title: Obesity Accelerates Endothelial-to-Mesenchymal Transition in Adipose Tissue of Mice and Humans

status: Public on Sep 19 2023

city: Charlottesville

first: Nicholas

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

summary: Vascular dysfunction and chronic inflammation are characteristics of obesity-induced adipose tissue dysfunction. Proinflammatory cytokines can drive an endothelial-to-mesenchymal transition (EndoMT), where endothelial cells undergo a phenotypic switch to mesenchymal-like cells that are pro-inflammatory and pro-fibrotic. In this study, we sought to determine whether obesity can promote EndoMT in adipose tissue. Mice in which endothelial cells are lineage-traced with eYFP were fed a high-fat/high-sucrose (HF/HS) or Control diet for 13, 26, and 52 weeks, and EndoMT was assessed in adipose tissue depots as percentage of CD45-CD31-Acta2+ mesenchymal-like cells that were eYFP+. EndoMT was also assessed in human adipose endothelial cells through cell culture assays and by the analysis of single cell RNA sequencing datasets obtained from the visceral adipose tissues of obese individuals. Quantification by flow cytometry showed that mice fed a HF/HS diet display a time-dependent increase in EndoMT over Control diet in subcutaneous adipose tissue (+3.0%, +2.6-fold at 13 weeks; +10.6%, +3.2-fold at 26 weeks; +11.8%, +2.9-fold at 52 weeks) and visceral adipose tissue (+5.5%, +2.3-fold at 13 weeks; +20.7%, +4.3-fold at 26 weeks; +25.7%, +4.8-fold at 52 weeks). Transcriptomic analysis revealed that EndoMT cells in visceral adipose tissue have enriched expression of genes associated with inflammatory and TGFb signaling pathways. Human adipose-derived microvascular endothelial cells cultured with TGF-β1, IFN-γ, and TNF-⍺ exhibited a similar upregulation of EndoMT markers and induction of inflammatory response pathways. Analysis of single cell RNA sequencing datasets from visceral adipose tissue of obese patients revealed a nascent EndoMT sub-cluster of endothelial cells with reduced PECAM1 and increased ACTA2 expression, which was also enriched for inflammatory signaling genes and other genes associated with EndoMT. These experimental and clinical findings show that chronic obesity can accelerate EndoMT in adipose tissue. We speculate that EndoMT is a feature of adipose tissue dysfunction that contributes to local inflammation and the systemic metabolic effects of obesity.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNA sequencing was performed on cells isolated from visceral adipose tissue after FACS or cultured human primary adipose-derived microvascular endothelial cells (described below). RNA was purified using the RNeasy MinElute kit (Qiagen, Cat # 74204). Purified RNA was submitted to the Yale Center for genome analysis for quality control analysis, low-input RNA sequencing amplification, PolyA RNA library preparation, and paired-end 100bp sequencing (NovaSeq v2, Illumina). Samples were multiplexed in sequencing runs to average 20M reads per sample. Raw sequencing reads were demultiplexed into sample specific Fastq files, which were analyzed by aligning to reference genomes (mouse mm10 or human hg38) by Kallisto v0.46.226. Differential gene expression analysis was performed with Sleuth v0.30.027. Gene set enrichment analysis was performed with GSEA v4.1 software (Broad Institute).

first: Kenneth

last: Walsh


title: Stepwise emergence of the neuronal gene expression program in early animal evolution

status: Public on Sep 20 2023

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed single-cell transcriptome analysis (using 10x) of four placozoan species (Trichoplax adhaerens, Trichoplax sp. H2, Cladtertia collaboinventa, Hoilungia hongkongensis). Additionally we performed bulk ATAC-seq experiments and anti-H3K4me2/anti-H3K4me3 ChIP-seq experiments the same species.

sample_organism:
Trichoplax adhaerens
Trichoplax sp. H2
Hoilungia hongkongensis
Hoilungia sp. H23

overall_design:
Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. Some samples were mixed (cross-species or cross-treatments) and processed together. Instructions for demultiplexing cells are provided.
Please note that the processed data for the scRNA-seq samples are generated from multiple samples (as indicated in the corresponding sample descriptionfield) and thus is linked to the Series records.

first: Sebastian

middle: R

last: Najle

first: Xavier

last: Grau-Bove


title: Global role of IGF2BP1 in controlling the expression of Wnt/β-catenin-regulated genes II

city: Hershey

first: Vonn

last: Walter

state: PA

address: 500 University Drive

department: Public Health Sciences

country: USA

institute: Penn State College of Medicine

summary: The purpose of this study was to determine how IGF2BP1 affects non-transformed and colorectal cancer (CRC) cells' expression of the genes regulated by Wnt/β-catenin signaling. The study established that while the majority of upregulated genes in non-transformed cells were activated by Wnt ligand treatment independent of IGF2BP1, a subset of Wnt-induced genes was regulated by IGF2BP1, including 11 direct binding targets. In contrast, in CRC cells where Wnt signaling is constitutively active, the majority of downregulated genes upon β-catenin/Tcf7l2 blockage were regulated by IGF2BP1, and 17 of these genes were identified as direct binding targets of IGF2BP1. Our iCLIP study identified a shift in the binding regions along target transcriptomes with modulations in Wnt signaling. Furthermore, the study found a significant change in the enrichment of 6-mer motifs associated with IGF2BP1 binding in response to Wnt signaling in both cell types, suggesting a role for Wnt signaling in regulating IGF2BP1 binding specificity. The study also revealed a signature of IGF2BP1-regulated genes that are significantly associated with colon cancer-free survival in humans, as well as potential targets for colon cancer treatment, including MGAT5 and MET. Overall, this study highlights the complex and context-dependent regulation of Wnt signaling target genes by IGF2BP1 in non-transformed and CRC cells and identifies potential targets for colon cancer treatment.

overall_design: To identify the interactome of IGF2BP1 in Wnt3a treated and untreated conditions.

first: Vikash

last: Singh

first: Irina

last: Elcheva

first: Yuka

last: Imamura Kawasawa

first: Vladimir

last: Spiegelman


title: Global role of IGF2BP1 in controlling the expression of Wnt/β-catenin-regulated genes [MEF_RNA-seq]

overall_design: To study the difference in DEG's between (MEF-Wnt3a Vs MEF) and (MEF-IGF2BP1-KO-Wnt3a Vs MEF-IGF2BP1-KO)


title: Global role of IGF2BP1 in controlling the expression of Wnt/β-catenin-regulated genes I

overall_design: To identify the interactome of IGF2BP1 in Wnt signaling active and suppressed condition


title: Global role of IGF2BP1 in controlling the expression of Wnt/β-catenin-regulated genes [G109_DLD1_RNA-seq]

overall_design: To study the difference in DEG's between (DLD1-dnTCF7L2 Vs DLD1) and (DLD1-dnTCF7L2-IGF2BP1 Vs DLD1)


title: Regulation of cohesin loop extrusion underlies changes in enhancer-promoter interactions during pancreatic cell differentiation

city: XIAMEN

first: XIAOWEN

last: LYU

state: FUJIAN

address: No.4221, Xiang'an South Road, Xiang'an District

country: China

institute: XIAMEN UNIVERSITY

summary: Transcriptional reprogramming during cell fate determination involves precise targeting of enhancers to tissue-specific genes. Enhancer-promoter interactions are regulated by different types of 3D chromatin organization, including compartmental domains and CTCF loops. To understand the contribution of these different levels of chromatin organization in cell lineage commitment, we analyzed changes in 3D organization during the differentiation of human embryonic stem cells (hESCs) into pancreatic islet organoids. We find that major events in chromatin reorganization, including decompaction of transposon-enriched heterochromatin, breakdown of poised enhancer-promoter interaction networks, gain or loss of CTCF loops and establishment of novel enhancer-promoter contacts, occur either sequentially or simultaneously. Transcriptionally activated transposons released from unstable heterochromatin compartments recruit CTCF to form new loops. In contrast, when released from poised long-range interaction networks, enhancers and genes crucial for cell differentiation recruit tissue-specific transcription factors by either direct binding or indirect 3D contacts containing RNA Polymerase II. Activation of stage-specific genes correlates with gain of CTCF binding at anchors of extended CTCF loops, suggesting changes in loop extrusion capacity. In agreement with this, we find a global increase in cohesin loading leading to longer residency on extended CTCF loops encompassing tissue-specific genes. Our findings provide new insights into how distinct types of chromatin organization affect the reprogramming of gene expression patterns to regulate cell lineage commitment.

overall_design: ChIP-seq, ATAC-seq, RNA-Seq, CUT&Tag

first: Xiaowen

last: Lyu

first: M

middle: J

last: Rowley

first: Michael

last: Kulik

first: Stephen

last: Dalton

first: Victor

middle: G

last: Corces


title: Therapeutic targeting of Chronic Kidney Disease-associated DAMPs differentially contributing to vascular pathology.

status: Public on Sep 18 2023

city: Cardiff

first: Anne-Catherine

last: Raby

state: Cardiff

address: Heath Park, Academic Avenue

country: United Kingdom

institute: Cardiff University

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

overall_design: Refer to individual Series


title: Effect of IDH1 mutation induced by doxycycline on gene expression during VSVΔ51 infection in LN-229-TRE-R132H glioblastoma cells

city: Guangzhou

first: Xueqin

last: Chen

address: Huangpu West Road 601

institute: Jinan University

summary: To investigate whether IDH1 mutation influence the effects of oncolytic virus VSVΔ51, we transduced doxycycline-inducible IDH1-R132H lentiviruses into LN-229 to establish the LN-229-TRE-R132H cell line. We then performed gene expression profiling analysis using data obtained from RNA-seq of LN-229-TRE-R132H cells infected with or without VSVΔ51 in the presence or absence of IDH1 mutation induced by doxycycline.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LN-229-TRE-R132H cells pretreated with or without doxycycline (1 μg/ml) for 48 h and then infected with or without VSVΔ51 (MOI = 1) for 12 h.


title: Transcriptional signature of islet neogenesis-associated protein peptide-treated rat pancreatic islets reveals induction of novel long non-coding RNAs

