title: Diurnal glycogen metabolism drives rhythmic liver protein secretion [in vitro]

city: St Lucia

first: Benjamin

last: Weger

state: QLD

address: 306 Carmody Road

department: IMB

institute: University of Queensland

summary: The liver secretes most circulating proteins, which are critical for inter-organ communication and systemic energy homeostasis. However, the regulatory mechanisms governing hepatic protein secretion are largely unknown. Using proteomics approaches in humans and mice, we here demonstrate that hepatic protein secretion follows a 24-hour rhythm which is modulated by the timing of food intake. Rhythmic variations in the expression of secretory pathway proteins, involved in protein glycosylation and folding in the endoplasmic reticulum and Golgi apparatus, mediate this process. We find that feeding rhythms and the circadian clock protein BMAL1 regulate diurnal hepatic protein secretion by driving glycogen breakdown which generates glycosylation substrates. Rhythmic secretion was attenuated in a mouse model of obesity and affected by genetic variants associated with glycogen storage disease and congenital disorders of glycosylation. Our study reveals a mechanistic link between glycogen-derived metabolites and the protein secretion pathway, thereby connecting nutrient intake with fundamental liver functions.

overall_design: AML12 cells (300,000 cells/well) were seeded into sterile 6-well plates, and all washes were performed with 1x PBS. Treatments included 67 μM CP-91149 and vehicle (0.03% DMSO). Cell were collected at 3, 6, 14 and 24 h after treatment.

first: Meltem

first: Benjamin D.

first: Dominic

last: Hoyle

first: Frédéric

last: Gachon


title: Canine morbillivirus infection of primary alveolar macrophages provides insights into mechanisms of viral interference with innate immune defense responses

status: Public on Dec 02 2025

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

type: Expression profiling by high throughput sequencing

summary: Morbillivirus canis (formerly: canine distemper virus, CDV) is a highly contagious pathogen with a broad host range among carnivore species. During respiratory infection, alveolar macrophages (AMs) are among the first cell types facing the virus, which has previously been shown for measles virus infection. While AMs contribute to pulmonary homeostasis, they likewise bear great potential in establishing a pro-inflammatory environment once confronted with viruses. This study aimed to investigate cellular defense responses by AMs, allowing assumptions on early pathogenesis of CDV.

overall_design: Primary canine AMs were obtained by post mortem bronchoalveolar lavage. Cells were subsequently infected with CDV Onderstepoort (Ond), a broadly used vaccine strain, and the virulent strain CDV R252. Samples from 1 day post infection were used for bulk RNA sequencing.

first: Pauline

last: Poepperl

first: Andreas

last: Beineke


title: Single Cell Profiling of Chromatin Accessibility in Cotton Ovule Epidermis Durring Early Fiber Development [scATAC-seq]

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

country: USA

institute: The University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Each cotton seed has approximately 25,000 singular fiber cells, which account for 25-30% epidermal cells. Understanding the basis of fiber cell initiation is critical for cotton yield improvement. However, it is difficult to separate and study fiber and non-fiber cells. Here we developed a reliable single-cell protocol to study chromatin accessiblity in fiber and epidermal cells of developing ovules.  We analyzed over 4,000 nuclei derived predominately from the epidermal layer of ovules during early stages of fiber development.

overall_design: Whole ovules of Gossypium were collected and briefly digested using macerozyme and cellulase enzyme mix to release protoplasts from the epidermal surrface, including developing fiber cells. Ovules from Gossypium hirsutum TM1 at 0, 1 and 2 days post-anthesis, The protoplasts were purified using differential gradient centrifugation, lysed, and nuclei were then isolated and analyzed using via 10x scATAC sequencing.

first: Ryan

middle: C

last: Kirkbride

first: Zenjian

middle: J


title: The multimerization pathway of the glucocorticoid receptor

city: Bethesda

first: Thomas

middle: A

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

summary: We propose a model of the glucocorticoid receptor for a structural pathway to tetramerization.

overall_design: We use crystallography along with microscopy and transcriptomics to study oligomerization of the glucocorticoid receptor.

first: Andrea

last: Alegre-Martí

first: Alba

last: Jiménez-Panizo

first: Agustina

middle: L

last: Lafuente

first: Inés

last: Montoya-Novoa

first: Montserrat

last: Abella

first: Paloma

last: Pérez

first: Juan

last: Fernández-Recio

first: Diego

middle: M

last: Presman

first: Gordon

last: Hager

first: Pablo

last: Fuentes-Prior

first: Eva

last: Estébanez-Perpiñá


title: Diurnal glycogen metabolism drives rhythmic liver protein secretion [in vivo]

first: Benjamin

middle: D

last: Weger

country: Australia

overall_design: C57BL/6J mice (n=4 per treatment and timepoint) were exposed to 12-hour night-restricted feeding for four days before receiving a subcutaneous injection of CP-91149 (40 mg/kg; volume of 10 µl per g body weight) or vehicle at ZT0. Serum and liver tissues were collected at ZT3, ZT6, ZT9, ZT12, and ZT24.

first: Meltem

first: Benjamin D.

first: Dominic

last: Hoyle

first: Frédéric

last: Gachon


title: Multi-omics analyses integration reveals a novel TRF2-miR-181a-5p-S100A10 regulatory axis in colon cancer.

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

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

overall_design: Refer to individual Series


title: Multi-omics analyses integration reveals a novel TRF2-miR-181a-5p-S100A10 regulatory axis in colon cancer [ChIP-seq]

summary: The Telomeric repeat-binding factor 2 (TRF2) binds to TTAGGG repeats located at chromosomes ends and ensures telomere protection together with the other members of shelterin. In addition to its well-known role in telomere maintenance, TRF2 can also bind to interstitial telomeric sequences (ITS) and regulate the expression of specific genes with a consequent impact on tumor formation and progression. However, a comprehensive analysis of the impact of TRF2 on global gene expression of human cancer cells is still missing and underlying mechanisms of TRF2-mediated gene expression regulation remain to be further elucidated. Here, by performing RNA sequencing analysis, we found that TRF2 alters the expression of 717 genes involved in various cancer-related pathways. Unexpectedly, Chromatin immunoprecipitation sequencing analysis revealed, that just a small portion of Differentially Regulated genes (DEGs) are directly bound by TRF2, suggesting the existence of alternative mechanisms of TRF2-mediated gene regulation. In particular, we found that TRF2 binds to various non-coding RNA (ncRNAs) regions, including miRNA host genes. Moreover, interactomic analysis unveiled that RNA binding proteins are well represented among TRF2 interactors, supporting the involvement of TRF2 in ncRNAs-mediated mechanisms. Through the intersection of omics-analyses, we provided here  experimental evidence of a multilayered mechanism of regulation where TRF2, interacting with TATA-box binding protein associated factor 15 (TAF15), regulates miR181A1 host gene and mature miR-181a-5p expression, which in turn targets S100A10, a known plasma membrane with oncogenic role. Our work shows, for the first time, a broad overview on the extratelomeric role of TRF2 in human cancer revealing, at the same time, a new axis through which TRF2 contributes to cancer progression.

overall_design: ChIP-Seq analysis of HCT116 cells by using an antibody directed against TRF2

first: Roberto

last: Dinami

first: Eleonora

last: Petti

first: Sara

last: Iachettini

first: Angela

last: Rizzo

first: Carmen

last: Maresca

first: Pasquale

last: Zizza

first: Serena

last: Di Vito

first: Manuela

last: Porru

last: D'Angelo

first: Maurizio

last: Fanciulli

last: Chambery

first: Eric

last: Gilson

first: Annamaria

last: Biroccio


title: Multi-omics analyses integration reveals a novel TRF2-miR-181a-5p-S100A10 regulatory axis in colon cancer [RNA-seq]

overall_design: RNA-Seq profiling of shTRF2-infected HCT116 cells vs shControl. Each condition was run in triplicate


title: Deregulated miRNAs in Hutchinson-Gilford Progeria Syndrome: Unraveling the Link of miRNAs to normal and premature aging.

city: Garching bei München

first: Felix

middle: Quirin

last: Fenzl

address: Boltzmannstraße 11

institute: Technische Universität München

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare, fatal disorder causing premature aging, affecting about 1 in 4–8 million births. Most cases are linked to a mutation in the LMNA gene, which leads to the production of a defective protein called progerin. In HGPS, progerin expression leads to the loss of heterochromatin, which significantly alters gene expression. This alteration particularly affects RNA polymerase II, a crucial enzyme in transcribing primary-miRNA (pri-miRNA) transcripts. As a result, changes in RNA polymerase II activity lead to aberrant levels of miRNAs that are a common feature in age-related diseases, including HGPS, where they contribute to the disease phenotype and progression. In this study, we investigate the molecular mechanisms underlying HGPS and normal aging using global miRNA sequencing to identify differentially expressed miRNAs associated with aging and/or premature aging conditions.

overall_design: The sequencing was conducted on 3 control and three HGPS (carrying a mutation on LMNA Exon 11, heterozygous c.1824C > T (p.Gly608Gly)) primary dermal fibroblast cell strains at both a young passage with relative senescence below 5% and an older passage with senescence levels between 15% to 20%.

first: Eva-Maria

last: Lederer

first: Peter

last: Krüger

first: Karima

last: Djabli


title: Comparing different administration routes for mesenchymal stromal cell infusion in an in vivo porcine ischemia-reperfusion injury model

city: Rotterdam

first: Henk

middle: P.

last: Roest

state: Choose State

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: Erasmus MC

summary: Hepatic ischemia-reperfusion injury is a complex pathophysiological process that occurs following reperfusion of blood supply in previously ischemic tissues. This form of injury plays a major role in cell dysfunction and death following hepatic surgery and liver transplantation. Mesenchymal stromal cells (MSC) seem to be a promising option for mitigation of this type of injury, as they possess anti-inflammatory and immune modulating capacities that may stimulate liver regeneration. The aim of this study was to demonstrate safety, feasibility and effectiveness of direct hepatic administration of MSC for treatment of ischemia-reperfusion injury in a pig model. After total vascular exclusion of the liver for 45 minutes, 3x10^6 human bone-marrow derived (BM)-MSC/kg were directly administrated into livers either via the intraportal route or hepatic artery route, whereas the control group did not receive any BM-MSC. Following reperfusion, hepatic blood flow and pulmonary pressures were continuously measured. Samples of blood and tissue of spleen, lung, and liver were taken among groups at the end of follow-up. Injection of BM-MSC did not result in obstruction of hepatic blood flow or increased pulmonary artery pressures. Blood flow in the portal vein was higher following injection BM-MSC in comparison to baseline blood flow. Arterially infused BM-MSC were more equal distributed over the different areas of the liver in comparison to the portal vein infused group (p=0,04). No BM-MSC were detected in pulmonary circulation nor in biopsies of spleen and lung. These results show that infusing therapeutic quantities of BM-MSC directly in the vascular bed of the liver is safe and feasible. Regarding risks of thrombosis or embolism, no differences between the routes of admission was observed.

