city: Bunkyo-ku, Tokyo

first: YUKI

last: YONEMOTO

address: 1-5-45 Yushima

institute: Tokyo Medical And Dental University

summary: Recent advances in research suggest that aging has a controllable chronic inflammatory disease aspect. Aging systemic T cells, which secrete pro-inflammatory factors, affect surrounding somatic cells, and accelerate the aging process through chronic inflammation, have attracted attention as potential therapeutic targets in aging. On the other hand, there are few reports on the aging of the intestinal immune system, which differs from the systemic immune system in many ways. In the current study, we investigated the age-related changes in the intestinal immune system, particularly in T cells. The most significant changes were observed in the CD4+ T cells in the small intestinal IEL, with a marked increase in the proportion of this fraction in old mice and reduced expression of the co-stimulatory molecules CD27 and CD28, which are characteristic of aging systemic T cells. The proliferative capacity of aging IEL CD4+ T cells was significantly more reduced than that of aging systemic T cells. Comprehensive transcriptome analysis showed that the expression of inflammatory cytokines such as TNF was not upregulated, whereas Cd8α, NK receptors, and Grazymes were upregulated in aging IEL CD4+ T cells. Functional analysis showed that aging IEL T cells had a higher cytotoxic function against intestinal tumor organoids in vitro than young IEL T cells. scRNAseq revealed that splenic T cells show a transition from naïve to memory T cells, whereas intestinal T cells show the emergence of a CD8αα+CD4+ T cell fraction in aged mice, which is rarely seen in young cells. Further analysis of the aging IEL CD4+ T cells showed that two unique subsets are increased, which are distinct from the systemic CD4+ T cells. Subset 1 has a pro-inflammatory component, with expression of IFNγ and upregulation of NFkB signaling pathways. Subset 2 does not express IFNγ, but upregulates inhibitory molecules and nIEL markers. Expression of granzymes and CD8α was common to both. These two fractions were in opposite positions in the clustering by UMAP and indeed had different TCR repertoires. They may be involved in the suppression of intestinal aging and longevity through anti-tumor immunity, elimination of senescent cells and stressed cells in the aging environment. This finding could be a breakthrough in aging research.

overall_design: SI-IELs or SP cells were collected and pooled from young (6-week-old) or old C57BL/6 mice (80-week-old), the cells from 3 young mice and 3 old mice were mixed and pooled as young SP, young IEL, old SP and old IEL. CD45+ cells were enriched from each group using CD45 microbeads (Miltenyi Biotec), followed by cell hashing with TotalSeq-C anti-mouse hashtag antibodies (hashtag1-young IEL, hashtag2-old IEL, hashtag3-young SP, hashtag4-old SP). After the Fc blocking, cells were stained with anti-CD3e-FITC mAbs and anti-CD4-APC mAbs, and the CD3+ cells and CD3+CD4+ cells were sorted from each group by FACSMelody. Dead cells removal was performed with 7-AAD. To enrich CD4+ cells, which are rare population in young IEL, CD3+ cells and CD3+CD4+ cells were mixed as 1:1 in young and old IEL.


title: DNMT3B PWWP mutations cause hypermethylation of heterochromatin (T7-DNMT3B ChIP-seq)

status: Public on Jan 22 2024

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies through its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here we find that knockout of DNMT3B causes losses of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1-alpha and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent manner that is facilitated by the protein's N-terminus through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.

overall_design: This series contains T7-DNMT3B ChIP-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT3B or expressing T7 tagged DNMT3B WT or mutant versions were grown before chromatin was extracted and T7-DNMT3B levels analysed by ChIP-seq.


title: Gene expression profile at single cell level of donor-matched primary bovine Mesenchymal Stromal Cells (MSCs)

city: Ithaca

first: Gerlinde

middle: R.

last: Van de Walle

state: NY

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

country: USA

institute: Cornell University

type: Expression profiling by high throughput sequencing

summary: Bovine MSCs were isoalted from adipose tissue, bone marrow and peripheral blood, from one donor. These cells were then subjected to scRNA-sequencing.

overall_design: Fresh tissue samples were collected and cultured to isolate MSCs. Upon MSC colony formation, the cells were detached and libraries were prepared for scRNA-seq.

first: Nikola

last: Danev

first: Guangsheng

last: Li

first: Jingyue

middle: E

last: Duan

middle: R


title: Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

type: Methylation profiling by high throughput sequencing

summary: Small-cell lung cancer (SCLC) is an aggressive malignancy composed of distinct transcriptional subtypes, each with unique therapeutic vulnerabilities. Implementing subtyping in the clinic has remained challenging due to limited tissue availability, particularly for longitudinal monitoring. Given the known epigenetic regulation of critical SCLC transcriptional programs, we hypothesized that there would be subtype-specific patterns of DNA methylation that could be detected in tumor or blood from SCLC patients. Using genomic-wide reduced-representation bisulfite sequencing (RRBS) in two cohorts of totally 179 SCLC patients and machine learning approaches, we developed a highly accurate DNA methylation-based classifier (SCLC-DMC) that could distinguish SCLC subtypes using clinical tumor samples with 95.8% accuracy in the testing set compared to mRNA-based profiling. We further adjusted the classifier for circulating-free DNA (cfDNA) to subtype SCLC from plasma. Using the cfDNA classifier (cfDMC) we could demonstrate that SCLC phenotypes can evolve during disease progression, highlighting the need for longitudinal tracking of SCLC during clinical treatment. Furthermore, methylation-based subtyping predicted response to a wide variety of drugs in preclinical models and clinical outcomes were indistinguishable in cohorts of patients subtyped using mRNA or SCLC-DMC. These data establish that tumor and cfDNA methylation can be used to identify SCLC subtypes and guide precision SCLC therapy.

overall_design: Reduced Representation Bisulfite Sequencing (RRBS) from Small Cell Lung Cancer Cell lines

first: Yuanxin

last: Xi

first: Simon

last: Heeke

first: Jing

last: Wang

first: Lauren

middle: A

last: Byers

first: John

middle: V

last: Heymach


title: Regulation of nuclear transcription by mitochondrial RNAs [scRNA-seq/snRNA-seq]

city: Duarte

first: Zhen

last: Chen

state: CA

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

summary: To understand the SncmtRNA-regulated endothelial gene expression. We performed single cell and single nuclear RNA-seq in endothelial cells with inhibition of SncmtRNA.

overall_design: Performing single-cell and single-nuclear RNA-seq in HUVECs upon knockdown of SncmtRNA and treatment with 25 mM high-glucose + 5ng/ml TNFa

first: Kiran

last: Sriram

first: Dongqiang

last: Yuan

first: Riccardo

last: Calandrelli

first: Sheng

last: Zhong

middle: B


title: Cis inhibition of NOTCH1 through JAGGED1 sustains embryonic Hematopoietic stem cell fate

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

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

overall_design: Refer to individual Series


title: Gene expression and VDJ profiling at single cell level of CD4 T cells isolated from the female reproductive tract (FRT) of Chlamydia muridarum infected WT (B6) and Bhlhe40-/- mice

status: Public on Jan 21 2024

city: Little Rock

first: Lin-Xi

state: AR

address: 4301 W. Markham St

department: Department of Microbiology and Immunology

institute: University of Arkansas for Medical Sciences

summary: CD4 T cells are recruited to the FRT following Chlamydia intravaginal infection.  We use single-cell RNA sequencing and VDJ profiling to compare CD4 T cells sorted from WT (B6) and Bhlhe40-/- mice at 14 days post Chlamydia muridarum intravaginal infection.

overall_design: Activated CD4 T cells in the FRT of Chlamydia-infected WT (B6) and Bhlhe40-/- mice were sorted by fluorescence-activated cell sorting (FACS) according to CD4+, CD44hi and CD90.2+ expression, and the absence of CD11b, B220 and F4/80 expression.  Sorted cells were analyzed using scRNAseq.

first: Miguel

last: Mercado

first: Qiang

first: Lu

last: Huang


title: Regulation of nuclear transcription by mitochondrial RNAs [bulkRNA-seq]

summary: In order to understand the SncmtRNA-regulated endothelial transcriptome, we performed loss and gain of function of SncmtRNA and profiled transcriptome.

overall_design: Performing polyA-enriched RNA-seq in HUVECs with SncmtRNA knockdown by LNA GapmeR or SncmtRNA overexpression with AAV9

first: Sriram

last: Kiran

first: Zhijie

last: Qi

first: Naseeb

middle: K

last: Malhi

first: Xuejing

last: Liu

first: Xiaofang

last: Tang


title: Parkinson's Disease Risk Enhancers in Microglia [RNA-seq]

city: Grand Rapids

first: Gerhard

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Institute

summary: Genome-wide association studies (GWAS) have uncovered thousands of single nucleotide polymorphisms (SNPs) that are associated with Parkinson's disease (PD) risk. The functions of most of these SNPs, including the cell type they influence, and how they affect PD etiology remain largely unknown. To identify functional SNPs, we aligned PD risk SNPs within active regulatory regions of DNA in microglia, a cell type implicated in PD development. Out of 6,749 ‘SNPs of interest’ from the most recent PD GWAS metanalysis, 73 were located in open regulatory chromatin as determined by both ATAC-seq and H3K27ac ChIP-seq.  We identified an active enhancer in microglia in intron two of SNCA that overlaps two PD risk SNPs, rs2737004 and rs2619356. In iPSC-derived microglia, CRISPR/Cas9 deletion of the open chromatin encompassing these SNPs caused reduced expression of multiple genes including SNCA and the adjacent gene MMRN1. Loss of the enhancer also led to upregulation of genes involved in glucose metabolism, a process that is known to be altered in PD patients. Our work expands the role of SNCA in Parkinson’s Disease and provides a connection between PD-associated genetic variants and underlying biology that points to a risk mechanism in microglia.

