title: Mating-type locus structure affects gene expression in unidirectional mating-type switching fungi

status: Public on May 08 2026

city: Pretoria

first: P

middle: Markus

last: Wilken

address: Lynnwood Rd, Hatfield

department: Department of Biochemistry, Genetics and Microbiology

country: South Africa

institute: Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria

summary: Fungal species are typically either fully self-fertile or self-sterile, but some filamentous ascomycetes can transition from self-fertility to self-sterility through unidirectional mating-type switching. In these fungi, the structure of the mating-type (MAT1) locus governs sexual behaviour: MAT-2 self-fertile individuals retain both MAT1-1 and MAT1-2 genes, while MAT-1 self-sterile isolates lose MAT1-2 genes during switching. A third type of isolate morphology also occurs under laboratory conditions: these are self-sterile isolates that retain both MAT1-1 and MAT1-2, but are unable to switch mating type. They are commonly referred to as MAT-2 self-sterile isolates. Two of the mating-type (MAT) genes, one of which is deleted during switching, encode transcription factors known to regulate not only the sexual cycle but also genes unrelated to mating. To test how MAT1 structural variations affects gene expression, we studied Ceratocystis albifundus, a species that switches mating type. To minimise variability caused by intraspecific genetic differences, two self-sterile isolates (MAT-1 and MAT-2 self-steriles) were derived from the same MAT-2 self-fertile parent, making all three isolates genetically identical, except at the MAT1 locus. Comparative transcriptomic analyses revealed that the MAT-2 self-fertile, MAT-1 self-sterile and MAT-2 self-sterile isolates all exhibited distinct expression patterns, including differences in MAT genes, the pheromone–receptor pathway, and other genes not directly linked to mating. The results show that MAT1 locus structure influences gene expression more broadly than those only related to the sexual cycle.

overall_design: This study compares gene expression among three isolate types of Ceratocystis albifundus that differ only in mating-type (MAT1) locus configuration. The isolate types include: (i) a MAT-2 self-fertile isolate (heterokaryotic, containing both and MAT1 locus configurations; CMW4068), (ii) a MAT-1 self-sterile isolate (homokaryotic, containing only MAT1-1 genes; CMW67508), and (iii) a MAT-2 self-sterile isolate (homokaryotic, containing both MAT1-1 and MAT1-2 genes but lacking the ability to undergo mating-type switching; CMW67509). The two self-sterile isolates were derived from the MAT-2 self-fertile parent, ensuring a uniform genetic background with variation restricted to the MAT1 locus. For each isolate type, three biological replicates were generated by pooling mycelium from independent cultures grown under identical conditions. RNA was extracted at 13 days post-inoculation, at which the MAT-2 self-fertile isolate was actively undergoing sexual development, while the self-sterile isolates remained in a vegetative state. The primary variable under investigation is MAT1 locus structure, and its effect on global gene expression and mating-related pathways.

first: F

last: Lane

first: B

last: Wingfield

first: M

middle: J


title: Tumor microbial burden drives immune responses through regulation of Interferon signaling

city: Houston

first: Haoyue

last: Liu

address: 6767 Bertner Ave.

country: USA

institute: University of Texas MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: To investigate the mechanisms involved in tumor microbial-associated immunotherapy sensitivity, we performed RNA sequencing on mouse MC38 tumor tissues upon local microbial depletion.

overall_design: vehicle control versus peri-tumoral ATBx (P.T. ATBx) treated mouse MC38 subcutaneous tumors


title: ATAC-seq of SRR2KO

status: Public on May 09 2026

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Stem cell maintenance and lineage commitment in the nervous system require precise regulation of transcription factors, among which SOX2 plays a central role. Its expression is controlled by multiple enhancers, including the Sox2 regulatory region 2 (Srr2), located downstream of the Sox2 locus. To dissect the role of Srr2 during neural development, we generated a CRISPR-Cas9 mouse model harboring a targeted deletion of this enhancer. We find reduced SOX2 in SEZ/SGZ niches and diminished ASCL1/OLIG2 progenitors, accompanied by fewer neurons and oligodendrocytes in vitro. Paired bulk RNA-seq and ATAC-seq at two defined transitions as 2 DIV (proliferation) and 2+1 DIV (early commitment) show that Srr2 loss causes widespread chromatin compaction during proliferation (6,393 DARs; 6,319 less accessible) that phenocopies wild-type differentiation, while accessibility largely converges by 2+1 DIV. Multi-omic integration reveals 115 neurogenic genes with persistent promoter closure and reduced induction at the transcriptional level in mutants, consistent with failure to activate proneural programs upon early differentiation. In vivo, SEZ cells of Srr2del/del mice exhibit lower SOX2 and FOXG1, fewer ASCL1/OLIG2 progenitors, and reduced neuronal and oligodendroglial markers. Together, our results uncover Srr2 as a critical enhancer of Sox2, required for establishing a chromatin environment permissive to neural differentiation, and underscore the importance of non-coding regulatory elements in controlling stem cell fate.

overall_design: 3 DIV proliferating WT and SRR2KO neurospheres and WT and SRR2KO NPs at the onset of differentiation (2+1 DIV). Isolated nuclei were subjected to ATAC-seq library preparation to evaluate genome-wide chromatin accessibility across genotypes and cellular states. Between 2 and 3 biological replicates per condition and genotype.

first: Sara

last: Cruces-Salguero

first: Ana

last: Domingo-Muelas

last: Jordán-Pla

first: Jose

middle: M

last: Morante-Redolat

first: Robin

last: Lovell-Badge

first: Isabel

last: Farinas

first: Verónica

last: Moncho-Amor


title: RNA‑seq of TREM1 pathway activation in human monocytes and neutrophils

city: South San Francisco,

first: Carolina

last: Galan

state: CA

address: 1 DNA Way

institute: Genentech

summary: This dataset contains bulk RNA‑sequencing profiles of primary human monocytes and neutrophils stimulated in vitro to activate the TREM1 signaling pathway. Monocytes from healthy donors were exposed to a plate‑bound TREM1 agonistic antibody or to a combination of purified peptidoglycan and PGLYRP1, alongside appropriate control conditions. RNA was collected after short‑term stimulation to capture early transcriptional responses. The resulting data can be used to characterize gene expression programs downstream of TREM1 in human myeloid cells and to derive pathway signatures for use in independent cohorts.

overall_design: RNA-seq profiling of monocytes upon TREM1 activation was performed after stimulation with a TREM1 agonist antibody, isotype control, or PGN-Ecndss+PGLYRP1 for 4 hours.

first: Warrison

last: Andrade

first: Saiyu

last: Hang


title: Type-2-immune history imprints local training in nerve-airway associated interstitial macrophages (NAMs) for disease tolerance during respiratory viral infection

city: New York

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

summary: Severe respiratory viral disease varies widely among individuals and often reflects immunopathology rather than inadequate pathogen control, suggesting that prior immune history can prime the lung’s inflammatory–regulatory balance to promote disease tolerance. Here we show that nerve- and airway-associated macrophages (NAMs), a subset of interstitial macrophages expand following type 2 inflammation induced by Nippostrongylus brasiliensis. We hypothesized that NAMs acquire epigenetically imprinted trained immunity and tested this in a heterologous challenge model in which mice infected with Nippostrongylus brasiliensis were challenged 4–6 weeks later with lethal H1N1 influenza. Remarkably, all Nb-conditioned mice survived, whereas all unconditioned controls succumbed by days 5–6 post-infection. Protection occurred without improved viral burden or enhanced T cell responses, and instead tracked with reduced immunopathology, amplified type 2 cues, increased efferocytosis and accelerated tissue repair. Using NAM-DTR mice, we show that conditioned NAMs are necessary and sufficient for protection: depletion or replacement with unconditioned NAMs abrogated survival, whereas adoptive transfer of conditioned NAMs conferred tolerance without enhancing viral clearance. Genomic analyses implicated an IL-4–STAT6–PPARγ and Arginase-1 chromatin program that imprints a pro-resolving and reparative NAM state driving programs of tissue repair, type 2 immunity and efferocytosis during lethal respiratory viral infections. Finally, meta-analysis of human lung single-cell atlases from healthy, IPF and COPD cohorts indicated that reparative NAM-like programs aligned with fibrotic remodeling in IPF but diverged in COPD, supporting context-dependent consequences of sustained repair states. These findings establish local trained immunity in lung-resident macrophages as a mechanism of disease tolerance and a therapeutic entry point for severe inflammatory respiratory infections.

overall_design:
NAMs from naïve and heminth trained mice were sorted for ATAC sequencing. A total of 50,000 purified macrophage populations per replicate were washed once in cold sterile PBS and resuspended in 20-50 µl of cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Cell lysates were centrifuged at 500g for 30 seconds to 1 min at 4 °C, and nuclei were resuspended in 25 µl of water. The transposition reaction mix consisted of 25 µl of TD buffer, 2.5 µl of Tn5 transposase (Illumina cat. 20034198), and 22.5 µl of nuclease-free water containing the nuclei. The mix was incubated for 30 min at 37 °C. Transposed DNA fragments were purified using a Qiagen Reaction MiniElute kit (Qiagen). Clean DNA was run with PCR amplification to incorporate the indexes, which were a universal index and a unique i7 index per sample. (IDT primers outlined in Buenrostro 2013 paper) and amplified by PCR for 11 cycles using NEBNext high fidelity 2× PCR master mix (New England Biolabs).  PCR products were cleaned with 0.9x volume of Ampure XP beads (Beckman Coulter), and amplified fragment size was verified on an Agilent 2100 Bioanalyzer system (Agilent) with high sensitivity DNA screentape. ATAC-seq libraries were quantified by quantitative PCR with the Roche-kapa Illumina quantification kit. Paired-end sequencing was performed on an Illumina Novaseq6000 system with an SP100 cycle kit sequenced as paired-end 50 bases.
Preprocessing of reads was done automatically by seq2science (v1.2.4) using the atac-seq workflow. Paired-end reads were trimmed with fastp (v0.23.2) with default options. Genome assembly mm10 was downloaded with genomepy (v0.16.3). Reads were aligned with bwa-mem2 (v2.2.1) with options '-M'. Afterwards, duplicate reads were marked with Picard MarkDuplicates (v3.0.0). General alignment statistics were collected by samtools stats (v1.16). Before peak calling, paired-end info from reads was removed with seq2science so that both mates in a pair get used. Peaks were called with macs2 (v2.2.7) with options '--shift -100 --extsize 200 --nomodel --buffer-size 10000' in BAM mode. The effective genome size was estimated by khmer (v3.0) by taking the number of unique k-mers in the assembly of the same length as the average read length for each sample.

