous Müller glia being present in all vertebrates including humans, Müller glia activation in mammals leads to glial scarring instead of neurogenesis. Therefore, understanding Müller glia cellular states and molecular processes during zebrafish regeneration may allow us to improve mammalian regeneration. Since only a subset of Müller glia activate following neuron loss, we asked whether a specialised subset of Müller glia might be genetically primed for activation. Single-cell RNA sequencing (sc-RNAseq) from integrated zebrafish Müller glia samples reveals heterogeneity of gene expression across the quiescent Müller glia pool with 4 main clusters emerging, two of which are genetically similar. Labelling for key differentially expressed markers identified that these main clusters correlated with glia spatially distributed across dorsal, central and ventral retina. Using a genetically driven, chemically induced nitroreductase approach, three distinct photoreceptor types were ablated: the long (Lws2), short wavelength-sensitive (Sws2) and rod (Xops) photoreceptors, which also differ in their abundance. As expected, histological analysis of the three injuries and sc-RNAseq data for the two cone photoreceptor ablations identified common genetic program involved in the transition of Müller glia quiescence to activation, and differential responses to injury related to either injury extent or subtype of photoreceptor targeted. Interestingly, despite differences in the distributed across the retina, biased activation of Müller glia was observed in dorsal and central regions. Gene ontology analysis revealed that these injury-responsive dorsal and central Müller glia express genes related to dorsal/ventral pattern formation, growth factor activity, and regulation of developmental process. Müller glia upregulated genes related to homeostasis as well as certain AP-1 and injury-responsive transcription factors, followed by expression of genes involved in cell cycle, chromatin remodeling, and microtubule organisation. Prior to cell cycle entry, Müller glia show a transient upregulation of genes involved in gliogenesis, and Notch signalling. These findings enhance our understanding of heterogeneous states of quiescent Müller glia, and how these differences relate to activation and regeneration potential following neural ablation. A comparison of the distinct quiescent Müller glia with glia states in mammals will reveal key molecular pathways that could be targeted for improved mammalian neural regeneration.

overall_design: Zebrafish lines Tg(her4.1:dRFP/gfap:GFP) for the uninjured control dataset,  Tg(her4.1:dRFP/gfap:GFP/lws2:nfsb-mCherry) for red cone ablation, and Tg(her4.1:dRFP/gfap:GFP/sws2:nfsb-mCherry) for blue cone ablation were used in this study. Zebrafish larvae at 6 days post-fertilisation (dpf) were swum in a 10 mM solution of metronidazole for 48 hours, to specifically eliminate the relevant subtype of cone photoreceptor. At 8 dpf, fish were rinsed in fresh system water under standard housing conditions. At 9 dpf (3 days post-injury; dpi), fish were humanely killed. The single-cell suspensions of 9 dpf zebrafish were prepared by following a published protocol (Lopez-Ramirez et al., 2016). Retinae were dissected and digested in 350 ml papain solution at 37°C for 15 minutes. The papain solution was prepared as follows: 100 ml papain (Worthington, LS003126), 100ul of 1% DNAse (Sigma, DN25), and 200 ml of 12mg/ml L-cysteine (Sigma, C6852) were added to a 5 ml DMEM/F12 (Invitrogen, 11330032). During digestion, retinal tissue was mixed by pipetting up and down 4 x 10 times. Following digestion, 1400 ml of washing buffer was added, containing 65 ml of 45% glucose (Invitrogen, 04196545 SB), 50ul of 1M HEPES (Sigma, H4034), and 500 ml FBS (Gibco, 10270106) in 9.385ml of 1x DPBS (Invitrogen, 14190-144). All solutions were filtered through a 0.22 mm filter (Millipore) and stored at 4°C prior to use.

first: Aaron

last: Krylov

first: Axel

last: Newton

first: Jie

last: He

first: Patricia

last: Jusuf


title: A cell state specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma

status: Public on Aug 16 2023

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Glioma cells hijack developmental transcriptional programs to control cell state. During neural development, lineage trajectories rely on specialized metabolic pathways. However, the link between tumor cell state and metabolic programs is poorly understood in glioma. Here we uncover a glioma cell state-specific metabolic liability that can be leveraged therapeutically. To model the diversity of glioma cell states, we generated genetically-engineered murine gliomas, induced by deletion of p53 alone (p53) or with constitutively active Notch signaling (N1IC), a pathway critical in controlling CNS cell fate. N1IC tumors harbored quiescent astrocyte-like transformed cell states while p53 tumors were comprised of proliferating progenitor-like cell states. N1IC cells exhibit distinct metabolic alterations, with mitochondrial uncoupling and increased ROS production rendering them more sensitive to inhibition of the lipid hydroperoxidase GPX4 and induction of ferroptosis. Importantly, treating patient-derived organotypic slices with a GPX4 inhibitor induced selective depletion of quiescent AC-like glioma cell populations with similar metabolic profiles.

overall_design: Mouse brain tumors and treated patient-derived tissue slices were dissociated for scRNA-seq analysis

first: Wenting

last: Zhao

first: Matei

last: Banu

first: Athanassios

last: Dovas

first: Michael

middle: G

last: Argenziano

first: Zhouzerui

last: Liu

last: Canoll


title: Short-term depletion of nicotinic acetylcholine receptor subunits in Drosophila enterocytes

first: Nadja

last: Katheder

summary: Bulk RNAseq from whole Drosophila melanogaster guts expressing either mCherry-RNAi (control) or RNAi against nicotinic acetylcholine receptor subunits β1 and β3 (nAchRβ1 and nAchRβ3)  under control of a enterocyte-specific driver to assess their role in barrier function.

overall_design: NP1::Gal4, tubGa80ts was used as a driver to induce mCherry (Bloomington line BL 35785), nAchRβ1(VDRC line v33825, pruned) or AchRβ3 (VDRC line v42742, pruned), knockdown by RNAi in enterocytes. Knockdown was induced for 3 days by shifting adult mated female flies (5 days old) to the permissive temperature (29ºC). 4 replicates were included for each genotype, consisting of 25 dissected whole midguts guts each (crop, malpighian tubules and hindgut were removed).