overall_design:
To assess the functionality of a PD risk enhancer in intron 2 of SNCA, RNA-seq was performed at three time-points across differentiation, (1) iPSCs (2) hematopoietic progenitors (HPCs) and (3) microglia, in wild-type cells and two clones generated via CRISPR/Cas9 deletion of 439 base pairs of the open chromatin region at the enhancer.
[contributor] Van Andel Institute Genomics Core

first: Alix

last: Booms

first: Steven

last: Pierce

first: Edwin

middle: J

last: van der Schans


title: Parkinson's Disease Risk Enhancers in Microglia [ATAC-seq]

overall_design:
Assay for transposase-accessible chromatin with sequencing (ATAC-seq) in iPSC-derived microglia cells was performed to map functional SNPs, classified based on their location in open chromatin at active enhancers and promoters.
[contributor] Van Andel Institute Genomics Core


title: Neuromorphic Electro-Stimulation Based on Atomically Thin Semiconductor for Damage-Free Inflammation Inhibition

status: Public on Jan 20 2024

city: shanghai

first: Shen

address: Yishan road 600

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Inflammation, caused by accumulation of inflammatory cytokines from immunocytes, is prevalent in a variety of diseases. Electro-stimulation emerges as a promising candidate for inflammatory inhibition. Although electroacupuncture is free from surgical injury, it faces the challenges of imprecise pathways/current spikes, and insufficiently defined mechanisms, while non-optimal pathway or spike would require high current amplitude, which makes electro-stimulation usually accompanied by damage and complications. Here, we propose a neuromorphic electro-stimulation based on atomically thin semiconductor floating-gate memory interdigital circuit. Direct stimulation is achieved by wrapping sympathetic chain with flexible electrodes and floating-gate memory are programmable to fire bionic spikes, thus minimizing nerve damage. A substantial decrease (73.5%) in inflammatory cytokine IL-6 occurred, which also enabled better efficacy than commercial stimulator at record-low currents with damage-free to sympathetic neurons. Additionally, using transgenic mice, the anti-inflammation effect is determined by β2 adrenergic signaling from myeloid cell lineage (monocytes/macrophages and granulocytes).

overall_design: There were 2D ES (tendon surgery, flexible electrode implantation and 2D ES), non-ES (tendon injury and flexible electrode implantation without ES) groups

first: Rong

last: Bao


title: Parkinson's Disease Risk Enhancers in Microglia


title: Large-scale whole blood RNA-Seq identifies transcriptional differences between primary sclerosing cholangitis and ulcerative colitis

city: Kiel

first: Florian

last: Uellendahl-Werth

address: Rosalind-Franklin-Straße 12

department: Institute of Clinical Molecular Biology (IKMB)

country: Germany

institute: Christian-Albrechts Universität zu Kiel

summary: Background: Patients suffering from primary sclerosing cholangitis (PSC) often also have ulcerative colitis (UC). Cross-disease genetic and microbiome studies across PSC und UC patients indicated that UC in PSC is a separate disease entity from primary UC, but expression studies for PSC are lacking. In this study, we performed a molecular comparison of whole blood expression levels in PSC only, PSC patients with additional UC diagnosis (PSC/UC), and UC, using a large collection of whole blood transcriptome data. Methods: We conducted whole blood RNA-Seq experiments for 495 UC patients, 220 PSC patients (of whom 177 have also a UC diagnosis), and 320 healthy controls from Germany and Norway. Differential expression analyses, gene ontology and coexpression analyses and random forest machine learning were performed to identify genes, ontologies and transcriptional features that discriminate diagnoses.  Results: The blood transcriptome in UC and PSC is dominated by neutrophil activation genes. In UC, but not in PSC (neither PSC alone nor PSC/UC), there is upregulation of genes for ribosomes, mitochondria and energy metabolism genes in conjunction with antibody transcript expression. In PSC, there is an increase in modules related to apoptosis and expression of genes of interferon-I-related ontologies. Random forest analysis could poorly discriminate PSC alone from PSC/UC (AUROC 0.56), but could discriminate PSC, UC, and controls with high accuracy (AUROC UC vs controls 0.95, PSC vs controls 0.88, UC vs PSC 0.986). The main coexpression modules are enriched in neutrophil degranulation and antibody production genes relevant for distinguishing PSC, UC, and controls.  Conclusions: PSC and UC share neutrophil-related transcriptional upregulation in whole blood (e.g. S100A12). UC is characterised by upregulation of modules involved in antibody production (MZB1, IGJ) and increased metabolic activity (PDK4, ribosomal genes), while PSC differs from UC by interferon (IFIT1) and apoptosis upregulation (G0S2). Supported by machine learning results, PSC and UC are interpreted as molecularly separate entities, while PSC/UC and PSC are indistinguishable.

first: Eike

middle: M

last: Wacker

first: Saptarshi

last: Bej

first: Olaf

last: Wolkenhauer

first: Mette

last: Vesterhus

first: Wolfgang

last: Lieb

first: Andre

last: Franke

first: Tom

middle: H

last: Karlsen

first: Trine

last: Folseraas

first: David

last: Ellinghaus


title: Blockade of C5aR1 resets M1 via gut microbiota-mediated PFKM stabilization in a TLR5-dependent manner

city: xuzhou

first: Jie

last: Zhao

address: xuzhou city

institute: xuzhou medical university

summary: Increased researches show that complement, the codominant central mediator of humoral immunity, is a critical factor in tumor initiation, development, and chemotherapy resistance. C5a/C5aR1 signaling has been shown to promote tumor progression by recruiting MDSCs in breast malignancies And blockade of C5aR1 resets M1 via gut microbiota-mediated PFKM stabilization in a TLR5-dependent manner. We here report that TLR5 as a key regulator of tumor associated macrophages M1 polarization. Flagellin, the protein subunit of the bacterial flagellum, stimulates the innate immune receptor Toll-like receptor 5 (TLR5) after pattern recognition. Receptor activity was turned by a TLR5-flagellin interaction distal to the site of pattern recognition. Thus, activation of downstream signaling pathway is promoted.

overall_design: To investigate the role of C5aR1 in regulating TAMs M1 polarization. We cultured the primary Bone marrow-derived macrophages from wild-type and C5ar1-/- mice.


title: Methylglyoxal-derived nucleoside adducts drive vascular dysfunction in a RAGE-dependent manner

status: Public on Jan 19 2024

first: Sarah

last: Shuck

address: 1500 Duarte Rd, Fox North Room 216

institute: Beckman Research institute at City of Hope

summary: Diabetic kidney disease (DKD) is a leading cause of death in patients with diabetes. An early precursor to DKD is endothelial cell dysfunction (ECD), a factor that often precedes and exacerbates vascular disease progression. We previously discovered that covalent adducts formed on DNA, RNA, and proteins by reactive metabolic by-product methylglyoxal (MG) predict DKD risk in patients with type 1 diabetes up to 16 years pre-diagnosis. However, the mechanisms by which MG-adducts contribute to vascular disease onset and progression remain unclear. Here, we report that the most predominant MG-induced nucleoside adducts, N2-(1-carboxyethyl)-deoxyguanosine (CEdG) and N2-(1-carboxyethyl)-guanosine (CEG), drive endothelial dysfunction. Following CEdG or CEG exposure, primary human umbilical vein endothelial cells (HUVECs) undergo endothelial dysfunction, resulting in enhanced monocyte adhesion, increased reactive oxygen species production, endothelial permeability, impaired endothelial homeostasis, and exhibit a dysfunctional transcriptomic signature. These effects were discovered to be mediated through the receptor for advanced glycation end products (RAGE), as an inhibitor for intracellular RAGE signaling diminished these dysfunctional phenotypes. Therefore, we find that not only are MG-adducts biomarkers for DKD, this study reveals they may also have a dual role as potential drivers of vascular disease onset and progression and a new therapeutic modality.

overall_design: Human unbillical vein endothelial cells (HUVEC) were treated with vehicle or either Mg-adduct with or without RAGE inhibitor Ri. Total RNA was isolated using Direct-zol RNA Miniprep Plus (Zymo). RNA se-quencing libraries were generated with Kapa RNA HyperPrep kit with RiboErase (Kapa Biosystems, KR1351) according to the manufacturer’s protocol. Total RNA (250 ng) from each sample was used for sequencing library preparation. The final libraries were val-idated with the Agilent Bioanalyzer DNA High Sensitivity Kit. Sequencing was per-formed on Illumina NovaSeq6000 with S4 Reagent Kit v1.5 (Illumina, 20028313) with the sequencing length of 2x101. Real-time analysis (RTA) 3.4.4 software was used to process the image analysis.

first: Seigmund

last: Wai Tsuen Lai

first: Supriyo

last: Bhattacharya

last: De Jesus Lopez Gonzalez

middle: C


title: Heat inactivation of Nipah virus for downstream single cell RNA sequencing

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: Single-cell RNA sequencing (scRNA-seq) has aided greatly in the study of viruses to distinguish responses from infected versus bystander cells in complex systems. Many of these workstreams, however, are not directly compatible with the more stringent biosafety regulations of BSL-3 and BSL-4 laboratories. Here we show that TCL buffer (Qiagen), inactivates both Ebola virus (EBOV) and SARS-CoV-2, representative BSL-4 and BSL-3 viruses. We show that additional heat treatment was additionally sufficient to inactivate EBOV-containing samples, and had minimal effects on extracted RNA quality and downstream sequencing results.

overall_design: Human induced pluripotent stem cell-derived alveolar epithelial type II cells were dissociated into single cells, FACS-sorted on live cells, and analyzed using scRNA-seq. After loading the cells onto the 10x Genomics chip, cDNA synthesis was performed with samples 2 and 3 undergoing an additional 60C heat step for 30 min. All 3 samples are frozen at -20C, and subsequently thawed, with Sample 3 thawed in 5% MicroChem Plus. All three samples were then processed for Illumina sequencing.

first: Adam

last: Hume

first: Judith

last: Olejnik

first: Mitchell

last: White

first: Jessie

last: Huang

first: Jacquelyn

last: Turcinovic

first: Baylee

last: Heiden

first: Yuriy

last: Alekseyev

first: John

last: Connor

first: Darrell

last: Kotton

first: Elke

last: Mühlberger


title: Unraveling the dynamics of hepatitis C virus adaptive mutations and their impact on antiviral responses in primary human hepatocytes

city: Bochum

first: Nicola

last: Frericks

address: Universitätsstraße 150

institute: Ruhr-Universität Bochum

summary: Long term cell culture adaptation of hepatitis C virus resulted in increased replication fitness in various human liver cell lines but in a moderate decrease in virus particle production upon infection of primary human hepatocytes (PHH). In order to identify molecular mechanisms conferring phenotypic differences in replicative fitness of the cell culture adapted virus strain p100pop, we infected PHH and Huh-7 cells with HCV, using the cell culture adapted strain p100pop or a Jc1 strain with similar genome organisation (Jc1-SP). Total RNA was extracted at 28 hours post inoculation and used for RNA sequencing. Transcriptome analyses, gene ontology enrichment analyses and KEGG pathway analyses revealed strong differences in the transcriptional signature of infected hepatoma cells and primary hepatocytes and the two virus strains used in this study. Wheras an innate immune response was induced in primary cells regardless of the infecting virus strain, this was not detectable in Huh-7 cells. Even though both viruses induce a similar host response in primary cells, the data indicate that the presence of cell culture adaptive mutations results in an increased expression of genes involved in the defense response to viral infection. In Huh-7 cells, differentially expressed genes associated with ER stress and apoptosis were solely enhanced upon p100pop infection but not upon Jc1-SP infection.

