title: SAM-synthase specific effects on metabolism and mitochondria underlie resistance to heat stress in C. elegans

city: Worcester

first: Amy

last: Walker

address: 373 Plantation Street

institute: UMass Medical School

summary: S-adenosylmethionine (SAM), produced by SAM synthases, is critical for various cellular regulatory pathways and the synthesis of diverse metabolites. Studies have often equated the effects of knocking down one synthase with broader SAM-dependent outcomes such as histone methylation or phosphatidylcholine (PC) production. However, many organisms express multiple synthase genes including humans and Caenorhabditis elegans. Evidence in C. elegans, which possesses an expanded family of SAM synthases, suggest that the enzymatic source of SAM impacts its function. For instance, loss of sams-1 leads to enhanced heat shock survival and increased lifespan, whereas reducing sams-4 adversely affects heat stress survival. Here, we reveal that loss of sams-1 exerts age-dependent effects on nuclear-encoded mitochondrial gene expression, mitochondrial metabolites, and mitophagy. Notably, we find that that SAMS-1 exerts synthase-specific effects on PC production. We propose a mechanistic framework wherein the reduced SAM from SAMS-1 acts through PC to impact mitochondrial fission and mitophagy, thereby enhancing survival during heat stress. This study highlights multifaceted roles of SAM across metabolic pathways and synthase-specific SAM functions.

overall_design: Lysis of young adult C. elegans was performed in 0.5% SDS, 5% β-ME, 10 mM EDTA, 10 mM Tris-HCl ph7.4, 0.5 mg/ml Proteinase K, before purification of RNA by TRI-Reagent (Sigma). cDNA was produced with Transcriptor First-strand cDNA kits (Roche), and RT-PCR was performed using Kappa SYBR Green 2X Mastermix. RNA for sequencing was purified using RNAeasy columns (Qiagen). RNA sequencing (including library construction was performed by BGI (Hong Kong). Reads were analyzed through the NextFlow analysis platform (https://github.com/DanHUMassMed/RNA-Seq-Nextflow), using DeSeq2 to identify differentially expressed genes. Gene set enrichment was performed using WormCat (http://www.wormcat.com).

first: Athena

middle: L

last: Munden

first: Dominique

last: Lui

first: Daniel

last: Higgins

first: Matthew

last: Fanelli

first: Thien-Kim

last: Ngyuen

first: Maria

last: Ericsson

first: Adwait

last: Godbole

first: Jessica

last: Spinelli

first: John

last: Haley

first: Caroline

last: Lewis

last: Promislow

first: Benjamin

last: Harrison

last: Raftery

first: Danijel

last: Djukovic

last: Miller


title: Injured epithelial cell states impact kidney allograft survival after T-cell-mediated rejection

status: Public on Nov 21 2025

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

type: Expression profiling by high throughput sequencing

summary: Background: T-cell mediated rejection (TCMR) remains a significant challenge after kidney transplantation and is associated with reduced allograft outcome. Previous research highlighted the critical role of TCMR-induced renal epithelial injury. Yet, the detailed cellular origin of these injury responses and the associated clinical implications remain poorly understood. Methods: To induce acute TCMR, we used mouse models of allogeneic (C57BL/6 to BALB/c and BALB/c to C57BL/6) kidney transplantation and syngeneic controls (C57BL/6 to C57BL/6 and BALB/c to BALB/c). Molecular changes were analyzed 7 days post-transplant using single-nucleus RNA sequencing and spatial transcriptomics. Results were compared with snRNA-seq data from three human TCMR biopsies and three stable allografts without rejection. The clinical impact of TCMR-induced epithelial injury was evaluated using marker gene sets on bulk transcriptomic data from 1292 kidney allografts, including 95 TCMR samples, with allograft outcome. Results: Mouse kidneys from allogeneic transplants exhibited all hallmark histological features of TCMR. Single-nucleus RNA sequencing revealed TCMR-induced injured cell states and significant gene expression changes particularly in proximal tubules (PT) and thick ascending limbs (TAL). Spatial transcriptomics showed a heterogeneous spatial distribution of these injured cell states and proximity to leukocytes. Cross-species analysis confirmed similar injured PT and TAL cell states in human TCMR. Signatures of a severely injured TCMR-induced TAL cell state correlated strongly with allograft survival in a large kidney transplant cohort specifically after TCMR. Conclusion: This is the first study showing kidney allograft outcome with distinct injured epithelial cell states. We found a particularly strong correlation between kidney allograft survival and TAL injury in TCMR, which occurred with reduced proximity to leukocytes, suggesting potential epithelial injury driven by non-immune mechanisms.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The presented data comprise single nucleus RNA sequencing data from mouse kidneys of syngeneic (C57BL/6 to C57BL/6 and BALB/c to BALB/c) and allogeneic (C57BL/6 to BALB/c and BALB/c to C57BL/6) transplantation, spatial transcriptomics data of the same and single nucleus RNA sequencing data from human kidney biopsies of stable kidney allografts and samples with T cell-mediated rejection.

first: Anna

last: Pfefferkorn

first: Lorenz

last: Jahn

first: Patrick

last: Gauthier

first: Janna

last: Leiz

first: Sadia

last: Safraz

first: Vera

last: Kuhlow

first: Izabela

last: Plumbom

first: Svjetlana

last: Lovric

last: Schmitz

first: Jan

last: Bräsen

first: Irina

last: Scheffner

first: Michael

last: Fähling

first: Igor

last: Sauer

first: Felix

last: Aigner

first: Janine

last: Altmüller

first: Thomas

last: Conrad

first: Kai

last: Schmidt-Ott

first: Wilfried

last: Gwinner

first: Philipp

last: Halloran

first: Muhammad

last: Ashraf


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (NNMT inhibition and SAM supplementation in TEC cells)

status: Public on Nov 20 2025

city: Amsterdam

first: Alessandra

last: Tammaro

state: AZ

address: Meibergdreef 05

department: Department of pathology

country: Netherlands

institute: Amsterdam University Medical Center

type: Methylation profiling by genome tiling array

summary: Renal tubular epithelial cells (TECs) are increasingly recognized as the central locus of chronic kidney disease and renal fibrosis. Here, we used conditionally immortalized TECs (expressing SV40 large T antigen at permissive conditions, 33°C with IFNγ, and behaving like normal primary cultures after 7 days in restrictive conditions, 37°C without IFNγ), stimulated with TGFβ to mimic the senescent and pro-fibrotic phenotypic shift of TECs during kidney disease. TGFβ stimulation and co-treatment with either the small-molecule NNMT inhibitor 5-amino-1-methylquinolinium iodide (NNMTi) or S-adenosyl methionine (SAM) altered the DNA methylation profile of the cells.

overall_design: 11 samples, 3 replicates (except 2 for TGFβ + SAM), 4 conditions. Control, TGFβ 10 ng/mL, TGFβ + NNMTi (5-amino-1-methylquinolinium) 50 µM, TGFβ + S-adenosyl methionine (SAM) 0.5mM. Cells treated for 48h.

first: Lucie

last: Chanvillard

first: Hildo

middle: C

last: Lantermans

first: Christopher

last: Wall

first: Jonathan

last: Thevenet

first: Loes

middle: M

last: Butter

first: Loic

last: Tauzin

first: Nike

last: Claessen

first: Stefan

last: Christen

first: Giulia

last: Lizzo

first: Sonia

last: Karaz

first: José

last: Sanchez-Garcia

first: Sylviane

last: Métairon

first: Valentina

last: Ferro

first: Sofia

last: Moco

first: Daniel

last: Raalte

first: Joris

last: Roelofs

first: Matthew

middle: J

last: Sanders

first: Jerom

middle: N

last: Feige

first: Vincenzo

last: Sorrentino


title: Pfkfb1 Selectively Identifies Macrophages Harboring Intracellular Growing Bacteria

city: shang hai

first: Li

last: Fan

address: song jiang qu

country: China

institute: Shanghai jiao tong university

summary: Through releasing virulence molecules into host cells, intracellular bacteria interfere with host cellular functions and grow in the cells that engulf them. To ensure survival and virulence, these pathogens also manipulate host factors, but this process is not fully understood. In this study, we investigated the host molecular mechanisms required for intracellular bacterial growth in macrophages using Salmonella typhimurium (Salmonella) infection model and bacterial division reporter system. Upon Salmonella infection, Protein Phosphatase 6 (Pp6) was significantly reduced in macrophages containing growing bacteria. Conditional knockout of Pp6 increased host susceptibility to Salmonella-mediated killing, which was attributed to the poor resistance in Pp6-deficient macrophages. MicroRNA-31 (miR-31) was identified as a negative regulator of Pp6, and its conditional deletion promoted Salmonella clearance. Moreover, a yeast two-hybrid screening identified 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (Pfkfb1), a key metabolic regulator, as a substrate of Pp6. Pp6-deficient macrophages exhibited elevated Pfkfb1 expression. Furthermore, we found that macrophages containing growing Salmonella exclusively exhibited high Pfkfb1 expression. Pfkfb1 deletion reduced bacterial growth, likely due to increased NO levels, while also downregulating arginase-1 (Arg-1) expression and impairing arginine biosynthesis and metabolism in macrophages. Together, we investigated the role of Pp6-Pfkfb1 axis in orchestrating host metabolic adaptions and intracellular bacterial survival, which may provide therapeutic targets for infectious diseases against intracellular multidrug-resistant bacteria.

overall_design: RNAseq profiling of WT  and Pfkfb1-/- BMDMs to explore the mechanistic basis

first: Yang

last: Sun


title: Transcriptomic analysis of ZMO_0422 in Zymomonas mobilis

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

country: USA

institute: University of Wisconsin - Madison

summary: Deletion of the IscR homolog ZMO_0422 was performed in Zymomonas mobilis to investigate the role of Fe-S cluster biogenesis in Zymomonas. Here we perform genome-wide transcirptomics study to examine transcript chagnes in delta-ZMO_0422 compared to WT Zymomonas mobilis under both aerobic and anaerobic growth conditions.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Transcriptomic analysis of WT and a deletion of ZMO_0422 of Zymomonas mobilis ZM4 under aerobic and anaerobic growth conditions.

first: Isabel

last: Askenasy

first: Patricia

last: Kiley


title: Synergistic Inhibition of CHK1 and MUS81 to target replicative stress in high-risk neuroblastoma

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

summary: Neuroblastoma (NB) is a pediatric tumor marked by genetic heterogeneity and frequent chromosomal alterations, including MYCN amplification and 17q gain, both linked to poor prognosis. These alterations affect key genes involved in transcriptional regulation and DNA damage response (DDR). NB cells experience high replicative stress (RS), making them particularly sensitive to DDR inhibition. Through integrative bioinformatics, genes such as EME1, RAD51C, and FANCJ on 17q were identified as critical in RS regulation. Targeting the downstream endonuclease MUS81, especially in combination with CHK1 inhibition, produced synergistic anti-tumor effects. This combination offers a promising strategy to exploit RS vulnerability in high-risk NB.

overall_design: RNA-sequencing of high dose Dyngo4a and combination drugging of Dyngo4a and prexasertib in IMR-32 neuroblastoma cell lines.

