title: Liver gene expression of rats intoxicated with pure fumonisin B1

city: Godollo

first: Tibor

last: Nagy

address: Páter Károly street 1.

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: Purified fumonisin B1 (FB1) mycotoxin was intraperitoneally administered at the no observed adverse effect level (NOAEL, 0.2 mg/kg bw/day, group 1X) and 5 and 10-times above (5X and 10X) to male rats, in a controlled (group C), 5-day study (n=8/group, total n=32), to study in vivo hepatotoxic effects.

overall_design: liver and kidney samples

first: Zoltán

last: Doleschall

first: András

last: Szabó


title: Adipose tissue gene expression profiling  in women with overweight or obesity following early vs. late time-restricted eating

status: Public on Sep 22 2025

city: Nuthetal

first: Michail

last: Lazaratos

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: Deutsches Institut für Ernährungsforschung Potsdam-Rehbrücke

type: Expression profiling by high throughput sequencing

summary: Time-restricted eating (TRE) is a promising strategy to prevent obesity and type 2 diabetes, but data on its effects on adipose tissue metabolism are limited. Therefore, we conducted a crossover study examined 31  women with overweight or obesity who followed both a two-week early TRE (eTRE) and a two-week late TRE (lTRE). Gene expression profiles in subcutaneous adipose tissue collected after both TRE interventions were compared using RNA sequencing. These data provide a first insight into the remodelling of the human adipose tissue transcriptome by the eating timing during TRE, warranting consideration in future dietary research and recommendations.

overall_design: Women with overweight or obese women have completed the randomized 10-weeks crossover clinical trial. After a 4-week baseline phase, two isocaloric 2-week interventions – (i) eTRE and (ii) lTRE - were conducted, separated by a 2-week washout phase. During the baseline phase, the participants consumed their usual food quality and quantity at their usual meal times. In the eTRE intervention, participants were asked to consume the same kind and amount of food as during the baseline but reduce their eating window to 8 h per day for a daytime from 8 am to 4 pm, while in the lTRE intervention, the 8-hour eating window shifted to 1 pm to 9 pm. Between the two interventions, participants returned to their usual eating times. Throughout the 10 weeks of the study, participants were asked to maintain their usual lifestyle habits in terms of physical activity and sleep. Subcutaneous adipose tissue samples were collected periumbilically at 9.30 a.m. after both interventions (visits 2 and 4) using a needle biopsy. Samples from 15 study participants were analysed using RNA-seq technology.

first: Olga

last: Pivovarova-Ramich

first: Markus

last: Jähnert


title: Spatiotemporal dynamics of the cardioimmune niche during lesion repair [spatial]

city: Würzburg

first: Andy

middle: Shing Fung

last: Chan

address: Gebäude E6,, Versbacher Str. 9

institute: Institute for Systems Immunology, University of Würzburg

summary:
[Important Note: Some files appear to have become corrupted during upload, and we are currently replacing them, which may take a few working days. In the meantime, if you need access to the raw data files, please email shing-fung.chan@uni-wuerzburg.de. We apologize for the inconvenience.]

The heart is one of the least regenerative organs in humans, and heart disease is the leading cause of death worldwide. Understanding the cellular and molecular processes during cardiac wound healing is an essential prerequisite to reduce health burden and improve cardiac function after myocardial tissue damage. By integrating single-cell RNA-sequencing with imaging-based spatial transcriptomics, we reconstructed the spatiotemporal dynamics of the fibrotic niche after ventricular injury in adult mice. Our analysis revealed dynamic regulation of local cell communication niches over time. We identified interactions that regulate cardiac repair, including fibroblast proliferation silencing by Trem2high macrophages that prevents excessive fibrosis. Moreover, we discovered a rare population of dedifferentiating cardiomyocytes early post-lesioning repair, sustained by signals from myeloid and lymphoid cells. Culturing non-regenerative mouse cardiomyocytes or human heart tissue with these niche factors reactivated progenitor gene expression and cell cycle activity. In summary, this spatiotemporal cell type atlas offers valuable insights into the heterocellular interactions that control cardiac repair.

overall_design: Cryoablation of the left ventricle (Cryo) was used as the mouse models to introduce ventricular lesions. After recovery of animals from lesion induction, we isolate the LV. 5μm formalin-fixed paraffin-embedded tissue sections (transverse plane of the LV) were mounted on a Xenium slide within the desired imaging region.

middle: S

first: Lisa

last: Marschhäuser

first: Wing

middle: L

last: Cheung

first: Franziska

last: Schneider-Warme

first: Dominic

last: Grün


title: Gene expression profile at single cell level of islets from two β-cell specific knockout mouse models (βZKO-Mip and βZKO-Rip), littermate controls (Zzef1f/f), and the MIP-Cre mice fed with normal-chow diet (NCD).

city: shanghai

first: jingminjie

state: CN

address: shanghai

country: China

institute: Ruijin Hospital

summary: Islet consists of multiple cell types that work in concert to orchestrate their endocrine function. To rule out of direct effect of diet or phenotype, we performed comparative single-cell RNA-sequencing (scRNA-seq) on 12-week βZKO-Mip, βZKO-Rip mice, littermate controls (Zzef1f/f) and MIP-Cre mice islets fed with normal-chow diet (NCD) by Chromium Next GEM Single Cell 3’ Reagent Kits.

overall_design: Briefly, two β-cell specific knockout mouse models (βZKO-Mip and βZKO-Rip) were generated by crossing the C57/BL6N mice harboring floxed exon 15 (Zzef1f/f) with MIP-Cre or RIP-Cre mice. Each islet sample was gathered from no less than three mice with the same genotype. Then, purified islets were treated with 2 ml 0.05% TryLE at 37℃ for 4 min, followed by gently pipetting for about 20 times. The cell suspension is stained with 0.4% trypan blue to assess cell viability under microscopic observation. The sorted cells with greater than 85% viability are qualified for 3’ digital gene expression by profiling ~10,000 individual cells per sample using 10x Chromium Single-Cell 3’ and V(D)J library construction (10x Genomics, USA), according to the manufacturer’s instructions.

first: Yanan

last: Cao

first: Jingminjie


title: Radiosensitization Following Valproic Acid and Gamma Rays in Anaplastic Thyroid Cancer Cells Increases the Expression of hsa-miR-26a-5p

city: Buenos Aires

first: Marina

last: Perona

address: Avenida General Paz 1499

department: Radiobiología

country: Argentina

institute: Comisión Nacional de Energía Atómica

summary: Background: Anaplastic thyroid cancer (ATC) is a rare lethal human malignancy with a poor prognosis. Multimodality treatment, including radiotherapy, is recommended to improve local control and survival. Valproic acid (VA) is a clinically available anticonvulsant and histone deacetylase inhibitor with a well-documented side effect profile. Furthermore, VA radiosensitizes various cancer cells, including thyroid cancer. MicroRNAs (miRs) are deregulated in several cancers and may modulate radiation response. Therefore, the aim of this study was to analyze the effect of VA combined with gamma radiation in radioresistant ATC cells at the expression level of miRs. Methods: ATC cells (8505c and KTC-2) were VA-treated and gamma-irradiated (2 Gy). The expression profile of miRs in 8505c was evaluated by microarray analysis 4 h after irradiation. Selected miRs were validated by RT-qPCR in both types of ATC cells. Results: We observed that after combined VA and gamma irradiation treatment, 8505c cells showed 109 differentially expressed miRs as compared to irradiated cells alone. These miRs exhibited a radiosensitization profile highlighted by upregulation of hsa-miR-26a-5p, which is usually downregulated in aggressive thyroid cancers. Moreover, hsa-miR-27a-3p and hsa-miR-486-5p, which are often deregulated in thyroid neoplasms, were downregulated after irradiation and VA treatment, respectively. The expression level of these three miRs was validated in 8505c and KTC-2 cells after treatments. Conclusion: The regulated miRs by VA and gamma irradiation reveal a novel miR expression profile with potential to be further studied in the radio-induced response and radiosensitization of ATC cells.

overall_design:
MicroRNA expression profiling by microarray analysis in anaplastic thyroid cancer cells after valproic acid and gamma rays combined treatment.
MiRNA expression was profiled on Affymetrix GeneChip® miRNA-4_0-st-v1 Array,  representing 723 human and 76 human viral miRNAs in 40 normal and 40 cancerous gastric tissues.

first: Irene

last: Ibañez

first: Hebe

last: Durán

first: Guillermo

last: Juvenal


title: Gene expression data of islets from Zzef1 global knockout (Zzef1_KO) mice and littermate controls (WT) mice fed with normal-chow diet (NCD) [bulk RNA-seq]

summary:
To understand the global molecular basis of the phenotype caused by the loss of Zzef1 in islets, we isolated pancreatic islets from 12-week-old Zzef1KO and WT mice fed with normal-chow diet (NCD). Then mice were sacrificed and total RNAs were isoloated from islets. We included at least 3-4 independent biological replicates, each composed of RNA isolated from islets of 5 animals with the same genotype.
We then performed gene expression profiling analysis using data obtained from islets RNA-seq of Zzef1KO mice and littermates fed a normal chow diet.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for islets of Zzef1KO mice and littermates.


title: A dynamic gene regulatory code drives synaptic development of hippocampal granule cells [snMO]

status: Public on Sep 21 2025

city: leuven

first: Danie

last: Daaboul

address: Herestraat 49

department: Department of Neuroscience

country: Belgium

institute: KU Leuven

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Connecting neurons into functional circuits requires the formation, maturation, and plasticity of synapses. While advances have been made in identifying individual genes regulating synapse development, the molecular programs orchestrating their action during circuit integration of neurons remain poorly understood. Here, we have employed a combination of single nuclei transcriptome and epigenome sequencing (single nuclei multiome)  to study the development of the hippocampus. The hippocampus contains several excitatory and inhibitory cell types, as well as astrocytes, glia and other immune cells of the brain. The hipocampal trisynaptic circuit (DG-CA3-CA1)  is essential for learning and memory. This study provides single-cell multiome data of hippocampal postnatal (P) development (P5, P10, P15, and P28), offering an in-depth analysis of gene regulatory networks during granule cell synapse formation. Together, these findings highlight the networks of key TFs and target genes orchestrating GC synapse development.

overall_design: Hippocampi from C57Bl6 mice were homogenized, nuclei were isolated and processed for both RNA sequencing and ATAC sequencing. This process was repeated using hippocampi from mice at postnatal day (P)5, P10, P15 and P28.