overall_design: Three biological independent passages of Huh-7 cells and primary human hepatocytes from  three independent donors were inoculated with HCV (Jc1-SP or p100pop). Apart from one PHH donor, hepatocytes from the same passage or donor were treated with conditioned medium and served as an uninfected control. The other  conditioned medium treated control derives from a different donor as the ones used for the infection experiments. At 28 hours post inoculation total RNA was extracted from cell lysates. Infection rates were determined using a HCV-probe based real time-quantitative PCR before RNA-sequencing was performed.  The resulting raw FASTQ files were aligned against the human reference genome GRh38 (version from 24.11.2021). Differentially expressed genes were identified by filtering on average expression for false discovery rate (FDR) correction by testing for differntilly expression due to infection while controlling for passage number of Huh-7 cells or the primary human hepatocyte donor. For the Gene Ontology enrichment analyses only differentially expressed genes with a mean RPKM value >0.5, fold change > 1.5 and FDR p-value<0.05 were considered. Further processing of these data for Gene set enrichment as well as KEGG pathway analyses were performed in R using the gseKEGG function from the RNA package 'clusterProfiler' v4.7.1.001.

first: Richard

last: Brown

first: Julie

last: Sheldon

first: Thomas

last: Pietschmann


title: Regulation of nuclear transcription by mitochondrial RNAs

first: Zhen

last: Chen


title: αO-conotoxin GeXIVA[1,2] reduced neuropathic pain and changed gene expression in chronic oxaliplatin-induced neuropathy mice model

status: Public on Jan 18 2024

city: Haikou

first: Huanbai

last: Wang

state: Hainan

address: Hai Dian Campus of Hainan University, No.58 of Ren Min Road, Mei Lan District, Haikou, Hainan Province,China

department: School of Life Sciences

institute: Hainan University

summary: Chemotherapy induced peripheral neuropathy (CIPN) is a dose-limiting painful neuropathy that occurs commonly during cancer management, which often leads to the discontinuation of medication. Previous studies suggest that the α9α10 nicotinic acetylcholine receptor (nAChR) specific antagonist αO-conotoxin GeXIVA[1,2] is effective in CIPN models, however the related mechanisms remains unclear. Here we analyzed the preventive effect of GeXIVA[1,2] on neuropathic pain in the long-term oxaliplatin injection induced CIPN model. At the end of treatment, lumbar (L4-L6) spinal cord was extracted, and RNA-sequencing and bioinformatic analysis were performed to investigate the potential genes and pathways related to CIPN and GeXIVA[1,2]. GeXIVA[1,2] inhibited the development of mechanical allodynia induced by chronic oxaliplatin treatment. Repeated injections of GeXIVA[1,2] for 3 weeks have no effect on mice normal pain threshold or locomotor activity and anxiety-like behavior as evaluated in the open field test (OFT) and elevated plus maze (EPM). Our RNA-sequencing results identified 209 differentially expressed genes (DEGs) in CIPN model, simultaneously injection of GeXIVA[1,2] with oxaliplatin altered 53 of the identified DEGs. These reverted genes were significantly enriched in immune-related pathways represented by cytokine-cytokine receptor interaction pathway. Our findings suggest that GeXIVA[1,2] could be a potential therapeutic compound for chronic oxaliplatin induced CIPN management.

overall_design:
We investigated the effect of chronic oxaliplatin and GeXIVA[1,2] treatment on mice L4-6 spinal cord gene expression.
Four groups were divided into GS+NS control group, GS+GeXIVA group, OXL+NS group, and OXL+GeXIVA group for RNA-seq analysis. Each group has 3 biological replicates.

first: Xiaodan

last: Li

first: Yamin

last: Qiao

first: Meiting

first: Wen

first: J

last: McIntosh

first: Dongting

last: Zhangsun

first: Sulan

last: Luo


title: Human iPSC-derived neurons reveal NMDAR-independent dysfunction following HIV-associated insults

city: Philadelphia

first: Kelly

last: Jordan-Sciutto

state: PA

address: 240 S. 40th St, Levy Building, Room 312

department: Oral Medicine

institute: University of Pennsylvania, School of Dental Medicine

summary: The central nervous system encounters a number of challenges following HIV infection, leading to increased risk for a collection of neurocognitive symptoms clinically classified as HIV-associated neurocognitive disorders (HAND). Studies attempting to identify causal mechanisms and potential therapeutic interventions have historically relied on primary rodent neurons, but a number of recent reports take advantage of iPSC-derived neurons in order to study these mechanisms in a readily-reproducible, human model. We found that iPSC-derived neurons differentiated via an inducible neurogenin-2 transcription factor were resistant to gross toxicity from a number of HIV-associated insults previously reported to be toxic in rodent models, including HIV-infected myeloid cell supernatants and the integrase inhibitor antiretroviral drug, elvitegravir. Further examination of these cultures revealed robust resistance to NMDA receptor-mediated toxicity. We then performed a comparative analysis of iPSC neurons exposed to integrase inhibitors and activated microglial supernatants to study sub-cytotoxic alterations in micro electrode array (MEA)-measured neuronal activity and gene expression, identifying extracellular matrix interaction/morphogenesis as the most consistently altered pathways across HIV-associated insults. These findings illustrate that HIV-associated insults dysregulate human neuronal activity and organization even in the absence of gross NMDA-mediated neurotoxicity, which has important implications on the effects of these insults in neurodevelopment and on the interpretation of primary vs. iPSC in vitro neuronal studies.

overall_design: Human iPSC-derived cortical neurons (WTC11 i3 neurons) were cultured for 19 days and exposed to either Veh (DMSO), Raltegravir (0.1 or 1 uM), Elivtegravir (1 or 10 uM), or supernatants from untreated and LPS+ATP treated ipSC-derived microglial supernatants (iMG Sups). Following a multi-day MEA recording experiment, total RNA was isolated from these neurons and analyzed via RNA-seq to observe transcriptional alterations associated with exposure to integrase inhibitor antiretroviral drugs and activated myeloid cell supernatants.

first: Alexander

last: Starr

first: Emily

last: Nickoloff-Bybel

first: Razan

last: Abedalthaqafi

first: Naela

last: Albloushi

middle: L


title: Mechanistic characterization of a Drosophila model of paraneoplastic nephrotic syndrome

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary:
Purpose: Paraneoplastic syndromes occur in cancer patients and originate from dysfunction of organs at a distance from the tumor or its metastasis.  In this study, using a Drosophila gut tumor model, we characterized a mechanism of tumor-induced kidney dysfunction.
Methods: snRNA-seq analysis of MT samples with and without Yki gut tumors and snRNA-seq analysis of MT samples with kidney principal cell-specific disregulation of PDGF/VEGF signaling
Results: we found that Pvf1, a PDGF/VEGF signaling ligand, secreted by gut tumors activates the PvR/JNK/Jra signaling pathway in the principal cells of the kidney, leading to mis-expression of renal genes and paraneoplastic renal syndrome-like phenotypes
Conclusions: Our study describes a novel mechanism by which gut tumors perturb the function of the kidney, which might be of clinical relevance for the treatment of paraneoplastic syndromes.

overall_design: 90 pairs of Drosophila MTs were dissociated for each sample and single nuclei were prepared. Ten thousand nuclei per sample were collected by FACS and loaded into a Chromium Controller (10X Genomics, PN-120223) on a Chromium Single Cell B Chip (10X Genomics, PN-120262), and processed to generate single cell gel beads in emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, CG000183). The library was generated using the Chromium Single Cell 3′ Reagent Kits v3.1 (10X Genomics, PN-1000121) and Chromium i7 Multiplex Kit (10X Genomics, PN-120262) according to the manufacturer’s manual. Quality control for the constructed libraries was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626). Quantification analysis was performed by Illumina Library Quantification Kit (KAPA Biosystems, KK4824). The library was sequenced on an Illumina NovaSeq system.

first: Jun

last: Xu

first: Ying

last: Liu

first: Weihang

first: Norbert

last: Perrimon


title: Changes in transcriptome and translatome upon YB-1 or YB-3 expression in double knockout HEK293T ΔYB-1ΔYB-3 cells

city: Pushchino

first: Ivan

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

summary: In this study, we generated transcriptome profiles from HEK293T,  HEK293T ΔYB-1ΔYB-3, and HEK293T ΔYB-1ΔYB-3 with the restored expression of YB-1 and/or YB-3. The data are used to explore YB-1 and YB-3 influence on transcriptome and translatome and their functional interchangeability in transcription and translation.

overall_design:
We established double knockout HEK293T ΔYB-1ΔYB-3 cells with the CRISPR/Cas approach. Next, we obtained derivatives of the double knockout HEK293TΔYB-1ΔYB-3 cells stably expressing full-length YB-1 and/or YB-3 mRNA.
RNA-Seq and Ribo-Seq data obtained from HEK293T, HEK293T ΔYB-1ΔYB-3, and HEK293T ΔYB-1ΔYB-3 with restored YB-1 and/or YB-3 expression in normal conditions.

first: Dmitry

middle: N

last: Lyabin

first: Irina

last: Eliseeva

first: Andrey

middle: I

last: Buyan


title: PAR-CLIP analysis of YB-1 RNA binding in HEK293T cells

summary: In this study, we performed PAR-CLIP experiment in HEK293T to explore RNAs directly bound by YB-1.

overall_design: YB-1 PAR-CLIP data was obtained in two replicates from HEK293T cells.


title: Reprogramming the Intrahepatic Cholangiocarcinoma Immune Microenvironment by Chemotherapy and CTLA-4 Blockade Enhances Anti-PD1 Therapy (scRNA-seq)

first: Dan

last: Duda

address: 55 Fruit St

department: Radiation Oncology

institute: Massachusetts General Hospital

summary: Intrahepatic cholangiocarcinoma (ICC) has limited therapeutic options and a dismal prognosis. Adding blockade of the PD1 pathway to gemcitabine/cisplatin chemotherapy has recently shown efficacy in biliary tract cancers but with low response rates. Here, we studied the effects of anti-CTLA-4 when combined with anti-PD1 and gemcitabine/cisplatin in orthotopic murine models of ICC. This combination therapy led to substantial survival benefits and reduction of morbidity in two aggressive ICC models that were resistant to immunotherapy alone. Gemcitabine/cisplatin treatment increased tumor-infiltrating lymphocytes and normalized the ICC vessels, and when combined with dual CTLA-4/PD1 blockade, increased the number of activated CD8+Cxcr3+IFNγ+ T cells. CD8+T cells were necessary for the therapeutic benefit because the efficacy was compromised when CD8+ T cells were depleted. Expression of Cxcr3 on CD8+ T cells is necessary and sufficient since CD8+ T cells from Cxcr3+/+ but not Cxcr3–/– mice rescued efficacy in T cell‒deficient mice. Finally, rational scheduling of anti-CTLA-4 “priming” with chemotherapy followed by anti-PD1 therapy achieved equivalent efficacy with reduced overall drug exposure. These data suggest that this combination approach should be clinically tested to overcome resistance to current therapies in ICC patients.