first: Luz

last: Orozco

first: David

last: Garfield

first: Yuxin

last: Liang

first: Heinrich

last: Jasper


title: Changes in chromatin accessibility in male mouse liver induced by naturally occurring endogenous pulses of plasma growth hormone (GH)-activated STAT5

city: Boston

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Sequencing files provided here are mouse liver DNase-seq for male mouse livers collected at either a peak or trough of GH/STAT5 activity. This is part of a larger study that includes DNase-seq in mouse liver from hypophysectomized males, females, and hypox-male mice given a single dose of GH. DNase hypersensitivity site (DHS) analysis of these livers established that the  naturally occurring, endogenous male rhythm of plasma GH pulse-stimulated liver STAT5 activation induces dynamic, repeated cycles of chromatin opening and closing at several thousand liver DHS and comprises a novel mechanism conferring male bias to liver chromatin accessibility.

overall_design: DNase-seq of individual male mouse livers obtained from mice euthanized either at a peak or at a trough of STAT5 DNA-binding activity ('STAT5-High' and STAT5-low', respectively), as determined by EMSA analysis. DNase-seq libraries for liver samples G74A_M1 and G74A_M2 differ from all of the other STAT5_High samples, and thus are marked 'outlier', insofar as their STAT5 DNA-binding (EMSA) activity is indicative of a STAT5-high liver, but their DNase-seq profiles were more similar to those of STAT5-low activity livers. In contrast, DNase-seq library for liver sample G92_M5 showed STAT5 DNA-binding (EMSA) activity indicative of a STAT5-low liver, but its DNase-seq profile was more similar to that of STAT5-high activity livers.

first: Andy

last: Rampersaud

first: Jeannette

last: Connerney

middle: J


title: Changes in chromatin accessibility in mouse liver following a pulse of GH-activated liver STAT5 activity

summary: This SuperSeries is composed of the SubSeries listed below. These files are part of a larger study where we establish that pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is a novel mechanism for establishing widespread sex differences in chromatin accessibility and transcription factor binding, which are closely linked to sex-biased gene expression and the sexual dimorphism of liver function.


title: Joint epigenome profiling reveals cell-type-specific gene regulatory programs in human cortical organoids

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

summary: Gene expression is regulated by multiple epigenetic mechanisms, which are coordinated in development and disease. However, current multiomic methods are frequently limited to one or two modalities at a time, making it challenging to obtain a comprehensive gene regulatory signature. Here, we describe a novel approach, 3DRAM-seq, which simultaneously interrogates spatial genome organization, chromatin accessibility, DNA methylation genome-wide and at high resolution. We combine 3DRAM-seq with immunoFACS and RNA-seq in cortical organoids to map the cell-type-specific regulatory landscape of human neural development across multiple epigenetic layers. Finally, we apply a massively parallel reporter assay (MPRA) to profile cell-type-specific enhancer activity in organoids and functionally assess the role of key transcription factors for human enhancer activation and function. More broadly, 3DRAM-seq can be used to profile the multimodal epigenetic landscape in rare cell types and different tissues.

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design: Simultaneous measurement of gene expression, DNA accessibility, DNA methylation and 3D genome architecture using 3DRAM-seq in mouse embryonic stem cells (mESC) and sorted cell populations, namely radial glia cells (RGC) and intermediate progenitor cells (IPC), from human cortical organoids. Additionally, massive parallel reporter assay  in NSC, IPC and PAX6/SOX2/EOMES triple negative cell population isolated from electroporated human cortical organoids.

first: Florian

last: Noack

first: Silvia

last: Vangelisti

first: Nora

last: Ditzer

first: Faye

last: Chong

first: Mareike

last: Albert


title: Gene expression repertoire of the human fetal gut and its effect due to HSCR associated polymorphisms

first: Sumantra

last: Chatterjee

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Grossman School of Medicine

summary: This is a gene expression study of human fetal gut at Carnegie stage (CS) 14 and CS22 classsfied by their HSCR associated enhancer haplotypes

overall_design: Frozen human fetal gut tissue were obtained from Human Biology Resource(HDBR) in the UK. RNA was extracted and sequenced at a depth of 50 million

first: Aravinda

last: Chakravarti


title: Single-Cell Transcriptome Analysis of Acute Myeloid  Leukemia Cells Using Methanol Fixation and Cryopreservation

status: Public on Aug 17 2023

city: MARSEILLE

first: MADACI

last: LAMIA

address: Parc Scientifique de Luminy case 928 163, avenue de Luminy

institute: INSERM/TAGC

summary: Introduction: The application of single-cell RNA sequencing has greatly improved our under-standing of various cellular and molecular mechanisms involved in physiological and pathophysi-ological processes. However, obtaining living cells for this technique can be difficult under certain conditions. To solve this problem, the methanol fixation method appeared as a promising alternative for routine clinical use. Materials and Methods: In this study, we selected two AML samples that had been fixed in methanol for 12–18 months. Once the cells were rehydrated, these samples were subjected to single-cell RNA sequencing. We then compared the results obtained from these samples with those obtained from the same samples cryopreserved in DMSO. Results: We used a previously validated methanol fixation protocol to perform scRNA-seq on DMSO cryopreserved cells and cells fixed in methanol for more than one year. Preliminary results show that methanol fixation induces some genetic and transcriptional modification compared with DMSO cryopreservation but remains a valuable method for single-cell analysis of primary human leukemia cells. Conclusions: The initial findings from this study highlight certain resemblances in methanol fixation over a 12-month period and cryopreservation with DMSO, along with associated transcriptional level modifications. However, we observed genetic degradation in the fixation condition when extending beyond one year. Despite certain study limitations, it is evident that short-term methanol fixation can be effec-tively used for leukemia blast samples. Its ease of implementation holds the potential to simplify the integration of this technique into routine clinical practice.