[UPDATE] The sample processed data files have been replaced on July 27, 2026.

first: Damani-Yokota

last: Payal

first: Nadorp

last: Bettina

first: Khanna

last: Kamal


title: The pro-inflammatory cytokines IFN-α and TNF-α inhibit extravillous trophoblast invasion

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Amsterdam UMC

summary: Impaired trophoblast differentiation and invasion are a hallmark of severe pregnancy complications such as preeclampsia and fetal growth restriction. Women with immune-mediated inflammatory diseases, in particular systemic lupus erythematosus (SLE), have an increased risk for adverse pregnancy outcomes. These diseases are characterized by high activity of pro-inflammatory cytokines, such as interferon alpha (IFN-α) and tumor necrosis factor alpha (TNF-α). Here, we investigated the direct effects of these cytokines on extravillous trophoblast (EVT) differentiation and invasion, using trophoblast stem cells (TSCs), trophoblast organoids, and first-trimester placental and decidual tissue. While neither cytokine impaired EVT differentiation, both significantly reduced EVT invasion into extracellular matrix and/or maternal decidua. Transcriptomic analysis revealed cytokine-induced alterations in gene expression associated with epithelial-mesenchymal transition (EMT), a key process in EVT invasion. These findings suggest that elevated IFN-α and TNF-α levels may directly impair placental development by inhibiting EVT invasion, providing a mechanistic link between inflammatory conditions such SLE and adverse pregnancy outcomes.

overall_design: Trophoblast organoids were treated with IFN-α or TNF-α in EVT differentiation medium for 14 days. As the expression of EVT markers was not affected by the presence of the cytokines, we isolated HLA-G-positive EVTs from the organoids. We performed transcriptome sequencing on these cells to investigate which genes/pathways are targeted by the cytokines that may explain the reduced EVT invasion. The dataset contains 3 experimental replicates of untreated, IFN-α-treated and TNF-α-treated EVTs.

first: Jantine

last: van Voorden

first: Gijs

middle: B

last: Afink


title: Post-transcriptional regulation of a protein chaperone by the mRNA encoding the major pneumococcal virulence factor PspA

city: Odense M

first: Jens

middle: Sivkær

last: Pettersen

state: Danmark

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary: This study investigates regulatory activity of the 3'UTR of the mRNA encoding the pneumocococal surface protein A.

overall_design: D39 wild type (WT), an isogenic pspA-3'UTR deletion mutant (Δ3UTR) and a strain with complementary constitutive overexpression of the pspA-'3UTR (Δ3UTR CEP:3UTR)  was inoculated in triplicates in C+Y media and grown at 40°C to an OD 0.5 before RNA extraction.

middle: S

first: Mikkel

middle: G

last: Jørgensen


title: A 3D Amphioxus Brain Atlas Illuminates the Blueprint of the Ancestral Chordate Brain and Highlights Unique Vertebrate Innovations

status: Public on May 07 2026

city: Taipei

first: Che-Yi

last: Lin

address: 128 Section 2, Academia Road, Nankang

country: Taiwan

institute: Academia Sinica

summary: Comparative studies of vertebrate brains have elucidated the evolution of morphological diversity; yet, the fundamental chordate brain blueprint and the emergence of vertebrate-specific innovations remain elusive. To reconstruct the cellular and molecular origins of brain architecture in chordates, we combined single-nucleus RNA-seq with spatial transcriptomics to generate a three-dimensional cell atlas of the central nervous system (CNS) in the early-branching chordate amphioxus. This atlas reveals a tripartite anterior-posterior organization comprising a rostral retinal/hypothalamic region, a di-mesencephalic domain, and a caudal hindbrain/spinal cord. Challenging previous views, we identify cell clusters resembling the vertebrate zona limitans intrathalamica and midbrain-hindbrain boundary regions that demarcate major brain compartments. Conversely, the absence of telencephalic marker expression in the amphioxus rostral forebrain suggests that the telencephalon is a vertebrate innovation. Collectively, our findings establish a spatial transcriptomic framework for the amphioxus CNS, providing crucial insight into the evolutionary origins of vertebrate brain complexity.

overall_design: High throughput RNA in situ hybridization performed with Xenium protocols on the amphioxus brain

first: Wen-Hsin

last: Hsu

first: Mei-Yeh

last: Lu

first: Yi-Hua

last: Chen

first: Yi-Hsien

last: Su

first: Shen-Ju

last: Chou

first: Jr-Kai

last: Yu


title: Mutant IDH1 blocks neutropoiesis by repressing myeloid progenitor programs [Nanopore sequencing]

city: Heidelberg

first: Daniel

middle: B.

last: Lipka

address: INF 581

department: Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology

country: Germany

institute: German Cancer Research Center

summary: IDH1 and IDH2 are frequently mutated in various cancers, including acute leukemias. However, the distinct mechanisms by which mutant IDH1 or IDH2 drive hematopoietic neoplasms remain poorly understood. Here, we analyzed DNA methylation in IDH1- and IDH2-mutant AML and found neutrophil lineage-specific epigenetic alterations in IDH1-mutant cases that went along with severely impaired neutrophil differentiation. Transcriptional analysis of normal hematopoiesis in humans and mice revealed a strong physiological upregulation of IDH1/Idh1 in myeloid progenitors. To study the functional effects of Idh1 mutations on hematopoiesis in a pre-leukemic setting, we used a genetically engineered inducible mouse model expressing a heterozygous Idh1 mutation under control of the endogenous promotor. Our study revealed a cell-intrinsic block in neutrophil differentiation caused by repression of myeloid transcription programs in neutrophil progenitors. This included impaired expression of Cebpe, which encodes a key transcription factor regulating neutrophil differentiation. Reactivation of Cebpe expression, by overexpression of its upstream regulator Cebpa or following treatment with hypomethylating agents restored differentiation, indicating that the differentiation block is reversible.

overall_design: Empty-vector or Idh1-R132H expressing 32D cells were cultured under steady-state conditions or were treated either with AGI-5198 or 5-acazitidine for 5 days. At the end of treatment period, 10^6 cells were harvested for DNA isolation. For each genotype (EV and Idh1-R132) and treatment condition (AGI and AZA), two biological replicates were collected. DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s protocol for cultured cells. DNA was eluted in 50 µL pre-warmed Buffer EB twice. DNA concentrationswas quantified using the Qubit High Sensitivity (HS) dsDNA Assay kit according to the manufacturer’s instructions.

first: Mariam

last: Hakobyan

first: Melissa

last: Türe

first: Maximilian

last: Schönung


title: Comparison of mRNA populations between mutants with and without active HIF-1, and with and without functional nonsense-mediated decay.

status: Public on May 06 2026

city: Cambridge

first: Charles

middle: Ara

last: Demurjian

state: MA

address: 31 Ames Street

institute: BioMicro Center at MIT

summary: This study looked at the interactions between the conserved hypoxia response pathway (controlled by EGL-9 and HIF-1) and the conserved nonsense-mediated decay (NMD) pathway in C. elegans. Given the role of HIF-1 as a transcription factor, and the role of NMD in degrading mRNA, we hypothesized that changes in both of these pathways would impact mRNA levels. To identify specific mRNAs that might be regulated by HIF-1 and/or NMD, we performed whole animal RNA-sequencing of samples of nine different genotypes, which had active or inactive HIF-1, and functional or nonfunctional NMD. Specifically, for HIF-1 activation samples were: wildtype [HIF-1 inactive], egl-9(-) [HIF-1 perpetually active] or egl-9(-) hif-1(-) [HIF-1 inactive]; and for NMD functionality samples were: wild type [functional NMD], smg-1(-) [NMD deficient] or smg-2(-) [NMD deficient]. Comparisons between genotypes can be used to identify HIF-1-dependent and NMD-dependent target mRNA.

overall_design: Detailed version: For each sample, 300-500 L4 larvae were picked onto NGM plates and allowed to grow for 6 hours, reaching young adulthood. Animals were washed off in M9, spun down at 2,000 rpm for 2 min, and excess liquid was removed by aspiration. Samples were then rinsed twice with 3 mL M9 and twice with 3 mL RNase-free water. Excess liquid was removed by aspiration, and the pellet frozen in liquid nitrogen. RLT buffer (QIAGEN) was added to the pellet, and worms were lysed using a BeadBug microtube homogenizer (Sigma) and 0.5 mm zirconium beads (Sigma). RNA was extracted using the RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. Following RNA isolation, RNA integrity and quantity were determined by Fragment Analyzer (Agilent). polyA RNA was isolated from ~500ng of RNA was prepared using NEBNext poly(A) mRNA Isolation at 1/5 reaction, fragmented for 10 minutes, and prepared for short read sequencing using NEBNext Ultra II Directional RNA Library Prep kit for Illumina at 1/10 reaction with 12 cycles of amplification56. Libraries were confirmed by fragment analysis and qPCR and sequenced with 75nt paired end reads on an Element AVITI.

first: Calista

last: Diehl

first: Duanduan

last: Ma


title: Gene-expression profiling of ACC

city: Munich

first: Alexandra

middle: Sophia

last: Triebig

address: Ziemssenstraße 1

department: Medizinische Klinik und Poliklinik IV

institute: LMU Klinikum München

summary: Custom gene expression analysis of 58 fixed-paraffin embeded ACC tissue samples

overall_design: To study the tumor microenvironment, total RNA was isolated from two to five sections per ACC FFPE tissue using the AllPrep DNA/RNA FFPE Kit (Qiagen). Samples meeting the quality criteria were analyzed for gene expression using a custom NanoString panel


title: Gene-expression profiling of ACC [1]

overall_design: To study the tumor microenvironment, total RNA was isolated from two to five sections per ACC FFPE tissue. Samples meeting the quality criteria were analyzed for gene expression using a custom NanoString panel


title: Molecular architecture of the tumor microenvironment caused by BRCA1 and BRCA2 somatic mutations in human lung adenocarcinoma

city: Guangzhou

first: Gaoming

last: Liao

state: Guangdong

address: No. 151, Yanjiang West Road, Yuexiu District, Guangzhou

department: National Center for Respiratory Medicine

country: China

institute: The First Hospital of Guangzhou Medical University

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq and scTCR-seq to study the heterogeneity and molecular architecture of tumor microenvironment (TME) caused by BRCA1 and BRCA2 somatic mutations in lung adenocarcinoma (LUAD). LUADs are considered to be a heterogeneity population in the lung epithelium. Homologous recombination repair (HRR) deficiency has been linked to enhanced immunotherapy responses in non-small cell lung cancer patients. The HRR genes BRCA1 and BRCA2 are key regulators of DNA repair, yet their impact on the TME in LUAD remains unclear.This study provides a comprehensive characterization of the BRCA-mutant TME in LUAD patients, uncovering distinct immune response mechanisms and potential therapeutic strategies. These findings enhance our understanding of BRCA1/2-driven molecular architecture and offer novel insights into improving therapy efficacy in LUAD.

overall_design: Single-cell transcriptome sequencing and TCR sequencing based on tumor tissue, adjacent tissue, and blood samples from LUAD patients.