overall_design: We isolated single cells from tumor tissues of 425-ICC in mice that received either gemcitabine/cisplatin (GC, n=2 mice) treatment alone or a combination of GC and dual ICB (anti-PD1 plus anti-CTLA-4, n=3 mice) on day 10 after treatment for single-cell RNA sequencing (scRNA-seq) analysis. A magnetically activated cell sorting (MACS) column was used to obtain CD45+ and CD45– cells from each tumor sample, and then the cells were mixed at a ratio of 1:1 and captured using the 10x Chromium controller.

first: Jiang

last: Chen

first: Xin

first: Stefan

last: Halvorsen

first: Zelong

first: Slim

last: Sassi

middle: G


title: Transcriptome and translatome changes upon restored YB-1 or YB-3 expression in double knockout HEK293T ΔYB-1ΔYB-3 cells


title: The impact of selective HDAC inhibitors on the transcriptome of early mouse embryos

city: Fukuoka

first: Ruiqi

last: Shao

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

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

summary: Histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), plays a crucial role in the control of gene expression. HDAC inhibitors (HDACi) have shown potential in cancer therapy; however, the specific roles of HDACs in early embryos remain unclear. Moreover, although some pan-HDACi have been used to maintain cellular undifferentiated states in early embryos, the specific mechanisms underlying their effects remain unknown. Thus, there remains a significant knowledge gap regarding the application of selective HDACi in early embryos. To address this gap, we treated early embryos with two selective HDACi (MGCD0103 and T247). Subsequently, we collected and analyzed their transcriptome data at different developmental stages. Our findings unveiled a significant effect of HDACi treatment during the crucial 2-cell stage of zygotes, leading to a delay in embryonic development after T247 and an arrest at 2-cell stage after MGCD0103 administration. Furthermore, we elucidated the regulatory targets underlying this arrested embryonic development, which pinpointed the G2/M phase as the potential period of embryonic development arrest caused by MGCD0103. Moreover, our investigation provided a comprehensive profile of the biological processes that are affected by HDACi, with their main effects being predominantly localized in four aspects of zygotic gene activation (ZGA): RNA splicing, cell cycle regulation, autophagy, and transcription factor regulation. By exploring the transcriptional regulation and epigenetic features of the genes affected by HDACi, we made inferences regarding the potential main pathways via which HDACs affect gene expression in early embryos. Notably, Hdac7 exhibited a distinct response, highlighting its potential as a key player in early embryonic development. Our study conducted a comprehensive analysis of the effects of HDACi on early embryonic development at the transcriptional level. The results demonstrated that HDACi significantly affected ZGA in embryos, elucidated the distinct actions of various selective HDACi, and identified specific biological pathways and mechanisms via which these inhibitors modulated early embryonic development.

overall_design: Four hours after insemination by IVF, zygotes were cultured for 6 h in HTF medium supplemented with BSA at 4 mg/ml and 10 μM MGCD0103 or T247. The zygotes treated with HDACi were further cultured under the same conditions as the normal zygotes, with non-treated normal zygotes serving as the control group. The zygotes obtained after IVF were collected at 12, 24, and 48 hpi, and categorized as 1-cell stage, 2-cell stage, and 4-cell stage embryos, respectively.

first: Takayoshi

last: Suzuki

first: Mikita

last: Suyama

first: Yuichi

last: Tsukada


title: Single-cell RNA sequencing analysis reveals CHOP as an early marker for conventional chondrosarcoma

city: Hong Kong

first: Zezhuo

last: Su

address: No. 21 Sasson Rd, Pokfulam

institute: The University of Hong Kong

summary: Chondrosarcoma is the malignant form of chondrogenic tumors that consist of cartilage producing cells. Chondrosarcoam can arise from benign chondrogenic lesion. Benign chondrogenic tumors are normally managed conservatively, while surgical intervention can improve clinical outcomes of patients with chondrosarcoma. Clinical decision making is mainly based on the grade of the chondrogenic tumor. However, interobserver viability is high. There is currently no clear molecular for the grading and clinical decision making. To tackle this clinical problem, we performed single-cell RNA sequencing on chondrosarcomas of different grades, an enchondroma, as well as a chondroblastic osteosarcoma and a fetal femur as comparison.

overall_design: Single-cell RNA sequencing from eight chondrosarcomas of different grade, an enchondroma, a chondroblastic osteosarcoma, and a fetal femur

first: Joshua

last: Ho

first: Kelvin

last: Cheung


title: Inflammasome signaling is dispensable for ß-amyloid-induced neuropathology in preclinical models of Alzheimer's disease

status: Public on Jan 17 2024

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Alzheimer's disease (AD) is the most common neurodegenerative disorder affecting memory and cognition. The disease is accompanied by an abnormal deposition of ß-amyloid plaques in the brain that contributes to neurodegeneration and is known to induce glial inflammation. Studies in the APP/PS1 mouse model of ß-amyloid-induced neuropathology have suggested a role for inflammasome activation in ß-amyloid-induced neuroinflammation and neuropathology. Here, we evaluated the in vivo role of microglia-selective and full body inflammasome signalling in several mouse models of ß-amyloid-induced AD neuropathology. Unexpectedly, microglia-specific deletion of the inflammasome regulator A20 and inflammasome effector protease caspase-1 in the AppNL-G-F and APP/PS1 models failed to identify a prominent role for microglial inflammasome signalling in ß-amyloid-induced neuropathology. Moreover, global inflammasome inactivation through respectively full body deletion of caspases 1 and 11 in AppNL-G-F mice and Nlrp3 deletion in APP/PS1 mice, also failed to modulate amyloid pathology and disease progression. In agreement, single-cell RNA sequencing did not reveal an important role for Nlrp3 signalling in driving microglial activation and the transition into disease-associated states, both during homeostasis and upon amyloid pathology. Collectively, these results question a generalizable role for inflammasome activation in pre-clinical amyloid-only models of neuroinflammation.

overall_design: CD45+ brain immune cells were isolated from 4 groups of mice: wild-type (WT), Nlrp3KO, APP/PS1 and Nlrp3KOxAPP/PS1 mice. The mice were profiled at the age of  3, 6 and 9 months for WT and Nlrp3KO mice, and at the age of 3 and 9 months for the APP/PS1 and the Nlrp3KOxAPP/PS1 groups. For each experimental condition,  3  mouse brains were pooled for  library construction.

first: Sahana

last: Srinivasan

first: Takashi

last: Saito

first: Isabelle

last: Scheyltjens

first: Maude

last: Jans

first: Fleur

last: Boone

first: Charysse

last: Vandendriessche

first: Roosmarijn

last: Vandenbroucke

first: Esther

last: Hoste

first: Sofie

last: Voet

first: Takaomi

last: Saido

first: Kiavash

last: Movahedi

first: Marius

last: Schwabenland

first: Marco

last: Prinz

first: Mohamed

last: Lamkanfi

first: Geert

last: van Loo


title: The Macrophage Landscape Across the Lifespan of a Human Cardiac Allograft

first: Xiao

last: Li

address: 6770 Bertner Ave

institute: Texas Heart Institute

summary: To examine the evolving landscape of immune cells in the human cardiac allograft over time, we collected left ventricular tissue from cardiac allografts at the time of repeat transplantation from 3 pediatric patients at 5 days, 15 months, and 12 years post transplantation and performed snRNA-seq profiling.

overall_design: We included 3 pediatric patients at 5 days (patient 1), 15 months (patient 2), and 12 years (patient 3) post transplantation (5dPT, 15mPT, and 12yPT). Left ventricular tissues were collected at the time of repeat transplantation surgeries and profiled using 10X Genomics snRNA-seq.

first: James

middle: F

last: Martin


title: High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing [ISS, Cartana]

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

summary: Spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ. We applied direct RNA hybridization-based in situ sequencing (ISS, Cartana) to compare male and female healthy mouse kidneys and the male kidneys injury and repair timecourse of ischemic reperfusion injury (IRI). A pre-selected panel of 200 genes were used to identify the dynamics of cell states and their spatial distributions during injury and repair. We developed a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting atlas allowed us to resolve distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. Projection of snRNA-seq dataset from the same injury and repair samples allowed us to impute the spatial localization of genes not directly measured by Cartana.

overall_design: Kidney spatial transcriptomics data were generated by RNA hybridization-based in situ sequencing (ISS, Cartana) and 10X Visium

first: Benjamin

last: Humphreys


title: High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing [10X Visium]


title: Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection

city: Stanford

first: Aaron

middle: James

last: Wilk

state: California

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

summary: HIV causes chronic inflammation and AIDS in humans, though the rate of disease progression varies between individuals. Similarly, simian lentiviruses vary in their pathogenicity based on characteristics of both the host (simian species) and virus strain. Here, we profile immune responses in pig-tailed macaques infected with variants of SIV that differ in virulence to understand the immune mechanisms underlying lentiviral pathogenicity. Compared to a minimally pathogenic lentiviral variant, infection with a highly pathogenic variant results in a more delayed, broad, and sustained activation of inflammatory pathways, including an extensive global interferon signature. Conversely, individual cells infected with highly pathogenic lentivirus upregulated fewer interferon-stimulated genes at a lower magnitude, indicating that highly pathogenic lentivirus has evolved to partially escape from interferon responses. Further, we identified distinct gene co-expression patterns and cell-cell communication pathways that implicate CXCL10 and CXCL16 as important molecular drivers of inflammatory pathways specifically in response to highly pathogenic lentivirus infection. Immune responses to highly pathogenic lentivirus infection are characterized by amplifying regulatory circuits of pro-inflammatory cytokines with dense longitudinal connectivity. Our work presents a model of lentiviral pathogenicity where failures in early viral control mechanisms lead to delayed, sustained, and amplifying pro-inflammatory circuits, which has implications for other viral infections with highly variable disease courses.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from 4 pig-tailed macaques. Two animals had been infected with minimally-pathogenic SIVMneCL8 and two animals had been infected with highly-pathogenic SIVMne170. From all animals, cells from pre-infection, and 8 post-infection time points (weeks 1, 2, 3, 4, 6, 8, 12, and 20) were thawed and processed for scRNA-seq on the Seq-Well platform. Animal key: 55 (CL8 A), 74 (CL8 B), 33 (170 A), 61 (170 B)

first: Catherine

last: Blish


title: High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila.

