title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-seq]

status: Public on Mar 25 2024

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

department: Department of Experimental Oncology

institute: European Institute of Oncology (IEO)

summary: Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.

overall_design: Gland forming (GL) and non-gland forming (NGL) tumor areas of 200-500 cells were collected from FFPE tissues in a cohort of 30 primary pancreatic ductal adenocarcinoma (PDAC) patients. Single or multiples areas were processed per patient for a total of 102 samples.


title: 5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma

status: Public on Feb 01 2024

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

country: USA

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary:
Purpose: Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high- risk neuroblastoma.

Methods: 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunopre- cipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models.

Results: In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found in- creased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma.

Conclusion: Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.

overall_design: This SuperSeries is composed of the SubSeries listed below; refer to individual Series


title: Dynamic histone modifications establish the two phase kinetics of glucosinolates against wounding stress in Arabidopsis plant

status: Public on Jan 31 2024

city: Anseong-si

first: Dasom

last: Choi

state: Gyeonggi-do

address: 4726, Seodong-daero

country: South Korea

institute: Chung-Ang University

summary: This study demonstrates that distinct composition of histone modifications between aliphatic and indolic GSL pathway genes contribute to the two phase activation of two different groups of GSL pathway genes in stress condition of Arabidopsis.

overall_design: Performed RNA-seq analysis between untreated control and wound-treated time course samples (harvested at 6 hrs, 12 hrs, 24 hrs, 3 days, 5 days after wounding treatment).

first: Sang

middle: W

last: Lee

first: Dong

middle: H

last: Kim


title: Effects of gene-by-environment interaction in light of differential susceptibility

status: Public on Jan 27 2024

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

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

overall_design: Refer to individual Series


title: Effects of gene-by-environment interaction on the mRNA profile in the light of differential susceptibility

summary:
Purpose: Investigation of effects of early adversity in mice deficient for serotonin transporter on mRNA expression in the context of differential susceptibility
Methods: Following prenatal stress and behavioural screening in adulthood, month old females, either wildtype or carrying a heterozygous knockout of the serotonin transporter gene, were sacrificed, brains extracted, the hippocampi of both hemispheres dissected, blended and separated in two protions. From one of these portions RNA was extracted. Extracted RNA was further processed by an external company, i.e. IGA Technologies (Udine, Italy). Following library preparation, samples were sequenced on the illumina HiSeq2000 platform (single end, 50 bp, 30 million reads/sample). Reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013). Following mapping, the reads per position were determined using HTSeq (Anders et al. 2015). These counts were then used for the analysis of differentially expressed genes (DEGs) using the R package DeSeq2 (Love et al. 2014).
Results: dependent on the serotonin transporter genotype and behaviourally determined susceptibility to early life adversity, animals displayed distinct gene expression. As expected, the effect sizes and significances were rather subtle.
Conclusion: the modulation of differential susceptibility seems to be modulated by distinct mRNA expression profiles, dependent on the serotonin transporter genotype

overall_design:
RNA expression affected in serotonin transporter deficient or wildtype offspring of prenatal stress that do or do  not succumb to the adverse effects of prenatal stress, i.e. vulnerable or resilient offspring
[contributor] IGA Technologies (Undine, Italy)

first: K

middle: P

last: Lesch

first: D

last: van den Hove

first: M

middle: T

last: Weidner

middle: U

first: L

last: Eijjsen


title: Spreading of inflammation: the skin-joint axis

status: Public on Jan 16 2024

city: Erlangen

first: Simon

last: Rauber

address: Ulmenweg 18

department: Medicine 3

summary: The spread of inflammation from the skin to the joints is a key issue in the pathogenesis of psoriatic arthritis (PsA). Psoriasis (PsO), one of the most common skin diseases, usually precedes joint manifestations, suggesting skin-joint disease spread, which occurs in about 30% of psoriasis patients. Until now, it has been unclear why the inflammatory process remains restricted to the skin in some patients with PsO, whereas it spreads to tendons and joints in others. Using a preclinical model of PsA, we aimed to elucidate the skin-joint axis, i.e. the spread of psoriatic inflammation from the skin to the joints. KAEDE transgenic mice expressing a photo-convertible fluorescent reporter were used to assess cell trafficking from inflamed skin to other organs in the mouse model of IL-23 overexpression (IL-23OE) induced PsA. Psoriatic skin lesions were irradiated with UV light to induce the photoswitch from KAEDE-GREEN to KAEDE-RED. Migrating cells were characterised by scRNAseq.

overall_design:
Stromal and immune cells from synovial joints and skin were isolated by fluorescence-activated cell sorting from minicircle-induced IL-23 overexpression on day 7. Two libraries were generated corresponding to either Balb/c or C67BL/6 background. Viable CD45+ Ly6G- and viable CD45- were isolated and labelled with hashtag antibodies against CD45 and B2m.
Please note that processed data genated from both GEX and HTO are linked to the corresponding *GEX sample records.

first: Maria

middle: G

last: Raimondo

first: Hashem

last: Mohammadian

first: Hannah

last: Labinsky

first: Aleix

last: Rius Rigau

first: Andreas

last: Ramming


title: Onocgenic cell marking and single-cell transcriptomics reveal cell type and time-resolved actions of von Hippel Lindau inactivation in the kidney

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: Defining the first events in oncogenesis and the cellular responses they entrain, even in advance of morphological abnormality, is a fundamental challenge in understanding cancer initiation. As a paradigm to address this we studied the tumor suppressor von Hippel Lindau (VHL), whose loss ultimately drives clear cell renal cancer. Vhl inactivation was directly coupled to activation of a tdTomato reporter within a single allele, allowing accurate visualization of affected cells in their native context and retrieval from the kidney for single-cell RNA sequencing. This strategy uncovered cell-type specific responses to Vhl inactivation, defined a novel proximal tubular class with oncogenic potential, and revealed longer term adaptive changes in the renal epithelium and the interstitium. Oncogenic cell marking also revealed markedly heterogeneous cellular effects including time-limited proliferation and elimination of specific cell types. Striking heterogeneity in these responses suggests that very early events define the tissue specificity of VHL tumor suppressor action.

overall_design: Vhl(wt/flox) (Control) and Vhl(KO/flox) (KO) mice carrying the renal tubular epithelium specific Pax8-CreERT2 were dosed with 5x 2 mg tamoxifen and harvested either at an early (1-3 weeks) or late (4-12 months) timepoints after dosing. Cre-mediated recombination marked Vhl recombination with the expression of tdTomato. tdTomato-positve and tdTomato-negative cells were retrieved by FACS and subjected to scRNA-seq using the 10X Chromium NextGEM platform.

first: Samvid

last: Kurlekar

first: Ran

last: Li


title: Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate [RNA-seq]

status: Public on Jan 10 2024

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF Forkhead box A (FOXA), required for endoderm lineage commitment, coordinates with the PR domain zinc finger 1 (PRDM1) TF to recruit Polycomb repressive complexes, which establish bivalent enhancers and repress alternative lineage programs. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to repress cell differentiation programs in pluripotent stem cells, suggesting this is a common feature of pioneer TFs. We propose that pioneer and PRDM TFs coordinate recruitment of Polycomb complexes to safeguard cell fate.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human PSCs, endoderm, mesoderm, and neuroectoderm and their KD derivatives (FOXA-TKD, PRDM1-KD, and OCT4-KD)

first: Satoshi

last: Matsui

first: Marissa

last: Granitto

first: Morgan

last: Buckley

first: Joseph

last: Shiley

first: William

last: Zacharias

first: Christopher

last: Mayhew

first: Makiko

last: Iwafuchi


title: Direct RNA sequencing experiment of humanized  liver mice with metabolic treatments

status: Public on Jan 23 2024

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary:
To make the human liver accessible to metabolic treatments, we employed a liver-specific humanized mouse model in which approximately 50% of the mouse hepatocytes were replaced by human ones.
To capture transcriptomes reflecting pathophysiology and therapeutic development of metabolic diseases, we subjected the humanized mice to  dietary intervention and the key metabolic transcriptional factor agonist treatments.  We then performed rna exoression profiling analysis using data obtained from nanopore direct RNA sequencing of these humanized mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
For the dietary treatment, the humanized mice were allowed free access to food (AL, n=4 for donor1, n=3 for donor2) or subjected to a twenty-four hours food withdrawal (Fast, n=4 for donor1, n=3 for donor2). For the transcription factor agonist treatments, the humanized mice were injected with DMSO (n=4), fenofibrate (n=4, 50mg/kg, Sigma-Aldrich, Cat. F6020), rosiglitazone (n=4,10mg/kg, Sigma-Aldrich, Cat. R2408) and GW4064 (n=4, 30mg/kg, Sigma-Aldrich, Cat. G5172) by i.p. injection. The livers were collected after 6 hours fasting and stored in liquid nitrogen immediately after mice sacrificed.The 75 ug of fresh Trizol isolated RNAs were adjusted to a volume of 100 μL with nuclease-free water. The polyadenylated RNAs were selected using the Dynabeads™ mRNA Purification Kit (Invitrogen, Cat. 61006) following the manufacturer's instructions. The 500 ng of fresh isolated polyadenylated RNAs were used for nanopore direct RNA sequencing (DRS) generally following the Oxford Nanopore Technologies (ONT) SQK-RNA002 kit protocol, including the optional reverse transcription step recommended by ONT. Libraries were loaded onto ONT R9.4 flow cells (Oxford Nanopore Technologies) and were sequenced using the GridION platform, with the standard MinKNOW/19.12.5 protocol script being used.