first: Xinbing

last: Yang

first: Qi

last: Liu

first: Shufeng

first: Yan

first: Jinwei

last: Li

first: Si

last: Huang

first: Wang

last: Ning

first: Xionghai

last: Qin

first: Gang

last: Xu


title: Soft matrix promotes ciliogenesis in human retinal pigment epithelial cells

status: Public on Jul 04 2026

first: Rida

last: Zahra

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies (COS), Cytoskeleton, Cell division and Signalling Unit

institute: Heidelberg University

summary: The primary cilium (PC) is a microtubule-based mechanosensory organelle involved in signal transduction. Although the signaling functions of PC have been well studied, its interaction with the cell´s mechanical environment remains unclear. Here, we used polyacrylamide hydrogels to investigate how extracellular matrix (ECM) stiffness influences ciliogenesis in human retinal pigment epithelial (RPE1) cells. We found that a soft hydrogel (1 kPa) induces cilia formation and elongation in RPE1 cells independent of serum starvation, a classical in vitro method to promote ciliogenesis. Transcriptome analysis of serum-fed RPE1 cells on soft matrix revealed cell cycle exit and alterations in ECM and cytoskeletal gene expression that favor ciliogenesis. Moreover, we observed that despite being very long, cilia formed on a soft substrate are functional, as they transduce Sonic hedgehog signal normally. Transcriptome and microscopy analysis of two cilia-inducing conditions (soft substrate and serum starvation) revealed upregulation of cilia-related genes and downregulation of proliferation markers on both conditions. Autophagy genes were more enriched in serum-starved cells, whereas upregulation of ECM genes and downregulation of actin-related genes were more pronounced on soft matrix. Our study demonstrates that PC biogenesis can be mechanically induced in RPE1 cells on soft substrates independent of external biochemical cues.

overall_design: (1) Bulk RNA-seq profiling of human retinal pigment epithelial cells cultured on soft matrix (1 kPa: polyacrylamide-fibronectin hydrogel system) or glass-control (glass coated with fibronectin only) in the presence of serum for 24 hours. (2) Bulk RNA-seq profiling of human retinal pigment epithelial cells cultured on uncoated glass in the presence or absence of serum (6 hours of serum depletion). (3) Bulk RNA-seq profiling of human retinal pigment epithelial cells cultured on uncoated glass in the presence or absence of serum (24 hours of serum starvation).

first: Natalie

last: Munding

first: Katrin

last: Domsch

first: Hannah

last: Braun-Lee

first: Camila

last: García-Navarrete

first: Motomu

last: Tanaka

first: Gislene

last: Pereira


title: Glucocorticoid polarization of primary human macrophages

first: Alexandra

summary: In vitro glucocorticoid-polarized peripheral blood monocytes isolated from healthy blood donors were characterized using NanoString nCounter gene expression analysis. Either dexamethasone or conditioned medium (CM) from an adrenocortical carcinoma cell line (NCI-H295R) was used as glucocorticoid treatment

overall_design: PBMC-derived macrophages of different healthy human blood donors were exposed to GM-CSF+IFNγ (=ctrl/M1 macrophage), GM-CSF+IFNγ+dexamethasone, GM-CSF+IFNγ+CM NCI-H295R cells or GM-CSF+IFNγ+CM NCI-H295R cells (pre-exposed to metyrapone)


title: Immune Modulation of Macular Degeneration Through Natural Killer Cell Activity

city: Dublin

first: Karsten

last: Hokamp

state: Dublin

address: Stephen's Green

department: Genetics

country: Ireland

institute: Trinity College Dublin

summary: Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in the world and can result in pathological neovascularization in late-stage disease. Discovery of new processes of disease pathogenesis are needed, as current gold-standard treatments have a therapeutic ceiling. Here we used a ‘human-first’ approach to uncover underlying mechanisms of disease and in doing so identify immunotherapy as a potential disease modifier for AMD.  Plasma cytokine analysis in The Irish Longitudinal stuDy on Ageing (TILDA), a large-scale population cohort, revealed an imbalance of peripheral lymphocytic type 1 and type 2 signature cytokines associated with severity of AMD. This led us to discover a skewed phenotype for innate lymphoid Natural Killer (NK) cells, but not T lymphocytes, in the peripheral blood of people with AMD, indicating peripheral NK cells may modulate retinal disease. Modelling retinal injury using a laser, we confirmed splenic NK cells were activated in response to distal retinal injury, with concordance between mouse and human lymphocytic activation patterns. scRNA-sequencing demonstrated expansion of a defined subset of activated cytolytic NK cells at the neovascular lesion site and found that NK cell proliferation, biogenesis and metabolic respiration is heightened during active resolution of retinal neovascular lesions. We find that NK cells play a critical role in remodelling neovascular lesions through their cytotoxic activity, limiting pathology. We find NK cells localize to the basolateral side of neovessels in human AMD donor eye tissue and show that primary human retinal endothelial cells can act as target cells for NK cell-directed cytolysis. NK cells in both peripheral blood and donor eye tissue exhibit a variety of markers of NK cell quiescence in AMD and indicate NK cells have limited capacity for replenishment at the site of disease, which may be a factor in disease progression. Adoptive NK cell immunotherapy with cytokine-activated NK cells reduces neovascular lesion volume and repairs neovessel barrier integrity in models of retinal neovascularization. Here, we propose that harnessing NK cells may represent a novel transformative therapeutic strategy for the prevention and treatment of neovascular eye disease.

overall_design: RNA seq profiling of wildtype C57Bl/6J mouse RPE/choroid tissue 3 days following intraperitoneal injection of recombinant IL-18 (100 mg/kg) and administration of laser-induced CNV

first: Sarah

middle: L

last: Doyle

first: Ema

last: Ozaki

first: Kiva

last: Brennan

first: Fiona

last: Roche


title: Safety and efficacy analysis of in vivo lentiviral gene therapy in pre-clinical ARC syndrome models

city: Non Hispanic / Latino

first: Andrei Claudiu

last: Cozmescu

address: 30 Guilford Street

department: Institute of Child Health

country: United Kingdom

institute: University College London

summary: Arthrogryposis, Renal dysfunction and Cholestasis (ARC) syndrome is a rare inherited disorder caused by defects in the VPS33B trafficking protein, leading to impaired bile flow, progressive liver disease and early death. No effective treatments are currently available. Gene therapy offers a potential approach by restoring the missing VPS33B protein in liver cells. Here, we show that liver-targeted lentiviral gene therapy safely and effectively rescues key features of ARC syndrome in a mouse model following in vivo administration by intravenous injection, combined with transient liver macrophage depletion. To assess the treatment efficacy, disease severity is exacerbated by 0.25% cholic acid diet feeds. A liver-specific vector shows a favourable safety profile over a ubiquitous vector. Mice receiving the safe liver-specific vector display improved survival, growth and liver function, reduced fibrosis and bile canaliculi restoration. These findings support targeted gene therapy as a promising treatment for ARC syndrome and related early-onset liver diseases.

overall_design: RNA-Seq gene expression disregulation analysis between tumoral and healthy liver samples collected at 9 months from mice treated with lentiviral gene therapy.

first: Sian

last: Goldsworthy

first: Sergi

last: Castellano

first: Claudiu

middle: A


title: Single-cell short- and long-read transcriptomic atlas of seven reproductive-axis tissues in male Baoshan pig

city: Kunming

first: Hai

last: Li

state: Yunnan

address: No. 452, Fengyuan Road, Panlong District

department: College of Animal Science and Technology

institute: Yunnan Agricultural University

summary: Single-cell transcriptomic data were generated from seven reproductive-axis tissues of an 18-month-old male Baoshan pig, including hypothalamus, pituitary, prostate, bulbourethral gland, seminal vesicle, epididymis, and testis. To characterize both gene-expression profiles and transcript isoform diversity across these tissues, single-cell short-read libraries were sequenced on an Illumina platform and single-cell long-read libraries were sequenced on an Oxford Nanopore platform. Short-read data were processed with Cell Ranger, whereas long-read data were processed with FLAMES and further assessed for isoform structure. The dataset provides cell-level gene expression matrices, transcript/isoform-level quantification, isoform annotation files, and accompanying cell metadata. These data may facilitate studies of cellular heterogeneity and transcript isoform usage across the porcine reproductive axis.

overall_design: This study includes seven tissue-derived single-cell samples from the reproductive axis of one 18-month-old male Baoshan pig: hypothalamus, pituitary, prostate, bulbourethral gland, seminal vesicle, epididymis, and testis. For each tissue, one single-cell short-read library was generated for Illumina sequencing and one single-cell long-read library was generated for Oxford Nanopore sequencing, resulting in 14 sequencing libraries in total. The submission therefore contains separate records for short-read and long-read libraries from each tissue.

first: Jinglong

last: Huo


title: Looping specificity of Polycomb response elements requires GAF and a combinatorial code of looping factors [micro-c]

city: Montpellier

first: Marco

last: Di Stefano

address: 141 Rue de la Cardonille

country: France

institute: CNRS

summary: Chromatin looping between cis-regulatory elements is essential for precise developmental gene expression, and its disruption is frequently linked to disease. Polycomb Response Elements (PREs) are specialized tethering elements that mediate chromatin loops and are bound by transcription factors like GAGA-associated factor (GAF), contributing to the recruitment of Polycomb group (PcG) proteins. While both PcG proteins and GAF have been implicated in looping, their specific roles and the mechanisms of loop specificity remain unresolved. Using genome-wide and locus-specific approaches, we show that high GAF occupancy is required for chromatin looping and gene regulation. However, GAF alone cannot establish loops without additional factors. Surprisingly, PRE looping does not require the PcG subunit Polyhomeotic (PH) or repressive histone marks (H3K27me3). Intriguingly, orthologous PRE sequences can rescue looping, while unrelated PREs with similar GAF levels cannot. This indicates that looping specificity depends on both GAF levels and compatible factor combinations at loop anchors. Our results support a combinatorial model in which GAF collaborates with additional looping factors, to drive PRE-specific interactions. We propose the existence of a “looping code” as a mechanistic basis that might explain why only a subset of PREs form loops and contribute to Polycomb-mediated gene silencing.

overall_design: Micro-C, Hi-C experiments at different developental stages and tissues (Drosohila embryos, larval imaginal eye, wing and leg discs

first: Gonzalo

last: Sabarís

first: Sandrine

last: Denaud

first: Lauriane

last: Fritsch

first: Ana-Maria

last: Popmihaylova

first: Giorgio-Lucio

last: Papadopoulos

first: Bernd

last: Schuettengruber

first: Giacomo

last: Cavalli


title: Symbiosome-targeted peptides enhance nitrogen fixation without terminal differentiation [Plant RNA-seq]

city: Braunschweig

first: Kevin

middle: D.

last: Oliphant

state: Niedersachsen

address: Humboldtstr. 1

department: Institut für Pflanzenbiologie

institute: Technische Universität Braunschweig

summary: Legumes have evolved lineage-specific peptides to control rhizobia and sustain nitrogen fixation. In inverted repeat-lacking clade (IRLC) legumes, nodule-specific cysteine-rich (NCR) peptides enforce terminal bacteroid differentiation, maximizing symbiotic output but restricting nodule lifespan. By contrast, Robinioid legumes, the IRLC’s sister clade, lack NCRs yet yet include perennial species that maintain productive nodules for decades. Here we identify a nodule-proline-glycine-rich peptide family (NPGs) as a conserved, genus-wide innovation of Robinia. NPGs are highly abundant, localize to the symbiosome membrane, and are intrinsically disordered. Exposure of Mesorhizobium robiniae to recombinant NPGs reprograms physiology, inducing nitrogenase expression while dampening growth without loss of viability. NPGs thus exemplify a distinct, reversible strategy of symbiont control, expanding the peptide repertoire that supports nitrogen fixation in perennial legumes.

overall_design: Plant RNA-seq (Robinia pseudoacacia): Transcriptomes of Robinia pseudoacacia tissues were profiled during nodulation with Mesorhizobium robiniae DSM 100022. RNA-seq was performed on nodules, roots, stems, and leaves at 24 h, 48 h, 96 h, 7 d, 14 d, 21 d, and 1 y post-inoculation. Spatial sampling included nodules and root segments at +5 cm and +10 cm from the nodule zone. Three biological replicates per condition were sequenced.