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

summary: Diabetes mellitus is characterized by chronic hyperglycemia with loss of β-cell function and mass. An attractive therapeutic approach to treat patients with diabetes in a non-invasive way is to harness the innate regenerative potential of the pancreas. The Islet Neogenesis-Associated Protein pentadecapeptide (INGAP-PP) has been shown to induce β-cell regeneration and improve their function in rodents. To investigate its possible mechanism of action, we report here the global transcriptional effects induced by the short-term INGAP-PP in vitro treatment of adult rat pancreatic islets. We identify 1,669 differentially expressed genes by INGAP-PP treatment, including dozens of previously unannotated rat transcripts. In-depth analysis suggests that INGAP-PP engages the transcriptional program regulated by vitamin D receptor activation, among other pathways relevant for β-cell function, ultimately leading to enhanced glucose-stimulated insulin release. Supported by epigenomic and single-cell RNA-seq data, we identify 9 previously unannotated long noncoding RNAs upregulated by INGAP-PP, some of which are also differentially regulated by IL1β and vitamin D in β-cells. These include Ri-lnc1, which is enriched in mature β-cells. Taken together, the results presented here reveal novel potential mechanisms that could underlie the positive physiological effects of INGAP on β-cell function and mass.

overall_design: We purified rat pancreatic islets and treated them in vitro with/without INGAP (50 μg/mL) for 4 days. Afterwards we purified RNA and processed it for RNA-seq.

first: Agustín

last: Romero

first: Ana

middle: C

last: Heidenreich

first: Carolina

middle: L

last: Roman

first: Algarañaz

last: Macarena

first: Ezequiel

last: Nazer

first: Juan

last: Gagliardino

first: Bárbara

last: Maiztegui

first: Luis

middle: E

last: Flores

middle: A

last: Rodríguez-Seguí


title: Global role of IGF2BP1 in controlling the expression of Wnt/β-catenin-regulated genes

first: Vonn

last: Walter

sample_organism:
Homo sapiens
Mus
Mus musculus

platform_organism:
Homo sapiens
Mus
Mus musculus


title: Therapeutic targeting of Chronic Kidney Disease-associated DAMPs differentially contributing to vascular pathology. [atherosclerosis AAN+sTLR2 aortas]

summary: Chronic Kidney Disease (CKD) is associated with markedly increased cardiovascular (CV) morbidity and mortality. Chronic inflammation, a hallmark of both CKD and CV diseases (CVD), is believed to drive this association. Pro-inflammatory TLR agonists, Damage-Associated Molecular Patterns (DAMPs), have been found elevated in CKD patients’ plasma and suggested to promote CVD, however, confirmation of their involvement, the underlying mechanism(s), the extent to which individual DAMPs contribute to vascular pathology in CKD and the evaluation of potential therapeutic strategies, have remained largely undescribed. A multi-TLR inhibitor, soluble TLR2, abrogated chronic vascular inflammatory responses and the increased aortic atherosclerosis-associated gene expression observed in nephropathic mice, without compromising infection clearance.  Mechanistically, we confirmed elevation of 4 TLR DAMPs in CKD patients’ plasma, namely Hsp70, Hyaluronic acid, HMGB-1 and Calprotectin, which displayed different abilities to promote key cellular responses associated with vascular inflammation and worsening of atherosclerosis in a TLR-dependent manner. These included loss of trans-endothelial resistance, enhanced monocyte migration, increased cytokine production, and foam cell formation by macrophages, the latter via cholesterol efflux inhibition. Calprotectin and Hsp70 most consistently affected these functions. Calprotectin was further elevated in CVD-diagnosed CKD patients and strongly correlated with the predictor of CV events CRP. In nephropathic mice, Calprotectin blockade robustly reduced vascular chronic inflammatory responses and pro-atherosclerotic gene expression. Taken together, these findings demonstrated the critical extent to which the DAMP-TLR pathway contributes to vascular inflammatory and atherogenic responses in CKD, revealed the mechanistic contribution of specific DAMPs and described two alternatives therapeutic approaches to reduce chronic vascular inflammation and lower CV pathology in CKD.

overall_design: Chronic nephropathy was induced in mice by repeated administration of Aristolochic Acid, and mice received soluble TLR2 treatment. Aortas from at least n=3 mice / group (including a PBS non-nephropathic group) were collected and analysed by RT2 profiler array

first: Morgane

last: Mazzarino

first: Esra

last: Cetin


title: Therapeutic targeting of Chronic Kidney Disease-associated DAMPs differentially contributing to vascular pathology. [atherosclerosis AAN+Paquinimod aortas]

overall_design: Chronic nephropathy was induced in mice by repeated administration of Aristolochic Acid, and mice received Paquinimod treatment . Aortas from at least n=3 mice / group (including a PBS non-nephropathic group) were collected and analysed by RT2 profiler array


title: Identifying gene combinations for targeting innate immune cells to enhance T cells activation [CITE-seq]

status: Public on Sep 17 2023

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: The Hebrew University of Jerusalem

summary: Genetic engineering of hematopoietic cells ex-vivo opens new opportunities for programming immune cells and improving their functionality in response to illness and infections. Molecular methods for genetic manipulation are constantly improving, but it is challenging to reveal which genes are the most beneficial to target and whether multiple genes tackling can further improve the desired outcome. Current screening methods are limited by scale, the number of perturbations, and low content readouts. We developed a hybrid platform called “high multiplicity of perturbations and cellular indexing of transcriptomes and epitopes by sequencing (HMPCITE-seq)” that allows for finding combinations of genes to target and improves desired cellular functions. We used antigen-presenting cells and performed two genome-wide CRISPR screens to enhance the activation and co-stimulation programs and restrict the suppressive programs. Five genes were found in both screens including Cebpb gene. We showed that targeting Cebpb in antigen-presenting cells enhances the expression of costimulatory molecules, prevents attenuate cell migration and phagocytosis, improves T cell proliferation, and restricts tumor growth. To find the genetic interactions between validated targeted genes, and identify gene combinations for targeting, we performed high-order perturbations of validated genes from the screens with single-cell RNA-seq readouts. We found that targeting both Cebpb and Med12 genes shows a better phenotype compared to the single KOs. Thus, the HMPCITE-seq platform, starting from a genome-wide screen, allows the finding of gene combinations to target as demonstrated by functional experiments in-vitro and in-vivo.

overall_design: The goal of this experiments was to find the effect of targeting Cebmb and Med12 on DCs, T cells, and tumor growth. We therefore generated perturb BMDCs from bone marrow or spleen incubate them with CD8 T cells or inject to tumors as detailed bellow.

first: Yehuda

last: Shovman

first: Arielle

last: Jacover

first: Lei

last: Xia

first: Anastasia

last: Komissarova


title: KRAS is required for placenta development

city: Brussels

first: Patrick

last: Jacquemin

address: 75 Avenue Hippocrate

country: Belgium

institute: de Duve Institute

summary: Besides its well-known roles in cancer, KRAS is important for embryogenesis, as its absence causes embryonic lethality. The precise mechanisms underlying the developmental functions of KRAS is still incompletely characterized. To address this issue, we analyzed Kras-/- mouse embryos. We observed that Kras-/- embryos show a lethality that starts around E13.5. Interestingly, a placental phenotype was observed in Kras-/- embryos. This phenotype was associated with a small placental size, and a marked decrease in glycogen trophoblast cells. It was related to the presence of hypoglycaemia and hypoxia in Kras-/- embryos. Thus, our study reveals hidden functions of KRAS4. Importantly, it identifies for the first time a role for KRAS in the differentiation process of a specific cell type and the biological defects caused by a loss of KRAS.

overall_design: Wild-type and Kras-/- mouse placenta were collected at e13.5. Cell nuclei were purified, RNA was extracted and submitted to snRNAseq.

first: Marie-Albane

last: Minati

first: Axelle

last: Loriot

first: Laurent

last: Gatto


title: Kaposi’s Sarcoma-associated Herpesvirus Viral Protein Kinase Augments Cell Survival

status: Public on Sep 16 2023

city: Chapel Hill

first: Xinjun

last: Wu

address: 450 West Drive

institute: UNC-Chapel Hill

summary: Human umbilical vein endothelial cells (HUVECs) expressing vPK (HUVEC-vPK) have a survival advantage over control HUVEC under conditions of extrinsic- and intrinsic-mediated apoptosis.

overall_design: Total RNA was extracted from two sample groups-HUVEC EV and HUVEC vPK (WT) under three different serum concentrations (0%, 2%, and 10%) (n=2). The Genewiz (AZENTA Life Sciences, (https://www.genewiz.com/) performed library preparation. RNA samples underwent RNA sequencing utilizing Illumina NovaSeq technology.

first: Zhigang

last: Zhang

first: Jason

middle: P

last: Wong

first: Ricardo

last: Rivera-Soto

first: Maria

last: White

first: Aryan

last: Rai

first: Blossom

last: Damania


title: Protocol for the purification and transcriptomic analysis of mouse astrocytes using GFAT

status: Public on Sep 15 2023

city: La Jolla

first: Nicola

last: Allen

state: CA

address: 10010 N Torrey Pines Rd

department: Molecular Neurobiology

institute: Salk Institute for Biological Studies

summary: Astrocytes are glial cells of the central nervous system that modulate neuronal function. Here, we present glyoxal-fixed astrocyte nuclei transcriptomics (GFAT), a protocol for the purification and transcriptomic analysis of astrocyte nuclei from the cortex and cerebellum of adult and aged fresh mouse brain. We describe steps for tissue dissection, glyoxal fixation, homogenization, nuclei isolation, antibody staining, fluorescence-activated cell sorting, and RT-qPCR or bulk RNA sequencing. GFAT does not require transgenic lines or viral injection and allows parallel astrocyte and neuron profiling.

overall_design: Bulk RNA-seq analysis of astrocyte and neuron nuclei in 4 month-old (adult) and 2 year-old (aged) WT C57BL/6 male mice

first: Lara

last: Labarta-Bajo

first: James

last: Deng

first: Minerva

last: Contreras


title: Therapeutic targeting of Chronic Kidney Disease-associated DAMPs differentially contributing to vascular pathology. [atherosclerosis AAN+PaqusTLR2 blood]

first: Anne-Catherine

last: Raby

overall_design: Chronic nephropathy was induced in mice by repeated administration of Aristolochic Acid, and mice received Paquinimod or soluble TLR2 treatment . Blood from at least n=3 mice / group (including a PBS non-nephropathic group) were collected and analysed by RT2 profiler array

first: Morgane

last: Mazzarino

first: Esra

last: Cetin


title: The effect of PLVAP knockdown in human liver sinusoidal endothelial cells (LSECs).

city: Berlin

first: Paul

last: Horn

address: Augustenburger Platz 1

department: Department of Hepatology and Gastroenterology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary:
To investigate the phenotypic consequences of PLVAP presence/absence in human LSEC, we utilised siRNA knockdown in 3 independent LSEC donors.
We then performed gene expression profiling analysis using data obtained from RNA-seq of LSEC with siRNA knockdown of PLVAP and siRNA Negative Control cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LSEC with siRNA knockdown of PLVAP and siRNA Negative Control cells.

