title: Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma [snRNA-seq]

summary:
Background & Aims: Hepatoblastoma is the most common pediatric cancer of the liver and the majority of cases display activating mutations in the Wnt/β-catenin pathway. Understanding the complex milieu of the tumor microenvironment has resulted in promising new therapies for adult cancers, but similar approaches in pediatric cancers are still lacking. We aimed to provide a comprehensive analysis of the tumor microenvironment of hepatoblastoma unveiling its spatial architecture and key signaling mechanisms.
Methods: Single-cell/-nucleus RNA-seq (n=15), spatial transcriptomics (n=22), and multiplex immunofluorescence stainings (n=7) of treated, untreated, and metastasized pediatric hepatoblastomas were performed. An RNA-seq validation cohort (n=110) including hepatoblastoma, non-tumor and fetal liver samples and single-cell RNA-seq data of healthy immune cells were used for further analysis. Western blotting and RNA-seq of hepatoblastoma and macrophage cell lines were conducted for experimental validation.
Results: Of four identified transcriptional tumor programs, “Developmental” and “Metabolic” reflected different hepatic differentiation stages, while “Cycling” was enriched in undifferentiated cells and relapsed samples, and “Intermediate” displayed high activity in samples from patients with poor outcomes. We discovered an increased ratio of anti- to pro-inflammatory immune cells and evidence of immune exclusion from tumor areas. Wnt-responsive upregulation of the immunomodulator midkine in hepatoblastoma cells was associated with a change in macrophage phenotype, which could be partially reversed through midkine inhibition.
Conclusions: Hepatoblastoma cells exist along a continuous spectrum of hepatic differentiation and inhabit an altered immune environment. Wnt signaling augments midkine expression, which appears to be involved in shaping the immune environment by modifying macrophages to enable immune evasion, thereby providing a potential therapeutic target.

overall_design: Single-nuclei gene expression profiles of human hepatoblastoma were generated from formalin-fixed, paraffin-embedded tissue samples (n=5) using Chromium Single Cell Flex Gene Expression (10x Genomics).

first: Daniel

last: Münter

first: Flavia

last: de Faria

first: Mathis

last: Richter

first: Irene

last: Aranda-Pardos

first: Marc

last: Hotfilder

first: Carolin

last: Walter

first: Enya

last: Paga

first: Clara

last: Inserte

first: Thomas

middle: K

last: Albert

first: Rajanya

last: Roy

first: Shariyah

last: Rahman

first: Nicole

last: Riedel

first: Volker

last: Müller

first: Andreas

last: Pascher

first: Karsten

last: Wiebe

last: Schmid

first: Christian

last: Vokuhl

first: Beate

last: Winkler

first: Eva

last: Jüttner

first: Simon

last: Vieth

first: Urs

last: Mücke

last: Kluiver

first: Weng

last: Chuan Peng

first: Claudia

last: Rossig

first: Jerome

last: Schlué

first: Omid

last: Madadi-Sanjani

first: Sarah

last: Sandmann

first: Wolfgang

last: Hartmann

first: Noelia

last: A-Gonzalez

first: Oliver

last: Soehnlein


title: RNAseq on hippocampal bulk tissue of Dclk3 KO mice

status: Public on Feb 07 2025

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

country: France

institute: CNRS

type: Expression profiling by high throughput sequencing

summary: To characterize hippocampal transcriptome of Dclk3 KO mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Dclk3 KO and WT adult mice (12 months)

first: Karine

last: Merienne

last: Decraene

first: Emmanuel

last: Brouillet


title: Spatially-structured inflammatory response in the presence of a uniform stimulus: RNAseq screen

city: Chicago

first: Elizabeth

middle: R

last: Jerison

state: Illinois

address: 929 E 57th St

department: Physics

country: USA

institute: University of Chicago

summary: Inflammatory responses occur within the complex spatial context of tissues and organs, and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here, we used single-cell RNA sequencing to screen for genes differentially expressed under LPS (lipopolysaccharide) and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis.

overall_design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS (P. Aeuruginosa, Sigma), or E3 alone (vehicle control), for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium 3' platform and reagents (v3.1 kit) was used for cell encapsulation, reverse transcription, and library preparation, according to manufacturer instructions (manual revision D), with 12 cycles of preamplification.


title: Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma [Spatial Transcriptomics]

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

overall_design: Spatial transcriptomics of human hepatoblastoma was performed from formalin-fixed paraffin-embedded (FFPE) tissue samples using Visium Spatial Gene Expression for FFPE (10x Genomics; n=10) and Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics; n=12).

first: Daniel

last: Münter

first: Flavia

middle: W

last: de Faria

first: Mathis

last: Richter

first: Irene

last: Aranda-Pardos

first: Marc

last: Hotfilder

first: Carolin

last: Walter

first: Enya

last: Paga

first: Clara

last: Inserte

first: Thomas

last: Albert

first: Rajanya

last: Roy

first: Shariyah

last: Rahman

first: Nicole

middle: C

last: Riedel

first: Volker

last: Müller

first: Andreas

last: Pascher

first: Karsten

last: Wiebe

last: Schmid

first: Christian

last: Vokuhl

last: Winkler

last: Jüttner

middle: A


title: Isogenic hiPSC models of Turner syndrome development reveal shared roles of inactive X and Y in the human cranial neural crest network

city: Farmington

first: Stefan

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

summary: Modeling the developmental etiology of viable human aneuploidy can be challenging in rodents due to syntenic boundaries, or primate-specific biology. In humans, monosomy-X (45,X) causes Turner syndrome (TS), altering craniofacial, skeletal, endocrine, and cardiovascular development, which in contrast remain unaffected in 39,X-mice. To learn how human monosomy-X may impact early embryonic development, we turned to human 45,X and isogenic euploid induced pluripotent stem cells (hiPSCs) from male and female mosaic donors. Because neural crest (NC) derived cell types are hypothesized to underpin craniofacial and cardiovascular changes in TS, we performed a highly-powered differential expression study on hiPSC-derived anterior neural crest cells (NCCs). Across three independent isogenic panels, 45,X NCCs show impaired acquisition of PAX7+SOX10+ markers, and disrupted expression of other NCC-specific genes, relative to their isogenic euploid controls. In particular, 45,X NCCs increase cholesterol biosynthesis genes while reducing transcripts that feature 5’ terminal oligopyrimidine (TOP) motifs, including those of ribosomal protein and nuclear-encoded mitochondrial genes. Such metabolic pathways are also over-represented in weighted co-expression gene modules that are preserved in monogenic neurocristopathy. Importantly, these gene modules are also significantly enriched in 28% of all TS-associated terms of the human phenotype ontology. Our analysis identifies specific sex-linked genes that are expressed from two copies in euploid males and females alike and qualify as candidate haploinsufficient drivers of TS phenotypes in NC-derived lineages. This study demonstrates that isogenic hiPSC-derived NCC panels representing monosomy-X can serve as a powerful model of early NC development in TS and inform new hypotheses towards its etiology.

overall_design: We differentiated human iPSCs to neural crest cells (NCCs) via moderate WNT and BMP activation, reported to enable reproducible derivation of anterior NCCs (PMID: 30095409). We applied this method to a total of 11 distinct human iPSC lines from all three of our cytogenomically validated isogenic hiPSC panels (PMID: 36161909). We next performed a highly-powered RNA-seq study, with a minimum of 4 replicates per cell line, grouped by a combination of donor and karyotype (“condition”), comprising 7-12 replicates each. This enables our analysis to assess monosomy-X driven changes within each isogenic context (or donor). RNA was extracted from NCCs using the PureLink RNA Mini Kit (ThermoFisher Scientific). Libraries were prepared at the UConn Center for Genome Innovation using the Illumina Strand mRNA Kit and 100bp paired-ends reads were sequenced to an average depth of 40 million reads/replicate on the NovaSeq 6000 (Illumina).

first: Darcy

middle: T

last: Ahern

first: Prakhar

last: Bansal

first: Isaac

middle: V

last: Faustino

first: Owen

middle: M

last: Chambers

first: Erin

last: Banda

first: Heather

last: Glatt-Deeley

first: Rachael

middle: E

last: Massey

first: Yuvabharath

last: Kondaveeti


title: Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma [scRNA-seq]

first: Kornelius

last: Kerl

overall_design: Gene expression profiles of human hepatoblastoma were generated from fresh tissue samples (n=10) using Chromium Single Cell Gene Expression (10x Genomics).

first: Daniel

last: Münter

first: Flavia

last: de Faria

first: Mathis

last: Richter

first: Irene

last: Aranda-Pardos

first: Marc

last: Hotfilder

first: Carolin

last: Walter

first: Enya

last: Paga

first: Clara

last: Inserte

first: Thomas

last: Albert

last: Roy

last: Rahman

last: Riedel

first: Beate

first: Eva

first: Simon

last: Vieth

first: Urs

last: Mücke

last: Kluiver

first: Weng

last: Chuan Peng

first: Claudia

last: Rossig

first: Jerome

last: Schlué

first: Omid

last: Madadi-Sanjani

first: Sarah

last: Sandmann

first: Wolfgang

last: Hartmann

first: Noelia

last: A-Gonzalez

first: Oliver

last: Soehnlein


title: Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma [RNA-seq]

first: Kornelius

last: Kerl

overall_design: To investigate the importance of Wnt signaling and MDK signaling in shaping the immune environment of hepatoblastoma, we performed RNA-seq of HepG2 and Huh6 hepatoblastoma cell lines treated with different concentrations of a Wnt inhibitor (PKF118-310) and an MDK inhibitor (iMDK) and of THP-1-derived macrophages co-cultured with HepG2 and Huh6 cells that had or had not been treated with iMDK. Per cell line, there is a control condition treated with the empty vehicle. PKF118-310 was used at concentrations of 0.2 µM, 0.3 µM and 0.4 µM (0.4 µM only for Huh6 cells). iMDK was used at concentrations of 5 µM and 10 µM. Each condition was tested in triplicates (except for HepG2 PKF118-310 0.3 µM due to low RNA concentrations in two out of the three samples).

first: Daniel

last: Münter

first: Flavia

last: de Faria

first: Mathis

last: Richter

first: Irene

last: Aranda-Pardos

first: Marc

last: Hotfilder

last: Walter

last: Paga

first: Rajanya

first: Shariyah

first: Nicole

first: Volker

last: Müller

first: Andreas

last: Pascher

first: Karsten

last: Wiebe

last: Schmid

first: Christian

last: Vokuhl

last: Winkler

last: Jüttner


title: Bulk RNA-seq after Overexpression of EFNB2 in U266 Multiple Myeloma Cells

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: EFNB2 is a cell transmembrane protein required for the survival of multiple myeloma cells. Specifically, we have previously shown that EFNB2 reverse signaling is required for myeloma proliferation and survival. Overexpressing EFNB2 increases myeloma survival, proliferation, and resistance to treatment. This effect is mediated partially through STAT5, but other mediators are likely invovled. To determine if other mediators and pathways might be involved, we performed RNA-seq on myeloma cells overepxressing EFNB2.