first: Kevn

middle: D


title: Symbiosome-targeted peptides enhance nitrogen fixation without terminal differentiation [Bacteria RNA-seq]

overall_design: Bacteria RNA-seq (Mesorhizobium robiniae) Transcriptomes of Mesorhizobium robiniae DSM 100022 were profiled following exposure to the nodule-proline-glycine-rich peptide (NPG). Mid-log cultures were treated with NPG2 peptide ( 250 µM), PBS control. Cells were harvested after 2 hours of exposure. Three biological replicates per condition were sequenced.


title: Looping specificity of Polycomb response elements requires GAF and a combinatorial code of looping factors [Hi-C]


title: Structural survey of HIF-2α reveals regulation of its subcellular localization and protein interactome

status: Public on May 05 2026

city: Lund

first: Stina

last: Östenberg

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary: Hypoxia‑inducible factor 2α (HIF‑2α) is a central regulator of cellular homeostasis and a known oncogenic driver in multiple cancers. Although HIF‑2α is canonically defined as a nuclear transcription factor, its cytoplasmic presence and potential non‑transcriptional functions remain poorly understood. Here, we dissect the structural determinants of HIF‑2α localization, stability, and activity using a deletion‑construct library, transcriptional assays, and in vivo xenograft models. We show that the oxygen‑dependent degradation domain (ODD), and N‑terminal intrinsically disordered region (IDR) and transactivation domain (NTAD) promote cytoplasmic localization, whereas the C‑terminal IDR drives nuclear accumulation. Notably, we demonstrate that HIF‑2α nuclear localization occurs independently of ARNT dimerization, resolving a long-standing question in the field. While both NTAD and C‑terminal (C)TAD contribute to transcriptional activation, only CTAD mediates hypoxia responsive element (HRE)   transactivation, and neither domain is required for tumor growth in vivo. These data suggest a dominant role for non‑canonical cytoplasmic mechanisms in HIF‑2α-driven tumorigenesis. Proteomic analyses reveal HIF‑2α interactions with regulators of mitochondrial function, translation initiation, RNA splicing, vesicular transport, and DNA replication. Together, these findings uncover previously unrecognized structural and functional complexity of HIF‑2α and expand its role beyond canonical transcriptional regulation

overall_design: RNA-seq profiling of SK-N-BE(2) wild‑type cells and of cells transfected with full‑length HIF‑2α, ΔN‑CTAD, or Δc‑IDR to examine how distinct HIF‑2α structural variants reshape the transcriptomic landscape.

first: Tomas

last: Gregor

first: Sinan

last: Karakaya

first: Anja

last: Zethraeus

first: Elina

last: Fredlund

first: Charlotte

last: Welinder

first: Emma

last: Hammarlund

first: Jenny

last: Hansson

first: Jared

last: Rosenblum

first: Sofie

last: Mohlin


title: Transcriptome and behavioral assessment in larval zebrafish (Danio rerio) following exposure to perfluorononanoic acid (PFNA)

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

summary: Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent chemicals widely detected in aquatic systems and drinking water. Perfluorononanoic acid (PFNA), a long-chain PFAS, has been reported globally in environmental matrices and fish tis-sues. Although PFNA has been linked to developmental, metabolic, and neurological toxicity, its effects on lipid-related pathways and neurotoxicity remain poorly charac-terized. This study evaluated the developmental and neurotoxic effects of PFNA ex-posure in zebrafish embryos and larvae following a 7-day exposure to environmentally relevant PFNA concentrations. PFNA exposure did not significantly affect survival or deformity rates. Apoptosis was significantly increased in larvae exposed to 1 µg/L PFNA compared to controls, whereas reactive oxygen species were unaffected. Each tested concentration (0.1 µg/L and 10 µg/L) showed a different effect on the zebrafish transcriptome.  Low-dose PFNA exposure primarily affected lipid transport, choles-terol metabolism, sphingolipid signaling, and neurodegeneration-related pathways, while high-dose PFNA altered synaptic signaling, axon guidance, and thyroid hormone synthesis. Hypoactivity was observed in the movement of larval zebrafish based on a visual motor response test.  Taken together, PFNA exposure leads to molecular changes related to neurotoxicity and lipid metabolism in zebrafish, which may con-tribute to adverse neurodevelopmental outcomes.

overall_design: Biological replicates were as follows: 0.1% DMSO controls (n = 3), 0.1 μg/L PFNA (n = 3), and 10 μg/L PFNA (n = 3).

first: Lev

last: Avidan

first: Cole

last: English

first: Katie

last: McDonnell

last: Ivantsova

first: Chris


title: Liver Endothelial Zonation Orchestrates Hepatic Steatosis Onset through Retinoic Acid-regulated FGF1

city: Xi'an

first: Zhiqiang

last: Fang

state: Shaanxi

address: No.169,Changle West Road

institute: Xijing Hospital

summary: The contribution of liver sinusoidal endothelial cell (LSEC) zonation to metabolic dysfunction-associated steatotic liver disease (MASLD) pathogenesis remains undefined. We identified selective lipid deposition in the pericentral zone during early MASLD. Multi-omics analyses confirmed enhanced pericentral lipid metabolism in both hepatocytes and LSECs. Mechanistically, pericentral LSEC marker c-Kit transcriptionally activated FGF1 via nuclear receptor RXRG, which suppressed hepatocellular lipid accumulation through FGFR4 signaling. Remarkably, retinoic acid (RXRG’s endogenous ligand and active vitamin A metabolite) phenocopied FGF1’s anti-steatotic effects. Clinical data revealed an inverse correlation between dietary vitamin A and MASLD severity, suggesting therapeutic potential of vitamin A supplementation for early intervention.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary c-Kit positive and c-Kit negative LSECs isolated from a 12-week HFD diet-induced MASLD mice liver using c-Kit immunomagnetic beads

first: Lin

last: Wang


title: Elevated plasma cholesterol improves sepsis outcome by promoting hepatic metabolic reprogramming

city: Lexington

first: Xiangan

last: Li

address: 741 S Limestone

institute: University of Kentucky

summary: Background: Sepsis is a life-threatening condition with high mortality and limited therapeutic options. This study investigated the association between plasma cholesterol levels and sepsis survival and explored the mechanisms by which elevated cholesterol confers protection. Methods: We analyzed 2,787 sepsis patients from the MIMIC-IV database, comparing cholesterol levels between 28-day survivors and non-survivors and assessing mortality risk using multivariable Cox regression. To test causality, C57BL/6J mice were fed either a high-cholesterol diet (HCD) or a regular diet (RD) before cecal ligation and puncture (CLP). Results: Survivors had significantly higher cholesterol than non-survivors (median 135 vs. 126 mg/dL; p < 0.001). High cholesterol (≥133 mg/dL) was independently associated with reduced 28-day mortality (adjusted HR = 0.80; 95% CI: 0.67–0.95; p = 0.012). In mice, HCD elevated plasma cholesterol and improved survival (52.5% to 90%), through a mechanism that is not primarily explained by broad immune activation. Hepatic transcriptomics revealed metabolic reprogramming, including enhanced oxidative phosphorylation and antioxidant pathways, with suppression of endoplasmic reticulum proteostasis. Inhibition of mitochondrial respiration abolished the survival benefit. Conclusions: Elevated plasma cholesterol is associated with improved sepsis outcomes, likely through promoting hepatic metabolic reprogramming. Targeting hepatic bioenergetics is a potential therapeutic approach.

overall_design: RNA-seq profiling of liver tissue from C57BL/6J mice fed a 3-day high-cholesterol diet versus a regular diet.


title: Transcriptome and Hormone Regulations Shape Drought Stress-Dependent Fusarium Head Blight Susceptibility in Different Barley Genotypes

status: Public on May 04 2026

city: Freising

first: Ralph

last: Hückelhoven

address: Emil-Ramann-Str. 2

department: Chair of Phytopathology

institute: Technische Universität München

summary: This dataset comprises 3'RNAseq data from a greenhouse experiment investigating the transcriptional responses of four spring barley genotypes (Avalon, Barke, Morex, and Palmella Blue) to Fusarium culmorum infection and drought stress. Plants were grown under controlled conditions and subjected to four treatment combinations: watered + mock (WM), watered + Fusarium (WFc), drought + mock (DM), and drought + Fusarium (DFc). Samples were collected at 4 and 7 days post-inoculation (dpi) from spikes and used for RNA extraction.

overall_design: RNA was extracted from barley spikes collected at  4 and 7 days post-inoculation (dpi) from four spring barley genotypes (Hordeum vulgare: Avalon, Barke, Morex, and Palmella Blue) under four treatment conditions: watered + mock (WM), watered + Fusarium culmorum (WFc), drought + mock (DM), and drought + Fusarium culmorum (DFc). Each sample represents a pool of four spikes from different pots, with four biological replicates per condition and time point. The experiment was designed to investigate the interaction between drought stress and Fusarium culmorum infection in barley, focusing on genotype-specific transcriptional responses. Plants were spray-infected with a Fusarium culmorum spore solution or mock-treated with water, and covered with plastic bags for 48 hours to ensure high humidity and promote successful infection. RNA was extracted from flash-frozen spike tissue and used for transcriptome profiling via RNA sequencing.

first: Sophia

last: Hein

first: Felix

last: Hoheneder

first: Christina

middle: E

last: Steidele

first: Christine

last: Wurmser


title: Histone Demethylase KDM6B Promotes Postnatal Oligodendrocyte Development and Cortical Myelination

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

summary: Myelination in the postnatal cortex requires epigenetic programs that activate oligodendrocyte gene networks. Here we show that the histone H3K27me3 demethylase KDM6B promotes this process in vivo. Conditional Kdm6b deletion (Kdm6b-cKO) in Emx1⁺ dorsal telencephalic progenitors caused delayed cortical myelination. Lineage-specific RNA-seq revealed that the oligodendrocyte master regulator Sox10 was significantly reduced, as well as myelination effectors, indicating impaired oligodendrocyte maturation. Chromatin immunoprecipitation assays of the same lineage showed increased H3K27me3 at promoter-proximal regions of Sox10, consistent with loss of KDM6B-mediated de-repression. Temporally controlled Sox10 induction partially rescued myelination in Kdm6b-cKO mice. These findings define a KDM6B→SOX10 axis that licenses oligodendrocyte development and cortical myelination by removing repressive H3K27me3 and sustaining active chromatin, with implications for KDM6B-related neurodevelopmental disorders.