first: Elien

last: Hilgert

first: Fien

last: Martens

first: Suzanne

last: Vanhauwaert

first: Christophe

last: Vanneste

first: Frank

last: Speleman

first: Lisa

last: Depestel

first: Kaat

last: Durinck


title: Epigenomic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of an Alzheimer's Mouse Model [BiSulfite-seq]

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

type: Methylation profiling by high throughput sequencing

summary: Detecting and understanding Alzheimer's disease (AD) in its early stages is essential for uncovering the initial mechanisms behind its neuropathology and devising effective interventions. In this study, we leveraged the humanized AppNL-G-F mouse which exhibits early-onset amyloid pathology along a predictable timeline, to investigate molecular changes in the hippocampus and blood before the onset of severe neuropathology and independent of aging. Employing a multi-omics approach, we identified alterations in chromatin accessibility, gene expression, and DNA methylation associated with early amyloidosis. Chromatin accessibility changes were prominent in excitatory neurons during early pathology, with a later shift to inhibitory neurons, potentially reflecting compensatory mechanisms to mitigate excitatory neuron dysregulation. Despite broadly comparable hippocampal cell composition, transcriptomic comparisons between wild-type and AppNL-G-F mice revealed major gene expression differences, particularly in pathways related to mitochondrial function and protein biosynthesis, preceding severe amyloid plaque deposition. In later stages, upregulation of immune and neuroinflammatory pathways was observed, aligning with established neuroinflammatory processes in AD. Additionally, we identified extensive DNA methylation differences in both the blood and hippocampus of AppNL-G-F mice during early and late stages of pathology. Many differentially methylated regions in the blood, even at early pathology stages, were associated with cis-regulatory elements in the brain and were located near differentially expressed genes in the hippocampus. These regions were enriched in pathways related to brain function, such as neuron development and synaptic processes, indicating a link between blood methylation patterns and brain function. This suggests the potential utility of blood methylation as a biomarker for early amyloidosis detection. Notably, we identified five candidate biomarker genes, including Rbfox1 and Camta1, with epigenetic dysregulation detectable in both the brain and blood prior to severe amyloid accumulation. Our study, leveraging a unique AD mouse model and a multi-omics approach, highlights epigenetic signatures of AD before the onset of clinical symptoms, providing a foundation for future research into early diagnosis and therapeutic strategies, as well as potential biomarkers.

overall_design: WGBS libraries were prepared using gDNA from both blood and hippocampus tissues of wildtype and APP_nlgf mice across three developmental stages (postnatal week 3, week 8, and week 24) and both sexes (n=5 per sex/age/genotype combination). For each tissue and time point, regions of significant differential methylation (DMRs) were identified by comparing the two genotypes, with sex included as a covariate in the analysis.

first: Lucia

last: Carbone

first: Brett

last: Davis


title: Epigenomic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of an Alzheimer's Mouse Model [RNA-seq]

overall_design: Bulk hippocampus from male and female AppNL-G-F and wild-type mice was collected across three postnatal time points (week 3, 8 and 24; W3, W8 and W24) for a total of 60 samples (5 replicates per age/sex/genotype). Males and females were combined to serve as biological replicates. Gene expression patterns were compared between the two genotypes at each of the three time points, by using sex as co-variate.


title: RNA-seq profiling of mouse lung endothelial cells to investigate ENG-dependent and ENG-independent BMP9-induced target genes.

city: Cambridge

first: Jingxu

last: Guo

address: Papworth Road

country: United Kingdom

institute: University of Cambridge

summary: The aim of this experiment is to dissect endoglin (ENG)-dependent and ENG-independent BMP9 target genes. We have shown previously (PMID: 31431534) that BMP9 in complex with soluble endoglin (sENG:BMP9) has compromised signalling in Eng knockout (KO) mouse lung endothelial cells (MLECs), but not in wild type (WT) MLECs, suggesting sENG:BMP9 signalling in WT MLECs is mostly ENG-dependent. Hence we designed this experiment to compare  sENG:BMP9 signalliing in WT cells with prodomain bound BMP9 (pro:BMP9) signalling in Eng-KO cells to tease out ENG-dependent and ENG-independent BMP9 target genes.

overall_design: MLECs were isolated from four independent Eng fl/fl:Rosa26-CRE:Immorto mice. Eng KO MLECs were generted by tamoxifen induction in vitro, along with vehicle treated cells to obtain wild type (WT) control. Treatment in WT cells include PBS-treatment and sENG:BMP9 treatment. Treatment in KO cells include PBS-treatment and pro:BMP9 treatment. All samples were processed in parallel for RNA extraction and RNAsequencing.

first: Wei

last: Li


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [ES_H3K9ac_ChIP-seq]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Spatiotemporal changes in the nuclear lamina and cell metabolism shape cell fate, yet their interplay is poorly understood. Here, we show that nuclear lamina dynamics regulate cysteine catabolic flux, crucial for proper stem cell fate and longevity. Lamin A/C loss in naïve pluripotent stem cells upregulates CTH and CBS enzyme expression, promoting de novo cysteine synthesis. Increased cysteine flux into acetyl-CoA fosters histone H3K9 and H3K27 acetylation, triggering a transition from naïve to primed pluripotency and abnormal cell fate. Conversely, gain-of-function mutation of lamin A/C, associated with premature aging, reduces CTH and CBS levels. This reroutes the cysteine catabolic flux and alters the balance between H3K9 acetylation and methylation, crucially impacting germ layer formation and genome stability. Importantly, modulation of cysteine metabolism rescues the abnormal cell fate, DNA damage repair defects, and the senescent phenotype upon lamin A/C mutation, highlighting the potential of modulating cell metabolism to mitigate epigenetic diseases.

overall_design: PLKO_LmnaKO，LmnaKO_shCbs and LmnaKO_shCth Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF. ESCs  were harvested to perform for H3K9ac ChIP-seq.

first: Julio

last: Cordero

first: Yinuo

last: Wang


title: Neuronal GDF-15 delivery alters peripheral CD4+ T cell phenotype

city: Hamburg

first: Jana

last: Sonner

state: Hamburg

address: Martinistr. 52

department: ZMNH

institute: UKE

summary: In this study we investigated the immunomodulatory properties of GDF-15 in the context of neuroinflammation. We exploited neuronal gene therapy to overexpress GDF-15 within the central nervous system, which protected mice from developing any clinical signs of neuroinflammation in the experimental autoimmune encephalitis (EAE) model. We discovered that GDF-15 delivery modulated the peripheral T cell response and prevented immune cells from transmigrating into the central nervous system.

overall_design: Female C57BL/6J mice were injected with an rAAV (PHP.eB) capsid to express eGFP or murine GDF-15 under the control of the human Synapsin 1 promoter to restrict expression to neurons. Three weeks later EAE was induced in half of the animals using MOG35-55/CFA and pertussis toxin. During the preclinical phase (day 9 post immunisation) EAE animals and healthy controls were sacrificed and spleens collected. CD4+ T cells were enriched using the MojoSort Mouse CD4 T Cell Isolation Kit.


title: NNMT promotes tubular senescence and fibrosis in chronic kidney disease (db/m and db/db mice kidney)

first: Alessandra

last: Tammaro

summary: Diabetic kidney disease is the leading cause of chronic kidney disease. db/db mice, which carry a deletion mutation resulting in a dysfunctional leptin receptor, exhibit hyperphagia, obesity, and elevated insulin levels, making them a widely used preclinical model of diabetic kidney disease. At 16 weeks of age, db/db mice showed enriched transcriptomic signatures of cellular senescence in their kidneys compared to control db/m mice.

overall_design: 2 groups of 8 (db/m) and 9 (db/db) animals. Kidney tissue from 16-week old male BKS.Cg-Dock7m +/+ Leprdb/J HE/HE (db/m) and BKS.Cg-Dock7m +/+ Leprdb/J WT/HO (db/db) mice.

first: Lucie

last: Chanvillard

first: Hildo

last: Lantermans

first: Christopher

last: Wall

first: Jonathan

last: Thevenet

first: Loes

last: Butter

first: Loic

last: Tauzin

first: Nike

last: Claessen

first: Stefan

last: Christen

first: Giulia

last: Lizzo

first: Sonia

last: Karaz

first: José Luis

last: Sanchez-Garcia

first: Sylviane

last: Métairon

first: Valentina

last: Ferro

first: Sofia

last: Moco

first: Daniel

last: Raalte

first: Joris

last: Roelofs

first: Matthew

last: Sanders

first: Jerome

last: Feige

first: Vincenzo

last: Sorrentino


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (young, old and NAM-supplemented old mice kidney) [Series_4]

first: Alessandra

last: Tammaro

summary: Aging is a major risk factor for chronic kidney disease. Aged mice (21 months old) exhibited enriched transcriptomic signatures of fibrosis and cellular senescence in their kidneys compared to young mice (4 months old), and dietary supplementation with nicotinamide (NAM) was insufficient to reverse these disease signatures.

overall_design: 3 groups of 6 (young) or 8 (old, old+NAM) animals. Kidney tissue from 4 months old (young) and 21 months old (old) wild-type (WT) C57BL/6JRj male mice. Some old animals supplemented with nicotinamide (NAM) mixed with the diet at a dose of 200 mg/kg bw/day, 1.6g/kg food for 14 weeks.

first: Lucie

last: Chanvillard

first: Hildo

last: Lantermans

first: Christopher

last: Wall


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (NAM and SAM supplementation in TEC cells) [Series_2]

summary: Renal tubular epithelial cells (TECs) are increasingly recognized as the central locus of chronic kidney disease and renal fibrosis. Here, we used conditionally immortalized TECs (expressing SV40 large T antigen at permissive conditions, 33°C with IFNγ, and behaving like normal primary cultures after 7 days in restrictive conditions, 37°C without IFNγ), stimulated with TGFβ to mimic the senescent and pro-fibrotic phenotypic shift of TECs during kidney disease. Co-treating the cells with nicotinamide (NAM) did not prevent the senescence and epithelial-to-mesenchymal transition in TGFβ-stimulated TECs, while co-treating with S-adenosyl methionine (SAM) attenuated this dysfunctional phenotype.

overall_design: 18 samples, 3 replicates, 6 conditions. Control, TGFβ 10 ng/mL, nicotinamide (NAM) 1mM, TGFβ + NAM, S-adenosyl methionine (SAM) 0.5mM, TGFβ + SAM. Cells treated for 48h.

first: Jonathan

last: Thevenet

first: Loes

last: Butter

first: Loic

last: Tauzin

first: Nike

last: Claessen


title: Human CRX Regulates Photoreceptor Cells Development via Bidirectional Transcriptional Control in Retinal Organoids

city: Guangzhou

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: CRX (cone-rod homeobox) is a key regulator of retinal photoreceptor development, yet its human-specific functions remain poorly understood due to scarce human retinal tissues and significant species differences. Here, we established a human CRX-mCherry fluorescent reporter retinal organoid (RO) model to dissect CRX-mediated gene regulation. Using FACS, RNA-seq, and CUT&Tag-seq, we identified CRX target genes and revealed its dual regulatory role: it activates photoreceptor-specific genes (e.g., RP1L1, linked to inherited retinal degeneration) in a dose-dependent manner, while suppressing non-photoreceptor genes (e.g., PCDH8 and PROX1). Notably, we first generated the human CRX CUT&Tag dataset, providing direct insights into CRX’s genome-wide regulatory landscape in photoreceptor cell development. These findings demonstrate that CRX functions as both a transcriptional activator and repressor, ensuring photoreceptor-specific gene expression and preventing aberrant cell fate transitions. Our study provides critical insights into the role of human CRX in retinal development and implications for retinal degenerative diseases.

