title: Investigating the molecular mechanisms underlying the therapeutic effects of Detumescence Analgesic Plaster on knee osteoarthritis through RNA sequencing technology

status: Public on Sep 01 2025

first: Chunxia

middle: ZL

last: Li

address: nstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiao Street, Dongzhimennei, Dongcheng District, Beijing, China

department: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary: In this study, transcriptome sequencing was used to study the mechanism of Detumescence Analgesic Plaster (DAP) in the treatment of Knee Osteoarthritis. We identified the key pathways and key genes for the treatment of Knee Osteoarthritis by transcriptome sequencing of rat cartilage issue, and completed qPCR validation. The results showed that genes such as NDUFA5, NDUFA6, NDUFS6, and COX6A2 were enriched in the oxidative phosphorylation signaling pathway. DAP intervention significantly increased the mRNA levels of NDUFA5, NDUFA6, NDUFS6, COX6A2, and MYL3 in rat cartilage tissue, alleviating damage and injury. This study provides a new idea for the molecular mechanism of Detumescence Analgesic Plaster in the treatment of KOA.

overall_design: Male SD rats without specific pathogen (SPF) were randomly divided into three groups: control group, KOA model group, and anti-inflammatory and analgesic patch group (0.1470 g/kg), with 12 animals in each group. According to previous literature, a KOA model was established in rats. 0.1 mL of a prepared 4% papain solution was extracted and injected into the lateral side of the patellar ligament on days 1, 4, and 7 of the modeling process. The rats were then fed normally and treated externally for 5 weeks. Differential expression genes (DEGs) were analyzed using DESeq2, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify important pathways. In addition, gene set enrichment analysis (GSEA) was used to identify the key signaling pathways of Xiaozhong Zhitong Tie, STRING functional protein association network analysis was used to analyze the interaction network and weighted gene co expression network (WGCN) analysis, and CytoHubba topology was used to screen DAP candidate targets targeting KOA. We conducted qPCR experiments on 5 key core genes and confirmed the accuracy of the analysis results.

first: Weijie

first: Yue

last: Yin

first: Xiaomei

last: Xiang

first: Lu

last: Fu

first: Ping

last: Wang

first: Yanqiong

first: Haiyu

last: Xu


title: MEK5/ERK5 inhibition sensitizes NRAS-mutant melanoma to MAPK-targeted therapy by preventing Cyclin D/CDK4-mediated G1/S progression

city: Wuerzburg

first: Rupesh

last: Paudel

state: Bavaria

address: Josef-Schneider Straße 2

department: Department of Dermatology, Venerology und Allergology

country: Germany

institute: University Hospital Wuerzburg

type: Expression profiling by high throughput sequencing

summary: Despite the advent of immune-oncological therapies, patients with advanced NRAS-mutant melanoma still have a significantly worse prognosis than their BRAF-mutant counterparts. This is mainly due to a high propensity for resistance to available therapies targeting the RAS/RAF/MEK/ERK mitogen-activated protein kinase (MAPK) pathway (MAPKi). Preclinical studies and mouse models have implicated the stress-activated MEK5/ERK5 MAPK cascade as a major resistance pathway activated by MAPKi-based targeted therapy in NRAS-mutant melanoma. Accordingly, MAPKi/ERK5i co-inhibition was capable of triggering a sustained cell cycle arrest in NRAS-mutant melanoma cells, but the key mediator(s) of its vigorous anti-proliferative effect remain elusive. Here, we further investigated the mechanism of MAPKi/ERK5i-induced cell cycle arrest in NRAS-mutant melanoma cells using both genetic methods and pharmacological inhibitors. Transcriptome analysis of human NRAS-mutant melanoma cells established that MAPKi/ERK5i-induced a near-complete shutdown of the mitotic machinery as consequence of a sustained G1 cell cycle arrest. This arrest was not only observed in diverse treatment-naïve melanoma cells but could also be induced in cells that already had developed resistance to therapeutic MEK inhibition (MEKi) and was accompanied by suppression of Cyclin D1 and E2F-mediated gene expression. Forced expression of Cyclin D1 and its effector kinase CDK4 restored cell cycle progression and mitotic gene expression in NRAS-mutant melanoma cells exposed to MEKi/ERK5i, implying Cyclin D/CDK4 activity as major target of combined MEKi/ERK5i. These findings suggest Cyclin D/CDK4 dependency as a major vulnerability of NRAS-mutant melanoma that could effectively be targeted by combined MAPKi/ERK5i.

overall_design: NRAS-mutant melanoma cell line FM79 were seeded in triplicate and transfected with either scrambled siRNA or siRNA against MEK5. The following day, siRNA-transfected cells were either mock-treated or treated with 5 nM Trametinib for 48 hours prior to lysis and RNA extraction. Total RNA was used to perform RNA-seq experiment.

first: Simon

last: Goller

first: Felix

last: Deutzmann

first: Alina

last: Gillitzer

first: Katharina

last: Meder

first: Andrea

last: Knorz

first: David

last: Schrama

first: Matthias

last: Goebeler

first: Marc

last: Schmidt


title: Similarities and Differences in the Intestinal Actions of Metformin and Imeglimin

city: Kobe

first: Kenji

last: Sugawara

state: Please Select

address: 7-5-1 Kusunoki-cho, Chuo-ku

country: Japan

institute: Kobe university graduate school of medicine

summary: We investigated the intestinal actions of metformin and imeglimin by transcriptomic profiling. Bulk RNA-seq was performed on intestinal tissues from C57BL/6J mice after single or chronic drug administration, and single-cell RNA-seq was conducted on colon samples after chronic treatment.

overall_design:
Bulk RNA-seq: Male C57BL/6J mice received (i) a single oral dose of metformin or imeglimin (600 mg/kg) with colon harvested at 6 h, or (ii) chronic exposure via drinking water (3 mg/mL) for 4 weeks, with proximal/middle/distal small intestine and colon collected.
Single-cell RNA-seq: Colonic cells from mice treated with metformin or imeglimin in drinking water for 12 weeks were dissociated and processed with 10x Genomics Chromium Fixed RNA Profiling; sequencing on NovaSeq 6000.


title: Master TFs in LUSC

status: Public on Sep 02 2025

city: Xi'an

first: Yihui

last: Zhang

state: Shanxi

address: No.229 Taibai North Road

country: China

institute: Northwest University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Fibrillin-Related Proteins Control Calcium Homeostasis in Dystrophic Muscle Across Species

city: Normal

first: Andres

last: Vidal-Gadea

state: Illinois

address: 125 S Fell Ave

department: School of Biological Sciences

country: USA

institute: Illinois State University

summary: Duchenne muscular dystrophy (DMD) involves progressive muscle degeneration associated with calcium dysregulation, but the mechanisms linking extracellular matrix (ECM) integrity to calcium homeostasis remain unclear. We investigated whether MUA-3, a fibrillin-related ECM protein in Caenorhabditis elegans, contributes to calcium regulation in dystrophic muscle. Using fluorescent calcium imaging in transgenic worms expressing muscle-specific GCaMP2, we found that downregulating mua-3 selectively elevated resting calcium levels in healthy muscle but had no effect in dystrophic (dys-1) muscle, suggesting impaired MUA-3 function in dystrophy. Despite altered calcium dynamics, mua-3 downregulation did not affect locomotor function. In human dystrophic myoblasts, we observed significantly elevated sarcoplasmic calcium levels concurrent with substantial downregulation of fibrillin genes FBN1/FBN2. These findings demonstrate that fibrillin-related proteins regulate calcium homeostasis across species, suggesting that ECM integrity directly contributes to cellular calcium control in muscle. This work identifies a conserved mechanism linking extracellular matrix stability to intracellular calcium regulation and suggests that targeting ECM-calcium coupling may offer new therapeutic approaches for muscular dystrophy.

overall_design: RNA Seq profiling of undifferentiated healthy and dystrophic human myoblasts

first: Damiano

last: Marchiafava


title: RNASeq analysis of eosinophils with IL33 or (and) SID26681509

city: Hangzhou

first: Yinling

last: Han

address: Jiefang Road

institute: Key Laboratory of Respiratory Disease of Zhejiang Province

summary: Eosinophils are the predominant immune cells implicated in asthma pathogenesis, highlighting the necessity for strategies to mitigate their effects. Previous studies have indicated a potential relationship between lysosomes and eosinophils, while the precise role of lysosomes in eosinophil activation during asthma remains insufficiently understood. Here, we used RNA-seq to analyze transcriptomic expression difference between IL33 or (and) SID26681509-stimulated eosinophils to find out what genes involved in the regulation of inflammation.

overall_design: To analyze transcriptomic expression difference between IL33 or (and) SID26681509-stimulated eosinophils to find out what genes involved in the regulation of inflammation.


title: Assessing T-Cell Profile Shifts via IL-23 Inhibition by Guselkumab on Psoriasis.

city: Nagoya

first: Yoshifumi

last: Kanayama

address: 1 kawasumi, Mizuho-cho, Mizuho-ku

institute: Nagoya City University Graduate school of Medical Sciences

summary: Anti-IL-23 antibody therapies result in improvements to the underlying immunopathology of psoriasis. However, the dynamics of the immune profile after the administration of anti-IL-23 biologics, along with their association with treatment response, remain unclear investigation. We focused on guselkumab, an anti-IL-23p19 antibody, and performed a comprehensive analysis of immune cells, serum inflammatory molecules, and transcriptomics of CD4+ T cells, aiming to identify disease-modifying drug effects in psoriasis. A total of 24 biologic-naive patients were enrolled. Peripheral and skin lesional blood samples were collected at baseline and after treatment with guselkumab. We conducted FACS analysis of regulatory T cells (Tregs), resident memory T cells (TRMs), and dendritic cells, measured serum cytokine and chemokine levels, and examined gene expression changes using RNA-seq data for peripheral CD4+ T cells.