overall_design: Examination of differential gene expression between wild-type and Kdm6b-deleted cortical neural cells derived from Emx1⁺ progenitors


title: Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways

city: Accra

first: Charles

middle: Ochieng'

last: Olwal

address: WACCBIP, Volta Road, University Of Ghana

department: Department of Biochemistry, Cell and Molecular Biology

country: Ghana

institute: West African Centre for Cell Biology of Infectious Pathogens

summary: Persistent infection with human papillomavirus (HPV) is the primary cause of cervical cancer worldwide. Notably, women co-infected with HPV and human immunodeficiency virus type 1 (HIV-1) have a six-fold higher lifetime risk of developing cervical cancer compared to those without HIV, even when adhering to antiretroviral therapy (ART) and achieving T-cell reconstitution. While chronic HIV-1 infection is known to cause inflammation, how paracrine signals from immune cells alter signaling in cervical cells remain poorly understood. To address this, we conducted global transcriptomics analysis on cervical swabs from Kenyan women with HPV, stratified by HIV-1 and cancer status. Strikingly, women with HIV-1 showed cancer-like gene expression patterns in non-cancerous cervical epithelial cells. Complementary global mass spectrometry (MS) proteomics of cervical cells exposed to the secretome of HIV-1–infected primary CD4+ T-cells revealed altered expression of proteins in MAPK, PI3K-AKT, and β-catenin signaling pathways. Integrative network analyses of transcriptomic and proteomic datasets revealed that HIV-1 altered gene expression in key pathways known to drive cervical cancer, including genes commonly mutated in HIV-1-naïve disease. Notably, IRS-1, a key PI3K-AKT pathway activator, was found to be consistently upregulated in both participant samples and cell culture models, as were interferon-stimulated genes. Phosphoproteomics MS analysis confirmed PI3K-AKT pathway activation in cervical cells exposed to conditioned media from HIV-1-infected T-cells. Together, our findings uncover how HIV-1 reshapes cervical cell signaling via paracrine mechanisms and highlights the PI3K pathway as a potential therapeutic target in HIV-associated cervical cancer.

overall_design: RNA-seq profiling of cervical samples from HIV-infected and HIV-uninfected Kenyan women who have normal cervix, precancerous cervical lesions or invasive cervical carcinoma

middle: O

first: Ujjwal

last: Rathore

first: Sara

last: Makanani

first: Prashant

last: Kaushal

first: Immy

last: Ashley

first: Manisha

middle: R

last: Ummadi

first: Vincent

last: Appiah

first: Alexandra

last: DjomkamZune

first: Sophie

last: Blanc

first: Declan

last: Winters

first: Yennifer

last: Delgado

first: Kapten

last: Muthoka

first: Jacqueline

last: Fabius

first: Manon

last: Eckhardt

first: Robyn

last: Kaake

first: Maureen

last: Su

first: Oliver

last: Fregoso

first: Judd

middle: F

last: Hultquist

first: Elkanah

last: Orang’o

first: Danielle

last: Swaney

first: George

middle: K

last: Boateng

first: Nevan

last: Krogan

first: Peter

last: Quashie

first: Yaw

last: Bediako

first: Mehdi

last: Bouhaddou


title: Single-cell transcriptomic analysis of lipoprotein transport in yolk sac membrane endodermal epithelial cells of chicken embryos

status: Public on May 01 2026

city: Taipei

first: Jie Ci

last: Wu

address: Roosevelt Rd.

institute: National Taiwan Unviersity

summary: This study investigates the transcriptional landscape of yolk sac membrane (YSM) endodermal epithelial cells in chicken embryos using single-cell RNA sequencing. The yolk sac membrane plays a critical role in nutrient absorption and transport, particularly in lipoprotein metabolism during early embryonic development.  Single-cell RNA sequencing was performed on YSM samples collected at embryonic day 4 (E4) and embryonic day 7 (E7). After quality control filtering, high-quality cells were retained for downstream analysis. Clustering analysis identified distinct cellular populations, and gene expression profiles were analyzed to characterize functional differences across developmental stages.  The processed data include filtered gene expression matrices, cell barcode annotations, gene feature annotations, and cell-level metadata including clustering assignments. Raw sequencing data are available in the Sequence Read Archive (SRA).

overall_design: Yolk sac membrane (YSM) tissues were collected from chicken embryos at embryonic day 4 (E4) and embryonic day 7 (E7). Single-cell suspensions were prepared and processed using the BD Rhapsody system.  Sequencing reads were processed to generate gene expression count matrices. Quality control filtering was applied to remove low-quality cells based on gene counts and sequencing depth. The filtered dataset was used for downstream analysis including normalization, dimensionality reduction, and clustering.  Processed data submitted to GEO correspond to the filtered dataset used in the analysis.

first: Jie-Ci

first: Zhao-Qi

last: Hu

first: Yuan-Yu

last: Lin

first: Harry John

last: Mersmann

first: Shih-Torng

last: Ding


title: CD109 is dynamically expressed in endothelial and endocardial subpopulations during heart development, modulates endothelial cell behavior in vitro, but is not required for cardiovascular morphogenesis

status: Public on May 03 2026

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: CD109 encodes a GPI-linked glycoprotein that acts as a signaling modulator in the TGF-β pathway. CD109 has emerged in several genome-wide association studies as linked to coronary artery disease, myocardial infarction, and angina pectoris. Heterozygous loss-of-function mutations in CD109 have also been reported in patients with congenital heart defects, suggesting potential developmental relevance, though CD109 has never been investigated in the context of cardiovascular development. We previously identified Cd109 upregulation in murine atrioventricular valves undergoing myxomatous degeneration following a reduction of epicardial-derived cells. Here, we characterize Cd109 expression in the murine cardiovascular system and assess its function during development using in vitro and in vivo approaches. We found that Cd109 is strongly expressed in the endothelium of the coronary vasculature and in an endocardial-derived subpopulation in the atrioventricular valves. This expression persists through key stages in cardiovascular development. Western blotting and immunostaining confirm endothelial expression in heart and lung tissues. siRNA knockdown of CD109 in primary human endothelial cells led to dysregulation of vascular development pathways and decreased tube formation capacity. We generated Tie2Cre;Cd109fl/fl mice, eliminating Cd109 expression from heart and lung tissues without overt morphological consequences. Together, these results establish Cd109 as a useful marker of coronary vasculature in the heart and indicate that endothelial lineage-specific deletion of Cd109 does not cause gross morphological defects during cardiac development. The transcriptional and functional changes observed in endothelial cells in vitro suggest that additional studies will be necessary to define contexts in which Cd109 influences vascular biology.

overall_design: RNA-seq profiling of Human Umbilical Vein Endothelial Cells (HUVECs) 72h after transfection with siRNA targeting CD109 or transfection with a scramble control.

first: Andrew

middle: B

last: Harvey

first: Andy

last: Wessels


title: Antigen-scaffolds loaded with hyper-stable Neoleukin-2/15 expand antigen-specific T cells with a favorable phenotype for adoptive cell therapy

city: Kgs. Lyngby

first: Kamilla Kjærgaard

last: Munk

address: Henrik Dams Allé, 204

department: Department of Health Technology

institute: Technical University of Denmark

summary: Adoptive cell therapy (ACT) has shown promising results in cancer treatment, however, achieving effective ex vivo expansion of potent, functionally active, and cytotoxic T cells remains challenging. To address this challenge, we recently developed artificial antigen-presenting scaffolds (Ag-scaffolds) capable of expanding antigen-specific T cells with phenotypes favorable for ACT.  In this study, we compared the established technology using IL2/IL21-loaded Ag-scaffolds (Ag-IL2/21) with Neoleukin-2/15-loaded Ag-scaffolds (Ag-Neo2/15). Neoleukin-2/15 (Neo2/15) is an engineered cytokine that selectively binds to IL-2Rβ/γ receptors, enhancing CD8+ T cell proliferation while limiting regulatory T cell expansion. Based on its favorable signaling properties, we hypothesized that incorporating Neo2/15 as part of the Ag-scaffolds would improve the quality and functionality of expanded T cells.  We showed that Ag-Neo2/15 scaffolds promoted significant T-cell expansion, with frequencies of antigen-specific CD8+ T cells comparable to those achieved with Ag-IL2/21 scaffolds. The CD8+ T cells expanded with Ag-Neo2/15 scaffolds exhibited potent TNFα and IFNγ, potentially enhancing their therapeutic potential. T cells expanded with Ag-Neo2/15 scaffolds had superior and durable cytotoxicity against tumor target cells compared to T cells expanded with Ag-IL2/21 scaffolds. These findings were further supported by our single-cell analysis revealing that T cells expanded with Ag-Neo2/15 scaffolds had higher cytotoxic scores and lower dysfunctionality scores compared to T cells expanded with Ag-IL2/21 scaffolds. The single-cell analysis also indicated increased expression of genes linked to cell division and enhanced proliferative capacity in Ag-Neo2/15 expanded T cells. Furthermore, TCR clonality analysis demonstrated that Ag-Neo2/15 scaffolds promoted the expansion of functionally superior T-cell clones, as the top clones of CD8+ T cells expanded with Ag-Neo2/15 scaffolds exhibited a favorable phenotype, essential for effective antigen recognition and sustained T-cell mediated cytotoxicity.  Our findings suggest that Ag-Neo2/15 scaffolds represent an advancement in ACT by producing high-quality, functional antigen-specific T cells. This method has the potential to improve clinical outcomes in cancer therapy by generating large numbers of highly functional T cells, thereby optimizing the balance between cytotoxicity and proliferation capacity with less exhausted T-cells in expansion protocols.

overall_design: We performed a single-cell analysis using antigen-specific T cells from two healthy donors to investigate differences between cells expanded with Ag-Neo2/15 scaffolds and those expanded using conventional strategies. In this analysis, we examined the transcriptome, surface proteome, and T-cell clonality of both unexpanded T cells, as well as T cells expanded using free peptide, IL-2 and IL-21, Ag-IL2/21 scaffolds, and two different Ag-Neo2/15 scaffolds (Neo-3x and Neo-12x).

first: Maria

last: Ormhøj

first: Kamilla

first: Siri

last: Tvingsholm

first: Keerthana

last: Ramanathan

first: Amalie

last: Bentzen

first: Georgios

last: Kladis

first: Gitte

middle: N

last: Aasbjerg

first: Grigorii

last: Nos

first: Tripti

last: Tamhane

first: Hólmfridur

last: Halldórsdóttir

first: Søren

last: Jakobsen

first: Marcus

last: Frej

first: Kristoffer

middle: H

last: Johansen

first: Mohammad

last: Kadivar

first: Sine

last: Hadrup


title: Airway immune signatures of protection and disease progression in recent human tuberculosis household contacts [bulk RNA-seq]

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

institute: Francis Crick

summary: The local early immune factors dictating whether individuals who have been infected with Mycobacterium tuberculosis remain healthy or progress to active TB have not been defined. We interrogated the airway immune response at single cell resolution in bronchoalveolar lavage (BAL) from PET-CT characterised recent TB household contacts, who either controlled the infection or progressed to TB disease, as well as of active TB patients at diagnosis. Single cell RNA-sequencing revealed type I IFN-dependent and -independent neutrophil signatures in BAL from active TB patients and TB progressors. We report an inverse relationship between airway neutrophils and T cells, with T cells showing signatures of exhaustion, cytotoxicity and cell death in progressors and active TB patients with a neutrophil dominated airway profile. Conversely, we identified T cell signatures of protection in non-progressor contacts dominated by genes related to regulation, quiescence and a stem-like profile. Both the signature of TB progression and the stem-like T cell signature of non-progressors from human airways were recapitulated in scRNA-seq data from non-human primate (NHP) granulomas, associated with disease or immune protection, respectively. Our findings from early human airway responses in TB contacts reveal genes, pathways and cell states that may dictate infection outcome and inform strategies for developing effective host-directed therapies and vaccines.