first: Alex

last: Wilkinson

first: Daniel

last: Patten

first: Shishir

last: Shetty


title: Gene expression analysis of FO B and ABCs of young and aged mice.

status: Public on Sep 14 2023

city: Fukuoka

first: Chisato

last: Ono

address: 3-1-1, maidashi, Higashi-ku

country: Japan

institute: Kyushu University

summary: We report the global gene expression in follicular (FO) B cells and age/autoimmunity-associated B cells (ABCs). We found that Fc-receptor like (Fcrl) 5 was highly expressed in ABCs isolated from 50-week-old mice, compared to FO B cells. This study provides a basis for understanding the relationship between autoimmune diseases and Fcrl5 expression in B cells.

overall_design: To investigate gene expression pattern of ABCs, we isolated FO B cells either from 8- and 50-wk-old mice and ABCs from 50-wk-old mice by FACS staining. These B cell subsets were subjected to generate cDNA libraries for RNA-seq analysis. We then performed comparative gene expression analysis to identify the characteristics of gene expression shaped in ABCs.


title: Integrated metabolic and transcriptomic analysis of the duckweed Lemna gibba growing under photomixotrophic conditions: Metabolic adjustments to different nitrogen sources

city: Cold Spring Harbor

first: Robert

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

summary: Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown in a photomixotrophic mode in liquid media under continuous light with 13C-labeled glucose as a carbon source. Two different conditions (nitrate vs. glutamine as nitrogen source) were compared by quantification of growth kinetics, metabolite levels, metabolic flux and transcript abundance.

overall_design: Fronds grown on inorganic nitrogen (nitrate) or on organic nitrogen (glutamine) medium were harvested and immediately frozen in liquid nitrogen. For each condition three biological replicates were analyzed.

first: Hai

last: Shi

first: Evan

last: Ernst

first: Nicolas

last: Heinzel

first: Sean

last: McCorkle

first: Hardy

last: Rolletschek

first: Ljudmilla

last: Borisjuk

first: Stefan

last: Ortleb

first: John

last: Shanklin

first: Jorg

last: Schwender


title: Translocator protein (18kDA) (TSPO) marks mesenchymal glioblastoma cell populations characterized by elevated numbers of tumor-associated macrophages

city: Regensburg

first: Markus

middle: J.

last: Riemenschneider

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

institute: Regensburg University Hospital

summary:
TSPO is a promising novel tracer target for positron-emission tomography (PET) imaging of brain tumors. However, due to the heterogeneity of cell populations that contribute to the TSPO-PET signal, imaging interpretation may be challenging. We therefore evaluated TSPO enrichment/expression in connection with its underlying histopathological and molecular features in gliomas.
We analyzed TSPO expression and its regulatory mechanisms in large in silico datasets and by performing direct bisulfite sequencing of the TSPO promotor. In glioblastoma tissue samples of our TSPO-PET imaging study cohort, we dissected the association of TSPO tracer enrichment and protein labeling with the expression of cell lineage markers by immunohistochemistry and fluorescence multiplex stains. Furthermore, we identified relevant TSPO-associated signaling pathways by RNA sequencing.
We found that TSPO expression is associated with prognostically unfavorable glioma phenotypes and that TSPO promotor hypermethylation is linked to IDH mutation. Careful histological analysis revealed that TSPO immunohistochemistry correlates with the TSPO-PET signal and that TSPO is expressed by diverse cell populations. While tumor core areas are the major contributor to the overall TSPO signal, TSPO signals in the tumor rim are mainly driven by CD68-positive microglia/macrophages. Molecularly, high TSPO expression marks prognostically unfavorable glioblastoma cell subpopulations characterized by an enrichment of mesenchymal gene sets and higher amounts of tumor-associated macrophages.
In conclusion, our study improves the understanding of TSPO as an imaging marker in gliomas by unveiling IDH-dependent differences in TSPO expression/regulation, regional heterogeneity of the TSPO PET signal and functional implications of TSPO in terms of tumor immune cell interactions.

overall_design:
IDH-wt WHO grade 4 solid glioblastoma tumors with high or low TSPO mRNA expression split by their median in TSPO LOW and TSPO HIGH group (nine solid tumors were analyzed for each of 2 conditions) - TSPO clusters for further analyses included 9 LOW I, 4 HIGH II, and 5 HIGH III solid tumors.
(Information regarding RNA-Seq RUN annotation used for Batch correction is provided within the metadata file or Suppl. Tab. 3 of the corresponding publication)

first: Lorraine

last: Weidner

first: Julia

last: Lorenz


title: Taste papilla cell differentiation requires the regulation of secretory protein production by ALK3-BMP signaling in the tongue mesenchyme

status: Public on Sep 13 2023

city: Athens

first: Hongxiang

last: Liu

state: Georgia

address: 425 Riverbend Pkwy, Apt 82

department: Animal and Dairy Science

institute: The University of Georgia

summary: Taste papillae are specialized organs, each of which comprises an epithelial wall hosting taste buds and a core of mesenchymal tissue. In the present study, we report that during early taste papilla development in mouse embryos, bone morphogenetic protein (BMP) signaling mediated by type 1 receptor ALK3 in the tongue mesenchyme is required for the epithelial Wnt/β-catenin activity and taste papilla differentiation.

overall_design: Separated mesenchymal and epithelial tissues from E12.0 Cre− littermate control and mesenchyme specific Wnt1-Cre mediated Alk3 conditional knock out (cKO) tongues were immersed in Trizol solution (15596018, Life Technologies) for RNA extraction using the RNeasy Plus kit (74136, Qiagen). For each experimental condition, a total of nine mesenchymal and epithelial tissues (pooled three tissues×three replicates) were used. RNA concentrations were measured using Nanodrop 8000 spectrophotometer (ThermoFisher Scientific). RNA sequencing was performed in Georgia Genomics and Bioinformatics Center at the University of Georgia using the NextSeq 500 system (Illumina)


title: KCNQ POTASSIUM CHANNELS MODULATE WNT ACTIVITY IN GASTRO-OESOPHAGEAL ADENOCARCINOMAS

city: London

first: David

last: Shorthouse

address: 29-39 Brunswick Square

department: School of Pharmacy

institute: UCL

summary: Voltage sensitive potassium channels play an important role in controlling membrane potential and ionic homeostasis in the gut and have been implicated in gastrointestinal (GI) cancers. Through large scale analysis of 897 patients with Gastro-oesophageal adenocarcincomas (GOA) coupled with in vitro models, we find KCNQ family genes are mutated in ~30% of patients, and play therapeutically targetable roles in GOA cancer growth. KCNQ1 and KCNQ3 mediate the WNT pathway and MYC to increase proliferation through resultant effects on cadherins junctions. This also highlights novel roles for KCNQ3 in non-excitable tissues. We additionally discover that activity of KCNQ3 sensitises cancer cells to existing potassium channel inhibitors, and that inhibition of KCNQ activity reduces proliferation of GOA cancer cells. These findings reveal a novel and exploitable role for potassium channels in the advancement of human cancer, and highlight that supplemental treatments for GOAs may exist through KCNQ inhibitors.

overall_design: Cell lines were established with overexpression of KCNQ3. These cell lines were then sequenced relative to controls. Cell lines were seperatey treated with 50um Amitriptyline or 30um Linopirdine for 6 days before being sequenced

first: Benjamin

last: Hall


title: Regulation of cohesin loop extrusion underlies changes in enhancer-promoter interactions during pancreatic cell differentiation (Hi-ChIP)

first: XIAOWEN

last: LYU

overall_design: Hi-ChIP, Mi-ChIP

first: Xiaowen

last: Lyu

first: M

last: Rowley

first: Michael

last: Kulik

first: Stephen

last: Dalton

first: Victor

last: Corces


title: Identifying gene combinations for targeting innate immune cells to enhance T cells activation [Med12 and Cebpb KO]

first: Oren

last: Parnas

overall_design: The goal of these experiments was to find the effect of knockout of specific genes and gene combinations on the whole transcriptome level. Genes of interest were knocked out using CRISPR and compared to controls that had non-targeting gRNA sequences. Each experiment was done in triplicate.

first: Yehuda

last: Shovman

first: Arielle

last: Jacover

first: Lei

last: Xia

first: Anastasia

last: Komissarova

first: Sebastian

last: Arcila-Barrera


title: Efficient Expansion and Delayed Senescence of Human Umbilical Cord Mesenchymal Stem Cells by Microcarrier-Bioreactor System

city: Shanghai, China

first: Liming

last: Ouyang

state: Shanghai

address: East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, China

summary: Human umbilical cord mesenchymal stem cells (hUC-MSCs) are widely used in cell therapy due to their powerful immunomodulatory and tissue regenerative capabilities. In order to meet the number and quality of cells for clinical applications, we developed a hUC-MSCs culture process based on homemade microcarriers and stirred bioreactors. In this study, the biological properties of hUC-MSCs amplified by planar culture and microcarrier bioreactor systems are systematically compared. It was found that microcarrier-expanded hUC-MSCs had a relatively lower degree of aging, relatively stronger proliferation capacity, and fewer cells stayed in the cell cycle retardation period. At the same time, RNA-seq was used to compare the differences in gene expression between the two cultures, and the pathways and genes related to cell aging were identified. Comparing the transcription levels of these aging-related gene sets can also confirm that cells cultured by microcarrier reactors are more youthful. Results show that our reactor culture method greatly improved the cell proliferation efficiency, while maintaining the basic properties and younger state of stem cells.

overall_design: Develop a culture process for hUC-MSCs based on homemade microcarriers and stirred bioreactors, systematically compare the biological characteristics of hUC-MSCs amplified by planar culture and microcarrier bioreactor systems, and compare gene expression differences between the two cultures by RNA-seq to identify pathways and genes associated with cellular senescence.

first: Xia

last: Wang

first: Wenxia

last: Cheng


title: Alloantigen Infusion Selectively Activates the Transcriptome of Type 2 Conventional Dendritic Cells"

city: Chicago

first: Samantha

last: Schroth

state: IL

address: 320 E Superior St

institute: Northwestern University Feinberg School of Medicine

summary: Recent studies have revealed novel molecular mechanisms by which innate monocytic cells acutely recognize and respond to alloantigen, and the significance of this to allograft rejection and immunologic tolerance. What remains unclear is the single cell heterogeneity of the innate allo-response, and particularly the contribution of dendritic cell (DC) subsets. To investigate the acute response of innate immune cells and DC subsets to exposure of alloantigen, experimental rodents were administered an intravenous injection of live allogenic cells versus isogenic cells. In parallel, we also infused apoptotic allogenic and isogenic cells, which have been reported to modulate immunity. Forty-eight hours after injection, recipient spleens were harvested, pooled by condition, enriched for DCs, and subjected to single cell mRNA sequencing and downstream analysis. Injection of live splenic cells induced a greater quantity of transcriptional changes across all DC subsets as identified by differential gene expression analysis and compared to apoptotic cell injection. In the setting of live cell infusion, type 2 conventional dendritic cells (cDC2s) were more transcriptionally responsive with a Ccr2+ cDC2 subcluster uniquely responding to the presence of alloantigen compared to isogenic control. Candidate receptors of allorecognition in other innate populations were interrogated amongst cDC2s and A-type paired immunoglobulin-like receptors (PIR-As) was found to be increased specifically in the cDC2 population following allo-exposure at the mRNA level and by flow cytometry. These results illuminate previously unclear distinctions between therapeutic infusions of live versus apoptotic allogenic cells and newly implicate cDC2 cells in innate allorecognition in the context of transplantation.