overall_design: We established a CRX-mCherry reporter fluorescent hiPSC line, which was subsequently differentiated into retinal organoids (ROs). On day 90 (D90), ROs were dissociated into single cells through enzymatic digestion. The cell suspension was then subjected to fluorescence-activated cell sorting (FACS) to isolate mCherry-positive and mCherry-negative cell populations. These two distinct populations were collected separately for RNA-seq analysis (designated as mN and mP). Furthermore, we performed ChIP-seq on D90 CRX-mCherry ROs to investigate CRX binding sites across the genome. Two experimental conditions were established: (1) a negative control group without CRX antibody (designated as -Ab), and (2) an experimental group with CRX antibody (designated as +Ab) to specifically capture CRX-associated chromatin regions.

first: Yuan

last: Wang

first: Bingbing

last: Xie

first: Xiaojing

last: Song

first: Guanjie

last: Gao

first: Yuanyuan

last: Guan

first: Dandan

last: Zheng

first: Ping

last: Xu


title: Epigenomic and Transcriptomic Alterations Precede Amyloidosis in the Hippocampus of an Alzheimer's Mouse Model

first: Mariam

last: Okhovat

overall_design: scATAC-seq libraries were prepared after pooling of n=5 biological replicates per genotype (wildtype and APP_nlgf), age (postnatal week 3, week 8, and week 24) and sex (male and female). For each tissue and time point, regions of significant differential methylation (DMRs) were identified by comparing the two genotypes, with sex included as a covariate in the analysis.

first: Lucia

last: Carbone

first: Brett

last: Davis


title: Genetic and dietary determinants of gut microbiome-bile acid interactions in BXD recombinant inbred mouse population

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

summary: Transcriptome data measured by microarray in proximal colon of  the BXD mouse genetic diversity model under a standard chow or a high fat diet at a postprandial state.

overall_design: At 29 weeks of age, previous euthanasia, mice were fasted overday and refed with their respective diet for 4h following their physiological cycle. Multi-organ were flash-frozen and bio-banked for future use, the assoiacted datasets are mentioned in the paper. In this study, proximal colon samples were collected and immediately frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.

first: Johan

last: Auwerx

first: Kristina

last: Schoonjans

first: Alessia

last: Perino

first: Hao


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [ES_ChIP_seq_H3K9me3_LA]

first: Gergana

last: Dobreva

summary: Spatiotemporal changes in the nuclear lamina and cell metabolism shape cell fate, yet their interplay is poorly understood. Here, we identify lamin A/C as a key regulator of cysteine catabolic flux essential for proper cell fate and longevity. Its loss in naïve mouse pluripotent stem cells leads to upregulation of the cysteine generating and catabolizing enzymes, cystathionine γ-lyase (CTH) and cystathionine β-synthase (CBS), thereby promoting de novo cysteine synthesis. Increased cysteine flux into acetyl-CoA fosters histone H3K9 and H3K27 acetylation, triggering a transition from naïve to primed pluripotency and abnormal cell fate and function. Conversely, the toxic gain-of-function mutation of Lmna, encoding lamin A/C and associated with premature aging, reduces CTH and CBS levels. This reroutes cysteine catabolic flux and alters the balance between H3K9 acetylation and methylation, crucially impacting germ layer formation and genome stability. Importantly, modulation of Cth and Cbs rescues the abnormal cell fate and function, restores the DNA damage repair capacity, and alleviates the senescent phenotype caused by lamin A/C mutations, highlighting the potential of modulating cell metabolism to mitigate epigenetic diseases.

overall_design: Control, Lmna KO and Lmna G609G/G609G  Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF. ESCs  were harvested to perform for H3K9me3 ChIP-seq.

first: Julio

last: Cordero

first: Yinuo


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [ES_ChIP_seq_H3K9ac_H3K27ac_LA]

overall_design: Control, Lmna KO nd CTH OE Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF. ESCs  were harvested to perform for H3K9ac and H3K27ac ChIP-seq.


title: Effects of lipopolysaccharide (LPS) or interferon gamma (IFNy) treatment on wild type or PILRA knock-out iPSC-derived human microglia after 24 hours

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: To study the effect of PILRA loss-of-function immune signaling pathways, we treated wildtype and PILRA knock-out (KO) iPSC-derived microglia (iMGs) with lipopolysaccharide (LPS) or interferon gamma (IFNy) for 24 hours and performed bulk RNA-seq analysis.

overall_design: iPSC-derived microglia (iMG) with either wildtype or PILRA knock-out genotypes were treated with either 1) LPS, 2) IFNg or 3) left untreated for 24 hours. The experiment was repeated five times, starting with freshly seeded iMG on different days.

first: David

last: Tatarakis

first: Tanya

last: Weerakkody

first: Kathryn

last: Monroe

first: Mathew

last: Blurton-Jones


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [04scRNA_seq_D10]

overall_design: Day10 EBs differentiated shControl, shControl Lmna-/-, shCth Lmna-/- mESCs were digested with Collagenase I.

first: Yonggang

last: Ren

last: Wang

middle: D

last: Cordero Henriquez


title: Transplantation of human glial progenitor cells into adult Huntington Disease mice rescues neuronal architecture and aspects of behavior

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Glial pathology is a significant contributor to disease pathogenesis in Huntington disease (HD), and neonatal glial replacement can delay disease progression and rescue aspects of behavior in mouse models of HD. Here we asked if the transplantation of normal human glial progenitor cells (hGPCs) into adult HD mice might similarly ameliorate phenotype. We found that the introduction of hGPCs into the striata of adult R6/2 HD mice significantly ameliorated their motor and cognitive phenotypes, extended their survival, and rescued aspects of medium spiny neuronal dendritic architecture. To establish the basis for this effect, we used retrograde labeling of striatal MSNs with glycoprotein-deleted rabies virus in hGPC-engrafted adult R6/2 mice to discover that the dendritic architecture of striatal MSNs was partially restored in adult-engrafted mice. These findings suggest that glial replacement may delay disease progression in HD, and that this is associated with the dynamic reorganization of medium spiny neuron dendritic architecture.

overall_design: WT mice or R62 mice (HD model) (n=2) were transplanted with human glia to investigate neuronal changes in response to glial transplantation. Unengrafted mice for both WT and R62 were used as control.

first: Carlos

middle: B

last: Villanueva

middle: A

first: Ashley

last: Tate

first: Signe

last: Lorenzen

first: Abdellatif

last: Benraiss

first: Nguyen

middle: P

last: Huynh

first: Benjamin

last: Mansky


title: A receptor kinase complex refines cambium activity in Arabidopsis

status: Public on Nov 19 2025

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: The largest reservoir of terrestrial biomass is the wood within plant stems. Consisting of xylem cells, wood is derived from the cambium, a stem cell population that is maintained by non-cell autonomous signalling. The central component of this system is PXY, a receptor protein present on the plasma membrane of cambium cells. Here, we show that PXY protein interacts with a second membrane-localised receptor kinase, ER, to promote cambium fate. Combinatorial mutations between ER, ERL1 and ERL2 and receptor kinases of a second family, PXY, PXL1, and PXL2, show severe cambial defects, but the mechanism underpinning these phenotypes is not known. Here we discovered that PXY and PXL proteins form protein complexes with ER family members. In genetic analyses, plant lines in which PXY signalling was constitutively active had dramatic phenotypic changes that required the presence of ER or ERL2. Our results demonstrate that PXY signalling mediated cambium regulation depends on ER signalling and explains ER function in the cambium. Because the cambium produces xylem, which constitutes the wood in vascular plants, our findings position PXY-ER complexes at the centre of the accumulation of this versatile biomaterial and essential carbon sink.

overall_design: RNA-Seq profiling of 7-day-old wild type, er mutant and XVE:ER transformed er mutant at 0h, 3h and 8h Estradiol induction.

first: Qing

last: He

first: Peter

last: Etchells


title: Dual developmental effects of ARX poly-alanine mutations in human cortical excitatory and inhibitory neurons

city: San Antonio

first: Jenny

last: Hsieh

state: Texas

address: One UTSA Circle

department: Department of Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

summary: Infantile spasms (IS), a severe childhood epilepsy with an incidence of 1.6–4.5 per 10,000 live births, often lead to lifelong intellectual disability. Up to 5% of affected males carry mutations in the Aristaless-related homeobox (ARX) gene. The lack of human-specific models for developmental epilepsy limits progress, making organoids a promising alternative. We use human cortical (CO) and ganglionic eminence organoids (GEO) to model poly-alanine expansion (PAE) mutations in ARX. PAE mutations increase cortical progenitor proliferation and accelerate early cortical development. ARX expression is upregulated in patient-derived COs at 30 DIV, correlating with altered cell cycle gene expression. We observe enhanced, cell-autonomous interneuron migration, which is rescued by CXCR4 inhibition. ARXPAE assembloids exhibit early network hyperactivity. These findings highlight the utility of human brain organoids in uncovering ARXPAE-driven mechanisms and represent a critical step toward developing targeted therapies for IS and related developmental epilepsies.

overall_design:
Human iPSC derived cortical organoids and ganglionic eminence organoids at 2 developmental timepoints (30DIV and 120DIV) were dissociated , single cell suspension was made and 10X genomics was used to perform single cell RNA sequencing
DIV = Days in vitro
Mapped to GRCh38 human assembly

first: Vanesa

last: Nieto-Estevez

first: Parul

last: Varma

first: Sara

last: Mirsadeghi

first: Jimena

last: Caballero

first: Sergio

last: Gamero-Alameda

first: Ali

last: Hosseini

first: Marc

last: Silvosa

first: Drew

last: Thodeson

first: Sonal

last: Goswami

first: Zane

middle: R

last: Lybrand

first: Michele

last: Giugliano

first: Christopher

last: Navara


title: Nutrigenomic profiling identifies ZIP10 (SLC39A10) as a regulator of erythroid zinc homeostasis with genetic associations to anemia risk

city: Seoul

first: Moon-Suhn

last: Ryu

address: 50 Yonsei-ro, Seodaemun-gu, Samsung Hall 611

country: South Korea

institute: Yonsei University

summary: To determine the physiological roles of ZIP10 and zinc in erythroid progenitor cells, Zip10 was depleted via nucleofector-mediated siRNA delivery into cells and cellular zinc was restricted by DTPA treatment. The transcriptome profiles acquired from RNA-seq were compared with those of control cells.

overall_design: Comparative gene expression profiling of control G1E-ER4 cells and those deficient in cellular zinc, ZIP10, or both (n = 3 biological replicates per group)

first: Juyoung

last: Kim


title: Anti-IL-15 treatment reduces acute lentivirus inflammation and signaling in the brain

city: Iowa City

first: Chen

middle: Sabrina

last: Tan

state: IA

address: 200 Hawkins Dr.