UPDATE: [12-13-2024] The following files were updated:
GSE224278_all.human.isoforms.donor1.bed.gz
GSE224278_all.mouse.isoforms.donor1.bed.gz
GSE224278_human.isoforms.donor1.gtf.gz
GSE224278_mouse.isoforms.donor1.gtf.gz
GSE224278_nanopore_human_transcripts_tpm_donor1.txt.gz

first: Chengfei

last: Jiang


title: High/low MNase-seq in foregut, Control and FOXA-TKD

summary: Nucleosome occupancy and positioning were examined in foregut stage to compare control and FOXA-TKD using high/low MNase-seq

overall_design: low-MNase-seq for identify accessible/fragile nucleosomes and high-Mnase-seq for identify stable nucleosomes


title: Single-cell RNA sequencing of total lung cells from Atg14f/f,Atg14f/f-CD11c-cre, Atg14f/f-LysM-cre mice

status: Public on Jan 07 2024

city: Beijing

first: Siwei

last: Feng

address: No.30,Shuangqing street

country: China

institute: Siwei Feng

summary: We found that several autophagy genes in myeloid cells are required to protect against high-dose Mtb (~1000cfu) infection. To understand the immune cell population in these mice after high-dose Mtb infection and what may contribute to the susceptibility, we did scRNAseq on naïve mice and mice infected with high-dose of Mtb strain Erdman.

overall_design: Lung cells from naive Atg14f/f,Atg14f/f-CD11c-cre, Atg14f/f-LysM-cre and 21dpi Atg14f/f,Atg14f/f-CD11c-cre, Atg14f/f-LysM-cre mice. Cells pooled from 4 mice each, age 8-10 wks.


title: Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate


title: Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC

status: Public on Feb 04 2024

city: Laval

first: Maya

last: Saleh

state: Qc

address: 531 Boulevard des Prairies

department: Armand Frappier Santé Biotechnologie

country: Canada

institute: INRS


title: Host and Microbe Blood Metagenomics Reveals Key Pathways Characterizing Critical Illness Phenotypes

status: Public on Jan 08 2024

city: San Francisco

first: Lucile

middle: P A

last: Neyton

state: CA

address: 505 Parnassus Ave

institute: UCSF

summary:
Two molecular phenotypes of sepsis and acute respiratory distress syndrome, termed hyperinflammatory and hypoinflammatory, have been consistently identified by latent class analysis in numerous cohorts, with widely divergent clinical outcomes and differential responses to some treatments; however, the key biological differences between these phenotypes remain poorly understood.
We used host and microbe metagenomic sequencing data from blood to deepen our understanding of biological differences between latent class analysis-derived phenotypes and to assess concordance between the latent class analysis-derived phenotypes and phenotypes reported by other investigative groups (e.g., SRS1-2, MARS1-4, reactive/uninflamed).
We analyzed data from 113 hypoinflammatory and 76 hyperinflammatory sepsis patients enrolled in a two-hospital prospective cohort study. Molecular phenotypes had been previously assigned using latent class analysis.
The hyperinflammatory and hypoinflammatory phenotypes of sepsis had distinct gene expression signatures, with 5,755 genes (31%) differentially expressed. The hyperinflammatory phenotype was associated with elevated expression of innate immune response genes, while the hypoinflammatory phenotype was associated with elevated expression of adaptive immune response genes, and notably, T-cell response genes. Plasma metagenomic analysis identified differences in prevalence of bacteremia, bacterial DNA abundance and composition between the phenotypes, with an increased presence and abundance of Enterobacteriaceae in the hyperinflammatory phenotype. Significant overlap was observed between these phenotypes and previously identified transcriptional subtypes of acute respiratory distress syndrome (reactive/uninflamed) and sepsis (SRS1-2). Analysis of data from the VANISH trial indicated that corticosteroids might have a detrimental effect in hypoinflammatory patients.
The hyperinflammatory and hypoinflammatory phenotypes have distinct transcriptional and metagenomic features that could be leveraged for precision treatment strategies.

overall_design:
Gene expression patterns comparison for hypoinflammatory and hyperinflammatory sepsis patients
*** Raw data not provided due to patient privacy concerns with making the raw data fully public in GEO. ***

first: Carolyn

middle: S

last: Calfee


title: Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate [CUT&Run and ChIP-seq]

overall_design: ChIP-seq or CUT&RUN for transcription factors, PRC components, and histone modifications in human PSCs, definitive endoderm, foregut cells, and their KD derivatives (FOXA-TKD and OCT4-KD) .


title: Deregulation of neuronal polarization promotes axonal growth after spinal cord injury

status: Public on Jan 01 2024

city: London

first: Franziska

last: Müller

address: Du Cane Road

department: Brain Sciences

institute: Imperial College London

summary: The developmental maturation of a neuron requires the completion of neuronal polarization preceding the formation of a synapse. Whether neuronal polarization marks the decline in growth competence in the injured mammalian adult nervous system remains elusive. Here we show that gene expression and epigenetic signatures associated with the regenerative growth ability of dorsal root ganglia (DRG) sensory neurons are lost during the transition from a non-polarized to a polarized state. The transcriptional co-factor Cited2 was found to be epigenetically upregulated in immature DRG and following a regenerative injury, but it remained unchanged by a non-regenerative spinal cord injury (SCI). Next, Cited2 was overexpressed in DRG neurons in a model of SCI in mice where it promoted sensory axon growth and reversed the gene expression signatures associated with neuronal maturation. Importantly, Cited2 expression stirred the maturation of DRG neurons towards a non-polarized state. Together, these data suggest that the transition from a non-polarized to a polarized state marks the reversible loss of the regenerative ability of a neuron, thus paving the way to targeted repair strategies relying on neuronal de-maturation.

overall_design: AAV-GFP or AAV-Cited2 was injected bilaterally into the sciatic nerve 4 weeks prior to a dorsal column axotomy. 24 hours post-injury, DRG were extracted and a neruonal enriched population processed for RNA-seq

first: Ilaria

last: Palmisano

first: Simone

last: Di Giovanni


title: Deregulation of neuronal polarization promotes axonal growth after spinal cord injury (ATAC-Seq)

overall_design: AAV-GFP or AAV-Cited2 was injected bilaterally into the sciatic nerve 4 weeks prior to a dorsal column axotomy. 24 hours post-injury, DRG were extracted and a neruonal enriched population processed for ATAC-seq

first: Matt

last: Danzi


title: CD146 as a potent target for anti-vascular therapies in lung cancer brain metastasis

status: Public on Dec 31 2023

city: Dalian

first: Wenzhe

last: Duan

address: Shahekou Zone, Zhongshan Road 467

institute: Second hospital of Dalian Medical University

summary: To investigate the function of CD146 in the lung cancer brain metastasis cells, we established PC9-BrM3 cells in which CD146 has been knocked down by shRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  PC9-BrM3 cells with or without AKR1B10 knockdown.

first: Wenwen

last: Liu

first: Shengkai

last: Xia

first: Qi

last: Wang


title: WT and RNE∆IDR mRNA half-life profiling in Sinorhizobium meliloti.

status: Public on Dec 25 2023

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: WT and RNE∆IDR strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Wild type(WT) was compared to RNE∆IDR strain.

overall_design: WT and RNE∆IDR strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Biological samples were taken before rifampicin treatment (0 minute), then at 1, 3, and 9 minutes after rifampicin treatment.  Two biologycal replicates were performed.

middle: M


title: Spatially resolved human kidney multi-omics single cell atlas highlights the key role of fibrotic microenvironment in kidney disease progression.

status: Public on Jan 17 2024

city: Philadelphia

first: Jonathan

last: Levinsohn

state: PA

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

summary: Kidneys possess come one of the most intricate three-dimensional cellular structures in the body, yet the spatial molecular principles of kidney health and disease remain inadequately understood. Here we generated high-quality single cell (sc), single nuclear (sn), spatial (sp) RNA expression and sn open chromatin datasets for 79 samples, capturing half a million cells from healthy, diabetic, and hypertensive diseased human kidneys. By combining the sn/sc and sp RNA data, we identify over 100 cell types and states and successfully map them back to their spatial locations. Computational deconvolution of spRNA-seq helps to identifies glomerular, tubular, immune, and fibrotic spatial microenvironments (FMEs). Although injured proximal tubule cells appear to be the nidus of fibrosis, we reveal the complex, heterogenous cellular and spatial organization of human FMEs, including the highly intricate and organized immune environment. We demonstrate the clinical utility of the FME spatial gene signature for the classification of a large number of human kidneys for disease severity and prognosis. We provide a comprehensive spatially-resolved molecular roadmap for the human kidney and the fibrotic process and demonstrate the clinical utility of spatial transcriptomics.

overall_design:
We provided human kidney atlas by generating the following datasets: (i) scRNA-seq (16 Control + 13 Disease), (ii) snRNA-seq (7 control + 11 Disease), (iii) snATAC-seq (10 Control + 8 Disease), (iv) Spatial Transcriptomics (3 Control + 11 Disease).

**Raw data were not provided due to privacy concerns**

Susztak_SC_SN_ATAC_merged_preSCVI_final.h5ad: merged object of snRNA/scRNA/snATAC
Susztak_SC_SN_ATAC_merged_PostSCVI_final.h5ad: integrated object via SCVI
Susztak_KPMP_SC_SN_ATAC_merged_PostSCVI_final.h5ad: integrated object via SCVI with KPMP samples as well
7_13_23_slide0_annotated_iPTsubclusters.h5ad: Annotated CosMx Object

first: Amin

last: Abedini

first: Konstantin

last: Kloetzer

first: Ziyuan

last: Ma

first: Julia

last: Frederick

first: Poonam

last: Dhillon

first: Michael

last: Balzer

first: Rojesh

last: Shrestha

first: Kishor

last: Devalaraja-Narashimha

first: Gurmannat

last: Kalra

first: Tanmoy

last: Bhattacharyya

first: Erding

last: Hu

first: Steven

last: Pullen

first: Carine

last: Boustany-Kari

first: Paolo

last: Guarnieri

first: John

last: Liles

first: Hanyung

last: Yu

first: Kyle

last: Coleman

first: Anil

last: Karihaloo

first: Daniel

last: Traum

first: Matthew

last: Palmer

last: Vitale

first: Lea

last: Sarov-Blat

first: Lori

last: Morton

first: Christopher

last: Hunter

first: Klaus

last: Kaestner

first: Mingyao

last: Li

first: Katalin

last: Susztak


title: Aberrant expression of the DCT gene is implicated in the hyperpigmentation of the visceral peritoneum of the chicken

city: guangzhou

first: xu

last: dong

state: Guangdong

address: wushan

institute: South China Agricultural University

summary: Hyperpigmentation of the visceral peritoneum (HVP) has recently garnered significant attention within the poultry industry due to its potential implications for the health of afflicted animals and its adverse effects on the appearance of commercial chicken carcasses.  Unfortunately, the heritable characteristics of HVP are not yet fully understood. Motivated by poultry industry demand, we deployed multi-omics comparing the clinical HVP and normal samples profiling the potential regulating molecular landscape in cell and genome resolution, specifically, aiming to decipher the precise molecular genomic marker. Specifically, we identified the signature genes for the HVP phenotype and found that the signature gene of melanogenesis strongly enriched in the HVP group. At the melanocyte level, overexpression of the DCT gene can promote the proliferation of melanocytes, with exogenous Tyr addition. On the contrary, significantly lower melanin content in the supernatant of cells was detected after siRNA interference relative to untreated cells. Through single-cell sequencing, the hyperexpression of melanogenesis-associated genes in melanocytes was echoed. In summary, molecular features of the HVP phenotype were systematically revealed, which may partially explain the strong heterogeneities of the peritoneum phenotype. The hyperpigmentation of the peritoneum is attributed to an excess deposition of melanin, where the DCT hyperexpression can be regarded as a molecular marker related to the deposition of peritoneal melanin. Future directions should deploy gene editing technology to alert the gene expression of DCT to change the phenotype of pigmentation in the visceral peritoneum.