first: Blanca

last: Lorente-Echeverría

first: Jeroen

last: Vandensteen

first: Gabriele

last: Marcassa

first: Willem

last: Naert

first: Joris

last: Vandenbempt

first: Elke

last: Leysen

first: Malou

last: Reverendo

first: Ine

last: Vlaeminck

first: Lise

last: Vervloessem

first: Jochen

last: Lamote

first: Suresh

last: Poovathingal

first: Kristofer

last: Davie

first: Keimpe

last: Wierda

first: Dan

last: Dascenco

first: Stein

last: Aerts

last: De Wit


title: Obesity promotes urinary tract infection by disrupting urothelial immune defenses

status: Public on Sep 19 2025

city: Columbus

first: John

middle: David

last: Spencer

state: OH

address: 700 Children's Drive

country: USA

institute: Nationwide Children's Hospital

summary: Obesity is a significant public health concern associated with increased infection risk, but the mechanisms remain unclear. Using a diet induced obesity mouse model, we investigate how obesity impacts urinary tract infection (UTI) susceptibility and bladder urothelial defenses. High fat diet-fed female and male C57BL/6 mice exhibit increased susceptibility to uropathogenic E. coli (UPEC) following experimental UTI. Transcriptomic analysis of bladder urothelial cells reveals sex-specific gene expression changes, but both sexes share activation of focal adhesion and extracellular matrix signaling. Western blot and immunostaining confirm activation of focal adhesion kinase (FAK), a central component of the focal adhesion pathway, in the bladders of obese female and male mice. Mechanistically, primary human urothelial cells overexpressing FAK exhibit increased UPEC invasion. These findings demonstrate that obesity enhances UTI susceptibility and identify FAK as a conserved pathway disrupted by obesity, contributing to increased UPEC vulnerability.

overall_design: Urothelium was isolated from bladders of female and male mice fed standard chow or high-fat diet for 8 or 12 weeks. RNA-seq was performed on urothelium, and comparisons were made between high-fat and standard chow-fed mice of the same sex and/or diet duration.

first: Laura

last: Schwartz

first: John David


title: Targeting of HIF2-driven cachexia in kidney cancer

city: Boston

first: Qinqin

last: Jiang

state: Ma

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Kidney cancer frequently causes paraneoplastic syndromes, including hypercalcemia and cachexia, but the underlying mechanisms are incompletely understood. The most common form of kidney cancer, clear cell renal cell carcinoma (ccRCC), is frequently caused by loss of the pVHL tumor suppressor protein and the resulting upregulation of the HIF2 transcription factor. We show that PTHLH, which resides on a ccRCC amplicon on chromosome 12p, is a direct HIF2 transcriptional target in ccRCC. Further, we show that the increased PTHLH expression is both necessary and sufficient for the induction of hypercalcemia and cachexia in preclinical orthotopic cell line tumor models. Consistent with these observations, two different allosteric HIF2 inhibitors, belzutifan and NKT2152, rapidly ameliorated hypercalcemia and cachexia in patients with ccRCC, including in some who did not exhibit objective tumor shrinkage. Our findings support prospective clinical studies to determine whether HIF2 inhibitors can be leveraged not only for tumor control, but also for the treatment of cancer-associated cachexia in renal cell carcinoma.

overall_design: We aim to systematically identify HIF-responsive genes by RNA-Seq in OS-RC-2 cells. We generated two isogenic comparisons to create HIF2 high and low status, for which cells 1) were treated with 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours, 2) underwent CRISPR-based gene editing with a HIF2a sgRNA or a contrl sgRNA (sgCtrl). We then performed RNA-Seq experiments to quantify gene expression for each condition in triplicates.

first: Muhannad

last: Abu-Remaileh

first: Zachary

middle: T

last: Herbert

first: William

middle: G

last: Kaelin Jr


title: HIF2-driven PTHrP Mediates Cachexia and Hypercalcemia in Renal Cell Carcinoma: Successful Treatment with HIF2 Inhibitors [polysome-seq]

summary: Kidney cancer frequently causes paraneoplastic syndromes, including hypercalcemia and cachexia, but the underlying mechanisms are incompletely understood.  The most common form of kidney cancer, clear cell renal cell carcinoma, is frequently caused by loss of the pVHL tumor suppressor protein and the resulting upregulation of the HIF2 transcription factor.  We show that PTHLH, which resides on a ccRCC amplicon on chromosome 12p, is a direct HIF2 transcriptional target in ccRCC.  Further, we show that the increased PTHLH expression is both necessary and sufficient for the induction of hypercalcemia and cachexia in preclinical orthotopic cell line tumor models.  Consistent with these observations, two different allosteric HIF2 inhibitors, belzutifan and NK-2152, rapidly ameliorated hypercalcemia and cachexia in ccRCC patients, including in patients who did not exhibit objective tumor shrinkage.


title: Extended PRF: impact of heat on gene expression in gingival fibroblasts

status: Public on Sep 20 2025

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

summary: Extended platelet-rich fibrin (e-PRF) combines the prolonged resorption properties of heat-coagulated platelet-poor plasma (PPP), becoming an albumin gel (Alb-gel) that is mixed back with the respective native cell-rich buffy coat layer (BC), the concentrated PRF (C-PRF). E-PRF or Alb-PRF is utilized as a barrier membrane in various clinical applications, such as guided tissue regeneration. Heating of PPP might lower its biological activity, but testing this hypothesis is necessary. To this end, we exposed gingival fibroblasts to lysates of regular PPP, heated PPP (hPPP), and BC, followed by bulk RNA sequencing. Gingival fibroblasts respond to PPP lysates with a total of 153 up- and 71 down-regulated genes when considering a minimum 3.0-fold log2 expression change and a significance level 2.0 log-10. In sharp contrast, the response to hPPP was characterized by only five up-regulated and five down-regulated genes, clearly indicating that heating almost completely abolished the biological activity of PPP. As expected, BC was more potent than PPP and broadened the spectrum of regulated genes. RT-PCR and immunoassays confirmed the heat sensitivity of PPP as exemplified by IL11 and other genes. Moreover, PPP, but not hPPP, drives the phosphorylation of p65, representing NF-κB signaling. Taken together, these findings extend previous observations that PPP causes a robust response in gingival fibroblasts and also strengthen the hypothesis that this response is heat-sensitive. These operations support the clinical concept of e-PRF by mixing back the heated inactive PPP with the bioactive buffy coat C-PRF layer.

overall_design: We exposed gingival fibroblasts to 30% lysates of regular PPP, heated PPP (hPPP), and BC, followed by bulk RNA sequencing, to identify changes in the genetic signatures of fibroblasts. In the indicated experiments, RT-PCR and immunoassays were conducted to verify some gene expression changes relevant to the RNA-seq. Moreover, the Western blot assay was applied to confirm that hPPP loses the capacity to induce NF-κB signaling.

first: Xiaoyu

last: Huang

first: Panahipour

last: Layla


title: Functional microRNA targeting without seed pairing

city: Cambridge

first: Matthew

middle: Harry

last: Hall

state: MA

address: 455 Main St

department: Biology

institute: Massachusetts Institute of Technology

summary: MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to serve as guides, directing binding to partially complementary sites in mRNAs, ultimately causing post-transcriptional repression. Complementarity to the miRNA seed (miRNA nucleotides 2–7) is typically necessary and sufficient for repression. Here, we investigate unusual sites with extensive complementarity to the miRNA 3′ region (nucleotide 9 and onwards) but without complementarity to the seed. The top examples of these 3′-only sites bind as well as top canonical sites and impart similar repression, which can be further boosted by as few as 2–3 additional pairs to the miRNA seed. Despite these similarities, 3′-only sites have slower association and dissociation rates than seed-matched sites. They also impart different conformations to bound AGO–miRNA complexes than do seed-matched sites, and individual miRNAs differ substantially with respect to how well they bind their respective 3′-only sites. Thus, pairing to the seed is not always required for binding and repression, or for a target to gain access to the 3′ region of the guide. For miRNAs that recognize 3′-only sites, those sites are estimated to constitute <1% of the set of endogenous target sites, a proportion resembling that of other rare but functional site types such as 3′-compensatory sites.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: AGO-RBNS: AGO-RBNS was conducted with various concentrations of purified AGO-miR-155 and AGO-miR-124 and a 100nM RNA pool consisting of 50nM random-sequence library and 50nM programmed library. Bound RNAs were captured, and libraries were prepared for high-throughput sequencing as in "The biochemical basis of microRNA targeting efficacy" (McGeary, Lin et al., 2019 Science) from both AGO-miR-bound and input RNA samples, and then sequenced on an Illumina HiSeq 2500. Relative abundance of sequence motifs in bound versus input RNA-derived sequencing reads were used to determine the relative AGO-miR binding affinity of each motif. MPRA: HeLa or F9 cells were transfected with miR-155, miR-124, miR-1, or mock transfected, as well as a massively parallel reporter library in which each library variant was the same mEGFP expression plasmid with a different target site to miR-155 or miR-124 cloned into the EGFP 3ʹ UTR. After 24 or 48h, total RNA was extracted, reverse-transcribed, and cDNAs containing library contant regions amplified by PCR, for sequencing on an Illumina Novaseq SP. Relative abundance of individual library members in miRNA-transfected versus mock-transfected samples were used to determine the relative repression imparted to the reporter mRNA by the presence of a given miRNA target site in its 3ʹ UTR

middle: H

first: Peter

middle: Y

last: Wang

first: Thy

middle: P

last: Pham

first: David

last: Bartel


title: Nanoscale Dynamics of Enhancer-Promoter Interactions during Exit from Pluripotency

city: Goettingen

first: Dimitra

last: Tsouraki

state: Lower Saxony

address: Am Fassberg 11

institute: Max Planck Institute for Multidisciplinary Sciences

summary: While compelling genetic evidence supports the role of enhancers in regulating promoter activity even over large genomic distances, it remains unclear to what extent physical proximity to promoters is required. To address this, we combined fluorescence in situ hybridization with super-resolution microscopy and Tri-C to examine enhancer–promoter (E–P) distances and regulatory element clustering at important loci (Nanog, Dppa3, Dnmt3a, Sox2, Prdm14) during the transition from naive to primed pluripotency in mouse embryonic stem cells. Despite transcriptional changes of several orders of magnitude, most genes show no major alterations in median E–P distances or in the probability of multiway contacts across states. However, Tri-C reveals a weak enrichment of multiway contacts at Nanog in naive cells, where it is highly expressed. Because transcription often occurs in transient bursts within a subset of cells, we combined RNA and DNA FISH to identify active alleles. For Nanog and Dppa3, reduced E–P distances correlate with more recent transcriptional activity. Together, these findings support models in which transcription is associated with transient E–P proximity and suggest that multiway contact formation among regulatory elements may contribute to gene regulation.

overall_design: Tri-C experiments. Study of multi-way chromatin interactions from key viewpoints during the exit of mouse embryonic stem cells from pluripotency.

first: Gabriela

last: Stumberger

last: Hörl

first: Clemens

last: Steinek

first: Marieke

middle: A

last: Oudelaar

first: Heinrich

last: Leonhardt

first: Hartmann

last: Harz


title: A dynamic gene regulatory code drives synaptic development of hippocampal granule cells [SS2]

first: Danie

last: Daaboul

summary: Connecting neurons into functional circuits requires the formation, maturation, and plasticity of synapses. While advances have been made in identifying individual genes regulating synapse development, the molecular programs orchestrating their action during circuit integration of neurons remain poorly understood. Here, we have employed a single-cell RNA sequencing (scRNAseq) method (Smart-seq2) to study the development of hippocampal GCs. GCs represent the first relay in the hippocampal tri-synaptic loop and play an essential role in processing spatial representations and memory acquisition. This study provides a high temporal resolution analysis of the transcriptome of GCs during early postnatal development (P5, P7, P10, P15, and P28). Together, these findings highlight the networks of key TFs and target genes orchestrating GC synapse development.