overall_design: U266 cells were transduced using a lentivirus to express dCas9-VPR. They were then transduced to express either control (non-targeting, scrambled) guide RNA (cgRNA) or guide RNA targeting the start site of EFNB2 ("gRNA2). There are 5 replicates of controls and 5 replicates of EFNB2 gRNA. We validated that the gRNA to EFNB2 causes a 80 - 100 fold increase in EFNB2 RNA by qPCR.

first: Joshua

last: Sasine

first: Jennifer

last: Dukov


title: Genomic G-Quadruplex folding and unfolding following global DNA demethylation

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

country: China

institute: Sun Yat-sen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We demonstrate that CpG methylation status may impact the genome-wide folding and stabilization of G-Quadruplex in human cancer cells.

overall_design: Examination of G-Quadruplex sites by using G4-specific ChIP-seq in 5aza-treated and untreated HCT116 cells


title: Senkyunolide A interrupts TRAF6-HDAC3 interaction to epigenetically suppress c-MYC and attenuate cholestatic liver injury

city: Beijing

first: Runping

last: Liu

state: Beijing

address: 11 Beisanhuandonglu

institute: Beijing University of Chinese Medicine

summary: Cholestatic liver diseases are highly prevalent and lack effective treatment, ultimately progressing to end-stage liver diseases. Our recent study indicates that the interplay between c-MYC and lncRNA H19 exacerbates the ductular reaction during cholestasis. However, the underlying mechanisms and their potential as therapeutic targets remain unclear. In this study, we demonstrate that senkyunolide A (SenA) effectively mitigates cholangiocyte hyperproliferation by epigenetically suppressing c-MYC expression and disrupting the downstream H19/Let-7a/Lin28a axis. Through comprehensive characterization using CHIP analysis, protein truncation, amino acid mutation or deletion, and the development of SenA derivatives, we identified a potential interaction between the carbonyl group in SenA and Arg483 in TRAF6, disrupting the TRAF6-HDAC3 complex. This dissociation facilitates the binding of HDAC3 to the MYC promoter region, resulting in enhanced histone deacetylation and transcriptional suppression. Here, we highlight the therapeutic potential of SenA in cholestatic liver diseases by elucidating its role in epigenetic regulation.

overall_design: Mice were administrated with Sham,  bile duct ligation(BDL) and BDL plus senkyunolide A. Cholangiocytes were isolated at the end of different treatment. Total cholangiocytes RNA was collected and RNA-sequecing was performed.


title: Mitochondrial regulator PGC-1a in neuronal metabolism and brain aging

city: Madison

first: Rozalyn

last: Anderson

state: WI

address: 2500 Overlook Terrace

institute: University of Wisconsin-Madison

summary: The brain is a high energy tissue, and the cell types of which it is comprised are distinct in function and in metabolic requirements. The transcriptional co-activator PGC-1a is a master regulator of mitochondrial function and is highly expressed in the brain; however, its cell-type-specific role in regulating metabolism has not been well established. Here, we show that PGC-1a is responsive to aging and that expression of the neuron-specific PGC-1a isoform allows for specialization in metabolic adaptation. Transcriptional profiles of the cortex from male mice show an impact of age on immune, inflammatory, and neuronal pathways and a highly integrated metabolic response associated with decreased expression of PGC-1a. Proteomic analysis confirms age-related changes in metabolism and further shows changes in ribosomal and RNA splicing pathways. We show that neurons express a specialized PGC-1a isoform that becomes active during differentiation from stem cells and is further induced during the maturation of isolated neurons. Neuronal but not astrocyte PGC-1a responds robustly to inhibition of the growth-sensitive kinase GSK3b, where the brain-specific promoter-driven dominant isoform is repressed. The GSK3b inhibitor lithium broadly reprograms metabolism and growth signaling, including significantly lowering expression of mitochondrial and ribosomal pathway genes and suppressing growth signaling, which are linked to changes in mitochondrial function and neuronal outgrowth. In vivo, lithium treatment significantly changes the expression of genes involved in cortical growth, endocrine, and circadian pathways. These data place the GSK3b/PGC-1a axis centrally in a growth and metabolism network directly relevant to brain aging.

overall_design: To investigate the transcriptional changes that occur in the brain with age, RNA-sequencing was conducted on cortical tissue from male mice at ages 10, 20, and 30 months of age. To investigate GSK3b inhibition in the brain, mice were fed 1 of 4 different doses of LiCO3. RNA-seq was conducted on cortical tissue from 4 mice per dose. To investigate the impact of GSK3b inhibition on neuronal growth and metabolism, primary cortical neurons were treated for 24 hours with LiCl and then collected for RNA-seq.

first: Dylan

last: Souder

first: Eric

last: McGregor

first: Timothy

last: Rhoads

first: Josef

middle: P

last: Clark

first: Tiaira

middle: J

last: Porter

first: Kevin

last: Eliceiri

first: Darcie

middle: L

last: Moore

first: Luigi

last: Puglielli


title: Decoding functional haematopoietic progenitor cells in the adult human lung

city: San Francisco

first: Mark

middle: Roberts

last: Looney

address: 513 Parnassus

institute: UCSF

summary: Comparative transcriptomic profiling of pulmonary and medullary CD34+ haematopoietic progenitor was performed to reveal shared and organ-specific gene signatures.

overall_design: Lin-CD34+ HSPCs were sorted from matched human lung and bone marrow and subjected to single-cell RNA sequencing.

first: Catharina

last: Conrad

first: Mélia

last: Magnen

first: Jessica

last: Tsui

first: Harrison

last: Wismer

first: Mohammad

last: Naser

first: Urmila

last: Venkataramani

first: Bushra

last: Samad

first: Simon

last: Cleary

first: Longhui

last: Qiu

first: Marco

last: De Giovanni

first: Nicole

last: Mende

first: Emmanuelle

last: Passegué

first: Elisa

last: Laurenti

first: Alexis

last: Combes


title: Spatially resolved RNA-sequencing of the injured murine heart

city: Jena

first: Dennis

middle: de

last: de Bakker

address: Beutenbergstraße 11

institute: FLI

summary: Myocardial infarction results in a massive loss of cardiomyocytes which will not be regenerated. Recent studies using models of regeneration show that cardiomyocytes at the border of the injury are most prone to proliferate. Which processes occur in this region and make these cells act as progenitors, remains to be elucidated. In addition, we lack molecular markers for the identification of these cells in the human heart. To create a transcriptional profile of the murine border zone, identifying local processes and enabling the discovery of marker genes which will allow the identification of human cardiomyocytes with potential proliferative capacity. Myocardial infarction (MI) was induced in mice and 3, 7 or 14 days later ventricular tissue was isolated ranging from the injured area into the remote myocardium. Tomo-sequencing was performed on these cardiac tissue samples, which comprises of tissue sectioning together with RNA-sequencing on individual sections. This resulted in spatially resolved transcriptome maps containing a dynamic, transcriptionally distinct border zone with reduced expression of genes involved in mitochondrial oxidative phosphorylation, fatty acid metabolism and sarcomere function and increased expression of myofibroblast and proliferation genes. Genes shared between the murine and zebrafish border zone, such as ANKRD1, UCHL1 and DES, were validated as molecular markers in injured human hearts. Unexpectedly, pronounced expression of these marker genes was found in surviving cardiomyocytes located at the sub-endocardium. The border zone is an evolutionary conserved, transcriptionally distinct and dynamic region.  With the use of newly identified markers, we discovered the existence of sub-endocardial cardiomyocytes in ischemic human hearts that share transcriptional characteristics with potential progenitor cells. This might have far reaching implications for the development of strategies to stimulate the regenerative capacity of patients suffering from ischemic injury.

overall_design: Under a fluorescent stereoscope, injured mouse hearts were isolated and cut open longitudinally and tissue was selected based on katushka signal. The katushka signal in these hearts is expressed by a Nppb promotor, thereby marking stressed tissue which was used to orient the tissue. Tissue was isolated from the injured hearts (1x 3dpi, 2x 7dpi, 2x 14dpi) containing part of the injury, katushka signal and part of the remote myocardium respectively. Tomo-seq was conducted as previously described (Junker, Noël, et al., 2014) whereby the tissue was embedded in Jung tissue freezing medium (Leica), sectioned at 20um from the injured area to the remote myocardium, of which every fifth section was collected into a single tube. RNA was extracted from each tube using Trizol (Ambion) after adding a defined amount of spike-in RNA to correct for technical variations during the downstream processing. RNA-seq was performed as previously described (Junker, Noël, et al., 2014) including the reverse transcription using primers containing a tube-specific barcode. The barcoding of the cDNA allowed for the pooling of material, since the barcode could later be used to determine the positional origin of the labeled transcript. The pooling of cDNA was followed by linear amplification and sequencing.

first: Jeroen

last: Bakkers


title: Secondary LPS stimulation of BMDMs differentiated from bone marrow of C57B/6J mice treated with 4xLPS, 1xLPS or PBS

city: Montreal

first: Przemyslaw

last: Sapieha

state: Quebec

address: 5345 Assumption Blvd

country: Canada

institute: Maisonneuve-Rosemont Research Center

summary: C57Bl/6J mice were treated with 4xLPS, 1xLPS, or PBS at 7 weeks of age and BM cells were collected at 11 weeks of age. BM cells were differentiated to bone marrow-derived macrophages (BMDMs) with M-CSF, and BMDMs were harvested after a secondary stimulation with LPS or PBS for 4 hours. Total RNA was extracted and analyzed for gene expressions by bulk RNA-seq

overall_design: 6 conditions were analysed: 1) PBS_NO (3 replicates, samples 1-3), 2) 1xLPS_NO (3 replicates, samples 4-6), 3) 4xLPS_NO (3 replicates, samples 7-9), 4) PBS_LPS (3 replicates, samples 10-12), 5) 1xLPS_LPS(3 replicates, samples 13-15), 6) 4xLPS_LPS (3 replicates, samples 16-18)

first: Masayuki

last: Hata


title: Dynamicdosage compensation of transposable elementsin mammals

status: Public on Feb 12 2025

city: Boston

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

summary: In mammals, X-linked dosage compensation involves two processes: X-inactivation to balance X chromosome dosage between males and females, and X-hyperactivation to achieve X-autosome balance. Transposable elements (TEs) are repetitive mobile DNA sequences and major sources of X chromosome dosage. Current studies in X-linked dosage compensation mainly focus on genes, with TEs still remaining elusive. Here we use “So-Smart-Seq” to comprehensively determine the allelic dynamics of TEs in the context of imprinted and random X-chromosome inactivation (XCI). We find that chromosomal loci and genetic backgrounds significantly impact TE silencing, and reveal putative roles of SINEs in shaping 3D chromatin architectures. We show remarkable difference in TE silencing between two forms of XCI and discover that X-hyperactivation is absent in TEs. Our data provide deep insight for TE studies and greatly contribute to complete understanding of X-chromosome wide dosage compensation.