overall_design: In this experiment, ten 40-day-old Huiyang Bearded Chickens, each with normal and black peritoneum color, were selected. Following humane slaughter in compliance with animal welfare requirements, peritoneum tissues were swiftly separated using scissors. The tissues were immediately rinsed 2-3 times in 4-degree pre-chilled 1×PBS on ice and then transferred to a 1.5mL centrifuge tube for scRNA-seq.

first: Zhenhui

first: Xu

last: Dong


title: Genome-wide CRISPR screening identifies SEC31A as a regulator of alpha cell survival

status: Public on Dec 23 2023

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Impairment of the glucagon response to hypoglycemia is among the severe clinical consequences in patients with type 1 or advanced type 2 diabetes. However, an incomplete understanding of the stress-response mechanism(s) in alpha cells has limited the insights into the pathophysiology underlying the dysregulated glucagon response and precluded the development of therapeutics. In this study, we undertook an unbiased, genome-wide screening by transducing alpha cells with a CRISPR lentiviral library to identify potential proteins that regulate stress resistance in alpha cells. We identified SEC31A, a gene responsible for the ER-Golgi transportation system, as a critical mediator of cell survival in response to stress. To provide clinical relevance to these findings, we performed transcriptome analysis using pseudoislets generated from sorted and re-aggregated human alpha cells with a knockdown of SEC31A. Our study offers insights into the regulatory mechanism(s) underlying ER stress resistance in pancreatic alpha cells with implications for treating hypoglycemia in T1D and advanced T2D

overall_design: Comparative gene expression profiling analysis of RNA-seq data for re-aggregated human alpha and beta islet  cells and its KD derivatives (SEC31AKD).

first: Kimitaka

last: Shibue

first: Sevim

last: Kahraman

first: Rohit

middle: N

last: Kulkarni


title: Global gene expression prolife of primary cultured murine stress erythroid progenitors.

city: University Pk

first: Robert

last: Paulson

address: 115 Henning Building, Penn State University

department: Veterinary and Biomedical Sciences

institute: Penn State University

summary: Inflammation inhibits steady state erythropoiesis, while at the same time it induces stress erythropoiesis to maintain erythroid homeostasis. Stress erythropoiesis relies on the rapid expansion of early progenitors that do not differentiate until the increase in serum Epo promotes a transition in progenitors to enable their synchronous differentiation. RNA-seq analysis allows us to identify an inflammatory transcriptome signature in early progenitors that induces iNOS-derived NO production. The accumulation of NO establishes a metabolism that promotes cell proliferation while inhibiting the differentiation of early progenitors. In contrast, the transition of progenitors to differentiation is marked by the suppressed inflammatory responses and a consequent decrease of iNOS-derived NO. We show that Epo initiates this transition response by altering progenitor metabolism to support itaconate production, resulting in the activation of Nrf2 that suppresses the inflammatory responses, which in turn alleviates the NO-mediated inhibition of erythroid program. Consequent differentiation of stress erythroid progenitors generates a bolus of new erythrocytes to maintain erythroid homeostasis until steady state erythropoiesis can resume.

overall_design: mRNA profiles of primary cultured stress erythroid progenitors in five conditions: WT expansion cultures treated with vehicle or 1400w, WT differentiation cultures treated with vehicle or 1400w, and Nrf2-/- differentiation cultures treated with vehicle.

first: Baiye

last: Ruan


title: Rational design of cyanobacteria aptamer sensitizes prostate cancer to hormone therapy

city: LOS ANGELES

first: Carlos

middle: David

last: Cruz-Hernandez

state: CALIFORNIA

address: 8700 Beverly Blvd #2900A

department: SOCC

institute: Cedars Sinai

summary: We performed RNA-seq to investigate gene expression changes in prostate cancer cells  treated with L-Gln and 56 mer Gln aptamer

overall_design: RNA-seq was performed in C4-2B and 22RV1 cells with biological triplicates under various conditions (56 mer 50 nM and L-Gln 2 mM).

first: Neil

middle: A

last: Bhowmick

middle: D


title: Th17 cells secrete TWEAK to trigger epithelial-mesenchymal transition and promote colorectal cancer liver metastasis (scRNA-seq)

status: Public on Jan 05 2024

city: Guangzhou

first: Lixia

last: Xu

address: 58 Zhongshan Road 2

institute: Sun Yat-sen University First Affiliated Hospital

summary: Liver metastasis is the leading cause of mortality in patients with colorectal cancer (CRC). Given the significance of both epithelial-mesenchymal transition (EMT) of tumor cells and the immune microenvironment in CRC liver metastasis (CRLM), the interplay between them could hold the key for developing improved treatment options. We employed multi-omics analysis of 130 samples from 18 synchronous CRLM patients integrated with external datasets to comprehensively evaluate the interaction between immune cells and EMT of tumor cells in liver metastasis. Single-cell RNA sequencing analysis revealed distinct distributions of non-malignant cells between primary tumors from patients with metastatic CRC (mCRC) and non-metastatic CRC, showing that Th17 cells were predominantly enriched in the primary lesion of mCRC. TWEAK, a cytokine secreted by Th17 cells, promoted EMT by binding to receptor Fn14 on tumor cells, and the TWEAK-Fn14 interaction enhanced tumor migration and invasion. In mouse models, targeting Fn14 using CRISPR-induced knockout or lipid-nanoparticle-encapsulated siRNA alleviated metastasis and prolonged survival. Mice lacking Il17a or Tnfsf12 (encoding TWEAK) exhibited fewer metastases compared to wild-type mice, while co-transfer of Th17 with tumor cells promoted liver metastasis. Higher TWEAK expression was associated with a worse prognosis in CRC patients. Additionally, CD163L1+ macrophages interacted with Th17 cells, recruiting Th17 via the CCL4-CCR5 axis. Collectively, this study unveils the role of immune cells in the EMT process and identifies TWEAK secreted by Th17 as a driver of CRLM.

overall_design:
In this study, single-cell analysis of more than 160,000 cells isolated from primary and metastatic colorectal cancer tissues, enabled us to unveil the interaction between tumor and immune cells in the context of liver metastasis in colorectal cancer.

***************************************************************
Please note that raw data have been deposited in the Genome Sequence Archive for Human under accession HRA005549
***************************************************************

first: Xin

last: Liu

last: Wang

first: Qingxia

last: Yang

first: Xinming

last: Song

first: Fang


title: Gene expression profiling of skin and blood in human acute Graft-versus host disease (GVHD) of the skin

status: Public on Dec 20 2023

city: Vienna

first: Johanna

last: Strobl

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary: GVHD following allogneeic hematopoietic stem cell transplantation is described as a T cell mediated disease. We analyze mononuclear phagocyte subsets and other leukocyte populations in blood and skin from patients with acyte cutaneous GVHD

overall_design:
Single cell suspensions were obtained from skin and blood of GVHD patients, FACS-sorted and sequenced using the 10XGenomics platform as previously described (Saluzzo et al. STAR Protoc. 2022 Jun 17;3(3):101470. doi: 10.1016/j.xpro.2022.101470. PMID: 35769924; PMCID: PMC9234085.
>>>Raw data not provided due to patient confidentiality.<<<

first: Laura

last: Gail

first: Ruth

last: Dingelmaier-Hovorka

first: Georg

last: Stary


title: Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells

status: Public on Dec 18 2023

first: Ashish

last: Lal

address: 37 Convent Drive, Bldg 3, Room 6134

department: Genetics Branch

institute: NCI, NIH

summary: Transcription factors play key roles in development and diseases by controlling gene expression. Forkhead Box A1 (FOXA1) is a pioneer transcription factor essential for mouse development that plays important roles in prostate and breast cancer. In colorectal cancer (CRC), we have found that FOXA1 is significantly downregulated, suggesting potential tumor suppressive functions. However, the mechanism(s) by which FOXA1 is downregulated in CRC cells remain largely unclear. We investigated the regulation of FOXA1 expression in CRC, focusing on well-differentiated CRC cells where it is robustly expressed. Genome-wide stability assays identified FOXA1 as an unstable mRNA in CRC cells. We validated FOXA1 mRNA instability in multiple CRC lines and patient-derived CRC organoids and found FOXA1 mRNA is degraded via its 3’UTR. Through FOXA1 3’UTR RNA pulldowns, we identified Staufen1 (STAU1) as a potential regulator of FOXA1. Indeed, knockdown of STAU1 results in increased expression of FOXA1 mRNA and protein due to increased FOXA1 mRNA stability. A subset of the STAU1-regulated transcriptome is enriched for FOXA1 targets, whose expression also increases upon STAU1 knockdown. Collectively, this study uncovers the molecular mechanism by which FOXA1 is regulated in CRC and provides insights into our understanding of the complex mechanisms of gene regulation in cancer.