overall_design: Splenic cells magnetically enriched for DCs and CD45+ cells from mice infused with live allo- (LA, Balbc), live iso- (LI, B6),  apopototic allo- (AA, Balbc), apoptotic iso- (AI, B6) antigen or saline control (C) 48 hours prior and subjected to single cell RNA sequencing.

first: Edward

last: Thorp


title: Identifying gene combinations for targeting innate immune cells to enhance T cells activation [Cebpb-KO CRISPR screen]

summary: Genetic engineering of hematopoietic cells ex-vivo opens new opportunities for programming immune cells and improving their functionality in response to illness and infections. Molecular methods for genetic manipulation are constantly improving, but it is challenging to reveal which genes are the most beneficial to target and whether multiple genes tackling can further improve the desired outcome. Current screening methods are limited by scale, the number of perturbations, and low content readouts. We developed a hybrid platform called “high multiplicity of perturbations and cellular indexing of transcriptomes and epitopes by sequencing (HMPCITE-seq)” that allows for finding combinations of genes to target and improves desired cellular functions. We used antigen-presenting cells and performed two genome-wide CRISPR screens to enhance the activation and co-stimulation programs and restrict the suppressive programs. Five genes were found in both screens including Cebpb gene. We showed that targeting Cebpb in antigen-presenting cells enhances the expression of costimulatory molecules, does not attenuate cell migration and phagocytosis, improves T cell proliferation, and restricts tumor growth. To find the genetic interactions between validated targeted genes, and identify gene combinations for targeting, we performed high-order perturbations of validated genes from the screens with single-cell RNA-seq readouts. We found that targeting both Cebpb and Med12 genes shows a better phenotype compared to the single KOs. Thus, the HMPCITE-seq platform, starting from a genome-wide screen, allows the finding of gene combinations to target as demonstrated by functional experiments in-vitro and in-vivo.

overall_design: Genome-wide CRISPR screen on Cebpb-KO DCs, secondary screen (based on RNA-seq results) on Cebpb-KO DCs and secondary screen on WT DCs.  In each screen, cells were sorted into two bins: 10% cells with highest CD86 level and 10% cells with lowest CD86 level. Genomic DNA was extracted from the sorted and unsorted cells and sequenced in order to verify the enrichment of the gRNAs.


title: A human alveolus-on-chip model for radiation induced lung injury

city: Boston

first: Amanda

last: Jiang

state: MA

address: 201 Brookline Avenue

institute: Wyss Institute

summary: Acute exposure to high-dose gamma radiation can result in radiation-induced lung injury (RILI), characterized by acute pneumonitis and subsequent lung fibrosis. A microfluidic organ-on-a-chip lined by human lung alveolar epithelium interfaced with pulmonary endothelium (Lung Alveolus Chip) is used to model acute, early stage RILI in vitro. Both lung epithelium and endothelium exhibit DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6h of radiation exposure, and greater damage is observed in the endothelium. The alveolus chips are exposed to radiation injury at 16 Gy and shows effects that resemble the human lung greater than animal preclinical models. The Alveolus Chip is also used to evaluate the potential ability of two drugs to suppress the effects of acute RILI.  These data demonstrate that the Lung Alveolus Chip provides a human relevant alternative approach for studying the molecular basis of acute RILI towards screening radiation countermeasure therapeutics.

overall_design: To assess the effect of radiation on the lung alveolar epithelium and the endothelium in a human lung alveolus chip. The study evaluates the effect of radiation on 2 cell types (human primary alveolar epithelium and lung microvascular endothelium) at two time-points (6 h and 7 d after radiation exposure). The controls are from human alveolus chips that receive no radiation exposure and are compared to alveolus chips that receive 16 Gy radiation. Each condition has 4 replicates: Alveolar epithelium (0 Gy) 6h, Alveolar epithelium (16 Gy) 6h, Microvascular endothelium (0 Gy) 6h, Microvascular endothelium (16 Gy) 6h, Alveolar epithelium (0 Gy) 7d, Alveolar epithelium (16 Gy) 7d, Microvascular endothelium (0 Gy) 7d, Microvascular endothelium (16 Gy) 7d

first: Queeny

last: Dasgupta

first: Donald

last: Ingber


title: Identifying gene combinations for targeting innate immune cells to enhance T cells activation [RNA-Seq]

overall_design: The goal of these experiments was to find the effect of knockout of specific genes and gene combinations on the whole transcrpitome level. Genes of interest were knocked out using CRISPR and compared to controls that had non-targeting gRNA sequences. Each experiment was done in triplicate.


title: Identifying gene combinations for targeting innate immune cells to enhance T cells activation

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

overall_design: Refer to individual Series


title: Neoadjuvant intratumoral immunotherapy with cowpea mosaic virus induces local and systemic antitumor efficacy in canine mammary cancer patients.

status: Public on Sep 12 2023

city: Hanover

first: Hugo

last: Arias-Pulido

state: NH

address: 621 Rubin Building - HB 7936 1 Medical Center Drive

department: Department of Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

summary: This study evaluated the efficacy, safety, and effects on treated and untreated tumors, and clinical impact of neoadjuvant intratumoral empty cowpea mosaic virus (eCPMV) immunotherapy in CMC patients.

overall_design: Impact of neoadjuvant intratumoral empty cowpea mosaic virus immunotherapy on canine mammary cancer  gene expression profiles generated by RNA-seq and tumor size in treated and untreated patients.

first: Guillermo

last: Valdivia

first: Daniel

last: Alonso-Miguel

first: Maria

middle: D

last: Perez-Alenza

first: Anna

middle: B

last: Zimmermann

first: Evelien

last: Schaafsma

first: Fred

middle: W

last: Kolling

first: Lucia

last: Barreno

first: Angela

last: Alonso-Diez

first: Veronique

last: Beiss

first: Jessica

middle: F

last: Affonso de Oliviera

first: María

last: Suárez-Redondo

first: Steven

last: Fiering

first: Nicole

last: Steinmetz

first: Johannes

last: vom Berg

first: Laura

last: Peña


title: Piperacetazine directly binds to the PAX3::FOXO1 fusion protein and inhibits its transcriptional activity

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: The tumor-specific chromosomal translocation product, PAX3::FOXO1, is an aberrant fusion protein that plays a key role for oncogenesis in the alveolar subtype of rhabdomyosarcoma (RMS). PAX3::FOXO1 represents a validated molecular target for alveolar RMS and successful inhibition of its oncogenic activity is likely to have significant clinical applications. Even though several PAX3::FOXO1 function-based screening studies have been successfully completed, a directly binding small molecule inhibitor of PAX3::FOXO1 has not been reported. Therefore, we screened small molecule libraries to identify compounds that were capable of directly binding to PAX3::FOXO1 protein using surface plasmon resonance technology. Compounds that directly bound to PAX3::FOXO1 were further evaluated in secondary transcriptional activation assays. We discovered that piperacetazine can directly bind to PAX3::FOXO1 protein and inhibit fusion protein-derived transcription in multiple alveolar RMS cell lines. Piperacetazine inhibited anchorage-independent growth of fusion positive alveolar RMS cells but not embryonal RMS cells. Based on our findings, piperacetazine is a molecular scaffold upon which derivatives could be developed as specific inhibitors of PAX3::FOXO1. These novel inhibitors could potentially be evaluated in future clinical trials for recurrent or metastatic alveolar RMS as novel targeted therapy options.

overall_design: RH30 cells were treated with 30 µM of piperacetazine or DMSO for 24 hours before harvest for RNA using RNAeasy kits (Qiagen Cat# 74104, Hilden, Germany). RNA-Seq libraries were constructed using Illumina TruSeq stranded mRNA sample preparation kits and sequenced on a NextSeq500 sequencer using 2x75bp paired-end protocol (Illumina). Genes with >10 total reads in these samples were kept, and raw read counts were transformed to regularized logarithm values using DESeq2 package (RRID:SCR_015687) (35). The ranked list of genes for the comparison between piperacetazine-treated and DMSO control were sorted by log2 fold change. The Gene Set Enrichment Analysis (GSEA) was performed using command “gsea-cli.sh GSEAPreranked” and curated gene sets

first: Jun

middle: S

last: Wei

first: Xinyu

last: Wen


title: Identifying gene combinations for targeting innate immune cells to enhance T cells activation [DNA]

first: Oren

last: Parnas

overall_design: CD86 screens - two repeats of the genome-wide CRISPR screen and one repeat of the secondary screen were performed. PDL1 screens - one repeat of the genome-wide CRISPR screen and two repeats of the secondary screen were performed. In each screen, cells were sorted into two bins: 10% cells with highest CD86/PDL1 level and 10% cells with lowest CD86/PDL1 level. Genomic DNA was extracted from the sorted cells and sequenced in order to verify the enrichment of the gRNAs.

first: Yehuda

last: Shovman

first: Arielle

last: Jacover

first: Lei

last: Xia

first: Anastasia

last: Komissarova


title: Effect of carcinogen exposure on gene expression of tumor-associated macrophages

city: Charlestown

first: Mei

last: Huang

address: Building 149 13th Street

institute: Massachusetts General Hospital

summary:
To investigate the carcinogen exposure in the regulation of macrophages in the tumor microenvironment, we inoculated DMBA3-4 and DMSO3-1 cell lines in Rag1 knockout mice and collect TAMs cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of tumor-associated macrophages  from DMBA3-4 and DMSO3-1 groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TAMs from DMBA3-4  and DMSO3-1 groups .

first: Shadmehr

last: Demehri


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [Cut&Run]

city: Umeå

first: Silvia

last: Remeseiro

state: Västerbotten

address: UNIVERSITETSTORGET 4

department: UCMM

country: Sweden

institute: Umeå University

summary: Glioblastoma (GBM) is the most aggressive of all primary brain tumours. Here, we perform a multi-omics approach to map the promoter-enhancer interactome and the regulatory landscape of glioblastoma, including RNA-seq, ChIP-seq of histone marks, HiChIP and ATAC-seq.

overall_design: CUT and RUN

first: Chaitali

last: Chakraborty

first: Itzel

last: Nissen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and POT1a deleted MSPCs Transcriptomes.

