title: Integration of metabolomic and transcriptomic analyses reveals novel regulatory functions of the ChREBP transcription factor in energy metabolism

city: Houston

first: Mark

last: Herman

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Carbohydrate Response Element-Binding Protein (ChREBP) is a transcription factor that activates key genes involved in glucose, fructose, and lipid metabolism in response to carbohydrate feeding, but its other potential roles in metabolic homeostasis have not been as well studied. We used liver-selective GalNAc-siRNA technology to suppress expression of ChREBP in rats fed a high fat/high sucrose diet and characterized hepatic and systemic responses by integrating transcriptomic and metabolomic analyses. GalNAc-siChREBP-treated rats had lower levels of multiple short-chain acyl CoA metabolites compared to rats treated with GalNAc-siCtrl containing a non-targeting siRNA sequence.  These changes were related to a sharp decrease in free CoA levels in GalNAc-siChREBP treated-rats, accompanied by lower expression of transcripts encoding enzymes and transporters involved in CoA biosynthesis. These activities of ChREBP likely contribute to its complex effects on hepatic lipid and energy metabolism. While core enzymes of fatty acid (FA) oxidation are induced by ChREBP knockdown, accumulation of liver acylcarnitines and circulating ketones indicate diversion of acetyl CoA to ketone production rather than complete oxidation in the TCA cycle.  Despite strong suppression of pyruvate kinase and activation of pyruvate dehydrogenase, pyruvate levels were maintained, likely via increased expression of pyruvate transporters, and decreased expression of lactate dehydrogenase and alanine transaminase. GalNAc-siChREBP treatment increased hepatic citrate and isocitrate levels while decreasing levels of distal TCA cycle intermediates.  The drop in free CoA levels, needed for the 2-ketoglutarate dehydrogenase reaction, as well as a decrease in transcripts encoding the anaplerotic enzymes pyruvate carboxylase, glutamate dehydrogenase, and aspartate transaminase likely contributed to these effects.  GalNAc-siChREBP treatment caused striking increases in PRPP and ZMP/AICAR levels, and decreases in GMP, IMP, AMP, NaNM, NAD(P), and NAD(P)H levels, accompanied by reduced expression of enzymes that catalyze late steps in purine and NAD synthesis.  ChREBP suppression also increased expression of a set of plasma membrane amino acid transporters, possibly as an attempt to replenish TCA cycle intermediates. In sum, combining transcriptomic and metabolomic analyses has revealed regulatory functions of ChREBP that go well beyond its canonical roles in control of carbohydrate and lipid metabolism to now include mitochondrial metabolism and cellular energy balance.

overall_design: All procedures were approved by Duke University Institutional Animal Care and Use Committee and performed according to the regulations of the committee. Breeding pairs of Obese Prone CD (OP/CD) Sprague Dawley rats were gifts from Dr. Warren Grill and Dr. Eric Gonzalez, Duke University, and a colony was established and maintained by Duke Laboratory Animal Resources (DLAR). Starting at 4 weeks of age, male OP/CD rats were single-housed with a light cycle of 7 AM on/7 PM off, and fed ad libitum with a high-fat/high-sucrose (HF/HS) diet (D12451i, Research Diets) containing 47% fat (kcal) and 17% sucrose (kcal).  Body weight and food intake were monitored weekly. After 9 weeks of feeding of the HF/HS diet, plasma samples were collected via saphenous vein bleeding. One week later, animals received an initial subcutaneous injection of one of two GalNAc-siRNA constructs at a dose of 9 mg/kg body weight, or an equal volume of the diluent (PBS), (see below for description of the two GalNAc-siRNA reagents).  Additional doses of each GalNAc-siRNA construct were injected at 10, 18 and 25 days after the first injection. Animals were fasted overnight one day after the third injection (day 19), and subjected to an intraperitoneal glucose tolerance test (IPGTT) on the following day. Animals were weighed and a glucose solution (1g/kg body weight) was administered via intraperitoneal injection.  Tail blood samples were obtained and glucose levels measured with a blood glucose meter (CVSHealth) immediately before and at 30,60, 90, 120, and 180 minutes after bolus injection of glucose.  One day after the fourth GalNAc-siRNA or saline injection on day 25, plasma samples were collected via saphenous vein bleeding.  A bolus of deuterium oxide (D2O, 10 ml/kg body weight, Sigma Aldrich) was then given by intraperitoneal injection and followed by free access to drinking water supplemented with 4% D2O for the rest of the experimental period. Saphenous plasma samples were collected again one day after the bolus delivery of D2O (day 27).  On day 28 between 8 AM-noon, animals were anesthetized with Nembutal (250 mg/kg) by intraperitoneal injection and sacrificed for collection of plasma and liver samples that were rapidly frozen in liquid nitrogen and stored at -80oC for further analyses.

first: Jie

last: An

first: Inna

last: Astapova

first: Guofang

last: Zhang

first: Andrew

last: Cangelosi

first: Olga

last: Ilkayeva

first: Hannah

last: Marchuk

first: Miachael

middle: J

last: Muehlbauer

first: Tabitha

last: George

first: Joseph

last: Brozinick

first: Christopher

middle: B

last: Newgard


title: Gene expression data from patients with peripheral arterial disease stenosis grade 1 vs 4 and 5

status: Public on Nov 06 2025

city: Atlanta

first: Luke

last: Brewster

state: GA

address: 101 Woodruff Circle

department: Surgery

country: USA

institute: Emory University

summary:
Human PAD arteries were obtained from patients undergoing amputation. This is an extension of a previously published data set from Dr. Lawson's lab. In total 39 arterial samples from 27 patients undergoing amputation were collected, including posterior tibial artery, anterior tibial artery, superficial femoral artery, peroneal artery, and popliteal artery. Histologic sections were graded for the degree of stenosis as follows: zero – none, one - 1-25%, two – 26-50%, three – 51-75%, four – 76-95%, five – 96-100%. The protocol was approved by the Duke University Health System Institutional Review Board and all the donors gave their permission by written consent.
We used microarrays to detail the global programme of gene expression underlying peripheral arterial disaes specifically in high-stenosis vessels vs. non-stenotic vessels.

overall_design: About 150 mg tissues were collected for RNA extraction using the standard TRIzol protocol and RNA quality was assessed by electropherogram using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Complementary DNA probes were generated without amplification and hybridized to Affymetrix U133A microarrays (Affymetrix, Santa Clara, CA) and signal intensity were processed by the GeneChip scanner.

first: Jeffery

last: Lawson


title: PDE4B deficiency aids macrophage Trojan horses to transfer Cryptococcus neoformans into the brain

city: nanjing

first: ying

last: gong

address: The Jiangning Campus of Nanjing Medical University is located at No. 101 Longmian Avenue, Jiangning District, Nanjing, China.

country: China

institute: nanjing medical university

type: Expression profiling by high throughput sequencing

summary: Cryptococcal meningitis (CM) is a fatal compliation. Macrophages work as Trojan horses transferring Cryptococcus neoformans (C. neoformans) into the brain. Mechanisms for C. neoformans Trojan horses are largely elusive. In this study, we performed scRNA-Seq on immune cells infiltrated into the brain in a murine model of CM. Bioinformatics analysis reveals that phosphodiesterase 4B (PDE4B) ranks top in regulating macrophage Trojan horses. Melanin, a virulence factor for Cn, decreased PDE4B in macrophages. PDE4B inhibitor promoted the Cn Trojan horse across the blood-brain-barrier (BBB) in vitro and in vivo. As similar, PDE4B knockout increased fungi burden in the brain, which is, at least partially, rescued by macrophages depletion. In contrast, PDE4B activation diminished C. neoformans brain infection. Mechanistically, PDE4B inhibition increased CXCR4 and CCR7 on C. neoformans macrophage Trojan horses, a process regulated by the cAMP/PKA signaling pathway. Dexamethasone, commonly used to treat Pneumocystis infections in AIDS patients, significantly decreased PDE4B expression in macrophages. Overall, this study reveals that PDE4B plays a crucial role in C. neoformans macrophage Trojan horses and serves as a potential therapeutic target for CM.

overall_design: To elucidate the characteristics of Trojan cells during Cryptococcus neoformans brain infection, we isolated CD45+ cells from the brain tissue of mice infected with the H99Tdtomato strain and conducted single-cell RNA sequencing (scRNA-Seq) analysis. Clustering analysis of the transcriptomic data, based on known marker genes and literature, followed by UMAP dimensionality reduction, revealed the composition of infiltrating cells in the brain tissue post-infection. To further identify the cell types associated with Cryptococcus infection, we analyzed the distribution of fungal RNA across different cell types.


title: Tungsten is Utilized for Lactate Consumption and SCFA Production by a Dominant Human Gut Microbe Eubacterium limosum

city: Athens

first: Michael

middle: W. W.

last: Adams

address: 120 East Green St.

department: Molecular Biology and Biochemistry

institute: University of Georgia

summary: Eubacterium limosum is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, making this microbe important for human health. Lactate is a primary source of gut SCFAs but its utilization by E. limosum has not been explored. We show that E. limosum growing on lactate takes up added tungstate rather than molybdate and produces the SCFAs acetate and butyrate, but not propionate. The genes encoding an electron bifurcating, tungsten-containing oxidoreductase (WOR1) and a tungsten-containing formate dehydrogenase (FDH), along with an electron bifurcating lactate dehydrogenase (LCT), lactate permease and enzymes of the propanediol pathway, are all up-regulated on lactate compared to growth on glucose. Lactate metabolism is controlled by a GntR-family repressor (LctR) and two global regulators, Rex and CcpA, where Rex in part controls W storage and tungstopyranopterin (Tuco) biosynthesis. Tuco-dependent riboswitches, along with CcpA, also control two iron transporters, consistent with the increased iron demand for many iron-containing enzymes, including WOR1 and FDH, involved in SCFA production. From intracellular aldehyde concentrations and the substrate specificity of WOR1, we propose that WOR1 is involved in detoxifying acetaldehyde produced during lactate degradation. Lactate to SCFA conversion by E. limosum is clearly highly tungstocentric and tungsten might be an overlooked micronutrient in the human microbiome and in overall human health.

overall_design: To investigate the effect of tungsten (W) and lactate on E. limosum and metabolic pathways, RNA sequencing was done comparing lactace vs glucose under conditions with and without additional W added.