overall_design: We performed scRNAseq on GCs from Rbp4-Cre:Ai9 mice at key timepoints during synapse development. Brain slices from Rbp4-Cre:Ai9 mice were made using a 500 μm brain matrix, and the dentate gyrus (DG) was dissected. Next, the DG was chopped in smaller pieces and digested using Pronase. Following the digestion, the tissue pieces were homogenized using two-size Pasteur pipettes and the mix was loaded in a 20% Percoll solution to remove debris. Following centrifugation, the pellet was resuspended in OptiMEM-trehalose, and DAPI was added. Fluorescence Activated Cell Sorting (FACS) was done based on DAPI and tdTomato signal, into 96-well plates containing lysis buffer

first: Blanca

last: Lorente-Echeverría

first: Jeroen

last: Vandensteen

first: Gabriele

last: Marcassa

first: Willem

last: Naert

first: Joris

last: Vandenbempt

first: Elke

last: Leysen

first: Malou

last: Reverendo

first: Ine

last: Vlaeminck

first: Lise

last: Vervloessem

first: Jochen

last: Lamote

first: Suresh

last: Poovathingal

first: Kristofer

last: Davie

first: Keimpe

last: Wierda

first: Dan

last: Dascenco

first: Stein

last: Aerts

last: De Wit


title: Effects of mechanical stretch and depletion of lamin A/C on gene expression in human myotubes (RNAseq)

city: Paris

first: Catherine

last: Coirault

address: 47 bd de l'Hôpital

country: France

institute: Inserm

summary: To investigate the effects of A-type lamins on chromatin accessibility during mechanical loading in human skeletal muscle, we established 72h differentiated muscle cells in which each target gene has been knocked down by siRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells in two conditions: baseline and after 4h cyclic mechanical stretch. Comparative gene expression profiling analysis of RNA-seq data for control and  siRNA known down myotubes.

first: Saline

last: Jabre


title: Effects of mechanical stretch and depletion of lamin A/C on chromatin accessibility in human myotubes (ATACseq)

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells in two conditions: baseline and after 4h cyclic mechanical stretch.Comparative gene expression profiling analysis of RNA-seq data for control and siRNA knockdown myotubes.


title: A dynamic gene regulatory code drives synaptic development of hippocampal granule cells [RNA-Seq]

first: Danie

last: Daaboul

summary: Connecting neurons into functional circuits requires the formation, maturation, and plasticity of synapses. While advances have been made in identifying individual genes regulating synapse development, the molecular programs orchestrating their action during circuit integration of neurons remain poorly understood. Here we have employed a bulk RNA sequencing method (RiboTag) to study the development of hippocampal GCs. GCs represent the first relay in the hippocampal tri-synaptic loop, and play an essential role in processing spatial representations and memory acquisition. This study provides a high temporal resolution analysis of the translatome of GCs during early postnatal development (P5, P7, P10, P15, P21, and P28). Together, these findings highlight the networks of key TFs and target genes orchestrating GC synapse development.

overall_design: Hippocampi from Rbp4-Cre:RiboTag mice were homogenized and the homogenate was incubated with anti-HA magnetic beads for RPL22-HA pull down. Ribosome-bound mRNA was separated from ribosomes, RNA was isolated and libraries prepared for bulk RNA sequencing. This process was repeated at post-natal day (P)5, P7, P10, P15, P21 and P28.

first: Blanca

last: Lorente-Echeverría

last: Vandensteen


title: A NEW DYSTROPHIN DEFICIENT RAT MODEL MIRRORING EXON SKIPPING IN PATIENTS WITH DMD EXON 45 DELETIONS

status: Public on Sep 18 2025

city: EVRY-COURCOURONNES

first: Tao

last: WANG

state: France

address: 1 bis, rue de l’Internationale

department: R & D

institute: genethon

summary: Mutations in the dystrophin (DMD) gene can cause muscle-wasting disorders ranging from the milder Becker muscular dystrophy (BMD) to the more severe Duchenne muscular dystrophy (DMD). Exon 45 deletion is the most frequently reported single-exon deletion in DMD patients worldwide. In this study, we generated a novel rat model with an exon 45 deletion using the CRISPR/Cas9 technology. The DmdΔ45 rat recapitulate key clinical and molecular features of DMD, including progressive skeletal muscle degeneration, impaired muscle and cardiac function, cognitive deficits, elevated circulating muscle damage biomarkers and an overall reduced lifespan. Transcriptomics analyses confirmed the deletion of exon 45 and revealed gene expression patterns consistent with dystrophin deficiency. In the skeletal muscle, RNA-seq profiles demonstrated a transition from early stress responses and regenerative activity at 6 months to chronic inflammation, fibrosis, and metabolic dysfunction by 12 months. Similarly, the cardiac transcriptomic shifted from an early inflammatory and stress-responsive state to one characterized by fibrotic remodelling and metabolic impairment. Despite these pathological features, the DmdΔ45 rats exhibited a milder phenotype than other DMD rat models. This attenuation may be attributed to spontaneous exon 44 skipping, which partially restores the reading frame and results in an age-dependent increase in revertant dystrophin-positive fibres. Further analysis indicated downregulation of spliceosome-related genes, suggesting a potential mechanism driving exon skipping in this model. In summary, the DmdΔ45 rat represents a valuable model for investigating both the molecular determinants of phenotypic variability and the endogenous mechanisms of exon skipping. These findings offer important insights for the development of personalized exon-skipping therapies, particularly for DMD patients with exon 45 deletions.

overall_design: To profile the transcriptome of a DMD exon 45 deletion rat model, we performed RNA-seq on four muscle types (diaphragm, heart, psoas, and soleus) from wild-type and mutant rats at 6 and 12 months of age, with three biological replicates per group.


title: A gene regulatory element modulates myosin expression and alters cellular response to stress [mouse]

city: Durham

first: Taylor

last: Anglen

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

summary: A hallmark of heart disease is gene dysregulation and reactivation of fetal gene programs. Reactivation of these fetal programs can provide cardioprotective or compensatory effects during heart failure depending on the type and stage of the underlying cardiomyopathy. Many putative cardiac gene regulatory elements have been identified that may control these programs, but their functions are largely unknown. We profile genome-wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element important for the regulation of MYH6 that encodes human fetal myosin and is critical to the pathogenesis of hypertrophic and dilated cardiomyopathies. Using chromatin conformation assays in combination with epigenome editing, we find that gene regulation is mediated through direct interaction between MYH6 and the enhancer. We also find that activation of the enhancer alters cardiomyocyte response to the hypertrophy-inducing peptide endothelin-1. Collectively, these results identify regulatory mechanisms of cardiac gene expression programs that act through critical developmental factors and modulate cellular response to stress.

overall_design: Differential analysis of chromatin looping after repression of an MYH6/MYH7 enhancer in mouse HL-1 cardiomyocyte line, assessed using HiCAR protocols.

first: Irene

middle: M

last: Kaplow

first: Baekgyu

last: Choi

first: Kevin

last: Hagy

first: Duc

last: Tran

first: Megan

middle: E

last: Ramaker

first: Svati

last: Shah

first: Ravi

last: Karra

first: Yarui

last: Diao

first: Charles

last: Gersbach


title: A gene regulatory element modulates myosin expression and alters cellular response to stress [RNA-seq]

overall_design: To identify differentially expressed fetal cardiomyocyte genes we profiled changes to gene expression in cardiomyocytes derived from human pluripotent stem cells following GSK3 inhibition.


title: A gene regulatory element modulates myosin expression and alters cellular response to stress

overall_design: Differential analysis of chromatin looping after repression of an MYH6/MYH7 enhancer in cardiomyocytes derived from human pluripotent stem cells, assessed using HiCAR protocols.


title: RNA tomography reveals spatial gene expression maps of Arabidopsis thaliana roots infected with Heterodera schachtii

city: Wageningen

first: Jose

last: Lozano-Torres

state: Gelderland

address: Radix, Building no. 107, Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

summary: Plant-parastic nematodes cause substantial crop losses worldwide. The sedentary endoparasite nematode Heterodera schachtii induces specialized feeding structures in host roots. The molecular mechanisms underlying feeding structure initiation and development remain poorly understood. High-resolution, spatially resolved transcriptomics is required to study localized gene expression patterns underlying feeding structure formation. Here, we introduce RNA tomography for plants, a powerful untargeted spatial transcriptomics technology that allows studying gene expression at cellular resolutions. We applied RNA tomography to Arabidopsis thaliana roots infected with H. schachtii at 1 and 2 days post inoculation. Our findings provide novel insights into early nematode parasitism.

overall_design: Four-day-old Arabidopsis seedlings grown in RoPod microscopic chambers were inoculated with ~20 H. schachtii infective stage juveniles (J2) per 3 seedlings. Roots with a single nematode infection at 1 and 2 days post inoculation were selected for RNA tomography library preparation.

first: Anna

last: Pijnacker

first: Yuhao

last: Wang

first: Jaap-Jan

last: Willig

first: Jonas

last: Mars

first: Steffen

last: Werner

first: Kelvin

last: Adema

first: Geert

last: Smant

first: Hendrik

middle: C

last: Korswagen


title: A gene regulatory element modulates myosin expression and alters cellular response to stress [HiCAR]

first: Taylor

last: Anglen

overall_design: Differential analysis of chromatin looping after activation of an MYH6/MYH7 enhancer and Endothelin-1 stimulus in cardiomyocytes derived from human pluripotent stem cells, assessed using HiCAR protocols.

first: Irene

last: Kaplow

first: Baekgyu

last: Choi


title: Integrated miRNA-mRNA Analyses of Triple-Negative Breast Cancer in Black and White Patients with or Without Obesity

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

type: Non-coding RNA profiling by high throughput sequencing

summary: Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous subtype of breast cancer. miRNAs play an essential role in TNBC pathogenesis and prognosis. Obesity is linked with an increased risk for several cancers, including breast cancer. Obesity is also related to the dysregulation of miRNA expression in adipose tissues. However, there is limited knowledge about race- and obesity-specific differential miRNA expression in TNBC. We performed miRNA sequencing of 48 samples (24 tumor and 24 adjacent non-tumor tissues) and RNA sequencing of 24 tumors samples from Black (AA) and White (EA) TNBC patients with or without obesity. We identified 55 miRNAs exclusively associated with tumors in obese EA patients and 33 miRNAs in obese AA patients, each capable of distinguishing tumor tissues from obese from lean individuals within their respective racial groups. In EA, we detected 41 significant miRNA–mRNA correlations. Notably, miR-181b-5p and miR-877-5p acted as negative regulators of tumor-suppressor genes (e.g., HEY2, MCL2, HAND2), while miR-204-5p and miR-143-3p appeared to indirectly target oncogenes (e.g., RAB10, DR1, PTBP3, NCBP1). Among AA patients, we found 28 significant miRNA–mRNA interactions. miR-195-5p, miR-130a-3p, miR-130a-5p, miR-424-5p, miR-148a-3p, miR-374-5p, and miR-30a-5p each potentially downregulated two or more genes (e.g., CLCN4, PLCB1, CDC25B, AEBP2, ERBB4). Pathway enrichment analysis highlighted KRAS, ESR1, ESR2, RAB10, TNRC6C, and NCAN as the most commonly differentially expressed in EA, whereas ERBB4, PLCB1, and SERPINE1 were most frequently in AA. These findings highlight the importance of considering race-specific miRNA–mRNA signatures in understanding TNBC in the context of obesity, offering insights into biomarker-driven patient stratification for targeted therapeutic strategies.