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate POT1a deleted MSPCs functions by using NGS-derived MSPCs transcriptome profiling (RNA-seq) in vitro and vivo.
Methods: In vitro, bone marrow cells flushed out from mouse femurs and tibiae were cultured, and adherent cells were collected. CD51+/PDGFRɑ+ cells were sorted and further cultured, and Cre Recombinase Gesicles were applied. After 48 hours culture, tdTomato fluorescently colored cells were re-sorted, cultured for about 4 weeks, and used for gene analyses. In vivo, bone marrow cells weer flushed out from mouse femurs and tibiae, and the flow-through fraction with tdTomato signals was sorted as an MSPC-enriched population.
Results: Gene set enrichment analysis of the differentially expressed genes revealed that several pathways related to bone development were significantly affected.
Conclusions: POT1a is essential for bone marrow MSPCs to maintain osteo- differentiation potential.

overall_design: In vitro, cultured POT1a deleted MSPCs mRNA profiles. In vivo, sorted bone marrow MSPCs mRNA profiles of NG2-cre / loxp-tdTomato / Pot1awt/fl and NG2-cre / loxp-tdTomato / Pot1afl/fl mice.

first: Kentaro

last: Nakashima

first: Yuya

last: Kunisaki

first: Jumpei

last: Nogami

first: Fumio

last: Arai


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [OPC_ChIP-seq]

summary: Glioblastoma (GBM) is the most aggressive of all primary brain tumours. Here, we perform a multi-omics approach to map the promoter-enhancer interactome and the regulatory landscape of glioblastoma,  including RNA-seq, ChIP-seq of histone marks, HiChIP and ATAC-seq.

overall_design: OPC ChIP-seq


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [OPC2 ATAC-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 15 GBM celllines (representative of 4 molecular subtypes) vs normal human Astrocytes


title: Genome-wide maps of hematopoietic stem and progenitor cells in mice bone marrow.

summary:
Purpose: To investigate whether the skeletal retardation observed in NG2-cre/Pot1afl/fl mice affected hematopoiesis.
Methods: Whole bone marrow cells mRNA profiles of 2-week-old wild-type (NG2-cre/Pot1awt/wt) and Pot1a knockout (NG2-cre/Pot1afl/fl) mice were generated by deep sequencing, using Illumina NextSeq 500.
Results: We compared the relative sizes of these subpopulations between the NG2-cre/Pot1afl/fl and control mice and found a significant reduction in cells of the B-cell lineage in NG2-cre/Pot1afl/fl marrow. Cell subpopulations associated with B-cell differentiation from hematopoietic stem/progenitor cells (HSPCs) were identified according to the expression of established marker genes.
Conclusions: Bone marrow microenvironments composed of POT1a-deleted MSPCs impair B-cell development.

overall_design: Single cell mRNA profiles of bone marrow HSCs and progenitor cells in NG2-cre/Pot1afl/fl  and control mice.


title: The endometrial trasccriptome transition accompanying acquisition of receptivity to embryo implantation in mice

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

summary: Receptivity of the uterus is essential for embryo implantation and progression of pregnancy. Acquisition of receptivity involves major molecular and cellular changes in the endometrial lining of the uterus from its non-receptive state at ovulation, to its receptive state four days later. The precise molecular mechanisms underlying this transition remain to be fully characterized. Here, we aimed to generate a comprehensive profile of the uterine transcriptome in the peri-ovulatory and peri-implantation states, and to define the differences between them, in the mouse. High throughput RNA-sequencing was utilized to identify genes and pathways expressed in the endometrium of C57Bl/6 female mice on day 3.5 post-coitum after mating with BALB/c males, compared to the endometrium of unmated estrous females (n=3-4 biological replicates). RNA-sequencing and analysis using Ingenuity Pathway Analysis software revealed that, compared to the endometrium at estrus, 388 genes were differentially expressed in the endometrium on day 3.5 post-coitum (FDR ≤ 0.05). Several upstream regulators are implicated in the transition to receptivity including several cytokines, steroid hormones, prostaglandin E2, and vascular endothelial growth factor A. The transcriptional changes indicate substantial changes in the uterine immune and vascular systems during the pre-implantation phase, with the functional terms Angiogenesis, Chemotaxis, and Lymphangiogenesis predominating. This analysis confirms that the transcriptome of a receptive uterus is vastly different to the non-receptive uterus and identifies several genes and regulatory pathways not previously associated with implantation. This dataset will serve as a valuable tool and resource for future research on the molecular mechanisms of uterine receptivity.

overall_design: We performed gene expression profiling using RNA-seq of endometrial tissues from estrous (CONT) females and mated (INT) females on day 3.5 post-coitum. There are three other experimental groups (VAS, SVX and SVXVAS) involving endometrial tissues from females mated with surgically modified males. These groups of samples will be used in a separate manuscirpt to elucidate the role of seminal fluid in transcriptomic changes in the uterus at the peri-implantation phase of pregnancy.

first: Sarah

last: Robertson

first: Hon

middle: Y

last: Chan

first: John

last: Schjenken

first: Jimmy

first: Ha

last: Tran


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [RNAseq]

summary:
Glioblastoma (GBM) is the most aggressive of all primary brain tumours. Here, we perform a multi-omics approach to map the promoter-enhancer interactome and the regulatory landscape of glioblastoma,
, including RNA-seq, ChIP-seq of histone marks, HiChIP and ATAC-seq.


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [HiChIP]

overall_design: HiChIP data for 15 GBM celllines (representative of 4 molecular subtypes) vs normal human Astrocytes


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [OPC_RNA-seq]

overall_design:
OPC_RNA-seq
Please note that the 'countmatrix_OPC_HGCC.csv' contains processed data for both GSE217348 and GSE234126 RNA-seq samples.


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [H3K27Me3.ChIPseq]

summary:
Glioblastoma (GBM) is the most aggressive of all primary brain tumours. Here, we perform a multi-omics approach to map the promoter-enhancer interactome and the regulatory landscape of glioblastoma,
including RNA-seq, ChIP-seq of histone marks, HiChIP and ATAC-seq.

overall_design: H3K27Me3.ChIPseq data for 15 GBM celllines (representative of 4 molecular subtypes) vs normal human Astrocytes


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [H3K4me3.ChIPseq]

overall_design: H3K4me3.ChIPseq data for 15 GBM celllines (representative of 4 molecular subtypes) vs normal human Astrocytes


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [H3K27Ac.ChIP]

overall_design: H3K27Ac.ChIP for 15 GBM celllines (representative of 4 molecular subtypes) vs normal human Astrocytes


title: A human alveolus-on-chip model for studying radiation induced lung injury

status: Public on Sep 11 2023

city: Houston

first: Queeny

last: Dasgupta

state: Texas

address: 2450 holcombe blvd

institute: Systemic Bio

summary: Acute exposure to high-dose gamma radiation often results in radiation-induced lung injury (RILI), characterized by acute pneumonitis and subsequent lung fibrosis. A microfluidic organ-on-a-chip device consisting of human lung alveolar epithelium and pulmonary endothelium (Lung Alveolus Chip) is used to recapitulate acute, early stage RILI in vitro. This RNA-seq data captures that both the lung epithelium and endothelium in this model capture key hallmarks of this disease particularly, DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6h of radiation exposure. The data also suggests that radiation affects the alveolar endothelium more significantly than the epithelium. The alveolus chips are exposed to radiation injury at 16 Gy and shows effects that resemble the human lung greater than animal preclinical models. These data demonstrate that the Lung Alveolus Chip provides a human relevant alternative approach for studying the molecular basis of acute RILI towards screening radiation countermeasure therapeutics.

overall_design: To assess the effect of radiation on the lung alveolar epithelium and the endothelium in a human lung alveolus chip. The study evaluates the effect of radiation on 2 cell types (human primary alveolar epithelium and lung microvascular endothelium) at two time-points (6 h and 7 d after radiation exposure). The controls are from human alveolus chips that receive no radiation exposure and are compared to alveolus chips that receive 16 Gy radiation. Each condition has 4 replicates: Alveolar epithelium (0 Gy) 6h, Alveolar epithelium (16 Gy) 6h, Microvascular endothelium (0 Gy) 6h, Microvascular endothelium (16 Gy) 6h, Alveolar epithelium (0 Gy) 7d, Alveolar epithelium (16 Gy) 7d, Microvascular endothelium (0 Gy) 7d, Microvascular endothelium (16 Gy) 7d

first: Donald

last: Ingber

first: Amanda

last: Jiang


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication [ATACseq]

first: Silvia

overall_design: ATACseq data for 15 GBM celllines (representative of 4 molecular subtypes) vs normal human Astrocytes


title: Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying the neurogliomal synaptic communication

summary: Glioblastoma (GBM) is the most aggressive of all primary brain tumours. Here, we perform a multi-omics approach to map the promoter-enhancer interactome and the regulatory landscape of glioblastoma, including RNA-seq, ChIP-seq of histone marks (H3K4me3, H3K27ac, H3K27me3), H3K4me3 HiChIP and ATAC-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data, comparative histone marks distribution, chromatin accessibility and loop formation around promoters, for 15 GBM cell lines (representative of 4 molecular subtypes) vs normal human Astrocytes


title: In depth analysis reveals promotion of human macrophage polarization towards a proinflammatory M1 phenotype by TRAIL

city: IZMIR

first: Duygu

last: Sag

address: Dokuz Eylül Üniversitesi 15 Temmuz Sağlık ve Sanat Yerleşkesi, Mithatpaşa Cad. 58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary:
The study aimed to investigate the impact of TRAIL on primary human M1, M2a and M2c macrophage polarization. Primary human monocyte-derived macrophages were pre-stimulated with TRAIL and then either left unpolarized (M0) or polarized into M1, M2a, or M2c phenotypes
Then, RNA sequencing analysis was performed in 4 healthy donors including treated and control groups for one time point  to analyze the differentially expressed M1 and M2 markers in TRAIL treated vs control groups.

overall_design: Differentially expressed genes in TRAIL treated M0 (unpolarized) and then M1, M2a and M2c polarized macrophages vs control group macrophages including M0 and only M1, M2a and M2c polarized macrophages was analyzed.