overall_design: PBMC (Peripheral Blood Mononuclear Cells) were obtained from the peripheral blood of samples UPN73 and UPN78. After centrifugation to separate them from plasma and other peripheral blood components, a ficoll-Hystopaque density gradient centrifugation method was used. The aim was to conduct a comparative study on the effect of methanol fixation of PBMC from patients with acute myeloid leukemia (AML) versus DMSO cryopreservation. This study was carried out using single cell RNA-seq technology. To carry out this study, we fixed the UPN73 and UPN78 samples in methanol for a period of 12 and 18 months respectively. At the same time, we also cryopreserved the same samples using DMSO before subjecting them to single-cell RNA-seq analysis.

first: Lamia

last: Madaci

first: Charlyne

last: Gard

first: Sébastien

last: Nin

first: Geoffroy

last: Venton

first: Pascal

last: Rihet

first: Denis

last: Puthier

first: Béatrice

last: Loriod

first: Régis

last: Costello

first: Céline

last: Baier


title: TOX induces T cell IL-10 production in a BATF-dependent manner

status: Public on Aug 14 2023

city: West Lafayette

first: D. Alejandro

last: Canaria

state: IN

address: 201 S University St

institute: Purdue University

summary: TOX is a member of the HMG-Box transcription factors and plays important roles in thymic T cell development. Outside of the thymus, however, TOX is also highly expressed by CD8 and CD4 T cells in various states of activation and in settings of cancer and autoimmune disease. In CD4 T cells, TOX has been primarily studied in T follicular helper (TFH) cells where it , along with TOX2 promotes TFH differentiation by regulating key TFH-associated genes and suppressing CD4 cytotoxic T cell differentiation. However, the role of TOX in other Th cell subtypes is less clear. In our study, we show that TOX is expressed in several physiologically-activated Th subtypes and its ectopic expression modestly enhances the in vitro differentiation of  Th2 and Treg cells. TOX overexpression also induced the expression of a small number of genes in unpolarized Th cells involved in cell activation (Pdcd1, PD-1), cellular trafficking (Ccl3, Ccl4, Xcl1) and in suppressing inflammation (Il10) that was conserved in multiple Th subtypes. We additionally show that TOX co-occupies these genes with the transcription factor BATF and that TOX-induced expression of IL-10, but not PD-1, is BATF-dependent. Based on these data, we propose a model where TOX regulates Th cell chemotactic genes involved in facilitating dendritic cell-T cell interactions and aids in the resolution or prevention of inflammation through the production of IL-10.

overall_design: We transduced naïve CD4 T cells that had been activated for 2 days with EV-RV or TOX-RV under non-polarizing (i.e. anti-CD3, anti-CD28 and IL-2 only) conditions as we initially wanted to explore non-Th lineage specific effects. After 5 days of culture, we re-stimulated the cells using anti-CD3 and anti-CD28 as previously reported, sorted the GFP+ cells and performed RNA-seq on RNAs isolated from these cells

first: D

first: Bingyu

last: Yan

first: Mengbo

last: Wang

first: Alejandra

last: Rodriguez

first: Charlotte

last: Campbell

first: Luopin

first: Majid

last: Kazemian

first: Matthew

middle: R

last: Olson


title: Effect of SREBP2 silencing on gene expression of THP-1 monocytes under hypoxic condition

city: Tokyo

first: Ryuichi

last: Nakahara

address: 4-6-1 Komaba, Meguro

department: the Research Center of Advanced Science and Technology

country: Japan

institute: the University of Tokyo

summary: Monocyte infiltrate hypoxic tumor center to initiate pro-tumorigenic immune response and angiogenesis, however the detailed mechanism and responsible metabolic pathway was not investigated. Here we report that monocyte macrophage lineage cells are uniquely responsive to hypoxia compared to cancer cells and fibroblasts, upregulating cholesterol biosynthesis through SREBP2 regulation. Disruption of SREBP2 offsets upregulation of hypoxia-induced cholesterol biosynthesis gene expression. In addition, hypoxia-induced SREBP2 activation is lineage-dependent, and this activation is lost when monocyte matures to macrophage, suggesting a metabolic switch during differentiation. Finally, inhibiting cholesterol synthesis using statin reduces tumor burden and infiltration of pro-tumor immune cells into tumor center. In summary, SREBP2 regulated hypoxic response in monocytes are essential for tumor growth and is a potent drug target for novel therapeutic strategies.

overall_design: To investigate if SREBP2 is the regulator for hypoxic response in monocyte, we transfected THP-1 cells with siRNA targeting SREBP2. After 48 hours of transfection, THP-1 cells were cultured in either control or hypoxic condition for 24 hours before extraction of total RNA for RNA-seq analysis. We then performed gene expression profiling analysis and pathway analysis using RNA-seq data.

first: Haruka

last: Hirose

first: Tsuyoshi

last: Osawa

first: Teppei

last: Shimamura


title: Increased RUNX3 expression mediates tumor-promoting ability of human breast cancer-associated fibroblasts

status: Public on Aug 15 2023

first: Takehiro

last: Yasukawa

address: 2-1-1 Hongo, Bunkyo-ku

institute: Juntendo University

summary: Cancer-associated fibroblasts (CAFs) are a major stromal component of human breast cancers and often promote tumor proliferation, progression and malignancy. We previously established an experimental CAF (exp-CAF) cell line equipped with a potent tumor-promoting ability. It was generated through prolonged incubation of immortalized human mammary fibroblasts with human breast cancer cells in a tumor xenograft mouse model. Herein, we found that the exp-CAFs highly express Runt-related transcription factor 3 (RUNX3), while counterpart fibroblasts do not. In breast cancer patients, the proportion of RUNX3-positive stromal fibroblast-like cells tends to be higher in cancerous regions than in non-cancerous regions. These findings suggest an association of RUNX3 with CAF characteristics in human breast cancers. To investigate the functional role of RUNX3 in CAFs, the exp-CAFs with or without shRNA-directed knockdown of RUNX3 were implanted with breast cancer cells subcutaneously in immunodeficient mice. Comparison of the resulting xenograft tumors revealed that tumor growth was significantly attenuated when RUNX3 expression was suppressed in the fibroblasts. Consistently, Ki-67 and CD31 immunohistochemical staining of the tumor sections indicated reduction of cancer cell proliferation and microvessel formation in the tumors formed with the RUNX3-suppressed exp-CAFs. These results suggest that increased RUNX3 expression could contribute to the tumor-promoting ability of CAFs through mediating cancer cell growth and neoangiogenesis in human breast tumors.