overall_design: mRNA profiles from LS180 upon siCTRL, or siSTAU1 after 72 + 72 hours of transfection. mRNA profiles from LS180 and HCT116 upon 5 ug/ml Actinomycin D treatment at different time points.

first: Katherine

middle: R

last: Pasterczyk

first: Meira

last: Zibitt

first: Corrine

last: Hartford

first: Xiao

middle: L

last: Li

first: Lorinc

last: Pongor

first: Lisa

last: Jenkins

first: Yue

last: Hu

first: Patrick

middle: X

last: Zhao

first: Bruna

last: Muys

first: Suresh

last: Kumar

first: Nitin

last: Roper

first: Mirit

middle: I

last: Aladjem

first: Yves

last: Pommier

first: Ioannis

last: Grammatikakis


title: Gene expression by RNA-seq in Liver of WT and panetch cell specific  P55 KO mice 18 hours after TNF

status: Public on Dec 15 2023

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: After a challenge with TNF, gene expression changes in the liver may result from direct effect of TNF, through liver TNF receptors, and indirect effect. Baterial infiltration of the liver due to leaky gut after TNF is a primary contributor of this effect. In order to evaluate only the direct effects of TNF on lier transcriptome, we performed TNF challenge in normal WT mice and P55 panetch cell KO mice, which do not show the leaky gut syndrome.

overall_design: To investigate the direct effects of TNF on liver gene expression, an RNA-seq was performed 18 hours after TNF or PBS (control) injection in P55 KO mice and P55 WT littermates (4 mice/group except KO+PBS: 3 mice/group)

first: Charlotte

last: Wallaeys

first: Natalia

last: Garcia-Gonzalez

first: Jolien

last: Vandewalle

first: Tineke

last: Vanderhaeghen

first: Hester

last: Dufoo

first: Melanie

last: Eggermont

first: Riet

last: De Rycke

first: Serge

last: Verbanck

first: George

last: Kollias

first: Richard

last: Blumberg

first: Takao

last: Iwawaki

first: Claude

last: Libert


title: Effects of gene-by-environment interaction on the H3K4me3 profile in the light of differential susceptibility

city: Cologne

first: Konrad

middle: U.

last: Förstner

address: Gleueler Str. 60

institute: ZB MED - Information Centre for Life Sciences

summary:
Purpose: Investigation of effects of early adversity in mice deficient for serotonin transporter on H3K4me3 enrichment in the context of differential susceptibility
Methods: Following prenatal stress and behavioural screening in adulthood, 3 month old females, either wildtype or carrying a heterozygous knockout of the serotonin transporter gene, were sacrificed, brains extracted, the hippocampi of both hemispheres dissected, blended and separated in two protions. For one of these portions  the material was split again in two portions, of which one was fixed using 1% PFA, and was subsequently processed using a standard Chromatin immuno precipitation protocol. Following ChIP, the samples were processed by Nxt-Dx Belgium. Library preparation was performed using the NEBNext Ultra II DNA Library prep kit for Illumina (NEB, Ipswitch, Massatchusettes, USA). Subsequently, the whole IP material was subjected to ends prep and ligation of Illumina adaptors. A clean up of the adaptor-ligated DNA with AMPure XP beads (Beckman Coulter) was performed without size selection. The eluted material was subjected to enrichment PCR (14 cycles) with the NEBNext Index primers, and a last clean up with AMPure XP beads followed. The quality of the final libraries was checked on a Bioanalyzer 2100 DNA 1000 chip (Agilent, Santa Clara, CA, USA). The concentration was determined by performing qPCR on the samples using a dilution of PhiX index3 as standard. The concentration of all indexed samples was adjusted to 10 nM and samples were pooled for sequencing. Sequencing was performed on an Illumina HiSeq4000 (read-length of 50 bp with 25-30 million reads/sample, paired-end).
Results: dependent on the serotonin transporter genotype and behaviourally determined susceptibility to early life adversity, animals displayed distinct H3K4me3 enrichment. As expected, the effect sizes and significances were rather subtle.
Conclusion: the epigenetic regulation by prenatal stress seems to be modulated by the serotonin transporter genotype

overall_design:
H3K4me3 enrichment affected in serotonin transporter deficient or wildtype offspring of prenatal stress that do or do  not succumb to the adverse effects of prenatal stress, i.e. vulnerable or resilient offspring
[contributor] Nxt-Dx (Ghent, Belgium)

first: K

middle: P

last: Lesch

first: D

last: van den Hove

first: M

last: Weidner

first: L

last: Eijjsen

first: R

last: Lardenoije


title: Multi-cellular phenotypic dynamics during the progression of breast tumors

status: Public on Dec 21 2023

city: Stockholm

first: Jean

last: Hausser

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institutet

summary: In cancer, improving diagnostics and therapeutic interventions can benefit from understanding the cellular and phenotypic heterogeneity of the tumor microenvironment (TME). In recent years, the TME has been profiled at an unprecedented level of detail by performing single-cell RNA sequencing (scRNAseq) on patient samples. However, from patient samples, studying the temporal dynamics of the TME has been challenging. Characterizing the temporal dynamics of the TME is critical to understand how inter-tumor heterogeneity is organized into a temporally ordered sequence of causes and consequences in cellular events. Here we survey the temporal dynamics of the TME by performing longitudinal scRNAseq on mouse breast tumors at different progression time points. We find multicellular phenotypic dynamics that follow one out of three possible temporal patterns: stable colonization, wave-like, or progressive increase. In particular, IFN-responsive cancer cells, GzmB+ cytotoxic T cells, as well as macrophages of a phagocytic phenotype, progressively increase as tumors progress. These findings establish the single-cell types and phenotypes in a progressing breast tumor, and determine when these players enter and leave the TME. This single-cell dataset could serve to position clinical samples where timing is unknown on a temporal axis of progression, and suggest optimal timing for different therapies.

overall_design: Clustering and comparative gene expression analysis on duplicate tumor samples from allograft model originally derived from a MMTV-PyMT GEMM of breast cancer in immunocompetent mice.

first: Louise

last: Gsell

first: Spencer

last: Watson

first: Iva

last: Sutevski

first: Matteo

last: Massara

first: Klara

last: Soukup

first: Antony

last: Cougnoux

first: Johanna

last: Joyce


title: Transcriptional profiling of intestinal tissue from mice with and without Npm1 deficiency.

status: Public on Dec 17 2023

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

institute: Cancer Research UK Scotland Institute

summary: A profile of gene expression differences in mouse intestine with the noted transgenic alleles, in the presence and absence of functional Npm1.

overall_design: Expression data from intestine with the noted transgenes with and without Npm1 deficiency.

first: Georgios

last: Kanellos

first: Owen

last: Sansom


title: Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion

status: Public on Jan 12 2024

city: Durham

first: Amanda

last: Hargrove

state: NC

address: 124 Science Dr

department: Chemistry

institute: Duke University

summary: The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) was previously identified as a predictive biomarker and potential driver of aggressive prostate cancer. Recent work suggests that SChLAP1 may bind the SWI/SNF chromatin remodeling complex to promote prostate cancer metastasis, though the exact role of SWI/SNF recognition is debated. To date, there are no detailed biochemical studies of apo SChLAP1 or SChLAP1:protein complexes. Herein, we report the first secondary structure model of SChLAP1 using SHAPE-MaP in vitro, in cellulo, and ex cellulo (protein-free). Comparison of the ex cellulo and in cellulo data via ΔSHAPE identified putative protein binding sites within SChLAP1. In addition, we identified primate conserved exons of SChLAP1 as well as regions that appear to have been incorporated through retroviral insertion. In particular, we characterized a complex structural landscape in a protein binding region at the 3′-end of SChLAP1 derived from a THE1B-type retroviral insertion, suggesting a role for an exapted RNA structure in SChLAP1:protein recognition and prostate cancer progression. This work lays the foundation for future efforts to selectively target and disrupt the SChLAP1:protein interface and to develop new therapeutic avenues in prostate cancer treatment.

overall_design:
DNA-seq of libraries derived from mock (DMSO) or SHAPE-probed SChLAP1 RNA. Biological duplicate obtained for in cellulo and ex cellulo samples, and unicate obtained of in vitro samples. DMS probing performed with ethanol control of in vitro SChLAP1 in biological unicate.
Please note that the processed data generated from both DMSO and SHAPE samples is linked to the corresponding DMSO sample records.

first: James

last: Falese

first: Emily

middle: J

last: McFadden

first: Christopher

last: D'Inzeo

middle: E


title: Monocyte gene expression in adult-onset Still's disease

status: Public on Dec 22 2023

city: Shanghai

first: Jinchao

last: Jia

address: No. 197 Ruijin Second Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Adult-onset Still’s disease (AOSD) is a rare autoinflammatory disease, characterized by fever, rash, arthritis and other systemic inflammatory manifestations like hepatosplenomegaly and serositis. One of the most serious complications AOSD is macrophage activation syndrome (MAS), a life-threatening condition caused by excessive activation of immune system and a cytokine storm. Clinical features of MAS include continuous high fever, hepatosplenomegaly, liver dysfunction, lymphadenopathy, hyperferritinemia, and hemophagocytosis. The prevalence of MAS in AOSD patients is estimated to be between 10–19%, but the mortality rate of AOSD-associated MAS is approximately 10–20%. The precise mechanism by which AOSD develops to MAS remains unclear. There is an unmet need to investigate the pathogenesis of MAS in AOSD in order to identify novel biomarkers and therapeutic targets to improve disease prognosis.

overall_design: Transcriptomes from peripheral blood monocytes of 12 treatment-naïve AOSD patients and 10 healthy controls

first: Qiongyi

last: Hu

first: Mengyan

last: Wang


title: Analysis of UV-induced DNA damage in human cells using CPD-seq 2.0

status: Public on Dec 01 2023

city: Stony Brook

first: Peng

last: Mao

state: NY

address: 101 Nicolls Rd

department: Department of Pathology

institute: Stony Brook University

summary: Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data shows prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5’ side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations.  Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identifies high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover new roles of often-overlooked mutation hotspots in perturbing gene transcription.