status: Public on Jan 16 2024

city: Ciudad de Buenos Aires

first: Nicolas

last: Frankel

state: Buenos Aires

address: Ciudad Universitaria

department: FMBC

country: Argentina

institute: CONICET


title: The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [CUT&RUN]

summary: Evolutionary analyses have estimated that ~60% of nucleotides in intergenic regions of the Drosophila melanogaster genome are functionally relevant, suggesting that regulatory information may be encoded more densely in intergenic regions than has been revealed by most functional dissections of regulatory DNA. Here, we approached this issue through a functional dissection of the regulatory region of the gene shavenbaby (svb). Most of the ~90 kilobases of this large regulatory region is highly conserved in the genus Drosophila, though characterized enhancers occupy a small fraction of this region. By analyzing the regulation of svb in different contexts of Drosophila development, we found that the regulatory information that drives svb expression in the abdominal pupal epidermis is organized in a different way than the elements that drive svb expression in the embryonic epidermis. While in the embryonic epidermis svb is activated by compact enhancers separated by large inactive DNA regions, svb expression in the pupal epidermis is driven by regulatory information distributed over broader regions of svb cis-regulatory DNA. In the same vein, we observed that other developmental genes also display a dense distribution of putative regulatory elements in their regulatory regions. Furthermore, we found that a large percentage of conserved non-coding DNA of the Drosophila genome is contained within regions of open chromatin. These results suggest that part of the evolutionary constraint on non-coding DNA of Drosophila is explained by the density of regulatory information, which may be greater than previously appreciated.

overall_design: CUT&RUN in Drosophila melanogaster pupal abdominal epidermis cells using an antibody that recognizes the H3K27ac histone modification to determine the genome-wide H3K27ac state.

first: Gonzalo

last: Sabarís

first: Daniela

last: Ortíz

first: Ian

last: Laiker

first: Ignacio

last: Mayansky

first: Sujay

last: Naik

first: Giacomo

last: Cavalli

first: David

last: Stern

first: Ella

last: Preger-Ben Noon

first: Nicolás


title: Gut complement induced by the microbiota combats pathogens and spares commensals

first: CBDM

last: Lab

department: Microbiology and Immunobiology

summary: Canonically, the complement system is known for its rapid response to remove microbes in the bloodstream. However, relatively little is known about a functioning complement system on intestinal mucosal surfaces. Herein we report the local synthesis of complement component 3 (C3) in the gut, primarily by stromal cells. C3 is expressed upon commensal colonization, is regulated by the composition of the microbiota in healthy humans and mice, leading to an individual host’s specific luminal C3 levels. The absence of membrane attack complex (MAC) components in the gut ensures that C3 deposition does not result in the lysis of commensals. Pathogen infection triggers the immune system to recruit neutrophils to the infection site for pathogen clearance. Basal C3 levels directly correlate with protection against enteric infection. Our study reveals the gut complement system as a novel innate immune mechanism acting as a vigilant sentinel that combats pathogens and spares commensals.

overall_design: To identify which intestinal cell types express C3 under homeostasis, we used single-cell RNASeq (scRNASeq) to perform a transcriptional survey of C3 expression across intestinal populations. We isolated C3-expressing cells (tdTomato-positive) from the subepithelial compartment of both male and female C3IRES-tdTomato C57BL/6 mice and performed scRNASeq on these cells.

first: Wu

last: Meng

first: Magill

last: Ian


title: The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [ATAC-seq]

overall_design: ATAC-seq of Drosophila melanogaster pupal abdominal epidermis to determine open chromatin regions across the genome.


title: The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [ChIP-seq]

overall_design: ChIP-seq using an antibody that recognizes the H3K27ac histone modification in D. melanogaster embryos (stages 14-15). Samples were enriched in cells with active 7 and E10 svb enhancers.


title: Dietary intervention reverses molecular signatures of hepatocellular senescence in the GAN diet-induced obese and biopsy-confirmed mouse model of NASH

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

summary:
We applied RNA sequencing (RNA-seq) to study the effects of dietary intervention on hallmarks of NASH and molecular signatures of hepatocellular senescence in the Gubra-Amylin NASH (GAN) diet-induced obese (DIO) mouse model of NASH. GAN DIO-NASH mice with liver biopsy-confirmed NASH and fibrosis received dietary intervention by switching to chow feeding (chow reversal) for 8, 16, or 24 weeks. Untreated GAN DIO-NASH mice and chow-fed C57BL/6J mice served as controls.
We find that chow reversal promoted substantial benefits on metabolic, biochemical and histological outcomes accompanied by marked suppression of gene expression markers of hepatocellular senescence in GAN DIO-NASH mice. These therapeutic benefits were reflected by progressive clearance of senescent hepatocellular cells, making the model suitable for profiling potential senotherapeutics in preclinical drug discovery for NASH.

overall_design: RNA-seq of poly A-enriched RNA isolated from GAN DIO-NASH mice or chow-reversal sampled at 8 weeks (n = 7), 16 weeks (n = 8), and 24 weeks (n = 8). Untreated GAN DIO-NASH mice at 8 weeks (n = 9), 16 weeks (n = 8), and 24 weeks (n = 7), and chow-fed C57BL/6J mice served as controls (24 weeks, n = 8)

first: Martin

last: Madsen

first: Emma

last: Rørbeck


title: Acetylation of the activated glucocorticoid receptor facilitates its proteasomal degradation thereby limiting hormonal signaling

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: The glucocorticoid (GC) receptor (GR) is a ligand-induced transcription factor regulating metabolism and inflammation. While homologous downregulation of ligand-bound GR limits the response, it also reduces hormone responsiveness resulting in glucocorticoid resistance. Regulatory mechanisms that refine this equilibrium are less understood. Here, we have identified seven lysine acetylation sites in the amino terminal domain of GR, lysine 154 within the regulatory AF-1 region being the dominant acetyl-acceptor. GR-Lys154 acetylation is mediated by p300/CBP in an exclusively agonist-induced manner and correlates with nuclear translocation and transcriptional activity. GR-Lys154 acetylation is removed by the NAD+ dependent deacetylase, SIRT1, indicating dynamic regulation of this mark. Notably, agonist-binding to both the wild type and acetylation-deficient mutant GR elicits similar short-term target gene expression. In contrast, upon extended treatment, the acetylation-deficient mutant shows impaired ubiquitination and higher protein stability with a concomitant increase in chromatin association and transactivation. Taken together, p300/CBP and SIRT1 fine-tune glucocorticoid response by siphoning acetylated GR for proteasomal degradation while GR deacetylation sustains the transcriptional cascade for prolonged periods.

overall_design: To determine the impact of GR-Lys154 acetylation on Dex-dependent regulation of target gene expression, we performed RNA sequencing in cells expressing wildtype (WT), acetylation-deficient (K154R) or acetylation -mimetic (K154Q) GR. For this, we used CRISPR/Cas9 to knock out endogenous GR (gene: NR3C1) in HepG2 cells to generate HepG2 GR-/-.Subsequently, we transduced these cells with doxycycline-inducible psedotyped lentiviral constructs harboring cDNAs for Ty1-tagged WT-, K154R- and K154Q-GR respectively. Cells were induced with doxycycline to express the variants of GR followed by treatment with vehicle or 1 µM Dex for 6 hours before harvesting, RNA isolation, library preparation and sequencing. For each genotype, four biological replicates indicate two independent experiments with two independent transductions each.

first: Aishwarya

last: Iyer-Bierhoff

last: Wieczorek

first: Sina

last: Peter

first: Dima

last: Ward

last: Bens

first: Sabine

last: Vettorazzi

first: Karl-Heinz

last: Gührs

first: Jan

middle: P

last: Tuckermann

first: Thorsten

last: Heinzel


title: Adipocyte p53 coordinates the adipose tissue immune cell landscape upon intermittent fasting

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: In obesity, sustained adipose tissue (AT) inflammation constitutes a cellular memory that limits the effectiveness of weight loss interventions. Yet, its fasting regimen-dependent regulation is unknown. Here, we show that cyclic intermittent fasting (IF) exacerbates the lipid-associated macrophage (LAM) inflammatory phenotype of visceral AT in obese mice. Importantly, we provide evidence that this increase in LAM abundance is almost entirely dependent on p53-driven adipocyte apoptosis. Adipocyte-specific deletion of p53 prevents LAM accumulation in AT during IF and increases the catabolic state of adipocytes, ameliorates metabolic flexibility, and insulin sensitivity. Finally, in cohorts of obese/diabetic patients, we describe a p53 polymorphism that links to long-term efficacy of a fasting-mimicking diet and that the expression of LAM markers and p53 in AT negatively correlates with maintaining weight loss after bariatric surgery. Overall, our results demonstrate that p53 signaling in adipocytes dictates LAM accumulation in AT under IF and that adipocyte p53 modulates fasting effectiveness in mice and humans.

overall_design: organism: mus musculus, tissue type: epididymal adipose tissue, data type: single-nuclei RNA sequencing data, groups: high-fat diet ad libitum fed (HFD-AL), high-fat diet fed and intermittent fasted (HFD-IF), high-fat diet fed and intermittent fasted, adipocyte-specific p53 KO mice

first: Isabel

last: Reinisch

first: Andreas

last: Prokesch


title: Nutrient-derived signals regulate eosinophil adaptation to the small intestine

city: New Haven

first: Vassily

middle: Igor

last: Kutyavin

state: CT

address: 1 Gilbert St

department: Immunobiology

institute: Yale University

summary: Eosinophils are commonly regarded as effector cells of type 2 immunity, yet they also accumulate in certain tissues during homeostasis - particularly in the gastrointestinal tract. Our understanding of the processes that govern homeostatic eosinophil accumulation and tissue-specific adaptation, and their functional significance, remains very limited. Here, we investigated how eosinophils adapt to the small intestine microenvironment and the local signals that regulate this process. We observed that eosinophils gradually migrate up the crypt-villus axis, giving rise to a villus-resident subpopulation with a distinct transcriptional signature. Genetic deficiency of eosinophils resulted in a reduction of villus area, as well as a reduction of multiple other immune cell populations, demonstrating their diverse functions in this environment. We determined that retinoic acid receptor signaling is specifically required for the maintenance of villus-resident eosinophils, while IL-5 is largely dispensable outside of its canonical role in eosinophil production. In addition, we unexpectedly found that high protein diet suppresses the accumulation of villus-resident eosinophils. Purified amino acids were sufficient for this effect, which was a consequence of accelerated eosinophil turnover within the tissue microenvironment and not due to altered development in the bone marrow. Our study provides new insight into the process of eosinophil adaptation to the small intestine and its dependence on nutrient-derived signals.