overall_design: To determine the relationship between the levels of microRNA (miRNA) expression and obesity in breast cancer, we perfomed miRNA-seq in tumor and adjacent non-tumor tissues in Triple Negative Breast Cancer (TNBC) samples of African American and Caucasian women dignosed with the disease.

first: Fokhrul

last: Hossain

first: Martha

middle: I

last: Gonzalez-Ramirez

first: Jone

last: Garai

first: Diana

last: Polania-Villanueva

first: Li

last: Li

first: Farzeen

last: Nafees

first: Md

last: Manirujjaman

first: Bolin

last: Bolin

first: Samarpan

last: Majumder

first: Xiao-Cheng

last: Wu

first: Chindo

last: Hicks

first: Luis

last: Del Valle

first: Denise

last: Danos

first: Augusto

last: Ochoa

first: Lucio

last: Miele


title: Lobe-less, a long noncoding RNA that regulates Drosophila mushroom body morphogenesis

status: Public on Sep 17 2025

city: Sapporo

first: Masanao

last: Sato

state: Hokkaido

address: Kita 9 jo Nishi 9 chome, Kita-ku, Sappro

country: Japan

institute: Hokkaido University

summary:
Investigation of the effects of lol mutation on Drosophila transcriptome.  w[1118] was used as the control strain.
The lol mutation used in this study were further described in Inagaki et al.

overall_design: A triplicated DNA microarray experiments were performed using total RNA from whole body or head of mutants (males or females were sorted), with three independent samples for each experiment. Same analysis was done for the control w[1118] strain.  The DNA microarray was designed for 16,637 transcripts with 8 probes per transcript based on flybase build DM5.7 (07/05/22)

first: Sachi

last: Inagaki

first: Yuji

last: Kageyama


title: Immunogenomic Diversity of Triple-Negative Breast Cancers in Obese and Non-obese Black and White Women

first: Jovanny

last: Zabaleta

summary: Racial disparities in incidence and outcomes of triple-negative breast cancer (TNBC) have been attributed to ancestry, socioeconomic factors and/or obesity. We studied 253 TNBCs from 128 Black and 125 White women. Arms were balanced for age, AJCC stage, histological grade and molecular subtypes, and differed significantly in BMI distribution, obesity, and Area Deprivation Index. We examined survival rates, whole-transcriptome RNASeq and genetic ancestry. In our sample, Black race or obesity were not intrinsically predictive of poor outcomes. TNBC molecular portraits varied with stage and biological aggressiveness, irrespective of race.  We identified a novel group of TNBCs with a distinctive luminal-like and stem-cell-like transcriptional profile that were equally distributed among Blacks and Whites. Genetic ancestry was highly admixed. Immune deconvolution showed a higher abundance of several immune cell populations in tumors from Blacks, which may have precision therapeutic significance, warranting further investigation of potential drivers of tumor immunity.

overall_design: Retrospective, two-arm observational study. The final sample set included  253 TNBCs - from 128 Black and 125 White women. The two arms were balanced with respect to age, AJCC stage, histological grade and molecular subtype. They differed significantly in BMI distribution, obesity rates and Area Deprivation Index. RNAseq was used to determine gene expression profiles associated with TNBC in African American (AA) and European American (EA), with and without obesity, from Louisiana. Gene profiles were used to determine associations with race/ethnicity, obesity stage, tumor stage, prediction of immune infiltration and survival

first: Fokhrul

last: Hossain

first: Jiande

first: Jerneja

last: Tomsic

first: Susan

last: Neuhausen

first: Yuan

last: Ding

first: Kavitha

last: Mukund

first: Zahra

last: Mesrizadeh

first: Shankar

last: Subramaniam

first: Victoria

last: Seewaldt


title: Rate Limiting Enzymes in Nucleotide Metabolism Synchronize Nucleotide Biosynthesis and Chromatin Formation [ATAC-Seq]

status: Public on Sep 16 2025

city: Chicago

first: SHASHANK

last: SRIVASTAVA

state: IL

address: 303 E Superior St, SQE Lab 7-400

institute: Northwestern University

summary: Fundamental cellular processes including replication, transcription, and repair rely on both an adequate nucleotide supply and sufficient availability of new histones. Chromatin disassembly and reassembly is crucial to maintain genome stability, and is regulated by the orderly engagement of histones with a series of histone chaperones that guide newly synthesized histones from ribosomes to DNA. Although the synthesis of nucleotides and the histone proteins are the two major biosynthetic processes to complete the formation of chromatin, our knowledge about the coordination of these processes is limited. Phosphoribosyl pyrophosphate synthetases (PRPSs) catalyze the rate-limiting step in the nucleotide biosynthesis pathway. PRPS enzymes form a complex with PRPS-associated proteins (PRPSAPs). In the present study, we discover that PRPS-PRPSAP enzyme complex are part of the histone chaperone network involving HSP70/90, NASP, HAT1/RBBP7 and importin-4 to regulate chromatin assembly. We show PRPS enzymes are essential not only for nucleotide biogenesis, but together with PRPSAP also play a key role in the heterodimerization of H3-H4 and posttranslational modification of nascent histones, early steps in the process of histone maturation. Depletion of PRPS proteins leads to limited histone availability and therefore to impaired chromatin assembly. Our discovery bridges nucleotide metabolism and chromatin regulation and provides first evidence on how nucleotide biogenesis and chromatin dynamics work in synchrony.

overall_design: ATAC seq-To evaluate the nucleosome positioning by measuring the fragment size, in response to dTAG47 mediated depletion  of PRPS1, for 24 h in HEK293T cells.

first: Shashank

last: Srivastava

first: Daniel

middle: R

last: Foltz


title: Transcriptomic profiles of biopsy-derived colon epithelial organoids from pediatric patients with ulcerative colitis

city: Palo Alto

first: Michael

middle: J.

last: Rosen

state: CA

address: 1701 Page Mill Rd, #262

institute: Stanford University

summary: Colon epithelial organoid lines were developed from pediatric patients with endoscopically active ulcerative colitis, inactive ulcerative colitis, and those without endoscopic or histologic evidence of colon inflammation (non-IBD controls). From each organoid line, RNA was processed from undifferentiated organoids (spheroids) and parallel organoids differentiated for 3 days (colonoids). Paired-end sequencing of poly-A enriched RNA libraries was carried out on the Illumina NovaSeq PE150 platform and the reads were aligned to the human reference hg38 genome. To determine differentially expressed genes, transcripts with Log2FC ≥ ±1, FDR P ≤ 0.1 were considered statistically significant.

overall_design: Bulk RNA-sequencing of colon epithelial organoid lines from eight pediatric patients with active UC, inactive UC, and non-IBD controls.

first: Babajide

last: Ojo

first: Lyong

last: Heo

middle: J


title: Rate Limiting Enzymes in Nucleotide Metabolism Synchronize Nucleotide Biosynthesis and Chromatin Formation [RNA-Seq]

overall_design: To evaluate the transcriptomic changes in response to PRPS1 or PRPSAP1 depletion. We treated  HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag cells with DMSO, dTAG47 (to deplete PRPS1) or AGB1 (to deplete PRPSAP1) for 24 hours and RNA seq was conducted.


title: Effect of depletion of PERK on gene expression in T cells after polyclonal or allogeneic stimulation

city: Milwaukee

first: Qiao

middle: cheng

last: Cheng

state: Wisconsin

institute: Medical College of Wisconsin

summary: PERK differentially regulates T cell allogeneic and anti-tumor responses. To further elucidate the mechanism, we performed transcriptomics analyses via bulk RNA sequencing on WT and PERK-deficient T cells after polyclonal or allogeneic stimulation. We here report that endoplasmic reticulum-associated degradation (ERAD)-associated genes, including Sel1l and Erlec1, were significantly increased in PERK conditional knock out (cKO) compared with WT T cells upon allogeneic but not polyclonal stimulation. SEL1L-HRD1 axis plays a central role in ERAD pathway, we also observed that PERK binds to SEL1L in activated human T-cell line. By using PERK-/-SEL1L-/- mice, we eluciated that PERK regulates T-cell allogeneic responses and GVHD induction through SEL1L-mediated ERAD pathway.

overall_design: RNA-seq profiling of wildtype or PERK-deficient T cells after stimulation with  anti-CD3 and anti-CD28 antibodies for 3 days or allogeneic antigen presenting cells (APCs) for 4 days.

first: Hee-Jin

last: Choi

first: Yongxia

last: Wu

first: Xue-Zhong

last: Yu


title: Targeting Siglec-10/α3β1 Integrin Interactions Enhances Macrophage-Mediated Phagocytosis of Pancreatic Cancer

first: Pratima

last: Saini

address: 300 E. Superior Street

summary: Tumor-associated macrophages (TAMs) in the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME) exhibit immunosuppressive phenotypes and impaired phagocytic activity, facilitating tumor progression and immune evasion. Here, we identify integrin α3β1, composed of ITGA3 and ITGB1 subunits, as a sialylated glycoprotein ligand for Siglec-10, an inhibitory glyco-immune checkpoint receptor highly expressed on TAMs in PDAC. The interaction between Siglec-10 on TAMs and α3β1 on PDAC cells suppresses macrophage-mediated phagocytosis, thereby promoting immune evasion. Consistently, disrupting Siglec-10 interactions with monoclonal antibodies significantly enhances macrophage phagocytosis of PDAC cells and alleviates myeloid cell-mediated inhibition of T cell proliferation and activation in vitro. In both a PDAC xenograft mouse model engrafted with human macrophages and a human Siglec-10 transgenic mouse model, targeting Siglec-10 with monoclonal antibodies reduces PDAC tumor growth. These findings suggest that the Siglec-10 interactions are key mediators of TAM-driven immune evasion in PDAC and highlight the therapeutic potential of targeting these interactions to restore anti-tumor immunity in PDAC.

overall_design: RNA-seq profiling of tumor-associated macrophages (TAMs) isolated from NSG mice co-injected with human TAMs and either isotype control or Siglec-10 antibody.

first: Mohamed

last: Abdel-Mohsen


title: Destruction of VISTA by TRIM25 ablation in T cells potentiates cancer immunotherapy

status: Public on Sep 15 2025

city: Wuhan

first: Yishuang

last: Sun

address: 115 Donghu Road

institute: Medical Research Institute

summary: To gain deeper insights into the role of Trim25 expression in T cells in regulating tumor microenvironment dynamics, we performed single-cell RNA sequencing on purified CD45+ immune cells isolated from MC38 xenografts harvested from either Trim25 cKO or WT C57BL/6 mice.

overall_design: MC38 tumors were generated by subcutaneous injection of 1×10^5 MC38 cells into 8-week-old WT and Trim25 cKO mice. CD45+ immune cells were then isolated from these tumors using a FACSAria III (BD) for scRNA-seq analysis.


title: RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [ZNF207_eCLIP-Seq]