overall_design: Bulk and single-cell RNAseq of bronchoalveolar lavage from human cohort of tuberculosis patients and their household contacts.

first: William

middle: J

last: Branchett

first: Jee-Whang

last: Kim

first: Jessica

last: Shields

first: Anver

last: Kamil

first: Jo

last: Lee

first: Ismail

last: Novsarka

first: Hubert

last: Slawinski

first: Katalin

last: Wilkinson

first: Robert

first: Raman

last: Verma

first: Pranabashis

last: Haldar

first: Anne

last: O'Garra


title: PGC-1alpha pathway dysregulation disrupts myofiber specification in a mouse model of SBMA

city: Ann Arbor

first: Andrew

middle: P

last: Lieberman

state: MI

address: 1150 W Medical Center Dr.

institute: University of Michigan

summary: Skeletal muscle pathology is a critical but poorly understood contributor to neuromuscular degeneration in spinal and bulbar muscular atrophy (SBMA), a CAG/polyglutamine (polyQ) expansion disorder caused by mutation in the androgen receptor (AR). Using a gene-targeted SBMA mouse model, we applied single-nucleus RNA sequencing to identify a previously unrecognized, disease-specific population of skeletal muscle myonuclei that replace normal myonuclear subtypes. This transition was driven by dysregulation of the PGC-1α pathway, a central regulator of myofiber specification and metabolic identity. PGC-1α dysfunction in SBMA muscle was age-, hormone-, and polyQ length–dependent and was partially rescued by subcutaneous delivery of AR-targeted antisense oligonucleotides. Integrated ChIP-seq and RNA-seq analyses revealed that aberrant PGC-1α activity promoted the expression of a distinct set of myofiber specification genes while downregulating those defining healthy Type IIb and Type IIx myonuclei. We propose a model in which this dysfunction arose downstream of polyQ-mediated sequestration of PGC-1α cofactors MEF2, CREB, and CBP, leading to transcriptional reprogramming and cellular dysfunction. These findings implicate PGC-1α dysregulation as a key event linking AR polyQ expansion to skeletal muscle degeneration and suggest a shared mechanism for polyQ-mediated muscle pathology across related neurodegenerative diseases.

overall_design: All mice used in this study were of the C57BL/6J strain. RNA was extracted and sequenced from male WT, R6/2 transgenic, or SCA1 Q154 mice. Tissue samples used were all skeletal muscle: tibialis anterior at 24 weeks for SCA1 Q154, quadriceps at 12 weeks for R6/2 transgenic, and an equal number of age- and tissue-matched controls from WT.

first: Curtis

last: Kuo

first: Laura

last: Chopp

first: Zhigang

last: Yu

first: Luhan

last: Ni

first: Hien

middle: T

last: Zhao

first: Janghoo

last: Lim


title: Dynamin 2 regulates mitochondrial mitotic fission in pulmonary hypertension

city: Kingston

first: Stephen

last: Archer

address: 94 Stuart Street

department: Department of Medicine

country: Canada

institute: Queen's University

summary: Dynamin-related protein 1 (DRP1) mediates mitochondrial fission and permits rapid cell cycle progression in hyperproliferative cells by coordinating nuclear and mitochondrial division, a process called mitotic fission. However, DRP1 alone appears insufficient to complete fission and the link between fission and cell cycle progression is unknown.We hypothesize Dynamin 2 (DNM2) interacts with DRP1 to complete mitochondrial fission and regulate cell cycle progression. We show that DNM2 is upregulated in pulmonary arterial smooth muscle cells in human and rodent pulmonary arterial hypertension (PAH PASMC), contributing to disease pathophysiology.

overall_design: We want to study the transcriptomic changes after silencing DNM2 in PAH PASMCs.

first: Ashish

last: Das Gupta

first: Kuang-Hueih

last: Chen

first: Danchen

last: Wu

first: Siddhartha

last: Yerramili

first: Patricia

last: Lima

first: Ashley

last: Martin

first: Rachel

last: Bentley

first: Benjamin

last: Ott

first: Tanvi

last: Nandani

first: Jeff

last: Mewburn

first: Lian

last: Tian

first: Ruaa

last: Al-Qazazi

first: Issac

last: Emon

first: Pierce

last: Colman

first: Lindsay

last: Jefferson

last: Noordhof

first: Oliver

last: Jones

first: Charles

last: Hindmarch


title: STAT1 expression in myeloid cells restrains murine norovirus-induced hepatitis and fibrosis

city: Vancouver

first: Lisa

middle: C

last: Osborne

state: BC

address: 3507-2350 Health Sciences Mall

department: Microbiology & Immunology

institute: University of British Columbia

summary: Rare cases of non-hepatotropic virus (NHV) infection in humans can cause severe hepatitis and even acute liver failure. Clinically relevant animal models of NHV-induced hepatitis are limited, contributing to the incomplete understanding of pathological mechanisms. Murine norovirus (MNV) elicits hepatosplenomegaly in mice lacking the antiviral immune effector Signal Transducer and Activator of Transcription-1 (STAT1), providing a model to investigate mechanisms of NHV-induced hepatic pathology. STAT1-sufficient and -deficient (Stat1Het, Stat1KO) littermates infected intravenously (i.v.) with MNV strain CR6 were assessed for hepatic inflammation and viral burden. Cell types and molecular pathways associated with hepatic pathology in CR6-infected Stat1KO mice were identified by flow cytometry and RNAseq of liver tissue. The relative importance of hematopoietic vs non-hematopoietic expression of STAT1 in restricting CR6 replication and maintaining tissue homeostasis was assessed in bone marrow chimeras. MNV CR6 Stat1KO mice developed severe hepatitis with patchy hepatocellular necrosis and localized enrichment of CR6-infected myeloid cells, particularly macrophages. Gene set enrichment analysis (GSEA) of hepatic biopsies isolated from CR6-infected Stat1KO mice suggested dysregulated myeloid cell activation and indicated similarities between murine and human hepatic pathologies. STAT1 expression in hematopoietic cells was protective against hepatic viral dissemination, but hematopoietic STAT1-deficiency permitted persistent hepatic MNV infection, facilitating dysregulated myeloid cell activation and hepatic fibrosis. These results demonstrate that the role of STAT1 extends beyond restricting MNV dissemination and suggest that STAT1-dependent regulation of myeloid cell activation prevents acute hepatic necroinflammation and secondary fibrosis. This model of MNV-induced hepatitis may prove valuable in elucidating mechanisms of rare clinical complications.

overall_design: RNA-seq profiling of liver biopsies following murine norovirus strain CR6 infection (day 5 post-infection).

first: A

last: Sharon

first: Madilyn

last: Portas


title: Airway immune signatures of protection and disease progression in recent human tuberculosis household contacts

first: Probir

last: Chakravarty

overall_design: Single-cell RNAseq of bronchoalveolar lavage from human cohort of tuberculosis patients and their household contacts.

first: William

last: Branchett

first: Jee-Whang

last: Kim

first: Jessica

last: Shields

first: Anver

last: Kamil

first: Jo

last: Lee

first: Ismail

last: Novsarka

first: Hubert

last: Slawinski

first: Katalin

last: Wilkinson

first: Robert

first: Raman

last: Verma

first: Pranabashis

last: Haldar

first: Anne

last: O'Garra


title: The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence [RNA-seq]

city: Grand Forks

first: Manu

last: Manu

state: ND

address: 10 Cornell Street, Stop 9019

department: Biology

institute: University of North Dakota

summary: The differentiation of hematopoietic progenitors into specialized types requires the transmittal of information from a few external or internal regulators to the thousands of genes that produce a cell type's characteristic phenotypes.  While the main signaling pathways, transcription factors, and the genes eliciting the terminal phenotypes are known, how information flows from a few regulators to thousands of genes to change the state of the cell remains to be fleshed out. To profile this information transfer process, we sampled the differentiation of the PUER myeloid cell line into macrophages and neutrophils at 27 time points over seven days.  There is extensive transient regulation; the number of transcripts modulated in time is twice the number differentially expressed between endpoints.  Differentiation is marked by two sharp transitions, at ~8h and ~80h, when transcriptomic state changes suddenly. We utilized non-negative matrix factorization to identify behaviors, characteristic temporal patterns of gene expression, and to classify transcripts by behavior. Only 10 distinct behaviors are sufficient to recapitulate the expression of ~36,000 transcripts with high fidelity. Gene expression in most of the behaviors occurs in pulses of varying initiation times and durations. This implies that information transfer during differentiation occurs in cascading waves of gene expression culminating in the permanent turning on of certain genes after ~80h. Each behavior is enriched in specific biological processes, so that physiological remodeling proceeds in a characteristic order---signal transduction, translation and mRNA processing, metabolism, and, ultimately, myeloid phenotypic processes. The sharp transition at 8h corresponds to the completion of transcriptional and translational remodeling and the initiation of metabolic remodeling; the one at 80h corresponds to the elicitation of myeloid phenotypes. Our analysis shows that differentiation relies upon a series of transient, rapid, and complex gene regulatory events and highlights the importance of profiling it at a high temporal resolution.

overall_design: Time series of RNA-seq during the differentiation of a mouse cell-line, PUER, into macrophages and neutrophils. RNA-seq was performed in triplicate over a course of 168h following tamoxofin (OHT) treatment. After sampling undifferentiated PUER cells (IL3-OHT 0h), cells were sampled every hour for the first four hours (1-4h), every 4 hours for the first 24h (8-24h), and every eight hours until 168h (32-168h) during both macrophage (IL3) and neutrophil (GCSF) differentiation.

first: Andrea

last: Repele

first: Joanna

last: Handzlik

first: Nimasha

last: Samarawickrama

first: Trevor

last: Long

first: Sunil

last: Nooti

first: Veena

last: Potluri

first: Yen Lee

last: Loh


title: The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence [CUT&RUN]

overall_design: CUT&RUN during the differentiation of a mouse cell-line, PUER, into macrophages. CUT&RUN was performed on undifferentiated PUER cells and 48 hrs after tamoxifen (OHT) treatment using PU.1, H3K4me3, and IgG antibodies.


title: A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis

city: San Francisco

first: Hanbing

last: Song

address: 513 Parnassus Ave, HSE

institute: UCSF

summary: Prostate cancer encompasses a spectrum of disease states driven by complex cellular heterogeneity. To delineate the transcriptional programs underlying lineage plasticity and metastasis, we constructed a comprehensive single-cell atlas of 128 patients, spanning localized, castration-resistant, and metastatic disease. Lineage plasticity was prevalent in localized disease, with subsets of tumor cells adopting distinct basal-like and club-like states. Luminal-like cancer cells also displayed extensive lineage infidelity, defined not by a binary loss of identity but by the combinatorial erosion of luminal gene modules associated with higher grade and stage. In the metastatic setting, gene program association analysis (GPAS) identified a broad induction of cell-cycle gene modules across organ sites as well as an induction of organ-specific gene modules, including osteomimetic signaling in bone, neuro-migratory genes in brain, and erythroid-like transitions in liver. Neuroendocrine prostate cancers (NEPCs) were not monolithic but defined by combinations of NE-associated gene modules including a novel HES6 program. Notably, these modules were detected at intermediate levels in localized samples, suggesting molecular plasticity precedes histological transformation. We also developed a refined NE signature that could distinguish NEPC tumors more accurately than previously published signatures. Within the tumor microenvironment (TME), we observed an elevation of pro-inflammatory Th17 T-cells in African American patients and identified a rare Schwann cell population. Finally, we present PCformer, a transformer-based foundation model trained on >500,000 cells to automate cell-state classification. Together, this comprehensive atlas demonstrates the complex nature of gene modules underlying lineage infidelity and plasticity in cancer cells and highlights distinct immune and stromal populations within the tumor ecosystem.