overall_design: Small intestine eosinophil populations (a4b7+, a4b7- CD22-, and CD22+) from wild type female B6 mice were isolated by FACS and their transcriptomes were analyzed by RNA-Seq (4 biological replicates per condition)

first: Lisa

last: Korn

first: Ruslan

last: Medzhitov


title: Transcriptome profiling of plasma-derived particles containing platelets in ME/CFS post exercise challenge

city: Ithaca

first: Jennifer

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: We profiled gene expression of pelleted material containing platelets from frozen plasma of healthy controls and ME/CFS cases for bulk RNA-seq, collected before and 24h after participants conducted a cardiopulmonary exercise test (CPET).

overall_design: Plasma samples collected from 3 ME/CFS cases and 3 healthy controls (all females) at 2 timepoints were included in the study.

first: Luyen

middle: T

last: Vu

first: Elizabeth

last: Fogarty

first: Hongya

last: Zhu

first: Faraz

last: Ahmed

first: David

last: Iu

first: Andrew

last: Grimson


title: miR-Blood - a small RNA sequencing atlas of purified human blood components

city: Heidelberg

first: Bruno

last: Steinkraus

state: Baden-Württemberg

address: Im Neuenheimer Feld 583

institute: HUMMINGBIRD DIAGNOSTICS GMBH

type: Non-coding RNA profiling by high throughput sequencing

summary:
miR-Blood is a high-quality, small RNA expression atlas for the major components of human peripheral blood (plasma, erythrocytes, thrombocytes, monocytes, neutrophils, eosinophils, basophils, natural killer cells, CD4+ T cells, CD8+ T cells, and B cells).

*** The data provided in this GEO dataset is licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). ***

overall_design: Small RNA expression analysis of EDTA-stabilized whole blood and purified blood component samples from 52 individuals.

first: Julia

last: Jehn

first: Franziska

last: Trudzinski

first: Rastislav

last: Horos

first: Judith

last: Schenz

first: Florian

last: Uhle

first: Markus

middle: A

last: Weigand

first: Maurice

last: Frank

first: Mustafa

last: Kahraman

first: Marco

last: Heuvelman

first: Tobias

last: Sikosek

first: Timothy

last: Rajakumar

last: Gerwing

first: Jasmin

last: Skottke

first: Alberto

last: Daniel-Moreno

first: Christina

last: Rudolf

last: Hinkfoth

first: Kaja

last: Tikk

first: Petros

last: Christopoulos

first: Laura

last: Klotz

first: Hauke

last: Winter

first: Michael

last: Kreuter

middle: R


title: Dedicated chaperone at the ribosome safeguards the proteostasis network during eEF1A biogenesis

first: Ilgin

last: Kotan

address: Im Neuenheimer Feld 329

institute: Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)

summary: Cotranslational protein folding depends on general chaperones that engage highly diverse nascent chains at the ribosomes. Here we find that the universal cotranslational machinery adapts to accommodate the challenging biogenesis of abundantly expressed eukaryotic translation elongation factor 1A (eEF1A). During eEF1A synthesis, chaperone Chp1 is recruited to the ribosome with the help of the nascent polypeptide-associated complex (NAC), where it safeguards eEF1A biogenesis. Aberrant eEF1A production triggers instant proteolysis, widespread protein aggregation, activation of Hsf1 stress transcription and compromises cellular fitness. The expression of pathogenic eEF1A2 variants linked to epileptic-dyskinetic encephalopathy is protected by Chp1. Thus, eEF1A is a difficult to fold protein that necessitates dedicated folding factor Chp1 at the ribosomal tunnel exit to protect the eukaryotic cell from proteostasis collapse.

overall_design: Selective Ribosome Profiling of Chp1 in S. cerevisiae (BY4741 Chp1-GFP strain, performed in two replicates, each consisting of an IP sample and a corresponding total translatome sample. As a negative control, IP and total translatome samples were prepared in WT untagged BY4741 cells also in two replicates). Ribosome profiling in S. cerevisiae (BY4741 WT or Chp1Δ cells, total translatomes in two replicates each)

first: Melania

last: Minoia

first: Jany

last: Quintana-Cordero

first: Katharina

last: Jetzinger

middle: E

first: Kathryn

last: Turnbull

first: Anna

last: Masser

first: Dorina

last: Liebers

first: Eloïse

last: Gouarin

first: Kai

last: Ehrenbolger

first: Jonas

last: Barandun

first: Vasili

last: Hauryliuk

first: Bernd

last: Bukau

first: Günter

last: Kramer

first: Claes

last: Andréasson

first: Michela

last: Ciccarelli


title: Single-cell RNA seq mapping of chicken leukocytes

city: Uppsala

first: Robert

last: Söderlund

address: Ulls väg 2B

country: Sweden

institute: National veterinary institute (SVA)

summary: The immune system is a complex infrastructure where many cells interact with each other and perform duties depending on their type and function. When using traditional immunological methods in studying non-traditional model organisms, such as birds, challenges arise. These are often associated with a lack of knowledge surrounding the organism in question—particularly, the expected leukocytes, their cell-specific marker genes, and associated reagents. Single-cell transcriptomics allows us to study the immune system at the level of each singular cell and create a profile of each cell present in a sample without as much prior knowledge of the organism. This project aimed to investigate the possibility of using single-cell transcriptomics as an alternative to traditional methods in avian immunology and using this as a basis for further research into avian medicine. The study was performed by sequencing the mRNA in approximately twenty thousand individual chicken blood cells from 4 healthy adult birds, performing unsupervised clustering of the cells, and attempting to annotate clusters based on expression profiles. Most of this study has been performed using the R-based software Seurat and 10 x genomics software Cell Ranger.  Resulting putative cell types include expected populations such as several different T-cells, B-cells, Monocytes, thrombocytes, red blood cells, and cells in various stages of the cell life cycle. After computational analysis, the number of cells per cell type corresponds to laboratory analysis of the cell types performed prior to sequencing. This indicates that the in-silico annotation of putative cell types is consistent with the actual cell types in the samples  This study of chicken leukocytes highlights the possibility of the usage of single-cell transcriptomics within non-traditional model organism immunology. It shows that using modern single-cell sequencing and existing software, sequencing-based characterisation of immune cells is possible and could prove a robust option in immunology study cases where traditional methods are limited.

overall_design: Blood samples from  chickens were purified to remove RBCs and Thrombocytes using gradient centrifugation on Ficoll and immunomagnetic cell separation respectively and analyzed using scRNA-seq. Read counting was performed using Cell Ranger count and data analysis was performed using Seurat.

first: Eva

last: Wattrang

first: Matilda

last: Maxwell


title: Safe and effective immunostimulatory therapy through vector-controlled cytokine delivery

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Systemic administration of interleukin (IL)-12 has been shown to induce potent anti-tumor immune responses in preclinical cancer models. Previous clinical trials using bolus IL-12 injection through maximal tolerable dosing (MTD) strategies indicated limited efficacy alongside unwanted side-effects. Our group developed IL-12-loaded PLGA nanospheres (IL12ns) that release their contents systemically in a slow, controlled manner. An immune diagnostic platform (IDP), capable of monitoring therapeutic response through peripheral blood sampling, was designed alongside this immunostimulatory therapy. The systemic immune responses from MTD and IL12ns dosing strategies were analyzed using this IDP in healthy mice. Importantly, the MTD was associated with aberrant peripheral immune stimulation, evidenced by increased IL-12, interferon gamma (IFNG), and IL-10 signaling. The immune-protective effects of IL12ns were supported by increases in pro-inflammatory plasma cytokines/chemokines without the maladaptive transcriptomic signatures in circulating peripheral immune cells. These data ultimately support the necessity of a vector system for safe immunostimulatory IL-12 therapy.

overall_design:
The purpose of this study was to assess the immunotoxicity of the IL12ns vector system in healthy BALB/c mice through repeated blood sampling over three weeks.
Both systemic and tissue-resident immune responses to IL12ns therapy, delivered at three doses (10, 0.1, and 0.001 mg), were compared to a daily MTD dosing strategy (10,000 ng/kg/day IL-12 – positive control) and control (negative) control.
The systemic IDP analysis included bulk PBMC RNA sequencing. Following peripheral blood processing into a PBMC single cell suspension, total RNA was isolated for downstream polyA mRNA sequencing.

first: Ryan

last: Lacinski

first: Sebastian

last: Dziadowicz

first: Halima

last: Akhter

first: Lei

last: Wang

first: Alyson

last: Prorock

first: Yongde

last: Bao

first: Katia

last: Sol-Church

first: Brock

last: Lindsey


title: Single-cell RNA-seq uncovers unique gene expression profiles in the spleen of hypoxic mice

city: Albuquerque

first: Laura

middle: Gonzalez

last: Gonzalez Bosc

state: NM

department: Cell Biology and Physiology

institute: University of New Mexico Health Sciences Center

summary: The stability of FOXP3 expression in Tregs influences the balance between tolerance and autoimmunity. Treg cell development and function are regulated by IL-2, which binds to IL-2Rα (also called CD25). Decreased expression of CD25 (Il2ra gene) characterizes Tregs that lose FOXP3 expression (exTregs) and undergo transdifferentiation into TH17 cells. This has been established under arthritic conditions but whether this Treg transdifferenciation into exTregs occur following hypoxia exposure, it is unknown. Therefore, single-cell RNA-seq (10x Genomics) was performed using a 10X Genomics Chromium system to test the hypothesis that hypothesis that chronic hypoxia initiates Treg transcriptional reprogramming.

overall_design: We used mice (Foxp3EGFP-cre-ERT2, Ai14-tdTomato) in which tamoxifen administration uncoveres 4 populations of CD4+ T cells; EGFP+, EGFP+ tdTomato+, EGFP-tdtomato+, and EGFP-tdtomato-. We performed single-cell RNA sequencing (scRNA seq) in isolated splenocytes from tamoxifen-treated mice following 5 days of CH or normoxia; tdTomato (WPRE sequence) predominated in the CD4+ memory T cell cluster. Treg marker Il2ra (CD25) was used to identify the Treg cluster and comparative gene expression profiling analysis of RNA-seq data was performed for normoxic and CH samples.