first: Saisuki

last: Putumbaka

first: Gerrit

last: Schut

middle: P

last: Thorgersen

first: Farris

middle: L

last: Poole

first: Nana

last: Shao

first: Dmitry

middle: A

last: Rodionov

middle: W


title: Long non-coding RNA UCA1 modulates chromatin remodeling via SMARCA2-containing SWI/SNF complex in human colorectal cancer

city: Lille, Cedex

first: Bernadette

last: Neve

address: Bâtiment ONCOLille, Bld du Professeur Jules Leclercq

department: CANTHER

country: France

institute: ONCOLille

summary: Differential lncRNA expression has been correlated to clinical characteristics of colorectal cancers (CRC), which are the second leading cause of cancer-related deaths. LncRNA UCA1 plays a role in epigenetic gene regulation in diverse cancers. We studied CRC cell properties in CRISPR/Cas9 HT29-derived models and, interestingly, UCA1-depleted HT29 cells presented an increased stem-cell phenotype. We show that loss of UCA1 modulates SWI/SNF chromatin remodeling complexes, which were previously shown to be involved in maintaining stem-cell properties. Not only was UCA1 permissive for induced SWI/SNF subunit SMARCA2 (BRM) expression upon chemo-drug treatment, but it also affected subunit compositions of SWI/SNF complexes by direct interaction of UCA1 with both ATP helicase BRM and BRG1. UCA1 is known to stimulate proliferation and decrease apoptosis, and we here show that it can restrain cells from a stem cell phenotype. The dual action of UCA1 revealed in this study highlights the complex actions of lncRNAs in cancer.

overall_design: RNAseq analysis of control ICP, dUCA1E1 and dUCA1E2 cells treated for 72h with or without 2 µM 5-Fluorouracil (5-FU).

first: Elsa

last: Hadj Bachir

first: Belinda

last: Duchêne

first: Mouloud

last: Souidi

first: Martin

last: Figeac

first: Jean-Pascal

last: Meneboo

first: Emmanuelle

last: Leteurtre

first: Nicolas

last: Jonckheere

first: Audrey

last: Vincent

first: Isabelle

last: Van Seuningen


title: Spatial transcriptomics of 12 tumor tissues from colorectal cancer

summary: To studied how transcript expression was distributed in heterogenous colorectal tumor tissues, we performed spatial transcriptome analysis of 12 CRC tumor samples. The OrgaRES consortium study includes tissues samples from patients at the university hospital of Lille (CHU Lille, France) obtained with the approval of the institutional review board and the Lille ALLIANCE-CANCER biobank. All patients gave their informed consent and signed a non-opposition statement to research use of a biological sample.

overall_design: Visium spatial expression analysis of 12 cryo-preserved colorectal cancer tissues

first: Charlotte

last: Dufour

first: Shéhérazade

last: Sebda


title: Single cell RNASeq analysis of bleomycin-injured mouse lung

city: Saint Louis

first: Jeffrey

last: Koenitzer

state: MO

address: 660 Euclid Ave.

institute: Washington University in St. Louis

summary: Bleomycin-induced lung injury results in monocyte infiltration and differentiation to pro-fibrotic monocyte-derived macrophages.

overall_design: Mice (n=3) were treated with intranasal bleomycin and lungs harvested at 14 days post-injury. Lungs were minced and digested in a solution containing 1 mg/ml collagenase A, 0.08 mg/mL DnaseI, 5% FBS, and 10 mM HEPES in PBS. Digests were passed through a 70 micron strainer followed by 10X Chromium encapsulation using v3'3.1 kits.

middle: R

first: Steven

last: Brody


title: MTHFD2-mediated ubiquitination and degradation of FOXO1 promote tongue squamous cell carcinoma progression

city: Wuhan

first: Aikebaier

last: Tuohuti

state: Hubei

address: shuiguohu

institute: Zhongnan Hospital of Wuhan University

summary: In recent years, there has been an increasing focus on Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2), a key enzyme in one-carbon metabolism, and its expression levels and mechanisms in tumors. Research has shown that MTHFD2 is upregulated in various malignant tumors and is closely associated with tumor onset, progression, and prognosis. However, the role and mechanisms of MTHFD2 in Tongue Squamous Cell Carcinoma (TSCC) remain unclear. Our study found that MTHFD2 expression is significantly elevated in TSCC and is closely linked to poor prognosis. Furthermore, the knockdown of MTHFD2 notably impacts the proliferation and migration capabilities of TSCC cells. Therefore, MTHFD2 holds promise as a crucial therapeutic target for TSCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCC-9 MTHFD2 wild-type and knock-out cells. There are 3 biological replicates per condition.


title: Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [Hi-C]

city: Worcester

first: Allana

last: Schooley

state: MA

address: 368 Plantation St

department: Systems Biology

institute: UMass Medical School

summary: Identity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how interphase folding is inherited, we developed an experimental approach that physically segregates mediators of G1 folding that are intrinsic to mitotic chromosomes from cytoplasmic factors. Proteins essential for nuclear transport, RanGAP1 and Nup93, were degraded in pro-metaphase arrested DLD-1 cells to prevent the establishment of nucleo-cytoplasmic transport during mitotic exit and isolate the decondensing mitotic chromatin of G1 daughter cells from the cytoplasm. Using this approach, we discover a transient folding intermediate entirely driven by chromosome-intrinsic factors. In addition to conventional compartmental segregation, the chromosome-intrinsic folding program leads to prominent genome-scale microcompartmentalization of mitotically bookmarked and cell type-specific cis-regulatory elements. The microcompartment conformation is formed during telophase and subsequently modulated by a second folding program driven by factors inherited through the cytoplasm in G1. This nuclear import-dependent folding program includes cohesin and factors involved in transcription and RNA processing. The combined and inter-dependent action of chromosome-intrinsic and cytoplasmic inherited folding programs determines the interphase chromatin conformation as cells exit mitosis.

overall_design: Hi-C libraries for RanGAP1-AID and Nup93-AID DLD-1 cells arrested in prometaphase or released to G1 for varying amounts of time. Replicates samples for control and Auxin-treated RanGAP1-AID cells in prometaphase, telophase, cytokinesis, early (5h) G1, or late (10h) G1.

first: Sergey

middle: V

last: Venev

first: Vasilisa

last: Aksenova

first: Job

last: Dekker


title: Transcriptional architecture of promoters and enhancers and the rapid unleash of heat shock response in Canis lupus familiaris [mRNA-seq]

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A, 17165 Solna, Sweden

department: Department of Gene Technology

country: Sweden

institute: Science for Life Laboratory, KTH Royal Institute of Technology

summary: Dogs exhibit high genetic diversity due to extensive breeding, and provide a versatile model for genetics, evolution, and complex traits. While RNA synthesis and transcriptional architecture of promoters and enhancers have been extensively analyzed in human, mouse, and fly, little is known about the mechanisms that coordinate gene and enhancer transcription in dog. Here, we combine precision run-on sequencing (PRO-seq) and strand-specific mRNA-seq (mRNA-seq) to measure nascent transcription, mRNA expression and mRNA stability in golden retriever macrophage (DH82) cells. Tracking transcription at nucleotide-resolution uncovers the precise transcription start nucleotides (TSN) genome-wide, identifies the exact locations of promoters and transcribed enhancers, and quantifies transcription machineries at initiation, promoter proximal pause, gene bodies, and termination windows. Moreover, we trigger an instant transcriptional reprogramming using heat shock, and track at nucleotide-resolution, how dog cells coordinate RNA synthesis and mRNA expression across the genome. Taken together, this study describes the transcriptional landscape at nucleotide-resolution, measures RNA synthesis, mRNA expression and mRNA-stability, and identifies mechanisms of gene and enhancer reprogramming in Canis lupus familiaris.

overall_design: RNA sequencing (RNA-seq) of macrophage-like cells from golden retriever (DH82) under normal growth conditions and heat shock.

first: Samu

last: Himanen


title: Transcriptional architecture of promoters and enhancers and the rapid unleash of heat shock response in Canis lupus familiaris [PRO-seq]

overall_design: Precision run-on sequencing (PRO-seq) of macrophage-like cells from golden retriever (DH82) under normal growth conditions and heat shock.


title: DRBD3 regulates long non-coding RNA abundance and cryptic splice site selection in trypanosomes

city: Armilla

first: Antonio

middle: M

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

country: Spain

institute: CSIC

summary: Trypanosomes are unicellular eukaryotes that rely heavily on post-transcriptional mechanisms to control gene expression. DRBD3 is an RNA-binding protein known to play important roles in mRNA processing, stability, transport and translation. It was found to associate with grumpy, a long non-coding RNA (lncRNA) recently characterized in Trypanosoma brucei. Here, we explore the role of DRBD3 in lncRNA metabolism and show that its depletion leads to the upregulation of a specific subset of approximately one hundred lncRNAs in both bloodstream and procyclic forms, likely through the activation of cryptic splice sites. The effect of DRBD3 depletion on lncRNA expression appears to be mostly indirect, and results from reduced levels of the poly(A) polymerase PAP1 following DRBD3 silencing. In addition to its impact on lncRNAs, DRBD3 loss also affects the processing of protein-coding genes, leading to alternative trans-splicing and protein truncation. Furthermore, we demonstrate that DRBD3 regulates the splicing of the newly identified intron in the transcript encoding the RNA-binding protein RBP20, and is important for maintaining the balance between trans- and cis-splicing. Our results position DRBD3 as a high-level regulatory factor that shapes the expression landscape of both coding and non-coding genes in trypanosomes

overall_design: Total RNA was obtained from three biological replicates corresponding to i) parental cell lines (bloodstream S16 or procyclic 449), or ii) cell lines in which DRBD3 was depleted by RNAi (bloodstream and procyclic). In addition, three biological replicates from a bloodstream cell line in which ZC3H41 was depleted by RNAi was included as a control

last: Estévez


title: A transposase-derived gene required for human brain development

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DNA transposable elements and transposase-derived genes are present in most living organisms, including vertebrates, but their function is largely unknown. PiggyBac Transposable Element Derived 5 (PGBD5) is an evolutionarily conserved vertebrate DNA transposase-derived gene with retained nuclease activity in cells. Vertebrate brain development is known to be associated with prominent neuronal cell death and DNA breaks, but their causes and functions are not well understood. Here, we show that PGBD5 contributes to normal brain development in mice and humans, where its deficiency causes disorder of intellectual disability, movement, and seizures. In mice, Pgbd5 is required for the developmental induction of post-mitotic DNA breaks and recurrent somatic genome rearrangements. In the mouse cortex, loss of Pgbd5 leads to aberrant differentiation and gene expression of distinct neuronal populations, including multiple types of glutamatergic neurons, potentially explaining the features of PGBD5 deficiency in humans. Together, these studies nominate PGBD5 as the long-hypothesized neuronal DNA nuclease and transposase-derived gene required for brain function in mammals.