overall_design: 36 localized prostate cancer patients and 2 metastatic prostate cancer patients (one liver metastatic and one sphenoid metastatic) enrolled in this study.

first: Sarah

last: Hsu

first: Julia

last: Pham

first: Yih-An

last: Chen

first: Hannah

last: Weinstein

first: Matthew

last: Cooperberg

first: Nancy

last: Greenland

first: Franklin

middle: W

last: Huang


title: Pervasive Enhanced Transcription in Inflammatory Breast Cancer Tumors and PBMCs Impacts RNA Splicing and Intronic RNAs in Plasma

city: Austin

first: Alan

last: Lambowitz

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary: Inflammatory breast cancer (IBC), the most aggressive and lethal breast cancer subtype, lacks unequivocal genomic differences or robust biomarkers that differentiate it from non-IBC. Here, Thermostable Group II Intron Reverse Transcriptase sequencing of RNA samples revealed myriad differences in tumors, PBMCs, and plasma that distinguished IBC from non-IBC patients and healthy donors across all tested non-IBC subtypes. By mapping reads to genome and transcriptome reference sequences and quantitating intron-to-exon read depth ratios, we developed methods for parallel analysis of transcriptional and post-transcriptional gene regulation. This analysis identified numerous protein-coding genes in IBC patient tumors and PBMCs with high intron-to-exon read depths, suggesting rate-limiting RNA splicing that negatively impacts mRNA production. Mirroring gene expression differences in tumors and PBMCs, over-represented protein-coding gene RNAs in IBC patient plasma were largely intron RNA fragments, while those in non-IBC patient and healthy donor plasma were largely mRNA fragments. Our findings provide new insights into IBC and should enable monitoring disease progression by liquid biopsy.

overall_design: Thermostable Group II Intron Reverse Transcriptase sequencing (TGIRT-seq) of RNA samples in tumors, PBMCs, and plasma collected from inflammatory breast cancer (IBC) and breast cancer (non-IBC) patients and healthy donors across all tested non-IBC subtypes.

first: Dennis

last: Wylie

first: Xiaoping

last: Wang

first: Jun

last: Yao

first: Hengyi

last: Xu

first: Elizabeth

middle: A

last: Ferrick-Kiddie

first: Toshiaki

last: Iwase

first: Savitri

last: Krishnamurthy

first: Naoto

last: Ueno

middle: M


title: RNA-seq analysis of human corneal epithelial cells under hyperosmotic stress modeling dry eye disease

city: Nanjing

first: Yun

last: Tang

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University

summary: We performed RNA-seq to investigate the transcriptomic changes in human corneal epithelial cells (HCECs) under hyperosmotic stress mimicking dry eye disease (DED).

overall_design: Comparison of gene expression profiles between control HCECs and HCECs treated with hyperosmotic medium (90 mM NaCl) for 24 hours. Three biological replicates per group.


title: Transient epigenetic changes promote cardiomyocyte differentiation of the subcutaneous adipose stromal vascular fraction

city: Kanazawa

first: Shinichiro

last: Takashima

address: 13-1 Takara-machi

department: Cardiovascular Medicine

country: Japan

institute: Kanazawa University

summary: Introduction: The subcutaneous adipose-tissue-derived stromal vascular fraction (Sa-SVF) contains stem/progenitor cells that rarely transdifferentiate into beating cardiomyocytes. Previously, we developed a culture protocol in which adult murine inguinal Sa-SVF cells reproducibly transdifferentiate into beating cardiomyocyte-like cells (beating CMs) without any specific induction in the primary culture. However, the mechanism underlying the differentiation of the Sa-SVF toward the cardiac lineage is unclear. Methods: To identify a key regulator of cardiac differentiation, we investigated sequential changes in global gene expression profiles of Sa-SVF cells during primary culture. Sa-SVF cells were isolated from adult murine inguinal subcutaneous fat pads and cultured using our beating CM induction method. At six time points during primary culture, total RNA was extracted and subjected to RNA-sequencing and quantitative polymerase chain reaction analysis. Results: Beating CMs appeared on day 14. Of 14,574 prefiltered genes, 749 showed significant expression changes (153 upregulated and 596 downregulated, > 2-fold) between days 7 and 14, coinciding with the appearance of beating CMs. Gene ontology analysis highlighted histone deacetylase (HDAC)-associated genes, expression of which was transiently suppressed during the period when cardiac sarcomere-related genes and the transcription factor Mef2c were upregulated. Treatment with an HDAC inhibitor increased cardiac troponin T expression on day 28. Furthermore, treatment of Mef2c-transduced Sa-SVF cells with an HDAC inhibitor markedly augmented cardiac troponin T expression (18-fold vs. control). Conclusions: We identified transient epigenetic modulation—particularly suppression of class II HDACs—as a key driver of Sa-SVF transdifferentiation into cardiomyocytes. These findings provide a mechanistic basis and a potential combinational strategy to enhance SVF-based cardiac regenerative approaches.

overall_design: Bilateral inguinal subcutaneous adipose tissues without lymph nodes, weighing approximately 500 mg, were obtained from female C57BL/6J mice (age 8–12 weeks). The Sa-SVF cells were isolated as described previously. Briefly, the tissues were digested using a Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) in serum-free Dulbecco’s modified Eagle’s medium (DMEM)/F-12 (Thermo Fisher Scientific, Waltham, MA, USA) for 30 min at 37°C using gentleMACS (Miltenyi Biotec). The digested tissue was thoroughly pipetted approximately 10 times in DMEM supplemented with 10% fetal bovine serum (FBS) (F7524, Sigma-Aldrich, St. Louis, MO, USA), filtered through a 100-μm nylon mesh, and then centrifuged at 400× g for 5 min. After washing with DMEM/F-12 with FBS and centrifugation, the cell pellet was resuspended in BD Pharm Lyse Lysing Buffer (BD Biosciences, Franklin Lakes, NJ, USA) and incubated for 5 min to lyse red blood cells. After a further round of centrifugation, the cell pellet was filtered through a 35-μm mesh and centrifuged at 400× g for 5 min; then, the Sa-SVF cells were resuspended in culture medium. Sa-SVF cells were counted using a TC20 automated cell counter (Bio-Rad Laboratories, Hercules, CA, USA) and seeded on a standard uncoated tissue culture plate (Nunc) (Thermo Fisher Scientific) in minimal growth medium (GM) consisting of Iscove’s Modified Dulbecco’s Medium (IMDM; I3390, Sigma-Aldrich), 10% fetal bovine serum (FBS), 2 mmol/L L-glutamine (Wako, Osaka, Japan), 100 units/mL penicillin, 100 μg/mL streptomycin, and 0.1 mmol/L 2-mercaptoethanol (StemSure) (Wako) at 5000 live cells/cm2, and then cultured under standard conditions (37°C with 5% CO2). To examine temporal changes in gene expression, we performed RNA-Seq analysis of Sa-SVF cell groups, from which total RNA was collected at days 0, 3, 7, 14, 21, and 28 of primary culture. Additionally, the Sa-SVF cell group at day 28 was also passaged and cultured for 28 days to collect total RNA as the P1 SaSVF group.

first: Yusuke

last: Shinjo

first: Soichiro

last: Usui

first: Masayuki

last: Takamura


title: Combined DNA and RNA profiling refines prognostic stratification independent of therapeutic actionability in cholangiocarcinoma

city: Montpellier

first: Simon

last: Cabello-Aguilar

address: Avenue du doyen Gaston Giraud

institute: CHU Montpellier

summary: Background Cholangiocarcinoma (CCA) exhibits marked biological heterogeneity. While genomic profiling identifies targetable alterations such as FGFR2 fusions and IDH1 mutations, transcriptomic analyses reveal distinct immune, proliferative and mesenchymal profiles. How these genomic and transcriptomic features jointly influence clinical outcomes remains unclear. Methods We performed integrated DNA and RNA profiling in 62 patients with intrahepatic and extrahepatic CCA treated at a single tertiary center. Targeted DNA sequencing assessed single-nucleotide variants, copy-number alterations, and microsatellite instability. Extended RNA sequencing evaluated gene fusions and pathway-level transcriptomic subtypes. Associations with progression-free survival (PFS) and overall survival (OS) were examined. Results Among 58 DNA-profiled tumors, the most frequent alterations were TP53 (43.1%) and KRAS (29.3%), followed by IDH1 (10.3%, restricted to intrahepatic CCA). Actionable alterations (IDH1, FGFR2 fusions, ERBB2 amplification, microsatellite instability-high) were detected in 25% of cases and associated with longer overall survival (67.5 vs 20.8 months; p=0.0004), consistent with benefit from matched therapies rather than intrinsic tumor biology. RNA profiling identified five transcriptomic subtypes: Immune (21%), Proliferative (18%), Mesenchymal (42%), Immune-Proliferative (8%), and Unclassified (11%). KRAS-TP53 co-mutation was the strongest adverse prognostic factor (38.1 vs 13.2 months; p=0.0004). The Mesenchymal subtype was associated with shorter PFS (5.9 vs 17.9 months; p=0.045) in patients treated with chemotherapy ± immunotherapy but did not significantly affect OS. Conclusions Integrated genomic and transcriptomic profiling refines prognostic stratification in cholangiocarcinoma independent of therapeutic actionability. KRAS-TP53 co-mutation and the Mesenchymal transcriptomic subtype represent independent high-risk markers detectable on routine FFPE tissue. These features complement actionable alterations and may inform patient selection and clinical trial design.

overall_design: Targeted RNA-seq

first: Julie

last: Vendrell

first: Inès

last: Dalmon

first: Jacques

last: Colinge

first: Eric

last: Assenat

first: Jérôme

last: Solassol


title: A Dual Approach to Evaluate the Performance of RNA-Seq Data Analysis Pipelines with Weak Signals

city: Fontenay-aux-Roses

first: Imène

last: GARALI

address: 31 Av. de la Division Leclerc

institute: ASNR

summary: RNA-Seq data analysis involves several critical steps, from quality control to differential expression analysis, each offering multiple algorithmic options. Selecting the optimal pipeline is particularly challenging in complex scenarios with weak signals.This study highlights the significant impact of pipeline selection on RNA-Seq data analysis, particularly in contexts characterized by weak transcriptional signals, as in this study for low-dose metallic particle exposure. By evaluating 90 bioinformatics pipelines using two complementary approaches — correlation with qRT-PCR data and classification performance — we were able to identify optimal configurations that ensure both analysis robustness for biological relevant observation.