last: Bosc

first: Benjamin

last: Lantz

first: David

last: Jones

first: Yan

last: Guo

first: Olufunmilola

last: Oyebamiji


title: Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation

first: Jennifer

middle: K

last: Grenier

state: NY

summary: ME/CFS is a serious and poorly understood disease. To understand immune dysregulation in ME/CFS, we used single-cell RNA-seq (scRNA-seq) to examine immune cells in cohorts of patients and controls. Post-exertional malaise (PEM), an exacerbation of symptoms following exercise, is a characteristic symptom of ME/CFS. Thus, to detect changes coincident with PEM, we also performed scRNA-seq on the same cohorts following exercise. At baseline, ME/CFS patients displayed dysregulation of classical monocytes suggestive of inappropriate differentiation and migration to tissue. We were able to identify both diseased and more normal monocytes within patients, and the fraction of diseased cells correlated with metrics of disease severity. Comparing the transcriptome at baseline and post-exercise challenge, we discovered patterns indicative of improper platelet activation from patients, with minimal changes elsewhere in the immune system. Taken together, these data identify immunological defects present at baseline in patients, and an additional layer of dysregulation following strenuous exercise.

overall_design: Blood samples were collected from 30 ME/CFS cases and 28 age- and activity-matched controls at two timepoints: prior to a cardiopulmonary exercise test (CPET) and 24h later. PBMCs were isolated and gene expression was profiled using the 10x Genomics single-cell RNAseq platform.

first: Faraz

last: Ahmed

first: Luyen

last: Vu

first: Hongya

last: Zhu

middle: S

last: Lu

first: Elizabeth

last: Fogarty

first: Andrew

last: Grimson


title: Transcriptome profiling of classical monocytes in ME/CFS post exercise challenge

summary: We collected classical monocytes from frozen PBMCs of healthy controls and ME/CFS cases for bulk RNA-seq. PBMCs were collected 24h after participants conducted a cardiopulmonary exercise test (CPET).

overall_design: Classical monocytes (CD14+) from 4 ME/CFS cases and 4 healthy controls (all females) were included in the study.


title: Gut-liver axis calibrates intestinal stem cell fitness via PEDF

city: Bethesda

first: Chuan

last: Wu

state: MD

address: 10 Center Drive, Building 10, RM 4B17

institute: National Cancer Institute

summary: The gut and liver are recognized to mutually communicate through the biliary tract, portal vein and systemic circulation, but it remains unclear how this gut-liver axis regulates intestinal physiology. Through hepatectomy, transcriptomic and proteomic profiling, we identified pigment epithelium-derived factor (PEDF), a liver-derived soluble Wnt inhibitor, that restrains intestinal stem cell (ISC) hyperproliferation to maintain gut homeostasis by suppressing the Wnt/b-catenin signaling pathway. Further, we found that microbial danger signals occurring as a result of intestinal inflammation can be sensed by the liver to repress PEDF production via peroxisome proliferator-activated receptor-a (PPARa), liberating ISC proliferation to accelerate tissue repair in the gut. Finally, treatment of mice with fenofibrate, a clinical agent of PPARa agonist for hypolipidemia enhances the susceptibility of colitis via PEDF activity. Therefore, we have identified a distinct role for PEDF in calibrating ISC expansion for intestinal homeostasis via reciprocal interactions between the gut and liver.

overall_design: Expression profiling by high throughput sequencing


title: Comparative Ribo-Seq of Staphylococcus aureus harboring A2058-unmodified ribosomes and m6A2058-modified ribosomes

city: Chicago

first: Mee-Ngan

middle: F.

last: Yap

state: IL

address: 320 E Superior St

department: Microbiology-Immunology

institute: Northwestern University Feinberg School of Medicine

summary:
A total of 10 cDNA libraries were constructed, representing 3 and 2 independent biological replicates of S. aureus strain KES34 (unmodified ribosomes) and KES30 (m6A2058-modified ribosomes), respectively. Translational efficiency (RPF/mRNA ratios),
total mRNA abundance and ribosome density of each ORFs were calculated.

overall_design: Investigating the translational efficiency and fidelity of unmodified- and m6A2058-modified ribosomes in a methicilin-resistant Staphylococcus aureus (MRSA).

first: K

last: Shields

first: M


title: Transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation

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

overall_design: Refer to individual Series


title: Defining key transcriptional regulators of extravillous trophoblast differentiation [RNA-seq]

city: Austin

first: Mijeong

last: Kim

address: 2506 Speedway, NMS 4.246

institute: The University of Texas at Austin

summary: During early human pregnancy, extravillous trophoblasts (EVT) play a central role in placental anchorage and blood vessel remodeling. Despite the essential roles in pregnancy, key factors and mechanisms underlying EVT differentiation remain largely unknown. Here, we defined key transcription factors (TFs) by monitoring the dynamics of transcriptome and enhancer usage during EVT differentiation. We confirmed the requirements of the defined TFs and identified their action mechanisms.

overall_design: Transcriptome profiling of human trophoblast stem cells (TSC) and EVT differentiating cells (multiple time-points) was conducted to monitor dynamics in the gene expression program during EVT differentiation. To investigate the requirements of the defined TFs (DLX5, DLX6, ASCL2, ZNF439, NRIP1, and TFAP2C) in proper EVT differentiation, we knocked down (KD) the individual TF in TSC and differentiated the cells to EVT. RNA-seq was performed on the individual key TF-KD EVT and non-targeting shRNA-expressing EVT (control). We also conducted RNA-seq of EVT overexpressing TFAP2C during days 2 to 8 of differentiation to monitor the effects of sustained expression of TFAP2C on EVT differentiation. The non-DOX-treated EVT was used as a control.

first: Jonghwan


title: Intraocular liver spheroids for non-invasive high-resolution in vivo monitoring of liver cell function

status: Public on Jan 15 2024

city: Solna

first: Nuria

last: Vilarnau

state: Outside AUS/NZ

address: Solnavägen 9

institute: Karolinska Institutet

summary: Longitudinal monitoring of liver function in vivo is hindered by the lack of high-resolution non-invasive imaging techniques. Using the anterior chamber of the mouse eye as a transplantation site, we have established a platform for longitudinal in vivo imaging of liver spheroids at cellular resolution. Transplanted liver spheroids engraft on the iris, become vascularized and innervated, retain hepatocyte-specific and liver-like features and can be studied by in vivo confocal microscopy. Employing fluorescent probes administered intravenously or spheroids formed from reporter mice, we showcase potential use of this platform exemplified by monitoring hepatocyte cell cycle activity, bile secretion and lipoprotein uptake. Moreover, we show that hepatic lipid accumulation during diet-induced hepatosteatosis is mirrored in intraocular grafts in vivo. The here described technology will provide a crucial tool to study liver physiology and disease progression in both pre-clinical and basic research as well as a drug screening platform in the pharma industry.

overall_design: To understand the suitability of this in vivo imaging platform to monitor different hepatocyte functions, we analyzed the transcriptome of the explanted liver spheroids at 2 months post-tx by RNA-seq.


title: Chromatin profiling of normal and HNF4A KO liver and NIH 3T3 mouse fibroblast cells

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

summary: We analyzed the effect on HNF4A loss on Histone modifications  (H3K4me1, H3K27ac) by ChIP-seq and CUT&Tag using control and HNF4A KO livers samples. We also examined chromatin accessibility by ATAC-seq in control and HNF4A KO livers. We also performed CUT&Tag and ATAC-seq of mouse fibroblast cells (NIH 3T3) treated with control or HNF4A expression vector.

overall_design: 17 Samples analyzed

first: Avinash

last: Thakur

first: Sibyl

last: Drissler

first: Pamela

last: Hoodless

last: Furglerud


title: Mixed cell-type spheroids endorse the generation and maintenance of heme-TAMs in an experimental tumor microenvironment [joint analysis]

first: Florence

last: Vallelian

address: Rämistrasse 100

institute: University Hospital Zürich

summary: Within the tumor microenvironment, heme exposure drives the transformation of macrophages into Arg1high Spp1high heme-TAMs with an enhanced matrix remodeling program and suppressed immunity, resisting inflammatory rewiring by INFγ and LPS.

overall_design: This is a joint analysis of two spheroids experiments (GSE236576 and GSE236995). Sample details can be found in the respective studies.

first: Dominik

last: Schaer

first: Livio

last: Baselgia

first: Elena

last: Duerst


title: Effect of loss of HNF4A in liver and effect of ectopic expression of HNF4A in mouse fibroblast cells

summary: To understand how HNF4A loss affects gene expression in mouse liver. We used control and HNF4A KO mouse livers for RNA sequencing. In addition, we also examined the effect of HNF4A gain in mouse fibroblast cells by ectropically expressing HNF4A in NIH3T3 cell to identify genes that are regulated by HNF4A.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.


title: Transcriptome analysis of control and SKOV3 floating sphere cells and sphere differentiated cells

city: Wuhan

first: Yurou

last: Chen

address: Donghu Road

institute: Zhongnan Hospital of Wuhan University

summary: We initiated this study with the aim of systematically identifying the biomarkers driving tumorigenesis and maintaining tumor dedifferentiation in human ovarian cancer.  To achieve that goal, SKOV3 cells were seeded in ultra-low-attachment 96-well plates in DMEM/F12 medium supplemented with 2% B27 serum replacement to allow the formation of floating spheres.  Then, these spheres were collected and recultured in a 6-well plate in DMEM with 10% FBS to allow the cells in the spheres to differentiate and attach to the bottom surface, and the genes in which transcription patterns were altered during the transition from OCSCs to differentiated cells.

overall_design: RNA-seq was performed in SKOV3-Adherent cells and SKOV3-stem cells with 3 replicates. Gene expression profiling was analyzed according to the sequencing results.

first: Yulong

last: Qiang

first: Wei

last: Zhang

first: Feng

last: Li


title: Transcriptome analysis of control and OTUD1 knockout SKOV3 Cells

summary: We have confirmed that high level of OTUD1 is important for retaining ovarian cancer stem cells (OCSCs) property. To investigate the exact mechanism of OTUD1 in the regulation of stemness maintain, we established SKOV3 cells with stable OTUD1 depletion by using sgRNA.

overall_design: RNA-seq was performed in SKOV3-sgNC and SKOV3-sgOTUD1 cells with 3 replicates. Gene expression profiling was analyzed according to the sequencing results.


title: ChIP-seq for Col-0 and pif4 using H3K9ac/H4K5ac antibodies.

status: Public on Jan 13 2024

city: Shanghai

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

summary: We analysed the effect of PIF4 on H3K9ac and H4K5ac.