overall_design: Motor cortices from 21 days old Pgbd5wt/wt (n=3) and Pgbd5-/- (n=3) littermates were disected and subjected to nuclei extraction. 10x Multiome was performed in the samples with the goal to understand Pgbd5 roles on neuronal physiology and numbers.

first: Luz

last: Jubierre Zapater

first: Rodrigo

last: Lopez Gutierrez

last: Hébert

first: Alex

last: Kentsis


title: Molecular Insights into HIV-associated Cardiac Dysfunction

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Antiretroviral therapy (ART) in human immunodeficiency virus (HIV) improved life expectancy in people living with HIV (PLWH) but cardiac diseases have emerged as a leading cause of death in this population. There is a notable increase in diastolic dysfunction and HF with preserved ejection fraction (HFpEF) attributed to the altered metabolic milieu seen in PLWH on ART. However, the specific role(s) that HIV itself, and/or ART may have on the cardiomyocyte phenotype is unknown. We investigated molecular pathways altered in cardiomyocytes in vitro in response to serum from ART-naïve and after ART-treated patients. Cardiomyocytes were treated for 24 hours with serum obtained longitudinally from HIV patients before and after receiving ART for 6 months. RNA sequencing revealed that differences between pre- and post-treatment with ART were related to processes involving cell death, cardiomyocyte calcium handling, and adverse remodeling. Apoptotic death was increased in cardiomyocytes treated with serum obtained from ART naïve HIV patients whereas those treated with serum from the same patients 6 months after ART presented changes in calcium-handling proteins and profibrotic markers, indicating altered contraction and relaxation, and adverse remodeling. These findings demonstrate altered molecular pathways in cardiomyocytes in response to active viremia and ART.

overall_design: Cardiomyocytes were treated for 24 hours with serum obtained longitudinally from HIV patients before and after receiving ART for 6 months, followed by RNA sequencing.

first: Maria

last: Munoz

first: Eng

last: Saw

first: Flora

last: Sam


title: Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [ATAC-seq]

last: Schooley

overall_design: ATACseq libraries for RanGAP1-AID DLD-1 cells arrested in prometaphase or released to G1 for 5h. Replicates samples for control and Auxin-treated RanGAP1-AID cells.


title: Comparative transcriptomics analysis of fatty acid-secreting Yarrowia lipolytica reveals importance of cell wall proteins

city: Gent

first: Inge

middle: N. A.

last: Van Bogaert

address: Coupure Links, 653

department: Department of Biotechnology

country: Belgium

institute: Ghent University

summary: Yarrowia lipolytica has been considered one of the most promising platforms for the microbial production of fatty acids and derived products. The deletion of the faa1 gene coding for an acyl-CoA synthetase leads to the accumulation and secretion of free fatty acids (FFAs) into the extracellular space. The secretion of products is beneficial for the development of microbial cell factories to avoid intracellular inhibitory effects and reduce downstream processing costs. However, the mechanism behind the secretion of fatty acids is not well known. In this research, we compared the transcriptome of this mutant showing FFA secretion to a wildtype-like strain not showing this phenotype. Both toxicity and growth assays, as well as deletion and overexpression mutants of candidate genes were used to assess the effects of candidate genes on the export of FFAs. Although no clear transporter of fatty acids was identified, the analysis of the transcriptomic data revealed an overrepresentation of cell wall-related proteins. Based on this results, a literature search allowed to retrieve proteins related to the cell wall previously associated to lipid. Experiments performed on these candidates proved their involvement in resistance to FFAs toxicity, with one of them being a potential acyl-CoA export protein.

overall_design: Quintuplates were analysed, comparing a wild-type strain with a mutant (faa1 knockout) able to secrete fatty acids when growing in high C/N ratio

first: Jose

last: Salvador Lopez

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce

middle: N


title: Declining FXR expression coordinates neonatal beta cell mass development with microbial bile acid metabolism maturation in mice

city: Shanghai

first: Chenyang

last: Fu

address: 197 Ruijin Road II

department: Department of Endocrine and Metabolic Diseases

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

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

overall_design: Refer to individual Series


title: Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm

first: Allana


title: Factors influencing variation in adult behavior of the tropical paper wasp Polistes canadensis

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

country: United Kingdom

institute: UCL

summary: The division of reproductive labor seen among individuals of the same colony in eusocial societies is one of the hallmarks of social evolution. These divisions have led to the evolution of distinct morphological or behavioral phenotypes known as ‘castes’. The establishment of a reproductive division of labor between individual colony members is a question of particular importance when studying simple eusocial societies. The classical paradigm of these societies is that all females are totipotent with the ability to exploit reproductive opportunities when they arise. Research has hypothesized that age variation in behavior could play an important role in how this division of labor is decided. Here, we provide the first systematic and statistical approach  to the study of adult behavior in the tropical paper wasp, Polistes canadensis.

overall_design: Whole brain RNA-Seq (pool of individuals)

middle: D

first: Seirian

last: Sumner

first: Emily

last: Bell

first: Andrew

last: Radford


title: In vivo anti-FAP CAR T therapy reduces fibrosis and restores liver homeostasis in metabolic dysfunction-associated steatohepatitis

status: Public on Nov 05 2025

city: New York

first: Scott

last: Friedman

state: NY

address: 1425 Madison Ave

department: Liver Diseases

institute: Icahn School of Medicine at Mount Sinai

summary: In this study, we aimed to determine the efficacy of in vivo chimeric antigen receptor (CAR) T cell therapy, generated by targeted lipid nanoparticles (t-LNPs), as an anti-fibrotic in metabolic dysfunction-associated steatotic liver disease. Hepatic fibrosis is a key predictor of mortality in liver disease, driven by fibrogenic hepatic stellate cells (HSCs). In heart, chimeric antigen receptor (CAR) T cells targeting fibroblast activation protein alpha (FAP) reduce murine cardiac fibrosis. However, the value of this approach in liver is unknown. We explored the anti-fibrotic potential of in vivo-generated anti-FAP CAR T cells in metabolic dysfunction-associated steatohepatitis (MASH), a highly prevalent disease with no approved anti-fibrotic therapies. We first established that FAP expression in both human and murine MASH is specific to HSCs. We then used flow cytometry, Sirius Red morphometry, digital pathology analysis, and single nuclear RNA-sequencing to assess the impact of anti-FAP CAR T cell therapy on murine MASH. Anti-CD5 targeted-LNPs carrying anti-FAPCAR mRNA generate activated, transient anti-FAP CAR T cells, which significantly reduced fibrosis by depleting pro-fibrogenic HSCs, and by modulating immune cells, endothelial cells and hepatocytes in a non-cell autonomous manner to mitigate inflammation and restore hepatic homeostasis. These findings reinforce the potential of in vivo CAR T therapy to attenuate a highly morbid and pervasive liver disease through its integrated, multicellular salutary effects.

overall_design: Samples used were frozen minced murine liver (left lobe). There are four expeirmental groups: Chow diet + vehicle, FAT MASH model + vehicle, FAT MASH model + IgG-FAPCAR LNP, and FAT MASH model + CD5-FAPCAR LNP. About 10-15mg of snap frozen liver tissue from four representative mice per group were pooled. Samples were prepared via an established protocol for nuclei isolation from murine MASH tissue(36). Solutions used included 2xST buffer (292 mM NaCl (Thermo Fisher Scientific, cat. no. AM9759)), 20 mM Tris-HCl pH 7.5 (Thermo Fisher Scientific, cat. no.15567027), 2 mM CaCl2 (VWR International Ltd, cat. no. 97062-820) and 42 mM MgCl2 (Sigma Aldrich, cat. no. 1028) in DNA/RNAse free water. 0.03% TST was prepared by adding 5mL of 2xST, 83uL Ribolock,83uL 2%BSA, 300uL of 1% Tween20, 4.6mL of H2O. The samples used for snRNAseq Chromium 3’ GEX were from snap frozen Chow + saline, MASH + saline, MASH + IgG-FAPCAR, and MASH + CD5-FAPCAR livers, about 3 months after euthanasia and cryopreservation. Each sample was chopped for 10 minutes over ice and passed through a strainer with 1mL TST. Samples were spun down at 500xg for 5 minutes at 4oC, supernatant was aspirated. Pellet was resuspended by pipetting 30 times with P1000 tips in 200uL of 0.4% BSA/PBS and then brought to the Genetics Core.

first: Chittampalli

last: Yashaswini

first: Li

last: Kenneth


title: Nucleophosmin 1 lactylation in graft kidney induces ferroptotic trigger waves that exacerbate delayed graft function

city: Chongqing

first: Xinyuan

last: Li

address: Chongqing

institute: The First Affiliated Hospital of Chongqing Medical University

summary: To identify the genome-wide binding sites of lactylated NPM1 and understand its role in transcriptional regulation.

overall_design: We generated NPM1-knockout (NKO) HK-2 cells followed by reconstitution with WT NPM1 (NKO-NPM1 WT) or the K257R mutant (NKO-NPM1 K257R).Fragmented chromatin was immunoprecipitated overnight at 4°C with anti-NPM1 antibody or rabbit IgG, followed by incubation with protein G-agarose beads.

first: Xin

last: Gou

first: Tianxin

last: Lin

first: Weiyang

last: He


title: Nucleophosmin 1 lactylation in graft kidney induces ferroptotic trigger waves that exacerbate delayed graft function [RNA-Seq]

summary: The effects of  NPM1 lactylation on transcriptional profiling in HK-2 cells

overall_design: We generated NPM1-knockout (NKO) HK-2 cells followed by reconstitution with WT NPM1 (NKO-NPM1 WT) or the K257R mutant (NKO-NPM1 K257R). RNA-sequencing analysis was performed to investigate the effect of NPM1-K257 lactylation on transcriptional profiling in HK-2 cells.


title: Identification of novel gene expression programs in thrombin-stimulated hepatic stellate cells

city: Piscataway

first: Lauren

last: Poole

state: NJ

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

summary: Transcriptional alterations of cultured hepatic stellate cells following 4, 24, or 48h control- or thrombin-stimulation were determined using RNA Sequencing. Illumina NovaSeq PE150 was used for sequencing.