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: Maryland

address: 1050 Boyles Street

institute: National Cancer Institute

summary: Despite progress in understanding pre-mRNA splicing, the regulatory mechanisms controlling most alternative splicing events remain unclear. We developed CRASP-Seq, a method that integrates pooled CRISPR-based genetic perturbations with deep sequencing of splicing reporters, to quantitively assess the impact of all human genes on alternative splicing from a single RNA sample. CRASP-Seq identified both known and novel regulators, enriched for proteins involved in RNA splicing and metabolism. As proof-of-concept, CRASP-Seq analysis of an LMNA cryptic splicing event linked to progeria uncovered ZNF207, primarily known for mitotic spindle assembly, as a regulator of progerin splicing. ZNF207 depletion enhances canonical LMNA splicing and decreases progerin levels in patient-derived cells. We further show that ZNF207’s zinc finger domain broadly impacts alternative splicing through direct interactions with U1 snRNP components. These findings position ZNF207 as a U1 snRNP auxiliary factor and demonstrate the power of CRASP-Seq to uncover key regulators and domains of alternative splicing.

overall_design: eCLIP sequencing of ZNF207 (tagged with FLAG at either the N-terminus (IP_B) or C-terminus (IP_D)) was performed in HEK293 Flp-In cells. FLAG-EGFP (IP_A) was used as a negative control.

first: Amit

middle: K

last: Behera

first: Jeongjin

last: Kim

first: Shreya

last: Kordale

first: Filip

last: Pekovic

first: Arun

last: Damodaran

first: Bandana

last: Kumari

first: Sandra

last: Vidak

first: Ethan

last: Dickson

first: Mei

middle: S

last: Xiao

first: Gerard

last: Duncan

first: Thorkell

last: Andresson

first: Tom

last: Misteli

first: Eugene

last: Valkov


title: RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [CRASP-Seq]

overall_design: CRASP-Seq assays of six different splicing minigene reporters (FAS exon-6, EZH2 exon-14, SRSF7 poison exon, PKM mutually exclusive exons, LMNA HGPS, LMNA WT) were performed in three different cell lines (HAP1, RPE1, and HepG2) at two different time points (T1 and T4).


title: RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [siZNF207_Rescue_mRNA-Seq]

overall_design: mRNA-Seq profiling was performed on HEK293 Flp-In cells treated with siRNAs (siNT or siZNF207) for 48 hours and induced to express either ZNF207 or an empty vector for 42 hours.


title: A gene regulatory element modulates myosin expression and alters cellular response to stress [ATAC-seq]

first: Taylor

last: Anglen

overall_design: To identify cis-regulatory elements important for regulating fetal cardiomyocyte gene expression we profiled genome-wide changes to chromatin structure in cardiomyocytes derived from human pluripotent stem cells following GSK3 inhibition.

first: Irene

last: Kaplow

first: Baekgyu

last: Choi

first: Kevin

middle: T

last: Hagy

first: Duc

last: Tran

first: Megan

last: Ramaker

first: Svati

last: Shah

first: Ravi

last: Karra

first: Yarui

last: Diao

first: Charles

last: Gersbach


title: Tyrosine kinase Ptk1 couples one carbon metabolism and virulence in an endogenous pathogen

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

summary: Endogenous pathogens can constrain virulence to ensure survival in the host.  Pathogenic state can be controlled by metabolic responses to the prevailing microenvironment; however, the coupling and effector mechanisms are not well understood. Flux through the One Carbon Metabolism (OCM) pathway can modulate virulence of the oral pathobiont Porphyromonas gingivalis, and here we show that this is controlled by tyrosine phosphorylation-dependent differential partitioning of gingipain proteases.  The OCM essential precursor pABA inhibits the low molecular weight tyrosine phosphatase Ltp1, and consequently relieves inhibition of its cognate kinase, Ptk1.  We found that in the absence of pABA, reduced Ptk1 kinase activity blocks extracellular release of gingipains.  Surface retention of gingipains confers resistance to neutrophil mobilization and killing, and virulence in animal models of disease is elevated.  Reciprocally, Ptk1 and gingipains are required for maximal flux through OCM, and Ptk1 can phosphorylate the OCM pathway enzymes GlyA and GcvT.  Further, ALP, an alkaline phosphatase involved in synthesis of DHPPP, which combines with pABA to make DHP, is phosphorylated and activated by Ptk1. Deletion mutants of ptk1 and pabC were more virulent in an in vivo virulence (murine abscess) model.   RNASeq was adopted to compare the transcriptional profile of ptk1 and pabC mutants recovered from abscess material.  We propose, that although the primary function of Ptk1 is to maintain OCM balance, it mechanistically couples metabolism with tunable pathogenic potential through directing the location of proteases.

overall_design: In order to investigate the role that the pABA synthesis enzyme PabC and the bacterial tyrosine kinase Ptk1 has on the transcriptome of Porphyromonas gingivalis during infection, mice were inoculated with either the parental wildtype (WT) ATCC 33277 strain or isogenic deletion mutants lacking either pabC (ΔpabC) or ptk1 (Δptk1) and abscess material collected and subjected to RNASeq.

first: Kendall

last: Stocke

first: Satya

last: Pandey

first: Shunying

last: Jin

first: John

middle: D

last: Perpich

first: Lan

last: Yakoumatos

first: Hirotaka

last: Kosaki

first: Daniel

middle: W

last: Wilkey

first: Zackary

last: Fitzsimonds

last: Miller

first: Mukesh

last: Sriwastva

first: Michael

middle: L

last: Merchant

first: Juhi

last: Bagaitkar

first: Silvia

last: Uriarte

first: Jan

last: Potempa


title: Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (RNA-Seq)

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

country: Italy

institute: University of Milan

summary: Lamina-associated domains (LADs) are megabase-sized portions of the genome anchored to the nuclear lamina (NL). Factors controlling the tethering of the genome to the NL have remained elusive. Here, we identified DNA Topoisomerase 2 beta (TOP2B) as a prominent regulator of genome-NL interactions. TOP2B depletion leads to the weakening of these interactions in LADs marked by H3K9me3 heterochromatin, and the repositioning of inter-LAD regions (iLADs) to the NL. TOP2B loss affects LAD interactions with Lamin B receptor (LBR) more prominently than with Lamins B1 and B2. LBR loss phenocopies the effects of TOP2B depletion, although the two proteins occupy different portions of the genome. Co-depletion of TOP2B and LBR causes partial LAD/iLADs inversion, mirroring changes typical of oncogene-induced senescence. We propose that a coordinated axis controlled by TOP2B in iLADs and LBR in LADs maintain proper partitioning of the genome between the NL and the nuclear interior.

overall_design: RNA-seq experiment were performed on RPE1SunTag control and depleted for TOP2B. RNA was extracted 5 days post transfection.

middle: G

first: Tom

last: van Schaik

first: Marcel

last: de Haas

first: Jeremie

last: Breda

first: Mikhail

last: Magnitov

first: Elzo

last: de Wit

first: Anna

last: Manjon

first: Rene

middle: H

last: Medema

first: Adam

last: Buckle

first: Catherine

last: Naughton

first: Nick

last: Gilbert

first: Bas

last: van Steensel


title: Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (bTMP-seq)

overall_design: bTMP-seq experiment were performed on hTERT-RPE1 cells control. bTMP intercaletes in negative supercoiled DNA and bTMP-seq provide genome-wide mapping of negative supercoiling in control RPE1 cells.


title: RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [siZNF207_mRNA-Seq]

first: Thomas

last: Gonatopoulos-Pournatzis

overall_design: mRNA-Seq profiling was performed on HEK293T cells treated for 48 hours with three independent ZNF207 siRNAs or a non-targeting control.

first: Amit

last: Behera

first: Jeongjin

last: Kim

first: Shreya

last: Kordale

first: Filip

last: Pekovic

first: Arun

middle: P

last: Damodaran

first: Bandana

last: Kumari

first: Sandra

last: Vidak

first: Ethan

last: Dickson

first: Mei

last: Xiao

first: Gerard

last: Duncan

first: Thorkell

last: Andresson

last: Misteli

first: Eugene

last: Valkov


title: Gene expression profiling by RNA-seq of control and TRIM21-knockdownHCT8 cells

status: Public on Sep 12 2025

city: Shanghai

first: Xintian

last: Zhang

address: 639 Zhi Zao Ju Road

institute: Shanghai Jiao Tong University

summary: In order to define the cohort of genes whose expression is regulated by TRIM21 in CRC,  we constructed HCT8 cells stably infected with lentivirus carrying control shRNA (shNC) or TRIM21 shRNA (sh1). Subsequently, total RNA was isolated and then performed transcriptome RNA sequence.

overall_design: We had two groups: (1) shNC and (2) sh1. Each group had 3 biological replicates.

first: Xiangjun

last: Meng


title: The role of PDE7A in Triple negative breast cancer (TNBC) growth and progression

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer, associated with poor response to therapies and high mortality. We identify that phosphodiesterase 7A (PDE7A) is overexpressed in the majority of TNBC, and a higher level of PDE7A associates with poor prognosis. The PI3K/AKT pathway, via the transcription factor IRF1, stimulates the expression of PDE7A in TNBC cells. PDE7A inhibition attenuates TNBC growth in both cell culture and mouse models of TNBC. Inhibition of PDE7A suppresses de novo pyrimidine biosynthesis, in part through the downregulation of the enzyme dihydroorotate dehydrogenase (DHODH). DHODH suppression attenuates TNBC tumor growth, mirroring the effects of PDE7A inhibition, and ectopic DHODH expression rescues PDE7A-inhibition-induced tumor suppression. Pharmacological co-targeting of PDE7A and DHODH potently inhibits TNBC tumor growth and metastasis. These findings identify the PDE7A→ DHODH→ de novo pyrimidine biosynthesis pathway as a key driver of TNBC, offering additional therapeutic opportunities for TNBC patients.

overall_design: MDA-MB-231 were treated with  PDE7A inhibitor (50 micomolar) BRL-50481 for 72 hours, samples were harvested and were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.

first: Narendra

last: Wajapeyee

first: Parmanand

last: Malvi

first: Suresh

last: Bugide

first: Roshan

last: Dutta

first: Kiran

last: Reddi

first: Yvonne

last: Edwards

first: Kamaljeet

last: Singh


title: Hypoxia promotes BCMA loss and a suppressive secretome thereby hindering CAR T cell therapy in multiple myeloma

status: Public on Sep 11 2025

city: Brussels

first: Eline

last: Menu

address: Bd de la Plaine 2

institute: Vrije Universiteit Brussel

summary: Multiple myeloma (MM) develops in a hypoxic bone marrow (BM) microenvironment, which alters tumor behavior and immune responses. While hypoxia is known to directly suppress immune function, its effect on immunotherapy-relevant antigen expression and the MM secretome remains underexplored. Here, we investigated how hypoxia affects BCMA expression and BCMA-targeted CAR T cell responses. MM cells cultured under hypoxia (1% O₂) showed reduced BCMA surface and total protein expression, resulting in reduced CAR-mediated signaling. Importantly, the hypoxic tumor secretome further reduced BCMA levels and significantly impaired CAR T cell killing and cytokine production, which was partially reversible by γ-secretase inhibition. To dissect the suppressive nature of the hypoxic secretome, we identified an increase in small extracellular vesicle (sEV) release under hypoxia. RNA profiling of sEVs revealed a hypoxia-induced RNA signature with potential immunomodulatory roles. In conclusion, hypoxia diminishes BCMA expression and enhances secretion of immunosuppressive factors, including sEVs, thereby limiting the efficacy of BCMA CAR T cell therapy in MM.