sample_organism:
Mus musculus
Mus musculus castaneus

platform_organism:
Mus musculus
Mus musculus castaneus

overall_design:
For the third-party data reanalysis, 188 GSM samples (GSM7980593-7980780) from GSE168455 were reanalyzed. Allelic expression of transposable elements during imprinted XCI was extracted from data GSE168455 that reveal full allelic transcriptome of single preimplantation embryos at various stages from WT and Xist mutant mouse. The allelic ratio between two X chromosome was calculated for each TE family.
To acquire allelic expression dynamics of transposable elements in random XCI, allelic bulk RNAseq was performed in differentiating TST ES cells, a mus/cas hybrid ES cell line where X chromosome from mus allele is progressively silenced during random XCI. Expression of transposable elements were determined  and the allelic ratio between two X chromosome was calculated for each TE family.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
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first: Barry

last: Kesner

first: Jeannie

last: Lee


title: The Aryl Hydrocarbon Receptor Directs the Differentiation of Progenitor Blastomeres

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Key regulatory decisions during cleavage divisions in mammalian embryogenesis determine the fate of preimplantation embryonic cells.  Single-cell RNA-sequencing of early stage—2-cell, 4-cell, and 8-cell—blastomeres show that the aryl hydrocarbon receptor (AHR), traditionally considered as an environmental sensor, directs the segregation of 4-cell blastomeres.  Disruption of endogenous AHR functions in Ahr knockout embryos or in embryos from dams exposed to dioxin, the prototypic xenobiotic AHR agonist, significantly impairs blastocyst formation by causing repression of OCT4 expression, decline of CDX2 expression, loss of OCT4 and CDX2 transcriptional heterogeneity, and incidence of nonspecific pluripotency downregulation.  Trajectory and gene variability analyses further confirm that deregulation of OCT4 functions and changes of transcriptional heterogeneity resulting from disruption of AHR functions restrict the emergence of differentiating blastomeres within these embryos.  It appears that AHR governs the differentiation of progenitor blastomeres and that interference with AHR functions significantly perturbs embryogenesis.

overall_design: Dysfunctional AHR may disrupt early blastomere differentiation and cause the impaired formation of Ahr-knockout and dioxin-exposed blastocysts.  Since mutual regulation between OCT4 and CDX2 is in place by the 16-cell stage, at a time when Ahr expression is undetectable, we aimed specifically at the early 2- to 8-cell stages to explore the potential role of the AHR in regulation of the transcriptome of progenitor blastomeres.  To achieve this purpose, we isolated 336 single blastomeres obtained from eight embryos of each of the nine groups: Wild-type control, Ahr-knockout, and dioxin-exposed each at 2-cell, 4-cell, and 8-cell stages individually, and subjected them to Single-Cell RNA-sequencing (scRNA-seq).

first: Chia-I

last: Ko

first: Jacek

last: Biesiada

first: Hesbon

last: Zablon

first: Xiang

last: Zhang

first: Alvaro

last: Puga


title: EGFR-induced lncRNA TRIDENT promotes drug resistance in non–small cell lung cancer via phospho-TRIM28-mediated DNA damage repair

status: Public on Feb 06 2025

first: Jonathan

middle: David

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: Long noncoding RNAs (lncRNAs) play numerous roles in cellular biology and alterations in lncRNA expression profiles have been implicated in a variety of cancers. Here, we identify and characterize a n lncRNA, TRIM28 Interacting DNA damage repair Enhancing Noncoding Transcript (TRIDENT), whose expression is induced upon epithelial growth factor receptor (EGFR) activation, and which exerts pro-oncogenic functions in EGFR-driven non–small cell lung cancer. Knocking down TRIDENT leads to decreased tumor-cell proliferation in both in vitro and in vivo model systems and induces sensitization to chemotherapeutic drugs. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to accumulation of DNA damage in cancer cells via decreased TRIM28 phosphorylation. Altogether, our results reveal a molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance. Our findings suggest that TRIDENT can be developed as a biomarker or therapeutic target for EGFR mutant non–small cell lung cancer.

overall_design: RNAseq profiling of H1975-TRE-dCas9-KRAB cells with NT control gRNA, TRIDENT gRNA1 AND TRIDENT gRNA2 after treating with 4ug/ml of doxycycline for 72 hours

first: Tanvi

last: Saxena

first: Anan

last: Quan

first: Erica

last: Chan

first: Nina

last: Kozlova

first: Latika

last: Matai

middle: D

first: Rajesha

last: Rupaimoole

first: Francisco

last: Beca

first: Taru

last: Muranen

first: Frank

last: Slack


title: Bile acid receptor FXR promotes intestinal epithelial ferroptosis and subsequent ILC3 dysfunction in neonatal necrotizing enterocolitis [IEC bulk RNA-seq]

city: Tianjin

first: yuchao

last: Jing

address: No.22, Meteorological Tai Road, Tianjin

institute: Tianjin Medical University

summary: Necrotizing enterocolitis (NEC) is a prevalent pediatric emergency characterized by the sudden onset of intestinal ischemia and necrosis resulting from hyperinflammation.The interactions between the bile acid receptor FXR with gut microbiota and mucosal immunity in early postnatal life, and its exact role in the pathogenesis of NEC, are unknown.Here we analyze the role of FXR in IECs under NEC.

overall_design: IECs (EpCAM+CD45-) from Fxrfl/fl naïve, FxrΔIEC naïve, Fxrfl/fl NEC and FxrΔIEC NEC pups were sorted via BD FACS. Sorted cells were subjeted to bulk RNA-seq

first: Yuxin

first: Yuchao

first: Juan

last: He


title: RNAseq on hippocampal bulk tissue of Dclk3 conditional KO mice

first: Charles

last: DECRAENE

summary: To characterize the effect of conditional inactivation of Dclk3 in adult mouse hippocampus.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for conditional Dclk3 KO and WT adult mice (6 months)

first: Karine

last: Merienne

last: Decraene

first: Emmanuel

last: Brouillet


title: Bile acid receptor FXR promotes intestinal epithelial ferroptosis and subsequent ILC3 dysfunction in neonatal necrotizing enterocolitis [scRNA-seq]

summary: We performed scRNA-seq to analyze the changes of IECs cell subsets and signaling pathways in neonatal mice after NEC

overall_design: IECs (EpCAM+CD45-) from Ctrl pups, NEC pups, Fxrfl/fl and FxrΔIEC NEC pups were sorted via BD FACS. Sorted cells were sequenced using the 10x Genomics platform.

last: Zhang


title: Bile acid receptor FXR promotes intestinal epithelial ferroptosis and subsequent ILC3 dysfunction in neonatal necrotizing enterocolitis [ILC3s bulk RNA-seq]

overall_design: Bulk RNA-seq analysis of small intestinal ILC3s pretreated with vehicle or PEox


title: Integration activity of evolutionarily recent human retroelements Alu and LINE in tumors

city: Moscow

first: Alexander

last: Modestov

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

summary: The activity of mobile elements can be considered as one of the aspects of tumor genomic instability. From that perspective, it has a potential as a prognostic or diagnostic marker. In this work we attempted to assess the levels of integration activity of evolutionarily recent human retroelements (RE) in tumors and their relationship with RE transcriptional activity as well as other potential regulatory factors.To determine the integration activity of RE in tumors and to assess its correlation with RE transcriptional activity we performed a genome-wide search for tumor-specific inserts. For that we selected 20 tumor samples with higher and 20 samples with lower LINE L1 L1Hs and L1PA2 expression for further sequencing of genomic flanks of L1Hs L1PA2 and AluYa5/8 elements. Corresponding matched norm samples were used as a control.

overall_design: All experimental biosamples were FFPE tumor tissue blocks. Histological materials were assessed by a pathologist and selected areas with at least 50% of tumor cells were dissected for further nucleic acids extraction. In some cases, adjacent non-tumour tissue was also marked and dissected. Total RNA was extracted from FFPE samples with RNeasy FFPE Kit (Qiagen) following the manufacturer’s protocol. For depletion of ribosomal RNA and library preparation, the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) was used. KAPA single-indexed adaptors (Roche) or KAPA unique dual indexed primers (Roche) were used for multiplexing samples in one sequencing run. Sequencing was performed on Illumina NextSeq 550(Illumina) with equipment for single-end 75-bp read length sequencing, for approximately 30 million raw reads per sample.

first: Maria

last: Suntsova

first: Anton

last: Buzdin


title: SFRP2+ CAFs Hinder Abscopal Effect from Combined Radiotherapy and Immunotherapy by Forming a Hostile Perivascular Niche [B16]

first: Yanpei

address: No.1023,South Shatai Road, Baiyun District, Guangzhou, Guangdong, China

institute: Southern Medical University

summary: Despite accumulating cases of radiotherapy-induced abscopal effect in the lung cancer with the introduction of immune checkpoint inhibitors (ICIs), the occurrence of this effect remains infrequent and unpredictable to be a therapeutic goal. Here, we showed that the combination of radiotherapy (8Gy*3F) and ICI alleviated the tumor burden at the irradiated site whereas no discernible benefit was observed in the abscopal tumors. RNA-sequencing data showed that extracellular structure organization pathways were enriched in the abscopal tumors after combined therapy, with Sfrp2 being identified as a central hub. SFRP2 expression was observed in cancer-associated fibroblasts (CAFs) and was elevated in abscopal tumors after combined therapy. Blockade of SFRP2 followed by combined radiotherapy and ICI reinvigorated infiltration and cytotoxicity of CD8+ T cells, and elicited regression of abscopal tumors, which was abrogated by CD8α depletion. Mechanistically, in vitro experiments demonstrated that SFRP2+ CAFs induced apoptosis of CD8+ T cells. The spatial transcriptome analysis showed that SFRP2+ CAFs were located in proximity to the vessels and surrounded by abundant macrophages and limited CD8Tex, thereby creating an immunosuppressive perivascular niche, which was validated in paraffin sections of human lung cancer. Lineage-tracing assays showed SFRP2+ CAFs were derived from pericytes. IGF-1 released by irradiated tumors facilitated the transition of pericytes into fibroblasts and stimulated the expression of SFRP2. In summary, SFRP2+ CAFs hijack the abscopal effect from combined radiotherapy and immunotherapy via inducing apoptosis of CD8+ T cells and orchestrating a hostile perivascular niche in the lung cancer. Targeting SFRP2+ CAF may recondition the TME and promote the abscopal effect.

overall_design: RNA-sequencing of B16 murine tumor specimens administered with different treatments: immune checkpoint inhibitor (3 replicates for this group) and radiotherapy combined with immunotherapy (3 replicates for this group).


title: Mitochondrial metabolism sustains DNMT3A-R882-mutant clonal haematopoiesis