overall_design:
Bulk RNA sequencing of cultured human hepatic stellate cells (LX-2) following stimulation timepoints:
Control-stimulated 4 h (n = 3)
Thrombin-stimulated 4 h (n = 3)
Control-stimulated 24 h (n = 3)
Thrombin-stimulated 24 h (n = 3)
Control-stimulated 48 h (n = 3)
Thrombin-stimulated 48 h (n = 3)

first: Noah

last: Mac

first: Sia

last: Prasad

first: Gina

last: Capece

first: Ricardo

last: Martínez-Zamudio

first: Conor

last: McClenaghan


title: A Single Day of Reduced Activity Alters the Next Day’s Transcriptomic and Metabolic Exercise Response

city: Cedarburg

first: Kevin

last: Gries

state: Wisconsin

address: W75N761 Tower Avenue Cedarburg, WI 5012

institute: Concordia University of Wisconsin

summary: Regular aerobic exercise decreases the risk of metabolic diseases, however reduced physical activity may attenuate these beneficial adaptations. This study investigated the influence of a single day of reduced activity on the skeletal muscle transcriptome (RNASeq) and systemic metabolism surrounding an acute bout of aerobic exercise. Utilizing a crossover design, subjects (n=9 [7M, 2F], 24±1y) exercised at 65% VO2max for 60-minutes following a day of reduced activity (IN; 3,581±1,185 steps) and normal activity (A; 11,069±3,631 steps). RNAseq from skeletal muscle biopsies was completed prior to and 4-hours post-exercise. Respiratory gas exchange analysis was completed at 20, 40, and 60 minutes of exercise. Blood samples for select metabolites were collected before, during, and throughout the 4-hour recovery. Inactivity resulted in nine Differentially Expressed Genes (DEG) at rest, while exercise altered 793 and 1,403 genes in A and IN, respectively. Gene set enrichment analysis revealed an interaction of exercise and trial that were related to inflammation, metabolism, cell cycle, and innate immunity. Respiratory exchange ratio (0.93±0.04 vs. 0.91±0.03; p<0.05) and carbohydrate utilization (2.16±0.79 vs. 1.96±0.72 g/min; p=0.09) was higher in the IN vs. A trial at 60-minutes of exercise. Triglycerides were higher in the IN trial (p<0.05),with no differences between trials observed in other measured metabolites. These findings indicate that a single day of reduced physical activity can elicit modest but significant changes in the metabolic and transcriptomic exercise response. Such alterations have implications for exercise guidelines and underscore the importance of controlling for daily step count when assessing exercise responses.

overall_design: RNAsequencing of human skeletal muscle before and 4 hours after exercise after a day of normal activity or inactivity.

first: Joseph

last: McGraw

last: Goetz-Sutinen

first: Jessica

last: Grimm

first: Jonathan

last: Baranowski

first: Mark

last: Berres


title: Serine tRNAs Compete to Regulate the mRNA Translation Of Serine-sensitive Codons

first: Robert

middle: S

last: Banh

address: 522 First Avenue, Smilow 907

department: Radiation Oncology

institute: New York University

summary: Differential mRNA translation efficiency (mTE) of codons is important in regulating protein synthesis, cellular states, and can change in response to amino acid (AA) availability. While the mTE of codons is canonically associated with their corresponding transfer RNA (tRNA) isoacceptors, its regulation by AAs in mammalian cells remains unexplored. We found that ELAC2, a 3’ tRNA maturation endonuclease, decreases the mTE of UC[U/C] serine (Ser) codons in response to Ser-limitation. Ablation of ELAC2 restored UC[U/C] mTE but reduced the mTE of AG[U/C] Ser codons. Among the tRNASer isoacceptors, tRNASer(GCU) decreased the most in ELAC2-deficient cells. Surprisingly, tRNASer(GCU) delivery restored AG[U/C] mTE and reduced UC[C/U] mTE in ELAC2-deficient cells. Finally, we deciphered the effects of Ser-sensitive codons on mRNA translation and the human proteome. Our study revealed that in response to Ser-limitation, regulation of tRNASer(GCU) levels fine-tune the mTE of UC[C/U] or AG[U/C] Ser-sensitive codons and shapes the proteome.

overall_design: Ribosome profiling and charged-tRNAseq was performed in PATU-8902 control (sgLUC) and ELAC2 KO (sgELAC2) cells grown with or without serine and glycine for 24hours.

first: Veronica

last: Costiniti

first: Wyatt

middle: C

last: Tran

first: Nandhini

last: Rajesh Babu

first: Kanshin

last: Evgeny

first: Beatrix

last: Ueberheide

first: Alec

last: Kimmelman


title: Uncovering the Roles of PPARγ and the Immunoproteasome in ILC2 Regulation

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: ILC2 cells were discovered less than 10 years ago. The activation and regulation of these cells have been extensively studied and some mechanisms have been discovered, but certain regulatory pathways have yet to be defined. PPARg and the immunoproteasome seem to play a major role in this regulation, but their exact function is still unknown. The aim of this project is to study the role of both the immunoproteasome and the transcriptional factor PPARg in ILC2 physiology using RNAseq.

overall_design: ILC2 cells were divided into three treatment groups: untreated control, IL-33 stimulation alone, and combined treatment with IL-33 and the PPARγ antagonist PKS3053. RNA-seq was performed to assess transcriptional changes across conditions.

first: Paoline

last: Laurent

first: Franck

last: Barrat


title: Multi-omics profiling of cachexia-target tissues reveals a spatio-temporal coordinated response to cancer

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

summary: Cachexia is a wasting disorder associated with high morbidity and mortality in cancer patients. Tumor-host interaction and maladaptive metabolic reprogramming are substantial, yet poorly understood, contributors to cachexia. We integrated metabolomics, RNA sequencing and 13C-glucose tracing data from multiple tissues and tumor of the C26 cachexia mouse model at different disease stages to provide a comprehensive overview of the spatio-temporal metabolic reprogramming during cachexia. We identified one-carbon metabolism as tissue-overarching pathway characteristic for metabolic wasting in mice and patients and linked to inflammation, promoting glucose hypermetabolism in muscle and atrophy. The same metabolic rewiring also occurred in a humanized cachexia mouse model. Together, our study provides a molecular framework to understand metabolic reprograming in cancer. It describes the first multi-tissue metabolite communication network during disease progression from the cachexia-free state to cachexia with one-carbon metabolism as tissue-overarching mechanism driving wasting.

overall_design: RNA-seq profiling of liver (L), heart (H), gastrocnemius muscle (GC), epididymal (E) and inguinal (I) adipose tissues from healthy control mice (PBS-injected), non-cachectic NC26 tumor mice (NC), pre-cachectic (Pre) and cachectic (Cax) C26 tumor mice

first: Pauline

last: Morigny

first: Michaela

last: Vondrackova

first: Honglei

last: Ji

first: Konstantinos

last: Makris

first: Radka

last: Trubacova

first: Tuna

middle: F

last: Samanci

first: Doris

last: Kaltenecker

first: Sophia

middle: E

last: Chrysostomou

first: Anna

last: Bidovec

first: Mariana

last: Ponce-de-Leon

first: Tanja

last: Krauss

first: Claudine

last: Seeliger

first: Olga

last: Prokopchuk

first: Marc

last: Martignoni

first: Melina

last: Claussnitzer

first: Hans

last: Hauner

first: Martina

last: Schweiger

first: Laure

last: Bindels

first: Mauricio

last: Berriel Diaz

first: Stephan

last: Herzig

first: Ondrej

last: Kuda

first: Maria

last: Rohm


title: Senolytic cell therapy identifies and reverses cellular senescence as a driver of aging-associated defects in intestinal regeneration and fitness

city: Cold Spring Harbor

first: Vyom

last: Shah

address: 1 bungtown road

department: Beyaz Lab

institute: Cold Spring Harbor Laboratory

summary: Organismal homeostasis is dependent on efficient tissue regeneration. Embedded within the highest self-renewing organ, intestinal stem cells (ISCs) drive the rapid regeneration of the gut epithelium. During aging, however, their regenerative capacity is significantly reduced albeit the exact mechanisms behind this decrease remain to be fully understood. Cellular senescence is a key feature of the aging process; yet little is known about the in vivo presence and functional consequences of senescent cells on the intestinal stem cell niche. Here, we identify, isolate and characterize the accumulation of senescent cells in the murine and human aging guts. To achieve their in vivo targeted ablation, we harness autologous senolytic CAR T cells, and uncover a detrimental impact of senescent cells on ISC function in natural aging and injury. Thus, therapeutic and prophylactic elimination of intestinal senescent cells is sufficient to either rejuvenate or prevent the functional decline in the regenerative potential of aged ISCs resulting in improvements in both epithelial integrity and mucosal immune function. Overall, these findings identify the in vivo deleterious role of senescent cells on the aged intestinal stem cell niche and provide proof of concept of the potential of targeted cell therapies to enhance tissue regeneration in aging organisms.

overall_design: Young (3 months) and old (18 months) mice were treated with 0.5x10^6 untransduced T cells (UT) or uPAR CAR T cells (m.uPAR-m.28z). Mice were harvested 8 weeks after infusion and organoids were generated from their intestinal crypts. 5 days after generation, organoids were harvested and subjected to bulk RNA sequencing.

first: C

last: Amor

first: J

last: Gewolb

last: Rousse

first: A

last: Harris


title: Transcriptional network analysis of PTEN protein-deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

city: Derio

first: Arkaitz

last: Carracedo

state: Biscay

address: Parque Científico Tecnológico de Bizkaia building 801A, POST-DOC Arkaitz, 4470

institute: CIC bioGUNE

summary: Among the extensive genomic alterations in prostate cancer, PTEN deletion stands out as one of the most consistently observed events. PTEN loss in prostate tumors is primarily associated with cancer cell proliferation and survival through the activation of the PI3K-AKT-mTOR signaling pathway. However, the use as a robust biomarker in clinical practice is hampered by its complex epigenetic, transcriptional, and post-translational regulation. In situ protein assessment by immunohistochemistry (IHC) captures PTEN protein status, but it does not report on associated tumor microenvironment remodeling.  Here, we undertook an approach that combined PTEN immunoreactivity analysis with high-throughput transcriptional analysis to gain insights into the downstream functional effects of PTEN protein loss in primary tumors. Our extensive bioinformatic analyses highlighted stromal remodeling as a prominent cancer cell-extrinsic process associated with PTEN loss. By extending our transcriptomic computational strategy to Pten-loss driven murine prostate cancer, we validated the causal role of Pten in the stromal reaction observed in clinical specimens. Mechanistically, we provide experimental evidence for the activation of a paracrine program that encompasses enhanced TGF-β signaling and that is compatible with the secretome of PTEN-deficient senescent cancer cells. Finally, our findings enable the sub-stratification of tumors with PTEN loss based on their senescence-associated stroma remodeling program to distinguish indolent from aggressive cases. Our study provides relevant biological context to the cellular and molecular alterations unleashed upon PTEN protein loss in prostate cancer.

overall_design: Transcriptomic profiles were generated from 197 primary prostate tumors to investigate molecular changes associated with PTEN protein loss, as determined by immunohistochemical (IHC) analysis.