overall_design: RNAseq of extracellular vesicles derived from RPMI-8226 and HS5 cells, placed in normoxia or hypoxia for 48 hours

first: Arne

last: Van der Vreken

first: Chenggong

last: Tu

first: Fien

last: Meeus

first: Lauren

last: van den Broecke

first: Jack

last: Brons

first: Karine

last: Breckpot


title: Microglia-astrocyte crosstalk regulates synapse remodeling via Wnt signaling

status: Public on Sep 10 2025

city: Worcester

first: Travis

middle: E.

last: Faust

address: 366 Plantation Street

department: Neurobiology

institute: University of Massachusetts Chan Medical School

summary: Unilateral whisker lesioning at age P4 leads to removal of thalamocortical synapses in layer IV of the barrel cortex over the course of the next 6 days. Synapse removal is mediated by microglia and induced by CX3CL1-CX3CR1 signaling between neurons and microglia. Downstream of CX3CL1-CX3CR1 activation, microglia induce astrocyte morphological changes and activation of canonical Wnt signaling in astrocytes. To explore the spatial pattern of microglia Wnt ligand expression and astrocyte Wnt receptor expression in astrocytes, we analyzed coronal sections containing the barrel cortex from 4 wild-type mice and 4 CX3CL1 knockout mice at 24 hours after whisker lesioning by multiplexed error-robust fluorescent in situ hybridization (MERFISH).

overall_design: Brains were isolated from P5 mice at 24 hours after unilteral whisker lesioning of the right side of the mouse's snout at age P4. Brains were extracted and embedded in OCT for sectioning onto specialized coverslips. Coronal sections containing the barrel cortex were collected for analysis by MERFISH. Each coverslip contained 1 coronal section from a wild-type mouse and 1 coronal section from a CX3CL1 knockout mouse.

middle: E

first: Margaret

middle: A

last: Boyle

first: Violeta

last: Durán-Laforet

first: Loris

last: Ferrari

first: Robert

last: Murphy

first: Dorothy

last: Schafer


title: Viral rebound in SHIV-infected infant macaques is predicted by immunovirologic features measured before and after antiretroviral therapy

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Evaluation of HIV cure strategies requires antiretroviral therapy (ART) interruption, but ethical and clinical considerations make this difficult in children. Uncovering predictors of time to viral rebound (TTR) and post-treatment control (PTC) of rebound viremia in a pediatric preclinical model may inform the design of studies testing novel cure interventions in these populations. We thus assessed 141 variables in SHIV-infected infant rhesus macaques (RMs) where ART initiation was staggered then followed by analytical treatment interruption (ATI). Viral rebound occurred in 25/30 RMs within 7-98 d of ATI, with TTR significantly delayed in the Early ART group compared to the Intermediate and Late ART groups (median TTR  84, 18, and 17 d, respectively; p<0.001). Peak plasma viral load pre-ART best described TTR, with increased predictive strength through the successive inclusion of six additional variables. Increased peak viral load pre-ART decreased the odds of no rebound and elevated Ki67+ effector memory CD8+ T cells in lymph nodes pre-ATI increased the odds of PTC. RNA sequencing of CD4+ T cells pre-ATI showed heme metabolism and IFNg response pathways were most upregulated in RMs with sustained suppression of viremia during ATI. Analysis of only the Early ART group also implicated TGFb pathway genes in lack of viral rebound off ART. This comprehensive investigation reveals major determinants of viral rebound dynamics following ART interruption that should be validated and explored as biomarkers to screen children with HIV being considered for ATI.

overall_design: 18 infant Indian rhesus macaques infected with SHIV.C.CH505.375H.dCT at 4 weeks of age divided into three groups (n=6) differing in timing of antiretroviral therapy (ART) initiation following infection: 8 wpi for Late ART, 2 wpi for Intermediate ART, and 4 or 7 dpi for Early ART. Animals were maintained on daily ART for a minimum of 52 weeks prior to treatment interruption. RNA sequencing was perfomed on CD4+ T cells isolated from blood and lymph nodes prior to treatment interruption.

first: Veronica

last: Obregon-Perko

first: Achal

last: Awasthi

first: Richard

last: Barfield

first: Stella

last: Berendam

first: Bhrugu

last: Yagnik

first: Tiffany

last: Styles

first: Greg

first: Prachi

last: Kumar

first: Mithra

first: Emily

last: Fray

first: Fan

last: Bu

first: Janet

last: Siliciano

first: Bob

first: Maud

last: Mavigner

first: Rama

middle: R

last: Amara

first: Steve

last: Bosinger

first: Genevieve

last: Fouda

first: Sallie

last: Permar

first: Cliburn

last: Chan

first: Ann

last: Chahroudi


title: Brown remodeling of white adipose tissue protects against abdominal aortic aneurysm via a novel batokine FSTL1 [CL316,243]

status: Public on Sep 06 2025

city: Guangzhou

first: Yao

last: Lei

address: 107 Yan Jiang West Road

department: Department of Cardiology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Abdominal aortic aneurysm (AAA) is a life-threatening vascular disease without effective medical therapies. Emerging evidences have suggested a crosstalk between adipose tissue and vascular cells and brown adipose tissue is beneficial for cardiovascular health. Nevertheless, whether brown remodeling of white adipose tissue would protect against AAA remains unclear. Here we showed that patients with AAA had a decreased browning level of adipose tissue and induction of adipose tissue browning significantly reduced AAA incidence and attenuated AAA development in mice. Using LC-MS/MS and proteomic analysis, we further identified Follistatin-like 1 (FSTL1) as a novel vessel-protective adipokine secreted by browning adipocytes. Mechanistically, FSTL1 inhibited VSMC apoptosis through DIP2A/AKT signaling. Furthermore, we demonstrated that adipocyte-specific deficiency of FSTL1 abrogated the protective effect of browning induction. Moreover, supplementation of FSTL1 either systemically or patched into hydrogel placing around abdominal aorta markedly limited aortic dilation and AAA progression. Our data suggest a protective role of adipose tissue browning and a novel batokine FSTL1 in the development of AAA, which may represent a novel intervention strategy for AAA.

overall_design: RNA sequencing of aortic tissues from Ang II-infused mice treated with or PBS.

first: Chunling

last: Huang

first: Yuna

first: Boshui

first: Lei

last: Yao


title: Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [scRNA-seq]

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

institute: Center for Genomics and Bioinformatics

summary: The bHLH transcription factors HAND1 and HAND2 are expressed in partially overlapping patterns during development. Studies have established evidence for significant functional redundancy between HAND1 and HAND2. To test redundancy fully, we engineered a Hand1 allele where we directly replace the exons and intron with those of Hand2. Results show that 2% of Hand1Hand2/ Hand2 mice are viable, and fertile. The remaining Hand1Hand2/Hand2 embryos exhibit neonatal lethality due to omphalocele, ventricular septal defects and conduction anomalies. Omphalocele can occur due to altered gut rotation and transcriptomic expression analysis reveals that established gene expression patterns associated with normal gut rotation are compromised. Interrogation of cardiac function in surviving Hand1Hand2/Hand2 mice reveals QRS abnormalities and accompanies cardiac morphogenic defects. These data support previous findings that HAND factors exhibit extensive functional overlap but do reveal that unique functions for HAND1 and HAND2 proteins within the Hand1 expression domain that are required for normal embryonic development.

overall_design: Four Control E13.5 day embryos that were sectioned transverse at the level of the umbilicus and four Hand1^Hand2/Hand2 E13.5 day embryos that were sectioned transverse at the level of the umbilicus were processed using the 10X Genomics FFPE flex protocols with six 25mm sections from each embryo. Libraries were made and sequenced and FASTQ files were processed using CellRanger

first: Anthony

middle: B

last: Firulli

first: Beth

first: Ram

last: Podicheti

first: Douglas

last: Rusch


title: Spatial transcriptomics reveals distinct role of monocytes/macrophages with high FCGR3A expression in kidney transplant rejections

status: Public on Sep 09 2025

city: Loma Linda

first: Yan

last: Chen Wongworawat

address: 11234 Anderson Street, Room 2516

institute: Loma Linda University

summary: Kidney transplant rejections are classified as active antibody mediated rejection (AMR) and cell mediated rejection (TCMR), with AMR primarily driven by antibodies produced by B cells, whereas TCMR is mediated by T lymphocytes that orchestrate cellular immune responses against the graft. Emerging evidence highlights the essential roles of innate immune cells in rejections, especially monocytes/macrophages and natural killer (NK) cells. However, the roles of specific innate immune cell subpopulations in kidney allograft rejection remain incompletely understood. Exploiting the spatial transcriptomics and formalin-fixed paraffin-embedded (FFPE) core needle biopsies from human kidney allografts, we demonstrated that non-rejection, AMR, acute TCMR and chronic active AMR have distinct transcriptomic features. Subclusters of monocytes/macrophages with high Fc gamma receptor IIIA (FCGR3A) expression were identified in C4d-positive active AMR and acute TCMR, and the spatial distribution of these cells corresponded to the characteristic histopathological features. Key markers related to monocyte/macrophage activation and innate alloantigen recognition were upregulated, along with metabolic pathways associated with trained immunity in AMR and TCMR. Taking together, these findings revealed that intragraft monocytes/macrophages with high FCGR3A expression play a critical role in kidney transplant rejections.

overall_design: We selected 8 cases based on histopathological and clinical features (Table 1), representing 4 diagnostic groups: 1) non-rejection conditions; 2) Active AMR; 3) Acute TCMR; 4) Chronic active AMR. The clinical diagnosis is interpreted by our renal pathologists based on the 2018 Banff Criteria. We performed 10x Genomic Visium spatial transcriptomics analysis on H&E - stained sections from archived FFPE core needle biopsies of human kidney allografts following Visium Spatial Gene Expression for FFPE workflow.


title: Mechanistic Study on the Restoration of Intestinal Barrier Integrity and Alleviation of Inflammatory Bowel Disease by Rhynchophylline via the AhR-NR4A1 Pathway

status: Public on Sep 05 2025

city: Urumqi

first: Xuwen

last: Mao

address: CollNo.567, Shangde North Road, Shuimogou District

institute: Xinjiang medical university

summary: Restoring intestinal barrier function is considered an effective strategy for the treatment of Inflammatory Bowel Disease (IBD). Rhynchophylline (Rhy), a bioactive alkaloid sourced from the traditional herbs Uncariarhynchophylla used in Chinese medicine, is known for its antihypertensive, anti-asthmatic, and antitumor properties. This study explores the pharmacological effects and molecular mechanisms of Rhy in treating IBD.

overall_design: In vitro cell inflammation injury model was established, and the inflammatory factors, cell permeability, cell proliferation, and intercellular tight junction protein expression were measured after Rhy intervention, which verified the anti-inflammatory activity and enhancement of intestinal barrier function of Rhy. In vivo animal model of acute and chronic colitis was established, and Rhy was administered orally at three dose levels to evaluate the protective effects of Rhy on acute and chronic colitis in animals. The signaling pathways that enhance the intestinal barrier function of Rhy were identified through transcriptomics, gene knockout techniques, and molecular dynamics simulations.