institute: University of Iowa

summary: In this study, we investigated the impact of IL15 on the brain’s immune and inflammatory milieu during acute SIV infection of rhesus macaques. Given the ongoing issue of HIV-associated neurocognitive disorders (HAND) in people living with HIV and the role of inflammation in its pathogenesis, understanding the brain’s immune response to lentiviral infections is crucial. We found that SIV infection stimulated a resident brain immune response in control animals, characterized by increased astrocyte activation and enhanced ramification of microbial morphology. However, animals treated with anti-IL15 antibodies (aIL15) prior to SIVmac239X infection showed significantly reduced brain inflammation without altering SIV levels in brain tissues. Specifically, aIL15 treatment resulted in 1) decreased overall microglial cell populations; 2) altered T lymphocyte dynamics in the brain; 3) reduced proinflammatory cytokine (IL6) expression in microglia; and 4) increased anti-inflammatory cytokine (TGF-β) expression in brain macrophages. RNA transcription profiles of aIL15-treated animals revealed an overall reduction in inflammatory signaling, alongside upregulation of genes associated with M1 macrophage signaling pathways. These results suggest that peripheral modulation of IL15 can attenuate neuroinflammation during acute lentiviral infection and may be therapeutic in conditions such as HAND. Our findings highlight the potential for targeting peripheral immune factors to modulate central nervous system inflammation in lentiviral infections.

overall_design: 11 adule male rhesus macaques were used. 8 were infected with SIVmac239. 3 were sacrificed on day 7, 5 were sacrificed on day 14. 3 were uninfected controls. Brain tissue from the frontal cortex and blood was sampled at necropsy. Basal ganglia and thalamus tissue were also collected from one animal.

first: Daniel

last: Ram

first: Raja

last: Gopalakrishnan

first: Malika

last: Aid

first: Kyle

middle: W

last: Kroll

first: Eunice

middle: K

last: Gikundiro

first: Caitlin

last: Davis

first: Marco

last: Hefti

first: Kimberly

last: Fiock

first: Brook

last: Tilahun

first: Yvette

last: Umotoniwase

first: Rhianna

last: Jones

first: Griffin

last: Woolley

first: Valerie

last: Varner

first: Michelle

last: Lifton

first: Steven

middle: E

last: Bosinger

first: Dan

middle: H

last: Barouch

first: Brandon

middle: F

last: Keele

first: R. Keith

last: Reeves

first: Sabrina


title: Nutrigenomic profiling identifies ZIP10 (SLC39A10) as a regulator of erythroid zinc homeostasis with genetic associations to anemia risk I

first: Moon-Suhn

last: Ryu

summary: To determine the effects of heme synthesis inhibition via different pathways in erythroid progenitor cells, heme synthesis was inhibited by 50 µM DTPA treatment (a zinc chelator), 50 µM DFO treatment (a  iron chelator), or 0.2 mM succinylacetone (SA, a ALAD inhibitor) for 24 hours in differentiating G1E-ER4 cells. G1E-ER4 Cells were divided into four groups: untreated control, 50 µM DTPA treatment, 50 µM DFO treatment, and 0.2 mM SA. The transcriptome profiles acquired from RNA-seq were compared with those of control cells.

overall_design: Comparative gene expression profiling of control G1E-ER4 cells and those deficient in cellular zinc, cellular iron, or ALAD activity (n = 3 biological replicates per group)

first: Juyoung

last: Kim


title: Nutrigenomic profiling identifies ZIP10 (SLC39A10) as a regulator of erythroid zinc homeostasis with genetic associations to anemia risk II

summary: To determine the physiological roles of zinc in erythroid progenitor cells, cellular zinc was restricted by 50 µM DTPA treatment (a zinc chelator) for 24 hours in differentiating G1E-ER4 cells. G1E-ER4 cells induced for differentiation by beta-estradiol were divided into two groups: control and 50 µM DTPA treatment. A sample from cells untreated with beta-estradiol was also included as an undifferentiated group.

overall_design: Comparative gene expression profiling of G1E-ER4 cells differentiating under control zinc and zinc restriction (n = 3 biological replicates per treatment), and undifferntiating cells without zinc intervention (n = 1)


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (Nnmt overexpressing TEC cells) [Series_3]

first: Alessandra

last: Tammaro

summary: Renal tubular epithelial cells (TECs) are increasingly recognized as the central locus of chronic kidney disease and renal fibrosis. Here, we used conditionally immortalized TECs (expressing SV40 large T antigen at permissive conditions, 33°C with IFNγ, and behaving like normal primary cultures after 7 days in restrictive conditions, 37°C without IFNγ) and genetically overexpressed Nnmt (Nnmt-OE) by means of lentiviral transduction of a mock or Nnmt expression construct. In the TGFβ model mimicking the senescent and pro-fibrotic changes in TECs, Nnmt overexpression resulted in an aggravated phenotype.

overall_design: 12 samples, 3 replicates, 4 conditions. Cells transduced with a mock or Nnmt expression construct and selected on puromycin. Some samples treated for 48h with TGFβ 10 ng/mL.

first: Lucie

last: Chanvillard

first: Hildo

last: Lantermans

first: Christopher

last: Wall

first: Jonathan

last: Thevenet

first: Loes

last: Butter

first: Loic

last: Tauzin

first: Nike

last: Claessen

first: Stefan

last: Christen

first: Giulia

last: Lizzo

first: Sonia

last: Karaz

first: José Luis

last: Sanchez-Garcia

first: Sylviane

last: Métairon

first: Valentina

last: Ferro

first: Sofia

last: Moco

first: Daniel

last: Raalte

first: Joris

last: Roelofs

first: Matthew

last: Sanders

first: Jerome

last: Feige

first: Vincenzo

last: Sorrentino


title: Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective [bulk RNA-seq]

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: Tyrosine kinase inhibitors (TKIs) have improved cancer outcomes but are limited by cardiovascular toxicity, most notably hypertension and heart failure. The underlying mechanisms remain poorly understood, hindering the development of protective strategies. Here, we investigated the role of endothelial mechanotransduction in mediating vascular and cardiac injury caused by the VEGFR-targeting TKI sunitinib. Using patient-specific induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) and a mouse model of TKI-induced hypertension, we identified downregulation of PIEZO1, a mechanically activated ion channel, as a central driver of endothelial dysfunction. Restoring PIEZO1 expression, either pharmacologically with Yoda1, a selective agonist, or through inducible overexpression in iPSC-ECs, reversed sunitinib-induced endothelial dysfunction and mitigated its hypertensive effects, providing both mechanistic and genetic validation of PIEZO1’s protective role against vascular toxicity. In mice, Yoda1 co-treatment prevented the long-term cardiac dysfunction observed following sunitinib exposure, and normalized elevations in circulating cardiac stress biomarkers. Single-nuclei multiomic profiling of mouse hearts revealed that sunitinib exposure activated chromatin remodeling and fibrogenic programs, which were reversed with PIEZO1 activation. Human engineered cardiac organoids further demonstrated that sunitinib impaired cardiomyocyte function only in the presence of endothelial cells, confirming a role for disrupted endothelial-cardiomyocyte crosstalk in TKI cardiotoxicity. Together, these findings identify endothelial PIEZO1 as a critical mediator of TKI-induced hypertension and cardiac dysfunction and highlight PIEZO1 activation as a potential therapeutic strategy for protecting cardiovascular health during cancer therapy.

overall_design: RNA-seq of patient-specific iPSC-ECs, primary endothelial cells, and iPSC-derived cardiac organoids

first: Nazish

last: Sayed


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (NNMT inhibition in TEC cells) [Series_1]

city: Amsterdam

first: Alessandra

last: Tammaro

address: Meibergdreef 05

institute: Amsterdam University Medical Center

summary: Renal tubular epithelial cells (TECs) are increasingly recognized as the central locus of chronic kidney disease and renal fibrosis. Here, we used conditionally immortalized TECs (expressing SV40 large T antigen at permissive conditions, 33°C with IFNγ, and behaving like normal primary cultures after 7 days in restrictive conditions, 37°C without IFNγ), stimulated with TGFβ to mimic the senescent and pro-fibrotic phenotypic shift of TECs during kidney disease. Co-treating the cells with the selective and membrane-permeable small molecule 5-amino-1-methylquinolinium iodide (NNMTi) significantly protected against senescence and epithelial-to-mesenchymal transition in TGFβ-stimulated TECs.

overall_design: 12 samples, 3 replicates, 4 conditions. Control, TGFβ 10 ng/mL, NNMTi (5-amino-1-methylquinolinium) 50 µM, TGFβ + NNMTi. Cells treated for 48h.

first: Lucie

last: Chanvillard

first: Hildo

last: Lantermans

first: Christopher

last: Wall

first: Jonathan

last: Thevenet

first: Loes

last: Butter


title: NNMT promotes tubular senescence and fibrosis in chronic kidney disease

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

overall_design: Refer to individual Series


title: Sex-Specific Angiogenic Responses in Endothelial Cells – Role of the Pluripotency Factor OCT4

city: Cleveland

first: Olga

last: Cherepanova

state: OH

address: 9500 Euclid Ave

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic

summary: The study investigates the sex-specific effects of the pluripotency factor OCT4 deficiency in endothelial cells (ECs) on angiogenesis. OCT4 is known for its role in embryonic stem cells, but we recently found that it plays a protective role in ECs during atherosclerosis. Herein, we utilized cultured mouse aortic ECs (MAECs) and several in vivo models, including skin wounding, melanoma tumor implantation, and hindlimb ischemia, to explore the role of OCT4 in angiogenesis in both male and female mice. Our findings show significant sexual dimorphism in angiogenic responses to OCT4 deficiency. Male mice with endothelial Oct4 knockout had faster skin wound healing, increased vascularization, and quicker blood flow recovery after hindlimb ischemia than wild-type mice. In contrast, female mice with endothelial Oct4 knockout experienced delayed wound healing, no significant change in blood flow recovery after hindlimb ischemia, and increased tumor growth. Mechanistically, MCP1, a key angiogenic chemokine, was differentially regulated in male and female Oct4 knockout compared to wild-type MAECs, suggesting OCT4-dependent regulation of MCP1 as a critical mechanism for sex differences in angiogenic responses. RNA sequencing (RNAseq) analysis revealed distinct gene expression profiles in male and female MAECs upon OCT4 deficiency, with female ECs showing upregulation of pro-inflammatory genes and male ECs exhibiting increased cell cycle and angiogenesis-related gene expression. Overall, the research provides novel insights into the sex-specific functional role of OCT4 in ECs during angiogenesis and emphasizes the need for developing sex-specific EC-targeting therapeutic strategies for cardiovascular diseases and cancer.

overall_design: To investigate the role of the pluripotency factor OCT4 in endothelial cells, we isolated endothelial cells from aortas of endothelial cell specific OCT4 knockout male and female mice. We established mouse aortic primary cultured endothelial cells. We then performed bulk RNA-seq. The wild-type male and female aortic endothelial cells were isolated from the littermate mice and cultured, processed, and sequenced in parallel. Raw data for wild type control cells can be found in GSE247364.