overall_design: RNA-seq of 1.0×10⁵ CD4 cells from peripheral blood before and at 4 and 12 weeks after Guselkumab administration.

first: Oki

last: Watanabe

first: Mai

last: Sakurai

first: Yuki

last: Enomoto

first: Aya

last: Yamamoto

first: Shunya

last: Mashiko

first: Yukako

last: Sugiura

first: Masahiko

last: Miyashiro

first: Junya

last: Masuda

first: Akimichi

last: Morita


title: Prenatal SMN-dependent defects in translation uncover a reversible primary ciliopathy in spinal muscular atrophy

city: Trento

first: Gabriella

last: Viero

address: Via Sommarive 18

department: Institute of Biophysics

country: Italy

institute: CNR

summary: Spinal muscular atrophy (SMA) is a neuromuscular disease caused by low levels of SMN protein resulting from mutations in the SMN1 gene. Several therapeutic approaches capable of boosting SMN are now approved for use in human patients, delivering remarkable improvements in lifespan and symptom severity. However, new and unexpected phenotypes are being reported in treated SMA patients, including growing evidence for significant neurodevelopmental comorbidities in some individuals, indicative of alterations in brain development. Here, using a mouse model of severe SMA, we reveal an underlying neurodevelopmental phenotype in SMA where prenatal SMN-dependent defects in translation drive a primary ciliopathy in the CNS. Cell proliferation was significantly reduced in the hippocampus of SMA mice at E14.5, accompanied by widespread perturbations in translation, disrupting genes associated with primary cilia. The density of primary cilia in vivo, as well as cilial length in vitro, was significantly decreased in prenatal SMA mice, revealing core morphological hallmarks of a primary ciliopathy. Prenatal transplacental therapeutic intervention with an SMN-restoring small molecule (Risdiplam) rescued primary cilia defects in SMA mouse embryos. We conclude that SMN protein is required for normal cellular and molecular development of the CNS, with low levels in SMA driving a primary ciliopathy. Early, systemic treatment with SMN-restoring therapies is likely to be required to target neurodevelopmental comorbidities.

overall_design: Ribosome profiling was obtained from control (Smn+/−; SMN2tg/0) and SMA Taiwanese mouse model (Smn−/−; SMN2tg/0, strain 005058) at embryonic day 14.5 from brain and spinal cord. Experiments were performed in biological triplicates for each tissue.

first: Federica

last: Genovese

first: Yu-Ting

last: Huang

first: Anna

last: Motyl

first: Martina

last: Paganin

first: Gaurav

last: Sharma

first: Ilaria

last: Signoria

first: Deborah

last: Donzel

first: Nicole

last: Lai

first: Marie

last: Pronot

first: Rachel

middle: A

last: Kline

first: Helena

last: Chaytow

first: Kimberley

middle: J

last: Morris

first: Kiterie

last: Faller

first: Thomas

middle: M

last: Wishart

first: Ewout

last: Groen

first: Michael

last: Cousin

middle: H

last: Gillingwater


title: The X-linked chromatin modifier SMC1A is deregulated in lupus female monocytes and promotes autoimmunity [RNA-Seq]

city: Heraklion

first: George

last: Bertsias

address: Andrea Kalokerinou 13

department: Medical School

country: Greece

institute: University of Crete

summary: Biological sex underlines the onset of autoimmunity yet the underlying molecular mechanisms remain ill-defined. Female susceptibility is prominent in systemic lupus erythematosus (SLE), an autoimmune disease of substantial burden. Herein we demonstrate that SMC1A, a subunit of the cohesin complex that escapes X-chromosome inactivation, exhibits female-biased expression in monocytes from SLE patients and those cultured under lupus-inducing stimulus. By altering SMC1A dosage, the expression of immune-related genes, particularly those responsive to lupus environment, was affected. Active enhancers of immune and inflammatory pathways showed widespread SMC1A redistribution in lupus-like monocytes, as revealed by integrated analysis of SMC1A binding, chromatin activity and accessibility. Our data support SMC1A as a sex-biased chromatin modifier that enhances inflammatory responses in lupus.

overall_design:
RNA-seq data from peripheral blood of 15 individuals in each of four groups -healthy male, healthy female and SLE male, SLE female- was analyzed to identify sexually differential gene expression in SLE patients compared to healthy controls. Some of these samples were previously published, with 20 of the total samples being analyzed for the first time in this study.
To investigate the role of SMC1A in gene transcription regulation in human monocytes during lupus-like inflammation, we silenced SMC1A in CD14+ monocytes isolated from blood of three healthy donors. The cells were treated  with IFNa and TNF for 18h and LPS for 3h and  RNA-seq was perfromed on cells from the following conditions: si_control unstimulated, si_control IFNa TNF LPS stimulated, si_smc1a unstimulated, si_smc1a IFNa TNF LPS stimulated.
Focusing on the whole blood-derived monocytes, we analyzed the transciptomic differences between monocytes from healthy donors and SLE patients by conducting RNA-seq on CD14+ monocytes isolated form the blood of 5 healthy donors and 6 SLE patients.
To delineate the sexually differential expressed genes in SLE monocytes, blood CD14+ monocytes were isolated from 10 male and 8 female patients with SLE, cultured with 10 ng/ml MCSF for 18 h and QuantSeq 3' mRNA sequencing was performed

first: Despoina

last: Kosmara

first: Sofia

last: Papanikolaou

first: Chrysoula

last: Stathopoulou

first: Giannis

last: Vatsellas

first: Aggelos

last: Banos

first: Prodromos

last: Sidiropoulos

first: Matthieu

middle: D

last: Lavigne

first: Dimitrios

last: Boumpas

first: Charalampos

last: Spilianakis

first: Dimitris

last: Konstantopoulos

first: Christoforos

last: Nikolaou


title: Master TFs bind SOEs to drive tumorigenesis in LUSC cells [ChIP-seq]

first: Yihui

last: Zhang

summary: These SOEs were highly enriched for  H3K27ac signals in H520/HCC95 cells. Binding of key TFs, also known as mater regulators, is usually enriched in cell fate determinant or disease-specific cis-regulatory elements, such as super-enhancers.To find out which TFs were essential for the tumorigenesis of LUSC, sequence motif enrichment analysis was performed in SOE using all CDE as background. As expected, the well-established master TFs of LUSC, i.e., SOX2 and TP63, exhibited the highest enrichment of binding sites among all tested TFs .To confirm their binding in SOEs, we performed ChIP-seq for these factors, including p63, SOX2, GRHL2 and KLF5, all of which exhibited significant and specific binding to most SOEs, compared to other non-SOE genomic regions.

overall_design: ChIP-seq of the H3K27ac in BEAS-2B, H520, HCC95, H226 cells and TP63, SOX2, GRHL2 and KLF5 in HCC95 cells.

first: Yongqiang

last: Ning

first: Jie

last: Wang


title: PPT1 is a negative regulator of STING signaling in cancer cells and its inhibition reactivates immune surveillance in cold tumors

city: Worcester

first: Emma

middle: V.

last: Watson

state: MA

address: AS7-1045 Albert Sherman Center, 368 Plantation St

department: Systems Biology

institute: UMass Chan Medical School

summary: Immunotherapy modalities have revolutionized cancer treatment for a number of metastatic and treatment-refractory tumor types. Still, many malignancies that are lacking in T cell infiltrates and immunologically “cold” fail to respond to these modalities. One approach to increase tumor immunogenicity has been to induce STING and downstream interferon signaling that is often dysregulated in “cold” tumors. Despite some early success of STING agonists in preclinical cancer models, these approaches have not been successful in the clinic due to poor tumor penetrance and systemic toxicities. Here we performed a genome-wide CRISPR screen to uncover novel therapeutic targets to activate STING expression in human tumors. We identified Palmitoyl Protein Thioesterase1 (PPT1) as a negative regulator of STING highly expressed in “cold” ovarian and prostate tumors. Genetic or pharmacological PPT1 suppression increased STING protein stability and its downstream activation of interferon and inflammatory cytokine signaling to enhance T cell migration. Treatment of preclinical prostate and ovarian cancer models expressing low levels of STING with the small molecule PPT1 inhibitor GNS561 enhanced STING expression and activation, leading to infiltration and activation of cytotoxic T cells that turned these tumors “hot” and reduced tumor growth, fibrosis, and dissemination without toxicity. Further analysis demonstrated that PPT1 is associated with reduced STING expression, CD8+ T cell numbers, overall survival, and immunotherapy outcomes in ovarian and prostate cancer patients. Thus, PPT1 inhibition may be a promising approach to activate STING and potentiate the effects of immunotherapy in “cold” tumors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq profiling of A1847, PC3, and MycCAP;p53KO cells treated with vehicle (DMSO) or 5 µM GNS561 for 24 hrs

first: Arshia

middle: N

last: Kaur

middle: V

first: Shreya

middle: R

last: Chowdhury

first: Marcus

last: Ruscetti


title: Co-mapping Clonal and Transcriptional Heterogeneity in Somatic Evolution via GoT-Multi.