overall_design: (1) To compare RNA expression between 522 and 544 cells. (2) To compare RNA expression between 544 cells with shCtrl and shGFP and those with RUNX3-targeting shRNAs (shRX3-4 and -5).

first: Hiroya

last: Okazaki

first: Yang

last: Shi

first: Akira

last: Orimo


title: Fecal microbiota transplantation from young donor mice rejuvenates hematopoietic stem cell in aged recipients by suppressing inflammatory signals while modulating gut microbiota and metabolites

city: Hangzhou

first: Xiangjun

last: Zeng

address: Zhejiang univerisity

institute: Zhejiang univerisity

summary: Hematopoietic stem cell (HSC) aging is accompanied by hematopoietic reconstitution dysfunction, including loss of regenerative and engraftment ability, myeloid differentiation bias and elevated risks of hematopoietic malignancies. Gut microbiota, a key regulator of host health and immunity, has been recently reported to impact hematopoiesis. However, there is currently no empirical evidence elucidating the direct impact of gut microbiome on aging hematopoiesis. To assess these potential effects, we performed fecal microbiota transplantation (FMT) from young mice to aged mice and observed an increment in both the absolute number and the engraftment ability of HSCs. Single cell RNA sequencing depicted overall transcriptional changes of HSCs as well as the bone marrow microenvironment and indicated that gut microbiota from young mice enhanced cell cycle activity of HSCs, attenuated canonical inflammatory signals and mitigated inflammation-associated phenotypes in aging hematopoiesis. Integrated microbiome-metabolome analysis uncovered that FMT reshaped gut microbiota construction and metabolite landscape, while the administration of Lachnospiraceae and tryptophan-associated metabolites promoted the recovery of hematopoiesis and rejuvenated aged HSCs. Together, our results highlighted the paramount importance of the gut microbiota in HSC aging and provided a strong rationale to limit hematopoietic exhaustion and treat hematologic disorders.

overall_design: Two samples from murine bone marrow cells by Single cell RNA sequencing: FMT-young and FMT-aged.

first: Xiaoqing

last: Li

first: Xia

first: Cong

last: Wei

first: Pengxu

last: Qian

first: He

last: Huang


title: Changes in chromatin accessibility due to hypophysectomy (hypox) and a single exogenous pulse of GH/STAT5 in mouse liver

first: David

last: Waxman

summary: Sequencing files provided here are mouse liver DNase-seq to identify DNase hypersensitive sites (DHS) in livers from intact and hypox female, hypox male, and hypox male mice given a single injection of GH and then euthanized 30, 90, or 240 minutes later. This is part of a larger study that includes DNase-seq in mouse liver from intact males determined to be STAT5-high or STAT5-low based on an endogenous pulse of GH/STAT5. This allows us to identify GH pulse-responsive DHS and better understand male-biased DHS regulation of sex-biased genes. Overall, our findings establish that pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is a novel mechanism for establishing widespread sex differences in chromatin accessibility and transcription factor binding, which are closely linked to sex-biased gene expression and the sexual dimorphism of liver function.

overall_design: DNase-seq analysis of mouse liver.

first: Andy

last: Rampersaud

first: Jeannette

last: Connerney


title: Sub-lethal apoptotic stress enables mtDNA release during senescence and drives the SASP

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary: Senescent cells drive age-related tissue dysfunction partially via the induction of a chronic senescence-associated secretory phenotype (SASP). Mitochondria are major regulators of the SASP; however, the underlying mechanisms have not been elucidated. Mitochondria also control apoptosis, a cell fate generally perceived as distinct from cellular senescence, which is apoptosis resistant. Here, we show that mitochondrial outer membrane permeability (MOMP) occurring in a small subset of mitochondria is a feature of cellular senescence. This process, called minority MOMP (miMOMP), depends on the formation of BAX and BAK macropores and results in release of mitochondrial DNA (mtDNA) into the cytosol, which in turn activates the cGAS/STING pathway, a major regulator of the SASP. Importantly, we found that inhibition of MOMP in vivo decreases inflammatory markers and improves healthspan parameters in aged mice. Our results propose the novel concept that apoptosis and senescence are regulated by similar mitochondrial-dependent mechanisms, and that sub-lethal mitochondrial apoptotic stress is a major driver of the SASP. We also provide proof-of-concept that inhibition of miMOMP may be a new therapeutic avenue to improve healthspan.

overall_design: mRNA profiles of senescent fibroblasts upon mitochondria clearance and following the re-introduction of mitochondrial DNA. We also examined the effects of Bax and Bak knockout on mRNA profile of proliferating and senescent fibroblasts.