title: 4EHP and NELF-E regulate factors required for ATF4 expression in the Drosophila fat body

city: New York

first: Hyung Don

last: Ryoo

address: 550 First Avenue, MSB 497

department: Cell Biology

institute: NYU School of Medicine

summary: Cells adapt to proteostatic and metabolic stresses, in part, by triggering the phosphorylation of eIF2alpha and the subsequent synthesis of ATF4. eIF2alpha phosphorylation facilitates translational induction of ATF4 by regulating reinitiation of the scanning ribosomes at the ATF4 mRNA’s 5’ leader. In addition to eIF2alpha, ATF4 induction requires other regulators that remain poorly understood. Here, we report an ATF4 regulatory network consisting of eIF4E-Homologous Protein (4EHP), NELF-E, the 40S ribosome, and eIF3 subunits. Specifically, 4EHP was required for ATF4 signaling in the Drosophila larval fat body and in disease models associated with abnormal ATF4 signaling. 4EHP’s mRNA cap-binding domain specifically interacted with NELF-E mRNA, which encodes a regulator of pol II-mediated transcription. Both NELF-E and 4EHP were required for the expression of ATF4 and enzymes that mediate the serine-one-carbon pathway. Knockdown of NELF-E also reduced several subunits of the 40S ribosome and the eIF3 translation initiation factor complex. Reduction of Rps12 and eif3h suppressed physiological ATF4 induction. These results uncover a previously unrecognized ATF4 regulatory network that impacts stress adaptation and pathological outcomes.

overall_design: We knocked down 4EHP in the Drosophila fat body using the dcg-Gal4 driver that drived 4EHP RNAi (VDRC #38399). NELF-E was knocked down by the expression of NELF-E RNAi (VDRC #21009) with the dcg-Gal4 driver. To identify 4EHP binding mRNAs, we expressed 4EHP fused to ADAR in the fat body (using dcg-Gal4) and compared the extent of mRNA editing with a negative control 4EHP-ADAR that has an impaired mRNA cap-binding domain. The fat bodies were dissected from late third instar male larvae and the RNAs were extracted using Trizol. PolyA mRNA was sequenced through Novaseq 6000.

first: Kristoffer

last: Walsh

first: Christoph

last: Dieterich


title: Dextran-based T-cell expansion nanoparticles for manufacturing CAR T cells with augmented efficacy

city: Kgs. Lyngby

first: Kamilla Kjærgaard

last: Munk

address: Henrik Dams Allé, 204

department: Department of Health Technology

country: Denmark

institute: Technical University of Denmark

summary: Adoptive T cell therapy (ACT) using chimeric antigen receptor (CAR) engineered T cells is currently being explored in multiple cancer types beyond leukemia/lymphoma. A key step in CAR-T cell manufacturing is the activation and expansion of T cells, which facilitates viral transduction, however, may hamper T cell fitness and reduce in vivo persistence. We developed “T-Expand” for T cell activation and expansion, comprising dextran-based nanoparticles (NPs) conjugated with anti-CD3 and anti-CD28 antibodies. The NPs triggered robust polyclonal expansion of human T cells with efficiency in the range of commercial microbeads (Dynabeads™). Engineered in the presence of T-Expand, CD19 CAR T cells exhibited enhanced proliferative capacity, cytotoxicity and persistence in vitro, and furthermore, showed superior anti-lymphoma activity in mouse models, resulting in complete tumor clearance at one fourth of the CAR T cell dose. Importantly, T-Expand is biocompatible with no observed toxicity, circumventing removal steps after T cell expansion compared to DynabeadsTM. As a biocompatible T cell expansion platform, T-Expand simplifies the manufacturing process while enhancing T cell persistence and functionality, and thereby holds promise for increasing clinical efficacy of CAR T cell therapy.

overall_design: RNA-seq profiling of CAR T cells expanded with T-Expand or Dynabeads in the presence of 20 IU/ml IL-2 for 10 days.

first: Tao

last: Zheng

first: Keerthana

last: Ramanathan

first: Maria

last: Ormhøj

first: Mikkel

last: Hansen

first: Hólmfridur

last: Halldórsdóttir

first: Hanxi

last: Li

first: Kamilla

first: Carlos

last: Rodriguez-Pardo

first: Rasmus

last: Friis

first: Seder

last: Islam

first: Peter

last: Heegaard

first: Klaus

last: Qvortrup

first: Hinrich

last: Abken

first: Yi

last: Sun

first: Sine

last: Hardup


title: Intestinal Macrophages Modulate Brain Synucleinopathy in Parkinson’s Disease

city: London

first: Daria

last: Gavriouchkina

state: London

address: UCL Cruciform Building, Gower Street

department: UK Dementia Research Institute at UCL

institute: University College London

summary: Emerging evidence suggests that Parkinson’s disease (PD) may have its origin in the enteric nervous system (ENS), from where alpha-synuclein (αS) pathology spreads to the brain. Decades before the onset of motor symptoms, PD patients suffer from constipation and present with circulating T cells responsive to αS, suggesting that peripheral immune responses initiated in the ENS may be involved in the early stages of PD. However, cellular mechanisms that trigger αS pathology in the ENS and its spread along the gut-brain axis remain elusive. Here, we demonstrate that muscularis macrophages (ME-Macs), housekeepers of ENS integrity and intestinal homeostasis, modulate αS pathology and neurodegeneration in models of PD. ME-Macs contain misfolded αS, adopt a signature reflecting endolysosomal dysfunction, and modulate the expansion of T cells that travel from the ENS to the brain via the dura mater as αS pathology progresses. Directed ME-Mac depletion leads to reduced αS pathology in the ENS and CNS, prevents T cell expansion, and mitigates neurodegeneration and motor dysfunction, suggesting a role for ME-Macs as early cellular initiators of αS pathology along the gut-brain axis. Understanding these mechanisms could pave the way for early-stage biomarkers in PD.

overall_design: In this study, single-cell RNA sequencing was performed on duodenal muscularis externa from wild-type and 3KL α-synuclein transgenic mice to capture transcriptional changes associated with α-synuclein pathology. 4 biologically independent samples were analyzed per genotype, each consisting of pooled tissue from 4 mice to ensure reproducibility. Macrophages and T cells were isolated from the muscularis externa and profiled in parallel to assess their transcriptional states and potential interactions. The design allowed direct comparison between disease and control conditions, with quality control and clustering used to define distinct cell populations. Main variable: genotype (WT vs 3KL).

first: Sebastiaan

last: De Schepper

first: Viktoras

last: Konstantellos

first: James A

last: Conway

first: Dimitra

last: Sokolova

first: Ludovica

last: Zaccagnini

first: Matthew V

last: Cowley

first: Annerieke

last: Sierksma

last: Yudina

first: Marisa

last: Edmonds

first: Bethany

last: Geary

first: Amber

last: Wallis

first: Meral

last: Celikag

first: Zeynep

last: Baykam

first: Monica

last: Vara-Perez

first: Gerard

last: Crowley

first: Fabian Tobias

last: Hager

first: Mitchell

last: Bijnen

first: David

last: Posner

first: Kelvin

last: Luk

first: Vuk

last: Cerovic

first: Menna

last: Clatworthy

first: Elizabeth J

last: Videlock

first: Zane

last: Jaunmuktane

first: Kiavash

last: Movahedi

first: Melanie

last: Greter

first: Benny

last: Chain

first: Dario R

last: Alessi

first: Soyon

last: Hong

first: Tim

last: Bartels


title: Quantifying Transcription Factor Specificity with Advanced DNA Universal Microarrays Featuring Long and Modified Binding Sites [974k]

city: Rehovot

first: Yuval

last: Bayer

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

summary: In the study, we have created new de Bruijn sequences for universal Protein Binding Microarrays with varying orders and DNA letter sets.

overall_design: The design is of probes which include a single de Bruijn of order 12. Layout is one chamber of 1824x534 probes. Each of all non-palindromic 10-mers is contained in at least 35 probes.

first: Ariel

last: Afek


title: Comparative analysis of shared and unique mechanisms important for diverse strains of Pasteurella multocida to cause systemic infection in mice

city: Clayton

first: Thomas

last: Smallman

state: Victoria

address: 19 Innovation walk

department: Microbiology

country: Australia

institute: Monash University

summary: Pasteurella multocida is a pathogen that causes a range of distinct diseases in livestock animals. Different P. multocida strains produce different capsule and lipopolysaccharide (LPS) structures. Different P. multocida diseases are associated with different capsule and LPS types, and little is known about what underpins this disease specificity. In this study, we utilised transposon-directed insertion site sequencing (TraDIS, also called Tn-Seq) to identify genes required for growth in rich media, and genes required for survival during systemic infections in BALB/c mice, for two diverse P. multocida strains, strain VP161 (capsule type A and LPS type L1) and strain M1404 (capsule type B and LPS type L2). Rich media analysis showed that both VP161 and M1404 shared 461 genes essential for growth in rich media, with comparison to the entire species showing that 95% of these rich media essential genes present in all publicly available closed P. multocida genomes. In vivo fitness analysis identified 63 and 94 genes important for VP161 and M1404 survival in BALB/c mice, respectively. Only 35 homologs were identified in both strains as important for survival, showing that conserved biological systems can be differentially important for different P. multocida strains. Investigation of proteins involved in the catabolite response showed that an active cyclic-adenosine monophosphate (cAMP) receptor protein (CRP) was required for maximal fitness in M1404.  Furthermore, disrupting CRP or cAMP production also reduced capsule production in M1404, but increased capsule production in VP161, showing different strains of P. multocida have different regulatory systems for crucial virulence factors.

overall_design: This study used transposon-directed insertion site sequencing (TraDIS, also called Tn-Seq) to investigate genes required for growth in rich media, and genes important for in vivo fitness, of two Pasteurella multocida strains, strain VP161 and strain M1404. A large VP161 Himar1 mutant library was grown in heart infusion broth, used to inject six-to-eight-week-old BALB/c mice via intraperitoneal injection with ~1 x 107 colony forming units. At the humane end point, surviving mutants were recovered from the bloodstream, liver and spleen, then plated on heart infusion agar and incubated overnight at 37ºC. The input library was also plated onto heart infusion agar and incubated overnight. The M1404 Himar1 mutant library was also used in the same way. Cells were recovered from the overnight growths, genomic DNA extracted and used to produce TraDIS libraries. TraDIS libraries were generated by shearing DNA to ~300 bp using Covaris sonication, using NEBNext kits to repair the ends of the DNA, A-tail, and then ligate adapters on the end. Specific amplification of transposon-chromosome junctions was performed using a Himar1-specific primer, and an adapter-specific primer. The adapter-specific primer contained index sequences specific for each dataset, and the primers contained Illumina P5 and P7 sequences to allow for Illumina sequencing. The TraDIS libraries were sequenced using an Illumina MiSeq, and the data analysed using the Bio-TraDIS toolkit. The data uploaded are the reads generated from the Illumina MiSeq, and the excel table that contains the analysed data shows the number of reads per gene, the number of unique Himar1 insertion sites per gene, and whether they were called as essential for growth in rich media or important for in vivo fitness in different tissues recovered from BALB/c mice.