status: Public on Sep 03 2025

city: New York

first: Anna

middle: S.

last: Nam

state: New York

address: Weiss Research Building, Floor 11

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

summary: Somatic evolution leads to clonal heterogeneity, which fuels cancer progression and therapy resistance. To decipher the consequences of clonal heterogeneity, we require a method that deconvolutes complex clonal architectures and their downstream transcriptional states. We developed Genotyping of Transcriptomes for multiple targets and sample types (GoT-Multi), a high-throughput, formalin-fixed paraffin-embedded (FFPE) tissue-compatible single-cell multi-omics for co-detection of multiple somatic genotypes and whole transcriptomes. We developed an ensemble-based machine learning pipeline to optimize genotyping. We applied GoT-Multi to frozen or FFPE samples of Richter transformation, a progression of chronic lymphocytic leukemia to therapy-resistant large B cell lymphoma. GoT-Multi detected heterogeneous cancer cell states with genotypic data of 27 mutations, enabling clonal architecture reconstruction linked with their transcriptional programs. Distinct subclonal genotypes, including therapy-resistant mutations, converged on an inflammatory state. Other subclones displayed enhanced proliferation and/or MYC program. Thus, GoT-Multi revealed that distinct genotypic identities may converge on similar transcriptional states to mediate therapy resistance.

overall_design:
Single-cell GoT-Multi (based on transcriptome and genotype profiling from 10x Genomics Fixed RNA Profiling)

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

first: Minwoo

last: Pak

first: Mirca

middle: S

last: Saurty-Seerunghen

first: Kellie

last: Wise

first: Tsega-Ab

last: Abera

first: Chhiring

last: Lama

first: Neelang

last: Parghi

first: Ted

last: Kang

first: Xiaotian

last: Sun

first: Qi

last: Gao

first: Liming

last: Bao

first: Mikhail

last: Roshal

first: John

last: Allan

first: Richard

last: Furman

first: Luciano

middle: G

last: Martelotto


title: Studying the long-term adaptation of Haloferax volcanii to low salt conditions: transcriptomic and genetic analyses

city: Frankfurt am Main

first: Andreas

last: Borst

address: Max-von-Laue-Str. 9

institute: Goethe-Universität Frankfurt

summary: Archaea are well known for inhabiting areas of our planet that are usually hostile for any form of life, hence they are often termed as “extremophiles”. Although also found in common soil or the digestive tract of vertebrates, some species thrive on acidic or alkaline grounds, in submarine black smokers with temperatures surpassing 100°C or live in aquatic areas with a very high salinity.Haloferax volcanii is a halophilic and mesophilic archaeon that was first discovered in the 1930s and isolated from the hypersaline environment of the Dead Sea. Its optimal growth conditions are at 42 °C in around 2 M NaCl and complex nutrient medium, however it can also grow in different synthetic media and at a wide range of temperatures and NaCl concentrations. While NaCl concentrations up to 0.7 M inhibit growth in synthetic glucose media, a concentration of 0.9 M is sufficient to sustain growth at a reduced rate.Here we show for the first time a transcriptome-wide analysis of differential gene expression of cells grown under low salt condition. We cultivated cells at an optimal NaCl concentration of 2.1 M in glucose media and compared the expression profile of these to cells grown in 0.9 M NaCl after 26 and 68 h.

overall_design: differential gene expression profiles of the halophilic archaeon Haloferax volcanii should be analysed as response to low salt conditions in glucose medium (2.1 M vs 0.9 M NaCl) after a short (26 h) and prolonged (68 h) period of time. RNA-Seq was done in duplicates of 3 Samples (2.1 NaCl M after 26h; 0.9 M NaCl after 26h and 0.9 M NaCl after 68 h). Key player genes involved in low salt stress response (26h at 0.9 M NaCl) and low salt adaption (68h at 0.9 M NaCl) shluld be identified.


title: Non-cell-autonomous control of gastruloid development by the lncRNA T-UCstem1 through DKK1-dependent modulation of WNT signalling

city: Basel

first: Edoardo

last: Sozzi

address: Klingelbergstrasse 48

country: Switzerland

institute: ETH Zurich

summary: The role and the mechanisms of long non-coding RNA (lncRNAs) in early mammalian embryogenesis remain unclear; this is mostly due to the complexity of the regulatory mechanism of lncRNAs and the limited availability of early embryo samples. The emergence of stem cell-based models of early mammalian embryogenesis offers new opportunities to address these challenging questions. Here we use mouse gastruloids to investigate the role of an ultraconserved lncRNA, T-UCstem1, in the formation of the mammalian body plan. Combining morphological and immunofluorescence analysis with bulk and single cells transcriptomics, we provide unprecedented evidence that T-UCstem1 is a key regulator of gastruloid development and is required for the extension of the anteroposterior axis. Specifically, knock down of T-UCstem1 results in aberrant gastruloid development, which is characterized by altered spatiotemporal expression of the differentiation markers and persistence of pluripotency genes. Single-cell analysis reveals higher cellular heterogeneity in T-UCstem1 KD gastruloids. Notably, the presence of cell populations characterized by the co-expression of pluripotency and differentiation markers points to a key role of T-UCstem1 in establishment and maintenance of proper cellular identity. Mechanistically, we show that T-UCstem1 acts non-cell autonomously through Dickkopf-related protein 1 (DKK-1)-dependent modulation of WNT pathway. Our findings highlight a previously unexplored role for ultraconserved lncRNAs in gastruloid development and open the way for using gastruloids to dissect the functions of lncRNAs in early mammalian development.

overall_design: Bulk RNA seq of mouse gastruloids derived from KD for an ultraconserved lncRNA, T-UCstem1, vs Ctrl. 3 biological replicates per group, 1 time point (5days).

first: Alessandro

last: Fiorenzano

first: Arianna

last: Coppola

first: Annalisa

last: Fico


title: Retinol Binding Protein 4 reactivates latent HIV-1 via the JAK/STAT5 and JNK pathways

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

institute: Ulm University Medical Center

summary: Reactivation of the latent viral reservoirs is crucial for a cure of HIV/AIDS. However, current latency reversing agents are inefficient and the endogenous factors that have the potential to reactivate HIV in vivo remain poorly understood. To identify natural activators of latent HIV-1, we screened a comprehensive peptide/protein library derived from human hemofiltrate, representing the entire blood peptidome, using J-Lat cell lines harboring transcriptionally silent HIV-1 GFP reporter viruses.  Fractions potently reactivating HIV-1 from latency contained human Retinol Binding Protein 4 (RBP4), the carrier of retinol (vitamin A). We found that retinol-bound holo-RBP4 but not retinol-free apo-RBP4 strongly reactivates HIV-1 in a variety of latently infected T cell lines. Functional analysis revealed that this reactivation depends on the JAK/STAT5 and JNK pathways but does not require retinoic acid production. High levels of RBP4 were detected in plasma from both healthy individuals and people living with HIV-1. Physiological concentrations of RBP4 induced significant viral reactivation in latently infected cells from individuals on long-term antiretroviral therapy with undetectable viral loads. As a potent natural HIV-1 latency-reversing agent, RBP4 offers a novel approach to activating the latent reservoirs and bringing us closer to a cure.

overall_design: RNA-seq profiling of J-Lat HIV reporter cells expressing , clone 10.6 and 8.4, treated with either RBP4 for 48 hours of left untreated.

first: Chiara

last: Pastorio

first: Markus

last: Jaritz

first: Moritz

last: Gaidt

first: Frank

last: Kirchhoff


title: JARID2 Inhibition Reprograms Human Hematopoietic Progenitor Cells To Enhance Bone Marrow Transplantation

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

summary: Hematopoietic stem cell transplantation is a common treatment for many blood disorders. Umbilical cord blood (UCB) serves as a valuable source of hematopoietic stem and progenitor cells (HSPCs), particularly for patients lacking a matched donor. However, the limited number of repopulating cells in UCB units restricts its clinical utility. Here, we demonstrate that JARID2 knockdown, distinct from EZH2 loss, increases both the number and functionality of human UCB-derived HSPCs in vitro and in vivo. After ex vivo culture, these functionally enhanced HSPCs were identified as CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻. Mechanistically, JARID2 knockdown promotes a quiescent, long-term self-renewal gene expression program by upregulating STAT1 and MHC class II. Notably, it also confers HSC-like potential to multipotent progenitors (MPPs), enhancing their regenerative capacity. These findings support JARID2 inhibition as a safe and reversible strategy to expand functional HSPCs from UCB ex vivo, potentially increasing access to this life-saving therapy for a broader patient population.

overall_design: To investigate the molecular mechanisms underlying JARID2-KD–mediated HSPC expansion and functional enhancement, we transduced enriched human CD34⁺ cells from umbilical cord blood with shRenilla, shJARID2, or shEZH2, and sorted hCD34⁺ cells for CITE-seq after 8 days of ex vivo culture. Based on CITE-seq results and other functional assays, we further sorted CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells after 8 days of ex vivo culture for bulk RNA-seq and CUT&Tag or CUT&RUN analysis. For scRNA-seq analysis, we transplanted CD34⁺ cells transduced with shRenilla or shJARID2 into NSG mice and collected hCD34⁺ cells from the bone marrow 20 weeks post-transplantation.