overall_design:
to investigate the feasability, saety and effectiveness of Mesenchymal Stromal Cells (MSCs) as an anti-inflammatory and immune-modulating moiety for liver regeneration after ischemia, pig livers were infused with human MSCs to discriminate infused cells from recipient cells..
Liver damage and loss-of-function was monitored in blood samples, and biopsies were taken at baseline (no ischemia) and 6 hours after a period of 45' of ischemia for expression profiling and histology.

first: Stef

middle: H

last: Luijmes

first: Job

middle: P

last: van Kooten

first: Kairon

last: Wang

first: Jorke

last: Willemse

first: Jubi

last: de Haan

first: Cornelia

last: Verhoeven

first: Luc

last: van der Laan

first: Monique

last: Verstegen

first: Jeroen

last: de Jonge


title: Transcriptional profile of the hippocampus from a polygenic obese mouse model compared to a reference mouse line

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

summary:
Obesity is often linked with low-level systemic inflammation. The polygenic mouse line DU6 has been selected for high body mass at 6 weeks of age for more than 180 generations. This mouse line does not develop diabetes despite pronounced obesity; the cellular and molecular mechanisms underlying this phenomenon remain unresolved.
Microarray analyses were conducted to profile the transcriptional signatures of hippocampi from the obesity mouse line DU6 versus a reference mouse line FztDU. Both lines are outbred mouse lines.

overall_design: The obesity mouse line and its reference mouse line were checked for immunological and behavioral differences.Since behavioral alterations in obesity have often been shown to be induced by hippocampal inflammation, transcriptional profiles of hippocampi of both mouse lines were analysed to detect inflammatory signatures.

first: Ulrike

last: Gimsa

first: Dirk

last: Koczan

first: Ellen

last: Kanitz

first: Armin

last: Tuchscherer


title: Loss of SIRT5 accelerates the development of pressure-overload induced heart failure upon dysregulating purine and pyrimidine metabolism

city: Birmingham

first: Sayan

last: Bakshi

state: Alabama

department: Department of Pathology

institute: University of Alabama at Birmingham

summary: Objectives: To explore how modulation of cardiomyocyte SIRT5 levels affects the development of pathological cardiac remodeling and dysfunction. Background: SIRT5 is a mitochondrial NAD+-dependent deacylase, which regulates metabolic enzymes upon desuccinylation, demalonylation, and deglutarylation. Its role in the development of heart failure is not completely understood. Methods: Mice with cardiomyocyte-specific Sirt5 deletion (Sirt5-/-) or Sirt5 overexpression (cSirt5-Tg) underwent transverse aortic constriction (TAC) or Sham surgery. Cardiac structure and function were assessed by echocardiography and quantification of myocardial fibrosis and cardiomyocyte cell size. Metabolomic analysis and RNA sequencing were performed to identify potential novel pathways regulated by SIRT5. Results: While cardiac structure and function were similar in cSirt5-Tg compared to control mice, cSirt5-/- mice displayed exacerbated cardiac dilation, dysfunction, and fibrosis following TAC. Accumulation of metabolites involved in purine metabolism, particularly inosine and hypoxanthine, and reductions in nucleosides, adenosine and adenine, and nucleotides, AMP and ADP, were observed in hearts of cSirt5-/- mice and following TAC. Moreover, transcriptional analysis revealed upregulation of purine-nucleoside phosphorylase (PNP) and 5' nucleotidase, ecto (NT5E) and downregulation of adenosine kinase (ADK), which is likely to contribute to enhanced degradation of purine nucleotides and resulting accumulation of inosine and hypoxanthine in hearts of cSirt5-/- mice following TAC. Lastly, reduced SIRT5 expression and protein succinylation in left-ventricular tissue of patients with heart failure correlates with reduced ADK expression. Conclusions: Loss of SIRT5 aggravates cardiac remodeling and dysfunction in response to chronic pressure-overload possibly by dysregulation of genes involved in purine and pyrimidine metabolism, resulting in impaired ATP regeneration from adenosine.

overall_design: All mice were housed with 12h daylight and night cycles at 22°C in individually ventilated cages in a specific pathogen free facility. Laboratory standard chow and water ad libitum were fed to all animals. Transgenic Sirt5 knockout (Sirt5-/-) mice were kindly provided by Johan Auwerx from the École Polytechnique Fédérale de Lausanne, Switzerland. David Lombard from University of Michigan, Ann Arbor, Michigan, USA kindly provided transgenic Sirt5 overexpressing (Sirt5-Tg) mice. Transgenic Sirt5-/- and Sirt5-Tg mice were crossed with hemizygote cardiomyocyte-specific recombinase expressing mice (Myh6-cre, Stock #011038, Jax) to generate cardiomyocyte-specific Sirt5 knockout (cSirt5-/-) and cardiomyocyte-specific Sirt5 overexpressing (cSirt5-Tg) mice, respectively. Recombinase non-expressing transgenic mice were used as controls.


title: Epigenetic profiling across hematopoietic stages identifies genomic loci with conserved chromatin alterations after infection

city: Houston

first: Pamela

last: Luna

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Infection leads to durable cell-autonomous changes in hematopoietic stem and progenitor cells (HSPCs), resulting in production of innate immune cells with heightened immune function. The mechanisms underlying this phenomenon, termed central trained immunity, remain poorly understood. We hypothesized that infection induces histone modifications in chromatin, leading to changes in chromatin accessibility that are passed down from HSPCs to myeloid progenitors, monocytes and macrophages. To test this hypothesis, we conducted genome-wide surveillance of activating histone marks H3K27Ac and H3K4me3 and transposon accessibility of chromatin in hematopoietic stem cells, multipotent progenitor 3, granulocyte-monocyte progenitors, monocytes and macrophages of naïve versus Mycobacterium avium infected mice. While activating histone marks and chromatin accessibility were increased broadly in biological responses to interferon and cytokine signaling. Consistent with this finding, transcription factor binding motifs related to interferon signaling, including IRFs, NF-kB, and CEBP, were highly enriched across cell types. However, activating histone marks and increased chromatin accessibility were commonly induced at only a few loci including Irf1 and Gbp6 across multiple stages of differentiation. In summary, processing of inflammatory signaling upon systemic infection leads to epigenetic changes in HSPCs, and these changes are conserved at a small number of genetic loci in downstream monocytes.

overall_design: To understand how the overall chromatin accessibility landscape is changed in myeloid cells and their progenitors upon M. avium infection, we performed single cell assay for transposase accessibility sequencing (scATAC-seq) on targeted HSPCs and downstream terminally differentiated cells, including Mo/Macs, neutrophils, and B cells, from pooled murine samples from M. avium infected and naïve mice.

middle: N

first: Brandon

middle: T

last: Tran

first: Katherine

middle: Y

last: King


title: Microbiome patterns analysis of Tuberculosis, Non-Tuberculous Mycobacteria and other respiratory patients

city: Asan

first: Jeong-An

last: Gim

address: 22 Suncheonhyang-ro

country: South Korea

institute: Soonchunhyang University

summary: Tuberculosis (TB) and non-tuberculous mycobacterial (NTM) infections, though clinically similar, require distinct management, highlighting the need for reliable biomarkers to differentiate them. In a study of 108 patients, 16S rRNA sequencing revealed distinct microbial signatures, with Enterococcus faecalis, Streptococcus mutans, and Snodgrassella alvi associated with TB, and Cardiobacterium hominis and Prevotella nigrescens linked to NTM. The absence of Mobiluncus curtisii, particularly with Olsenella phocaeensis also absent, suggested a higher probability of NTM, offering promising insights for diagnostic and therapeutic advancements.

overall_design: Total 38 patients with TB, 29 NTM, and 41 others samples were analyzed. All patients were selected by the Pulmonology Department at the Korea University Guro Hospital to undergo bronchoalveolar lavage fluid (BALF) collection for diagnostic purposes. 16S metagenomics sequencing was performed on 108 samples. The raw 16S amplicon sequences were processed by QIIME2 v1.8.0 with default parameters. Then, we obtained the abundance corresponding to each taxon.

first: Oh

last: Jee Youn

first: Ko

last: Young Kyung

first: Jeon

last: Min Ha

first: Gim

last: Jeong-An


title: STAT3 overexpression lentivirus infect human broncho epithelial cells

city: Chapel Hill

first: Ling

last: Sun

state: NC

address: 125 Mason Farm RD 7230K Marsico Hall 7230K Marsico Hall

institute: UNC at Chapel Hill

summary: To find the role of STAT3 in human broncho epithelial cell, we extracted RNA from HBE infected with NC, WTSTAT3 and MuSTAT3 overexpression lentivirus

overall_design: Gene expression profiling analysis was performed on RNA obtained from HBE infected with lentivirus

first: Hong

last: Dang

first: Gang

last: Chen


title: RPL6 interacts with HMGCS1 to stabilize HIF-1α by activating cholesterol biosynthesis in hepatocellular carcinoma II

city: Chongqing

first: Li

middle: Min

last: Yang

state: Chongqing

address: 1 Yixueyuan Road, Yuzhong District

country: China

institute: Chongqing Medical University

summary: The identification of predictive markers to determine the premetastatic phase before metastasis is critical for developing effective strategies for early detection and prevention. By applying the dynamic network biomarker (DNB) approach to analyze time-series transcriptomic data from a pulmonary metastasis HCC mouse model, we revealed that the premetastatic phase occurred during the fourth week after implantation. A total of 142 DNB genes were identified as functionally important biomarkers of this critical phase, among which 60S ribosomal protein L6 (RPL6) was a core DNB member. RPL6 was significantly upregulated in HCC tissues with extrahepatic metastasis and was strongly correlated with poor prognosis in HCC patients. RPL6 promoted the invasion and metastasis of HCC cells, both in vitro and in vivo. Mechanistically, RPL6 directly bound to the HMGCS1 mRNA 3’UTR, a rate-limiting enzyme in cholesterol biosynthesis, thus increasing HMGCS1 mRNA stability and protein expression and subsequently elevating intracellular cholesterol level. Elevated cholesterol inhibited of the ubiquitin-dependent degradation of HIF-1α by binding to PHD2 and reducing PHD2-mediated hydroxylation of HIF-1α, which further resulted in HIF-1α signaling pathway activation. Moreover, RPL6, HMGCS1 and HIF-1α were coexpressed in HCC tissues with extrahepatic metastasis. Taken together, this study provides new insights into the dynamic transcriptome profiles of HCC pulmonary metastasis and establishes an important role for the RPL6-HMGCS1-HIF-1α axis in HCC metastasis, suggesting potential prognostic biomarkers and therapeutic targets in HCC.

overall_design: To identify the critical state and driving genes during HCC metastasis process, we systematically monitored gene expression profiles at four stages in a pulmonary metastasis HCC mouse model, in which GFP-labeled MHCC97H cells with high metastatic potential were orthotopically transplanted into the livers of nude mice.