overall_design: The data were obtained from an in vivo experiment conducted on an adult male Sprague-Dawley rat model, which was exposed via inhalation of a particulate aerosol at different doses (low and high) of an environmental chemical pollutant (tungsten) to assess its biological effects on the brain. This project is the subject of an experimental study in our laboratory. The animal ethics committee approved the study protocol, which has been published. More details are available in Exposure to tungsten particles via inhalation triggers early toxicity marker expression in the rat brain. Inhalation Toxicology, 36(4):261–274, 2024. "Leo Mace, Chloe Brizais, Florence Bachelot, Annabelle Manoury , Sébastien Thomé , Celine Gloaguen, Imene Garali Zineddine, Victor Magneron, V. Monceau, Amandine Sache, Frederic Voyer, Christelle Elie, Laurence Roy, Francois Gensdarmes, Dmitry Klokov , Michelle L Block, Chrystelle Ibanez".

first: Chrystelle

last: IBANEZ


title: The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

country: Italy

institute: IRBM

summary: The transition of embryonic stem cells (ESCs) from pluripotency to lineage commitment involves complex regulatory mechanisms, including chromatin dynamics and transcriptional/post- transcriptional processes. These mechanisms often interact within intricate networks that require thorough investigation. In this study, we highlight the critical role of the mouse RNA-binding protein LIN28A in neuronal differentiation. LIN28A mediates RNA-dependent interactions with thePolycomb repressive complex 2 (PRC2), leading to the eviction of PRC2 from chromatin andactivation of a neuronal lineage-specific transcriptional program. Proteomic analyses revealed thatthe LIN28A interactome undergoes substantial remodeling during differentiation, corresponding to changes in LIN28A localization. In undifferentiated ESCs, LIN28A primarily resides in the nucleus,interacting with PRC2 components in an RNA-dependent manner, assisting in chromatin dynamics. The absence of LIN28A results in persistent PRC2 association with chromatin, impairing theexpression of genes critical for neuronal differentiation. Chromatin immunoprecipitationsequencing further confirmed that loss of LIN28A results in preferential PRC2 occupancy at thepromoters of differentiation-associated genes. These findings reveal a novel role of LIN28A inepigenetic remodeling, crucial for proper neuronal differentiation of ESCs.

overall_design: Chip-Seq of H3K27ME3 Mouse Embrional Stem Cells (ESC) and serum-free embryoid bodies (sFEBs)  KO/Wt  of LIN28A

first: Silvia

last: Piscitelli

first: Emanuela

last: Cascone

first: Chiara

last: D’Ambrosio

first: Giuseppina

last: Divisato

first: Emilia

last: Giannino

first: Laura

last: De Lisio

first: Daniel

last: D'Andrea

first: Danilo

last: Swann Matassa

last: Lanzuolo

first: Valentina

last: Rosti

first: Maria Chiara

last: Zizolfi

first: Monica

last: Matuozzo

first: Emanuele

last: di Patrizio Soldateschi

first: Paolo

last: Maiuri

first: Andrea

last: Scaloni

first: Fabiana

last: Passaro

last: Parisi


title: Exercise suppresses breast cancer and reprograms the immune tumor microenvironment, cancer cell intrinsic features, and their interaction

city: Burnaby

first: Graeme

middle: J.

last: Koelwyn

address: 8888 University Drive

department: Faculty of Health Sciences

institute: Simon Fraser University

summary: Exercise links with improved cancer outcomes following a diagnosis of primary breast cancer but experimental evidence from preclinical studies and molecular mechanistic insights are limited. Here, we show that exercise inhibits breast cancer growth and metastases across multiple syngeneic mouse models compared to sham control. Utilizing the Met1-iRFP model to interrogate tumor microenvironmental (TME) and tumor-specific effects, exercise decreased intratumoral immune cell content, particularly tumor-associated macrophages, and prompted an activated anticancer innate immune response. Cancer cell-intrinsic effects were characterized by broad transcriptomic reprogramming including downregulation of metabolic pathways and upregulation of pathways regulating proliferation and apoptosis. Metabolomic analyses unveiled broad shifts in tumor metabolism including decreased NAD+ and lactate, as well as availability of biosynthetic precursors. Finally, in silico analyses identified TME ligands such as Hmgb2 as drivers of downstream gene expression changes in cancer cells. Collectively, our findings show that exercise suppresses breast cancer progression and does so via broad reprogramming of TME-cancer components and their interaction.

overall_design: RNA-Seq profiling of Met1-iRFP tumor cancer (iRFP+) and tumor microenviroment (TME, iRFP-) cells from exercised and sedentary mice.

first: Sayyed Hamed

last: Shahoei

first: Courtenay

last: Graham

first: Claudia

last: Siguenza

first: Geoffrey

last: Nonis

first: Seyed Milad

last: Vahedi

first: Puneet

last: Sidhu

first: Emily

last: Brown

first: Juan

last: Liu

first: Elisa De

last: Stanchina

first: Kathryn

last: Moore

first: Jason

last: Locasale

first: Erik

last: Nelson

first: Lee

last: Jones


title: Dual Orexin Receptor Antagonism with Lemborexant Enhances Microglial Clearance of β-Amyloid in Mice

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: Background: Sleep regulates brain amyloid-beta (Aβ) levels, and disruption of sleep is a risk factor for Alzheimer’s Disease (AD) and can exacerbate amyloid pathology. The orexin/hypocretin system, a key sleep-wake regulator, represents an emerging therapeutic target in AD, though the effects of FDA-approved dual orexin receptor antagonist drugs (DORAs) on amyloid pathology are unknown. Here, we assessed and compared the effects of lemborexant (LEM), an FDA-approved DORA, and doxepin, an anti-histaminergic sleep drug, on amyloid pathology and glial responses in the APP/PS1 mouse model of AD. Methods: APP/PS1 mice were treated with lemborexant (10 or 30mg/kg daily) or doxepin (35mg/kg daily) for 3 months, starting just before the onset of amyloid plaque accumulation, or for 1 month after plaque pathology was established. Sleep was measured using a piezoelectric system, and amyloid pathology and glial responses were quantified by immunohistochemistry and confocal microscopy, as well as single cell RNAseq of isolated microglia. Amyloid plaques were labeled with methoxy-X04 to monitor plaque growth, and microglial plaque phagocytosis was assessed by flow cytometry. Microglial elimination was performed using the CSF1r inhibitor PLX3397. Results: Despite equivalent total sleep enhancement, LEM more effectively prevented formation of and slowed growth of both fibrillar and diffuse Aβ plaques. LEM enhanced peri-plaque microglial activation and enhanced microglial amyloid phagocytosis in vivo. Single-cell microglial transcriptomics showed a LEM-mediated shift toward pro-phagocytic and antigen-presentation gene signatures. Depleting microglia via CSF1R inhibition abolished LEM’s anti-amyloid effects, underscoring microglia as essential mediators. Conclusions: These results demonstrate that dual orexin receptor antagonism with lemborexant can augment microglial function to mitigate AD pathology.

overall_design: Microglia from APPswe/PS1δE9 mouse brains were labeled with CD45 and CD11b antibodies and isolated by fluorescence-activated cell sorting (FACS). Microglia from five mice per group (VEH and LEM) were pooled into a single sample per condition and processed for scRNA-seq.

first: Sharma

last: Ashish

first: Segawa

last: Emiko

first: Chen

last: Xiaoying

first: Park

last: Sohui

first: Wang

last: Shoutang

first: Irmen

middle: E

last: Riley

first: Constantino

last: Nicholas

last: Chanung

first: Kanan

last: Michael

first: Macauley

middle: L

last: Shannon

first: Colonna

last: Marco

first: Hatanaka

last: Ken

first: Cheng

middle: Y

last: Jocelyn

first: Moline

last: Margaret

first: Musiek

middle: S

last: Erik


title: Selective reduction of Nav1.7 with divalent small interfering RNA delivers strong and durable analgesia in thermal and pinprick models of acute pain

city: Yes

first: Wimalanathan

last: Kokulapalan

state: Massachusetts

address: 51 SLEEPER ST FL 7

department: Neuroscience Biology

institute: Atalanta Therapeutics

summary: Humans missing the SCN9A gene encoding the Nav1.7 sodium ion channel are wholly insensitive to pain, but inhibitors of Nav1.7 tested clinically have not produced strong analgesia. Here we investigated whether pharmacological challenges of selectivity, CNS distribution, and target engagement might be addressed by transcript knockdown with divalent small interfering RNA (di-siRNA), a modality with efficient distribution in the brain following dosing into cerebrospinal fluid. SCN9A_2544 di-siRNA sequence catalyzing SCN9A transcript cleavage was identified by in-vitro screening. Following intrathecal dosing in rats, di-siRNA was internalized into over 90% of neuronal cell bodies within the dorsal root ganglion, knocked down cytoplasmic transcript with no detectable off-target knockdown, and reduced Nav1.7 protein up to 75% in DRG and up to 85% in spinal cord. Results show that SCN9A_2544 di-siRNA reduces Nav1.7 function in vivo selectively and to a level that produces powerful analgesia.

overall_design: We investigated the specificity of siRNA SCN9A_2544 using RNA-seq that compared the SCN9A_2544 treated rats to PBS treated rats.

first: Corrie

last: Gallant-Behm

first: Kokulapalan

last: Wimalanathan

first: Stefan

middle: I

last: McDonough


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [ChIP-seq]

city: Oxford

first: I-Jun

last: Lau

address: Old Rd

department: Botnar Research Centre

institute: University of Oxford

summary: Transcription factors (TFs) are key effectors of enhancer activity. MYB is a critical hematopoietic TF that is frequently dysregulated in cancer. Despite its well-established role, the exact mechanisms by which MYB influences enhancer function—and the specific stages of enhancer activation at which it operates—remain poorly understood. Using high resolution Micro-Capture-C, we show that upon MYB degradation, highly defined enhancer-promoter interactions at specific MYB binding sites are lost. Loss of these interactions, together with other hallmarks of enhancer activity—reduced H3 lysine-27 acetylation and enhancer RNA transcription—correlates with significant downregulation of target gene expression in leukemia, indicating that MYB mediates transcription activation via maintenance of enhancer function. When anchored to DNA within a gene desert region that is devoid of histone marks and active transcription, the MYB transactivation domain is sufficient and necessary for the nucleation of an enhancer-like region. This results in the activation of transcription from distal cryptic elements and the establishment of long-range chromatin interactions up to 400 kb away from the anchor point. Together, these results indicate that MYB activity alone is sufficient to induce long-range interactions and transcription, achieving this through highly precise enhancer-promoter crosstalk.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq in the following cell lines: 1. WT SEM cells; 2. SEM cells with MYB endogenously tagged with FKBP12(F36V) ±dTAG13; 3. WT E14 (TOT2N variant) cells; 4. WT E14 (TOT2N variant) cells containing stable integration of TetR constuct ±doxycycline; 5. WT E14 (TOT2N variant) cells containing stable integration of TetR-MybTA constuct  ±doxycycline.

first: Nicholas

last: Crump

first: Thomas

last: Milne


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions

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

overall_design: Refer to individual Series


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [RNA-seq]

overall_design: polyA minus RNA-seq in E14 (TOT2N variant) cell lines containing 1) stable integration of TetR constuct, 2) TetR-MYBTA constuct or 3) wild type.


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [ATAC-seq]

overall_design: ATAC-seq in E14 (TOT2N variant) cell lines: 1) wild type, 2) containing stable integration of TetR constuct or 3) containing stable integration of TetR-MYBTA constuct