first: Xiaochu

last: Wang

first: Xenia

last: Kostoulias

first: Amy

last: Wright

first: Faye

last: Morris

first: Marina

last: Harper

first: John

last: Boyce


title: Molecular and spatial integration of algal endosymbionts of the freshwater sponge, Ephydatia muelleri, throughout development in light and dark conditions

city: Lewiston

first: April

middle: L

last: Horton

email: ahorton@bates.edu, ahill5@bates.edu

state: Maine

address: 44 Campus Avenue, Carnegie Science Hall

department: Biology

institute: Bates College

summary: Animal-algal photosymbioses are a unique group of symbiotic relationships in which animals harbor photosynthetic algae within their cells and tissues. Both marine and freshwater sponges host algal endosymbionts. In previous work, we demonstrated that freshwater sponges can acquire these endosymbionts horizontally through algal infection and that potentially conserved evolutionary pathways may lead to the establishment of the endosymbioses including those involved in endocytosis, ion transport, vesicle-mediated transport, innate immunity, redox regulation, and metabolic processes.  Here, we show that algal symbionts can be transferred vertically from algal-bearing overwintering gemmules to adult sponges, and that their proliferation is enhanced by light. Sponges grown under light conditions harbored higher algal loads than those in the dark; however, algae were still able to proliferate and persist in sponges reared in the dark, occupying similar spatial locations to those grown in light. RNA-Seq analysis of algal-bearing sponges across developmental stages in light and dark conditions revealed genetic regulatory pathways involved in the transmission and establishment of the endosymbiosis. Differential expression analysis indicated that the endocytosis and SNARE pathways regulate the internalization and transport of algae  at the earliest stage of hatching under light conditions and later in development under dark conditions, potentially contributing to the recruitment of endosymbiotic algae. In sponges hatched in the dark, genes involved in vesicle acidification are regulated, alongside changes in the expression of genes in the pentose phosphate pathway - a key metabolic route involved in redox homeostasis and circadian rhythm regulation via NADPH metabolism, is observed. E. muelleri serves as a versatile model system, supported by robust genomic and transcriptomic resources, for studying host-symbiont interactions. It offers a unique opportunity to investigate the molecular signaling and environmental factors that shape symbiosis in a system where the host can exist with or without algal endosymbionts, symbionts can be acquired either horizontally or vertically, and proliferation of the algae can occur with or without photosynthesis.

overall_design: RNASeq profiling of freshwater sponges with algal endosymbionts at four developmental stages and grown under light:dark conditions.

first: April L

first: Sally P

last: Leys

first: Ana

last: Riesgo


title: Quantifying Transcription Factor Specificity with Advanced DNA Universal Microarrays Featuring Long and Modified Binding Sites [420k]

overall_design: The design is of probes which include three de Bruijn sequences of order 9, two of order 10, and two of order 11.  The layout is two chambers, each of 796x528 probes.  We used part of the entire design that includes a single de Bruijn of order 9, where each of all 9-mers is contained in 2 probes on average.  The rest of the de Bruijn sequences are denoted as PBM, where each of the 9-mers is contained in 105 probes on average.


title: Quantifying Transcription Factor Specificity with Advanced DNA Universal Microarrays Featuring Long and Modified Binding Sites [48k]

overall_design: The design comprises probes with a single de Bruijn of order seven over seven letters. The layout is one chamber of 320x150 probes. Each non-palindromic 6-mers over {A, C, M, W, G, T} is contained in at least 33 probes. M represents 5-methylcytosine (5mC) and W represents guanine paired with 5mC.

first: Irina

last: Miodownik


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [bulkPolyA_RNA_seq_LA_ES]

city: Mannheim

first: Gergana

last: Dobreva

address: Ludolf-Krehl-Str. 7-11

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Spatiotemporal changes in the nuclear lamina and cell metabolism shape cell fate, yet their interplay is poorly understood. Here, we identify lamin A/C as a key regulator of cysteine catabolic flux essential for proper cell fate and longevity. Its loss in naïve mouse pluripotent stem cells leads to upregulation of the cysteine generating and catabolizing enzymes, cystathionine γ-lyase (CTH) and cystathionine β-synthase (CBS), thereby promoting de novo cysteine synthesis. Increased cysteine flux into acetyl-CoA fosters histone H3K9 and H3K27 acetylation, triggering a transition from naïve to primed pluripotency and abnormal cell fate and function. Conversely, the toxic gain-of-function mutation of Lmna, encoding lamin A/C and associated with premature aging, reduces CTH and CBS levels. This reroutes cysteine catabolic flux and alters the balance between H3K9 acetylation and methylation, crucially impacting germ layer formation and genome stability. Importantly, modulation of Cth and Cbs rescues the abnormal cell fate and function, restores the DNA damage repair capacity, and alleviates the senescent phenotype caused by lamin A/C mutations, highlighting the potential of modulating cell metabolism to mitigate epigenetic diseases.

overall_design:
Total RNA was isolated  from ES_shControl , ES_shControl Lmna_KO, ES_shCth Lmna_KO, and CTH OE Nkx2-5-GFP mES cell lines
Total RNA was isolated from ES_shCbs_Lmna_KO Nkx2-5-GFP mES cell lines to process for polyARNA-seq

first: Julio

last: Cordero

first: Yinuo


title: Gasdermin E is Dispensable for H1N1 Influenza Virus Pathogenesis in Mice

city: Columbus

first: Jacob

last: Yount

address: 460 w 12th Ave.

department: Department of Microbial Infection and Immunity

institute: The Ohio State University College of Medicine

summary: Targeting cell death pathways, including pyroptosis and necroptosis, has been shown to mitigate influenza virus infection severity. Here, we examined whether pyroptosis specifically driven by the pore-forming protein gasdermin E (GSDME) is involved in regulating influenza virus infection outcomes. We found that Gsdme-/- mice showed similar weight loss and survival in severe A/PR/8/34 (H1N1) virus infections compared to WT counterparts. Likewise, lung dysfunction, histopathological damage, viral titers, and inflammatory cytokine levels were similar in the two groups. Global transcriptomic analysis also revealed similar gene expression programs in WT versus Gsdme-/- mouse lungs at baseline and in response to infection. To confirm the generality of these findings, we infected mice with 2009 pandemic H1N1 virus and again observed similar weight loss, mortality, and lung dysfunction in WT and Gsdme-/- mice. Our results overall demonstrate that GSDME contributes negligibly to the host response against H1N1 influenza virus, refining our understanding of cell death pathways in influenza pathogenesis.

overall_design: Bulk RNAseq performed on the lungs of WT and Gsdme-/- mice at day 7 post infection with 50 TCID50 PR8 (H1N1) intranasally.

first: Speaks

last: Samuel

first: McFadden

last: Matthew

first: Forero

last: Adriana

first: Yount

last: Jacob


title: Bulk RNA-seq of primary tumor biopsy samples from prostate adenocarcinoma patients

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

summary: This dataset contains bulk RNA sequencing data from primary tumor biopsy samples of patients with prostate adenocarcinoma. TPM-normalized expression values are provided along with sample metadata. The data were generated to support transcriptomic profiling of human prostate tumors and are related to a companion single-cell RNA-seq dataset from the same cohort.

overall_design:
RNA was extracted from fresh primary tumor biopsy samples of prostate cancer patients using the Maxwell CSC RNA FFPE kit. cDNA libraries were prepared using the SureSelect XT HS2 RNA kit and sequenced on the Illumina NovaSeq 6000 platform in paired-end mode (2×101 bp). After quality control (FASTQC), trimming (Trimmomatic), alignment (STAR, GRCh38), and quantification (RSEM), TPM-normalized expression values were generated.

***************************************************************
No raw data files: RNA sequencing data derived from human prostate biopsy samples would be submitted, due to patient privacy concerns.
***************************************************************

first: Hyunho

last: Han

first: Jongsoo

last: Lee

first: Jihee

last: Jung

first: Ayoung

last: Yoo

first: Jungchan

last: Jun

first: Dongwook

last: Song

first: Yeonsue

last: Jang

first: Baek

middle: G


title: Next Generation Sequencing Facilitates Quantitative Analysis of B73 and Zmcryq mutant in dark or blue light treat Transcriptomes

city: Shenzhen

first: Zhao

last: Zhiwei

state: Guangdong

address: 1066, Xueyuan Rd

department: College of Life Sciences and Oceanography

institute: Shenzhen univerisity

summary: Analysis of differential gene expression regulated by Blue light. The hypothesis tested in the present study was that ZmCRYs mediate mostly Blue light regulated genes' expression

overall_design: mRNA profiles of 7 days of B73 and Zmcryq seedlings  grown in longday white light, pretreated with 48h dark, then moved to blue light for 1 hour or kept in dark were generated by deep sequencing, in triplicate, using Illumina Hiseq6000

first: Zhiwei

last: Zhao

first: Hongtao

last: Liu


title: Single-nucleus multiomics reveals the regulatory programs in three brain regions of sporadic early-onset Alzheimer's Disease

city: Houston

first: Zhongming

address: 7000 Fannin St.

institute: The University of Texas Health Science Center at Houston

summary: Sporadic early-onset Alzheimer’s Disease (sEOAD) represents a significant but less-studied subtype of Alzheimer’s Disease. In this study, we generated a single-nucleus multiome atlas from over 70,000 nuclei derived from the postmortem prefrontal cortex, entorhinal cortex, and hippocampus of four sEOAD patients and five control donors. Comprehensive analyses were conducted to delineate cell type-specific transcriptomic changes and linked candidate cis-regulatory elements (cCREs) across these brain regions. We identified and prioritized seven conservative transcription factors in glial cells and neurons in multiple brain regions, including RFX4 in astrocytes and IKZF1 in microglia, which are implicated in the regulation of sEOAD-associated genes. Moreover, we investigated altered intercellular signaling between glial cells and neurons, highlighting their regulatory potential on gene expression in receiver cells. Finally, we reported an enrichment of late-onset Alzheimer’s Disease risk loci within microglial cCREs linked to sEOAD-associated genes. This atlas enhances our understanding of the transcriptional and chromatin dynamics in sEOAD and provides a foundational resource for further pathological investigations.

overall_design: Nuclei were isolated from postmortem prefrontal cortex (PFC,n=9), entorhinal cortex (EC, n=6), and hippocampus (HIP, n=5) of sprodic early-onset Alzheimer's Disease patient (n=4) and matched controls (n=5). The isolated nuclei were then subjected to single-nuclei multiome sequcing. ll tissues were de-identified under The Health Insurance Portability and Accountability Act of 1996 (HIPAA) privacy rules. The tissue donation consent was obtained from all participants by UTHealth.


title: Effect of neuropeptide substance P on gene expression in the hippocampal tissue of mice after fecal microbiota transplantation

city: Beijing

first: Jing

last: Lan

address: No. 2 Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

summary: To explore how SP affects the function of the hippocampus mediated via intestinal flora, we performed RNA-seq analysis on the hippocampus of mice subjected to FMT treatment.