first: Minli

first: Dapeng

last: Zhang


title: RNA modifications, alternative splicing and circular RNA landscape in the mouse brain: inosine and beyond

city: Beijing

first: Erika

last: Larrea de Orte

state: Beijing

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

department: DNA & RNA Modifications

institute: Chinese Institute for Brain Research (CIBR)

type: Non-coding RNA profiling by high throughput sequencing


title: effects of depeltion of Tim-4 on gene expression in Peritoneal macrophages (PEMs)

city: Jinan

first: Wen

last: Liu

address: 6699 Qingdao Road

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

summary: T-cell immunoglobulin domain and mucin domain 4 (Tim-4) is known to suppress macrophage inflammatory responses in various diseases, but its role and underlying mechanism in peritoneal macrophage with LPS stimulation are unknown.

overall_design: Primary macrophage Peritoneal macrophages (PEMs) isolation from  Tim-4fl/fl mice and LysM-Cre; Tim-4fl/fl mice

first: Xiao

last: Wang

first: Fuxiang

last: Bai

first: Baohui


title: IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration [RNA-seq PDX]

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

summary: We have previously shown that IKKa coordinates the activation of several oncogenic and therapy-resistant pathways, including ATM/DDR, BRD4, and JAK/STAT3, independently of canonical NF-kB signaling. Here, we found that IKKa suppression, either genetically or pharmacologically, led to stabilization of ZO-1 protein and increased CLDN2 expression, resulting in altered tight junction distribution. IKKa KO cells showed a shift in their migratory mode towards collective migration, which is associated with superior metastatic capacity in vivo. Analysis of single-cell (sc)RNA-seq data from a mouse model of CRC revealed an accumulation of the tight junction signature, including ZO-1 and CLND2, in the metastatic populations. scRNA-seq analysis of patient-derived organoid (PDO5)  identified three distinct epithelial cell clusters (C2, C4 and C8) that show a significant enrichment for the metastasis-specific EpiHR signature and the tight junction signature. In particular, C2 and C8 display unique genetic signatures that are significantly upregulated in IKKa KO cells and enriched in the PDO5 IKKa KO-derived metastases. Analysis of human paraffin-embedded CRC specimens led to the identification of vascular tumor infiltrates with ZO-1 and CLDN2-positive cluster-like or glandular phenotypes. The concomitant presence of low CHUCK (IKKa)  and high TJP1 (ZO-1) RNA levels is sufficient to predict poor prognosis in CRC patients. These results suggest that the presence of collectively migrating cancer cells in the vascular infiltrates, characterized by high levels of tight junction proteins, could be standardized as a prognostic tool to predict metastasis. We anticipate the use of drugs targeting tight junction elements for metastasis prevention.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We analyzed bulk RNAseq samples obtained from hepatic metastasis (mouse PDX) derived from Patient Derived Organoid (Colorectal Tumoroid) in two different conditions: 3xWT untreated and 3xIKKa KO untreated.

first: Daniel

last: Alvarez-Villanueva

first: Mónica

last: Larrubia-Loring

first: María

last: Maqueda

first: Anna

last: Tramuns

first: Evelyn

last: Andrades

first: Teresa

last: Lobo-Jarne

first: Eric

last: Canton

first: Josune

last: Alonso-Marañón

last: Martínez-Iniesta

first: Luis

middle: G

last: Palma

first: Alberto

last: Villanueva

first: Mar

last: Iglesias

last: Bigas


title: IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration [RNA-seq Tumoroid]

overall_design: We analyzed bulk RNAseq samples obtained from Patient Derived Organoid (Colorectal Tumoroid) in two different conditions: 2xWT untreated and 2xIKKa KO untreated.


title: RPL6 interacts with HMGCS1 to stabilize HIF-1α by activating cholesterol biosynthesis in hepatocellular carcinoma

first: Li

last: Yang

overall_design: To investigate the underlying molecular mechanisms by which RPL6 promotes HCC metastasis, we first performed RNA sequencing (RNA-seq) analysis in RPL6 knockdown MHCC97H cells and control cells.

first: Minli


title: IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration


title: IKKa modulates colorectal cancer metastasis by preventing tight junction stabilization and collective cell migration [scRNA-seq]

overall_design: We analyzed 3x scRNAseq 10x samples obtained from Patient Derived Organoid (Colorectal Tumoroid) in three different conditions: 1xWT untreated, 1xIKKa KO untreated and 1xIKKa KO treated with CLDN2 inhibitor


title: Unmasking budgerigar splenic leukocyte populations with single cell transcriptomics

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: Budgerigar splenic leukocyte populations have not been examined yet. With single cell transcriptomics we aimed to identify the different immune subpopulations and compare the immune system of these psittacine birds with chickens.

overall_design: Splenocytes were isolated after an enzymatic digest of budgerigar spleen tissue, followed by a lymphoprep gradient centrifugation purification. Dead cells and cell aggregates were excluded from further analysis using FACS.

first: Anne

last: De Meyst

first: Niels

last: Vandamme

first: Daisy

last: Vanrompay


title: Multimodal Analysis of Human Submandibular Gland Offers Novel Insight into Gene Regulatory Networks that Characterize Homeostatic State

city: Buffalo

first: Rose-Anne

last: Romano

state: NY

address: Main Cir

institute: SUNY University at Buffalo

summary: Bulk ChIP-sequencing was performed on human submandibular glands looking at known epigenomic markers. Complementary transcriptomic analyses are performed at a bulk and single cell resolution using previously published datasets.

overall_design: The characterization of the epigenetic landscape of human salivary gland epithelial cells via histone modification ChIP-Seq

first: Erich

last: Horeth

first: Jonathan

last: Bard

first: Theresa

last: Wrynn

first: Jason

last: Osinski

first: Satrajit

last: Sinha


title: ROS activates NETs release of bone marrow CD55+ neutrophils to promote early bone aging

first: Yutong

last: Guo

address: No.22, Zhongguancun South Avenue, Haidian District, Beijing, 100081, PR China.

institute: Peking University

summary: Bone marrow neutrophils are highly heterogeneous cells and we used sing cell RNA-sequencing to analyze the diversity of BM neutrophils of SAMP6 and SAMR1 mice femur bone.

overall_design: Femour of 3-month male SAMP6 and SAMR1 mice were separately flushed out, and after lysing red cells, BM cells were analyzed by sc-RNA seq.


title: Single cell chromatin accessibility profiles of the chick embryonic ectoderm

city: London

first: Eva

last: Hamrud

address: Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Campus, Great Maze Pond

country: United Kingdom

institute: King's College London

summary: The embryonic ectoderm gives rise to four fates: neural, neural crest, placodal and epidermal. The derivatives of these fates give rise to the entire vertebrate nervous system and skin. To explore how these cell fates emerge, we profiled single cell chromatin accessibility in the chick embryonic ectoderm at five developmental timepoints.

overall_design: Ectoderm pieces was microdissected from chick (Gallus gallus) embryos at five developmental timepoints: HH5, HH6, HH7, ss4 and ss8.

first: Andrea

last: Streit


title: CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma (spatial)

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: Mutations in KRAS are a dominant driver of pancreatic ductal adenocarcinoma (PDAC), with over 40% of PDAC patients presenting with KRASG12D mutations. The recent development of small molecule inhibitors targeting KRASG12D, has enabled effective targeting of mutant KRAS signaling and suppression of PDAC; however, the contribution of the tumor microenvironment (TME) to the therapeutic efficacy of KRASG12D inhibition and mechanism/s of resistance to KRASG12D suppression remain to be elucidated. Here, we employed spatial transcriptomics and CODEX-based spatial proteomics to evaluate cancer cell intrinsic and extrinsic responses to KRASG12D inhibition with MRTX1133. MRTX1133 treatment was associated with increased CD11c+ cells, T cells, and tumor-restraining fibroblasts within proximity to cancer cells, suggesting that antigen presentation and remodeling of the local microenvironment is associated with an effective response to KRASG12D inhibition. In the context of emergence of MRTX1133 therapy resistance, CDK8, a multiprotein mediator complex associated kinase, was identified as a mediator of resistance in part through induction of downstream CXCL2 chemokine secretion, inhibition of FAS expression, and remodeling of the TME to promote immune evasion. Targeting CDK8 in combination with aCTLA-4 immunotherapy overcomes resistance to small molecule mediated targeted KRASG12D inhibition with prolonged survival of mice with PDAC.

overall_design: Pancreas tissue from mice treated with vehicle or MRTX1133 was collected in formalin and processed into paraffin blocks. HY19636 samples are orthotopic tumors and KC samples are from LSL-KrasG12D; Pdx1-Cre genetic models. 5 um thick sections were generated, stained with H&E, and scanned with an Zeiss Axio Scan.Z1.

first: Kathleen

last: McAndrews

first: Bingrui

last: Li

first: Raghu

last: Kalluri


title: RNA modifications, alternative splicing and circular RNA landscape in the mouse brain: inosine and beyond [RNA-seq]

first: Erika

last: Larrea de Orte

summary: RNA modifications, including adenosine-to-inosine (A-to-I) editing, are fundamental for normal brain physiology, as they participate in multiple biological processes and pathological conditions. These modifications can alter RNA secondary structures and affinity for RNA-binding proteins, thereby influencing RNA processing mechanisms such as alternative splicing. In this study, we investigated A-to-I RNA editing and its impact on alternative splicing regulation in the mouse brain using ADAR enzyme-deficient mice. We analyzed the brain transcriptome of ADAR2 knockout (Adar2−/−Gria2R/R), as well as double ADAR1 catalytically inactive / ADAR2 knockout (Adar1E861A/E861A Ifih−/− Adar2−/−Gria2R/R) mice compared to wild-type controls, identifying alternative splicing events associated with the absence of ADAR1 and ADAR2 specific A-to-I editing.

overall_design: Total RNA from whole brains from adult 3–4-month-old male mice was used for RNA-seq as described in the Methods section of this publication. Three biological replicates for each genotype were sequenced. ADAR2 knockout  (Adar2−/−Gria2R/R), double ADAR1 catalytically inactive/ADAR2 knockout (Adar1E861A/E861A Ifih−/−Adar2−/−Gria2R/R) and wild-type controls. All mice were C57BL/6J on a background.

last: Larrea

first: Maitena

last: Tellaetxe-Abete

first: Yan

last: Peng

first: Yujie

last: Zhang

first: Shuangshuang

last: Feng

first: Kaidong

last: Lu

first: Liang

last: Xue

first: Taisuke

last: Nakahama

first: Yukio

last: Kawahara

first: Magdalena

last: Koziol


title: CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma (scRNA)

overall_design: Orthotopic PDAC models (PKC-HY19636 or KPC689 resistant) were treated with vehicle, or the KRASG12D inhibitor MRTX1133 alone or in combination with aCTLA4 and/or CDK8i for the indicated timeframes. 2-3 pancreata/tumors were pooled per sample.