overall_design: Human skin fibroblast cells were grown in DMEM/F-12 medium with 10% FBS. Media was removed and cells were exposed to UV-C at 6 and 8 J/m2 to induce UV damage. A portion of the cells were harvested immediately after UV treatment as time 0 (i.e., no repair). The rest of cells were incubated in fresh DMEM for repair. Repair time points were taken at 6 and 24 h post UV irradiation. Genomic DNA was isolated from cells and used for the preparation of CPD-seq 2.0 libraries. After Illumina sequencing, locations of UV-induced photolesions were identified using our published protocol. Formation and repair of UV damage was analyzed in gene promoters, particularly those containing ETS binding sites.

first: Mingrui

last: Duan


title: Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination [blood]

city: Cleveland

first: Richard

last: Silver

state: OH

address: 10900 Euclid Ave

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center

summary: RNA-Seq was utilized to provide an unbiased assessment of systemic and mucosal immunity using blood cells from LTBI subjects and recipients of ID and oral (PO) BCG.

overall_design: Blood CD4+ T cells were studied from groups of Mtb/BCG-naïve, BCG-vaccinated and LTBI subjects. We combined the pre-vaccination studies of individuals who subsequently received ID and/or PO BCG.  Blood was drawn into CPT tubes and PBMC isolated, aliquoted and frozen.  Following thawing, CD4+ T cells were isolated using Miltenyi positive selection kits.  Autologous monocyte-derived dendritic cells (MDDC) were prepared (Hoft et al, Mucosal immunology. 2018;11(2):486-95).  MDDC were cultured overnight with autologous CD4+ T cells (20:1, T cell:MDDC ratio), in presence of either Danish BCG (Statens Serum Institut, Copenhagen, MOI 20:1), or medium alone. Cell pellets were lysed for RNA extraction.

first: Daniel

last: Hoft

first: Chad

last: Storer

first: Rich

last: Head


title: Unraveling the role of sex in endothelial cell dysfunction – Evidence from lineage tracing mice and cultured cells

status: Public on Nov 30 2023

first: Olga

last: Cherepanova

state: OHIO

address: 9620 Carnegie Ave N Bldg

department: Cardiovascular and Metabolic Science

institute: Cleveland Clinic Lerner Research Institute

summary: Background: Biological-sex differences play a vital role in cardiovascular diseases, including atherosclerosis. The endothelium is a critical contributor to cardiovascular pathologies since endothelial cells (EC) regulate vascular tone, redox balance, and inflammatory reactions. Although EC activation and dysfunction play an essential role in the early and late stages of atherosclerosis development, little is known about sex-dependent differences in EC. Methods: We used aortic EC that was isolated from 13-week-old female and male mice as well as EC-lineage tracing (Cdh5-CreERT2 Rosa-YFP) atherosclerotic Apoe‒/‒ mice to investigate the biological sexual dimorphism of the EC functions in vitro and in vivo. RNA sequencing (RNAseq) analyses were performed on male and female mouse aortic EC and human lung EC. Results: In vitro, female mouse aortic EC (F_MAEC) showed more apoptosis and higher cellular ROS levels, lower mitochondrial membrane potential (ΔΨm), and lower levels of mitochondrial transcription factor A (TFAM) than male aortic EC (M_MAEC). Additionally, F_MAEC had decreased angiogenic potential (tube formation, cell viability, and proliferation) compared to M_MAEC. In vivo, female mice had significantly higher lipid accumulation within the aortas, less efficient outward vessel remodeling, and lower endothelial-mediated vasorelaxation than males. Using the EC-lineage tracing approach, we found that female lesions had significantly lower rates of intraplaque neovascularization and Endothelial-to-Mesenchymal (EndoMT) transition within advanced atherosclerotic lesions but higher incidents of missing EC lumen coverage and higher levels of oxidative products and apoptosis. RNAseq analyses revealed that both mouse and human female EC had higher expression of genes associated with inflammation and apoptosis and lower expression of genes related to angiogenesis and oxidative phosphorylation than male EC. Conclusions: Our study delineates critical sex-specific differences in EC relevant to pro-inflammatory, pro-oxidant, and angiogenic characteristics, which are entirely consistent with a vulnerable phenotype in females. Our results provide a biologic basis for sex-specific pro-atherosclerotic mechanisms.

overall_design: To investigate the sexual dimorphism of endothelial cells, we isolated endothelial cells from male and female mouse aortas. We established mouse aortic primary cultured endothelial cells. We then performed gene expression profiling analysis of RNA-seq data for sexual dimorphism of endothelial cells.

first: Junchul

last: Shin


title: Tumor-driven stromal reprogramming in the pre-metastatic lymph node

status: Public on Nov 29 2023

city: Cambridge

first: Michelle

last: Piquet

state: MA

address: 250 Massachusetts Ave,

institute: Novartis Institutes for BioMedical Research

summary: Metastatic dissemination is critically reliant on the formation of a receptive niche, a process which is thought to rely on signals derived from the primary tumor. Lymph nodes are continuously exposed to such signals through the flow of afferent lymph, allowing the potential reprograming of lymphoid tissue stroma in support of metastases or immunosuppression. We utilize single cell RNA sequencing to profile reprograming of the stromal support network within the pre-metastatic lymph node. Transcriptomic changes of the tumor-draining LN are compared against those of the contralateral non-draining LN. Additionally, we include experimental conditions for comparison in which LNs are exposed to fixed tumor cells, mimicking antigenic challenge without active tumor growth, thereby allowing us to distinguish between active tumor-elicited reprograming and general immune responses to tumor antigen.

overall_design: Single Cell RNA sequencing was performed on enriched PDPN+ stromal cells isolated from enzymatically dissociated lymph nodes. Tumor-draining and non-draining inguinal lymph nodes were harvested from mice bearing subcutaneous MC38 tumors. Draining and non-draining inguinal lymph nodes were also harvested from mice inoculated with fixed (non-viable) MC38 cancer cells. For both conditions, 5 x 105 cells were implanted subcutaneously on the animal’s lower-right flank. Mice were euthanized and LNs were collected on day 12 after treatment.

first: David

last: Ruddy

first: Viviana

last: Cremasco

first: Jonathan

last: Chang


title: The intrinsically disordered region of the E3 ubiquitin ligaseTRIP12 induces the formation of chromatin condensates and interferes withDNA damage response.

status: Public on Nov 11 2023

city: Toulouse

first: Claire

last: Vargas

address: 2 Avenue Hubert Curien

country: France

institute: Centre de Recherches en Cancérologie de Toulouse

summary: Chromatin compaction is crucial for the expression and the integrity of the genome. We previously showed that the nuclear HECT-type E3 ubiquitin ligase TRIP12 (Thyroid hormone Receptor Interacting Protein 12) is tightly associated to chromatin. Overexpressed in several types of cancers, we explored herein the consequences of TRIP12 overexpression on chromatin homeostasis. First, we established the proxisome of TRIP12 by BioID and unveiled its pleiotropic role in chromatin regulation. Second, we demonstrated that an overexpression of TRIP12, via its intrinsically disordered region, leads to the formation of chromatin condensates enriched in heterochromatin epigenetic marks. We further discovered that the formation of TRIP12 mediated-chromatin condensates is highly dynamic and driven by a mechanism of polymer-polymer phase separation (PPPS). Chromatin condensates formation is dependent not only on the concentration, the length of TRIP12-IDR but also electrostatic interactions. Chromatin compaction is a determinant parameter in several biological processes. Indeed, we measured that the formation of TRIP12 mediated-chromatin condensates alters cell cycle progression, genome accessibility, transcription as well as DNA damage response (DDR) by inhibiting the accumulation of Mediator DNA Damage Checkpoint (MDC1). Altogether, this study reveals a novel dynamic role for TRIP12 in chromatin compaction independently of its ubiquitin ligase activity with important consequences on cellular processes.

overall_design: Comparative gene accessibility analysis of ATAC-seq data from two experiments of HeLaS3 cells transfected with TRIP12-IDR-GFP versus non transfected HeLaS3 cells.

first: Jérôme

last: Torrisani

first: Marlène

last: Dufresne


title: Self-Assembling Hematopoietic Niche on a Chip: Bulk sequencing to investigate effect of proton radioablation

status: Public on Nov 25 2023

city: Philadelphia

first: Andrei

last: Georgescu

state: Pennsylvania

address: 315 Skirkanich Hall, 210 S. 33rd Street

institute: University of Pennsylvania

summary: (Radiation Experiments: bulk sequencing data) Here we present an integrative, bottom-up approach towards emulating the human bone marrow in vitro. Our method harnesses the regenerative capacity of adult stem cells to self-assemble a complex, specialized microenvironment of human hematopoietic stem cells (HSCs) in a vascularized three-dimensional microphysiological system. Through flow cytometry and single-cell transcriptomic interrogation, we show that the microengineered niche can reconstitute HSC self-renewal, multilineage hematopoiesis, and complex ligand-receptor signaling pathways of the native human marrow. The ability of our model to generate functionally mature myeloid cells also makes it possible to mimic the key physiological processes of innate immunity including neutrophil chemotaxis and intravascular mobilization. To demonstrate the advanced application of the bone marrow-on-a-chip, we present i) a specialized model of bone marrow ablation by proton beam radiotherapy and ii) a multiorgan model of innate immune response against bacterial lung infection. This work advances our ability to reconstruct, probe, and deconvolve the complexity of the bone marrow niche, and may enable new capabilities to model human hematopoiesis and immunity for biomedical and pharmaceutical applications.

overall_design: Bone marrow hematopoietic niche models cultured in vitro were irradiated with 0 Gy, 0.2 Gy, 2 Gy, and 20 Gy of proton radiation, with each group comprising 3 independent biological replicates that were multiplexed.

first: Joseph

middle: H

last: Oved

first: Samira

last: Mehta

first: Jeongyun

last: Seo

first: Michele

last: Kim

first: Eric

last: Diffenderfer

first: George

last: Worthen

first: Dan

last: Huh


title: Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination

first: Richard

last: Silver

overall_design: BAL cell gene expression was evaluated after overnight culture in medium alone (baseline conditions), or with virulent Mtb strain H37Rv in patients with latent tuberculosis infection (LTBI) and in BCG-vaccinated (ID and PO groups) and Mtb/BCG-naive patients.