first: Stella

last: Victorelli

first: Helene

last: Martini

first: Maria

last: Vizioli


title: CaBlCaXi: MSL2 is an allelic dosage sensor in mammals

status: Public on Aug 10 2023

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Allele-specific gene expression have been observed in genomic imprinting, X chromosome inactivation, allelic exclusion of immunoglobulin loci and non-canonical random monoallelic expression. Here we show that MSL2 can regulate allele specific gene expression and we elucidate its mechanism of action. MSL2 is known to regulate gene dosage up to two fold in drosophila and mammals. In addition to its canonical role as a milder modulator, we found that the loss of MSL2 switches off gene expression completely in an allele specific way and results in biallelic to monoallelic gene expression, which will be ignored as classical down regulated genes without applying the mouse hybrid F1 system. It indicates that MSL2 can activate the expression of the allele which is otherwise inactive intrinsically. We further found this is achieved by the interplay between MSL and KANSL complex. MSL2 acts as a methylation-insensitive factor, which can prevent DNA methylation of the inactive allele, thus facilitating occupancy of methylation-sensitive factor KANSL3 and activating the gene expression. The novel mechanism of MSL2 provides a safeguarding system to warrant biallelic gene expression of intrinsically monoallelic expressed genes including X-inactivated and imprinting genes. These genes are further discovered as sex bias genes such as X-inactivation escaped genes (escapees) are expressed higher in females. Furthermore, the biallelic expression of MSL2 regulated escapees may protect females from single loss of function mutation and contribute to male severer or predominance neurodevelopmental diseases.

overall_design: Allele specific differential analysis of various sequencing data from ESCs and NPCs of female and male hybrid clones.

first: Yidan

last: Sun

first: Raed

last: Hmad

first: Meike

last: Wiese


title: Noncanonical MAVS signaling restrains dendritic cell-driven antitumor immunity by inhibiting IL-12

city: shanghai

first: Lingling

last: Wu

address: 227 Chongqing South Road, Huangpu District, Shanghai

department: School of Medicine

institute: Shanghai Jiaotong University

summary: MAVS-mediated cytosolic RNA sensing plays a central role in tumor immunogenicity. However, the effects of host MAVS signaling on antitumor immunity remains uncertain. Here, we demonstrate that host MAVS pathway drives accelerated tumor growth and impairs antitumor immunity, while MAVS knockout in dendritic cells (DCs) promotes tumor-reactive CD8+ T cell responses. Specifically, the CD8+ T cell priming capacity is enhanced by lack of functional MAVS in a type I interferon-independent, but IL-12-dependent, manner. Mechanistically, loss of RIG-I/MAVS cascade activates non-canonical NF-κB pathway and in turn induces IL-12 production by DCs, resulting in CD8+ T cell: DC crosstalk licensed by IFN-γ and IL-12. Moreover, ablation of host MAVS sensitizes tumors to immunotherapy and attenuates radiation resistance, thereby facilitating the maintenance of effector CD8+ T cells. These findings identify that host MAVS pathway acts as an immune checkpoint of DC-driven antitumor immunity, indicating the development of DC-based immunotherapies through MAVS signaling antagonism.

overall_design: To investigate the role of  the effects of host MAVS signaling on antitumor immunity, MC38 tumor cells were inoculated to WT and MAVS KO mice. Ten days after tumors inoculation, tumor infiltrated dendritic cells were isolated.Total RNA from each sample was extracted using Trizol Reagent following standard protocols and mRNA sequencing was performed.

first: Xiaochuan

last: Hong


title: Differential Gene Expression in Monocyte macrophage lineage cells, cancer cells and fibroblasts under control or hypoxic condition

first: Ryuichi

last: Nakahara

summary: DNA Microarray data of THP-1, HeLa and NHDF under control or hypoxic condition

overall_design: Gene expression in THP-1, HeLa and NHDF was measured after 24 hours of treatment under control or hypoxic condition.

first: Tsuyoshi

last: Osawa


title: Difference of gene expression in Malpighian tubules (MTs) betweeen control, "yki3SA" tumor, and "yki3SA+ITP-i" tumor-bearing flies

status: Public on Aug 11 2023

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

summary: To investigate the function of malpighian tubule in tumor-induced host wasting, we established a wasting model in fly by activation of Yki in adult midgut ISCs, in which the host flies present the sysytmeic organ wasting and metabolic abnormalities.

overall_design:
We performed gene expression profiling analysis using data obtained from RNA-seq of Malpighian tubules of control , "yki3SA" tumor, and "yki3SA+ITP-i" tumor-bearing flies .
Comparative species composition and diversity analysis,gene expression profiling analysis of meta-seq data for control and yki3SA tumor-bearing flies.


title: MSL2 is an allelic dosage sensor in mammals

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series

last: Hmadi


title: Expression of PVRL4, a molecular target for cancer treatment, is transcriptionally regulated by FOS family protein [ATAC]

first: Kiyoshi

last: Yamaguchi

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

department: Division of Clinical Genome Research

institute: The University of Tokyo

summary: Nectin-4 or PVRL4 is a promising therapeutic target because its augmented expression has been found in a wide range of human cancers. It is of note that Enfortumab Vedotin, an ADC for PVRL4 is clinically used for the treatment of urothelial bladder cancer. In addition, rMV-SLAMblind, a genetically engineered oncolytic measles virus, can infect cancer cells and induce apoptosis through an interaction with PVRL4. Although the transcripts of PVRL4 are elevated in breast, lung and ovarian cancer, the mechanism(s) of its overexpression has not been uncovered. To clarify the regulatory mechanism(s) of its elevated expression in breast cancer cells, we searched for its regulatory region(s) using ATAC-seq and ChIP-seq data. Using breast cancer cells, we identified an enhancer region. Additional analyses disclosed that FOS interacted with the enhancer region, and the alterations of the FOS-binding motifs decreased the reporter activity. Consistent with these data, exogenous expression of FOS enhanced not only the reporter activity but also PVRL4 expression in breast cancer cells. Furthermore, RNA-seq analysis using breast cancer cells treated with PVRL4-siRNA revealed its possible involvement in cytokine response and immune systems. These data suggest that FOS is involved, at least partly, in the regulation of PVRL4 expression in breast cancer cells, and that elevated PVRL4 expression may regulate response of the cancer cells to cytokines and immune systems.

overall_design: ATAC-seq was used to profile open chromatin in SKBR3, T47D, HCT116, and RKO cells.