title: RNA modifications, alternative splicing and circular RNA landscape in the mouse brain: inosine and beyond [circRNA-seq]

summary: RNA modifications, including adenosine-to-inosine (A-to-I) editing, are fundamental for normal brain physiology, as they participate in multiple biological processes as well as in pathological conditions. These modifications can influence RNA secondary structure and alter affinity for RNA-binding proteins, thereby modulating RNA processing mechanisms such as backsplicing, which gives rise to circular RNAs (circRNAs). In this study, we investigated the impact of A-to-I editing on circRNAs in the mouse brain using Adar enzyme–deficient mice, as ADARs catalyze A-to-I RNA editing. We applied a self-developed protocol to sequence full-length circRNAs using Oxford Nanopore Technologies (ONT) and performed a comprehensive characterization of these molecules. In addition, Illumina sequencing was used to conduct a robust differential expression analysis of circRNAs upon ADAR depletion.

overall_design: Total RNA from whole brains of adult 3–4-month-old male mice was used for circRNA sequencing. Total RNA was enriched for circular RNAs and sequecing libraries for ONT and Illumina were prepared as described in the Methods section of this publication. Three biological replicates per genotype were sequenced: ADAR2 knockout (Adar2−/−Gria2R/R), double ADAR1 catalytically inactive/ADAR2 knockout (Adar1E861A/E861A Ifih−/− Adar2−/−Gria2R/R), and wild-type controls. All mice were on a C57BL/6J background.

last: Tellaetxe-Abate


title: Enhancing prohibitin peptide with D-arginine for improved structural stability and in vivo metabolic effects on obesity

city: St Lucia

first: Benjamin

last: Weger

address: 306 Carmody Road

institute: University of Queensland

summary: Obesity is a global epidemic and the primary risk factor for type 2 diabetes, ranking as the fifth leading cause of death worldwide. While lifestyle changes can address body fat accumulation, pharmacotherapies are essential for sustained weight loss. In this study, we report the design of a new generation of cationic-rich peptide-based therapeutics engineered to target white adipose tissues. Our findings demonstrate remarkable efficacy in significantly reducing body weight in a high-fat diet-induced mouse model. Notably, a prohibitin peptide substituted with D-arginine represents a paradigm shift by inducing mitochondrial uncoupling. This study heralds a promising avenue for developing the next generation of prohibitin-targeting peptides, capable of curbing adipocyte expansion and body weight, with favorable preclinical safety profiles. Altogether, these peptides hold immense potential for addressing obesity and metabolic syndrome.

overall_design: 2 organs (WAT and liver) of female (F) and male (M) mice that have been injected with vehicle or PTP-r.

first: Lai

last: Chan

first: Meltem

first: Junqiao

last: Du

first: Nicole

last: Lawrence

first: Marlon

last: Cardoso

first: Samilla

middle: B

last: Rezende

first: Jéssica

last: AI Muller

first: Kuok

last: Yap

first: Brian

last: Tse

first: Kamil

last: Solowski

first: Robert

last: Sullivan

first: Jennifer

last: Gunter

first: Octávio

last: Franco

first: Frédéric

last: Gachon

first: David

last: Craik


title: Investigation of Extracellular Vesicular Small RNAs to Identify Biomarkers for Pancreatic Ductal Adenocarcinoma

city: Ulsan

first: Semin

last: Lee

address: 50, UNIST-gil

department: Biomedical Engineering

institute: Ulsan National Institute of Science and Technology

summary:
Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis and unmet needs for clinical biomarkers. Extracellular vesicles (EVs) contain diverse biomolecules, including several kinds of small RNAs (smRNAs). We investigated EV-containing smRNAs (EV-smRNAs) as novel PDAC biomarkers.
SmRNA-seq showed that the total count of EV-smRNAs was remarkably downregulated in PDAC when it was compared with normal controls. Among them, the expression of microRNAs (miRNAs) including miR-125a-5p, miR-30e-5p, miR-16-2-3p, miR-98-5p and let-7 family were considerably attenuated in PDAC, and especially decreased miR-142-5p and let-7f-5p were significantly related to the early stage of PDAC. Also, upregulated long non-coding RNAs (lncRNAs) such as DDX59-AS1, SNHG25, LDLRAD4-AS1, and LYPLAL1-DT, and downregulated miRNAs such as miR-766-3p, miR-148b-3p and miR-337-3p were associated with metastatic PDAC. Considering the prognosis, lncRNA CARS1-AS1 and miRNA miR-142-5p were upregulated in patients with better responses to treatment. Moreover, we found a set of miRNA-lncRNA-target gene candidates, consisting of miRNA let-7c-5p and miR-98-5p, lncRNA OLMALINC, and target genes BACH1 and CCND1. In PDAC cell lines and PDAC organoids, they played a role in mainly cell migration during PDAC progression.
We suggested some potential EV-smRNA biomarkers involved in PDAC development, metastasis and prognosis, and also underlined mechanistic insights into PDAC progression.

overall_design: Peripheral blood was collected from 51 patients with PDAC and 15 normal controls. Extracted EV-smRNAs were analyzed using small RNA sequencing (smRNA-seq), and their target genes were validated with PDAC cell lines and organoids.

first: Hyemin

last: Kim

first: Sabin

last: Park

first: Younghoon

last: Choi

first: Jinho

first: Minjee

first: Junghyun

first: Eunmi

first: Sehoon

first: Jongkyun

first: Kyutaek

first: Kwanghyuk

first: Jookyung


title: Mouse lung gene expression comparison between mesenchymal Flcn deletion and wild type control.

city: Los Angeles

first: Brendan

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

summary: Loss of functional FLCN mutations are known to be the cause of Birt-Hogg-Dubé (BHD) syndrome, in which pulmonary cysts are presented in up to 90% of the patients. Lack of the related disease models in vivo poses a significant barrier to understanding the pathogenic mechanisms, including how the cysts develop and what molecular signaling pathways are involved.   In this study, we selectively deleted Flcn specifically in lung mesenchymal cells using a Tbx4-rtTA/TetO-Cre driver. These mice exhibit defective postnatal lung alveolarization. Most strikingly, alveolar enlargement continues into adulthood in these mice, accompanied by bilateral pulmonary cyst formation that resemble human BHD. Interestingly, Flcn deletion in lung epithelial cells alone did not exhibit any alveolar enlargement. No synergistic or additive effects were detected in mouse lungs with combined Flcn deletion in both epithelial and mesenchymal compartments compared to the mice with lung mesenchymal Flcn knockout. We have compared differential gene expression of lung tissues between Flcn knockout in mesenchyme and wild type control mice by RNA-seq.

overall_design: The middle lobes of the de-blood lungs from the mice at postnatal day 7 and 4 months of ages were isolated and flash-frozen in liquid nitrogen. mRNAs from wild type and Flcn knockout lungs were prepared by using the TRIzol RNA extraction reagent (ThermoFisher, #15596026). The RNeasy Micro Kit (Qiagen, #74004) was then used to clean up the extracted mRNA. Total RNA quality was checked with a bioanalyzer (Agilent) with RIN greater than 7.0 being acceptable. RNA-sequencing was performed at Novogene (Sacremento, CA).

first: Wei

last: Shi

first: Yongfeng

last: Luo

first: Matthew

last: Thornton


title: Lipid metabolism associated with efficacy of metronomic capecitabine and camrelizumab in gastrointestinal cancer: an exploratory clinical trial

city: Shanghai

first: Chenfei

last: Zhou

address: Ruijin No.2 Road

institute: Ruijin Hospital

summary: Lipid accumulation of skeletal muscle can be modulated after treatment of metronomic chemotherapy, while the detail molecular mechanisms are unclear. We used metronomic dose of 5-FU to treat C2C12 cell in vitro. RNA sequencing showed the expression of lipid metabolism related genes was changed after treatment.

overall_design: Mouse myocytes C2C12 was treated with metronomic dose of 5-FU (5ug/L) for 24 hours, and PBS treatment was used as control. After treatment, cells were collected for RNA sequencing.


title: Insights into the transcriptional cascade involved in the initial and early phases of glandular trichome development in Nicotiana tabacum [RNAseq_MIXTA]

city: Louvain-la-Neuve

first: Charles

last: Hachez

address: Croix du Sud 4

department: LIBST

institute: UCLouvain

summary: Glandular trichomes play a pivotal role in plant defense against a wide range of biotic and abiotic stresses. This study aims to employ AmMIXTA as a transcriptional switch to explore the genetic network that triggers glandular trichome development by leveraging its known role in promoting glandular trichome development when heterologously expressed in Nicotiana tabacum. To this end, we conducted a comprehensive RNA-seq analysis on transgenic tobacco lines expressing AmMIXTA under the control of a β-estradiol-inducible promoter across key time points. Our findings reveal a significant upregulation of a suite of genes, predominantly transcription factors, following the induction of AmMIXTA, providing insights into the transcriptional cascade involved in the initial and early phases of glandular trichome development. Moreover, through confocal live cell imaging of transcriptional reporter lines, interaction studies and DAP-seq assays, we confirmed the involvement of NtZFP8, a gene identified in our study, in glandular trichome development. Our data support a synergistic model where AmMIXTA and NtZFP8 co-regulate a network of genes critical for glandular trichome formation. Our study opens new lead to investigate the complex genetic network controlling glandular trichome formation in tobacco and related Solanaceae species of agronomical interest.

overall_design: By employing AmMIXTA as a transcriptional switch under the regulation of a β-estradiol inducible promoter, we aimed to dissect the molecular mechanisms governing glandular trichome initiation and development on the cotyledons of tobacco, which are naturally devoid of trichomes. Two timepoints were analyzed: 4h and 48h post-MIXTA induction. While the 4h time point post-AmMIXTA induction should capture genes involved in the initiation and early stages of glandular trichome development, the later time point (48 hrs post-induction) should capture the trans-differentiation of cells into glandular trichome cells.

first: Alice

last: Berhin

first: Aldana

last: Ramirez


title: A Novel Dominant Negative Variant of IRF8 in a Mother and Son: Clinical, Phenotypic and Biological Characteristics

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

summary: Background: Genetic testing of a child with persistent EBV viremia identified a novel variant c.1279dupT (p.*427Leuext*42) in interferon regulatory factor 8 (IRF8). The same variant was also found in his mother, who shortly thereafter was diagnosed with an HPV+ tumor. The maternal grandparents lacked this variant. Objective: We sought to examine the pathogenicity of the identified IRF8 variant and its phenotypic and functional characteristics in the proband and his mother. Methods: Immune cell enumeration, immunophenotypic and functional flow cytometry, NK cell cytotoxicity, MALDI-TOF mass spectrometry, TCRVb spectratyping, RNA sequencing, OLink proteomics, Sanger sequencing, Immunoblotting, Molecular cloning, Immunofluorescence microscopy and Image analysis were used in this study.