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

summary: Somatic DNMT3A R882 codon mutations drive the most common form of clonal haematopoiesis (CH) and are associated with increased acute myeloid leukaemia (AML) risk. Preventing expansion of DNMT3A-R882-mutant haematopoietic stem/progenitor cells (HSPCs) may therefore avert progression to AML. To identify DNMT3A-R882-mutant-specific vulnerabilities, we conducted a genome-wide CRISPR screen on primary mouse Dnmt3aR882H/+ HSPCs. Amongst the 640 vulnerability genes identified, many were involved in mitochondrial metabolism and metabolic flux analysis confirmed enhanced oxidative phosphorylation usage in Dnmt3aR882H/+ vs Dnmt3a+/+ (WT) HSPCs. We selected citrate/malate transporter Slc25a1 and complex I component Ndufb11, for which pharmacological inhibitors are available, for downstream studies. In vivo administration of SLC25A1 inhibitor CTPI2 and complex I inhibitors IACS-010759 and metformin, suppressed post-transplantation clonal expansion of Dnmt3aR882H/+, but not WT, LT-HSCs. The effect of metformin was recapitulated using a primary human DNMT3A-R882 CH sample. Notably, analysis of 412,234 UK Biobank participants revealed that individuals taking metformin had markedly lower prevalence of DNMT3A-R882-mutant CH, after controlling for potential confounders including glycated haemoglobin, diabetes and body mass index. Collectively, our data propose that modulation of mitochondrial metabolism as a therapeutic strategy for prevention of DNMT3A-R882-mutant AML.

overall_design: RNA-seq of WT and DNMT3A R882 mutant mice under metformin treatment and control

first: Malgorzata

last: Gozdecka

first: Monika

last: Dudek

first: Sean

last: Wen

first: Justyna

last: Rak

first: Brian

last: Huntly

first: George

last: Vassiliou


title: SFRP2+ CAFs Hinder Abscopal Effect from Combined Radiotherapy and Immunotherapy by Forming a Hostile Perivascular Niche [II]

overall_design: RNA-sequencing of LLC1-sgLkb1 murine tumor specimens and LLC1 murine tumor specimens administered with different treatments: radiation, immune checkpoint inhibitor, or their combination. 3 replicates for each group.


title: Chronic Salmonella Infection Contributes to Gallbladder Carcinogenesis by Host Epigenetic Modifications

city: New Delhi

first: Pramod

middle: Kumar

last: Garg

state: Delhi

address: Ansari Nagar

department: Gastroenterology

country: India

institute: AIIMS, New Delhi

summary: The present study aimed to understand the pathways involved in gallbladder cancer through genome-wide expression profiling (microarray) of human GBC

overall_design: Tissue samples were collected from GBC and gallstone patients during surgery. H&E staining was done to confirm the presence of tumor area

first: Kajal

last: Jain

middle: K


title: Single-cell RNA sequencing reveals a novel CD4+T cell subset in papillary thyroid cancer

city: Shanghai

first: Zhengshi

last: Wang

address: No.301 Middle Yanchang Road

institute: Shanghai Tenth People's Hospital

summary: Papillary thyroid cancer (PTC) is the most common thyroid malignancy. Although PTC patients usually show a favorable prognosis, some still have a high rate of recurrence and a relatively low survival rate. We aimed to reveal the mechanisms involved in the development of thyroid cancer using single-cell RNA sequencing (scRNA-seq).scRNA-seq data was collected from 15 samples, including primary tumors of PTC, metastatic lymph nodes (LNs), and adjacent normal tissues. The results from scRNA-seq data were further validated with flow cytometry, proliferation, invasion, and migration assays, and bulk RNA-seq data.A novel CD4+T cell subset was identified, termed as EGR1+CD4+T cells. It produced high levels of IL-10 and IFN-γ in response to phorbol 12-myristate 13-acetate (PMA) and ionomycin, and showed a distinct molecular pathway activity compared to CD4+Tregs. CD4+T cell-specific over-expression of EGR1 in vitro enhanced tumor cell proliferation, invasion, and migration when co-cultured with PTC cell lines. The expression profiling analysis of immune checkpoint molecules indicated that CD96 was commonly up-regulated in EGR1+CD4+T cells, CD4+Tregs, and other T cell subsets, especially in tumor tissues. Single CD96 blockade significantly increased the levels of IFN-γ, IL-17a, and IL-10 in EGR1+CD4+T cells, and inhibited the proliferation of PTC tumor cells. Co-blockade of CD96/TIGIT significantly enhanced the production of IFN-γ, TNF-α, and IL-17a in both EGR1+CD4+T and CD3+CD4+T cells, which also suppressed cell proliferation, invasion, and migration when co-cultured with PTC tumor cells. These findings indicated that EGR1+CD4+T cell was a novel CD4+T cell subset with specific functions. Single CD96 blockade or co-blockade of CD96/TIGIT enhanced antitumor immunity of EGR1+CD4+T cells, which might be promising therapeutic strategies in PTC treatment.

overall_design:
Cells were firstly stained with two fluorescent dye, Calcein AM and Draq7, for precisely determination of cell concentration and viability via BD Rhapsody™ Scanner (BD Biosciences) before single cell multiplexing labelling.     Cell of each sample were sequentially labeled with BD Human Single-Cell Multiplexing Kit (Cat.     No. 633781) which utilizing the cell-hashing technology  mainly to provide higher sample throughput and eliminate batch effect for single cell library preparation and sequencing.     Briefly, cells from each sample were labeled by antibodies with different sample tags respectively and washed twice with Stain Buffer (FBS) (BD Biosciences, Cat.     No. 554656) before pooling all samples together.     Pooled samples were loaded in one BD Rhapsody micro-well cartridge based on Fan et al .     Cell capture beads were then loaded excessively to ensure that nearly every micro-well contains one bead, and the excess beads were washed away from the cartridge.     After lysing cells with lysis buffer, Cell capture beads were retrieved and washed prior to performing reverse transcription.     Microbeads-captured single cell transcriptome and SampleTag molecules were generated into cDNA library and SampleTag library separately containing cell labels and unique molecular identifiers (UMI) information.We then performed gene expression profilinf analysis use data obtained from scRNA-seq of 15 samples, including primary tumors of PTC, metastatic lymph nodes (LNs), and adjacent normal tissues.
Please note that each sample record represents mixed-samples and the sample_metadata.txt contains the sample information for 15 samples (SAMPLE1-SAMPLE15).

first: Wenli

last: Jiang


title: TNBC organoid sc-multiome seq data treated with epigenetic drugs

city: Chapel Hill

first: Elizabeth

last: Brunk

state: NC

address: 250 Bell Tower Dr.  4352 Genome Sciences Bldg.

department: Pharmacology, Lineberger Comprehensive Cancer Center, UNC School of Medicine

institute: University of North Carolina at Chapel Hill

summary: Identifying biologically relevant signals from single-cell omics data to ultimately promote precision medicine is one current grant challenge. To address this challenge, we focused on triple-negative breast cancer (TNBC), integrated bulk and single-cell RNA-seq data from a large global population, and identified subpopulation identities that were able to provide responsive trajectories upon treatment. As a proof of principle, we applied our computational frame work on a TNBC organoid treated with two epigenetic drugs, JQ1 and MS177. We used this model to highlight how different components within the tumor responded molecularly differently to drug treatment.

overall_design: 10X sc-multiome sequencing was performed on the TNBC organoid in the control, JQ1-treated and MS177-treated conditions

first: Yue

first: Santiago

last: Haase

first: Austin

last: Whitman

first: Adriana

last: Beltran

first: Philip

last: Spanheimer


title: Alteration of BRN3A expression influences the expression of genes involved in the regulation of important biological processes in the HPV induced cervical Cancer

city: Varanasi

first: Jagat

last: Roy

state: Uttar Pradesh

address: Institute of Science

department: Zoology

institute: Banaras Hindu University

summary: Cervical cancer is the fourth most common cancer worldwide in females. This occurs primarily due to the infection of high-risk human papillomavirus (HPV) although in advanced stages it requires support from host cellular factors. BRN3A is one such host cellular factor that upregulates tumorigenic high-risk HPV expression. The expression of BRN3A in cervical cancer remains high where it enhances tumorigenicity. The effect of BRN3A on HPV-mediated cervical cancer and the underlying mechanism remains obscure. Thus, we have investigated the overall effect of BRN3A on genes associated with cancer-related different biological processes. In approach, we have altered the expression of BRN3A through overexpression and knockdown in cervical cancer cells following transcriptome profiling through next-generation RNA-sequencing. This study revealed a substantial change in the expression of several genes associated with cancer-promoting biological processes including viral processes, immune response, cell-death, cell-proliferation, and different signaling pathways, etc. Additionally, promoter analysis through in silico mode revealed that a total of 32.7% of genes possess BRN3A binding sites at their promoters. Physical interaction of BRN3A with IFITM1, OAS3, ISG15, BCL2L1, and HSP90AB1 genes was also confirmed. Thus, the present study identified molecular targets of BRN3A and provided new insight into the pathogenesis of cervical cancer. According to our knowledge, this is the first report on the effect on eukaryotic transcriptomes after over-expression and knocking down BRN3A.

overall_design: Method: Total RNA was isolated from transfected SiHa cells in both conditions: (i) Over expression (OE) of BRN3A was done through expression vector pCDNA3.1; and (ii) knock down (KD) of BRN3A expression was done through siRNA oligos (5’-GCCAUAAUCUGCAACUUCAdTdT-3’) in biological treplicates. Further, RNA profiles were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform using 51bp pair-end reads in flowcell (Flowcell ID: C7K52ACXX).This resulted in a sequencing depth of 15-20 million reads. The resulting sequencing fastq files were mapped to the Human genome (hg19) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to merge with Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012).

first: Anand

last: Prakash

first: Yashvant

last: Patel


title: Paraventricular nucleus CRH neurons regulate acute lung injury via sympathetic nerve–neutrophil axis

city: Changsha

first: Dai

last: Ruping

state: Hunan

address: Ren-Min Central Road

department: Anesthesiology

institute: The Second Xiangya Hospital of Central South University

summary: Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are severe conditions with high morbidity and mortality, and effective treatments are limited. Neuroimmune interactions play a critical role in lung homeostasis, but it remains unclear if specific brain regions regulate lung inflammation. Here, we unveil the critical role of neuroimmune signaling in ALI, focusing on the regulatory function of corticotropin-releasing hormone (CRH) neurons in the paraventricular nucleus (PVN) of the hypothalamus. Using viral tracing, chemogenetic modulation, and pharmacological interventions in mouse models of ALI induced by intranasal lipopolysaccharide and cecal ligation and puncture (CLP), we found that lung injury activated CRHPVN neurons that projected to the lung. Activation of these neurons protected mice from ALI and death, reducing neutrophil infiltration and effector functions in the lung. In contrast, inhibiting CRHPVN neurons exacerbated ALI. Notably, the beneficial impact of CRHPVN neuron activation is compromised by the pulmonary chemical sympathectomy or inhibition of the β2-adrenergic receptor. These protective effects were dependent on sympathetic nerves, with norepinephrine released locally to modulate neutrophil functions via β2-AR–β-arrestin2 signaling, inhibiting the NF-κB pathway. Our findings reveal a brain-lung axis that regulates immune responses in ALI, suggesting novel therapeutic targets for ALI and ARDS.

overall_design: CRH-IRES-Cre mice were injected with AAV2/9-Ef1α-DIO-mCherry (control group) or AAV2/9-Ef1α-DIO-hM3Dq-mCherry (experimental group) into the paraventricular nucleus (PVN). After viral expression, CNO was intraperitoneally injected, and 1 hour later, LPS (20 mg/kg) was administered intranasally to induce acute lung injury (ALI). Lung tissues were collected 8 hours post-LPS for RNA sequencing.