first: Tomoyuki

last: Nanamiya

first: Kiyoko

last: Takane

first: Yoichi

last: Furukawa


title: Urinary bladder in F344 rats: Control vs dimethylarsinic acid

status: Public on Aug 09 2023

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

institute: Osaka Metropolitan University Graduate School of Medicine

summary: The gene expression profling between Control and dimethylarsinic acid for 4 weeks in urinary bladder epithelium of F344 male rats.

overall_design: Male 6-week-old F344 rats were treated with 0 (Control) or 200 ppm dimethylarsinic acid (DMA) in drinking water for 4 weeks. After treatment, rats were sacrificed, and removed urinary bladder. Control and DMA treatment: 7 control and 7 DMA-treated male rats. Mixed 7 samples from each group for each array.

first: Min

last: Gi


title: Epigenetic regulation during cancer transitions across 11 tumour types.

city: St Louis

first: Alla

last: Karpova

state: MO

address: 700 Rosedale avenue Campus Box 1000

institute: Washington University St Louis

summary: Chromatin accessibility plays an essential role in regulating gene expression and cellular identity, and its alterations have been implicated in driving oncogenic processes such as cancer initiation, progression, and metastasis1–4. While genetic aspects of cancer transitions have been explored, the role of epigenetic drivers remains less understood. To investigate the influence of chromatin architecture on cancer transitions, we generated an atlas of single-nucleus chromatin accessibility data (snATAC-seq) from 225 samples and matched single-cell/single-nucleus RNA expression (sc/snRNA-seq) from 206 samples across 11 cancer types. Analyzing over 1 million cells, we identified pan-cancer epigenetic drivers and transcriptional programs associated with transitions (regulatory regions of ABCC1, VEGFA, and GATA6, KLF6 and FOX-family TFs), as well as cancer type specific programs (regulatory regions of FGF19, ASAP2, EN1 and PBX3 TF). Differentially-accessible chromatin regions pinpointed genes and enriched pathways associated with major cancer transitions. For example, TP53, hypoxia, and TNFA signaling were linked to cancer initiation, while estrogen response, epithelial-mesenchymal transition (EMT), myogenesis, and apical junction were linked to metastatic transition. We also observed correlations between regulatory regions and genetic drivers across cancer types, suggesting their cooperation in cancer transition programs. This atlas furnishes a valuable resource for further investigation of the role of epigenetic programs in cancer initiation, progression, and metastasis.

overall_design:
Data includes snATAC-seq and snRNA-seq for 24 clear cell renal carcinoma samples, 4 normal kidney samples, 18 glioblastoma samples from the Clinical Proteomic Tumor Analysis Consortium (CPTAC)

***Will submit raw data files to either GDC or CDS***

first: Li

last: Ding


title: Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [bulk RNA-Seq]

city: Syracuse

first: Samantha

middle: Jane

last: England

address: 107 College Place

department: Biology

institute: Syracuse University

summary: Background: V0v spinal interneurons are highly-conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and scRNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild-type siblings.  Results: Our data reveal two molecularly-distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly-distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.

overall_design: Ten samples were analysed in total, all at 27 hours post fertilization (hpf). Five biological repicates were performed for V1 and dI2 spinal interneurons from uninjected wild-type control embryos in the Tg(hmx CNEIII:cfos:GAL4-VP16,UAS:EGFP)SU41 background. Five biological replicates were performed for V1 and dI2 spinal interneurons from hmx2;hmx3a double knock-down (DKD) morphant embryos in the Tg(hmx CNEIII:cfos:Gal4-VP16,UAS:EGFP)SU41 background.

first: Amber

last: Woodard

first: Amra

last: Mujcic

first: Angelica

last: Kowalchuk

first: Sarah

last: de Jager

first: William

middle: C

last: Hilinski

first: José

last: Juárez-Morales

first: Matthew

middle: E

last: Smith

first: Ginny

last: Grieb

first: Santanu

last: Banerjee

first: Katharine

last: Lewis


title: Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids

status: Public on Aug 07 2023

city: Raleigh

first: Thomas

last: Rudibaugh

state: North Carolina

address: 840 Main Campus Dr, Partners II Room 3700

institute: North Carolina State University


title: Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids [Rudibaugh2022]

summary: Dopamine signaling in the adult ventral forebrain regulates behavior, stress response, and memory formation and in neurodevelopment regulates neural differentiation and cell migration. Excessive dopamine levels including due to cocaine use both in utero and in adults could lead to long-term adverse consequences. The mechanisms underlying both homeostatic and pathological changes remain unclear, partly due to the diverse cellular responses elicited by dopamine and the reliance on animal models that exhibit species-specific differences in dopamine signaling. To address these limitations, 3-D cerebral organoids have emerged as human-derived models, recapitulating salient features of human cell signaling and neurodevelopment. Organoids have demonstrated responsiveness to external stimuli, including substances of abuse, making them valuable investigative models. In this study we utilize the Xiang-Tanaka ventral forebrain organoid model and characterize their response to acute and chronic dopamine or cocaine exposure. The findings revealed a robust immune response, novel response pathways, and a potential critical role for reactive oxygen species (ROS) in the developing ventral forebrain. These results highlight the potential of cerebral organoids as in vitro human models for studying complex biological processes in the brain.

overall_design:
To investigate the effects of acute and chronic dopamine exposure on ventral forebrain cerebral organoids, we grew organoids to 83 days before exposing them to acute or chronic doses of dopamine.
We then flash froze our samples, before the organoids were fixed and total RNA was removed. Each condition had three replicates and we used two different cell lines. The samples transcriptomes were compared against vehicle controls.

first: Albert

last: Keung


title: BL6Mousei: MSL2 is an allelic dosage sensor in mammals

first: Asifa

last: Akhtar

first: Yidan

last: Sun

first: Raed

last: Hmad

first: Meike

last: Wiese


title: H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana

city: Kannapolis

first: Tzung-Fu

last: Hsieh

state: NC

address: Tzung-Fu Hsieh, 600 Laureate Way

department: Plant and Microbial Biology

summary: H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction. H2A.X is encoded by two genes in Arabidopsis genome, HTA3 and HTA5. We generated h2a.x double mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However, h2a.x mutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under the H2A.X promoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation in h2a.x developing seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide in h2a.x mutant seeds. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling. h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA. Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Alternatively, H2A.X may be involved in recruiting methyltransferases to those sites. Overall, our data show that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.