first: Daniel

last: Hoft

first: Chad

last: Storer

last: Head


title: Gene expression analysis of BCG-vaccinated and CoMtb mice

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

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

overall_design: Refer to individual Series


title: Transcriptional reprogramming during human osteoclast differentiation identifies regulators of osteoclast activity

status: Public on Nov 05 2023

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

summary:
Enhanced osteoclastogenesis and osteoclast activity contribute to the development of osteoporosis, which is characterized by increased bone resorption and inadequate bone formation. As novel anti-osteoporotic therapeutics are needed, understanding the genetic regulation of human osteoclastogenesis could help identify potential treatment targets. This study aimed to provide an overview of the transcriptional reprogramming during human osteoclast differentiation. Osteoclasts were differentiated from CD14+-monocytes from eight female donors. RNA-sequencing during differentiation demonstrated 8980 differentially expressed genes grouped into eight temporal patterns conserved across donors. These patterns showed distinct molecular functions, associated with postmenopausal osteoporosis susceptibility genes based on RNA from iliac crest biopsies, and bone mineral density SNPs. Network analyses showed mutual dependencies between the temporal expression patterns and provides insight into subtype-specific transcriptional networks. Donor specific expression patterns identified genes at monocyte stage, such as filamin B (FLNB) and oxidized low density lipoprotein receptor 1 (OLR1, encoding LOX-1), that are predictive for the resorptive activity of mature osteoclasts. Differentially expressed G-protein coupled receptors showed strong expression during osteoclast differentiation and associated with bone mineral density SNPs, implying a pivotal role in osteoclast differentiation and activity. The regulatory effects of three differentially expressed G-protein coupled receptors were exemplified by in vitro pharmacological modulation of complement 5A receptor 1 (C5AR1), somatostatin receptor 2 (SSTR2), and free fatty acid receptor 4 (FFAR4/GPR120). Activating C5AR1 enhanced osteoclast formation, while activating SSTR2 decreased resorptive activity of mature osteoclasts, and activating FFAR4 decreased both number and resorptive activity of mature osteoclasts.
In conclusion, we report the transcriptional reprogramming during human osteoclast differentiation and identified SSTR2 and FFAR4 as anti-resorptive G-protein coupled receptors as well as FLNB and LOX-1 as potential molecular markers of osteoclast activity. These data can help future investigations to identify molecular regulators of osteoclast differentiation and activity and provide the basis for novel anti-osteoporotic targets.

overall_design: RNA-expression profiles from 4 time points during human osteoclasts differentiated in vitro from CD14 positive peripheral blood cells of 8 anonymous donors.

first: Morten

last: Hansen

first: Kaja

last: Madsen

first: Maria

last: Price

first: Kent

last: Søe

first: Yasunori

last: Omata

first: Mario

last: Zaiss

first: Caroline

last: Gorvin

last: Frost


title: RNA-Seq of BRQ-treated and control B16F10 cells

status: Public on Nov 01 2023

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

institute: Northwestern Polytechnical University

summary: B16F10 cells treated with DMSO or BRQ were collected and then the total RNA was isolated. After removal of the remaining genomic DNA, mRNA was purified from total RNA using polyT and then fragmented with 10× RNA fragmentation buffer and the RNA-seq library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit and was sequenced.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BRQ treated group and control group. Each group was replicated for three times.

first: Ruizhuo

last: Lin

first: Gaofei

last: Wei


title: Self-Assembling Hematopoietic Niche on a Chip: Single Cell Sequencing

first: Andrei

last: Georgescu

summary: (Single Cell Sequencing Data) Here we present an integrative, bottom-up approach towards emulating the human bone marrow in vitro. Our method harnesses the regenerative capacity of adult stem cells to self-assemble a complex, specialized microenvironment of human hematopoietic stem cells (HSCs) in a vascularized three-dimensional microphysiological system. Through flow cytometry and single-cell transcriptomic interrogation, we show that the microengineered niche can reconstitute HSC self-renewal, multilineage hematopoiesis, and complex ligand-receptor signaling pathways of the native human marrow. The ability of our model to generate functionally mature myeloid cells also makes it possible to mimic the key physiological processes of innate immunity including neutrophil chemotaxis and intravascular mobilization. To demonstrate the advanced application of the bone marrow-on-a-chip, we present i) a specialized model of bone marrow ablation by proton beam radiotherapy and ii) a multiorgan model of innate immune response against bacterial lung infection. This work advances our ability to reconstruct, probe, and deconvolve the complexity of the bone marrow niche, and may enable new capabilities to model human hematopoiesis and immunity for biomedical and pharmaceutical applications.

overall_design: Two samples were sequenced, each of which used bone marrow hematopoietic stem cells from a different donor to establish the in vitro model of the hematopoietic niche and emergent immunity. We provide here the raw sequencing data from each donor, and the processed feature matrix that results when both samples are aggregated

first: Joseph

last: Oved

first: Samira

last: Mehta

first: Jeongyun

last: Seo

first: Michele

last: Kim

first: Eric

last: Diffenderfer

first: George

last: Worthen

last: Huh


title: Tumor and immune cell types interact to produce heterogeneous phenotypes of pediatric high grade glioma

status: Public on Nov 03 2023

city: Aurora

first: John

last: DeSisto

state: CO

department: Pediatrics

institute: University of Colorado


title: A critical role for Hepatocyte Nuclear Factor 4 alpha in polymicrobial sepsis-associated metabolic reprogramming and death: ATAC-seq after CLP sepsis model

status: Public on Oct 31 2023

first: Steven

last: Timmermans

summary: In sepsis, limited food intake and increased energy expenditure induce a starvation response, which is compromised by a quick decline in expression of hepatic PPARα, a transcription factor essential in intracellular catabolism of free fatty acids. The mechanism upstream of this PPARα downregulation is unknown. We found that sepsis causes a progressive hepatic loss-of-function of HNF4α, which has strong impact on the expression of several important nuclear receptors, including PPARα. HNF4α depletion in hepatocytes dramatically increases sepsis lethality, steatosis and organ damage and prevents an adequate response towards IL6, which is critical for liver regeneration and survival. An HNF4α agonist protects against sepsis at all possible levels, irrespectively of bacterial loads, suggesting HNF4α is crucial in disease tolerance to sepsis. In conclusion, hepatic HNF4α fails in sepsis, causing PPARα downregulation and metabolic problems and a disturbed IL6-mediated acute phase response. The data open new insights and therapeutic options in sepsis.

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) tot determine the changes in chromatin accessibility in the liver of mice after CLP using 4 biological replicates in CLP and SHAM (control) conditions

first: Céline

last: Van Dender

first: Ville

last: Paakinaho

first: Tineke

last: Vanderhaeghen

first: Jolien

last: Vandewalle

first: Maarten

last: Claes

first: Bart

last: Roman

first: Jan

last: De Waele

first: Siska

last: Croubels

first: Karolien

last: De Bosscher

first: Jorma

last: Palvimo

first: Claude

last: Libert


title: The effects of host-microbe interactions on the transcriptomic signatures of cervicovaginal epithelial cells [RNA-seq]

status: Public on Dec 14 2023

city: New York

first: Michal

last: Elovitz

address: 1468 Madison Ave

department: Obstetrics, Gynecology and Reproductive Sciences

institute: Icahn Mount Sinai

summary: To elucidate the molecular pathways altered by host-microbe interactions in cervicovaginal epithelial cells we performed whole genome RNA-sequencing. We identified genes and functional pathways that were altered in cervicovaginal epithelial cells after exposure to G. vaginalis or L. crispatus or their supernatant.

overall_design: We performed functional pathways analysis using the transcriptomic data from RNA-seq on three cell types treated with live bacteria or bacterial supernatants from different bacterial strains.

first: Lauren

last: Anton

first: Briana

last: Ferguson


title: A subset of pro-inflammatory spiny mice macrophages promotes a regenerative phenotype in mouse fibroblasts

status: Public on Oct 23 2023

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Macrophages play an essential role in tissue regeneration. However, the ability to dissect the role of macrophages in regeneration from their role in wound healing with scar has been hampered by a lack of comparative systems. In this study, we use a mammalian model of tissue regeneration and scar formation to contrast the role of macrophages in both wound healing paradigms. The African Spiny mouse (A. cahirinus) can regenerate tissue of the external ear pinnae after 4mm biopsy punch. The common lab mouse (M. musculus) forms a scar after the same injury. We test the potential of bone marrow derived macrophages from both species to activate local ear fibroblasts and find macrophages from A. cahirinus are able to induce a matrix turnover phenotype in fibroblasts from both species. We identify growth factors and cytokines specific to macrophages derived from A. cahirinus, and using single cell RNAseq and screening with these factors, we identify populations of macrophages unique to a regenerating injury compared to scar forming injury. Finally we test how macrophage populations change over time in a regenerating injury and how they differ from each stage in a scar forming system

sample_organism:
Acomys cahirinus
Mus musculus

platform_organism:
Acomys cahirinus
Mus musculus

overall_design: Injured Mus and Acomys ear tissues were analyzed using 10X single-cell rna-seq

first: Steve

last: Potter

first: Ashley

last: Seifert


title: Gene expression analysis of alveolar macrophages from BCG-vaccinated and CoMtb mice stimulated ex vivo [exvivoRNAseq]

first: Aderem

last: Lab

summary: The aim of this study was to measure the response of alveolar macrophages (AMs) from BCG-vaccinated mice and mice with CoMtb to LPS, PAM3CSK4, and Mtb stimulation ex vivo.

overall_design: Mice were vaccinated sub-cutaneously with BCG-Pasteur (1e6 CFU), or inoculated in the dermis of the ear with H37Rv (1e4 CFU)  and allowed to rest for 8 weeks. To characterize the  macrophage transcriptional response to each stimulus, AMs were isolated by bronchoalveolar lavage followed by plate adherence for 24 hours. AMs were stimulated with either LPS (10 ng/mL), Pam3CSK4 (10 ng/mL), or Mtb-H37Rv for 6 hours prior to RNA isolateion.