first: Sinem

last: Gunalp

first: Derya

last: Helvaci

first: Aysenur

last: Oner

first: Ahmet

last: Bursali

first: Alessandra

last: Conforte

first: Huseyin

last: Guner

first: Gokhan

last: Karakulah

first: Eva

last: Szegezdi


title: Single-cell transcriptomics identifies new blood cell populations in Drosophila released at the onset of metamorphosis

city: Marburg

first: Katja

last: Rust

address: Emil-Mannkopff-Str. 2

institute: Phillips-University Marburg

summary:
Drosophila blood cells called hemocytes form an efficient barrier
against infections and tissue damage. During metamorphosis,
hemocytes undergo tremendous changes in their shape and
behavior, preparing them for tissue clearance. Yet, the diversity and
functional plasticity of pupal blood cells have not been explored. Here,
we combine single-cell transcriptomics and high-resolution
microscopy to dissect the heterogeneity and plasticity of pupal
hemocytes. We identified undifferentiated and specified hemocytes
with different molecular signatures associated with distinct functions
such as antimicrobial, antifungal immune defense, cell adhesion or
secretion. Strikingly, we identified a highly migratory and immuneresponsive
pupal cell population expressing typical markers of the
posterior signaling center (PSC), which is known to be an important
niche in the larval lymph gland. PSC-like cells become restricted to
the abdominal segments and are morphologically very distinct from
typical Hemolectin (Hml)-positive plasmatocytes. G-TRACE lineage
experiments further suggest that PSC-like cells can transdifferentiate
to lamellocytes triggered by parasitoid wasp infestation. In summary,
we present the first molecular description of pupal Drosophila blood
cells, providing insights into blood cell functional diversification and
plasticity during pupal metamorphosis.

overall_design: Three replicates of single cell RNA-sequencing of 2-10h APF Drosophila pupae using the Takara ICELL8 platform.

first: Alexander

last: Hischhäuser

first: Darius

last: Molitur

first: Gabriela

last: Salinas

first: Jörg

last: Großhans

first: Sven

last: Bogdan


title: Spliceosome mutations are associated with clinical response in a Phase 1b/2 study of the PLK1 inhibitor onvansertib in combination with decitabine in relapsed or refractory acute myeloid leukemia.

city: San Diego

first: Peter

last: Croucher

address: 11055 Flintkote Avenue

institute: Cardiff Oncology Inc

summary: Background: PLK1 is overexpressed in acute myeloid leukemia (AML). A Phase 1b trial of the PLK1 inhibitor onvansertib (ONV) combined with decitabine (DAC) demonstrated initial safety and efficacy in patients with relapsed/refractory (R/R) AML. The current study aimed to identify molecular predictors of response to ONV + DAC in R/R AML patients. Patients and methods: A total of 44 R/R AML patients were treated with ONV+DAC and considered evaluable for efficacy. Bone marrow (BM) samples were collected at baseline for genomic and transcriptomic analysis (n=32). A 10 gene expression-signature, predictive of response to ONV + DAC, was derived from the leading-edge genes of gene set enrichment analyses (GSEA). The gene signature was evaluated in independent datasets and used to identify associated mutated genes. Results: 20% of the patients achieved complete remission, with or without hematologic count recovery (CR/CRi) and 32% exhibited a ≥50% reduction in bone marrow blasts. Patients who responded to treatment had elevated mitochondrial function and OXPHOS. The gene signature was not associated with response to DAC alone in an independent dataset.  By applying the signature to the BeatAML cohort (n=399), we identified a positive association between predicted ONV + DAC response and mutations in splicing factors (SF). In the Phase 1b/2 trial, patients with SF mutations (SRSF2, SF3B1) had a higher CR/CRi rate (50%) compared to those without SF mutations (9%). Conclusion: PLK1 inhibition with ONV in combination with DAC could be a potential therapy in R/R AML patients, particularly those with high OXPHOS gene expression and SF mutations.

overall_design: Peripheral blood samples from patients with relapsed or refractory AML were taken prior to treatment with the combination of the PLK1 inhibitor onvansertib and the hypomethylating agent decitabine. The samples were retrospectively used to explore potential biomarkers and gene signatures of response to the treatment.


title: Spatial tramscriptomics of xenograft tumor tissues

city: San Antonio

first: Tim

middle: Hui-Ming

last: Huang

state: TX

address: 7703 Floyd Curl Dr

institute: University of Texas Health at San Antonio

summary: Xenograft tumors were generated in J:Nu mice by injecting C4-2 prostate cancer cells and hybrid cells derived from cultured C4-2 prostate cancer cells and U937 derived macrophages

overall_design: Investigate the differential pathways between C4-2 parental xenograft tissue and tumor-macrophage hybrid xenograft tissue.

middle: H

first: Chun-Liang

last: Chen

first: Chia-Nung

last: Hung

first: Zhang

last: Zhao


title: Differential gene expressions of various interferon, antiviral response genes as well as tissue factor (F3) and TMPRSS genes in primary airway epithelial cells infected with SARS-CoV-2

city: Rockville

last: Sun

address: 5625 Fishers Lane

department: National Institute of Allergy and Infectious Diseases (NIAID)

institute: National Institutes of Health (NIH)

summary: Clinical data show SARS-CoV-2 infection causes activation of host inflammatory antiviral response, including the type I interferon pathway and the expression of many inflammatory cytokines, as well as the infiltration of neutrophils and macrophages. It has been hypothesized that the overt host inflammatory response is at least partially responsible for COVID-19 associated diffuse alveolar damage (DAD). Our research focuses on one defining feature of DAD, hyaline membrane formation which is characterized by fibrin deposition in lung airspace. With primary normal human bronchial/tracheal epithelial (NHBE) cells and human small airway epithelial cells (HSAEC) as in vitro models, we have evidence of turbidity assay, confocal microscopy, and scanning electron microscopy (SEM) proving that infection with field isolates of SARS-CoV-2 variants and SARS-CoV-2 spike pseudotyped lentiviruses (pSARS2) induces fibrin clot formation in the NHBE and HSAEC cells. We have also observed that the infection-induced fibrin formation in NHBE and HSAEC cells requires thrombin but is independent of tissue factor and other classical plasma coagulation factors. In addition, we have validated involvement of type II transmembrane serine proteases (TMPRSS) in the activation of thrombin, the last enzyme in the coagulation cascade.    Therefore, we performed RNA sequencing analyses to infected NHBE and HSAEC cells and further investigated how SARS-CoV-2 variants and pSARS2 regulate type I interferon response, antiviral innate response, and expression of TMPRSS genes. By doing this, we found both pSARS2 and the field delta variant viruses upregulated type I interferon and innate antiviral responses in the infected NHBE and HSAEC cells compared to their uninfected controls. However, we did not observe significant upregulation in the tissue factor transcription in both pSARS2 and the delta variant infected samples.

overall_design: To investigate how viral infection regulates type I interferon response, antiviral innate response, and expression of TMPRSS genes in lung epithelial cells, we cultured two types of lung epithelial cells, NHBE and HSAEC in vitro and uninfected or infected these cells.    We then performed gene expression profiling analysis using data obtained from RNA-seq of these 2 different cells either uninfected or infected with SARS-CoV-2 delta variant or SARS-CoV-2 spike pseudotyped lentiviruses.     Comparative gene expression profiling analysis of RNA-seq data for infected NHBE and HSAEC cells and their uninfected counterparts. Each condition contains duplicate samples .

first: Chang


title: Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity

status: Public on Sep 09 2023

city: Berkeley

first: Ben

last: Williams

address: 2151 Berkeley Way

institute: UC Berkeley

type: Methylation profiling by high throughput sequencing

summary: Background: In diverse eukaryotes, DNA methylation is deposited within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance has remained unclear. Results: We report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages (>100 million years), indicating evolutionary conservation. Furthermore, we demonstrate that Dynamic GbM is tightly associated with the presence of a promoter/regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. Lastly, we find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Conclusions: This study proposes a new model for GbM in regulating gene expression plasticity, including a newly discovered type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state. We propose that Dynamic GbM is a hallmark of genes that can navigate a greater landscape of transcriptional states by maintaining regulatory flexibility.

overall_design: NEBNext® Enzymatic Methyl-seq

first: Clara

middle: J

first: Dawei

last: Dai

first: Kevin

last: Tran

first: Grey

last: Monroe


title: Single-cell sequencing of tumor-associated macrophages in a Drosophila model

status: Public on Sep 08 2023

city: Stockholm

first: Mubasher

last: Mohammed

state: Stockholm lan

address: Svante Arrhenius Väg 20c, MBW, Stockholms University

department: Department of Molecular Biosciences, the Wenner-Gren Institute

institute: Stockholm University

summary: Tumor-associated macrophages may act to either limit or promote tumor growth, yet the molecular basis for either path is poorly characterized. Using a Drosophila model for dysplastic growth during tumor early progression in combination with single-cell RNA sequencing of macrophage-like hemocytes, we identified 5 cell clusters. We included a second tumor model in our analysis where we inhibited the activation of effector caspases, partially mimicking apoptosis-resistant tumor cells. Circulating hemocytes from both tumor models differ qualitatively from control wild-type cells – they display an enrichment for genes involved in cell division, which was confirmed using proliferation assays. Split analysis of the tumor models further reveals that proliferation is strongest in the caspase-deficient setting. Similarly, depending on the tumor model, hemocytes that attach to tumors activate different sets of immune effectors – antimicrobial peptides dominate the response against the tumor alone, while caspase inhibition induces a shift toward members of proteolytic cascades. Finally, we find evidence for transcript transfer between hemocytes and possibly other tissues.

overall_design: Here, to identify genes that are differentially expressed in hemocytes from tumor larvae, we profiled the transcriptome of circulating single-cell hemocytes from wild-type and tumor larvae, as well as from tumor-associated hemocytes (TAHs), which were extracted manually from tumorous salivary glands (Fig 1A). Since we had previously observed strong activation of caspases in RasV12-expressing SGs (20), and in light of the bi-edged nature of caspase activation and apoptosis in cancer (see above), we included larvae where effector caspases were inhibited by the expression of the specific inhibitor p35

first: Dilan

last: Khalili

first: Martin

last: Kunc

first: Martina

last: Šindlerová

first: Johan

last: Ankarklev

first: Ulrich

last: Theopold


title: Comparative RNA-Seq transcriptome analyses of diabetic nerve and kidney disease II