first: Ruping

last: Dai

first: Hui

last: Li


title: Light-sensitive short hypocotyl genes confer symbiotic nodule identity in the legume Medicago truncatula

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

institute: Max Planck Institute for Plant Breeding Research

summary: Legumes grow specialized root nodules that are distinct from lateral roots in  morphology and function, with nodules intracellularly hosting beneficial nitrogen-fixing  bacteria that provide the plant with nitrogen. We have previously shown that a lateral  root-like program underpins nodule initiation, but there must be additional  developmental programs that confer nodule identity. Here, we show that two members  of the LIGHT SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family,  known to define organ boundaries and meristem complexity in the shoot, function as  regulators of nodule organ identity. LSH1/LSH2 function upstream of and together  with the known nodule regulators Nuclear Factor Y A1 and NODULE ROOT1/2. The  principal outcome of LSH1/LSH2 function is the production of cells able to  accommodate nitrogen-fixing bacteria, a unique nodule feature. We conclude that the  coordinate recruitment of a pre-existing shoot developmental program, in parallel to a  root program, underpins the divergence between lateral roots and nodules.

overall_design: RNAseq of M. truncatula genes after rhizobia (S. meliloti 2011) treatment in wild type (R108), and mutants: lsh1-1, lsh1lsh2, noot1noot2, nf-ya1-1, RNAseq of M. truncatula genes with the ectopic expression of LSH1LSH2 and NOOT1NOOT2

first: Katharina

last: Schiessl


title: Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits

city: Mohali

first: Rita

last: Sharma

state: Punjab

address: Sector 81

department: Food Biotechnology

institute: National Agri-Food Biotechnology Institute

summary: We report a comprehensive transcriptomics analysis across five temporal stages of pistil and seed development in Sorghum bicolor variety M35-1. Sequencing of fourteen libraries (three replicates from all stages and two replicates from 30 DAP stage) yielded >608 billion paired-end reads. A total of 31337 genes expressed in these five stages of pistil and seed development.

overall_design: Transcriptomic analysis of pistils collected before pollination and four temporal stages of seed development in Sorghum bicolor variety M35-1

first: Rubi

first: Namrata

last: Dhaka

first: Kushagra

last: Krishnan

first: Manoj


title: SFRP2+ CAFs Hinder Abscopal Effect from Combined Radiotherapy and Immunotherapy by Forming a Hostile Perivascular Niche (scRNA-Seq)

city: Guangzhou

first: Yanpei

last: Zhang

overall_design: Lung metastatic lesions were constructed as unirradiated side by tail vein injection of LLC1-sgLkb1 tumor cells in Sfrp2fl/fl mice and Sfrp2ΔCol1a2 mice. Three weeks later, LLC1-sgLkb1 tumor cells were subcutaneously inoculated into these mice as the irradiation side, followed by single ICI treatment or a combination of RT and ICI. Upon completion of the therapy regimen, the unirradiated lung tumor status was assessed using micro-CT scans, and the tissues were collected.


title: Targeting zinc metabolism for breast cancer inhibition in mice

city: Zhengzhou City

first: Yuan

last: Wang

state: Henan

address: No.1 Jianshe East Road, Jinshui District

institute: First Affiliated Hospital of Zhengzhou University

summary: The breast cancer prognosis remains challenging, with an increased zinc level reported in some breast tumor tissue. This study investigated the impact of a zinc chelator, (9-anthrylmethyl) bis(2-pyridylmethyl) amine (APA) on breast cancer cells both in vitro and in vivo. We report that APA application inhibits breast cancer cell proliferation and zinc metabolism. Our RNA-seq analysis demonstrated that APA treatment influenced cell cycle progression and division by downregulating DNA synthesis and DNA damage repair processes. Further, qPCR and western blot analyses showed that the mRNA and protein expression of cyclins were downregulated by APA application. Interestingly, the addition of zinc chloride (Zncl2) did not decrease APA toxicity but instead significantly enhanced its’ effect. Furthermore, the zinc exporter, slc30a1, was upregulated after APA treatment. By using Fluozin3 staining, we detected that zinc concentration in the cytoplasm of SLC30A1 knockdown MDAMB231 cells was significantly elevated. Moreover, the reduction of slc30a1 enhanced the APA inhibitory effect on MDAMB231 cells in vitro. Finally, we found that APA combined with slc30a1 blockage significantly suppressed MDAMB231 tumor growth in a xenograft mouse model. Overall, this study suggests that APA disrupts cellular zinc metabolism. Combination with APA and slc30a1 inhibition providing a promising clinical approach for breast cancer treatment.

overall_design: MDAMB231 cells were treated with DMSO or APA (40 μM) for 24 h

first: Fei

first: Yongjuan

first: Chen

last: Ni

first: Xixi

last: Duan

first: Xiaohan

last: Luo

first: Yaping

last: Gao

first: Ming

first: Yanru

last: Qin

first: Zhihai


title: Sustained-release anti-JUN therapeutic abrogates post-operative adhesions

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

institute: Stanford University

summary: Post-operative abdominal adhesions are the leading cause of bowel obstruction and a major cause of chronic pain and infertility. Further, adhesion formation complicates any re-operative strategy, increasing the length of surgery and rendering a safe minimally invasive approach impossible. Despite the prevalence of abdominal adhesions, which form following 50-90% of abdominal operations, no proven preventative or treatment strategy has been developed. Our group previously established a mouse model to study adhesive disease in vivo and explored adhesion biology across mouse and human tissues. We established that adhesions derive primarily from the visceral peritoneum, are composed of poly-clonally proliferating tissue-resident fibroblasts, and identified that modulation of JUN signaling regulates abdominal adhesiogenesis following surgery. We identified a small molecule JUN inhibitor (T-5224) that decreases adhesion formation. Here, we encapsulated T-5224 in a shear-thinning hydrogel with anti-adhesion properties for intra-peritoneal delivery and sustained-release for post-operative adhesion prevention. We extensively characterized this novel therapeutic system, and found it to be safe, systemically well-tolerated, and efficacious in reducing adhesions in our mouse model. Furthermore, this therapeutic system minimizes not only the quantity of adhesions that form, but also limits the maturation of adhesion fibrosis at an ultrastructural level. Critical towards clinical translation, we developed a large mammal (porcine) preclinical model of adhesions with bowel resection and showed that the T-5224-hydrogel therapeutic provides robust adhesion prevention without deleterious effects on bowel anastomosis or abdominal wall (laparotomy) wound healing. At a single-cell transcriptomic level, treated fibroblasts in our pig model show decreased JUN and associated pathway signaling. Adhesion biology shares close similarities across surgical sites (e.g. thoracic, joint space, neurological); as such, this formulation has significant potential for applicability across the body. Material properties of the T-5224-hydrogel formulation, such as shear-thinning and self-healing, also facilitate ease of open or minimally invasive application. Therefore, these results are promising for immediate and high-impact translation to patient care to address a common, unmet clinical need.

overall_design: scRNA-seq of unsorted cells from pig abdominal adhesios specimens either treated with T-5224-hydrogel or untreated controls

first: Deshka

middle: S

last: Foster

first: Daniel

last: Delitto


title: Small molecule inhibitor combination treatment effectively represses global B-cell signaling in diffuse large B-cell lymphoma

city: Nijmegen

first: Melde

last: Witmond

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

summary: Cells sense their environment via signaling networks and malignant cells often hijack signaling pathways for their growth, which complicates defining the effects of drugs. Here, we map the state of the signaling network of B-cell lymphoma cells via simultaneous quantification of 111 (phospho-)proteins. We demonstrate that the B-cell signaling network can be disrupted with specific clinical small molecule inhibitors (iBTK, iSYK, iNFκB), thereby inducing a repressed state of the network. Principal component analysis identifies how the three inhibitors work along subtly different repression axes through the signaling state landscape. Finally, we observe that 1 µM combination treatment with all three inhibitors is more effective in inducing the repressed state than 10 µM of the single inhibitors. These results emphasize that cellular signaling occurs in complex networks, and underscore how quantification of the signaling state landscape provides insights into how combination drug treatments can bring cells in a desired network state.

overall_design: We performed comprehensive ID-seq experiments to define a DLBCL-specific signaling state landscape. The HBL1 cell line (RRID: CVCL_4213) was used as model for ABC-DLBCL. Cells were treated with different doses and combinations of the inhibitors ibrutinib (iBTK), R406 (iSYK), and QNZ (iNFkB) for 60 min (0, 0.1, 1, 10, 100 uM) and subsequently activated with anti-Ig + hydrogen peroxide for 20 min (triplicate samples). Samples were then measured with ID-seq to quantify 111 intracellular (phospho-)proteins.

first: Babet

last: Bollen

first: Pam

last: Heijmans

first: Annemiek

last: van Spriel

first: Jessie

last: van Buggenum

first: Wilhelm

last: Huck


title: The brain endothelial cell translatome analysis in the visual cortex at plastic and nonplastic ages

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

summary: In this study, we provide the translatome data in the brain endothelial cells (BECs) of the visual cortex at 3 different time points (pre-critical period (P10), critical period (P30), post-critical period (P100)) by using translating ribosome affinity purification (TRAP) combined with high-throughput RNA sequencing analysis in Tie2-Cre:Ribo-Tag mice, which are designed for expressing hemagglutinin A (HA)-tagged RPL22, a ribosomal protein in endothelial cells depending on CRE recombinase. To obtain a high-quality BEC pool, we modified the TRAP method by adding the capillary isolation process before the immunoprecipitation step and finally verified BEC-specific translating mRNA purification using RT-PCR.

overall_design: The translatomic profiles of brain endothelial cells obtained from the visual cortex of mice at three different developmental stages (P10, P30, and P100).

first: Won-Jong

last: Oh

first: Namsuk

last: Kim

first: Mi-Hee

last: Jun


title: pTDP-43 levels correlate with cell type specific molecular alterations in the prefrontal cortex of C9orf72 ALS/FTD patients

city: Atlanta

first: Hsiao-Lin

middle: V.

last: Wang

state: GA

address: 615 Michael Street,, Whitehead Biomedical Research Building, Room 355,

department: School of Medicine, Department of Human Genetics

institute: Emory University

summary: Repeat expansions in the C9orf72 gene are the most common genetic cause of amyotrophic lateral sclerosis and familial frontotemporal dementia (ALS/FTD). To identify molecular defects that take place in the dorsolateral frontal cortex of patients with C9orf72 ALS/FTD, we compared healthy controls with C9orf72 ALS/FTD donor samples staged based on the levels of cortical phosphorylated TAR DNA binding protein (pTDP-43), a neuropathological hallmark of disease progression. We identified distinct molecular changes in different cell types that take place during FTD development. Loss of neurosurveillance microglia and activation of the complement cascade take place early, when pTDP-43 aggregates are absent or very low, and become more pronounced in late stages, suggesting an initial involvement of microglia in disease progression. Reduction of layer 2-3 cortical projection neurons with high expression of CUX2/LAMP5 also occurs early, and the reduction becomes more pronounced as pTDP-43 accumulates. Several unique features were observed only in samples with high levels of pTDP-43, including global alteration of chromatin accessibility in oligodendrocytes, microglia, and astrocytes; higher ratios of premature oligodendrocytes; increased levels of the noncoding RNA NEAT1 in astrocytes and neurons, and higher amount of phosphorylated ribosomal protein S6. Our findings reveal previously unknown progressive functional changes in major cell types found in the frontal cortex of C9orf72 ALS/FTD patients that shed light on the mechanisms underlying the pathology of this disease.