overall_design: RNAseq data from 3 human untreated samples: Control (n=1)  and IRF8 variant (mother and son; variant c.1279dupT (p.*427Leuext*42), n=2) donors

first: Amir

last: Sadighi Akha

first: Atilla

last: Kumanovics

first: Hu

last: Li

first: Kevin

last: Halling


title: The late chromatoid body component TSSK2 associates with translational machinery in elongating spermatids in mice

city: Turku

first: Lin

last: Ma

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

summary: Spermatogenesis culminates in a dramatic morphological transformation, including a tight compaction of the chromatin and nuclear re-shaping that largely silences transcription. Due to transcriptional silencing, the production of the sperm-specific proteins needed for the morphological transformation requires active storage and translational regulation of mRNAs transcribed in earlier cell types. The germline-specific RNP granule, the chromatoid body (CB), accumulates RNAs and has a role in RNA storage in early haploid cells (round spermatids). In late haploid cells (elongating spermatids), the CB is transformed to so-called late-CB, whose function in RNA regulation has remained elusive. Here we characterized the function of the late-CB by identifying proteins and RNAs interacting with the known late-CB marker, Testis-Specific Serine Kinase 2 (TSSK2). We showed that TSSK2 interacts with eukaryotic translation initiation factors and the late-CB associates with active, localized protein synthesis. Furthermore, we revealed an association of TSSK2 with a specific set of mRNAs that are enriched in polysome fractions in elongating spermatids, supporting the role of the late-CB in the temporally regulated translation. These results link the function of the late-CB to the RNA regulation during late spermatogenesis for the first time, providing important novel information about the RNA regulatory processes required for spermatogenesis and male fertility.

overall_design: To identify TSSK2-associated mRNAs, we sequenced two TSSK2-IP samples and two control IgG IP samples.

first: Mari

middle: S

last: Lehti

first: Salli

last: Kärnä

first: Matthieu

last: Bourgery

first: Panyi

last: Tran

first: Anu

last: Sironen

first: Noora

last: Kotaja


title: Endothelial-to-mesenchymal transition: A targetable mechanism that contributes to portal vein thrombosis in cirrhosis

first: Genís

last: Camprecios

state: Catalonia

address: Rosselló 153

department: Hepatic Hemodynamics

institute: IDIBAPS

summary: Portal vein thrombosis (PVT) is a prevalent thrombotic complication in cirrhosis, yet its pathophysiology remains elusive, hindering effective treatment strategies. Unlike thrombosis in other vascular beds, anticoagulation often fails to achieve complete recanalization in PVT, highlighting the need of alternative therapeutic approaches. We investigated portal vein endothelium involvement in PVT pathogenesis, identifying potential therapeutic targets. We isolated for the first time primary human portal vein endothelial cells (PVEC) from explanted livers of cirrhotic patients with and without PVT, as well as from a control group without portal hypertension and conducted RNA sequencing. Transcriptomic analysis unveiled endothelial-to-mesenchymal transition (EndMT) pathway as a key mechanism underlying PVT in cirrhosis, predominantly induced through TGFβ/SMAD mechanism. Remarkably, coagulation markers remained unaffected. In silico drug repurposing identified statins as potential agents targeting these alterations. Our study elucidates significant endothelial changes in the portal vein of cirrhotic patients, particularly pronounced in those with PVT, with EndMT emerging as a pivotal process. Simvastatin emerges as a promising therapeutic option for PVT treatment and prevention by modulating EndMT in PVEC.

overall_design:
To investigate the role of the portal vein endothelium in the pathogenesis of portal vein thrombosis (PVT) we isolated human portal vein endothelial cells (PVEC) from the explanted liver from patients with cirrhosis without and with PVT undoergoing liver transplantation (LT). As controls we used patients undergoing LT due to polychistosis, a condition without portal hypertension.
We then expanded the obtained cells and performed bulk RNAseq with cells at passage 1.
Comparative gene expression analysis was performed between control PVECs vs PVEC without PVT, and between PVEC without PVT and PVEC with PVT (CT-PVEC, CH-PVEC and PVT-PVEC).

first: Virginia

last: Hernández-Gea

first: Aina

last: Anton

last: Campreciós


title: Insights into the transcriptional cascade involved in the initial and early phases of glandular trichome development in Nicotiana tabacum [DAPseq_MIXTA_ZFP8]

first: Charles

last: Hachez

overall_design: In order to unravel downstream pathways regulated by AmMIXTA and NtZFP8 and so identify the transcriptional targets of both transcription factors, we employed DNA affinity purification sequencing (DAP-seq), a technique that facilitates the identification of DNA sequences directly bound by transcription factors (Bartlett et al., 2017). DNA reads from the NGS platform were filtered and mapped to the N.tabacum genome (Sierro et al., 2014) with an average mapping of 98% suggesting a high quality of the samples (Supplemental Table S4). Hits were identified by comparing against the negative control (nlsGFP protein), using criteria of a peak shape score greater than 2 and a p-value less than 0.05, to delineate significant binding regions.

first: Alice

last: Berhin


title: Effect of PACT knockout on LNCaP protate cancer cells

city: Nedlands

first: Andrew

middle: Jonghan

last: Woo

state: WA

address: 6 Verdun Street

department: UWA Centre for Medical Research

institute: University of Western Australia

summary: PACT, encoded by the PRKRA gene, is a double-stranded RNA binding protein which has two main mechanisms of action; functioning as an activator of both protein kinase RNA (PKR) and retinoic acid-inducible gene 1 (RIG-1) to facilitate innate antiviral defense mechanisms in mammals; and PACT is also an integral member of the cytoplasmic RNA-induced silencing complex (RISC) which enables the processing of pre-microRNAs into mature microRNAs (miRNAs). We previously described an alternate role for PACT as a nuclear receptor (NR) co-activator, which when recruited to hormone-regulated promoters can modulate the expression of NR-regulated genes. Here we employed a loss of function approach to investigate the role of PACT in prostate cancer (PCa). Depletion of PACT in human PCa cell lines resulted in a significant reduction in cell proliferation. RNA-sequencing analysis of LNCaP PCa cells ± PACT revealed that in the absence of PACT, various biological processes involved in proliferation were depleted, including cell cycle progression and division.

overall_design: To investigate the gene expression changes upon the depletion of PACT in prostate cancer cells, we used CRISPR/Cas9 to knockout PACT in LNCaP cells, followed by comparative gene expression profiling analysis using the wild-type LNCaP cells as the control.

first: Dianne

last: Beveridge

first: Peter

last: Leedman


title: OTUD1 downregulates PD-L1 expression by deubiquitinating STAT3 and promotes the immune response in ccRCC

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: Renal cell carcinoma (RCC) is a common urinary malignancy. It has the highest mortality rate among urologic malignancies, and its incidence has been increasing in recent years, and its common subtype is renal clear cell carcinoma (ccRCC). Ovarian tumor domain protease 1 (OTUD1) is known as a member of the OTUD deubiquitinase family and has the ability to remove ubiquitin modifications from target proteins. The OTUD family consists of 10 members, including OTUD1, all of which have the function of deubiquitinating target proteins. In this study, we determined the correlation between OTUD1 and the immune pathway through bioinformatics analysis. Subsequently, by mass spectrometry analysis and immunoprecipitation experiments, we demonstrated that OTUD1 can interact with STAT3 and regulate the expression of PD-L1 in kidney cancer cells through STAT3. OTUD1 can also inhibit the activity and nuclear translocation of STAT3 by regulating the K63 ubiquitination modification of STAT3. Finally, we found that OTUD1 can deubiquitinate STAT3 and inhibit its activity and nuclear translocation, thereby regulating the PD-1 signaling pathway, and ultimately promoting the immune response of renal cancer tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the ACHN cells after kncokdown of OTUD1

first: Wentao

last: Liu


title: Small non-coding RNAs encapsulating mammalian cells fuels innate immunity

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Our study addresses the void in understanding surface RNAs, notably glycan-RNAs, abundant on the cell exterior yet lacking precise mapping, particularly in rare cell populations. We present AMOUR, a technique uniting RNA capture with T7-based linear amplification, facilitating accurate profiling of surface RNAs while maintaining plasma membrane integrity. Validation via surface fluorescence in-situ hybridization and RNA aptamer imaging confirms their presence on the outer membrane, autonomously associating in vitro, independent of protein scaffolding. Our work reveals non-coding RNAs as integral components of diverse human and murine hematopoietic cell surface RNAs. Single-cell sequencing of human umbilical cord blood mononuclear cells identifies prevalent Y RNAs on monocyte surfaces. Notably, these Y RNAs interact with histones, critically regulating interleukin-6 (IL-6) gene expression and subsequent protein secretion upon histone stimulation. Highlighting the pivotal role of Y RNAs, our findings clarify their involvement in innate immune activation by capturing and presenting extracellular histones.

overall_design:
Surface RNAs are profiled utilizing the AMOUR strategy developed by us across various murine hemotopoietic cell types isolated from C57BL/6 mouse bone marrow cells.
Total RNASeq of mouse PBMC

first: Jiang

last: Xiao

first: Lulu

last: Hu


title: Comparative analysis of AMOUR and other strategies for profiling surface RNAs

summary: Conventionally limited to proteins, lipids, and polysaccharides, cell membranes have recently revealed the presence of protein-coding RNAs and glycan small RNAs on the surface of mouse and human cells. Despite glycan-RNA's prevalent presence on the cell exterior, a comprehensive method for accurately mapping all surface RNAs, particularly for rare cell populations has been lacking, leaving their physiological roles largely unexplored. We developed AMOUR, an RNA capture technique coupled with T7-based linear amplification, enabling precise profiling of surface RNAs in mammalian cells while preserving plasma membrane integrity.To ensure both sensitivity and specificity, we developed two supplementary strategies: WGA-Pd and RT-Amp, for surface RNA profiling alongside AMOUR.

overall_design: To ensure both sensitivity and specificity, we developed two supplementary strategies for surface RNA profiling alongside AMOUR. The first employs a wheat germ agglutinin pull-down assay (WGA-Pd), utilizing WGA to capture modified plasma membranes rich in N-acetylglucosamine and N-acetylneuraminic acid (sialic acid), followed by surface RNA extraction. The second involves a modified AMOUR method, substituting T7 RNA polymerase with reverse transcriptase during surface RNA capture. We also compared the surface RNA profiles post-protein deprivation with trypsin treatment (WGA-T).


title: Control of Renal Central Carbon Metabolism  by Heme Oxygenase-1

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: Metabolic adaptation refers to the regulation of cellular metabolism to prevent tissue dysfunction in response to different forms of stress. Heme, an iron-containing porphyrin, is indispensable for oxygen transport and for the activity of hemoproteins such as catalases. Cytotoxic “labile” heme is readily degraded by two distinct heme oxygenases (HO). The conditional deletion of Hmox-1, the gene encoding the inducible heme-degrading enzyme heme oxygenase (HO)-1, impairs metabolic adaptation to malaria and to polymicrobial infection. Embryonic deficiency in HO-1 is partially lethal in mice and surviving animals show progressive chronic inflammatory disease making them an unsuitable model to study metabolic adaptation. Here we found that mice with an inducible deletion of Hmox1 (Hmox1R26Δ/Δ) but not control mice rapidly succumbed to sterile hemolytic stress. Mortality was associated with heme-driven kidney failure, hypoglycemia, and disruption of adaptive thermoregulation. RNA sequencing and targeted metabolomics combined with data-driven in silico metabolic modeling revealed that failed renal metabolic adaptation is driven by altered oxidative phosphorylation and impaired pentose phosphate pathway. Heme-induced kidney failure and mortality in Hmox1R26Δ/Δ mice was not prevented with impairment of the inflammatory response, nor with antioxidants. Our results emphasize the critical importance of Hmox1 expression in hemolytic stress leading to acute kidney injury and death.