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: Diabetic kidney disease (DKD) and diabetic peripheral neuropathy (DPN) are common complications of type 1 (T1D) and type 2 (T2D) diabetes. However, the mechanisms underlying the development and progression of these complications are unclear. Thus, the goal of the current study was to use system biology approaches to examine DKD and DPN pathogenesis in T1D and T2D mouse models on the same genetic background. We optimized a streptozotocin-induced db/+ murine model of T1D and compared it to our established db/db T2D mouse model of the same C57BLKS/J background and confirmed both develop DKD and DPN. Transcriptomic data from glomeruli and sciatic nerve tissue from T1D and T2D mice were analyzed by self-organizing map and differential gene expression analysis followed by functional enrichment. Consistent with prior literature, pathways related to immune function and inflammation were dysregulated in both DKD and DPN in T1D and T2D mice. The gene-level analysis identified a high degree of concordance in DEGs in both DKD and DPN and across diabetes type, suggesting genetic background influences diabetic complications. These findings offer new insight as the influence of genetic background on DPN in mouse models has not been well defined. Collectively, these findings support the role of inflammation and genetic background in complications of both T1D and T2D.

overall_design: mRNA profiles of four diabetic complication-prone tissues (sciatic nerve, dorsal root ganglia, kidney glomeruli and kidney cortex) from 16-week old BKS.Cg-m +/+ Leprdb/J mice with/without pioglitazone treatment of 15 mg/kg for 11 weeks. For type 1 diabetes model, a single high-dose 150 mg/kg (i.p.) streptozotocin (STZ) injection at 5 weeks of age, while db/db genetic model was used for type 2 diabetes model. Deep sequencing of six biological replicates in each tissues using Illumina HiSeq 2000.

first: Eva

last: Feldman


title: Single cell RNA-seq of seizure-affected brain tissue with mosaic copy number gain of chromosome 1q

city: Columbus

first: Katherine

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary: Somatic mosaicism is a known cause of neurological disorders, including developmental brain malformations and epilepsy. Brain mosaic copy number gain of chromosome 1q is associated with cortical malformations, early-onset epilepsy, and developmental delay. Pathogenic brain mosaicism is traditionally attributed to post-zygotic genetic alterations arising in a neural progenitor cell during fetal development. However, in our cohort, in at least five of six patients with brain mosaic copy number gain of chromosome 1q, the alteration occurred pre-conception. We observed a third non-constitutive, but parentally-derived, haplotype for chromosome 1q in patient brain tissue, demonstrating that the copy number alteration occurred in a gamete pre-conception. The altered cells had no representation in parental buccal or proband blood or buccal samples, but were prominently observed in proband brain tissue, suggesting the copy number gain was lost in most cell lineages during embryonic development. Single-nuclei genotyping coupled with gene expression profiling revealed a strong enrichment of the chromosome 1q gain in astrocytes, which correlated with the unusual finding of hyaline astrocytic inclusions in all six cases.

overall_design: We used surgically resected brain tissue from children with epilepsy to dissociate single nuclei (from frozen tissue) and prepare for sequencing using 10x Genomics single cell 3' v3.1. In most tissues, we previously identified a chr1q gain at mosaic levels; some tissues do not have the chr1q gain and are from adjacent brain sections.

first: Tracy

last: Bedrosian

first: Erin

last: Heinzen


title: Mechanism of Hyperproteinemia-Induced Damage to Female Reproduction in a Genetic Silkworm Model

status: Public on Sep 06 2023

city: Suzhou

first: Guihua

last: Jiang

address: Renai Road 199, Dushu Lake Higher Education Town

institute: Soochow University

summary: Hyperproteinemia is a metabolic disorder characterized by abnormally elevated plasma protein concentrations (PPC) in humans and animals. Here, a genetic silkworm model with high PPC was employed to investigate the effect of elevated PPC on female reproduction. Transcriptomic analysis revealed that high PPC induces downregulation of the ovarian development-related genes and disrupts ovarian sugar metabolism. Biochemical and endocrinal analyses revealed that high PPC increases trehalose and glucose levels in hemolymph and glycogen content in the fat body through activation of the gluconeogenic pathway and inhibition of the IIS-AKT pathway, thus disrupting characteristic metabolic homeostasis of sugar in the ovary. These resulted in ovarian developmental delay as well as reduced number and poor quality of eggs. Insulin supplementation effectively increased egg numbers by lowering blood sugar. These collective results provide new insights into the mechanisms by which high PPC negatively affects female reproduction and support the potential therapeutic effects of insulin.

overall_design: To identify the molecular targets of high PPC that affect female reproduction, RNA-seq analysis was performed on ovarian tissues at the P2 and P4 stages

first: Gui-Hua

first: Guang

last: Wang

first: Cheng

last: Luo

first: Yong-Feng

first: Jian-Feng

last: Qiu

first: Ru-Ji

last: Peng

first: Yang-Hu

last: Sima

first: Shi-Qing

last: Xu


title: High-dimensional deconstruction of pancreatic cancer identifies tumor microenvironmental and developmental stemness features that predict survival

city: St. Louis

first: Erik

last: Storrs

state: MO

address: 660 S Euclid Ave

institute: Washington University

summary: Numerous cell states are known to comprise the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME). However, the developmental stemness and co-occurrence of these cell states remain poorly defined. Here, we performed single-cell RNA sequencing (scRNA-seq) on a cohort of treatment-naive PDAC time-of-diagnosis endoscopic ultrasound-guided fine needle biopsy (EUS-FNB) samples (n=25). We then combined these samples with surgical resection (n=6) and publicly available samples to increase statistical power (n=80). Following annotation into 25 distinct cell states,  cells were scored for developmental stemness and a customized version of the Ecotyper tool was used to identify communities of co-occurring cell states in bulk RNA-seq samples (n=268). We discovered a tumor microenvironmental community comprised of aggressive basal-like malignant cells, tumor-promoting SPP1+ macrophages, and myofibroblastic cancer-associated fibroblasts associated with especially poor prognosis. We also found a developmental stemness continuum with implications for survival that is present in both malignant cells and cancer-associated fibroblasts (CAFs). We further demonstrated that high-dimensional analyses predictive of survival are feasible using standard-of-care, time-of-diagnosis EUS-FNB specimens. In summary, we identified tumor microenvironmental and developmental stemness characteristics from a high-dimensional gene expression analysis of PDAC using human tissue specimens including time-of-diagnosis EUS-FNB samples. These reveal new connections between tumor microenvironmental composition, CAF and malignant cell stemness, and patient survival that could lead to better upfront risk stratification and more personalized upfront clinical decision-making.

overall_design: We performed scRNA-seq of PDAC from standard-of-care time-of-diagnosis endoscopic ultrasound guided fine needle biopsy (EUS-FNB) specimens at the time-of-diagnosis and from surgical samples obtained from tumor resections to enable a clinically integrated, comprehensive view of PDAC

first: Chaudhuri

last: Aadel

first: Das

last: Koushik


title: Gene expression analysis of Zymomonas mobilis ZM4 for promoter strengths prediction

status: Public on Sep 07 2023

city: Wuhan

first: Wenfang

address: No.368 Youyi Avenue

institute: Hubei University

summary: Looking at the expression levels of all the genes of Zymomonas mobilis ZM4; and in particular we would like to predict the strengths of the genes located on the native plasmids.

overall_design: RNA seq was performed based on 3 colonies of Zymomonas mobilis ZM4. And we performed gene expression profilling analysis using the obtianed from the RNA-seq.

first: Yuejie

last: Bian


title: Transcriptional and epigenetic landscape of the mouse intestine during aging identifies key molecular drivers of aging -associated dysfunctions and diseases

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

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

overall_design: Refer to individual Series


title: Gene expression profiles of endometrium from women across the menstrual cycle

city: Parkville

first: Peter

last: Rogers

state: VIC

address: Level 7, University Department, Royal Women's Hospital, Crn Grattan Street and Flemington Rd

department: Department of Obstetrics and Gynaecology

institute: University of Melbourne

summary: Natural variability in menstrual cycle length, coupled with rapid changes in endometrial gene expression, makes it difficult to accurately define and compare different stages of the endometrial cycle. We have developed and validated a novel method for precisely determining endometrial cycle stage based on global gene expression. Our ‘molecular staging model’ reveals significant and remarkably synchronized daily changes in expression for over 3,400 endometrial genes throughout the cycle, with the most dramatic changes occurring during the secretory phase.

overall_design: Total RNA from endometrial biopsy was obtained from women across the menstrual cycle. Cycle stages were evaluated using histopathology. Menstrual cycle stage definitions, assuming a standardized 28 day cycle, and numbers of samples in each group were as follows: Stage 1 = menstrual (days 1–4), 2 = early proliferative (days 5–7), 3 = mid proliferative (days 8–11), 4 = late proliferative (days 12–15, includes ‘interval’), 5 = early secretory (days 16–19, or post ovulation days 2-5), 6 = mid secretory (days 20–23, or post ovulation days 6-9), 7 = late secretory (days 24–28, or post ovulation days 10-14).

first: Jessica

last: Chung

first: Wan

middle: T

last: Teh

first: Sally

last: Mortlock

first: Jenny

middle: N

last: Fung

first: Grant

last: Montgomery


title: Single cell RNA sequencing of pancreastic cancer associated fibroblasts (CAFs) exposed to hypoxia

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

summary: Single cell RNA sequencing of cancer associated fibroblasts cultured in hypoxia and normoxia environments

overall_design:
Total 81 HCCs with PET information were sequenced to identify gene expressions. Cancer associated fibroblasts isolated from two pancreatic cancer patients were cultured and exposed to hypoxia and normoxia environments, respectively. Then single cell RNA sequencing was performed.
*** Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns. ***

first: Dakeun

last: Lee

first: Chang

middle: O


title: The Glucocorticoid Receptor regulates behaviour, DNA methylation and gene transcription in the adult zebrafish brain

city: Sheffield

first: Vincent

middle: Trevor

last: Cunliffe

state: South Yorkshire

address: Western Bank

department: School of Biosciences

institute: University of Sheffield

summary: The Glucocorticoid Receptor (GR) is a transcriptional regulator which co-ordinates behavioural, metabolic and immune responses to stressors. Previous studies have shown that wild-type and grs357 mutant zebrafish exhibit a range of behavioural differences, implying possible roles for GR function in the brain. As part of a study to elucidate the mechanisms underlying the behaviours that are regulated by GR, we compared the brain transcriptomes of wild-type and grs357 mutant adults. RNA-seq analysis identified 19 Biological Process and 4 Molecular Function Gene Ontology (GO) terms that were particularly sensitive to loss of GR function. Foremost among the Biological Process terms linked to GR function are Chaperone-mediated Protein Folding, Regulation of Circadian Rhythm and Regulation of Primary Metabolic Process, each of which is accompanied by several other closely related GO terms. In addition, the Biological Process GO term Behavior was significantly associated with 32 genes exhibiting GR-regulated gene transcription. The Molecular Function terms most closely linked to GR function are Heat Shock Protein Binding, Protein Serine/Threonine Kinase Activity, Transcription Regulator Activity and Unfolded Protein Binding. Taken together, our results identify key biological processes and novel molecular mechanisms through which the GR likely regulates responses to stress in the zebrafish adult brain.