first: Ivana

last: Rondon-Lorefice

first: Jose

middle: I

last: Lopez

first: Aitziber

last: Ugalde-Olano

first: Maite

last: Zufiaurre

first: Ianire

last: Astobiza

first: Natalia

last: Martin-Martin

first: Laura

last: Bozal-Basterra

first: Saioa

last: Garcia-Longarte

first: Amaia

last: Zabala

first: Sofia

last: Rey

first: Aida

last: Santos-Martin

first: Miguel

last: Unda

first: Ana

last: Loizaga-Iriarte

first: Mariona

last: Graupera

first: Paolo

last: Nuciforo

first: Isabel

last: Mendizabal


title: Strain Matters: Host Responses Reflect Symbiont Origin in the Squid-Vibrio Symbiosis

city: Pasadena

first: Vera

last: Beilinson

state: CA

address: 1200 E. California Blvd

department: Biology and Bioengineering

institute: Caltech

summary: Bacterial strains within a species can differ in traits that shape host–microbe interactions. Using the squid–vibrio symbiosis, we examined how strain-level variation influences host responses. Strains from squid and fish light organs were compared for their effects on Euprymna scolopes gene expression and development. Non-native strains showed reduced colonization success and delayed host phenotypes. Transcriptomic responses were most similar with native isolates and most divergent with a fish-derived strain. These findings demonstrate that fine-scale strain differences shape host compatibility and underscore the importance of strain-level diversity in the establishment of beneficial symbioses.

overall_design: Juvenile squid from the same clutch where exposed to 1 of 5 bacterial strains used in this study. Squid were considered part of the same clutch if their eggs were laid by the same parental pair at the same time and the hatchlings emerged synchronously. Clutch identity was tracked to account for genetic background in downstream analyses.

first: Grischa

middle: Y

last: Chen

first: Alexis

last: Hargadon

first: Edward

last: Ruby

first: Margaret

last: McFall-Ngai


title: The Metabolostasis System Regulates the Aggregation and Toxicity of Essential Metabolites

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Although metabolites are essential across all branches of life, it has been recently reported that they can form cytotoxic aggregates that resemble those formed by proteins in misfolding diseases. The phenomenon of metabolite aggregation suggests the existence of a metabolite homeostasis (metabolostasis) system capable of maintaining metabolites within a concentration range optimal for cellular function. To investigate this system, using Saccharomyces cerevisiae as a model organism, we identified the critical upper limits of metabolite consumption, beyond which metabolostasis is disrupted, leading to toxicity and growth inhibition. By enforcing a metabolite intake near the upper limits, we monitored the changes at the metabolome, transcriptome, and proteome levels, enabling us to map the metabolostasis system. Among the most affected pathways, we identified oxidative phosphorylation and intracellular membrane trafficking, particularly within the vacuole, which emerges as a containment and detoxification hub for potentially toxic metabolites. Near the upper limits of metabolite consumption, we observed the formation of amyloid-like metabolite aggregates, suggesting that the cytotoxicity is, at least in part, related to the conformational state of the metabolites and, in turn, the physicochemical properties that determine their solubility. Our findings characterize metabolostasis as the cellular system that maintains metabolites within their safe concentration limits and prevents their aberrant accumulation into cytotoxic aggregates.

overall_design: In this study, we investigate the metabolostasis system by performing a comprehensive analysis of the cellular responses associated with acute metabolostasis imbalance. Using Saccharomyces cerevisiae as a model system, we report a dose-dependent toxicity of many of the twenty coding amino acids and assess their upper limit for consumption. Our findings demonstrate that overfeeding many of these essential metabolites induces toxicity and growth inhibition, accompanied by significant accumulation of the same metabolites and broad disruptions to the amino acid pool. We further characterize the effects of metabolite overfeeding on transcriptomic and proteomic levels, revealing extensive changes in gene expression, impacting up to a half of the coding genes. We then report that growth inhibition is associated with the formation of amyloid-like aggregates, suggesting a potential mechanism for the observed toxicity.

first: Shon

last: Levkovich

first: Maoz

last: Lahav

first: Keila

last: Kaplan

first: Myra

last: Gartner

first: Ilana

last: Sogolovsky-Bard

first: Hanaa

last: Adsi

first: Yasmin

last: DeRowe

first: Alexander

last: Brandis

first: Michele

last: Vendruscolo

first: Ehud

last: Gazit

first: Dana

last: Laor Bar-Yosef


title: scRNA seq of Pdgfra+ cells from the mouse intestine

city: Cambridge

first: Alok

last: Jaiswal

state: MASSACHUSETTS

address: 415 Main Street

institute: The Broad Institute of MIT and Harvard

summary: Sorted PDGFRA+cells  that were lineage-negative for other major intestinal cell type markers (EPCAM1, TER119, CD45, PECAM1) were obtained from the colon of 5 mice. Briefly, mice were given 2.0% (weight/volume) DSS (Thermo Fisher Scientific, #J14489-22) dissolved in water for 7 days for the acute model of DSS. In the chronic model, DSS-administration was followed by a water recovery phase lasting for another 7 days. This cycle was repeated 2 more times, with mice weights being recorded daily.

overall_design: 3 Acute DSS treated vs. 2 Chronic DSS treated  samples from Il11mNG reporter mice

first: Vladislav

last: Pokatayev

first: Daniel

last: Graham

first: Ramnik

last: Xavier


title: Tissue-adhesive, antibacterial and antioxidant hydrogel sealant for sealing colorectal anastomotic leakage and preventing postoperative adhesion

city: Chang Chun

first: Zhen

last: Wang

address: 1 xin min street

institute: The First Hospital of Jilin University

summary: Surgical treatment of colorectal diseases typically involves excising the diseased portion of the bowel and anastomosing the remaining sections to re-establish continuity. Surgical suturing has limitations in preventing anastomotic leakage and postoperative adhesion. To address these challenges, a tissue-adhesive, antibacterial, and antioxidant hydrogel was designed to cover and seal colorectal anastomotic wounds. The hydrogel was formed in situ by simply mixing oxidized hyaluronic acid (OHA), adipic acid dihydrazide-modified hyaluronic acid (HA-ADH), ε-poly-L-lysine (ε-PLL), and tannic acid (TA). The hydrogel exhibited a rapid gelation rate and self-healing ability. Compared with commercial fibrin glue, the hydrogel had superior tissue adhesive strength and wound sealing performance. The hydrogel displayed potent reactive oxygen species scavenging ability and antibacterial activity against both gram-positive and gram-negative bacteria. The hydrogel also exhibited good biodegradation and biocompatibility. In a cecum-abdominal wall adhesion model in rats, the hydrogel attached firmly to the injured tissues and served as a physical barrier to prevent adhesion formation. In anastomotic leakage models after colon resection in rats and rabbits, the hydrogel effectively sealed the anastomotic leakage, prevented postoperative adhesion, and promoted anastomotic healing. Thus, this multifunctional hydrogel has strong clinical potential for preventing anastomotic leakage and adhesion formation after colorectal surgery.

overall_design: RNA sequencing experiments were conducted to explore the potential mechanisms by which the HA/TA10/ε-PLL50 hydrogel prevents postoperative adhesion formation and promotes intestinal anastomotic healing. The experiment was divided into three groups: “Suture” group, “Suture + FG” group, “Suture + Gel” group. Collect anastomotic tissue on the 7th day after surgery and each group has 3 parallel samples for detection.

last: Zhang

first: Liang

last: He

first: Quan


title: Androgen receptor drives polyamine synthesis creating a vulnerability for prostate cancer

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: The androgen receptor (AR) enacts metabolic effects of the anabolic steroid testosterone, but how AR-directed metabolic changes affect prostate cancer progression is not well understood. Here, we show that the AR increases de novo polyamine synthesis by direct transcriptional regulation of ornithine decarboxylase (ODC) expression across cell types, including prostate cancer cells. Likewise, androgen treatment of prostate cancer models increased intracellular and secreted polyamines, a process that was critical for tumor development as both genetic and pharmacologic inhibition of AR-induced polyamine synthesis enhanced growth inhibition of prostate cancer by supraphysiological androgens. This polyamine reduction lessened negative feedback regulation of S-adenosylmethionine synthase 1 (AMD1), enhancing its utilization of S-adenosylmethionine (SAM), which reduced global protein methylation patterns and expression of the protooncogene MYC. The ODC inhibitor difluoromethylornithine (DFMO) was effective in reduction of polyamines in patients with metastatic CRPC even despite treatment with bipolar androgen therapy, supporting further study of this therapy combination. Thus, the AR is a critical regulator of polyamine synthesis, which may constitute a vulnerability in prostate cancer treated with bipolar androgen therapy.

overall_design: LNCaP cell line was obtained from American Type Culture Collection (ATCC) and grown in RPMI 1640 (Gibco; 11835-055) supplemented with 10% fetal bovine serum (Corning), sodium lactate 1.6mM, sodium pyruvate 0.5mM, L-alanine 0.43mM, 1% pen-strep (Gibco). The vector pCDH-puro-cMyc vector (Addgene; 46970, J Wang laboratory) and pCDH-EF1-FHC empty vector control (Addgene, 64874, R Wood laboratory) were transfected into 293T cells (ATCC) along with pMD2.G (Addgene; 12259) and psPAX2 (Addgene; 12260) packaging vectors using lipofectamine (Invitrogen) to produce cMyc-puro, control-puro, and Tet-On-shAR-puro lentivirus particles. Two days after transduction with indicated virus, vector-expressing cells were selected with puromycin 1ug/ml for 72 hours. Cells were maintained at 37 ⁰C in 5% CO2. They regularly tested negative for mycoplasma contamination using MycSensor PCR Assay kit (Agilent Technologies). R1881, DFMO, Putrescine and vehicle control were supplemented into the media of duplicate cultures and RNA obtained from the cells as processed as indicated.

first: Laura

last: Sena

first: David

last: Sanin


title: RNA-seq of fetal testes of Sox9-eGFP mice treated with DEHP

city: Providence

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

summary: RNA-seq analysis was conducted as part of an experiment investigating the effects of the phthalate, di(2-ethylhexyl) phthalate (DEHP), on the mouse fetal testis. The goal of the study was to investigate the mechanism by which phthalates interfere with Sertoli cell function, following exposure to 0, 20, 500 mg/kg/d DPeP from gestational day (GD) 17-21.

overall_design: Timed pregnant Sox9-eGFP+ mice were treated with 0 (vehicle corn oil), 20, or 500 mg/kg/d DEHP in a 6 mL/kg solution by daily oral gavage from GD 14- GD 17. fetal testes were collected on GD17  one hour after administration of the final dose.  Each biological replicate consists of total RNA extrated from 1 testis or 2 pooled testes from the same litter (pregnant dam).