first: Lufeng

last: Cheng

first: Yu

last: Liu

first: Yuche

last: Wu


title: Brown remodeling of white adipose tissue protects against abdominal aortic aneurysm via a novel batokine FSTL1

overall_design: RNA sequencing of  VSMCs treated with or without recombinant FSTL1.


title: Gene expression profile of B55a/PPP2R2A knocked-down Parkin-expressing HeLa cells

status: Public on Sep 07 2025

city: Rome

first: Valentina

last: Cianfanelli

address: Viale Marconi 446

institute: University Roma TRE

summary: Or study identified the PP2A-B55a/PPP2R2A Ser-Thr phosphatase as a regulator of Parkin-dependent mitophagy and mitochondrial biogenesis. HeLa cells expressing Parkin and knocked-down for B55a/PPP2R2A induce a lysosome- and mitochondria-related transcriptional programmes down-stream TFEB and PGC-1a transcription factor activation.

overall_design: Total RNA was extracted from B55a/PPP2R2A kncked-down cells, induced for Parkin expression with Doxycycline. Cells transiently transfected with a control oligo were used a control sample.

first: Cianfanelli

last: Valentina

first: Nanni

last: Monica

first: De Cegli

last: Rossella


title: MicroRNAs induced by IFNα in HepG2 cells

city: Changchun City

first: Le

last: Wang

state: Jilin Province

address: No. 1 Xinmin Street

institute: the First Hospital of Jilin University

summary: Interferon-α (IFNα) plays a key role in innate immunity by inducing interferon-stimulated genes (ISGs). Beyond protein-coding ISGs, non-coding RNAs such as microRNAs are also modulated by IFNα. Here, we profiled differentially expressed microRNAs in HepG2 cells following IFNα stimulation, providing new insights into interferon signaling and antiviral regulation.

overall_design: RNA sequencing of HepG2 hepatocellular carcinoma cells treated with IFNα (20 ng/mL) for 0, 3, 8, and 24 hours.

first: Guangyun

last: Tan


title: Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP

city: Copenhagen

first: Mariia

last: Metelova

address: Blegdamsvej 3b

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: Copenhagen University

summary: The regulation of cell-type-specific transcription programs is a highly controlled and complex process that needs to be fully understood. The gene regulation is often influenced by distal regulatory elements and their interactions with promoters in three-dimensional space. Although proximity ligation techniques like Hi-C have revolutionized our understanding of genome organization, the genomic resolution for many of these methods is limited by both experimental and financial constraints. Here, we introduce Micro-C-ChIP to provide extremely high-resolution views of chromosome architecture at genomic loci marked by specific covalent histone modifications. This is achieved by affinity isolation of specific chromatin states in order to target chromosome folding libraries to focus on chromatin domains (regulatory elements, heterochromatin, etc.) of interest, yielding extremely high sequencing depth at these loci. We applied Micro-C-ChIP to mouse embryonic stem cells (mESC) and hTERT-immortalized human retinal epithelial cells (hTERT-RPE1), revealing architectural features of genome organization with comparable or higher resolution than Micro-C datasets sequenced to 10X higher depth. In particular, we discovered extensive promoter-promoter networks in both cell types and characterized the specific architecture of bivalently bookmarked promoters in mESC. Together, these data highlight Micro-C-ChIP as a cost-effective approach to exploring the landscape of genome folding at extraordinarily high resolution.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Micro-C-ChIP was performed against H3K4me3 and H3K27me3 in two cell types, mESC and hTERT-RPE1. Each condition (histone marks and cell types) has two biological replicates.The replicates for each condition were merged and converted to mcool format.

first: Nils

last: Krietenstein


title: Base-resolution profiling of 5-glyceryl-methylcytosine in Chlamydomonas reinhardtii via deaminase-assisted sequencing [RNA-Seq]

first: Fanchen

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

summary: 5gmC (5-glyceryl-methylcytosine), a vitamin C-derived hypermodified base, has been identified in the genome of Chlamydomonas reinhardtii. However, the global distribution of 5gmC and its role as an epigenetic mark remain poorly understood. In this study, we employed a DNA deaminase to distinguish 5gmC from 5mC (5-methylcytosine) and cytosines, enabling precise profiling of 5gmC across the genome. This deaminase-assisted sequencing (DEA-seq) demonstrates superior performance compared to the previously proposed TET-coupled bisulfite sequencing. Using both methods, we identified numerous confident 5gmC sites. Unlike 5mC, which predominantly occurs at CpG sites, 5gmC is preferentially located in CHH contexts. Remarkably, over half of 5gmC sites are mutually exclusive from 5mC, suggesting a role in active DNA demethylation. Additionally, 5gmC is enriched within introns, contrasting with the more extensive localization of 5mC in intergenic and promoter regions. Importantly, 5gmC levels are positively correlated with transcription, while 5mC typically exhibits an inverse relationship with gene expression, consistent with the enrichment of 5mC but loss of 5gmC at repressive H3K9me1 sites. Collectively, these findings suggest that 5gmC is not only an intermediate for active DNA demethylation but also functions as a stable epigenetic mark, potentially influencing transcriptional regulation independently of 5mC.

overall_design: RNA-seq of C. reinhardtii strains (CC125, CC5325 and CC5325KO).

first: Baodan

last: He

first: Zixin

first: Xuan

last: Deng

first: Tong

last: Ge

first: Hui

last: Chen

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Guoliang

last: Xu

first: Kaiyao

last: Huang

first: Jianhuang

last: Xue


title: Lysosomal exocytosis by macrophages as a druggable mechanism for anti-inflammatory clearance of dead adipocytes in adipose tissue

status: Public on Sep 03 2025

city: Leipzig

first: Raphaela

last: Wehr

state: Saxony

address: Liebigstraße

department: Institute of Anatomy

institute: Leipzig University

summary: The clearance of dead adipocytes in adipose tissue (AT) poses a major challenge due to their large size, which exceeds the phagocytic capacity of macrophages and prevents classical, anti-inflammatory efferocytosis. Instead, adipose tissue macrophages (ATMs) accumulate around dying adipocytes, forming crown-like structures (CLS), and engage in lysosomal exocytosis – the extracellular degradation of adipocytes. In this study, we used an ex vivo explant model of murine epididymal white AT, cultured over seven days to investigate pharmacological strategies that modulate lysosomal exocytosis. We observed a progressive increase in CLS formation, secretion of the lysosomal enzymes ß-Hexosaminidase A (HEXA) and lysosomal acid lipase (LAL), and surface abundance of LAMP1 and LAMP2, confirming ATMs as key mediators of this process. Notably, activation of lysosomal exocytosis with the mTOR inhibitor Rapamycin enhanced adipocyte clearance and significantly reduced inflammatory ATM abundance and TNF-α secretion. Bulk RNA sequencing of ATMs revealed a highly significant impact of Rapamyin on ATM proliferation.  In contrast, inhibition of lysosomal exocytosis with PIKfyve inhibitor Apilimod or targeted inhibition of LAL using Lalistat-2 disrupted lysosomal function and promoted a pro-inflammatory ATM phenotype. Our findings highlight lysosomal exocytosis as a critical pathway for the resolution of dead adipocytes and the regulation of inflammation in adipose tissue. Pharmacological enhancement of this process may represent a promising therapeutic approach to attenuate inflammation in AT and its metabolic consequences, including insulin resistance and type 2 diabetes.

overall_design: After sacrificing the mice, the rostral eWAT was dissected under sterile conditions and cut into small pieces (explants) of ≈ 1 mm3 (10 mg per explant) in PBS. Five AT explants per well were transferred to six-well plates prepared with 1 ml cell culture medium: RPMI 1640 with 10 % fetal bovine serum and 1 % antibiotics (100 U/ml penicillin and streptomycin). Explants were over casted with cell culture inserts and cultured at 37 °C with 5 % CO2 and 21 % O2 for seven days. On day one of AT explant culture, 100 µl treatment (Rapamycin 0.5 µM or Apilimod 0.5 µM or Lalistat 10 µM or DMSO-control 0.5%) solution was added in each well. Treated AT explants were digested using collagenase. SVF was resuspended in staining buffer and the Fc-receptors blocked by anti CD16/32 (1:100) for 10 min on ice. After centrifugation (300 g, 5 min, 4 °C, slow deceleration) cells were stained with labeled F4/80 antibody (1:200) on ice for 20 min, centrifugated (300 g, 5 min, 4 °C, slow deceleration), resuspended in staining buffer. Living, F4/80+ cells were sorted (~50,000 cells per sample) using a BD FACSAria SORP and frozen at −80 °C in TRIzol. RNA isolation and purification was performed using RNeasy Micro Kit by Quiagen. RNA sequencing and analysis was performed at Leipzig University’s Core Unit ‘DNA Technologien’. RNA extraction and library preparation was performed with a sequencing depth of 10 million reads/sample. Results were then analyzed using the DESeq2 package on Galaxy2. Differentially expressed genes (DEG) were considered as significant with a p-adj. value < 0.01 and a log2(fold change) > 0.5 or < -0.5. Gene set enrichment analysis was performed with datasets from the DAVID Database. For each condition, AT from 8 animals was pooled in groups of two, so that 4 samples were analyzed for each treatment.

first: Andreas

last: Lindhorst

first: Lilli

last: Arndt

first: Martin

last: Krueger

first: Nora

last: Raulien

last: Gericke


title: RNA-seq of primary cardiomyocytes under ischemia-reperfusion injury reveals altered expression in DNA damage repair genes including Xrcc6

status: Public on Sep 04 2025

city: Xiamen

first: Hongwen

last: Xiao

state: Fujian

address: No. 1999, Guankou Middle Road, Jimei District

department: Department of Basic Medicine

institute: Xiamen Medical College

summary: To investigate the molecular response of cardiomyocytes to ischemia-reperfusion (I/R) injury, we established an in vitro I/R model using primary neonatal mouse cardiomyocytes. Oxidative stress was simulated by treating the cells with 100 μM hydrogen peroxide (H₂O₂) for 24 hours, followed by a 24-hour recovery period in complete medium to mimic the ischemia and reperfusion phases, respectively. Bulk RNA sequencing was performed on both control (n = 3) and I/R-treated (n = 4) cardiomyocytes. Transcriptomic profiling identified differentially expressed genes and enriched pathways associated with oxidative stress response, DNA damage repair, and regulation of cell death. This dataset provides valuable insights into the molecular mechanisms underlying myocardial I/R injury and may help identify potential therapeutic targets.

overall_design: Primary cardiomyocytes were isolated from 1–3-day-old C57BL/6 neonatal mice and cultured under standard conditions. The ischemia-reperfusion (I/R) injury model was induced in vitro using 100 μM H₂O₂ in serum-free medium for 24 hours to simulate ischemia, followed by replacement with normal culture medium for another 24 hours to mimic reperfusion. RNA was extracted from untreated control (n=3) and I/R-injured(n=4) cells, and RNA-seq libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit. Sequencing was performed on the Illumina NovaSeq 6000 platform. Differential expression and pathway analyses were conducted to identify genes associated with oxidative stress, DNA damage, and potential drug targets.