overall_design: Nuclei were isolated from post-mortem brain samples from the dorsolateral prefrontal cortex (DLPFC) of C9orf72 ALS/FTD patients and control patients, followed by single-nucleus multiome library preparation and sequencing.

first: Victor

middle: G

last: Corces


title: Expression changes in the XY fetal gonads due to iron deficiency

status: Public on Feb 05 2025

city: Suita

first: Naoki

last: Okashita

address: 1-3 Yamadaoka

country: Japan

institute: Osaka university

summary: Iron plays an important role in epigenome regulation by acting as a cofactor.We developed a method to enrich pre-Sertoli (Nr5a1 positive(+)) cells from mouse embryonic gonads carrying Nr5a1-hCD271 transgene. To examine mRNA expression in pre-Sertoli cells treated with the iron chelator Deferoxamine (Dfo), pre-Sertoli cells were purified and introduced into RNA seq analyses. As a result, we found that the expression of many genes, including Sry, changes due to iron deficiency.

overall_design: RNA-seq profile of XY/XX gonads cultured in medium with/without Dfo.

first: Ryo

last: Maeda

first: Makoto

last: Tachibana


title: mRNA stability factor HuR promotes immune evasion in pancreatic ductal adenocarcinoma [RIP-seq]

city: Portland

first: Yifei

last: Guo

address: 2730 S Moody Ave

institute: Oregon Health & Science University

summary: The limited infiltration of tumor-specific T cells into the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME) is hypothesized to limit immunotherapy responses. The RNA-binding protein, HuR (ELAVL1), is over-abundant in PDAC, and its expression negatively correlates with T cell infiltration. In the immunocompetent Kras-p53-Cre (KPC) model, we found HuR depletion impairs tumor growth. To investigate the impact of the immune cells on tumor growth, we analyzed the infiltrated immune population in tumors and found that HuR-depleted tumors had increased T cell infiltration and activation. Mechanistically, HuR mediated stabilization of mTOR pathway and enhanced PDAC nutrient consumption, which impaired local T-cell antitumor function. We found that HuR suppression of antitumor immunity has profound consequences, as HuR-deficient tumors are sensitive to immune checkpoint blockade, while isogenic, wildtype tumors are resistant. These findings describe a novel role of HuR in PDAC facilitating tumor immune suppression in the PDAC TME by inhibiting T cell infiltration and function.

overall_design: RIP-seq profiling of HuR-binding transcripts in KPC8069 cells.

first: Jonathan

middle: R

last: Brody

first: Robert

last: Eil


title: mRNA stability factor HuR promotes immune evasion in pancreatic ductal adenocarcinoma

overall_design: RNA-seq profiling of wildtype KPC8069 cells and their HuR knockout derivatives.

first: Jennifer

last: Finan


title: Discrimination of initiator tRNA and start codon by mammalian mitochondrial initiation factor 3 in leaderless mRNA translation

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

institute: RIKEN

summary: The mammalian mitochondrial protein synthesis system produces thirteen essential subunits of oxidative phosphorylation (OXPHOS) complexes. Translation initiation in mammalian mitochondria is characterized by the use of leaderless mRNAs and non-AUG start codons, where the proofreading function of IF-3mt still remains elusive. Here, we developed a reconstituted mammalian mitochondrial translation system using in vitro transcribed and native mitochondrial tRNAs to investigate IF-3mt’s proofreading function. Similar to bacterial IF-3, IF-3mt permits initiator tRNA to participate in initiation by discriminating the three G-C pairs in its anticodon stem, and the cognate interaction of its anticodon with the AUG start codon. As a result, IF-3mt promotes the accurate initiation of leaderless mRNAs. Nevertheless, IF-3mt can also facilitate initiation from the non-AUG(AUA) start codon through its unique N- and C-terminal extensions in concert with the 5-methylcytidine (m5C) or 5-formylcytidine (f5C) modification at the anticodon wobble position of mt-tRNAMet. This is partly because the IF-3mt-specific N- and C-terminal extensions and the KKGK-motif favor leaderless mRNA initiation and relax non-AUG start codon discrimination. Analyses of IF-3mt-depleted cells revealed that, in human cells, IF-3mt indeed participates in translating the ORFs of leaderless mRNAs, as well as the internal ORFs of bicistronic mRNAs.

overall_design: Ribo-Seq and RNA-Seq were performed in Naïve and IF-3mt KO HEK293 cells.

first: Muhoon

last: Lee

first: Qimin

last: Jia

first: Chang

last: Liu

first: Ruiyuan

last: Huang

first: Shuai

first: Asuteka

last: Nagao

first: Tsutomu

last: Suzuki

first: Kozo

last: Tomita

first: Shintaro

last: Iwasaki

first: Nono

last: Takeuchi-Tomita


title: Interaction of the endogenous antibody response with activating FcgRs enhance control of Mayaro virus through monocytes

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Mayaro virus (MAYV) is an emerging arbovirus. Previous studies have shown antibody Fc effector functions are critical for optimal monoclonal antibody-mediated protection against alphaviruses; however, the requirement of Fc gamma receptors (FcgRs) for protection during natural infection has not been evaluated. Here, we showed mice lacking activating FcgRs (FcRg-/-) developed prolonged clinical disease with more MAYV in joint-associated tissues. Viral clearance was associated with anti-MAYV cell surface binding antibodies rather than neutralizing antibodies. Lack of Fc-FcgR engagement increased the number of monocytes through chronic timepoints. Single cell RNA sequencing showed elevated levels of pro-inflammatory monocytes in joint-associated tissue with increased MAYV RNA present in FcRg-/- monocytes and macrophages. Transfer of FcRg-/- monocytes into wild type animals was sufficient to increase virus in joint-associated tissue. Overall, this study suggests that engagement of antibody Fc with activating FcgRs promotes protective responses during MAYV infection and prevents a pro-viral role for monocytes.

overall_design: Mice were infected with 10^3 FFU of MAYV and, at 10 dpi, mice were sacrificed, perfused with PBS, and the ipsilateral feet were dissociated into a single cell suspension, as described above. Cells were stained with anti-CD45 BUV395 (BD Biosciences clone 30-F11; 1:200) and a viability dye. Viable, unfixed, CD45+ or CD45- cells were sorted on a BD FACSAria into RPMI supplemented with 10% FBS. Sorted CD45+ immune cells were centrifuged and resuspended in 1X PBS with BSA 0.04% to analyze using scRNA-seq.

first: Megan

last: Dunagan

first: Nathânia

last: Dábilla

first: Colton

last: McNinch

first: Jason

last: Brenchley

first: Patrick

middle: T

last: Dolan

first: Julie

last: Fox


title: Akkermansia muciniphila outer membrane protein Amuc_0904  promotes goblet cell differentiation

city: 天津市

first: Liu

last: yang

state: 天津市

address: qixiangtai Road

institute: Tianjin medical university

summary: Akkermansia muciniphila is recognized as a promising probiotic that improves the symptoms of a variety of diseases. However, the role and mechanism of A. muciniphila in regulating intestinal homeostasis remain to be explored. Here, we discovered that A. muciniphila was dramatically increased during colitis recovery, and its colonization greatly increased goblet cells to protect the intestinal barrier in mice. Amuc_0904, a previously uncharacterized A. muciniphila outer membrane protein, was identified to induce goblet cell differentiation.

overall_design: Total RNA was extracted from HT-29 cells using TRIzol Reagent according the manufacturer’s instructions. The RNA quality was determined using a 2100 Bioanalyser (Agilent), and the RNA concentration was quantified using the ND-2000 (NanoDrop Technologies). RNAseq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA). Paired-end RNAseq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2×150 bp read length) according to the standard protocols by Majorbio Bio-Pharm Technology Co. Ltd. The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml). The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.


title: Comprehensive Single-Cell Chromatin and Transcriptomic Profiling of Peripheral Immune Cells in Non-Segmental Vitiligo

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

summary: This study integrates single-cell RNA and ATAC sequencing to profile peripheral immune cells in nonsegmental vitiligo, providing insights into systemic immune dysregulation.

overall_design: We performed scRNA-seq and scATAC-seq on peripheral blood mononuclear cells (PBMCs) isolated by Ficoll-Paque density gradient centrifugation from vitiligo patients and healthy controls.

first: Jesus

last: Gay-Mimbrera

first: Juan

last: Ruano


title: Early transcriptomic changes at the skin interface during Powassan virus transmission by Ixodes scapularis ticks

city: Syracuse

first: Saravanan

last: Thangamani

state: New York

address: 505 Irving Ave

institute: SUNY Upstate Medical University

summary: Powassan virus (POWV), a vector-borne pathogen transmitted by Ixodes ticks in North America, is the causative agent of Powassan encephalitis. As obligate hematophagous organisms, ticks transmit pathogens like POWV at the tick bite site, specifically during the initial stages of feeding. Tick-feeding and salivary factors modulate the host's immunological responses, facilitating blood feeding and pathogen transmission. However, the mechanisms of immunomodulation during POWV transmission remain inadequately understood. In this study, we investigated the global cutaneous transcriptomic changes associated with tick bites during POWV transmission. We collected skin biopsies from the tick attachment sites at 1-, 3-, and 6-hours post-feeding by POWV-infected and uninfected ticks, followed by RNA sequencing of these samples. Differentially expressed genes were analyzed for pathway enrichment using gene ontology and pathway enrichment analyses. Our findings reveal that tick feeding alone significantly impacts the skin transcriptome within the first 1 to 3 hours of tick attachment. Although early POWV transmission induces minimal changes in the local environment, a pronounced shift toward a proinflammatory state is observed 6 hours post tick attachment, characterized by neutrophil recruitment and interleukin signaling. These transcriptomic data elucidate the dynamic changes at the tick bite site, transitioning from changes that assist blood meal acquisition to a proinflammatory phase that may facilitate viral dissemination.

overall_design: Either POWV infected ticks, or uninfected ticks were allowed to feed on the backs of BALB/C mice for 1, 3, or 6 hours. After that time frame, the bite sites were collected in 4mm biopsies, and processed for RNA sequencing.

first: Dakota

last: Paine

first: Meghan

last: Hermance


title: Real-time quantitative PCR analysis of EV-containing miRNA from human adipocytes SGBS cells

city: Marseille

first: Lourdes

last: Mounien

address: 27 Boulevard Jean Moulin

institute: Aix Marseille University

summary: Mature adipocytes were pretreated with VD for 24h and/or treated with TNFα during 24h. EVs released by adipocytes after TNF treatment were isolated and the miRNAs contained in it were extracted for qPCR analysis.