middle: J

first: Susan

last: Hall

first: Maha

last: Alhasnani


title: PRMT3-mediated cellular and molecular regulation in brain tumour stem cells.

city: Calgary

first: Ravinder

last: Bahia

state: Alberta

address: 3330 Hospital drive NW

department: Cell Biology and Anatomy

institute: University of Calgary

summary:
Effect on gene expression profilng of BTSCs following PRMT3 inhibition with SGC707.
To investigate the role of PRMT3 in regulating the cellular and molecular features of BTSCs, we performed RNA-seq using samples obtained from SGC707 treated versus XY1 treated GBM BTSCs.

overall_design: Comparative gene expression profiling of RNA-seq data obtained from SGC707 treated versus XY1, negative probe, treated BT248 cells (3 biological replicated).

middle: K

first: Kyle

last: Heemskerk

first: Samir

last: Assaf

first: Orsolya

last: Cseh

first: Xiaoguang

last: Hao

first: Rozina

last: Hassam

first: Panagiotis

last: Prinos

first: Hema

middle: A

last: Luchman

first: Samuel

last: Weiss


title: Identifying the molecular basis for functional divergence of duplicated SOX factors controlling endoderm formation and left-right patterning in zebrafish

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

institute: University of Warwick

summary: Endoderm, one of three primary germ layers of vertebrate embryos, makes major contributions to the respiratory and gastrointestinal tracts and associated organs, including liver and pancreas. Placement and patterning of these organs relies on the left-right organiser – known as Kupffer’s Vesicle (KV) in zebrafish. Transcription factors Sox32 and Sox17 are members of the zebrafish SoxF subfamily. Sox32 and sox17 arose from duplication of ancestral Sox17 in the teleost lineage. Sox32 induces sox17 expression in early embryos and is required for specification of endoderm and KV progenitors. Zebrafish Sox17 is implicated in KV morphogenesis. In mammals, Sox17 is vital for endoderm organ formation and can induce endoderm progenitor identity. Phenotypic evidence therefore suggests functional similarities between zebrafish Sox32 and Sox17 with mammalian SOX17. We sought to explore the functional differences and potential similarities between these proteins in the early zebrafish embryo. Our results indicate that, unlike Sox32, human SOX17 cannot induce endoderm specification in zebrafish. Furthermore, using hybrid protein functional analyses, we show that Sox32 specificity for the endoderm gene regulatory network is linked to evolutionary divergence in its HMG domain from its paralogue Sox17. Additionally, changes in the C-terminal regions of Sox32 and Sox17 underpin their differing target specificity and divergence in mediating differential gene regulatory programmes. Finally, we establish that specific conserved peptides in the C-terminal domain are essential for the role of Sox17 in establishing correct organ asymmetry. Overall, our results provide novel insights into vertebrate endoderm development, left-right patterning, and the evolution of SoxF transcription factor function.

overall_design: To investigate the functional differences between SOX family transcription factors implicated in endoderm formation and left-right patterning (mammalian SOX17 and zebrafish Sox17 and Sox32) we injected equimolar quantities of mRNA encoding these factors into zebrafish embryos at the one-cell stage and performed RNA-seq analyses at 6 hours post-fertilisation.  To determine whether differences in the HMG domains between zebrafish Sox17 and Sox32 were critical to their distinct functions we produced mRNAs for Sox32 lacking the HMG domain, or where the Sox32 HMG domain had been substituted for that of Sox17.  We then performed RNA-seq analyses as previous.

first: Simaran

last: Johal

first: Randa

last: Elsayed

first: Kristen

last: Panfilio


title: TGF-β-Driven Mafb Induces Ovarian Cancer Metastasis and Immune Dysregulation by Competitively Binding WTAP to Weaken the Degradative Modification of IGFBP2

first: Qinke

last: Li

state: 重庆

address: No. 76, Yuzhong District, Chongqing

institute: The second affiliated hospital of Chongqing Medical University

summary: This ChIP-seq dataset examines the genome-wide binding profile of transcription factor MAFB in ovarian cancer cells to investigate its role in tumor progression and immune dysregulation. Using ID8 mouse ovarian cancer cells with MAFB overexpression, we performed chromatin immunoprecipitation followed by high-throughput sequencing to identify MAFB binding sites. Surprisingly, our analysis revealed that IGFBP2, a key mediator of MAFB-driven tumor metastasis and immune modulation, was not a direct transcriptional target of MAFB. The ChIP-seq data was generated using an anti-MAFB antibody, with IgG as control. Peak calling was performed using MACS2 (version 2.2.7.1), and peak annotation was conducted using the ChIPseeker R package. Motif analysis was performed with HOMER (v4.11.1), and differential analysis was conducted with MAnorm.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for transcription factor MAFB in ID8 mouse ovarian cancer cells with MAFB overexpression and control cells, using anti-MAFB antibody and IgG control for immunoprecipitation.

first: Qiang

last: Yi

first: Siying

last: Zhang

first: Zhu

last: Yang


title: GAPDH Controls Transcript Stability, Protein Translation and Drives Proliferation in Acute Myeloid Leukemia [CLIP-seq]

city: Dortmund

first: Jeffrey

middle: Lesslie

last: Schloßhauer

address: Otto-Hahn-Straße 11

department: Chemical Genomics Centre

institute: Max Planck Institute of Molecular Physiology

summary:
Dysregulation of RNA binding proteins (RBPs) is a hallmark in cancerous cells.
In acute myeloid leukemia (AML) RBPs are key regulators of tumor proliferation. While classical RBPs have defined RNA binding domains, RNA recognition and function in AML by non-canonical RBPs (ncRBPs) remains unclear. Given the inherent complexity of targeting AML broadly, our goal was to uncover potential ncRBP candidates critical for AML survival using a CRISPR/Cas-based screening. We identified the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a pro-proliferative factor in AML cells. Based on cross-linking and immunoprecipitation (CLIP) we are defining the global targetome detecting novel RNA targets mainly located within 5’UTR including GAPDH, RPL13a, PKM and ENO1. The knockdown of GAPDH unveiled genetic pathways related to ribosome biogenesis, translation initiation, and regulation. Moreover, we were able to demonstrate a stabilizing effect through the GAPDH binding to target transcripts including its own mRNA, unveiling GAPDH’s pivotal role in cancer. The present findings provide new insights on the pathophysiological role of GAPDH in AML.

overall_design: To investigate the influence of GAPDH on RNA-binding we conducted CLIP-seq under low glucose,  normal glucose and galactose culturing conditions.


title: Extracellular Vesicle Transcriptome in Ischemic Stroke Rat with Intra-arterial Transplantation of Human Neural Stem Cells (microRNA)

city: Beijing

first: Chuheng

last: Chang

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

institute: Peking Union Medical College Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Extracellular vesicles (EVs) can cross the blood–brain barrier and enter the systemic circulation, potentially acting as peripheral biomarkers of stroke neuropathology. Here, we investigated alterations in EV RNA cargoes extracted from rat brain and plasma before and after stroke induction via middle cerebral artery occlusion and subsequent human neural stem cells (hNSCs) transplantation. EV RNA coexpression profiles were assessed, and digital source tracking was used to determine EV origin. The therapeutic effects of intra-arterial delivery of hNSCs on ischemic rat brains were quantified, focusing on functional recovery, resolution of ischemic lesions, and the microenvironment. Stroke induced distinct EV secretion patterns, with a notable increase in EV secretion from non-neuronal cells. hNSCs transplantation caused minimal immune rejection and transplanted cells survived in the brain for over a week. Stem cell-derived EVs were detected in peripheral blood, indicating prolonged systemic distribution after transplantation. Gene regulatory network analyses identified specific EV miRNAs that play crucial roles in neurogenesis, wound healing, angiogenesis, and blood–brain barrier integrity. An integrated analysis of EV RNAs in brain and plasma samples revealed that stroke increased correlations in RNA expression between brain and plasma and that hNSCs transplantation reversed the effect. Brain- and plasma-derived EVs carry similar molecular information after stroke, suggesting that plasma-derived EV RNAs reflect stroke pathophysiology. Intra-arterial transplantation of hNSCs improved outcomes after stroke in rats, by promoting endogenous neurogenesis and maintaining blood–brain barrier integrity. The identified EV miRNAs provided a new mechanism by which hNSCs transplantation regulates neural regeneration through the miR-204-5p/EFNB3 axis.
https://onlinelibrary.wiley.com/doi/10.1002/mco2.70400

overall_design:
Eighteen adult male Sprague-Dawley rats, aged 8-12 weeks, were subjected to transient middle cerebral artery occlusion (tMCAO, 90 minutes occlusion ). Three days after tMCAO, rats were injected with either a suspension of 2×10^5 hNSCs or saline randomly (9 rats in each group) using a 31-gauge needle.
Three animals per group were sacrificed for sample collection (brain and plasma) at 4, 10, and 31 days post-tMCAO. Brain and serum EVs were extracted for RNA isolation and sequencing.
Three healthy adult male Sprague-Dawley rats were sacrificed for brain and plasma sample collection, serving as healthy controls.
Temporal expression profiles of brain- and plasma-derived EV-RNA before and after stroke were analyzed. Comparative analysis between treatment and control group at different time points post-stroke were also conducted.

first: Yiqing

last: Wang

first: Renzhi

first: Xinjie

last: Bao


title: GLIS3 RNA-seq

first: Alok

last: Jaiswal

summary: Define the transcriptome of fibroblasts perturbed for GLIS3 in response to fibrotic stimuli.

overall_design: IL-11mNG CRISPRko Ctrl/Glis3KO, and IL-11mNG CRISPRa Ctrl/Glis3A fibroblasts were treated with a combination of TGFb and IL1b (10ng/ml) over a timecourse of 24 hours. Cells were collected, RNA isolated, and submitted for bulk RNA-seq.

first: Vladislav

last: Pokatayev

first: Daniel

last: Graham

first: Ramnik

last: Xavier


title: GLIS3 ChIP-seq

summary: Define the DNA targets of fibroblast GLIS3 in response to fibrotic stimuli.

overall_design: IL-11mNG GLIS3-FLAG fibroblasts were treated with a combination of TGFb and IL1b (10ng/ml) over a timecourse of 24 hours. Cells were collected and ChIP Seq was performed. Sheared DNA lysate was incubated with anti-H3K4me3, -FLAG, or -IgG for the procedure.


title: GAPDH Controls Transcript Stability, Protein Translation and Drives Proliferation in Acute Myeloid Leukemia [GAPDH_KD_RNAseq]

overall_design: To investigate the influence of GAPDH depletion a knockdown of GAPDH was induced by shRNA under low glucose, normal glucose and galactose culturing conditions.


title: Arabidopsis cationic amino acid transporter (CAT) is a high affinity transporter for a systemic herbicide L-Phosphinothricin

city: Singapore

first: Grace

middle: Zi Hao

last: Tan

address: 1 Research Link National University of Singapore, 03-48

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: L-phosphinothricin (PPT) is a broad-spectrum herbicide, however its transportation mechanisms remain unidentified. Here we present cationic amino acid transporters (CAT) as the high affinity transporter of PPT, explaining the different sensitivities of flowering and non-flowering plants. Comparative analysis between Arabidopsis thaliana and Marchantia polymorpha revealed non-target site mechanisms for PPT resistance in the latter. LC-MS analysis showed minimal PPT uptake by M. polymorpha, while transcriptomic analysis identified four candidate transporters for PPT uptake. Overexpression of AtCAT1 and AtCAT5 in M. polymorpha increased PPT susceptibility and uptake. Protein molecular dynamics simulation revealed the modes of PPT transportation, allowing for mutagenesis strategies to reduce PPT susceptibility. This study reports the first high affinity PPT transporter, AtCAT, and highlights the natural diversity of PPT susceptibility due to transportation.