overall_design: The mice were divided into the FMT-CON group, the FMT-DSS group, and the FMT-DSS+SP group. After the fecal microbiota transplantation treatment, we used RNA-seq to detect gene expression in hippocampal tissue of each group.


title: Small Extracellular Vesicles From Platelet-Rich and Platelet-Poor Plasma Are Primarily From Platelets and Protect Synoviocytes From IL-1β–Induced Inflammation

city: Naples

first: Logan

last: Piening

state: FL

address: 1370 Creekside Blvd

department: Orthobiologics

institute: Arthrex Inc.

type: Non-coding RNA profiling by high throughput sequencing

summary: This study sought to investigate the miRNA content of various extracellular vesicles derived from plasma fluids in order to better understand their functions in musculoskeletal injuries.

overall_design: To determine the miRNA content of extracellular vesicles derived from various plasma based devices. Compare the miRNA content between each of the groups.

first: Preston

last: Wolfe

first: David

last: Shepard

first: Lisa

last: Fortier

first: Michael

last: Baria


title: Establishment of a simple, efficient, and scalable method to generate oocyte-like cells in vitro

city: Kofu

first: Mizuki

last: Sakamoto

country: Japan

institute: University of Yamanashi

summary: Understanding the molecular basis of oocyte identity and function is essential not only for basic biology but also for clinical applications, as it is closely linked to female infertility. However, technical challenges remain in advancing this understanding, mainly due to the difficulty of obtaining a sufficient number of oocytes. In this study, we established a two-dimensional culture method that efficiently generates oocyte-like cells, referred to as mini-oocytes, from mouse embryonic stem cells. This method requires minimal labor and leverages a transcription factor-mediated approach for oocyte-like cell generation. Our analyses revealed significant similarities between in vitro-derived mini-oocytes and in vivo oocytes. Furthermore, we demonstrated the utility of mini-oocytes for investigating oocyte-specific molecular features through a small-scale knockout screen targeting the subcortical maternal complex. Given the simplicity, efficiency, and scalability of the mini-oocyte induction method, it offers a practical alternative for conducting experiments that are otherwise challenging with in vivo oocytes.

overall_design: Total RNA-seq were performed using mini-oocytes.

first: Takashi

last: Ishiuchi

first: Ami

last: Banno


title: Single-cell transcriptomic profiles of metastatic lesion biopsies and PBMCs from M1-stage prostate cancer patients

city: Seoul

first: Baek Gil

last: Kim

institute: Yonsei University

summary: This dataset contains single-cell RNA sequencing (scRNA-seq) data generated from patients with M1-stage metastatic prostate cancer, comprising two complementary sample types: metastatic lesion biopsies from five patients and peripheral blood mononuclear cells (PBMCs) from seven patients. Together, these datasets support integrated profiling of the metastatic tumor microenvironment and the systemic immune landscape. The processed data include log-normalized gene expression matrices and detailed cell-level metadata, enabling analyses of tumor–immune interactions, circulating immune phenotypes, and molecular features associated with metastatic disease progression. A related bulk RNA-seq dataset from primary tumor biopsies is available (see Related Series: GSE297742), providing opportunities for comparative transcriptomic analyses between primary and metastatic disease states.

overall_design: This Series contains single-cell RNA sequencing (scRNA-seq) data generated from metastatic biopsy samples (n = 5) and peripheral blood mononuclear cells (PBMCs; n = 7) collected from patients with M1-stage metastatic prostate adenocarcinoma. Metastatic lesion biopsies were enzymatically dissociated into single-cell suspensions, while PBMCs were isolated using density gradient centrifugation. All samples were processed using the 10x Genomics Chromium Single Cell 3’ v3 platform for single-cell library construction and sequenced on the Illumina NovaSeq 6000 with paired-end reads (2 × 101 bp). Raw sequencing data were processed using the Cell Ranger pipeline (10x Genomics) for alignment to the GRCh38 reference genome and generation of gene-by-cell count matrices, followed by downstream analyses in Seurat for quality control, normalization, dimensionality reduction, clustering, and cell-type annotation. The resulting dataset includes high-quality log-normalized gene expression matrices and comprehensive cell-level metadata across both biopsy- and PBMC-derived single-cell populations, enabling integrated analysis of metastatic tumor biology and systemic immune remodeling in advanced prostate cancer.

first: Hyunho

last: Han

first: Jongsoo

last: Lee

first: Jihee

last: Jung

first: Ayoung

first: Jungchan


title: Developmental regulation of ERK signaling by mitotic kinases

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

summary: The morphogenesis of the mouse epiblast during implantation can be recapitulated by culturing its counterpart ES cells in growth factor reduced Matrigel. We analysed the transcripts level changes using Next-generation sequencing (NGS) technique with ES cells grown in Matrigel in N2B27 medium supplemented with 2iLif, FGF2/Activin, PD03259021, Aurka inh and PD032+ Aurka inh for 2 days.  We found cells delayed exit of naïve pluripotency by inhibiting Aurka activity and this effect can be strengthened by combing Mek and Aurka inhibitors. By further pathways enrichment analysis, we found down regulation of MAPK signalling pathway after Aurka inhibition which is validated by Q-PCR and immunofluorescence. Our findings demonstrate the pluripotent cells continuously generate and perceive two types of Erk-mediated pro-differentiation cues - autocrine signals of the Fgf/Mek cascade and cell-intrinsic cues via the mitotic kinase Aurka.

overall_design: We performed bulk RNA-sequencing on ES cells grown in growth factor reduced Matrigel with 5 different culture conditions and each culture condition has 3 replicates.

first: Fei

last: Chen

first: Jan

last: Bruder

first: Niraimathi

last: Govindasamy

first: Rui

first: Devila

last: Prit

first: Hannes

middle: C

last: Drexler

first: Sebastian

last: Leidel

first: Hans

last: Schöler

first: Ivan

last: Bedzhov


title: Transcriptomic analysis of SW620-conditioned medium-treated THP-1 macrophages

status: Public on Nov 18 2025

city: Taipei

first: Yung-Chi

last: Chang

address: Rm 736, No. 1, Sec. 1, Jei-Ai Rd

country: Taiwan

institute: National Taiwan University, College of Medicine

summary: Siglec-5 and Siglec-14, expressed on myeloid cells, share ligand-binding domains but have opposing signaling functions. While these paired receptors regulate macrophage immune responses against bacterial infection, their role in the tumor microenvironment remains unclear. We found that Siglec-14 expression in THP-1 macrophages, when exposed to CRC tumor-conditioned medium, induces a protumoral SPP1+ tumor-associated macrophage phenotype, with enrichment of angiogenic pathways.

overall_design: RNA-seq profiling of human monocytic THP-1 cells engineered to express either an empty vector (EV/THP-1), human Siglec-5 (S5/THP-1), or human Siglec-14 (S14/THP-1) were differentiated with PMA and then treated with SW620-conditioned medium for 48 h

first: Lin

last: Kuan-Yu

first: Chang

last: Yung-Chi


title: Secretory kinase FAM20C triggers adipocyte dysfunction inciting insulin resistance and inflammation in obesity

first: Ankit

last: Gilani

state: New York

address: 413E 69th Street

institute: Weill Cornell Medical College

summary: Obesity is a major driver of type 2 diabetes (T2D) and related metabolic disorders, characterized by chronic inflammation and adipocyte dysfunction. However, the molecular triggers initiating these processes remain poorly understood. We identify FAM20C, a serine/threonine kinase, as an early obesity-induced mediator of adipocyte dysfunction. Fam20c expression is substantially upregulated in adipocytes in response to obesity, correlating with a proinflammatory transcriptional signature. Forced expression of Fam20c in adipocytes promotes robust upregulation of proinflammatory cytokines and induces insulin resistance that is dependent on its kinase activity. Conversely, deletion of adipocyte Fam20c after established obesity and hyperglycemia improves glucose tolerance, augments insulin sensitivity, and reduces visceral adiposity, without altering body weight. Phosphoproteomic studies reveal that FAM20C regulates phosphorylation of intracellular and secreted proteins, modulating pathways critical to inflammation, metabolism, and extracellular matrix remodeling. We identify FAM20C-dependent substrates, such as CNPY4, whose phosphorylation contributes to proinflammatory adipocyte signaling. Of translational relevance, we show that in humans visceral adipose FAM20C expression positively correlates with insulin resistance. Our findings establish FAM20C as an early regulator of obesity-induced adipocyte dysfunction and systemic metabolic impairment. Our studies provide proof of concept that inhibition of FAM20C may serve as a potential therapy for T2D by restoring adipocyte health.

overall_design: RNA-Seq profiling of primary differentiated adipocytes from control and adipocyte-specific Fam20c KO mice.


title: Inhibition of Acetyl-CoA metabolic enzymes by EVT0185 impairs hepatic stellate cell activation and reverses MASH and fibrosis in mouse models [nanostring]

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

summary: Metabolic Dysfunction-Associated Steatohepatitis (MASH) is characterized by liver steatosis and inflammation which lead to fibrosis following hepatic stellate cell (HSC) activation. Acetyl-CoA is fundamental for de novo lipogenesis (DNL) and cholesterol synthesis and can be derived from citrate via ATP citrate lyase (ACLY), or from acetate via acetyl-CoA synthetase (ACSS2). Here, we find that EVT0185, an ACLY and ACSS2 inhibitor, leads to resolution of MASH and fibrosis while lowering insulin and glucose in four distinct mouse models. EVT0185 also reduces fibrosis alone and in combination with semaglutide and more effectively than bempedoic acid in a model not characterized by steatosis or insulin resistance. Spatial transcriptomic and scRNAseq reveal marked downregulation of cholesterol synthesis in HSCs with EVT0185 treatment in vivo and in vitro. These data indicate a critical role for ACLY and ACSS2 in HSCs and suggest further clinical evaluation of EVT0185 for reducing MASH and fibrosis may be warranted.

overall_design: Liver RNA from Vehicle (n = 8) and EVT0185-treated (100 mg/kg; n = 8) MASH mice was analyzed using the NanoString nCounter Fibrosis Panel (760 genes). Data were normalized in nSolver 4.0 using global geometric mean normalization, with pathway scores computed from normalized expression values. The dataset therefore includes 16 total samples (8 biological replicates per group) with one treatment group and one vehicle control group for comparative analysis.

first: Fiorella

last: Di Pastena

first: Jaya

last: Gautam

first: James

last: Lally

first: Gregory

last: Steinberg


title: APOBEC3B enhances the efficacy of PARP inhibitors in elimination of ovarian cancer stem cell

city: LA JOLLA

first: QINGFEI

last: JIANG

address: 2880 TORREY PINES SCENIC DR

institute: UNIVERSITY OF CALIFORNIA SAN DIEGO

summary: Late detection and tumor recurrence are major factors driving the lethality of high-grade serous ovarian carcinoma (HGSOC). PARP inhibitors (PARPi) have achieved significant clinical efficacy by selectively targeting DNA repair deficiencies in HGSOC patients with BRCA mutations and homologous recombination deficiency (HRD). However, a subset of patients ultimately develops resistance to PARPi, necessitating alternative effective treatment options. The mutational signatures of APOBEC3 family of DNA deaminases are widespread across a broad array of cancer types. Here, we report that cancer stem cell (CSC)-like tumorspheres exhibit reduced A3B expression compared to non-CSC adherent counterparts. Importantly, inhibition of A3B leads to PARPi resistance, elevated frequency of CSCs, and enhanced expression of stemness factors. In addition, we found that high A3B-expressing cells are under strong replication stress and thus synchronize efficiently with PARPi. In this study we knocked down of A3B in A2780 3D tumorsphere by lentiviral tranduction, followed by treated of DMSO control or Olaparib, and performed bulk RNA-sequencing to compare gene expression changes (n=3 for each condition).