overall_design: An equal volume of culture media was used to isolate EV and process to miRNA extraction according to manufacturer protocol (Qiagen)

first: Thomas

last: Payet

first: Julien

last: Astier

first: Lorrine

last: Bournot

first: Flavie

last: Sicard

first: Stéphane

last: Robert

first: Romaric

last: Lacroix

first: Martin

last: Wabitsch

first: Jean-François

last: Landrier


title: Gut microbe-derived short-chain fatty acids regulate joint inflammation and osteoclast activation after alphavirus infection

first: Michael

middle: S.

last: Diamond

state: MO

address: 425 S. Euclid Ave

department: Immunology and Pathology

institute: Washington University School of Medicine

summary: Although oral antibiotics can predispose to joint inflammation, this phenomenon remains poorly understood. Here, we leverage mouse models of alphavirus arthritis to investigate the gut commensals, metabolites, and host mechanisms that promote musculoskeletal inflammation. Mice treated with a short course of oral antibiotics exhibited worsened arthritis after chikungunya virus (CHIKV) infection. This phenotype was associated with loss of short chain fatty acids (SCFA) and greater intestinal permeability, and required TLR4 signaling, MyD88 expression, monocytes, antigen-specific and bystander CD4+ T cells, and pro-inflammatory cytokines. Administration of exogenous SCFA or colonization of mice with bacterial species that generate SCFA mitigated CHIKV-induced joint inflammation. Single cell RNA sequencing revealed that gut-derived SCFA restrain the inflammatory phenotype of synovial CD4+ T cells and limit activation of monocytes and osteoclast-like cells. Thus, antibiotic-triggered gut dysbiosis exacerbates alphavirus arthritis by shaping the inflammatory profile of both infiltrating and resident immune cells in joint tissues.

overall_design: 3-4-week-old mice were treated with either water, antibiotics (vancomycin and ampicillin [AV]), AV supplemented with propionate, or AV after CD4+ T cell depletion (4 mice per group), prior to infection with Mayaro virus. At 5 days post infection, tissues from the ipsilateral feet were grossly dissected and single cell suspensions were obtained. Cells were labeled with TotalSeq anti-mouse hashtag antibodies (one distinct hastag per mouse sample in each group) and fluorescently conjugated antibodies against cell surface antigens, and individual samples were pooled according to experimental treatment group. CD4+ T cells and myeloid cells were then sorted, pooled by experimental group, and submitted for single cell RNA sequencing.

first: Fang

last: Zhao

first: Maksim

last: Kleverov

first: Emma

last: Winkler

first: Russell

middle: B

last: Williams

first: Hana

last: Janova

first: Lindsay

last: Droit

first: Leran

last: Wang

first: Ting-ting

last: Li

first: Leah

last: Heath

first: Ana

last: Jung

first: Matthias

last: Mack

first: Megan

last: Baldridge

first: Thaddeus

last: Stappenbeck

first: Larissa

last: Thackray

first: Chyi-Song

last: Hsieh

first: Scott

middle: A

last: Handley

first: Chun-Jun

last: Guo

last: Fischbach

first: Maxim

middle: N

last: Artyomov


title: Identification of Transcriptional Regulators and Signaling Pathways Mediating Postnatal Rumen Growth and Functional Maturation in Cattle

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 175 W Campus Dr

department: School of Animal Sciences

institute: Virginia Tech

summary: The rumen plays an essential role in ruminant digestion, absorption, metabolism, and health. The rumen undergoes substantial changes in size and function from birth to adulthood. The molecular mechanisms underlying these changes are not fully understood. This study was aimed to identify the transcription factors and signaling pathways mediating these changes in cattle. We used 6 neonatal bull calves and 6 adult steers, all Angus-crossbred, in this study. We found that the ratios of the emptied rumen, reticulum, omasum, and abomasum to total body weight in adult steers were 4.8 (P < 0.01), 3.1 (P < 0.01), 6.0 (P < 0.01), and 0.8 (P = 0.9) times those in neonatal calves, respectively. Histological examinations showed a 7.4-, 2.0-, 3.0-, 2.9-, and 4.6-fold increase (P < 0.01 for all) in the length of the rumen papillae and the thickness of the rumen epithelium, tunica mucosa and submucosa, tunica muscularis, and tunica serosa, respectively, from neonatal calves to adult steers. Papilla density was lower in adult steers than in neonatal calves (P < 0.05). The size of the rumen epithelial cells was not different between neonatal calves and adult steers (P = 0.57). RNA sequencing identified 2,906 genes differentially expressed (adjusted P < 0.05 and |log2fold change| ≥ 1) in the rumen between neonatal calves and adult steers, of which 1,586 were downregulated and 1,320 upregulated in adult steers. Bioinformatic analyses indicated organ development and morphogenesis, neuronal differentiation, blood vessel development, Ras signaling, and Wnt signaling were among the functional terms enriched in genes downregulated in adult steers, while fatty acid metabolism, ketogenesis, immune responses, PPAR signaling, and Rap1 signaling were among those enriched in genes upregulated in adult steers. Bioinformatic analyses also indicated that SRF, IRF4, SPI1, ETS1, and PURA were the major transcription factors mediating gene upregulation and that TCF4, MESP1, TCF3, ID4, and SNAI2 were the major transcription factors mediating gene downregulation in the rumen from neonatal calves to adult steers. Taken together, these results suggest that the rumen grows by increasing the number, not by the size, of individual cells from birth to adulthood, that the absorptive, metabolic, immune, and motility functions of the rumen are attained or enhanced during the postnatal life, and that the changes in rumen size and function from birth to adulthood are mediated by many transcription factors including SRF and TCF4 and many signaling pathways including the PPAR and Wnt signaling pathways.

overall_design:
To investigate the gene expression profile, signalling pathways and transcription factors that are responsible for mediating the postnatal rumen growth in cattle
We performed RNA-seq on rumen tissues from four newborn calves and four adult steers to analyze their comparative gene expression profiles.
We then identified the signaling pathways and transcription factors responsible for the differentially expressed genes based on the gene expression data.

first: Binod

last: Pokhrel

first: Zhendong

last: Tan


title: Nanostructured Lipid Carriers based mRNA vaccine leads to a T cell–inflamed tumor microenvironment favorable for improving PD-1/PD-L1 blocking therapy and long-term immunity in a cold tumor model

city: La Tronche

first: Carole

last: Fournier

address: Site Santé - Allée des Alpes

institute: Institute for Advanced Biosciences

summary: Using RNA-seq analysis, we have described the impact of a mRNA based vaccine on intratumoral immune-related transcriptional signature in a B16-OVA cold model

overall_design: After euthanasia of the mice, B16-OVA tumors were collected and immediately frozen in liquid nitrogen. Tumors were sent to BGI genomics in dry ice where extraction of total RNA and bulk RNA-seq were performed.

first: Christine

last: Charrat

first: Patrice

last: Marche


title: HMGA1 acts as an epigenetic gatekeeper of ASCL2 and Wnt signaling during colon tumorigenesis [RNA-seq]

city: Baltimore

first: LI

last: LUO

address: 720 Rutland Ave, Ross Build

department: Hematology

institute: Johns Hopskins University

summary: Mutated cells undergo changes in chromatin accessibility and gene expression, resulting in aberrant proliferation and differentiation, although how this occurs is unclear.  HMGA1 chromatin regulators are abundant in stem cells and oncogenic in diverse tissues; however, their role in colon tumorigenesis is only beginning to emerge.  Here, we uncover a previously unknown epigenetic program whereby HMGA1 amplifies Wnt signaling during colon tumorigenesis driven by inflammatory microbiota and/or Adenomatous polyposis coli (Apc) inactivation.  Mechanistically, HMGA1 “opens” chromatin to up-regulate the stem cell regulator, Ascl2, and downstream Wnt effectors, promoting stem and Paneth-like cell states while depleting differentiated enterocytes.  Loss of just one Hmga1 allele within colon epithelium restrains tumorigenesis and Wnt signaling driven by mutant Apc and inflammatory microbiota.  However, HMGA1 deficiency has minimal effects in colon epithelium under homeostatic conditions.  In human colon cancer cells, HMGA1 directly induces ASCL2 by recruiting activating histone marks.  Silencing HMGA1 disrupts oncogenic properties, whereas re-expression of ASCL2 partially rescues these phenotypes.  Further, HMGA1 and ASCL2 are co-expressed and up-regulated in human colorectal cancer.  Together, our results establish HMGA1 as an epigenetic gatekeeper of Wnt signals and cell state under conditions of APC inactivation, illuminating HMGA1 as a potential therapeutic target in colon cancer.

overall_design: Comparative single cell RNAseq data for enriched colon crypt cells from CDX2P-CreERT2Apcfl/fl Hmga1+/+,CDX2P-CreERT2Apcfl/fl Hmga1+/- or CDX2P-CreERT2Apcfl/fl Hmga1-/- mice.

first: Li

middle: Z

last: Luo

first: Linda

last: Resar

first: Leslie

last: Cope

first: Cynthia

last: Sears


title: Beclin 1 prevents ISG15-mediated cytokine storms to secure fetal hematopoiesis and survival

city: Suzhou

first: Wen

last: Wei

state: Jiangsu Province

address: No. 199, Ren Ai Road

institute: Soochow University

summary: Proper control of inflammatory responses is essential for embryonic development, but the underlying mechanism is poorly understood. Here, we show that under physiological conditions, inactivation of ISG15, an inflammation amplifier, is associated with the interaction of Beclin 1 (Becn1), via its ECD domain, with STAT3 in the major fetal hematopoietic organ of mice. Conditional loss of Becn1 caused sequential dysfunction and exhaustion of fetal liver hematopoietic stem cells, leading to lethal inflammatory cell-biased hematopoiesis in the fetus. Molecularly, the absence of Becn1 resulted in the release of STAT3 from Becn1 tethering and subsequent phosphorylation and translocation to the nucleus, which in turn directly activated the transcription of ISG15 in fetal liver hematopoietic cells, coupled with increased ISGylation and production of inflammatory cytokines, whereas inactivating STAT3 reduced ISG15 transcription and inflammation but improved hematopoiesis potential, and further silencing ISG15 mitigated the above collapse in the Becn1 null hematopoietic lineage. The Becn1-STAT3-ISG15 axis remains functional in Atg5/7-disrupted fetal hematopoietic organs. These results suggest that Becn1, in an autophagy-independent manner, secures hematopoiesis and survival of the fetus by directly inhibiting STAT3-ISG15 activation to prevent cytokine storms. Our findings highlight a previously undocumented role of Becn1 in governing ISG15 to safeguard the fetus.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for p-STAT3 (Tyr 705) in E14.5 Becn1-/- fetal livers.

first: Xueqin

last: Gao

first: Yixuan

last: Fang

last: Yuan

first: Jianrong

last: Wang


title: HMGA1 acts as an epigenetic gatekeeper of ASCL2 and Wnt signaling during colon tumorigenesis

overall_design: Comparative chromatin accessibility analysis of ATAC-seq data for enriched colon crypt cells from CDX2P-CreERT2Apcfl/fl Hmga1+/+,CDX2P-CreERT2Apcfl/fl Hmga1+/- or CDX2P-CreERT2Apcfl/fl Hmga1-/- mice.