first: Wentao

last: Han

first: Hassan

last: Bjeije

first: Hamza

last: Celik

first: Michael

last: Rettig

first: Nancy

last: Issa

first: Andrew

middle: L

last: Young

first: Yanan

last: Li

first: Infencia

last: Xavier Raj

first: Christine

last: Zhang

first: Aishwarya

last: Krishnan

first: Tyler

last: Parsons

first: Samantha

middle: C

last: Burkart

first: Jason

last: Arand

first: Wei

last: Yang

first: Jeffrey

last: Magee


title: Tripotent Lgr5 stem cells in the posterior tongue generate non-taste lingual, taste and salivary gland cells [scRNA-seq]

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

summary: The circumvallate papillae (CVP) and foliate papillae (FoP) of the posterior tongue contain taste buds in close proximity to specialized salivary glands, known as von Ebner and minor salivary glands, respectively. The developmental relationship between taste buds and these salivary glands remains largely unexplored. Lineage tracing studies in mice have revealed that Lgr5 marks taste bud stem cells. Here, we report single-cell RNA sequencing of the entire CVP and FoP of mice, yielding transcriptional profiles of cells from tongue surface epithelium, taste buds and the associated salivary glands. We unveiled a developmental trajectory in which taste buds, the associated salivary glands and the non-taste tongue surface epithelium originate from a common Lgr5+ cell. We describe long-term organoid culture conditions for these cells and confirm their tripotency at the clonal level in vitro. CVP and FoP harbor chemosensory units consisting of taste bud and salivary gland cells derived from the same parental Lgr5+ stem cell.

overall_design: Circumvallate papillae (n=20) and foliate papillae (n=40) were send for single-cell RNA seq. Lineage trajectory analysis revealed a potential bi/tripotent Lgr5+ stem cell in the posterior tongue. Subsequent scRNA-seq analysis of clonal cultures derived from a single Lgr5+ stem cell presented its tripotent nature. Next, in-vivo mulitcolour lineage tracing confirmed this phenomenon. Studying the cell fate decisions resulted in a putative role for Foxe1 in the lineage trajectory. Bulk RNA-sequencing of knock-out of Foxe1 in the posterior tongue organoids revealed an ablation of mature saliva markers and a more progenitor-like phenotype.

first: Laurens

last: Verweij

first: Seok-Young

last: Kim

first: Dimitrios

last: Laskaris

first: Lin

last: Lin

first: Femke

last: Ringnalda

first: Chris

last: Winkel

first: Jay

last: Slack

first: Karin

last: Sanders

first: Jacco

last: van Rheenen

first: Marc

last: van de Wetering

first: Hans

last: Clevers


title: Transcriptomic effects of INTS1 knockout in zebrafish larvae

city: Tel Aviv

first: Shir

last: Confino

address: Chaim Levanon St 55, Tel Aviv-Yafo

department: Neurobiology, Biochemistry and Biophysics

country: Israel

institute: Tel Aviv University

summary: Precise regulation of RNA polymerase II (RNAPII) is fundamental to transcriptional fidelity in eukaryotes. The Integrator complex, a conserved multi-subunit assembly, safeguards transcriptional integrity through its interaction with RNAPII, mediating transcription initiation, nascent RNA cleavage, and 3′ end processing. INTS1, the largest subunit of the Integrator complex, is critical for its function, and its mutations are linked to human neurodevelopmental disorders, yet, the underlying transcriptional effects remain poorly defined. Here, we characterize the global transcriptional effects of INTS1 deficiency in zebrafish. INTS1 loss leads to widespread gene expression changes, including of genes linked to hyperactivity and pathways associated with Attention-Deficit/Hyperactivity Disorder. We observe mutant-specific first intron retentions and transcript extensions. These findings underscore a central role for INTS1 in coordinating transcriptional regulation, and highlight the essential function of the Integrator complex in maintaining transcriptome integrity. Together, they offer insights into how INTS1 disruption may contribute to behavioral and physiological abnormalities.

overall_design: Global transcriptomic analysis of head pools from 120 hpf INTS1 knockout zebrafish larvae and their wild-type siblings


title: The X-linked chromatin modifier SMC1A is deregulated in lupus female monocytes and promotes autoimmunity [ChIP-Seq]

first: George

last: Bertsias

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for the cohesin complex member protein SMC1A and the histone modification H3K27ac in blood CD14+ monocytes unstimulated and stimulated with IFNa TNF (18h) and LPS  (1h)

first: Despoina

last: Kosmara

first: Sofia

last: Papanikolaou

first: Chrysoula

last: Stathopoulou

first: Giannis

last: Vatsellas

first: Aggelos

last: Banos

first: Prodromos

last: Sidiropoulos

first: Matthieu

last: Lavigne

last: Boumpas

first: Charalampos

last: Spilianakis

first: Dimitris

last: Konstantopoulos

first: Christoforos

last: Nikolaou


title: The novel tRF-23 promotes osteogenic differentiation of hBMSCs and protects against bone loss in ovariectomized mice

status: Public on Aug 31 2025

city: Jiujiang

first: Tao

last: Wang

address: No. 551, Qianjin East Road

institute: Jiujiang University

type: Non-coding RNA profiling by high throughput sequencing

summary: The pathogenesis of osteoporosis is closely related to the impaired human bone marrow-derived stromal cells (hBMSCs) osteogenic differentiation. No studies to date, however, have established whether tRNA-derived fragments (tRFs) can influence osteogenic differentiation of hBMSCs or the onset of osteoporosis. Here, tRF-23 was found to control hBMSC osteogenesis through its ability to target suppressor of cytokine signaling 1 (SOCS1) via the Janus kinase 2/signal transducer and activator of transcription 3(JAK2/STAT3) signaling pathway. tRF-23 was then further established as a potential target for efforts to protect against bone loss and marrow adipose tissue (MAT) accumulation in osteoporotic model mice, and its molecular mechanism was also verified in vivo. Together, these results suggest a model in which tRF-23 can protect against bone loss induced by ovariectomized (OVX) through the augmentation of hBMSC osteogenesis, providing a foundation for further characterizing the pathogenesis of osteoporosis and seeking new therapeutic targets for this disruptive condition.

overall_design: After using Trim Galore to remove any low-quality reads and adapter sequences, the remaining sequences 12-50 nucleotides long were aligned with miRBase (http://www.mirbase.org/). Known miRNAs were identified with BWA followed by the alignment of unmapped reads to rRNAs (https://rnacentral.org/). An in-house tRNA sequence database (using sequences from http://gtrnadb.ucsc.edu/ and https://cm.jefferson.edu/MINTbase/) was then employed for analyses of all other reads that were unmapped. Intronic sequences were initially removed, followed by the addition of CCA to the end of all tRNA sequences. Ultimately, 50 genomic nucleotides were added behind these CCA residues, and the resulting sequences were selected as possible tRFs, followed by classification with tRFdb (http://genome.bioch.virginia.edu/trfdb/) and MINTBase (https://cm.jefferson.edu/MINTbase/). Differentially expressed tRFs during osteogenesis (at days 0, 7, 14 and 21 of osteogenic differentiation) were identified with the EB-Seq algorithm based on the following criteria: fold change > 2 or < 0.5 and P < 0.05, FDR < 0.05. The miRanda and RNAhybrid tools were used to identify predicted targets of these tRFs of interest.

first: Haichun

last: Liao

first: Wen

last: Li

first: Lin

last: Xu

first: Chao

last: Zhao

first: Xingnuan

first: Jianjun

last: Xiong


title: Cross-species cellular mapping and humanization of Fcγ receptors to advance antibody modeling

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

summary: Fc receptors mediate the effector functions of therapeutic antibodies. Immunoglobulin G (IgG), the predominant antibody in circulation and clinical use, engages diverse Fc gamma (Fcγ) receptors that are expressed by multiple immune and structural cells. Here, we provide a comprehensive overview of Fcγ receptors and FcRn expression at both the transcriptomic and proteomic level in humans, macaques, and mice. We reveal species-specific differences in both Fcγ receptor diversity and cell-specific expression profile that compromise the translation of mouse and macaque preclinical models for antibody research. To overcome this, we generated a new mouse model in which human FcγRI (hCD64), FcγRIIA (hCD32A), FcγRIIB (hCD32B), FcγRIIIA (hCD16A), FcγRIIIB (hCD16B) is expressed under control of the relevant human promotors, replacing the murine counterparts (FcγRI, FcγRIIB, FcγRIII, and FcγRIV). Furthermore, to improve human antibody pharmacokinetics, murine FcRn was replaced by its human analog. We comprehensively mapped the expression of the knock-in receptors, and found that humanization led to much more faithful cell-specific Fcg receptor expression. We validated the functionality of these knock-in human receptors through in vitro and in vivo antibody-dependent cellular cytotoxicity, anaphylaxis and antigen presentation assays. This cross-species Fcγ receptor atlas and humanized mouse model with refined Fcg  receptor expression and antibody pharmacokinetics will improve the preclinical assessment of antibody-based therapeutics.