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana

overall_design: To identify transcriptional response to GS-inhibiting herbicides, RNAseq analysis was perform on Arabidopsis seedlings and Marchantia gemmalings treated with glutamine, phosphinothricin, or methionine sulfoxime for 48h. Untreated plants were used as controls. n=3

middle: Z

first: Daisuke

last: Urano


title: Liver transcriptomic profile of 6 months old wild type and hepatocyte-specific ATF6 overexpression mice

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We generated hepatocyte specific n-ATF6 overexpression transgenic mice via Cre-mediated recombination. At 6 months age, livers from the transgenic mice and their wild type controls were harvested for RNA isolation and followed with RNA-sequencing.

overall_design: In total 13 samples were included, 6 from wild type mice and 7 from ATF6 transgenic mice.

first: Mathias

last: Heikenwälder

first: Xin


title: IAF scRNA seq

summary: Human fibroblast cells were treated with a combination of fibrotic cytokines (TGF-b and IL-1b) over a time course of 0, 6, 12 and 24 hours. Live cells were collected and submitted to single cell sequencing.


title: Liver transcriptomic profile of 3 months old wild type and hepatocyte-specific ATF6 overexpression mice

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We generated hepatocyte specific n-ATF6 overexpression transgenic mice via Cre-mediated recombination. At 3 months age, livers from the transgenic mice and their wild type controls were harvested for RNA isolation and followed with RNA-sequencing.

overall_design: In total 12 samples were included, 5 from wild type mice and 7 from ATF6 transgenic mice.


title: Single-cell transcriptomic characterization of immune cells from livers of wild type and ATF6 transgenic mice

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We isolated CD45+ cells from livers of wild type and hepatocyte-specific nATF6 overexprerssion mice for scRNAseq to decrible the the immune cell population.

overall_design: In total 8 samples were included, 4 from wild type mice and 4 from ATF6 transgenic mice.


title: Repeated behavioral testing and the use of summary measures reveal trait anxiety in preclinical rodent models

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

summary: The reliability and validity of preclinical anxiety testing is essential for translating animal research into clinical use. However, the commonly used anxiety tests lack inter-test correlations and face challenges with repeatability. While translational animal research should be able to capture stable individual anxiety traits - the core feature of anxiety disorders - the conventional approach employs a single type of test at a single time, which primarily reflects transient states of animals that are heavily influenced by experimental conditions. Here, we propose a validated, optimized test battery capable of reliably capturing trait anxiety in rats and mice of both sexes. Instead of developing novel tests, we combined widely used tests (elevated plus-maze, open field and light-dark test) to provide instantly applicable adjustments for better predictive validity. We repeated these tests three times to capture behavior across multiple challenges, which we combined to generate summary measures (SuMs). Our approach resolved inter-test correlation issues and provided better predictions for subsequent outcomes under more anxiogenic conditions or fear conditioning. SuMs were also shown to be more sensitive markers of stress-induced anxiety following social isolation. Finally, we tested our method's efficacy in discovering anxiety-related molecular pathways through RNA sequencing of the medial prefrontal cortex. SuMs revealed four-times more molecular correlates of trait anxiety than transient states, highlighting novel gene clusters. Furthermore, 16% of these correlates were also found in the amygdala. In summary, we provide a novel approach to capture trait anxiety in rodents, offering improved predictions for potential therapeutic targets for personalized medicine. We also provide recommendations to enhance feasibility without compromising validity or animal ethics, tailored to various scientific goals.

overall_design: Gene expression profiles from the medial prefrontal cortex of Wistar rats were assessed via RNA sequencing to identify molecular correlates of trait anxiety. This analysis correlated gene expression with summary behavioral measures (SuMs), derived from multiple repeated anxiety tests, allowing more effective capture of stable anxiety traits and their underlying molecular signatures. Raw count values of RNA sequencing data (10.5281/zenodo.14236344) and the corresponding behavioral data (10.5281/zenodo.15469973) is publicly available at the Zenodo online data repository as related datasets.

first: Zoltán

last: Varga

first: Diána

last: Pejtsik

first: Máté

last: Tóth

last: Balogh

first: Manó

last: Aliczki

first: László

last: Szente

first: Gyula

last: Balla

first: Levente

last: Kontra

first: Zsófia

last: Eckert

first: Huba

last: Szebik

first: Zsolt

last: Borhegyi

first: Éva

last: Mikics


title: APOBEC3 promotes squamous differentiation and metastases via IL1A/AP-1 signaling

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

summary: In urothelial carcinoma, up to 70% of mutations are caused by mutagenic activity of the APOBEC3 deaminases. To dissect the role of APOBEC3 in the progression of UC, we generated a mouse model UPPA with conditional knock out of Pten and Trp53 in addition to mouse Apobec3 (mA3) overexpression and scRNAseq was performed on the mouse bladder tumors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
UPPA and UPP mouse bladder tumors are anlyzed using scRNAseq
human bladder tumor scRNAseq

>>>Raw data for human samples are deposited in dbGaP due to patient privacy concerns<<<

first: Andrew

last: Truong

first: Mi

last: Zhou


title: Kaposi’s sarcoma-associated herpesvirus modulates the pseudouridine pathway to enhance lytic replication

city: Leeds

first: Timothy

last: Mottram

address: Faculty of Biological Sciences

institute: University of Leeds

type: Methylation profiling by high throughput sequencing

summary: Pseudouridylation is a prevalent RNA modification shown to occur in tRNAs, rRNAs, snoRNAs and most recently mRNAs and ncRNAs. Emerging evidence suggests that this dynamic RNA modification is implicated in altering gene expression by regulating RNA stability, modulating translation elongation and modifying amino acid substitution rates.  However, the role of pseudouridylation in infection is poorly understood. Here we demonstrate that Kaposi’s sarcoma-associated herpesvirus (KSHV) manipulates the pseudouriylation pathway to enhance replication. We show the pseudouridine synthases (PUS), PUS1 and PUS7 are essential for efficient KSHV lytic replication, supported by the redistribution of PUS7 to viral replication and transcription complexes. Here we present a comprehensive analysis of KSHV RNA pseudouridylation revealing hundreds of modified RNAs at single-nucleotide resolution. Notably, we further demonstrate that pseudouridylation of the KSHV-encoded polyadenylated nuclear RNA (PAN) plays a significant role in the stability of PAN RNA and in the association of the KSHV ORF57 protein. Our findings reveal a novel and essential role of pseudouridine modification in the KSHV replication cycle.

overall_design: Samples are compared between respective Non-bisulfite control and Bisulfite treated samples and further compared between latent and doxycyline reactivated TREx-BCBL1-RTA cells, identifying deletion signatures indicative of pseudouridine modification presence.

first: Adrian

last: Whitehouse


title: Genomic copy number number characterisation of liver tissues in wildtype mice and ATF6-transgenic mice.

first: Kristian

last: Unger

summary: We compared the genomic copy number profiles of liver tissues of wild type mice with that of ATF6-transgenic mice after 3 and 12 months, respectively.

overall_design: Genomic DNA from tissue samples was hybridised against a pooled reference DNA from healthy mice.

first: Mathias

last: Heikenwälder


title: Genetic vulnerabilitis study in VHL mutant cells

first: Jianfeng

last: Ge

state: Cambridgeshire

address: 37, ST THOMAS'S SQUARE

institute: University of Cambridge

summary: VHL has been known as a tumour suppressor gene, also is an essential gene for some proteolysis-targeting chimera (PROTAC) degraders. Here by using CRISPR-cas9 genome wide screening we find that VHL mutation results in strong proliferation defect by HIF1A . VHL MUT shows malfunction of mitochondria which can be restored by HIF1A inhibition. VHL MUT bear specific genetic vulnerabilities which are druggable and mainly HIF1A dependent. In OE33 and MCF7, additional HIF1A inhibition on VHL MUT allows a complete ARV-771 drug resistance acquisition. Our study reports the consequence of VHL mutation and HIF1A dependent druggable genetic vulnerabilities in VHL mutant renal epithelial cells and possible PROTAC resistance acquisition mechanism in breast and oesophageal cancers, provides potential therapeutic targets and strategies for early precancerous and established cancerous cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VHL WT HK2 clones (D-C8, D-C10, D-C35) and VHL KO HK2 clones (C8, C10, C35).

first: Sakari

last: Vanharanta


title: Multipotent progenitors with distinct origins, clonal lineage fates, transcriptomes, and surface markers yield two hematopoietic trees

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: Multipotent progenitors (MPP) are the quantitative source of native hematopoiesis that have been thought to be replenished slowly by hematopoietic stem cells (HSC). However, recent fate mapping studies have revealed two developmentally distinct populations of MPP, HSC-derived MPP (hMPP), and HSC-independent, embryonic MPP (eMPP). These data raise fundamental questions on the distinctions and functions of these progenitors. Here, we mapped the clonal dynamics of the two independent MPP systems, using in situ barcoding, and barcode linkage (hMPP), or disconnect (eMPP), with HSC. The cumulative output of eMPP to hematopoiesis was 35%, and their output was enriched for lymphoid fates. Conversely, hMPP output was enriched for myeloid-restricted fates. Distinguishing HSC from eMPP outputs revealed that only ~15% of adult HSC clones underwent multilineage differentiation (lymphoid, myeloid, and erythroid). To prospectively identify eMPP, we developed PolySMART for joint profiling of PolyloxExpress RNA barcodes, surface markers, and transcriptomes, and we found that the plasma cell marker CD138 enriches for eMPP. CD138+ MPP are primed for self-renewal and toward lymphoid fate, and become largely but not completely replaced by CD138− MPP over time, which may contribute to the loss of lymphoid output with age. Taken together, adult hematopoiesis consists of two distinct lineage trees. The source of the “eMPP tree” substantially contributes to hematopoiesis before it declines, while the HSC-hMPP tree supplies hematopoiesis life-long. Our molecular determinants distinguishing the two MPP systems may open avenues to further explore these unexpected layers of hematopoiesis.