overall_design: RNA-sequecning of A2780 following lentiviral knockdown of A3B and the backbone control, followed by treatment of DMSO or Olaparib (n=3 for each conditon, total n=12).

first: Maria

last: Rivera

first: Lucy

last: Liu

first: Sabina

last: Enlund

first: Chae-Eun

last: Lim

first: Haoran

last: Zhang

first: Kaifu

last: Yang

first: Roman

last: Sasik

first: Leslie

last: Crews

first: Kathleen

last: Fisch

first: Ramez

last: Eskander

first: Frida

last: Holm

first: Qingfei

last: Jiang


title: Differentiation-induced reduction in functional diversity restricts the ability of cytomegalovirus-specific CD8 T cells to eliminate virus-infected cells

city: Hannover

first: Ahmed

last: Hassan

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

summary: Individuals with expanded CD8 T cells recognizing the pp65-HLA-A*02:01–restricted viral epitope NLVPMVATV (NLV-T cells) have weakened immune control of human cytomegalovirus (HCMV) reactivation. Here, we characterized NLV-T cells from healthy HCMV-positive donors, dividing them into two groups: those with low and those with high NLV-T cell frequencies (LF and HF, respectively). Our comprehensive multimodal analysis revealed that NLV-T cells from HF donors preferentially exhibit a phenotype of advanced differentiation, characterized by granzyme B and perforin expression. Although these cells were more efficient in eliminating peptide-loaded target cells than NLV-T cells from LF donors, the latter were more potent in cytokine secretion and the elimination of HCMV-infected cells with virus-induced HLA class-I downregulation. Overall, these findings suggest that HCMV exploits CD8 T cell differentiation to evade immune protection and explain the previously observed decline in HCMV reactivation control in individuals with NLV-T cell accumulation.

overall_design:
For single cell RNA seq: PBMCs were thawed and either used for staining directly (HF donors) or CD8+ T cells were enriched using magnetic activated cell sorting (MACS) (LF donor samples). The PBMCs from HF donors and the enriched CD8+ T cells from LF donors were stained with NLV-peptide loaded MHC class I tetramers for 15 minutes at 37°C, followed by staining for extracellular markers, Totalseq antibodies, and cell-hashing antibodies (Table 4) for 25 minutes at RT. The samples were washed and up to 8 samples were pooled and cells were sorted for CD19-, CD14-, CD16-, CD56-, CD3+, CD8+, NLV-tetramer+ cells on a Becton-Dickinson FACSAria III Fusion or Becton-Dickinson FACSAria IIu cell sorter.
For bulk RNA and TCR sequencing: The NLV-T cells were expanded via NLV-peptide stimulation for 9 days and frozen. For sequencing, the cells were thawed and the NLV-T cells were isolated with NLV-loaded MHC class I streptamers.

first: Lea

last: Fritz

first: Berislav

last: Čuvalo

first: Bibiana

last: Costa

first: Britta

last: Wieland

last: Eiz-Vesper

first: Christine

last: Falk

first: Lennart M

last: Roesner

first: Thomas

last: Werfel

first: Thilo

last: Dörk-Bousset

first: Ulrich

last: Kalinke

first: Hristo

last: Georgiev

first: Reinhold

last: Förster

last: Bošnjak


title: BAF60A KO RNA seq (primary cells)-Highly discriminative globin gene activation by the non-canonical BAF chromatin remodeling complex

city: Philadelphia

first: Eugene

last: Khandros

state: PA

address: 3615 Civic Center Blvd.

department: Hematology

institute: The Children's Hospital of Philadelphia

summary: The regulation of beta-like globin genes, including the switch from fetal (HBG) to adult (HBB and HBD) genes has served as a paradigm of developmental transcriptional control. While HBG repressors such as BCL11A and LRF have been well characterized, recent discoveries of HIF1a and BGLT3 as HBG-specific activators have raised interest in finding new activators as potential therapeutic targets. The ATP-dependent chromosome remodeler BRG1 has previously been demonstrated as necessary for hemoglobin gene transcription. In loss of function studies in adult-like HUDEP2 cells, we found that BRG1 depletion preferentially decreased fetal HBG and the minor adult HBD. BRG1 forms multisubunit complexes with combinations of 27 subunits in 3 families - canonical BAF, polybromo BAF, and non-canonical BAF (ncBAF) - to regulate chromatin accessibility and gene transcription in a cell and condition-specific manner. Using CRISPR loss of function studies in HUDEP2 cells and primary adult erythroid cells, we identified the non-canonical BAF complex as a positive regulator of HBG and HBD. Loss of the non-canonical BAF complex subunits BRD9 and BAF60A/SMARCD1 preferentially decreased HBG and HBD in HUDEP2 cells and primary adult erythroid cultures, while accelerating erythroid differentiation and hemoglobinization. Pharmacological depletion of BRD9 led to acute decreases in chromatin accessibility at HBD and HBG promoters and reduced their primary transcripts, while longer treatment recapitulated  genetic ablation effects. This surprising demonstration of BAF complex selectivity within a multi-gene cluster extends our understanding of globin gene transcriptional regulation and identifies a potential target for therapeutic manipulation of beta-like globins.

overall_design: We performed RNA seq analysis in 3 healthy donor erythroid cells derived from CD34+ HSPC after BAF60A knockout. Total RNA was isolated form erythoid cells after 10 days of erythroid differentiation targetted with CRISPR control sgRNA (AAVS1 targetting) or BAF60A targetting. Transcriptome changes were analysed by bulk RNA-seq after ribosomal RNA removal.

first: Abhirup

last: Bagchi

first: Sindhu

last: Billakanti

first: Vanessa

last: Shehu

first: Kathryn

middle: M

last: Farrell

first: Sarah

last: Cotteta

first: Bailey

last: Godfrey

first: Micaela

last: Alpert

first: Jacob

last: Zeranski

first: Krista

last: Budinich

first: Zhuangzhuang

last: Geng

first: Osheiza

last: Abdulmalik

first: Belinda

last: Giardine

first: Cheryl

last: Keller

first: Ross

last: Hardison

first: Junwei

last: Shi


title: Efferocytosis-induced metabolic shift in bone macrophages drives lactate production and modulates inflammation and osteoclastogenesis

city: ANN ARBOR

first: Hernan

last: Roca

state: MI

address: 1011 N. University Ave.

department: Periodontics and Oral Medicine

institute: University of Michigan

summary: During the critical process of homeostatic efferocytosis, macrophages clear apoptotic cells and subsequently transition to reparative functions that promote the resolution of inflammation and support tissue repair. Their inherent plasticity enables rapid changes in macrophage activity suited to specific microenvironments. However, the heterogeneity in their cell states also presents challenges in characterizing subsets of macrophages and analyzing their specific contributions post-efferocytosis. In this study, single-cell RNA sequencing data from bone-marrow derived macrophages engulfing apoptotic osteoblasts (OB) was used to characterize macrophage subpopulations enriched during efferocytosis. Clustering analysis revealed two subpopulations (c3 and c9) that were unique to efferocytic macrophages. These distinct subpopulations displayed a transcriptional profile characterized by enhanced glycolytic energy metabolism, along with an anti-inflammatory gene signature. Notably, HIF-1 signaling, glycolysis/gluconeogenesis, and carbon metabolism were among the top five most significantly enriched pathways in c3 and c9 macrophages. qRT-PCR analysis revealed that macrophages engulfing apoptotic OBs exhibited increased expression of key glycolytic enzymes and solute carriers, including Slc2a1, Pdk1, Ldha, and Slc16a3. Metabolomics analysis revealed a significant increase in intracellular lactate, phosphoenolpyruvic acid, glycerol-3-phosphate, 2-/3-glycerophosphate, and fructose-6-phosphate, indicative of enhanced glycolysis. In addition, efferocytic macrophages showed increased extracellular lactate production compared to control macrophages, as confirmed by lactate ELISA. The effects of lactate (0-20mM) on osteoblast mineralization, osteoclast differentiation and function, and macrophage-derived inflammatory factors were evaluated through various in vitro experiments. While no effect was seen in osteoblast mineralization, high lactate concentrations significantly reduced the number of multinucleated osteoclasts and their resorptive activity. Interestingly, extracellular lactate also significantly upregulated M2-like macrophage markers (Arg1, Il1rn, Klf4). These results support the concept that macrophage efferocytosis of apoptotic osteoblasts alters macrophage energy metabolism, which in turn plays a distinct and pivotal role in modulating the bone microenvironment.

overall_design: single-cell RNA sequencing (scRNA-seq) was performed using the 10X Genomics platform on flow-sorted control macrophages (F4/80-APC+) and efferocytic macrophages engulfing Cell-Trace-stained apoptotic osteoblasts, 1 sample per group

first: Nicholas

middle: J

last: Carruthers

first: Rahasudha

last: Kannan


title: Spatially resolved single-cell analysis uncovers protein kinase Cδ-expressing microglia with anti-tumor activity in glioblastoma [Spatial Transcriptomics]

city: Charlestown

first: Reid

last: Mcneil

state: MA

address: 149 13th Street

department: Cancer Research

institute: Mass General Hospital

summary: The glioblastoma (GBM) microenvironment contains resident immune cells with intrinsic anti-tumor potential, particularly microglia. Understanding the single-cell spatial heterogeneity and interactions between immune cells and brain tumor–initiating cells (BTICs) is essential for identifying therapeutic targets to reprogram immune responses and suppress BTIC growth. Using single-cell and spatial transcriptomics, we mapped immune cell populations in the GBM microenvironment and identified signaling networks mediating immune–cancer cell interactions. We discovered a previously unrecognized subset of microglia expressing protein kinase Cδ (PKCδ) with anti-tumor activity against BTICs. The presence of PKCδ-expressing microglia was validated in human GBM specimens. Enhancing PKCδ in microglia via adeno-associated virus or niacin increased phagocytosis of patient-derived BTICs in vitro and improved survival in GBM-bearing mice. Data from The Cancer Genome Atlas (TCGA) revealed that high PKCδ expression correlates with increased apoptosis, phagocytosis, and immune signaling pathways. These findings offer highlight PKCδ+ microglia as a promising therapeutic target in GBM.

overall_design: Using GBM mouse modelts, mice were either treated with niacin or untreated, the tumors were resected from the mice and analyzed using spatial transcriptomics.

first: Reza

last: Mirzaei

last: McNeil

first: Charlotte

last: D’Mello

first: Britney

last: Wong

first: Susobhan

last: Sarkar

first: Frank

last: Visser

first: Candice

last: Poon

first: Pinaki

last: Bose

first: Wee

last: Yong