overall_design: We carried out single-cell RNA sequencing (BD Rhapsody platform; sequenced using NovaSeq6000) on magnetically cell enriched (MagniSort) and fluoresence-activated cell sorted (FACS; BD Symphony S6) splenocytes of C57BL/6J female mice

first: Karel

last: Van Damme

first: Victor

last: Bosteels

first: Clint

last: De Nolf

first: Bart

last: Lambrecht


title: Tripotent Lgr5 stem cells in the posterior tongue generate non-taste lingual, taste and salivary gland cells [Bulk RNA-seq]

first: Gijs

last: van Son

first: Laurens

last: Verweij

first: Seok-Young

last: Kim

first: Dimitrios

last: Laskaris

last: Lin

first: Femke

last: Ringnalda

first: Chris

last: Winkel

first: Jay

last: Slack

first: Karin

last: Sanders

first: Jacco

last: van Rheenen

first: Marc

last: van de Wetering

first: Hans

last: Clevers


title: RNA-Seq profiles of human prostate cancer PC3 cells with TTC3 knockdown.

city: Saint Petersburg

first: Ranjan

last: Perera

state: FL

address: 600 5th St S

department: Oncology Center

institute: Johns Hopkins All Childrens Hospital

summary: The TTC3 gene is located at 21q22.2, and its protein product functions as an E3 ubiquitin protein ligase, mediating the ubiquitination and subsequent degradation of phosphorylated Akt in the nucleus. TTC3 was reported to play a role in neuronal differentiation inhibition and asymmetric cell division in cancer cells. We found that silencing TTC3 can significantly suppress prostate cancer cell proliferation and growth in vitro and in vivo. To identify targets regulated by TTC3, we performed global gene expression profiling analysis in TTC3-silenced PC3 cells.

overall_design: Expression profiling by high throughput sequencing, using Illumina NextSeq 2000.

first: Menglang

last: Yuan

first: Kandarp

last: Joshi


title: Single Cell RNAseq of adult and stem cell derrived iris muscle

city: Kgs. Lyngby

first: Anne

middle: Zebitz

last: Eriksen

address: Produktions Torvet 423

department: Health Technology

country: Denmark

institute: Technical University of Denamrk

summary: We performed single-cell RNA sequencing (scRNAseq) on iris tissue from three adult human donors and human embryonic stem cell (hESC)-derived whole eye organoids, termed “SEAM,” using the 10X Genomics Chromium platform.  From the adult human datasets, we identified an iris muscle population based on the co-expression of PAX6 and smooth muscle proteins (ACTA2 and TAGLN). This dataset was further used to characterize the expression profile of the non-neuronal, crest-derived iris muscle.  Additionally, we differentiated hESCs into whole eye organoids (SEAM) and performed scRNAseq after 7 weeks of differentiation. In the organoids, we identified cell populations corresponding to most ocular cell types, spanning neurons, distal optic cup, periocular mesenchyme, and ocular surface epithelium. Notably, we identified iris muscle-like cells in the developing eye organoids.  We conducted an integrated analysis using the Seurat R package to compare the hESC-derived eye organoids with one of the adult donor irises (IRIS91 and SRAM48). This analysis revealed a shared iris muscle cluster containing cells from both datasets. The hESC-derived iris muscle represents a developing tissue with lower expression of mature muscle genes and higher expression of transcription factors, such as PAX6 and LHX2.  Human globes from donors aged 50–74 years were obtained within 24 hours postmortem from the Eye-Bank for Sight Restoration, NY, and Miracle in Sight, NC, with informed consent provided by the donors or their next of kin. This study was reviewed by the Icahn School of Medicine at Mount Sinai IRB oversight and deemed not to be human subject research. We received approval for use of H9 cell lines by WiCell.

overall_design:
This study involves single-cell RNA sequencing (scRNAseq) of two sample types: adult human iris tissue from three donors and human embryonic stem cell (hESC)-derived SEAM whole eye organoids collected at week 7 of differentiation.  Sample Preparation:  Frozen vials of freshly isolated adult human iris tissue and SEAM cultures were used. Cell viability was assessed using Trypan Blue staining, and only debris-free cell suspensions with >80% viability were processed. Approximately 10,000 cells were used as input for each sample. Library Preparation:  Cells were processed using the 10X Genomics Chromium Controller (v3.16) and Chromium Single Cell 3’ Library and Gel Bead Kit (v3.0). Gel beads in oil microdroplets (GEMs) were created to encapsulate single cells. Reverse transcription was performed inside GEMs to generate cDNA tagged with unique molecular indices (UMIs) and cell barcodes. GEMs were broken, and cDNA was amplified and quantified using an Agilent Bioanalyzer High Sensitivity chip and Qubit analysis (Thermo Fisher). Sequencing:  Libraries were sequenced on an Illumina NovaSeq 6000 platform using S4 flow cells (100 bp paired-end reads). Target sequencing depth was 50,000–100,000 reads per cell. Data Processing:  FASTQ files were generated using the Cell Ranger Single-Cell Software Suite (v3.1). Reads were aligned to the GRCh38 human reference genome. Filtered matrices of unique gene counts were produced for downstream analysis. Data Filtering and Normalization:  Low-quality cells (fewer than 500 unique genes) and potential doublets (more than 5,500 unique genes) were excluded. Final analysis included an average of 1,523 cells from adult human iris tissue and 6,039 cells from SEAM organoids. Data were normalized using a global-scaling method (LogNormalize) with a scale factor of 10,000. Analysis:  Principal component analysis (PCA) was performed, and clustering was conducted. Dimensionality reduction was visualized using Uniform Manifold Approximation and Projection (UMAP). Differential expression analysis was performed to identify cluster-specific genes, and heatmaps were generated to visualize the top 20 differentially expressed genes per cluster. Annotation and Enrichment:  Cluster annotation was based on manual curation of gene expression patterns and complemented with Enrichr gene set enrichment analysis (using the GO Biological Process 2018 database).

***************************************************************
Submitter states that missing raw files are due to file loss.
***************************************************************

first: Timothy

last: Blenkinsop

first: Bar

last: Markovoz

middle: Z


title: Nuclear compression-mediated DNA damage drives ATR-dependent Lamin expression and mouse ESC differentiation

city: Mumbai

first: Shamik

last: Sen

state: Maharashtra

address: Powai

department: Biosciences and Bioengineering

country: India

institute: IIT Bombay

summary: Embryonic stem cells (ESCs) which are susceptible to DNA damage depend on a robust and highly efficient DNA damage response (DDR) mechanism for their survival. However, the implications of physical force-mediated DNA damage on ESC fate remains unclear. Here we assessed the importance of DNA damage in ESC differentiation by culturing mouse ESCs (mESCs) on substrates of varying stiffness, which has been shown to induce stem cell differentiation. We show that stiffness-dependent mESC spreading induces DNA damage through nuclear compression that leads to loss of pluripotency, expression of Lamin A/C and germline markers. DNA damage and induction of Lamin A/C are observed in the presence of differentiating agents, as well as during mESC differentiation on cell derived matrices, identifying DNA damage as an early event in differentiation. Differentiation was also associated with reduction of DNA damage and activation of the DDR factor – ATR. While ATR is typically known to play roles in DDR pathway, its role during stiffness-mediated nuclear compression and mESC differentiation is unknown. Nuclear enrichment of activated ATR on stiff substrates and reduction of Lamin A/C expression due to ATR inhibition suggests that mESC differentiation is driven by nuclear compression-mediated DNA damage and involves ATR-dependent modulation of Lamin A/C.

overall_design: To probe the effect of stiffness mediated mechanoadaptation on Tg2A mouse embryonic stem cells (mESCs), we cultured mESCs on gels of varying stiffnesses (0.6 kpa, 4 kPa and 33 kpa) coated with fibronectin. RNA isolation of whole cell lysates was done at different timepoints (3hrs, 6 hrs, 24 hsr and 72 hrs) and compared with a pluripotent control which was cultured on gelatin coated dish in presence of LIF. A DNA damage positive control was used by treating the cells with etoposide (ETO) on 0.6 kPa for 24 hrs. Samples were pooled from 3 independent experiments and run as 2 replicates.

first: Tanusri

last: Roy

first: Sayak

last: Dhar

first: Niharika

last: Tiwary

first: Priya

last: Singh

first: Divya

middle: T

last: Sowpati

first: P

last: Shekar

first: Sushil

last: Kumar


title: Gene expression profile of CPT2-knockdown HCT116 colorectal cancer cells

city: Shenyang

first: Juan

last: Li

address: No.44 Xiaoheyan Road

institute: Liaoning Cancer Hospital & Institute

summary: CPT2 knockdown induced accumulation of glycerophospholipids and promoted CRC progression. We conducted transcriptomic sequencing of CPT2-knockdown HCT116 CRC cells to explore the underlying mechanism.

overall_design: HCT116 cells in the logarithmic growth phase were treated with either negative control siRNA (NC) or siCPT2 for 48 hours. The cells were collected, washed three times with PBS, and lysed with 1 mL of TRIzol for 5 minutes on ice. The samples were preserved on dry ice and sent to Biomarker Technologies for high-throughput sequencing.

first: Kuo


title: HNF4α contributes to hepatic CAR dysfunction in polymicrobial sepsis

city: Gent

first: Steven

last: Timmermans

institute: VIB-UGent

summary: Constitutive androstane receptor (CAR) is a xenobiotic nuclear receptor mainly expressed in the liver, where it regulates drug metabolism and energy homeostasis. CAR has emerged as a promising therapeutic target for diabetes, fatty liver disease, and alcoholic liver disease, but it has not been investigated in the context of sepsis. Here, we show that sepsis impairs CAR function in the liver, partly due to reduced transcription mediated by HNF4α, the key liver identity transcription factor, and partly due to decreased DNA binding, caused by chromatin remodelling, also mediated by HNF4α. This impairment leads to the downregulation of several genes involved in monocarboxylic acid, fatty acid, and xenobiotic metabolism, contributing to increased sepsis lethality, and is associated with an  elevated hepatic acute phase response. NCT protects against sepsis by enhancing HNF4α binding to the CAR promoter, thereby increasing both CAR transcription and activity.