overall_design: Using the Polylox barcoding system, we first showed independent evidence of the existence of embryonic MPP.  Then, combining CITEseq experiments, we analyzed the difference between embryonic MPP and HSC-derived MPP in lineage fate, transcriptome and surface markers. In this study, we collected data from five Tie2PolyExpress E9.5-induction mice, six Tie2PolyExpress adult-induction mice, and fourteen RosaCreERT2PolyExpress  E14.5-induction mice (of which five were analyzed at E18.5, nine were analyzed at adult age).

first: Fuwei

last: Shang

first: Hans-Reimer

last: Rodewald


title: Role of Solute carrier family 37 member 3 in hepatocellular carcinoma

city: Tianjin

first: Ziyu

last: Meng

address: North Huairui, 6#

institute: Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology

summary: We selected si-SLC37A3-transfected HuH-7 cells in vitro to investigate the role of solute carrier family 37 member 3 in the progression of HCC

overall_design: HuH-7 cells were plated in 6-well plates and transfected with si-SLC37A3 and si-NC

first: Yutong

last: Sui


title: Transcriptional profile of Mycobacterium tuberculosis peptide-specific T cells in pulmonary granulomas

status: Public on Nov 04 2025

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: The function of Mycobacterium tuberculosis peptide-specific T cells in granulomas is incompletely understood. Here we profiled rhesus macaque and human Mtb-specific T cells by performing single cell RNA sequencing on granuloma cells stimulated with Mtb peptide pools. Mtb-specific T cells express pro-inflammatory cytokines, chemokines, TNF superfamily molecules, SLAM family molecules, semaphorins, growth factors, proteases and collagen. Peptide recognition by Mtb-specific T cells also drives expression of FLT3LG, LTA and XCL1 in bystander and unconventional CD8 T cells. Granuloma T cells express transcripts encoding multiple cytotoxic molecules, while peptide-specific T cells primarily express granzyme B. In granulomas from a patient that underwent a pneumonectomy to remove tuberculosis-destroyed lung, we identify a population of peptide-specific T cells similar to macaque peptide-stimulated T cells. Thus, Mtb peptide-specific T cells may mediate protection against Mtb infection through the combined effects of many functions as well as the induction of bystander responses by neighboring T cells.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Scale Bio single-cell RNA seqsequencing of granulomas from human and Rhesus macaque

first: Christine

last: Nelson

first: Keith

last: Kauffman

first: Kevin

last: Osum

first: Shunsuke

last: Sakai

first: Jay

last: Buchanan

first: Jean

middle: M

last: Chanchu

first: Melanie

last: Cohen

first: Julie

last: Laux

first: Iyadh

last: Dougi

first: Katherine

last: Barrows

first: Ifeanyichukwu

middle: U

last: Anidi

first: Cecilia

last: Lindestam Arlehamn

first: Alessandro

last: Sette

first: April

last: Walker

first: Amirhossein

last: Shamsaddini

first: Justin

middle: B

last: Lack

first: Joel

last: Ernst

first: Carl

middle: G

last: Feng

first: Laura

last: Via

middle: P

last: Fennelly

first: Shamus

middle: R

last: Carr

first: Daniel

middle: L

last: Barber


title: Generation of spinal cord organoids from human induced pluripotent stem cells caudalised to a lumbar fate

city: Parkville

first: Samantha

middle: Katherine

last: Barton

state: Victoria

address: 30 Royal Parade

country: Australia

institute: The Florey Institute of Mental Health and Neuroscience

summary: Organoids offer a powerful platform to model human development and disease in vitro while preserving key features of in vivo tissue architecture and complexity. In this study, we developed a novel, reproducible protocol to generate human induced pluripotent stem cell (iPSC)-derived spinal cord organoids specifically patterned to the lumbar region, a segment rarely modelled in vitro. These organoids recapitulate the ventral spinal cord’s cytoarchitecture and exhibit functional neuronal activity, providing a physiologically relevant system for investigating human spinal cord development and neurodegenerative disease mechanisms. Furthermore, we applied 10x Genomics single-cell RNA sequencing to generate the first high-resolution transcriptional map of human lumbar spinal cord organoids, revealing their cellular diversity and molecular signatures.

overall_design: Human iPSC-derived spinal cord organoids at day 60 of differentiation were enzymatically dissociated into a single-cell suspension and processed for transcriptomic profiling using the 10x Genomics single-cell RNA sequencing (scRNA-seq) platform.

first: Li Jun

last: Loh

last: Mason

first: Pratibha

last: Panwar

first: Shila

last: Ghazanfar

first: Kwaku

last: Dad Abu-Bonsrah

first: Forough

last: Habibollahi

first: Brett

last: Kagan

first: Bradley

last: Turner


title: Disparate Leukemia Mutations Converge on Nuclear Phase-Separated Condensates

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

summary: During cancer development, mutations promote gene expression changes that cause transformation. Leukemia is frequently associated with aberrant HOXA expression driven by translocations in nucleoporin genes or KMT2A, and mutations in NPM1. How disparate mutations converge on this regulatory pathway is not understood. Here we demonstrate that mutant NPM1 (NPM1c) forms nuclear condensates in multiple human cell lines, mouse models, and primary patient samples. We show NPM1c phase separation is necessary and sufficient to recruit NUP98 and KMT2A to condensates. Through extensive mutagenesis and pharmacological destabilization of phase separation, we find that NPM1c condensates are necessary for regulating gene expression, promoting in vivo expansion, and maintaining the undifferentiated leukemic state. Finally, we show that nucleoporin and KMT2A fusion proteins form condensates that are biophysically indistinguishable from NPM1c condensates. Together, these data define a new condensate underlying leukemias that we term coordinating bodies (C-bodies), and propose C-bodies as a therapeutic vulnerability.

overall_design: NPM1WT/Degron OCI-AML3 cells were transduced with the lentiviral particles to induce FL-NPM1c, “C-body null”, or mCherry overexpression after endogenous NPM1c degradation with dTAG-13. mCherry positive cells were FACS isolated

first: Gandhar

last: Datar

first: Elmira

last: Khabusheva

first: Archish

last: Anand

first: Joshua

last: Beale

first: Marwa

last: Sadek

first: Chun-Wei

last: Chen

first: Evdokiia

last: Potolitsyna

first: Nayara

last: Alcantara-Contessoto

first: Guangyuan

last: Liu

first: Josephine

last: De La Fuente

first: Christina

last: Dollinger

first: Anna

last: Guzman

first: Alejandra

last: Martell

first: Katharina

last: Wohlan

first: Abhishek

last: Maiti

first: Nicholas

last: Short

first: S. Stephen

last: Yi

first: Vibeke

last: Andresen

first: Bjørn Tore

last: Gjertsen

first: Brunangelo

last: Falini

first: Rachel

middle: E

last: Rau

first: Lorenzo

last: Brunetti

first: Nidhi

last: Sahni

last: Riback


title: Dissecting the epigenome dynamics in human immune cells upon viral and chemical exposure by multimodal single-cell profiling

city: Saarbrucken

first: Irem

middle: Begüm

last: Gündüz

state: Saarland

address: Building A2.4

department: Bioinformatics

institute: Saarland University

summary: Pathogen and chemical exposures lead to profound remodeling of the gene-regulatory landscape across human immune cell populations. Here, we present a single-nucleus chromatin accessibility atlas of human immune cells of individuals exposed to HIV-1, COVID-19, Influenza virus, organophosphates as well as healthy controls that provides insights into gene regulation driven by these cell-extrinsic stimuli. This atlas comprises 271,299 cells and 319,420 candidate regulatory elements that exhibited dynamic accessibility associated with gene expression across immune cell states. Our longitudinal HIV cohort revealed epigenetic signatures of T cell exhaustion, manifested in changes in the accessibility of binding sites for the FOXP family transcription factors. We further identified changes in the accessibility of candidate regulatory elements in CD14 monocytes upon SARS-CoV-2 exposure that are associated with a switch in NF-κB to AP-1-based regulation of cytokine networks. By integrating single-cell profiles of DNA methylation from matched samples we create a multimodal epigenome atlas of human immune cells across exposure states using the accessibility-derived candidate regulatory elements. Both modalities exhibit complementary epigenetic signatures at transcription factor binding sites associated with cell state, as exemplified in the process of memory formation in T-cells. Finally, by linking potentially regulatory DNA methylation signatures to changes in chromatin accessibility in monocytes, we identify AP1 motifs exhibiting epigenetic dynamics, indicating selective remodeling in TF networks in severe cases of COVID-19.

overall_design:
Single-cell ATAC-seq was performed on PBMCs from three human cohorts: (i) four HIV-infected individuals sampled longitudinally at pre-infection, acute, and chronic stages with ART administered between acute and chronic phases; (ii) five individuals challenged with live influenza virus and sampled at baseline (day -2), and 3, 6, and 28 days post-challenge; (iii) individuals with varying organophosphate exposure grouped by urinary TCPY levels (low: n=9, medium: n=6, high: n=20). Nuclei were processed using the 10x Genomics Chromium platform and sequenced on an Illumina NovaSeq 6000.

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

last: Gunduz

first: Bei

last: Wei

first: Aaron

last: Wilk

first: Madeline

last: Lee

first: Catherine

last: Blish

first: Fabian

last: Muller

first: William

last: Greenleaf


title: Impact of cranial bone-derived mesenchymal stem cell transplantation for functional recovery in experimental spinal cord injury

city: Hiroshima

first: Kiyoharu

last: Shimizu

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Neurosurgery

country: Japan

institute: Graduate School of Biomedical and Health Sciences Hiroshima University

summary:
We compared the therapeutic effects and mechanism of transplanted rat cranial bone-derived mesenchmay stem cell (rcMSCs) and rat bone marrow-derived mesenchymal stem cell (rbMSCs) in a rat cervical spinal cord injury (cSCI) model.
We  performed gene expression profiling analysis using data obtained from RNA-seq of rcMSCs and rbMSCs

overall_design: Comparative gene expression profiling analysis of RNA-seq data for rcMSCs and rbMSCs