overall_design: To determine the molecular function of GR in the adult brain, we compared the brain transcriptomes of adult grs357 mutant zebrafish brains versus wild-type age matched sibling brains through RNA sequencing analysis.

first: Helen

middle: L

last: Eachus

first: Lara

last: Oberski

first: Jack

last: Paveley


title: A first-in-class fully modified version of miR-34a with outstanding stability, activity, and anti-tumor efficacy

status: Public on Sep 05 2023

city: West Lafayette

first: Ikjot Singh

last: Sohal

state: IN

address: 4332 Foal Dr

department: Biological Sciences

institute: Purdue University

summary: Altered by defects in p53, epigenetic silencing, and genomic loss, the microRNA miR-34a represents one of the most clinically relevant tumor-suppressive microRNAs. Without question, a striking number of patients with cancer would benefit from miR-34a replacement, if poor miR-34a stability, non-specific delivery, and delivery-associated toxicity could be overcome. Here, we highlight a fully modified version of miR-34a (FM-miR-34a) that overcomes these hurdles when conjugated to a synthetically simplistic ligand. FM-miR-34a is orders of magnitude more stable than a partially modified version, without compromising its activity, leading to stronger repression of a greater number of miR-34a targets. FM-miR-34a potently inhibited proliferation and invasion, and induced sustained downregulation of endogenous target genes for >120 hours following in vivo delivery. In vivo targeting was achieved through conjugating FM-miR-34a conjugated to folate (FM-FolamiR-34a), which inhibited tumor growth leading to complete cures in some mice. These results have the ability to revitalize miR-34a as an anti-cancer agent, providing a strong rationale for clinical testing.

overall_design: This experiment is designed to compare the effect of partially- and fully-modified miR-34a on gene expression relative to a negative control (scramble siRNA) or untreated through mRNA profiling of MB231 cells transfected with the different oligos.

first: Ahmed

middle: M

last: Abdelaal

first: Ikjot

first: Shreyas

last: Iyer

first: Kasireddy

last: Sudarshan

first: Harish

last: Kothandaraman

first: Nadia

middle: A

last: Lanman

first: Philip

last: Low

first: Andrea

last: Kasinski


title: Attenuated IL-2 muteins promote regulatory T cell adaptation of the effector phenotype and function in vivo via modified IL-2 responses

city: South San Francisco

first: Shining

last: Ma

state: CA

address: 1120 Veterans Blvd

institute: Amgen Inc.

summary: Interleukin-2 (IL-2), along with T-cell receptor (TCR) signaling, are required to control regulatory T cell (Treg) homeostasis and function in vivo. Due to the heightened sensitivity to IL-2, Tregs retain the ability to respond to low-dose or attenuated forms of IL-2, as currently being developed for clinical use to treat inflammatory diseases. While attenuated IL-2 increases Treg selectivity, the question remains as to whether a weakened IL-2 signal sufficiently enhances Treg suppressive function(s) toward disease modification.  To understand this question, we characterized the in vivo activity and transcriptomic profiles of two different attenuated IL-2 muteins in comparison with wildtype (WT) IL-2. Our study showed that, in addition to favoring Tregs, the attenuated muteins induced disproportionately robust effects on Treg activation and conversion to effector Treg (eTreg) phenotype. Our data furthermore suggested that Tregs activated by attenuated IL-2 muteins showed reduced dependence on TCR signal, at least in part due to the enhanced ability of IL-2 muteins to amplify the TCR signal in vivo. These results point to a new paradigm wherein IL-2 influences Tregs’ sensitivity to antigenic signal, and that the combination effect may be leveraged for therapeutic use of attenuated IL-2 muteins.

overall_design: Four different IL-2 treatment conditions (PBS, WT IL-2, H16R, and 3x mutein) within 2 antibody treatment groups (isotype and MHC II blocking antibodies) were evaluated with 4 mice in each group, resulting in a total of 32 Treg samples. CD25- Tcons from two mice from each group were included for comparison.

first: Michelle

last: So

first: Aazam

last: Ghelani

first: Rohith

last: Srivas

first: Anupama

last: Sahoo

first: Robyn

last: Hall

first: Wenjun

last: Liu

first: Hao

last: Wu

first: Sherman

last: Yu

first: Shiping

last: Lu

first: Elly

last: Song

first: Taryn

last: Cariaga

first: Marcus

last: Soto

first: Hong

last: Zhou

first: Chi-Ming

last: Li

first: Ashutosh

last: Chaudhry

first: Xin

last: Luo

first: Sue

last: Sohn


title: A molecular staging model for accurately dating the endometrial biopsy

first: Peter

last: Rogers


title: scRNA-seq of young and aged lungs following influenza A virus infection

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary: Aging is known to alter the host repsonse to influenza infection. Here, we use single-cell RNA sequencing (scRNA-seq) to identify cellular changes in the lungs of young (16-week-old) and aged (80-week-old) mice following influenza infection.

overall_design: Mice were infected with influenza A/PR8/34 (~50 PFU/mouse) to establish acute infection. Infections were performed by intranasal (i.n.) administration under anesthesia as described before (Sun et al., 2009). Mice were then euthanized and the right ventricle was perfused with 10 mL cold DPBS (Corning). The lung lobes were cut into fine pieces and digested at 37 °C with collagenase IV (1 mg/mL; Worthington) for 40 minutes. The tissue pieces were further ground and homogenized in a 70 μm cell strainer. After spinning down, red blood cells were removed by addition of ACK lysis buffer (Lonza) for 10 minutes on ice. Cells were kept in 10% RPMI (Lonza) at all times. Only day 9 post-infection samples were sorted for scRNA-seq. Single-cell suspensions were incubated with antibodies against surface markers for 30 minutes at 4 °C in 10% RPMI, followed by 2 washes in 10% RPMI. Samples were then run on an Aria IIIu cell sorter (BD Biosciences). For day 9 post-infection samples, single-cell suspensions of lung tissue were FACS sorted (see above), and Lin+ cells and Lin– cells from each sample were individually pooled at a 1:1 ratio. For day 3 post-infection samples, cells were not sorted as the ratio of Lin+:Lin– cells was approximately 1:1. Cells were loaded onto the Chromium Controller (10x Genomics), then the 10x Genomics 3’ v2 Reagent Kit (day 9 post-infection samples) or the 10x Genomics 3’ v3.1 Reagent Kit (day 3 post-infection samples) was used to generate cDNA libraries. Barcoded libraries were sequenced on an Illumina NextSeq 500 instrument using a NextSeq 500/550 High Output Kit v2 (150 cycles) (20024907, Illumina) with the following cycle counts: 28 (read 1), 8 (index), and 91 (read 2) (day 9 post-infection samples) or 28 (read 1), 10 (index 1), 10 (index 2), 90 (read 2) (day 3 post-infection samples). Data were demultiplexed and aligned to the mm10 2020-A reference transcriptome (10x Genomics) using Cell Ranger (v6.0, 10x Genomics). Analysis was performed in R using Seurat (v4.0) (Butler et al., 2018), with tidyverse (v1.3.1) used for data organization (Wickham et al., 2019). Receptor-ligand analysis was performed using CellChat (v1.1.3) (Jin et al., 2021) with default settings.

first: Moujtaba

last: Kasmani


title: Bulk RNA-seq of young and aged lungs following influenza A virus infection

summary: Aging is known to alter the host repsonse to influenza infection. Here, we use bulk RNA sequencing (bulk RNA-seq) to identify cellular changes in the lungs of young (16-week-old) and aged (80-week-old) mice following influenza infection.

overall_design: Mice were infected with influenza A/PR8/34 (~50 PFU/mouse) to establish acute infection. Infections were performed by intranasal (i.n.) administration under anesthesia as described before (Sun et al., 2009). Mice were then euthanized and the right ventricle was perfused with 10 mL cold DPBS (Corning). For bulk RNA-seq, pieces of right lung were harvested after ventricular perfusion and snap frozen on dry ice. RNA was extracted using an RNAEasy Mini Kit (Qiagen). Reverse transcription was performed and the resultant cDNA was enzymatically fragmented and indexed using a Nextera XT DNA Library Preparation Kit (Illumina). Barcoded cDNA libraries were sequenced on an Illumina NextSeq 500 instrument using a NextSeq 500/550 High Output Kit v2 (75 cycles) (20024906, Illumina) with the following cycle counts: 37 (read 1), 8 (index 1), 8 (index 2), 37 (read 2). Demultiplexing was performed using bcl2fastq (v2.20, Illumina). Alignment was performed using Salmon (v1.4.0) (Patro et al., 2017) and the GRCm39 reference genome (Ensembl) with default settings. Downstream analysis was performed in R using DESeq2 (v1.28.1) (Love et al., 2014).


title: RNA sequencing data after simultaneous transactivation of M-opsin and knockout of rhodopsin upon subretinal injection of mice with the REVeRT dual AAV system

city: Munich

first: Elvir

last: Becirovic

address: Butenandtstr. 5-13

department: Department of Pharmacy - Center for Drug Research

institute: LMU Munich

summary: Large genes including several CRISPR-Cas modules, such as gene activators (CRISPRa), require dual adeno-associated viral (AAV) vectors for efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). REVeRT is flexible in split site selection and can efficiently reconstitute different split genes in numerous in vitro models, in human organoids and in vivo. Furthermore, REVeRT can functionally reconstitute a CRISPRa module targeting genes in various mouse tissues and organs in single or multiplexed approaches upon different routes of administration. Finally, supplementation of ABCA4 (6.8 kb) via REVeRT improves retinal degeneration and function in a mouse model of inherited blindness. Due to its flexibility and efficiency REVeRT harbors great potential for basic research and clinical applications.

overall_design: Examination of two different groups of mice heterozygous for the P23H mutation subretinal injected at post natal day 21 with dual AAV encoding for Cas9-VPR and sgRNAs for either the knockout of Rhodopsin and transactivation of M-opsin (sgRho-3xsgOpn1mw, n = 3) or a control sgRNAs targeting the bacterial lacZ locus (sglacZ, n = 4). Retinas were isolated 4 weeks after subretinal injection.

first: Klara

last: Hinrichsmeyer


title: A molecular staging model for accurately dating the endometrial biopsy [RNA-seq]

first: Jessica

last: Chung

first: Wan

last: Teh

first: Sally

last: Mortlock

first: Jenny

last: Fung

first: Grant

last: Montgomery