overall_design: Whole genome sequencing using h2ax mutant, corresponding wild-type sibling, and h2ax female (Col-0) crossed with wild-type pollen (Ler) embryo, endosperm, and seedling were performed to examine the effect of H2AX loss on endosperm and embryo methylation profiles.

first: Jennifer

middle: M

last: Frost

first: Robert

last: Fischer

first: Yeonhee

last: Choi


title: Single nucleus ATAC-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

summary: This dataset contains single nucleus Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat nucleus accumbens tissue. Rats received repeated cocaine injections (20mg/kg, intraperitoneal injection), or saline injections as a control. Single-nucleus ATAC-seq was carried out with FACS-sorted nuclei using the 10X Genomics Chromium single cell sequencing platform using the Chromium Next GEM Single Cell ATAC Kit v2.

overall_design: This experiment contains 4 biological samples. Samples were adult rat nucelus accumbens brain tissue isolated from rats 1hr after the final (7th) daily treatment with either saline or cocaine. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding followed by preparation of snATAC-seq libraries using the Chromium Next GEM Single Cell ATAC Kit v2. Libraries underwent paired-end sequencing on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2, R3). Additional index files are also provided for each sample and each lane (I1).

last: Phillips

first: Lara

last: Ianov


title: RNA-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer" [RNA-seq]

summary: This dataset contains RNA-seq results from rat embryonic striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 4 h.

overall_design: This experiment contains 8 biological samples, each of which underwent RNA-seq on an Illumina NextSeq500 instrument. Samples were treated with neurobasal media (vehicle; samples V1, V2, V3, V4), or 10mM KCl (samples K1, K2, K3, K4) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID. Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.


title: RNA-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

summary: This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 4 h.

overall_design: This experiment contains 18 biological samples, each of which underwent ATAC-seq on an Illumina NextSeq500 instrument. Data are from two experiments. In the first experiment, samples were treated with neurobasal media (vehicle; samples V1, V3, V4), or 10mM KCl (samples K2, K3, K4) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID. In the second experiment, samples were treated with anisomycin (40µM) or DMSO control 30 minutes prior to depolarization with 10mM KCl. "DV" samples received DMSO followed by vehicle. "DK" sample received DMSO followed by 10mM KCl. "AK" samples received 40µM anisomycin followed by 10mM KCl.  Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.


title: RNASeq samples of OSKM reprogrammable MEFs treated with or without vitamin B12

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Examination of the impact of vitamin B12 supplementation during in vitro OSKM reprogramming

overall_design: Three replicates were generated from the following conditions: MEF, doxy-OSKM, MEF + B12 and doxy-OSKM + B12. Each sample sequenced in six different flowcells to obtain sufficient coveragae.

first: Marta

last: Kovatcheva

first: Nacho

last: Pons


title: ChIPSeq of H3k36me3 samples of OSKM reprogramming mouse embryonic fibroblasts treated with B12

summary: Examination of the impact of vitamin B12 supplementation during in vitro OSKM reprogramming on H3K36me3

overall_design: One biolgical replicate was generated from each condition. Libraries were sequenced in two flowcells to achieve sufficient coverage.


title: Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells.

first: Samantha

last: England


title: Urinary bladder in F344 rats: Control vs dimethylarsinic acid-induced tumors

first: Shugo

last: Suzuki

summary: The gene expression profling between non-treated urinary bladder epithelium (Control) and dimethylarsinic acid-induced urinary bladder tumors of F344 male rats.

overall_design: Male 10-week-old F344 rats were treated with 0 (Control) or 200 ppm dimethylarsinic acid (DMA) in drinking water for 2 years. After treatment, rats were sacrificed, and removed urinary bladder. Control and DMA-tumor: 5 control urinary bladder epithelium and 6 DMA-induced urinary bladder carcinomas of male rats. Mixed 5 or 6 samples from conrol or DMA-induced tumor group, respectively, for each array.

first: Min

last: Gi


title: Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids [Rudibaugh2023]

first: Thomas

last: Rudibaugh

overall_design:
To investigate the role of reactive oxygen species in cerebral organoids transcriptomic response to chronic dopamine or cocaine exposure, we grew organoids to 83 days before exposing them to chronic doses of dopamine or cocaine with or without an ROS inhibitor.
We then flash froze our samples, before the organoids were fixed and total RNA was removed. Each condition had three replicates and we used two different cell lines. The samples transcriptomes were compared against vehicle controls with or without an ROS inhibitor.

first: Albert

last: Keung


title: Rapid transcriptional changes of ROS1 fusion positive cells in response to crizotinib treatments

city: Aurora

last: Doebele

state: CO

address: 12801 E. 17th Ave, Building RC1-S, Rm L18-8401A

department: Devision of Medical Oncology

institute: University of Colorado Anschutz Medical Campus

summary: Despite the initial benefit of tyrosine kinase inhibitors targeting ROS1 fusion kinase in non-small cell lung cancer, the complete responses are rare and resistance ultimately develops from residual tumor cells. Although several acquired resistance mechanisms after disease progression have been reported, the adaptative resistance mechanism that contributes to residual diseases before the onset of acquired resistance is less clear. Cellular adaption through the signaling rewiring under primary oncogene inhibition is considered a major mechanism contributing to residual disease. To explore the rapid signaling reprogramming under acute ROS1 inhibition, we treated a panel of ROS1 fusion-positive cells, mostly derived in our lab, with crizotinib for 24 hours and profiled transcriptional changes by RNA-seq. Understanding the molecular mechanism that supports residual disease could help us better target and eliminate drug-tolerant cells, thus improving the responses to ROS1 targeted therapies.