overall_design: A total of four conditions were used: SHAM+CTRL, SHAM+TCPOBOP, CLP+CTRL and CLP+TCPOBOP, with 4 biological replicates each, for a total of 16 samples. Livers were isolated and processed for transcriptional profiling by RNA-seq

first: Céline

last: Van Dender

first: Claude

last: Libert


title: Anti-Müllerian Hormone Ameliorates Uterine DNA Damage Response and Prevents Pregnancy Complications in Doxorubicin-Treated Mice

city: Boston

first: Ngoc Minh Phuong

last: Nguyen

address: 55 Fruit st

department: Pediatric Surgical Research Laboratory

institute: Massachusetts General Hospital andHarvard Medical School

summary: Anti-Müllerian hormone (AMH) has emerged as a potential fertoprotective agent, demonstrating its strongest protective effects against Doxorubicin (DOX)-induced ovarian toxicity. While chemotherapy’s gonadotoxic impact on ovaries has been extensively studied, its effects on the uterus remain poorly understood. In this study, we investigated DOX-induced uterine damage and assessed the protective role of AMH co-treatment. DOX triggered DNA double-strand breaks in the uterine myometrium, activating Cdkn1a and other Tp53 pathway genes, and was linked to increased dystocia in pregnant mice. AMH co-treatment counteracted these effects by reducing γ-H2AX-positive DNA damage foci, suppressing Tp53 pathway activation, and improving pregnancy outcomes. These findings establish AMH as a promising therapeutic agent for preserving uterine integrity during chemotherapy, opening new avenues for fertility preservation and improved reproductive health in cancer patients.

overall_design: To elucidate the impact of DOX and AMH on prepubertal uterine function, we administered two weekly doses of DOX (3mg/kg) to prepubertal mice (postnatal day 25). A comparative group received concurrent administration of AMH. Uteri were harvested at 4 and 24 hours post-treatment for bulk RNA sequencing analysis.

first: David

last: Pepin


title: The interaction of CDC6 and Tmod3 accelerates resistance to paclitaxel through focal adhesion assembly

city: Jinan

first: Yue

last: Liu

state: Shandong

address: No. 44 West Wenhua Road

department: School of Pharmaceutical Science

institute: Shandong University

summary: The widespread clinical application of paclitaxel (PTX) in cancer treatment has been significantly limited by the emergence of drug resistance and drug-tolerant persisters. Through genome-wide CRISPR/Cas9 screening, we identified cell division cycle 6 (CDC6) as a critical determinant of cell adhesion-mediated paclitaxel resistance. CDC6, an essential DNA replication licensing factor, functions through a pathway distinct from well-characterized resistance mechanisms. The depletion of CDC6 considerably increases paclitaxel-induced cell death. Beyond its established role in stabilizing chromosomes, our findings indicate that tropomodulin-3 (Tmod3) interacts with CDC6 in the cytoplasm. This interaction enhances CDC6 protein stability and drives drug-resistant phenotypes through regulating actin cytoskeleton remodeling and facilitating focal adhesion assembly. In addition, pharmacological or genetic inhibition of CDC6 notably sensitizes the antitumor efficacy of paclitaxel both in vitro and in vivo. Collectively, our studies elucidate the mechanisms through which CDC6 functions as a key regulator of paclitaxel resistance and provide a potential strategy to enhance paclitaxel efficacy through cytoskeletal-adhesion axis modulation.

overall_design: RNA sequencing was performed on paclitaxel-sensitive and resistant cell lines to identify differentially expressed genes.

first: Huirui

last: Wang

first: Jie

last: Zhan

first: Jiabo

last: Sun

first: Yan

first: Xiaojie

last: Fu

first: Dongxue

last: Lv


title: Transferrin Receptor contributes to PANoptosis in thyroid cancer

city: Dali

first: Zhiqiang

last: Ma

state: Yunnan

address: No.35 Renmin South Road

institute: Dali Bai Autonomous Prefecture People's Hospital

summary: PANoptosis is a novel type of cell death triggered by the cross-talk of three types of cell death (necrosis, apoptosis, and pyroptosis). Nevertheless, the molecular mechanisms associated with PANoptosis in thyroid cancer (TC) remain uncharted. Therefore, this study explored the effect of TFRC on PANoptosis in TC cells in vitro.

overall_design: This study performed an mRNA-seq for K1 cells from the KD-NC (K1 cells transfected with negative vector) and KD-TFRC (K1 cells transfected with TFRC shRNA) groups

first: Shungao

first: Jingwei

last: Shen

first: Hong

first: Hua

last: Yang

first: Yuqin

last: Hu

first: Simeng

last: Ying


title: Extracellular matrix-myCAF signatures correlate with resistance to neoadjuvant aPD-L1 immune checkpoint inhibition with durvalumab + metformin in HPV+ HNSCC

status: Public on Aug 29 2025

city: Philadelphia

first: Alban

last: Linnenbach

state: PA

address: 233 S. 10th Street, Building BLSB 412

department: Kimmel Cancer Center

institute: Thomas Jefferson University

summary: In HPV-positive head and neck squamous cell carcinoma (HNSCC), early resistance to neoadjuvant durvalumab plus metformin therapy is associated with baseline enrichment of extracellular matrix–associated myofibroblastic cancer-associated fibroblasts (ECM-myCAF) within the tumor compartment. In contrast, treatment responders exhibit a distinct tumor microenvironment marked by baseline enrichment of Langerhans-like dendritic cells and post-treatment upregulation of antigen presentation pathways. These findings highlight the tumor-stroma interface as a key determinant of immunotherapy response and provide a foundation for biomarker-driven patient selection. Identifying stromal and immune signatures predictive of response to neoadjuvant aPD-L1 therapy supports future strategies targeting the tumor microenvironment to improve outcomes in HNSCC.

overall_design: Unbiased GSEA

first: Pablo

last: Llerena

first: Hani

last: Samarah

first: Kathryn

last: Nunes

first: Zhao

last: Lin

first: Kelly

last: Bridgham

first: Sruti

last: Tekumalla

first: Amiti

last: Jain

first: Larry

middle: A

last: Harshyne

first: Sanket

last: Shukla

first: Ioannis

last: Vathiotis

first: Madalina

last: Tuluc

first: Stacey

middle: M

last: Gargano

first: John

last: Eisenbrey

first: Scott

middle: W

last: Keith

last: Cognetti

first: Voichita

last: Bar-Ad

first: Adam

middle: J

last: Luginbuhl

first: Rita

last: Axelrod

first: Rajanikanth

last: Vadigepalli

first: Hushan

first: Diana

last: Whitaker-Menezes

first: Megan

last: Roche

first: My

last: Mahoney

first: Athanassios

last: Argiris

first: Charalambos

last: Solomides

first: Jennifer

last: Johnson

first: Mouadh

last: Barbirou

first: Amanda

last: Miller

first: Andrew

middle: P

last: South

first: Ramkrishna

last: Mitra

first: Ubaldo

last: Martinez-Outschoorn

first: Joseph

last: Curry


title: Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma

city: Cambridge

first: Cissy

last: Yong

state: I am not in the U.S. or Canada

address: Hills Road

department: Surgery

country: United Kingdom

institute: University of Cambridge

summary: Human isotopic tracer studies are fast becoming the gold standard model to study cancer metabolism in vivo. Analysed tissues are typically retrieved after surgical resection, which exposes them to a variable extent of warm ischaemia. Although standardised protocols are emerging, the effects of sampling conditions on the tissue metabolome remain understudied. Here, we perform a 13C-glucose study coupled with metabolomic, transcriptomic, and proteomic profiling in patients with clear cell renal cell carcinoma (ccRCC) to assess the metabolic profile of tissues sampled intraoperatively, when blood supply is intact, versus post-surgical resection, which exposes the tissue to ischaemia. We show that ischaemia significantly affects the metabolic landscape of ccRCC, masking some critical features, such as suppressed gluconeogenesis. Furthermore, in orthotopic ccRCC-derived xenografts, we identified that prolonged exposure to ischaemia disrupts the tissue metabolome stability. Therefore, minimising tissue ischaemia is pivotal in accurately profiling cancer metabolism in these important and resource-intense patient studies.

overall_design: To investigate the impact of ischaemia (induced by tissue sampling conditions) on the molecular characterisation of ccRCC, patient tissues (normal adjacent kidney and ccRCC) were sampled at two timepoints: in vivo (tissues perfused) and post-surgical resection (tissues ischaemic). Each patient, where feasible, underwent multiregional sampling (n= 1-3) of their tumour and kidney. We then performed differential gene expression analysis and gene set enrichment analysis  of RNA-seq data between ccRCC and kidney tissues and between timepoints.