title: Autonomous function of Antennapedia (Antp) in adult muscle precursors directly connects Hox genes to adult muscle development

city: Heidelberg

first: Katrin

last: Domsch

address: INF 230

department: COS - Developmental Biology

institute: Heidelberg University

summary: The evolutionarily conserved Hox genes define segment identities along the anterior-posterior axis and are expressed in most cell types within each segment, performing specific functions tailored to cellular needs. It has been suggested previously that Drosophila adult flight muscles in the second thoracic segment (T2) develop without direct Hox gene input, relying instead on ectodermal signals to shape their identity. However, our research, leveraging single-cell transcriptomics of Drosophila wing discs and Hox perturbation experiments using CRISPR technology and gain-of-function assays, unveiled a more intricate regulatory landscape. We found that the Hox protein Antennapedia (Antp) is essential for adult flight muscle development, acting in two critical ways: by regulating the cell cycle rate of adult muscle precursors (AMPs) through repression of proliferation genes, and by guiding flight muscle fate via regulation of Hedgehog (Hh) signalling during cell fate establishment. Antp, along with its cofactor Apterous (Ap), directly interacts with the patched (ptc) locus to control its expression in AMPs. These findings challenge the notion of T2 as a "Hox-free" zone, highlighting the indispensable role of low-level Antp expression in adult muscle development.

overall_design: to investigate the regulatory function of Antp in the adult muscle precursors (AMPs). We performed whole wing disc RNA-Seq in Antp AMP CRISPR conditions.

first: Aakriti

last: Singh

first: Ingrid

last: Lohmann


title: Transcriptomic profiling of Aurora Kinase B inhibition in lupus-prone mice

city: Nanjing

first: YUE

last: ZHAO

address: 305 East Zhongshan Road

institute: National Clinical Research Center of Kidney Diseases, Jinling Hospital

summary: Lupus nephritis (LN) is one of the most common and severe complications of systemic lupus erythematosus (SLE). Multitarget therapy (MT) has demonstrated a 20% higher rate of complete remission (CR) compared to conventional treatments for LN. Using a signature-based approach for drug repurposing, we identified and validated that the specific Aurora Kinase B (AURKB) inhibitor AZD1152 exhibits therapeutic efficacy comparable to that of MT therapy. To elucidate the therapeutic mechanism of AZD1152, we conducted transcriptome sequencing on renal tissues from MRL/lpr mice treated with AZD1152 and control vehicle. ,

overall_design: Bulk RNA-seq was performed on renal tissues from four MRL/lpr mice treated with AZD1152 and three MRL/lpr mice treated with vehicle.

first: Y

last: Zhao


title: SIV infection induces alterations in gene expression and loss of interneurons in Rhesus Macaque frontal cortex during early systemic infection

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

summary: We performed single nuclei transcriptomics frontal cortex samples of rhesus macaques 10- and 20-days post-SIV infection, compared to non-infected controls, to understand alterations of cell type specific neural transcriptomes during acute infection period.

overall_design: Fresh frozen postmortem frontal cortex samples from non-infected, 10-day post-infection, and 20-day post-infection rhesus macaques were used to generate single nuclei suspensions and the nuclei were processed for the 10x Genomics 3' gene expression assay v3.1.

middle: C

first: Richard

last: Crist

first: Dennis

middle: L

last: Kolson


title: Segment specific loss of NFAT5 function in the kidneys

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

summary: Nuclear factor of activated T-cells 5 (NFAT5) is a transcription factor known for its role in osmotic stress adaptation in the renal inner medulla, due to osmotic gradient that is generated between renal cortex and renal inner medulla. However, its broader implications in kidney injury and chronic kidney disease (CKD) are less understood. Here we used two different Cre deleter mice (Ksp1.3-Cre and Aqp2-Cre) to generate tubule segment and even cell type specific NFAT5 deficient mice in the principal cells of the collecting duct (CD) and in the distal nephron starting in the TAL up to the CD and performed extensive gene expression profiling. In both Nfat5 knockout models, we observed massive changes in gene expression pattern, with heightened inflammatory responses and renal injury, culminating in renal fibrosis. Interestingly, inflammatory responses and fibrosis were much more prominent in the Aqp2Cre+/-Nfat5fl/fl mice that lack NFAT5 only in the collecting duct. By analyzing gene expression in the medullary and cortical regions of the kidney separately, we confirmed that the loss of NFAT5 results in kidney injury that extends beyond hypertonic areas. The correlation between the levels of inflammatory response, injury severity, and fibrosis indicates that cytokines are key mediators of stress signals in the kidney. Thus, NFAT5 is essential not only for adapting to osmotic stress but also for regulating cytokine signaling.

overall_design:
To explore the impact of spatial Nfat5-KO, we compared transcriptomic data from two different Nfat5-KO mouse models and distinguished between cortex and inner medulla. The first transgenic model involved a knockout driven by the Aqp2-promoter, causing Nfat5-KO in the principal cells of the collecting duct (CD). The second model used a knockout driven by the Ksp-promoter, leading to Nfat5-KO in the distal nephron starting in the TAL up to the CD.
We performed differentially expression analyses using data from RNA-seq of renal cortex (CTX) and inner medulla (IM) of control mice (4 from Aqp2-Cre+/-; 4 from  Nfat5fl/fl, 4 from WT) and 6 from the  in the distal nephron (TAL up to the CD) Nfat5-KO mice (KspCre+/-Nfat5fl/fl). The RNA-seq data from Nfat5-KO in the principal cells of the CD (Aqp2Cre+/-Nfat5fl/fl) and control (Aqp2-Cre+/-) were collected in a previous study (GSE195881).

first: Kristina

last: Engel

first: Vera

last: Kulow

first: Dmitry

last: Chernyakov

first: Edith

last: Willscher

first: Michael

last: Fähling


title: Using RNA-seq to analyze gene expression in the mouse lens epithelial cells alpha-TN4 overexpressing Vector, WT-CREB, KCREB, R314A-CREB, S133A-CREB, S133A-KCREB and S133A/R314A -CREB before and after TGFβ treatment

city: Guangzhou

first: Lan

last: Zhang

address: Jinsui Road 7#

institute: 中山眼科中心

summary: CREB regulates lens EMT in both S133 phosphorylation dependent and independent manners. We found that S133A-CREB activated, while R314A-CREB attenuated lens mesenchymal marker gene Fn1 and Snail2. To better understand the mechanism by which S133A and R314A mutations modulate EMT gene expression. RNA-seq on the alpha-TN4 overexpressing Vector, WT-CREB, KCREB, R314A-CREB, S133A-CREB, S133A-KCREB and S133A/R314A -CREB before and after TGFβ treatment.

first: Jing-Miao

first: Ling

first: Shuyu

last: Zheng


title: Analyzing CREB binding motif and sites in the mouse lens epithelial cells alpha-TN4 overexpressing Vector, WT-CREB, S133A-CREB, R314A-CREB and S133A/R314A –CREB.

summary: Transcription factor CREB regulates lens Epithelial-Mesenchymal Transition（EMT）in both S133 phosphorylation dependent and independent manners. We found that S133A-CREB can activate lens EMT, while R314A-CREB attenuated it. To understand the mechanism by which S133A-CREB and R314A-CREB modulates EMT gene expression. ChIP assay using CREB antibody in the in the mouse lens epithelial cells alpha-TN4 overexpressing Vector, WT-CREB, S133A-CREB, R314A-CREB and S133A/R314A-CREB, and ChIP-seq was conducted on the ChIP DNA. We found that WT-CREB, S133A-CREB as well as R314A-CREB binds to the promoter regions of mesenchymal genes, and S133A-CREB retained canonical CREB binding motif, while R314A-CREB exhibited shifted binding motif preference to ATF1.

overall_design: Chromatin immunoprecipitation-DNA sequencing for CREB in in the mouse lens epithelial cells alpha-TN4 overexpressing Vector, WT-CREB, S133A-CREB, R314A-CREB and S133A/R314A –CREB.

last: Wang


title: Genotype-Driven Sensitivity in Mice to Tick-Borne Encephalitis Virus Correlates with Differential Host Responses in Peripheral Macrophages and Brain

city: Brno

first: Daniel

last: Růžek

address: Žerotínovo nám. 617/9

country: Czech Republic

institute: Masaryk University

summary: Tick-borne encephalitis (TBE) is the most common tick-borne viral infection in Eurasia, with outcomes ranging from asymptomatic to fatal encephalitis. While the reasons for this variability are unclear, host genetics likely plays a role. Our previous research showed that BALB/c mice have intermediate susceptibility to TBE virus (TBEV), STS mice are highly resistant, and the recombinant congenic strain CcS-11, which has 12.5% of the STS genome on the BALB/c background, is more susceptible than the BALB/c. In this study, we used these three mouse strains to investigate the host response to TBEV infection in both peripheral macrophages, one of the initial target cell populations, and in the brain, the terminal target organ for the virus.

overall_design: We analyzed 16 different RNA samples using Affymetrix Mouse gene 1.0 ST arrays extracted from virus-infected and mock-infected mouse brain homogenates.   For each mouse strain, RNA from 3 virus-infected mice and 2 or 3 mock-infected mice was examined on individual microarrays.

first: Michaela

last: Berankova

first: Jiri

last: Holoubek

first: Vaclav

last: Hönig

first: Zuzana

last: Matusova

first: Martin

last: Palus

last: Salat

first: Jaroslava

last: Vojtiskova

first: Lukas

last: Valihrach

first: Marie

last: Lipoldova

last: Ruzek


title: RPRD1B’s direct interaction with phosphorylated RNA Polymerase II regulates polyadenylation of cell cycle genes and drives cancer progression

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

summary:
RNA Polymerase II (Pol II) regulates eukaryotic gene expression through dynamic phosphorylation of its C-terminal domain (CTD). Phosphorylation at Ser2 and Thr4 on the CTD is crucial for RNA 3’ end processing and facilitating the recruitment of cleavage and termination factors. However, the transcriptional roles of most CTD-binding proteins remain poorly understood. In this study, we focus on RPRD1B, a transcriptional regulator that interacts with the phosphorylated CTD and has been implicated in various cancers. We investigated its molecular mechanism during transcription and found that RPRD1B modulates alternative polyadenylation of cell growth transcripts by directly interacting with the CTD. RPRD1B is recruited to transcribing Pol II near the 3’ end of the transcript, specifically in response to Ser2 and Thr4 phosphorylation, but only after flanking Ser5 phosphorylation is removed.
Transcriptomic analysis of RPRD1B knockdown cells revealed its role in cell proliferation via termination of the key cell growth genes at upstream polyadenylation sites, leading to the production of tumor suppressor transcripts that lack AU-rich elements (AREs) with increased mRNA stability. Overall, our study uncovers previously unrecognized connections between the Pol II CTD and CID, highlighting their influence on 3’ end processing and their contribution to abnormal cell growth in cancer.

overall_design: ChIP-Sequencing of RPB1-subunit of RNA Pol II, two biological replicates per sample (HEK293 cells).

first: Rosamaria

middle: Y

last: Moreno

first: Jessie