overall_design:
To investigate the relevance of kidney Hmox1 expression during hemin stimulation, we utilized and inducible whole body KO for Hmox1 ( Rosa26Cre-ERT2 Hmox1).
We then performed gene expression profile analysis using RNA-seq of 4 different time points . Comparative gene expression analysis of RNA-Seq data for WT mice vs. Hmox1 KO at each different time point.

first: Joel

last: Guerra

first: Elisa

last: Jentho

first: Sasha

last: Schäuble

first: Wolfgang

last: Vivas

first: Dania

last: Martinez

first: Marco

last: Groth

first: Emma

last: King

first: Michael

last: Bauer

first: Verena

last: Hoerr

first: Sebastian

last: Weis


title: Single-cell transcriptome sequencing of porcine adipose tissue

first: Yunxia

last: Li

state: Hunan

address: No. 1 Nongda Road

department: College of Animal Science and Technology

institute: Hunan Agricultural University

summary: Single-cell RNA sequencing of adipose tissue from SPF, GF, and humanized flora (HFA) pigs provides high-resolution transcriptome data, that provide a unique view for the interactions of gut microbiota and lipid metabolism.

overall_design: SPF pig（n=3）;GF pig (n=3); HFA pig(n=3)

first: Jie

last: Yin


title: Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Validation cohort

city: Antwerpen

first: Nicolaas

last: Van Renne

address: Universiteitsplein 1

institute: Laboratory of Experimental Medicine and Pediatrics (LEMP)

summary: We used RNA-seq to map the transcriptomes of archived formalin-fixed paraffin-embedded (FFPE) liver biopsies from precancerous chronic viral hepatitis patients with known clinical outcome. This Series contains the validation cohort used to validate the predictive transcriptomic signature.

overall_design: Transcriptomic profiles of 51 patients with at least 1 million mapped reads were retained in the validation dataset.

first: Stijn

last: Van Hees

first: Bart

last: Cuypers

first: Arno

last: Furquim d’Almeida

first: Axelle

last: Vanderlinden

first: Pieter

last: Meysman

first: Jordan

middle: J

last: Feld

first: Paloma

last: Sangro del Alcázar

first: Stefan

last: Bourgeois

first: Dirk

last: Sprengers

first: Geert

last: Robaeys

first: Luisa

last: Vonghia

first: Peter

last: Michielsen

first: Sven

last: Francque

first: Bruno

last: Sangro

first: Owen

last: Cain

first: Ahmed

last: Elsharkawy

first: Rob

last: De Man

first: Andre

last: Boonstra

first: Harry

last: Janssen

first: Ann

last: Driessen

first: Kris

last: Laukens

first: Thomas

last: Vanwolleghem


title: Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Training cohort

first: Nicolaas

last: Van Renne

summary: We used RNA-seq to map the transcriptomes of archived formalin-fixed paraffin-embedded (FFPE) liver biopsies from precancerous chronic viral hepatitis patients with known clinical outcome. This Series contains the training cohort used to generate the predictive transcriptomic signature.

overall_design: Transcriptomic profiles of 56 patients with at least 1 million mapped reads were retained in the training dataset.

first: Stijn

last: Van Hees

first: Bart

last: Cuypers

first: Arno

last: Furquim d’Almeida

first: Axelle

last: Vanderlinden

first: Pieter

last: Meysman

first: Jordan

last: Feld


title: Engineering nuclear elasticity to manipulate somatic cell fate

city: San Francisco

first: Susanna

last: Rosi

address: 2200 Island Dr

institute: Altos labs

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

overall_design: Refer to individual Series


title: Engineering nuclear elasticity to manipulate somatic cell fate [ATAC-seq]

overall_design: ATAC-seq

first: Benjamin

middle: A

last: Yang

first: Carlos

last: Aguilar


title: Autophagy regulates neuronal differentiation by controlling WNT/DVL signal pathway

city: Bongmyeongdong

first: Vincencius

last: Vidyawan

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

summary: Development of human embryonic stem cells (hESCs) technology provides a powerful tool to understand the mechanism of various diseases, as well as a model for human developmental study in vitro. In this study, we generated neurons from hESCs with previously established protocol and we observed that autophagy-related genes were upregulated at neuroepithelial/NPC stage. To check the importance of autophagy activation, bafilomycin was treated at a specific time point. We found that inhibition of autophagy at NPC stage delayed neuronal differentiation, as indicated by the downregulation of neuronal marker TUJ1 and upregulation of NPC marker NESTIN. Further investigation revealed that WNT signaling might be involved as part of the underlying mechanisms. Autophagy negatively regulates WNT signaling by promoting Disheveled-2 (DVL-2) degradation. Disruption of autophagy might lead to failure in the downregulation of WNT signaling and consequently, delaying neuronal differentiation. Dysregulation of autophagy has been associated with a variety of neurological diseases, including Vici syndrome. Here, we developed cerebral organoids culture to model Vici syndrome by introducing loss of function mutation in EPG5 gene. Mutation in EPG5 gene disturbed autophagy process, subsequently induced defect in progenitor cells migration and cortical layer generation in organoids. The results showed how damaged autophagy leads to smaller organoids, recapitulating Vici syndrome-associated microcephaly, and therefore validating the disease relevance of our study.

overall_design: To investigate role of autophagy RNA sequencing analysis was performed  the transcriptome profiles of bafilomycin-treated NPC (BafA1; day 11 of differentiation)

first: Lesly

last: Puspita

first: Virginia

last: Juwono

first: Magdalena

last: Deline

first: Mi-Yoon

last: Chang

first: Sang-Hun

last: Lee

first: Jae-won

last: Shim


title: RNA-sequencing of FACS-sorted hematopoietic stem and progenitor cells (LSK) from bone marrow of WT and Sucnr1 knock-out mice

city: Oslo

first: Lorena

last: Arranz

address: Forskningsveien 1

department: CRESCO - Centre for Embryology and Healthy Development

country: Norway

institute: University of Oslo

summary: Succinate is a metabolic signal that links hypoxia to IL-1β and cell responses in myeloid cells through intracellular mechanisms, but also autocrine/paracrine processes through succinate receptor 1 (Sucnr1). Succinate and its receptor have been scarcely studied in the context of hematopoiesis under health or disease. We investigated the in vivo role and molecular mechanisms of succinate and Sucnr1 in normal and malignant hematopoiesis, using an in vivo knock-out (KO) of Sucnr1.

overall_design: We profiled FACS-sorted hematopoietic stem and progenitor cells (HSPC) identified as  Lin−Sca-1+c-Kit+ (LSK) from bone marrow (BM) of males C57BL6/J WT (n = 4) and Sucnr1-KO (n = 3) aged 7 months by RNA-sequencing (RNA-seq). 27000-75000 cells were FACS-sorted in Arcturus Picopure RNA isolation kit (Thermo Fisher) extraction buffer.

first: Aurora

last: BERNAL

first: Vincent

last: CUMINETTI

first: Ruth

last: PAULSSEN

first: Manuel

last: GÓMEZ

last: ARRANZ


title: Reversing myeloid-derived suppressor cells mediated immunosuppression via p38α inhibition enhances immunotherapy efficacy

city: Chengdu

first: Yumei

last: Wang

address: 1166 LiuTai

institute: Chengdu University of TCM

summary:
By combining the tumor immunological phenotype (TIP) gene signature and high throughput sequencing based high throughput screening (HTS2), we identified that ponatinib significantly inhibits the expression of “cold” tumor associated chemokines CXCL1 and CXCL2 in cancer cells.
To investigate how ponatinib regulates the expression of “cold”-tumor related genes CXCL1 and CXCL2, we conducted RNA-seq study to examine transcriptome-wide effects of ponatinib with both MDA-MB-231 cells and 4T1 cells.

overall_design: Comparative transcriptome analysis of RNA-seq data for TNBC cells treated with ponatinib or DMSO.

first: Qianyu

first: Dong


title: Lysine metabolism reprogramming reshapes the immune microenvironment and induces immunotherapy tolerance in liver cancer

city: Xi'an, Shaanxi Province

first: Yungang

last: Xu

state: Shaanxi

address: Xi'an, Shaanxi Province

institute: Xi'an Jiaotong University

summary: Liver cancer is one of the most common malignant tumors worldwide, and its high aggressiveness and recurrence rate pose a major challenge. Metabolic reprogramming is one of the cancer hallmarks and allows tumor cells to adapt to drastic changes, supporting their rapid growth, survival, and proliferation under various conditions. The metabolic reprogramming of several amino acids within tumors profoundly affects the function of the immune cells. Furthermore, arginine and various other amino acids are now being widely studied as potential targets for anti-tumor therapy. However, the role of lysine metabolic reprogramming in tumors remains largely unexplored. This study aims to reveal the relationship between lysine metabolism reprogramming and the prognosis of liver cancer, the tumor immune microenvironment (TIME), and responses to immunotherapy through multi-omics analysis. Combined transcriptomic and proteomic analyses revealed a significant downregulation of lysine metabolism in tumor tissues against normal tissue adjacent to the tumor from liver cancer patients. Subsequently, we constructed a lysine metabolism score (LM score) based on nine lysine metabolic genes to stratify liver cancer patients into high and low lysine metabolism subtypes. The LM score exhibited potential in predicting both survival and immunotherapy response in liver cancer. Furthermore, significant differences were observed in prognosis, clinical staging, TIME, and immunotherapy outcomes between the subtypes with low and high lysine metabolism. In the subtype of low lysine metabolism, an immunosuppressive TIME predominated, correlating with poorer patient survival and anti-tumor immune responses. In conclusion, we uncover that disturbed lysine metabolism promotes the formation of the immunosuppressive TIME, thereby inducing immunotherapy resistance and advancing liver cancer progression. This provides an effective theoretical reference for elucidating the mechanism of immunotherapy resistance in liver cancer and seeking new therapeutic strategies.

overall_design: We analyzed gene expression profiles using RNA-seq in hepatocellular carcinoma tumor tissues and normal tissue adjacent to the tumor(NAT).