first: Julien

last: Bauer

first: Stephanie

last: Wenlock


title: Preadipocyte uncoupling protein 1 expression invoked by fibroblast growth factors imprints on post-differentiation white and brown adipocyte function [2]

city: Freising

first: Katharina

last: Küllmer

address: Gregor-Mendel Straße 2

institute: Technical University of Munich

summary: The presence of uncoupling protein 1 (UCP1) is a hallmark of thermogenic adipocytes and enables heat production by dissipating energy from mitochondrial proton motive force as heat. The purpose of its recently discovered presence in preadipocytes in response to certain fibroblast growth factors (FGFs) remains elusive. In this study, we systematically investigated the potential of all paracrine FGFs to invoke Ucp1 expression in murine preadipocytes derived from interscapular brown and inguinal white adipose tissue. The factors FGF2, FGF4, FGF8, and FGF9 induced Ucp1 expression in undifferentiated preadipocytes, with FGF2 acting most potently and rapidly. This premature Ucp1 induction did not translate into increased Ucp1 thermogenic activity after full adipogenic differentiation. Notably, preadipocyte treatment with FGFs and parallel Ucp1 expression led to a sustained suppression of interferon-stimulated genes after differentiation. Preadipocyte Ucp1 was required and sufficient for this lasting imprint. Thus, FGF-induced Ucp1 expression in preadipocytes programs a lasting post-differentiation anti-inflammatory status.

overall_design: Stromal vascular fraction (SVF) cells were isolated from interscapular brown adipose tissue (iBAT) of C57BL/6N wild-type and Ucp1 knockout mice. Cells were cultured to 70–80% confluency and treated at the preadipocyte stage with either 5.5 nM FGF2, 250 nM of the FGFR inhibitor LY (LY2874455), or left untreated for 48 hours. Subsequently, differentiation into mature brown adipocytes was induced (Gantert et al. 2021). Total mRNA was extracted using the SV Total RNA Isolation System (Promega). For each condition, mRNA from three biological replicates was pooled prior to library preparation and sequencing, which were performed by Novogene.

last: Kuellmer

first: Tobias

last: Fromme


title: Preadipocyte uncoupling protein 1 expression invoked by fibroblast growth factors imprints on post-differentiation white and brown adipocyte function [1]

overall_design: We used 20-day-old male C57BL/6N wild-type (WT) and Ucp1 knockout (Δ/Δ) mice. For each genotype, interscapular brown adipose tissue (iBAT) from three animals was pooled to generate one sample. Total mRNA was isolated using the Promega kit, and library preparation and sequencing were performed by Novogene.


title: Invasive properties of patient-derived glioblastoma cells after reversible electroporation in vitro

city: Ljubljana

first: Anja

last: Blažič

address: Tržaška cesta 25

country: Slovenia

institute: University of Ljubljana, Faculty of electrical engineering

summary:
Background. Electroporation-based therapies are being explored in glioblastoma (GB) treatment, as means of enhancing drug delivery or achieving nonthermal ablation. Yet, little is known about how sublethal exposure affects the invasive behaviour of GB tumour cells.

Materials and methods. Five patient-derived GB cell lines were initially screened for intrinsic invasive potential, and two most invasive (NIB140 CORE and NIB216 CORE) were selected for further experiments with electroporation treatment. Cells in suspension were exposed to bursts of high-frequency biphasic electric pulses resulting in electric field strength of 1 kV/cm, which corresponded to conditions of reversible electroporation. Changes in cell invasion and gene regulation were assessed 24 hours after electro-poration using transwell assay and RNA transcriptome analysis, respectively.

Results. Reversible electroporation at 1.0 kV/cm enhanced invasion in a cell line-dependent manner. NIB140 CORE showed a consistent and pronounced increase, with a median of 3.74-fold (274 %) higher number of invading cells compared to sham control. In contrast, NIB216 CORE exhibited only a modest increase in invasion (1.30-fold; 30 %). Transcriptomic profiling identified modulation of genes linked to extracellular matrix or-ganization and ion channel activity in NIB140 CORE, and cytoskeletal remodelling in NIB216 CORE, indicating the activation of invasion-related pathways.

Conclusions. These findings highlight a potential risk of pro-invasive responses in GB cells. In tumour ablation with irreversible electroporation, this concern relates to cells in the pe-ripheral zone that may experience only sublethal electric fields, while in electrochemo-therapy, a similar risk may arise if permeabilized cells are not effectively eliminated due to insufficient local drug delivery. Nevertheless, the two tested cell lines responded differ-ently, underscoring patient-specific heterogeneity and the need for validation in more physiologically relevant models.

overall_design: RNA-seq profiling of non-treated (no exposure) and with electroporation-treated (exposure to 200 V) patient-derived glioblastoma cells (NIB140 CORE and NIB216 CORE) using H-FIRE pulses 24 hours upon the treatment

first: Bernarda

last: Majc

first: Metka

last: Novak

first: Barbara

last: Breznik

first: Lea

last: Rems


title: Elevated VAMP8 Expression Promotes Cervical Cancer Progression by Enhancing Autophagy via HIF-1 Pathway

status: Public on Aug 30 2025

city: shanghai

first: dan

last: wu

address: shengyang road

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: Background: Cervical cancer, prevalent in low- and middle-income countries, is primarily caused by high-risk HPV16. Vesicle-Associated Membrane Protein 8 (VAMP8), involved in vesicle trafficking and autophagy, may influence HPV16-related cervical cancer progression.  Methods: VAMP8 expression was evaluated in cervical tissue specimens from patients with HPV16-positive lesions (including low- and high-grade squamous intraepithelial lesions and cancer) and HPV-negative normal controls using proteomics, qPCR, and immunohistochemistry. A Cox proportional hazards model for prognosis was developed using immunohistochemical data from a cohort of cervical cancer patients. The clinical significance of VAMP8 was further assessed using RNA-seq and clinical data from The Cancer Genome Atlas-Cervical Cancer (TCGA-CESC) cohort. The effects of VAMP8 on autophagy and tumor progression were examined in HPV16 E6/E7-immortalized cervical epithelial cells (Ect1/E6E7) and cervical cancer cell lines (SiHa, HeLa, C-33A) in vitro, and in a SiHa xenograft model in vivo. Transcriptomic analysis of Ect1/E6E7 and SiHa cells identified VAMP8-regulated pathways. Chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays in SiHa cells were used to confirm the regulation of the HIF-1 pathway.  Results: VAMP8 was upregulated in HPV16-positive samples, particularly in low-grade squamous intraepithelial lesions (LSIL). Elevated VAMP8 correlated with poor survival outcomes and advanced tumor stages. VAMP8 enhanced autophagy and reduced proliferation and invasiveness in HPV16-positive cervical cells but increased in established cancer cell lines. In vivo, VAMP8 overexpression promoted tumor growth and autophagy. The HIF-1 pathway emerged as a key regulatory axis of VAMP8, enhancing hypoxic responses and angiogenesis.  Conclusion: Elevated VAMP8 in HPV16-associated cervical cancer promotes tumor progression by enhancing autophagy via the HIF-1 pathway, suggesting its potential as a diagnostic and prognostic biomarker.

overall_design: RNA-seq Profiling of Wild-Type ECT-1/E6/7, siHA Cells, and Their VAMP8-Overexpressing  Derivatives (OEVAMP8)

first: Yue

last: Wang

first: Dan

last: Wu

first: Jinxia

last: Gai

first: Yiying

last: Cai

first: Keqin

last: Hua

first: Zhiling

last: Zhu

first: Weijuan

last: Xin


title: The transcriptional differences between mCAR-T and cmCAR-T cells

first: kaicheng

last: Zhou

state: shanghai

address: Jinke road 3728

department: Pharmacy school

institute: Fudan University

summary: The study investigates the transcriptional differences between mCAR-T and cmCAR-T cells to understand their distinct cell-killing and cytokine release behaviors. RNA-seq experiments revealed that untransfected T cells, cmCAR-T, and mCAR-T cells exhibit significant transcriptomic differences on days 2 and 4. Notably, the GZMB gene, associated with cytotoxicity, was expressed at higher levels in cmCAR-T cells compared to mCAR-T cells. Analysis of gene signatures related to T cell activation and exhaustion showed distinct patterns between the two cell types. Differentially expressed genes (DEGs) highlighted enriched cytokine signaling in cmCAR-T cells on day 2 and interferon signaling on day 4. These findings suggest that while both CAR-T cell types have transient functional signals, cmCAR-T cells demonstrate enhanced and prolonged cytotoxicity compared to mCAR-T cells.

overall_design: Control T cells (untransfected), Linear mRNA CAR-T or cmRNA CAR-T cells (n=3) were harvested at day 2 and day 4 post electroporation transfections. Subsequently, the total RNA was extracted from cell samples using TRIzol Reagent (Thermo Fisher Scientific, 15596026CN) for preparing RNA libraries using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605-0). Sequencing was performed using the Illumina NovaSeq 6000 platform.

first: Qinchao

last: Hu

first: Hui

last: Zhao

first: Kaicheng

first: Xuyao

last: Zhang


title: Myocardial Reprogramming by HMGN1 Underlies Heart Defects in Trisomy 21 (CutnRun)

status: Public on Aug 28 2025

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

summary: Congenital heart defects (CHD) are the most common form of developmental abnormalities, occurring in ~1% of live births, and can arise due to altered dosage of genes essential for cardiogenesis. Aneuploidy accounts for nearly 15% of CHD and the most frequent form involves trisomy of chromosome 21 (Ch21), resulting in Down Syndrome (DS). Here we used single cell RNA-seq, CRISPR-activation with single cell RNA-seq, single cell ATAC-seq and Cut&Tag epigenomic profiling to define the molecular disruptions occuring with Trisomy 21 and upregulation of the Ch21 epigenetic factor HMGN1. These experiments were performed in human pluripotent stem cells (hiPSCs) or in directed differentiation to cardiomyocyte lineages at days 10 and 20.