first: Yijie

last: He

first: Jin

last: Li

first: Linlong

last: Guo

first: Mu

first: Haiqing

last: Pan

first: Zhanqing

first: Hua

last: Tian

first: Huan

last: Yu

first: Yuhong

last: Zhou


title: A spatial transcriptomics dataset of the endometrium from repeated implantation failure patients

city: Beijing

first: Peng

last: Wang

address: No.5 Ankang Hutong, Deshengmenwai, Xicheng District

institute: Beijing Anding Hospital affiliated to Capital Medical University

summary: Repeated implantation failure (RIF) presents a significant challenge in vitro fertilization (IVF) treatment, and abnormalities in the endometrium often play a crucial role in RIF. To enhance and deepen our understanding of tissue context in the endometrium underlying RIF, we applied spatial transcriptomics (ST) sequencing using the 10x Visium platform to 8 endometrial tissues from 4 normal individuals (CTR) and 4 RIF patients during the mid-luteal phase in this study. We achieved 10131 high-quality spots, with a median detected gene number was 3156. Seven distinct cellular niches (Niche 1-7) with specific characteristics were identified in our data. Deconvolution of ST data was performed by integrating with a public single-cell RNA (scRNA) dataset, and it was found that unciliated Epithelia were the dominant components in our data. To the best of our knowledge, this is the first spatial transcriptomics atlas of endometrial tissue in normal and RIF conditions, and the spatial data can provide a valuable source for further studies investigating the RIF mechanism.

overall_design: Fresh endometrial tissues from 4 normal (named CTR) and 4 RIF samples were processed by 10x Visium Spatial Transcriptomics Sequencing. The CTR group (CTR1-CTR4) comprised non-smoking subjects aged 25, 24, 32, and 31 years, with corresponding BMIs of 18.14, 20.25, 24.37, and 20.32 kg/m². The RIF group (RIF1-RIF4) consisted of non-smoking subjects aged 31, 33, 25, and 29 years, with BMIs of 22.18, 24.47, 21.64, and 20.35 kg/m². The CTR group reported no previous embryo transfers. In the RIF group, RIF1, RIF3, and RIF4 had undergone 3 prior transfers of good-quality embryos, while RIF2 had experienced 5. Regarding obstetric history, CTR1 and CTR2 were primiparous, while CTR3 and CTR4 were multiparous. All RIF subjects were nulliparous. All participants were confirmed free of uterine pathologies (including endometriosis and adenomyosis), endocrine, metabolic, auto-immune diseases and infection. Endometrial samples were collected via Pipelle biopsy from the uterine fundus and upper cavity at 7 days after the Luteinizing Hormone (LH) surge (LH + 7).


title: PRDM16 reduces cellular senescence by upregulating GSTM1

status: Public on Sep 02 2025

city: Wuhan

first: Yuting

last: Zhu

state: Hubei

address: 1277 Jiefang Avenue

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Cellular senescence is a hallmark of aging and the accumulation of senescent cells (SnCs) accelerates the aging process, contributing to aging-related organ disorders. The PRDF1 and RIZ1 homology domain (PRDM) protein exhibits robust transcriptional regulatory activities and governs a wide range of biological processes. However, its roles in cellular senescence remain unclear. Here, we demonstrated that PRDM16, a member of the PRDM protein family, decreased significantly in multiple organs of aged mice compared to young mice. Global Prdm16 deletion contributed to cellular senescence in various organs, including the kidneys, heart, lungs, hippocampus, stomach, and gut, leading to accelerated aging-related organ injury. Furthermore, tubular-specific Prdm16 deletion aggravated irradiation-induced kidney aging and aging-related kidney diseases in irradiated mice subjected to ischemia-reperfusion surgery. Exogenous PRDM16 gene delivery by lentivirus effectively attenuated cellular senescence in vitro and in vivo. Mechanistically, PRDM16 improved glutathione metabolism and inhibited oxidative DNA damage, which is a driving force of senescence. Specifically, PRDM16 upregulated the transcription of glutathione S-transferase mu 1 (GSTM1) by binding to its promoter region. Transfection with GSTM1 reversed PRDM16 deficiency-induced cellular senescence and kidney aging. Collectively, our results provide a potential target for the investigation of anti-aging therapies.

overall_design: The renal cortex of 9-month-old wild type (WT) and Prdm16 global knockout (Prdm16 ko) mice were isolated and analyzed using single-cell RNA sequencing.

first: Qian

last: Yuan

first: Chun

last: Zhang


title: 2B4 Co-Stimulation and Dasatinib Modulation  Enhance Anti-CD19 CAR-NK Cell Cytotoxicity

city: Ribeirão Preto

first: Matheus

middle: Henrique

last: dos Santos

state: SP

address: R. Ten. Catão Roxo, 2501

department: Oncology

country: Brazil

institute: University of Sao Paulo

summary: Chimeric Antigen Receptor (CAR)-cell-based therapies have shown remarkable achievements in cancer treatment, especially for hematological malignancies. In CAR-T cells, the costimulatory[P1]  domain is a key factor that significantly affects their therapeutic success. However, the effects of different costimulatory domains on the activation and performance of CAR-natural killer (CAR-NK) cells have not been sufficiently studied. We designed novel CAR constructs incorporating NK-specific costimulatory domains, such as 2B4 (CD244) and DAP12, to enhance CAR NK functionality. We evaluated their efficacy using in vitro cytotoxicity assays, cytokine profiling, and in vivo tumor models. We further investigated dasatinib, a tyrosine kinase inhibitor, as a pharmacological modulator of CAR NK cell activity. Short-term dasatinib exposure temporarily and reversibly suppressed CAR-NK activity yet enhanced function upon withdrawal. Accordingly, 2B4-DAP12 CAR-NK cells demonstrated superior tumor control and survival compared to conventional 4-1BBζ CAR-NK cells in vivo following dasatinib pretreatment. Our findings highlight that NK-optimized co-stimulation (2B4-DAP12) with reversible dasatinib pharmacological control synergistically enhanced CAR-NK cytotoxic function, providing an innovative strategy for next-generation cellular therapies.

overall_design: The cells were then co-culture against CD19+positive Nalm-6 cells for 4 hours. After co-culture, cells were magnetically separated and the RNA of CAR-NK cells were purified for differencial gene expression analisys.

first: Virgínia

last: Picanço Castro


title: FGF1-FGFR2 axis regulated by nuclear receptor RORγ represents an effective strategy in intrahepatic cholangiocarcinoma

first: Zhanfeng

last: Gu

state: Guangzhou

address: No. 183, Zhongshan Avenue West

department: Department of Hepatobiliary surgery

institute: The Third Affiliated Hospital of Southern Medical University

summary: Intrahepatic cholangiocarcinoma (iCCA) is a highly aggressive malignancy with limited therapeutic options. Although targeted therapies like pemigatinib provide partial clinical benefits, acquired resistance remains a significant challenge. Through integrative bioinformatics analysis of public datasets and immunohistochemical validation, we identified the retinoid-related orphan receptor gamma (RORγ) as markedly upregulated in iCCA. Genetic silencing and pharmacological inhibition of RORγ (GSK805/XY101) suppressed proliferation, induced apoptosis in vitro, and significantly reduced xenograft tumor growth in vivo. Mechanistically, RORγ promoted fibroblast growth factor receptor 2 (FGFR2) signaling via two complementary mechanisms: direct transcriptional activation of FGFR2 and induction of fibroblast growth factor 1 (FGF1) expression and secretion, which in turn activated FGFR2. Inhibition of RORγ markedly decreased FGF1 levels in conditioned media, whereas exogenous FGF1 restored tumor growth. Notably, RORγ antagonists synergized with pemigatinib to overcome resistance in pemigatinib-refractory models. Collectively, these findings identify the RORγ-FGF1-FGFR2 axis as a critical oncogenic driver in iCCA and highlight RORγ inhibition as a promising therapeutic strategy to suppress tumor progression and enhance sensitivity to FGFR inhibitors.

overall_design: HUCCT-1 cells were treated with vehicle, XY101 (5 µM) for 48 hours. Total RNA was extracted, and RNA-seq libraries were constructed using Illumina TruSeq Kit. RNA sequencing (RNA-seq) was performed by Beijing Genomics Institute (BGI, Shenzhen, China). Briefly, poly(A)⁺ mRNA was enriched using oligo(dT) magnetic beads. cDNA was synthesized under high-temperature conditions and purified by the kit. Sequencing was carried out on the BGISEQ platform. The resulting reads were aligned to the reference human genome assembly (GRCh37/hg19) using BWA and Bowtie 2. Gene expression levels were quantified from the RNA-seq data using RSEM, and a heatmap was subsequently generated to visualize the expression profiles.

first: Xiaojuan

first: Hong

first: Junhua

first: Zhaorong

last: Huang

first: Dongyue

first: Zhenhua

first: Yechun

last: Zeng

first: Guodi

last: Cai

first: Huizi

last: Sun

first: Jun

last: Zheng

first: Yichu

last: Nie

first: Qingwen

first: Haolong

first: Franky Leung

last: Chan

first: Junjian

first: Jianwei

first: Yingfang

last: Fan


title: Genome-wide inter-chromosomal contacts of rDNA units detected by 4C procedure in human Mel Z melanoma cells.

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: 4C-rDNA procedure was used for analysis of whole-genomic inter-chromosomal contacts of rDNA units in human Mel Z melanoma cells grown either on the plastic or Matrigel.

overall_design: Analysis of rDNA genome-wide contacts in Mel Z melanoma cells using 4C approach.

first: Yuri

middle: V

last: Kravatsky


title: Base-resolution profiling of 5-glyceryl-methylcytosine in Chlamydomonas reinhardtii via deaminase-assisted sequencing [Bisulfite-Seq]

city: Shanghai

first: Fanchen

last: Wang

type: Methylation profiling by high throughput sequencing

overall_design: WGBS of 5mC (BS) and 5gmC (DEA/TET-BS) in the C. reinhardtii strains (CC125, CC5325 and CC5325KO).

first: Baodan

last: He

first: Zixin

first: Xuan

last: Deng

first: Tong

last: Ge

first: Hui

last: Chen

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Guoliang

last: Xu

first: Kaiyao

first: Jianhuang

last: Xue


title: RNA-seq of Epithelial cells treated with siRNA and irradiation or cytokine treatment

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon GU

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences

summary: RNA-seq of lung epithelial cells with EGFR or ErbB deletion, harvested 3 days after irradiation or cytokine treatment. RNA was extracted, libraries were prepared using a stranded RNA-seq protocol, and sequencing was performed on the Illumina platform.

overall_design: RNA-seq analysis of lung epithelial cells with EGFR or Erbb3 deletion, 3 days after irradiation or cytokine treatment.

first: Ji-Hee

last: Kim

first: Seo-Hyun

last: Choi

first: Jae-Kyung

last: Nam

first: Haeng Ran

last: Seo

first: Min-sik

last: Park

first: Inhee

first: Jeeyong


title: RNA-seq of mouse lung tissue after irradiation

summary: High-dose ionizing radiation-induced pulmonary injury. To characterize these changes, we performed RNA sequencing (RNA-seq) on lung tissues isolated from mice exposed to 90 Gy irradiation. Samples were collected at 8, 11, and 14 days post-irradiation, and non-irratied controls. RNA was extracted and libraries were prepared using a stranded RNA-seq protocol, followed by sequencing on the Illumina platform. 해석

overall_design: RNA sequencing (RNA-seq) analysis conducted on selectively sampled lung tissues exclusively from irradiated areas during the 8 to 14-d period postirradiation