overall_design: Comparative H3K9ac/H4K5ac occupancy analysis of ChIP-seq data for Col-0 and pif4 at 22℃ and 28℃.

first: Aiwu

last: Dong

first: Chengzhang

first: Jiachen

last: Wang


title: Analysis of peri-prosthetic breast tissue bewteen subjects with and without breast implant illness (BII)

status: Public on Jan 14 2024

city: Indianapolis

first: Mithun

last: Sinha

state: IN

address: 340 West 10th Street

institute: Indiana University School of Medicine

summary: Peri-prosthetic breast tissues were obtained from women with breast implants. Total RNA was extracted and cDNA library was prepared.

overall_design: Transcriptome profile of peri-prosthetic breast tissues

first: Imran

last: Khan


title: Placental gene expression data from human fetuses with isolated spina bifida and fetuses with no congenital anomalies

status: Public on Jan 12 2024

city: Ottawa

first: Kristin

middle: L

last: Connor

state: Ontario

address: 1125 Colonel By Drive

institute: Carleton University

summary:
Fetal spina bifida can associate with reduced fetal growth. However, little is known about placental development and function in pregnancies with fetal spina bifida, despite that the placenta is a critical regulator of fetal growth.
We used data from a case-control study to determine how the placental transcriptome differs in fetuses with isolated spina bifida (cases), compared to fetuses without any congenital anomalies (controls).

overall_design: Pregnant people carrying a fetus with isolated SB (cases) or a fetus with no congenital anomalies (controls) were recruited at Mount Sinai Hospital, Toronto. Clinical data and placental samples were collected. Placental transcriptome profiles for mRNA, lncRNA and miRNA were determined for the following samples: preterm (PT) controls (n=12; fetuses with no congenital anomalies, born preterm), controls (n=9; fetuses with no congenital anomalies born full-term), and cases (n=12; fetuses with isolated spina bifida). The Clariom D microarray (human) and the GeneChip® WT Pico Kit were used and two batches were run: controls and cases in September 2020, and PT controls in September 2021. Raw expression files (.CEL files) were processed in Transcription Analysis Console software (version 4.0.2). Data were summarised using the signal space transformation algorithm and normalised using the robust multiple-array average method.

first: M

last: White

first: J

last: Arif-Pardy

first: T

last: Van Mieghem

first: K


title: Heterogeneity of hepatocyte dynamics restores liver architecture after chemical, physical or viral damage

first: Carlos

last: Fernandez-Hernando

address: 10 Amistad St

institute: Yale University

summary: The liver has a remarkable capacity for regeneration after injury. Midlobular hepatocytes have been proposed as the most plastic hepatic cell type, providing definitive evidence that zone 2 of the liver lobule acts as a reservoir for hepatocyte proliferation during homeostasis and regeneration. However, the implication of other mechanisms beyond hyperplasia that contribute to liver repair have been little explored and the collaboration of another hepatocyte subpopulation has differed among previous studies depending on the model of liver injury used. Thus, re-examination of dynamics of hepatocytes during regeneration is critical to get a better understanding of underlaying mechanisms for potential cell therapy and treatment of liver diseases. Here, using a mouse model of hepatocyte- and non-hepatocyte-specific multicolor lineage tracing, we demonstrate that hepatocytes located in the midlobular region also undergo hypertrophy besides cell division in response to chemical, physical, and viral insults. Our study shows for first time that this subpopulation also combats liver impairment after infection with coronavirus. Furthermore, we demonstrate that pericentral hepatocyte subpopulation also expands in number and size during the repair process in collaboration with midlobular hepatocytes and Galectin-9-CD44 pathway may be critical for driving these processes. Interestingly, we identified transdifferentiation and cell fusion processes during liver regeneration after severe injury that may be key to recover hepatic function.

overall_design: Single-cell transcriptomic profiling of liver cells from male Alb-CreERT2 Rosa26rbw mice after acute CCI4 treatment

first: Inmaculada

last: Ruz-Maldonado

first: Hanming

first: Jonathan

last: Sun


title: MBD2 couples DNA methylation to Transposable Elements silencing during male gametogenesis

city: Los Angeles

first: Shuya

address: 610 Charles E Young Dr S

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: DNA methylation is an essential component of transposable element (TE) silencing, yet the mechanism by which methylation causes transcriptional repression remains poorly understood. Here we study the Arabidopsis thaliana Methyl-CpG Binding Domain (MBD) proteins MBD1, MBD2, and MBD4, and show that MBD2 acts as a transposable element (TE) repressor during male gametogenesis. MBD2 bound chromatin regions containing high levels of CG methylation, and MBD2 was capable of silencing the FWA gene when tethered to its promoter. MBD2 loss caused TE activation in the vegetative cell (VC) of mature pollen without affecting DNA methylation levels, demonstrating that MBD2-mediated silencing acts strictly downstream of DNA methylation. Loss of silencing in mbd2 became more significant in the mbd5 mbd6 or adcp1 mutant backgrounds, as well as in plants with chemically induced genome-wide DNA demethylation, suggesting that MBD2 acts redundantly with other silencing pathways to safeguard TEs from activation. Overall, our study identifies MBD2 as a novel methyl reader that acts downstream of DNA methylation to silence TEs during male gametogenesis.

overall_design: Use ChIP-seq, RNA-seq, snRNA-seq, WGBS, and MNase-seq

first: Zhenhui

last: Zhong


title: Understanding Bovine Embryo Elongation: A Transcriptomic Study of Trophoblastic Vesicles

status: Public on Jan 11 2024

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

country: France

institute: INSERM UMRS-1139

summary:
Background: During the process of elongation, the embryo increases in size within the uterus  while the extra-embryonic tissues (EET) develop and differentiate in preparation for implantation. As it grows, the ovoid embryo changes shape into first a tubular and then a filamentous form. This process is directed by numerous genes and pathways, the expression of which may be altered in the case of developmental irregularities such as when the conceptus is shorter than expected or when the embryo develops after splitting. In bovines, efforts to understand the molecular basis of elongation have employed trophoblastic vesicles (TVs)—short tubular EET pieces lacking an embryo—which also elongate in vivo. To date, however, we lack molecular analyses of TVs at the ovoid or filamentous stages that might shed light on the expression changes involved.
Methods: Following in vivo development, we collected bovine conceptuses from the ovoid (D12) to filamentous stages (D18), sectioned them into small pieces with or without their embryonic disc (ED), and then transferred them to a receptive bovine uterus to assess their elongation abilities. We also grew spherical blastocysts in vitro up to D8, and subjected them to the same treatment. We then assessed differences in gene expression between the different samples and fully elongating controls at different stages of elongation using a bovine array (10K) and an extended qPCR array comprising 224 genes across 24 pathways.
Results: In vivo, TVs elongated more or less depending on the stage at which they had been created and the time spent in utero. Their daily elongation rates differed from control EET, with the rates of TVs sometimes resembling those of earlier-stage EET. Overall, the molecular signatures of TVs followed a similar developmental trajectory as intact EET from D12–D18. However, within each stage, TVs and intact EET displayed distinct expression dynamics, some of which were shared with other short epithelial models.
Conclusions: Differences between TVs and EET likely result from multiple factors, including a reduction in the length and signaling capabilities of TVs, delayed elongation from inadequate uterine signals, and modified crosstalk between the conceptus and the uterus. These findings confirm that close coordination between uterine, embryonic, and extraembryonic tissues is required to orchestrate proper elongation and, based on the partial differentiation observed, raise questions about the presence/absence of certain developmental cues or even their asynchronies.

overall_design: Amplified material was indirectly labelled using “random” hexamers. One independent target was generated and hybridized onto one array. 2 measurements per DayPregnancy & TissueType were generated.

first: S

first: F

last: Liu

first: D

last: Laloe

first: C

last: Richard

last: Le Bourhis

first: MN

last: Rossignol

first: I

last: Hue


title: Defining key transcriptional regulators of extravillous trophoblast differentiation

first: Mijeong

last: Kim


title: Effect of depletion of ATG7 on gene expression in IAV-infected A549 cells

city: Fuzhou

first: JiLong

last: Chen

address: Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University

summary: To analyse differential expression genes（LncRNA and mRNA） in ATG7 knockdown cells and control cells upon influenza virus infection, transcriptome RNA sequencing was performed

overall_design: ATG7 knockdown cells and control cells were infected with PR8 influenza virus(MOI=0.5) for 16 hours .Comparative gene expression profiling analysis of RNA-seq data for ATG7 KD cells and control cells.

first: Biao

first: Yuhai

first: Ji-Long


title: Gluten induces rapid reprogramming of natural memory αβ and γδ intraepithelial T cells to induce cytotoxicity in celiac disease

city: New York

first: Arnold

last: Han

state: New York

institute: Columbia University

summary: Celiac disease (CD) is an autoimmune disease in which intestinal inflammation is induced by dietary gluten. The means through which gluten-specific CD4+T cell activation culminates in intraepithelial T cell (T-IEL)–mediated intestinal damage remain unclear. Here, we performed multiplexed single-cell analysis of intestinal and gluten-induced peripheral blood T cells from patients in different CD states and healthy controls. Untreated, active, and potential CD were associated with an enrichment of activated intestinal T cell populations, including CD4+follicular T helper (TFH) cells, regulatory T cells (Tregs), and natural CD8+αβ and γδ T-IELs. Natural CD8+αβ and γδ T-IELs expressing activating natural killer cell receptors (NKRs) exhibited a distinct TCR repertoire in CD and persisted in patients on a gluten-free diet without intestinal inflammation. Our data further show that NKR-expressing cytotoxic cells, which appear to mediate intestinal damage in CD, arise from a distinct NKR-expressing memory population of T-IELs. After gluten ingestion, both αβ and γδ T cell clones from this memory population of T-IELs circulated systemically along with gluten-specific CD4+T cells and assumed a cytotoxic and activating NKR-expressing phenotype. Collectively, these findings suggest that cytotoxic T cells in CD are rapidly mobilized in parallel with gluten-specific CD4+T cells after gluten ingestion.

overall_design: scRNA-seq and scTCR-seq were performed on intestinal biopsies from 11 patients with newly diagnosed or active CD (ACD), 19 celiac patients treated with a GFD, 7 patients with PCD, and 17 healthy controls. scRNA-seq and scTCR-seq were also performed on sorted CD38+CD103+B7integrin+ CD8+ and γδ T cells isolated from the peripheral blood of 5 celiac patients who underwent oral gluten challenge. CITE-seq was also performed on T cells from patients ACD 1-10, GFD 1-14, PCD 1-2, CONTROL 1-16, and GC 1-3.

first: Adam

last: Kornberg