first: Alissa

middle: C

last: Rothchild

first: Alan

last: Diercks

last: Aderem


title: Influence of evernic acid alone and in combination with temozolomide on gene expression of U-87 glioblastoma cell line

status: Public on Oct 24 2023

city: Bonn

first: Anastasiia

last: Shcherbakova

state: NRW

address: Sigmund-Freud-Straße, 25

institute: University Clinic Centre Bonn, Medical Clinic III

summary: to investigate the sensitization mechanism of temozolomide-resistant U-87 cells by evernic acid, we established gene expression of U-87 cells treated with evernic acid, temozolomide and their combinations compared to the gene expression of untreated cells. The NGS-core facility of the University Hospital Bonn of Bonn University performed the RNA-sequencing.

overall_design: cells were treated with evernic acid at 30 µM and 45 µM, with temozolomide at 600 µM, and with combinations of evernic acid and temozolomide at 35 µM + 320 µM, 20 µM + 380 µM and 20 µM + 580 µM

first: Gudrun

last: Ulrich-Merzenich


title: The effects of host-microbe interactions on cervicovaginal epithelial cells


title: Single-cell RNA sequencing reveals a hierarchical transcriptional regulatory network of terpenoid biosynthesis in cotton secretory glandular cells

status: Public on Oct 12 2023

first: Longxian

last: Chen

address: 300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

summary: Plants can synthesize a wide range of terpenoids in response to various environmental cues. However, the specific regulatory mechanisms governing terpenoid biosynthesis at the cellular level remain largely elusive. Herein, we employed single-cell RNA sequencing (scRNA-seq) to comprehensively characterize the transcriptome profile of cotton leaves and established a hierarchical transcriptional network regulating cell-specific terpenoid production.

overall_design: Gene expression profiling of scRNA-seq data from cotton leaves

first: J

middle: Q

last: Huang


title: Attenuation of PTBP2 facilitates fibroblast to neuron conversion by promoting alternative splicing of neuronal genes

city: Buffalo

first: Jian

last: Feng

state: NEW YORK

address: 955 Main St, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

summary: The direct conversion of human skin fibroblasts to neurons has a low efficiency and unclear mechanism. Here, we show that the knockdown of PTBP2 (nPTB) significantly enhanced the transdifferentiation induced by ASCL1, MiR124-9/9* and p53 shRNA to generate mostly GABAergic neurons. Longitudinal RNAseq analyses identified the continuous induction of many RNA Splicing Regulators (RSRs). Among these, the knockdown of RBFOX3, which encodes the mature neuronal marker NeuN, significantly abrogated the transdifferentiation. Overexpression of RBFOX3 significantly enhanced the conversion induced by AMp; the enhancement was occluded by PTBP2 knockdown. We found that PTBP2 attenuation significantly favored neuron-specific alternative splicing (AS) of many genes involved in synaptic transmission, signal transduction, and axon formation. RBFOX3 knockdown significantly reversed the effect, while RBFOX3 overexpression enhanced it. The study reveals the critical role of neuron-specific AS in the direct conversion of human skin fibroblasts to neurons by showing that PTBP2 attenuation enhances this mechanism in concert with RBFOX3.

overall_design: Transcriptomic profiling of induced neurons mediated by ASCL1, miR124-9/9*, p53 shRNA and PTBP2 shRNA at day 3, 7, and 14 using human skin fibroblasts.

first: Binglin

last: Zhu

first: Li

last: Li

first: Emily

last: Fisher

first: Ping

last: Zhong

first: Zhen

last: Yan


title: RNA sequencing identifies human placentalIL3RAas a potential predictor of adverse cardiovascular outcomes in patients with severe preeclampsia

status: Public on Nov 09 2023

city: La Jolla

first: Mariko

last: Horii

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Background: Mortality from preeclampsia (PE) and PE-associated morbidities are 3-to 5-fold higher in persons of African ancestry than in those of Asian and European ancestries. The placenta is central to the etiology of PE. However, how and to what extent the placenta contributes to worse PE outcomes in persons of African ancestry is yet to be fully elucidated.  Objective: We aimed to identify molecular pathways that are unique or enriched in placentas of parturient persons of African ancestry with PE with severe features (sPE) compared to those of Asian and European ancestry with sPE. Study design: Bulk RNA sequencing was performed on 50 placentas from parturient persons with sPE of African (n=9), Asian (n=18) and European (n=23) ancestries and 73 normotensive controls of African (n=9), Asian (n=15) and European (n=49) ancestries. Results: Metabolism, hormone regulation and hypoxia/angiogenesis genes, previously described to be upregulated in PE, including: LEP, PAPPA2, INHA, FSTL3, FLT1, PHYHIP and ENG, were upregulated in sPE across ancestries, with high expression of FSTL3 being additionally associated with intrauterine growth restriction (p<.0001). Notably, LEP, FLT1 and PHYHIP were more highly upregulated in sPE placentas from parturient persons of African versus Asian ancestry. Genes associated with allograft rejection and adaptive immune response were selectively upregulated in placentas from African ancestry parturitions and not in those of Asian and European ancestries. Among the allograft rejection/adaptive immune response genes, IL3RA was of particular interest because the patient with the highest placental IL3RA level, a woman of African ancestry with IL3RA levels 4.5-fold above the average for African ancestry parturitions with sPE, developed postpartum cardiomyopathy, and was the only patient out of 123, that developed this condition. Interestingly, the sPE patients of Asian and European ancestries with the highest IL3RA levels for their ancestries developed unexplained tachycardia peripartum, necessitating echocardiography in the European ancestry patient. The association between elevated placental IL3RA levels and unexplained tachycardia or peripartum cardiomyopathy was found to be significant in the 50 sPE patients (p=.0005). Conclusions: African ancestry parturitions are associated with higher placental upregulation of metabolism (LEP) and hypoxia/angiogenesis (FLT1) genes, and selective upregulation of allograft rejection/adaptive immune response genes, including IL3RA. High placental expression of IL3RA may predict worse maternal cardiovascular outcomes, including peripartum cardiomyopathy. Studies evaluating placental IL3RA levels in peripartum cardiomyopathy cohorts are therefore warranted, as are broader studies evaluating placental factors in maternal cardiovascular outcomes postpartum.

overall_design:
Total RNA-seq of placental RNA from non-hypertensive control and severe preeclampsia from different ancestry

UPDATE: [Jan-10-2024] The Sample ancestry and sex characteristics were updated.

first: Omonigho

last: Aisagbonhi


title: KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism.

status: Public on Nov 08 2023

city: Bronx

first: Matanel

last: Yheskel

address: 1300 Morris Park

department: Genetics

institute: Albert Einstein College of Medicine

summary: Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we generated five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles showed effects on neuroanatomical development, cognition, and other behaviors, in addition to a transcriptional signature that included the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout human glutamatergic neurons derived from induced pluripotent stem cells (iPSCs), suggesting a conserved role for KDM5 proteins in regulating ribosomal protein genes. Loss of ribosomal protein gene expression resulted in changes to neuronal ribosome composition. Moreover, we find that the translation efficiency of mRNAs required for mitochondrial metabolism was particularly affected upon reduction KDM5 in Drosophila neurons. Altered mitochondrial activity was confirmed through metabolomic studies that revealed decreased citric acid cycle activity. KDM5 therefore plays a key role in maintaining mitochondrial function that, when altered, could contribute to cognitive and behavioral phenotypes.

overall_design: To understand how patient Claes-Jensen Syndrome (CJS) associated variants in KDM5C modeled in Drosophila affect transriptional programs in neurons, we created 5 CJS variant strains as well as a synthetic demethylase-dead strain and performed paired-end RNA-Sequencing. All variants were compared to WT KDM5. We dicovered that ribosome protein genes were downregulted acorss all ID variants. To understand how loss of KDM5 function affected translation efficiency, we performed Ribo-Seq on control and kdm5-knockdown neurons.

first: Julie

last: Secombe


title: Self-supervised learning for predicting transcriptomic groups on whole slides images in intrahepatic cholangiocarcinoma

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

institute: INSERM

summary: Backgrounds & Aims: Transcriptomic classification of intrahepatic cholangiocarcinoma (iCCA) has been recently improved from two classes to five classes, associated with pathological features, targetable genetic alterations and survival. Despite its prognostic and therapeutic value, the classification is not routinely performed due to technical limits such as insufficient material or the cost of molecular analyses. Our aim was to predict iCCA transcriptomic classes on whole-slide digital histological images (WSI) using a self-supervised learning (SSL) model. Methods: Gene expression was investigated using RNA sequencing to class samples in the five transcriptomic classes. We then used a SSL method called GigaSSL. We first trained our model on a discovery set of 769 slides (biopsy and surgical samples, 246 patients) in a 5-fold cross-validation scheme. We then validated the model in a TCGA (n= 29) and a French external validation set (n=32). Results: Our model showed good performance for predicting each transcriptomic class in the discovery set (Area under the curve, AUC: 0.55-0.81), particularly for the Hepatic stem-like class (most frequent group, 37% of cases), with AUC 0.81. The model generalised well for the prediction of four on five of the transcriptomic classes into the two validation sets with AUCs ranging from 0.76 to 0.80 in the TCGA set and from 0.62 to 0.92 in the French external set. Conclusion: We have developed and validated a SSL based model able to predict iCCA transcriptomic classes on routine histological slides (biopsy and surgical samples), which could have an impact on the management of patients.