first: Xinlan

last: Lu

first: Min

last: Qiang


title: Single cell sequencing of out of thaw bone marrow derived MSC cells

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

summary:
Purpose: A Multiomics-based Unbiased Computational Modeling Platform Identifies Predictive Attributes of Mesenchymal Stromal Cell Immunomodulatory Potency
Methods: scRNAseq from MSCs with dropseq method on BioRad ddseq platform
Results: framework for identifying putative CQAs and generating MoA hypotheses for therapeutic cells and may help overcome current challenges in advancing large-scale, quality-driven manufacturing of cell therapies for broad clinical use. We used SureCell app to align the reads to human reference genome and used SEURAT for downstream analysis.
Conclusions: Cell therapies are complex “living medicines” with potential to treat chronic, incurable diseases. Despite their success and promise, quality-driven reproducible manufacturing and identification of Mechanisms-of-Action (MoA) remain significant challenges. Specifically, it is difficult to identify which set of cell attributes, among the thousands of proteins, RNA, lipids, and metabolites, are most correlative to their function in a specific disease setting. Here, we report a multiomics-driven unbiased computational platform to identify multivariate features that are predictive of their immunomodulatory functions.

overall_design: BM-MSCs single cell RNAsequences

first: Paramita

last: Chatterjee

first: Carolyn

last: Yeago


title: Human microglia differentially respond to ß-amyloid, tau, and combined Alzheimer's disease pathologies in vivo [scRNA-Seq]

status: Public on Dec 01 2025

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: Recent studies have identified important species-dependent differences in the response of microglia to beta-amyloid pathology. Yet, whether human microglia also interact differently with the pathognomonic combination of amyloid and tau pathologies that occurs in Alzheimer’s Disease (AD) remains unclear. We generated a xenotolerant mouse model of AD that develops both plaque and tangle pathologies, transplanted stem cell derived microglial progenitors and examined the interactions between human microglia and AD pathologies with scRNA sequencing, immunohistochemistry, and in vitro modeling. Combined amyloid and tau pathologies induced robust type-I interferon and proinflammatory cytokine responses, as well as an increased adoption of a distinct “rod” morphology in human microglia. The Rod morphology could be induced with type-I interferon treatment in vitro. We provide new insights into human microglial responses to combined AD pathologies and a novel platform to investigate and manipulate human microglia in vivo.

overall_design: xenotolerable hWT, h5XFAD, hPS19 and hPPS5X mice were transplanted with human iPSC-derived HPCs, aged to 6 months, and human xMG was then sorted out and subjected to scRNAseq analysis.

first: Morgan

last: Coburn

first: Ghazaleh

last: Eskandari-Sedighi

first: Jonathan

last: Hasselmann

first: Whitney

last: England


title: miRNA expression profiling of intestinal epithelial cell-derived extracellular vesicles from mice following Paneth cell ablation by dithizone

city: Jinan

first: Xiaofang

last: Huang

state: Shandong Province

address: 107 Western of Wenhua Road

institute: Qilu Hospital of Shandong University

summary: Paneth cells, critical sentinels of the innate immune system within the intestinal epithelium, play a vital role in maintaining intestinal homeostasis and defending against pathogens. Their dysfunction is implicated in the pathogenesis of sepsis. However, the specific mechanisms by which Paneth cells communicate with and regulate the surrounding intestinal microenvironment, particularly via extracellular vesicles (EVs), remain poorly understood. This study aims to characterize the global miRNA expression profile of intestinal epithelial cell-derived EVs (IEC-EVs) in a mouse model of acute Paneth cell loss, to identify key intercellular signaling molecules that may mediate intestinal barrier response to injury. We employed a well-established model of Paneth cell ablation by a single intraperitoneal injection of dithizone in C57BL/6 mice. Control mice received a vehicle solution. Intestinal epithelial cells were isolated six hours post-injection, and IEC-EVs were subsequently purified from these cells. Small RNA from the purified IEC-EVs was extracted and subjected to next-generation sequencing to comprehensively profile the miRNA cargo. Our comparative analysis reveals a distinct set of miRNAs that are differentially expressed in IEC-EVs following Paneth cell ablation. These candidate miRNAs are predicted to target signaling pathways crucial for epithelial cell proliferation, apoptosis, and inflammatory responses. We hypothesize that the alteration of the miRNA landscape in IEC-EVs represents a novel mechanism of intercellular communication that orchestrates the intestinal epithelial response to damage. This dataset provides the comprehensive resource of miRNA expression in IEC-EVs under conditions of Paneth cell deficiency. The findings are expected to elucidate novel pathways in intestinal pathophysiology and may identify potential miRNA biomarkers or therapeutic targets for conditions involving intestinal barrier dysfunction, such as sepsis.

overall_design: miRNA sequencing of intestinal epithelial cell-derived extracellular vesicles from C57BL/6 mice (n=3 per group) following Paneth cell ablation with dithizone versus vehicle control.

first: Jie

last: Yang

first: Siyu


title: Engineering nuclear elasticity to manipulate somatic cell fate [scRNA-seq]

first: Susanna

last: Rosi

overall_design: single-cell RNA-seq

first: Benjamin

first: Carlos

last: Aguilar


title: In situ piezoelectricity induces M2 polarization of macrophages to regulate Schwann cells for alleviating neuropathic pain of CCI rats

first: Guihua

last: Wei

address: No.111, North 1st Section, 2nd Ring Rd

institute: Southwest Jiaotong University

summary: Peripheral nerve injuries often lead to neuropathic pain (NP), which is influenced by macrophage polarization, impacting Schwann cell function. Bioelectric signals, particularly from piezoelectric materials like polyvinylidene fluoride (PVDF), play a pivotal role in modulating macrophage polarization. In this study, we demonstrate that PVDF's piezoelectric properties enhance M2 polarization during hypoxia macrophage model, as indicated by increased CD206 (M2 marker) expression and decreased CD8 (M1 marker). This shift in polarization is linked to enhanced secretion of Arg-1 and IL-10 from M2 macrophages, and reduced levels of ROS, iNOS, and TNF-α from M1 macrophages. The underlying mechanism driving this polarization shift involves the activation of the AMPK signaling pathway. In vitro, M2-conditioned medium significantly promoted Schwann cell proliferation and migration. In a chronic sciatic nerve constriction (CCI) rat model, PVDF treatment improved pain sensitivity, as shown by increased mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL). Additionally, PVDF treatment reduced the CD80/CD206 (M1/M2) ratio, promoting an anti-inflammatory environment, and increased the NF200/S100 ratio, indicating enhanced axonal regeneration. RNA sequencing revealed that Schwann cells co-cultured with M2-conditioned medium upregulated Cell Adhesion Molecule (CAM), Ca+ signaling pathway, and Mitogen Activated Protein Kinases (MAPK), critical signal pathway for Schwann cell regeneration and nerve repair. Our findings suggest that PVDF's piezoelectric properties offer a novel strategy for modulating macrophage polarization and enhancing Schwann cell activity, providing a potential therapeutic approach for NP.

overall_design: RSC96 Schwann cells were treated for 24 hours with macrophage-conditioned medium to model an hypoxia environment. RNA-seq was performed on cells under three conditions: Control (C), Hypoxia + non-piezoelectric material (B,PCL@PDA), and Hypoxia + piezoelectric material (A, PVDF@PDA). This design allows for the assessment of the piezoelectric effect on Schwann cell transcriptomes under hypoxic stress.

first: Chunlan

last: Chen

first: Xi

last: Li

first: Haoyan

first: Zaiqi

first: Xue

last: Gou

first: Pu

last: Zhang


title: Dietary Salt Impairs Circadian Physiological Metabolic Adaptations in Salt-Sensitive Hypertension

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

summary: The body's circadian rhythm is coordinated by a central hypothalamic and peripheral molecular clocks, which involve clock proteins (PER, CRY, CLOCK, and BMAL1). Our recent study demonstrated that deletion of Per1 in Dahl salt-sensitive (SS) rats (SSPer1-/-) exacerbated SS hypertension (HTN), kidney injury, and disrupted blood pressure rhythms. To define time-of-day, genotype-, and diet-dependent alterations in the renal transcriptome and proteome associated with SS HTN, we collected kidney cortex from SS and SSPer1-/- rats fed either a normal salt (NS, 0.4% NaCl) or high salt (HS, 4% NaCl) diet. Samples were obtained during both the active (night) and inactive (day) phases. The diet challenges were conducted for 3 weeks in male rats. Bulk RNA-sequencing was performed on both NS and HS-fed groups, and proteomic analyses were performed in HS-fed groups. In SS rats, HS intake markedly blunted time-of-day-dependent transcriptional changes, including reduced differential expression of core circadian genes such as Bmal1 and Nr1d1 when transitioning from the inactive to the active phase. Pathway analyses revealed significant stress and immune response, as well as metabolic adaptations caused by the HS diet. Specifically, the remodeling of the pyruvate dehydrogenase complex was identified as a key prediction in both transcriptomic and phosphoproteomic datasets. As anticipated, Per1 deletion further exacerbated disruptions in immune regulation and metabolic adaptation. Collectively, our findings demonstrate that numerous renal genes exhibit diurnal oscillations under physiological conditions and are profoundly disrupted in SS HTN, likely contributing to impaired kidney function and circadian misalignment of blood pressure regulation.

last: Staruschenko


title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization

city: Daejeon

first: Wonki

last: Cho

address: 291 Daehak-ro Yuseong-gu

institute: KAIST


title: Modeling Liver Cancer Molecular and Histological Features by CRISPR Editing of Primary Porcine Hepatocytes

city: Chicago

first: Lobna

last: Elkhadragy

state: Illinois

address: 2201 W Campbell Park Dr,

department: Radiology

institute: University of Illinois at Chicago

summary: Preclinical models are essential for advancing therapeutic strategies in hepatocellular carcinoma (HCC), an aggressive disease with poor survival outcomes. Here, we established genetically defined HCC models by ex vivo CRISPR editing of porcine hepatocytes. Hepatocytes were isolated from Yucatan minipigs and subjected to combinations of 2-4 gene alterations, including CRISPR-mediated knockout of tumor suppressor genes (TP53, PTEN, CDKN2A, AXIN1), with or without c-myc overexpression. Edited hepatocytes were expanded in culture, and those harboring at least three gene alterations formed tumors in SCID mice that recapitulated human HCC histologically. Clonal derivatives from the cell pools generated mouse xenograft tumors with distinct liver cancer histological features. Transcriptomic profiling of the cell models and xenograft tumors revealed activation of cell cycle pathways and similarity with human HCC. Further, autologous intrahepatic implantation of edited hepatocytes into pigs produced tumors with prominent immune infiltration, establishing an immune-competent large-animal model of HCC. Collectively, this HCC modeling platform provides insights into cooperative gene alterations underlying HCC pathogenesis and enables preclinical testing of systemic and locoregional therapies in a clinically relevant large-animal context.

overall_design: RNA-seq profiling of primary porcine hepatocytes, cell lines developed by subjecting the hepatocytes to gene alterations, xenograft tumors developed in SCID mice, intrahepatic pig tumors, normal pig liver tissues.