overall_design: RNA was extracted from cells treated with DMSO or crizotinib for 24 hours in three biological replicates and subjected to RNA-seq.

first: Logan

last: Tyler

last: Chen

first: Anh

last: Le


title: Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA-Seq]

overall_design: Two samples were analysed in total, both at 48 hours post fertilization (hpf). These two samples represent two biological replicates of all V0v spinal interneurons (isolated from embryos from an incross of heterozygous evx1i232/+;evx2sa140/+;Tg(evx1:EGFP)SU2 parents.

first: Amber

last: Woodard

first: Amra

last: Mujcic

first: Angelica

last: Kowalchuk

first: Sarah

last: de Jager

first: William

last: Hilinski

first: José

last: Juárez-Morales

first: Matthew

last: Smith

first: Ginny

last: Grieb

first: Santanu

last: Banerjee

first: Katharine

last: Lewis


title: Organotypic 3D cell-architecture architecture impacts the expression pattern of miRNAs-network in breast cancer SKBR3 cells  [miRNA-seq]

status: Public on Aug 04 2023

city: Chihuahua

first: Mercedes

last: Bermúdez

state: Chihuahua

address: Chihuahua

department: Dentistry

country: Mexico

institute: Universidad autónoma de Chihuahua

type: Non-coding RNA profiling by high throughput sequencing

summary: The transcriptomic assays showed that cell growth in organoids significantly affected (all p < 0.01) the gene expression patterns of both, miRNAs and mRNAs, finding 20 upregulated and 19 downregulated DE-microRNAs, as well as 49 upregulated and 123 downregulated DE-mRNAs. In silico analysis showed that a subset of 11 upregulated DE-microRNAs target 70 downregulated DE-mRNAs. These genes are involved in 150 gene ontology (GO) biological processes such as regulation of cell morphogenesis, regulation of cell shape, regulation of canonical Wnt signaling pathway, morphogenesis of epithelium, regulation of cytoskeleton organization, as well as in the MAPK and AGE-RAGE signaling KEGG-pathways. Interestingly, hsa-mir-122-5p (Fold Change (FC)=15.4), hsa-mir-369-3p (FC=11.4), and hsa-mir-10b-5p (FC=20.1) regulated up to the 81 % of the 70 downregulated DE-mRNAs

overall_design: We evaluated the effect of 3D cell organization on the expression pattern of miRNAs (by Small-RNAseq) and mRNAs (by microarrays) in the breast cancer SKBR3 cell line and analyzed the biological processes and signaling pathways regulated by the differentially expressed protein-coding genes (DE-mRNAs) and miRNAs (DE-microRNAs) found in the organoids.

first: Maria

last: Gastelum

first: Maribel

last: Aguilar-Medina

first: Rosalio

last: Ramos-Payan

last: Bermudez


title: Consequences of depleting core RNAi factors on miRNA profiles

status: Public on Aug 08 2023

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Rd

department: Pharmacology

institute: UT Southwestern Medical Center

summary: In this study, we used CRISPR/Cas9 to deplete HCT116 cells of DROSHA, AGO1, AGO2, AGO1/2, AGO1/2/3, TNRC6A/B, TNRC6/B + siTNRC6C,  TNRC6A/B-/- + siGL2, WT, WT + siGL2, WT + siTNRC6C. Then, we used these KO and siRNA KD cell lines to measure resulting miRNA profiles.

overall_design: Comparative gene expression profiling analysis of small-RNA-seq data for HCT116 cells and its KO derivatives (DROSHA-/-, AGO1-/-, AGO2-/-, AGO1/2-/-, AGO1/2/3-/-, TNRC6A/B-/-, TNRC6/B-/- + siTNRC6C, TNRC6A/B-/- + siGL2, WT, WT + siGL2, WT + siTNRC6C).

first: Krystal

last: Johnson

first: Samantha

first: Jing

last: Liu

first: Yongjun

last: Chu


title: Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer

status: Public on Aug 02 2023

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

overall_design: Refer to individual Series


title: Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer [ATAC]

summary: To investigate the EBV genome after Decitabine treatment by reduced representation bisulfite sequencing, ATAC-seq, and RNA-seq

overall_design: Two EBV positive gastric cancer cell lines were treated with decitabine for 1 and 3 days and ATAC-seq was performed

first: Italo

last: Tempera

first: Paul

last: Leiberman


title: Compact engineered human mechanosensitive transactivation modules enable potent and versatile synthetic transcriptional control

status: Public on Jul 31 2023

city: Houston

first: Isaac

last: Hilton

address: 6500 Main Street

department: Bioengineering

institute: Rice University

summary: Engineered transactivation domains (TADs) combined with programmable DNA binding platforms have revolutionized synthetic transcriptional control. Despite recent progress in programmable CRISPR/Cas-based transactivation (CRISPRa) technologies, the TADs used in these systems often contain poorly tolerated elements and/or are prohibitively large for many applications. Here we defined and optimized minimal TADs built from human mechanosensitive transcription factors (MTFs). We used these components to construct potent and compact multipartite transactivation modules (MSN, NMS, and eN3×9) and to build the CRISPR-dCas9 recruited enhanced activation module (CRISPR-DREAM) platform. We found that CRISPR-DREAM was specific, robust across mammalian cell types, and efficiently stimulated transcription from diverse regulatory loci. We also showed that MSN and NMS were portable across Type I, II, and V CRISPR systems, TALEs, and ZF proteins. Further, as proofs of concepts, we used dCas9-NMS to efficiently reprogram human fibroblasts into iPSCs and demonstrated that MTF TADs are efficacious and well tolerated in therapeutically important primary human cell types. Finally, we leveraged the compact and potent features of these engineered TADs to build new dual and all-in-one CRISPRa AAV systems. Altogether, these compact human TADs, fusion modules, and new delivery architectures should be valuable for synthetic transcriptional control in biomedical applications.

overall_design: mRNA sequencing for accessing CRISPR-DREAM specificity in HEK293T cells

first: Barun

last: Mahata