overall_design: populational analysis

first: Aurélie

last: Beaufrère


title: Concordant B and T Cell Heterogeneity Inferred from the Multiomic Landscape of Peripheral Blood Mononuclear Cells in a Crohn's Disease Cohort

status: Public on Oct 10 2023

city: Atlanta

first: Greg

last: Gibson

state: GA

address: North Ave NW

institute: Georgia Institute of Technology

summary: Crohn’s disease is characterized by inflammation in the gastrointestinal tract due to a combination of genetic, immune, and environmental factors. Transcriptomic and epigenomic profiling of intestinal tissue of Crohn’s disease patients have revealed valuable insights into pathology, however have not been conducted jointly on less invasive peripheral blood mononuclear cells (PBMCs). Furthermore, the heterogeneous responses to treatments among individuals with Crohn’s disease imply hidden diversity of pathological mechanisms. We employed single nucleus multiomic analysis, integrating both snRNA-seq and snATAC-seq of PBMCs with a variety of open source bioinformatics applications. Our findings reveal a diverse range of transcriptional signatures among individuals, highlighting the heterogeneity in PBMC profiles. Nevertheless, striking concordance between three heterogeneous groups was observed across B cells and T cells. Differential gene regulatory mechanisms partially explain these profiles, notably including a Crohn’s disease-specific signature involving TGFß signaling in two individuals. A mutation mapped to a transcription factor binding site within a differentially accessible peak associated with the expression of this pathway, with implications fora personalized approach to understanding disease pathology. This study highlights how multiomic analysis can reveal common regulatory mechanisms that underlie heterogeneity of PBMC profiles, one of which may be specific to inflammatory disease.

overall_design: To investigate the heterogeneity of gene regulation in Crohn's disease and healthy  PBMC using multiome snRNA-seq and snATAC-seq.

first: Margaret

last: Brown

first: Anne

last: Dodd

first: Fang

last: Shi

last: Greenwood

first: Sini

last: Nagpal

first: Subra

last: Kugathasan


title: Tumor and immune cell types interact to produce heterogeneous phenotypes of pediatric high grade glioma [bulkRNA-seq]

first: John

last: DeSisto

summary: Bulk RNA-Seq of pediatric high-grade glioma patient samples

first: Adam

last: Green


title: Tumor and immune cell types interact to produce heterogeneous phenotypes of pediatric high grade glioma [scRNA-seq]

summary: Single-cell RNA-Seq was conducted on 19 pediatric high-grade glioma patient samples to study tumor heterogeneity and tumor/immune cell interaction.

overall_design: scRNA-Seq on 19 patient samples of pediatric high grade glioma


title: A critical role for Hepatocyte Nuclear Factor 4 alpha in polymicrobial sepsis-associated metabolic reprogramming and death: HNF4A ChIP-seq in the CLP sepsis model (ChIP-Seq)

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

overall_design: Chromatin Immunoprecipitation (ChIP-seq) of HNF4A to determine the changes in chromatin occupancy in the liver of mice after CLP using 4 biological replicates in CLP and SHAM (control) conditions

first: Céline

last: Van Dender

first: Ville

last: Paakinaho

first: Tineke

last: Vanderhaeghen

first: Jolien

last: Vandewalle

first: Maarten

last: Claes

first: Bart

last: Roman

first: Jan

last: De Waele

first: Siska

last: Croubels

first: Karolien

last: De Bosscher

first: Jorma

last: Palvimo

first: Claude

last: Libert


title: Gene expression profile at single cell level of mononuclear cells from skeletal muscle (gastrocnemius) of non-PAD controls and PAD patients

status: Public on Oct 05 2023

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: The molecular and cellular mechanisms of skeletal muscle from peripheral artery disease (PAD) patients are not completely understood. We used single cell RNA sequencing (scRNA-seq) to characterize the skeletal muscle diversity between control and PAD patients.

overall_design: Live mononuclear cells (Calcein+) from human skeletal muscle were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Guillermo

last: Turiel

first: Thibaut

last: Desgeorges

first: Evi

last: Masschelein

first: Jing

last: Zhang

first: Stephan

last: Engelberger

first: Katrien

last: De Bock


title: c-MYC-dependent transcriptional inhibition of autophagy is implicated in Cisplatin sensitivity in HPV-positive Head and Neck Cancer

city: Milano

first: Susanna

last: Chiocca

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology, IEO

summary: Autophagy is important for removal, degradation and recycling of damaged organelles, proteins, and lipids through the degradative action of lysosomes. In addition to its catabolic function, autophagy is important in cancer and viral-mediated tumorigenesis, including Human Papillomavirus (HPV) positive cancers. HPV infection is a major risk factor in a subset of Head and Neck Cancer (HNC), for which no targeted therapies are currently available. Herein, we assessed autophagy function in HPV-positive HNC. We showed that HPV-positive HNC cells presented a transcriptional and functional impairment of autophagic process compared to HPV-negative cells, which was reactivated by knocking-down HPV E6/E7 oncoproteins, the drivers of cellular transformation. We found that the oncoprotein c-MYC was stabilized and triggered in HPV-positive cell lines. This resulted in the reduced binding of the MiT/TFE transcription factors to their autophagy targets due to c-MYC competition. Thus, knock-down of c-MYC induced the upregulation of autophagic and lysosomal genes in HPV-positive HNC cells, as well as the increase of autophagic markers at the protein level. Moreover, HPV oncoprotein E7 upregulated the expression of the phosphatase inhibitor CIP2A, accounting for c-MYC upregulation and stability in HPV+ HNC cells. CIP2A mRNA expression negatively correlated with autophagy gene expression in tumor tissues from HNC patients, showing, for the first time, its implication in a transcriptional autophagic context. Both CIP2A and c-MYC knock-down, as well as pharmacological downregulation of c-MYC, resulted in increased resistance to Cisplatin treatment. Our results not only show a novel way by which HPV oncoproteins manipulate the host machinery, but also provide more insights on the role of autophagy in chemoresistance, with possible implications for targeted HPV-positive HNC therapy.

overall_design: 4 biological replicates of Primary human keratinocytes were transduced with the retroviral vector pLXN Empt, HPV16 E6, HPV16 E7, or HPV16 E6/E7. After 5 days of selection with G-418 at the appropriate concentration cells were harvested and RNA extracted.RNA was used to generate the library using Truseq kit from Illumina.

first: Alessandro

last: Medda

first: Ottavio

last: Croci


title: RBM25 affects the immune and inflammatory progress by binding to and modulating alternative splicing levels of associated genes in rat H9C2 cells [ABL2020-10020-ABF_H9C2_RBM25_iRIP]

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Alternative splicing (AS) enables genes to be translated into a vast diversity of proteins while aberrant AS predisposes cells to abnormal biological processes. As is closely associated with AS, RNA binding proteins (RBPs) are gradually gaining attention. RBM 25 was reported to participate in the cardiac pathophysiological process via AS regulation. Nonetheless, gaps still existed in whether RBM 25 functions in heart failure by its splicing factor role. H9C2 cells with excessively expressed RBM25 were used to filtrate different expression genes (DEGs) and analyze for RBM25-regulated AS by RNA-seq. Next, iRIP-seq was performed to examine its binding targets. For genes screened, further RT-qPCR-based validation was conducted. RBM25 overexpression caused expressive alteration in 80 genes mainly involved in the inflammatory response and virus response. Notably, RBM25 partially modulated AS of differential genes enriched in the apoptotic process and bound to genes clustered at inflammation response. Further, qRT-PCR verified Slc38a9, IL-17RC, Csf1, and Coro6 as targets of RBM25 being bound to and AS-regulated.

first: Xin

last: Tian

first: Guangli

last: Zhou

first: Hao

last: Li

first: Ping

last: Yang


title: Hyperactive PI3K-delta in Th1 and Th2 differentiation

status: Public on Oct 04 2023

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

summary: While inputs regulating CD4+ T helper cell (Th) differentiation are well-defined, the integration of downstream signaling with transcriptional and epigenetic programs that define Th-lineage identity remain incompletely resolved. PI3K signaling is a critical regulator of T-cell function; activating mutations affecting PI3Kd result in an immunodeficiency with multiple T-cell defects. Using mice expressing activated-PI3Kd, we found aberrant expression of proinflammatory Th1-signature genes under Th2-inducing conditions, both in vivo and in vitro. This dysregulation was driven by a PI3Kd-IL-2-Foxo1 signaling amplification loop, fueling Foxo1-inactivation, loss of Th2-lineage restriction and extensive epigenetic reprogramming. Surprisingly, ablation of Fasl, a Foxo1-repressed gene, normalized both Th2 differentiation and TCR signaling. BioID and imaging revealed Fas interactions with TCR-signaling components, which were supported by Fas-mediated potentiation of TCR signaling that could occur in the absence of FADD. Our results highlight Fas-FasL signaling as a critical intermediate in phenotypes driven by activated-PI3Kd, thereby linking two key pathways of immune dysregulation.

overall_design: CD45+ cells isolated from lungs in 4 samples. Each sample consists of cells from 3 mice, sequenced as one pool per sample. Comparisons made between WT & MT, & between Naïve & HDM.

first: Pamela

last: Schwartzberg

first: Dominic

last: Golec

first: Pedro

last: Gazzinelli Guimaraes

first: Thomas


title: RBM25 affects the immune and inflammatory progress by binding to and modulating alternative splicing levels of associated genes in rat H9C2 cells [ABL2020-10020-ABF_RBM25_OE]

summary: Alternative splicing (AS) enables genes to be translated into a vast diversity of proteins while aberrant AS predisposes cells to abnormal biological processes. As is closely associated with AS, RNA binding proteins (RBPs) are gradually gaining attention. RBM 25 was reported to participate in the cardiac pathophysiological process via AS regulation. Nonetheless, gaps still existed in whether RBM 25 functions in heart failure by its splicing factor role. H9C2 cells with excessively expressed RBM25 were used to filtrate different expression genes (DEGs) and analyze for RBM25-regulated AS by RNA-seq. Next, iRIP-seq was performed to examine its binding targets. For genes screened, further RT-qPCR-based validation was conducted. RBM25 overexpression caused expressive alteration in 80 genes mainly involved in the inflammatory response and virus response. Notably, RBM25 partially modulated AS of differential genes enriched in the apoptotic process and bound to genes clustered at inflammation response. Further, qRT-PCR verified Slc38a9, IL-17RC, Csf1, and Coro6 as targets of RBM25 being bound to and AS-regulated. Herein, our work demonstrated that by exerting its binding capability, RBM25 may serve as a regulator of related RNA expressive levels and AS process to confer negative impacts on cardiac inflammation in cardiomyocytes. Our study provided preliminary evidence regarding the understanding of RBM25 in heart failure complicated by inflammation.