first: Olayinka

last: David

first: Caitlyn

middle: C

last: Castillo

first: Luke

last: Redlon

middle: R

last: Jordan

first: Kyle

last: Schachtschneider

first: Ron

last: Gaba


title: Upper Airway Gene Expression in Hospitalized Children with Rhinovirus-induced Respiratory Illnesses

city: Ann Arbor

first: Marc

last: Hershenson

state: MI

address: 1150 W. Medical Center Drive

department: Department of Pediatric Pulmonology

institute: Michigan Medicine

summary: In this study, we collected nasal swabs from infants and children hospitalized with RV infection and assessed gene expression by next generation sequencing, comparing profiles to swabs obtained from control subjects undergoing otolaryngologic procedures.  We also compared gene expression patterns to those obtained from children with respiratory syncytial virus (RSV) infection, another common respiratory virus well-studied in children.

overall_design:
Flocked nasal swab samples were obtained from children age 0-18 hospitalized with single-virus respiratory infections, as well as uninfected children for comparison.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Jordan

middle: E

last: Kreger

first: Alex

middle: L

last: Sliwicki

first: Saly

last: Essoh

first: Yiran

first: Chaandini

last: Jayachandran

first: Jessica

last: Czapla

first: Toby

last: Lewis

first: Erin

middle: M

last: Kirkham

first: Rodney

last: Vergotine

first: Antonia

last: Popova

first: Heidi

last: Flori


title: Uterine epithelial ERα regulates preimplantation uterine luminal epithelial (LE) and uterine mRNAs

city: Athens

first: Xiaoqin

last: Ye

address: 501 D.W. Brooks Drive

department: Physiology and Pharmacology

institute: The University of Georgia

summary: Uterine epithelial estrogen receptor α (ERα) deficiency in epiERα-/- (Esr1f/-Wnt7aCre/+) mice leads to dysregulated environment of uterine lumen, which is lined by uterine luminal epithelium (LE). We hypothesized that LE transcriptomes held molecular keys to understanding ERα in regulating preimplantation uterine environment. Day 0.5 post-coitum (D0.5) and D3.5 LE (isolated via enzymatic digestion), digested uterus (DU), and flash-frozen uterus (U) from Esr1f/- (control) and epiERα-/- mice were processed for mRNA-seq. There were minimal differentially expressed genes (DEGs, TPM>1, FC>2, FDR<0.05) between DU and U. Between D0.5 and D3.5 Esr1f/- LE, the top upregulated and downregulated GOBP pathways were on cellular processes and on innate immune responses, respectively, with the later also seen in Esr1f/- U. Compared to Esr1f/- LE, the most upregulated and downregulated pathways in D0.5 epiERα-/- LE were on innate immune responses and on biosynthesis and metabolism, respectively; while those in D3.5 epiERα-/- LE were on cell division and on signaling and metabolic processes, respectively. Na+ transmembrane transport was among shared upregulated pathways in D0.5 and D3.5 epiERα-/- LE. Between Esr1f/- and epiERα-/-, most DEGs in U were also DEGs in LE, limited DEGs in U only with higher expression than in LE were related to immune responses, implicating potential paracrine effects of uterine epithelial ERα. Selected DEGs were verified by realtime PCR and immunohistochemistry. This mRNA-seq dataset provides molecular keys to understanding temporal (e.g., innate immunity) and constituent (e.g., uterine fluid movement) functions, and potential paracrine effects of uterine epithelial ERα in regulating the preimplantation uterine environment.

overall_design: Virgin Esr1f/- and epiERα-/- female mice at ~2-6 months old were mated with wild type stud males (Esr1f/f or C57BL/6). They were checked every morning for the presence of a vaginal plug, an indication of mating activity during the previous night. The day of plug identification is defined as day 0.5 post-coitum (D0.5). The plugged females were separated from the stud males and randomly assigned into D0.5 and D3.5 time points, with same genotype littermates assigned into different timepoint groups. There were four groups of mice: D0.5 Esr1f/- group, D0.5 epiERα-/- group, D3.5 Esr1f/- group, and D3.5 epiERα-/- group. The mice were dissected at 11~12 h on both days. For each uterus, ¼ of one uterine horn was fixed in 10% formalin and ¼ of the other uterine horn was flash-frozen on dry-ice, designated as “U” (uterus), the remaining ¾ uterine horns connected by the cervix were slit open, immersed in 0.5% dispase (REF#17105-041, gibco, Waltham, MA, USA) in 1xHBSS buffer without calcium or magnesium (REF#1415-052, gibco, Waltham, MA, USA) for 30 min in a 6-cm culture dish, modified from our previous procedure (3-5). To determine the effects of enzymatic digestion process on uterine gene expression, we collected a small piece of digested uterine tissue prior to being processed for LE isolation. The small piece of digested uterine tissue was frozen on dry-ice and designated as “DU” (digested uterus). The LE layer in the remaining uterine tissue was gently scraped. The dislodged LE sheets were collected into a 1.5 ml microcentrifuge tube using a 200 μl pipette tip under a dissection microscope, centrifuged at 2000g for 3 minutes at 4C. Upon the removal of the buffer, 1 ml of TRIzol (REF# 15596018, Invitrogen, Carlsbad, CA, USA) was added to the LE pellet, which was gently vortexed to disperse the LE pellet, and kept at -20C. The U and DU tissues were carefully powdered in liquid N2 using a mortar and pestle, collected into a 1.5 ml microcentrifuge tube, in which 1 ml of TRIzol was added, and upon gentle vortexing to disperse the uterine powder, the tube was kept at -20C. At the conclusion of tissue collection, the LE, DU, and U samples in TRIzol were processed as one batch per tissue for total RNA isolation.

first: Jonathan

last: Hancock

first: Tong

last: Zhou

first: Yuehuan

last: Li

first: Taylor

last: Martin

first: Moya

last: Zhang


title: A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure [Micro-C]

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

summary: Atrial fibrillation (AF) and heart failure (HF) frequently co-occur and exacerbate each other's morbidity, yet the underlying molecular mechanisms remain incompletely understood. Here, we compared atrial gene regulatory networks across multiple mouse models of AF (Tbx5 cKO, Zfhx3 KO, Scn1b-null) and HF (TAC, AngII), revealing unexpected transcriptional and genomic convergence between Tbx5 cKO and HF models. Notably, Tbx5 was significantly downregulated in atrial tissue from both murine and human HF samples. We identified over 100 coordinately dysregulated Tbx5- and TAC-dependent transcription factor genes, with cell-type resolution achieved through single-cell transcriptomics. Loss of a TBX5-driven cardiomyocyte gene regulatory network—including Klf15, a transcriptional repressor of hypertrophy—was observed in both AF and HF models, while a shared disease-specific network emerged in activated fibroblasts, notably involving the pro-fibrotic regulator Sox9. These findings define a conserved TBX5-dependent atrial genomic injury response that may underlie the reciprocal pathophysiological relationship between AF and HF.

overall_design: Micro-C performed on untreated HL1 cells

first: Sonja

last: Lazarevic

first: Carlos

last: Perez-Cervantes

first: Alexander

last: Ruthenburg


title: The local cellular response to Human Papillomavirus focuses on basal layer restoration as visualized in situ by specific cellular neighborhoods near infected cells

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

institute: Leiden University Medical Center

summary: We applied spatial single-cell spatial transcriptomics to formalin-fixed paraffin-embedded healthy vulvar tissue (n=5) and HPV16+ high grade vulvar lesions (vHSIL, n=31).      lesions (vHSIL, n=31).  We applied spatial single-cell spatial transcriptomics to formalin-fixed paraffin-embedded healthy vulvar tissue (n=5) and HPV16+ high grade vulvar

overall_design: CosMx SMI 1k Plex

first: Ziena

last: Adbulrahman

first: Saskia

last: Santegoets

first: Mariette

last: van Poelgeest

first: Marij

last: Welters

first: Sjoerd

last: van der Burg


title: Small non-coding RNAs encapsulating mammalian cells fuels innate immunity

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Our study addresses the void in understanding surface RNAs, notably glycan-RNAs, abundant on the cell exterior yet lacking precise mapping, particularly in rare cell populations. We present AMOUR, a technique uniting RNA capture with T7-based linear amplification, facilitating accurate profiling of surface RNAs while maintaining plasma membrane integrity. Validation via surface fluorescence in-situ hybridization and RNA aptamer imaging confirms their presence on the outer membrane, autonomously associating in vitro, independent of protein scaffolding. Our work reveals non-coding RNAs as integral components of diverse human and murine hematopoietic cell surface RNAs. Single-cell sequencing of human umbilical cord blood mononuclear cells identifies prevalent Y RNAs on monocyte surfaces. Notably, these Y RNAs interact with histones, critically regulating interleukin-6 (IL-6) gene expression and subsequent protein secretion upon histone stimulation. Highlighting the pivotal role of Y RNAs, our findings clarify their involvement in innate immune activation by capturing and presenting extracellular histones.

overall_design: Gene expression profiling analysis of RNA-seq data  after Histone treatment

first: Jiang

last: Xiao


title: Transcriptomic profiling of Adcy7-knockout bone marrow-derived macrophages

city: Shanghai

first: Guofang

last: Xia

address: NO. 600 Yishan road

institute: Shanghai Jiaotong University School of Medicine Affiliated Sixth People's Hospital

summary: Myocardial ischemia/reperfusion (I/R) injury remarkably thwarts the therapeutic efficiency of percutaneous coronary intervention for myocardial ischemia disorders, and cardiac macrophages have been shown to play critical roles during the injury process. Here, we identified adenylyl cyclase 7 (ADCY7) in macrophage as a critical candidate for I/R injury based on spatial transcriptomics analysis and multi-parameter flow cytometry and confirmed the expression changes in I/R injury mouse model and patients with myocardial infarction. Taking advantage of depletion/reconstitution of macrophages in male mice, we demonstrated that macrophage Adcy7 deficiency significantly exacerbated myocardial I/R injury and impaired cardiac function, while Adcy7 overexpression attenuated these pathological manifestations. Notably, we observed that macrophage Adcy7 deficiency led to more infiltration of leukocytes and production of pro-inflammatory cytokines. To gain insight into how ADCY7 regulates inflammation, we performed transcriptomic and phosphor-proteomic analysis on Adcy7-deficient bone marrow-derived macrophages, and found that ADCY7 induced protein kinase A activation, leading to inhibition of nuclear translocation of NF-κB, thus restraining pro-inflammatory response. We further developed photoactivated adenylyl cyclase activation system combined with the macrophage depletion/reconstitution procedure and achieved substantial effect to alleviate cardiac inflammation and myocardial I/R injury. Together, our study identified ADCY7 as a promising therapeutic target for developing effective anti-inflammatory strategy to ameliorate myocardial I/R injury.

overall_design: The bone marrow cells were incubated with Adcy7-targted or Rosa-tageted CRISPR-CAS9 lentivirus at an MOI of 30 on day 1 post-isolation and differentiated into BMDMs in 5 days. The total RNA of BMDM was isolated with TRIZOL reagent and reverse transcripted with SuperScript™ II for following RNA-sequencing.

first: Congfeng

last: Xu