overall_design: Cut and Run samples for HMGN1-Flag. Cardiomyocytes differentiated from human induced pluripotent stem cells (hiPSCs) were collected at day 20 for CUT&RUN analysis. Cells were dissociated using 0.25% Trypsin-EDTA (1X) (Gibco, 25200-072) and neutralized with 1% FBS in PBS. For each condition, 150,000 cells per sample were processed according to the manufacturer’s instructions using the CUTANA™ CUT&RUN Kit (Epicypher, 14-1048). Cells were first washed and bound to activated Concanavalin A (ConA)–coated magnetic beads in the Bead Activation Buffer. Nuclei were permeabilized with Digitonin-containing buffer, and all buffers were supplemented with cOmplete™ Mini, EDTA-free Protease Inhibitor Cocktail (Millipore Sigma, 11836170001).  Samples were incubated with 0.5 µg of H3K4me3 primary positive control antibody (Epicypher 13-0060), 1 µL of IgG control antibody, and 1 µg of Monoclonal ANTI-FLAG M2 antibody (Sigma-Aldrich, F1804-200 µG) per sample at 4 °C overnight on a rotating mixer. After antibody binding, samples were washed by cell permeabilization buffer. Protein A-MNase fusion enzyme was added to each sample and incubated at 4 °C for 1 hour with mixing. Targeted chromatin digestion was initiated by adding calcium-containing digestion buffer and incubating at 0 °C for 30 minutes. Reactions were stopped with Stop Buffer supplemented with glycogen and RNase A, followed by incubation at 37 °C for 10 minutes to release digested chromatin fragments.  DNA was purified using phenol-chloroform extraction or DNA Clean & Concentrator kit (Zymo Research), followed by SPRIselect bead cleanup (Beckman Coulter, B23317) and 80% ethanol washes. Elution was performed with 0.1X TE buffer, and DNA concentration was measured using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645), indexed with i5/i7 dual indices, and amplified by PCR. Library DNA size distribution was assessed using the Agilent Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626). Final libraries were pooled and sequenced on an Illumina NextSeq 500/550 using the Mid Output v2 kit (Illumina, 20024904) with the following cycle configuration: Read 1: 75 bp, Index 1: 8 bp, Index 2: 8 bp, Read 2: 75 bp.

first: Sanjeev

last: Ranade

first: Deepak

last: Srivastava


title: FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer

city: Uxbridge

first: Alessandro

last: Esposito

state: Select a State/County

address: Kingston Lane

department: Centre for Genome Engineering and Maintanance

institute: Brunel University of London

summary: Mutations in KRAS, particularly at codon 12, are frequent in adenocarcinomas of the colon, lungs and pancreas, driving carcinogenesis by altering cell signalling and reprogramming metabolism. However, the specific mechanisms by which different KRAS G12 alleles initiate distinctive patterns of metabolic reprogramming are unclear. Using isogenic panels of colorectal cell lines harbouring the G12A, G12C, G12D and G12V heterozygous mutations and employing transcriptomics, metabolomics, and extensive biochemical validation, we characterise distinctive features of each allele. We demonstrate that cells harbouring the common G12D and G12V oncogenic mutations significantly alter glutamine metabolism and nitrogen recycling through FOXO1-mediated regulation compared to parental lines. Moreover, with a combination of small molecule inhibitors targeting glutamine and glutamate metabolism, we also identify a common vulnerability that eliminates mutant cells selectively. These results highlight a previously unreported mutant-specific effect of KRAS alleles on metabolism and signalling that could be potentially harnessed for cancer therapy.

overall_design: We have done RNA sequencing (transcriptomics) to reveal differences between different KRAS mutants. We used a commercially available isogenic cell line based on the colorectal cancer SW48 line with heterozygote knockin mutations G12A, G12C, G12D and G12V. Having identified FOXO1 as a possible mediator of metabolic reprogramming induced by KRAS mutants, we have repeated the work in low nutrient conditions, and with a FOXO1 inhibitor.

first: Suzan

last: Ber

first: Khushali

last: Patel

first: Annie

last: Howitt

first: Shamith

last: Samarajiwa


title: Eupatilin Ameliorates Spinal Cord Injury by Inhibiting Damage-associated Microglia and Optimizing the Regenerative Microenvironment

city: Xi'an

first: Beibei

last: Yu

state: Shannxi

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

institute: Xijing hospital

summary: Microglia represent critical therapeutic targets in spinal cord injury (SCI), with damage associated microglia (DAM) playing key roles in neuroinflammation and tissue repair.Through integrated in-silico analysis of scRNA-seq and microarray datasets, we identified DAM subsets specific to acute SCI characterized by hub genes Fcer1g, Grn, and Gusb. Using a C57BL/6 mouse spinal cord contusion model, we validated increased DAM accumulation post-injury and demonstrated their propensity to transition toward homeostatic microglia (MG2). Eupatilin treatment promoted DAM-toMG2 differentiation, as confirmed through bulk and single-cell RNA sequencing analyses revealing supportive gene expression changes. These findings establish DAM as functionally distinct microglial populations in acute SCI and identify Eupatilin as a therapeutic agent that facilitates beneficial microglial polarization. This work provides mechanistic insights into microglial dynamics during SCI and suggests targeted modulation of DAM-to-MG2 transitions as a promising therapeutic strategy for promoting inflammation resolution and functional recovery.

overall_design: Prior to surgery, mice were fasted for 6 hours received anesthesia with a single intraperitoneal injection of 270-330 mg/kg Avertin (Sigma-Aldrich, MO, USA, T48402). The T9 lamina was surgically exposed while preserving the integrity of the dura mater, followed by a 30-second aneurysm clip compression for all injured groups. The muscle and skin were then sutured closed. Following SCI, manual bladder  expression was performed 3 times daily until bladder function recovered. For the first 3 days, intrathecal injections were administered: the treatment group received Eupatilin (30 μl, 1.5 mg/mL, Bide, Shanghai,  China, BD298186), while the SCI control group received an equivalent volume of saline.

first: Weitao

last: Man

first: Zide

last: Wang


title: PRDM16 controls smooth muscle cell fate in atherosclerosis: Fixed-cell scRNAseq datasets [scRNA-seq]

first: Ryan

middle: Patrick

last: Calhoun

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Vascular smooth muscle cells (SMCs) normally exist in a contractile state but can undergo fate switching to produce a variety of cell phenotypes in response to pathologic stimuli. In atherosclerosis, these phenotypically modulated SMCs play a critical role in determining plaque composition and the risk of major adverse cardiovascular events. We found that PRDM16, a transcription factor that has been genetically implicated in cardiovascular disease, is highly expressed in arterial SMCs, and downregulated during SMC fate switching in human and mouse atherosclerosis. Deletion of Prdm16 in SMCs of mice activates the synthetic modulation program in arteries under homeostatic conditions. Upon exposure to atherogenic conditions, these mice form strikingly dense, SMC-rich, fibroproliferative plaques that contain few foam cells. Acute deletion of Prdm16 in SMCs triggers a similar fibrotic response, resulting in the formation of collagen-rich lesions with thick fibrous caps – a hallmark of enhanced lesion stability. Reciprocally, ectopic expression of PRDM16 in cultured cells is sufficient to block SMC synthetic processes, including migration, proliferation, and fibrosis. Mechanistically, PRDM16 binds to chromatin and decreases activating histone marks at synthetic genes. Altogether, our results define PRDM16 as a specific gatekeeper of the synthetic SMC switch and reveal that PRDM16 levels in SMCs predetermine atherogenic lesion composition.

overall_design: All mice for this study were male of the C57BL6/J background. The Prdm16 floxed mouse line was bred with Tagln Cre or Myh11 CreER. Floxed animals without Cre were used as controls. Animals were raised at room temperature on standard chow (LabDiet, 5010) with a 12-h light–dark cycle at room temperature (22 °C) unless specified otherwise. For atherosclerosis experiments, mice were placed at thermoneutrality (30 °C) at weaning (21 days old) and kept at thermoneutrality until the end of the experiment. For iKO studies, tamoxifen (Sigma, T5648; stock 20 mg/mL in corn oil) was injected intraperitoneally at a dose of 100 mg/kg for 4 consecutive days.

first: Josephine

last: Tan

first: Patrick

last: Seale


title: B-Cells Derived EVs Shape Melanoma Response to Immune Checkpoint Therapy

city: Zurich

first: Richard

last: Chahwan

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

institute: University of Zurich

summary: In recent years, the understanding of the immune tumor microenvironment has evolved to include B cells as active participants rather than mere bystanders. Retrospective studies investigating the presence of B cells and B cells-associated signatures within tumors have revealed a significant correlation with therapeutic outcomes. Although conflicting data exist regarding whether B cells act as pro-tumor or anti-tumor agents, it is becoming increasingly clear that understanding B cells as a heterogeneous population, shaped by tumor microenvironment cues, is essential. This study explores the crucial roles played by B cells and their extracellular vesicles (EVs) in shaping responses to immune checkpoint blockade (ICB) therapy. We have independently verified the significant enrichment of B cells in ICB therapy responders in comparison to non-responder in tumors of melanoma patients. B cell depletion experiments in an in vitro tumor-killing assay demonstrate a clear impairment of T cell-mediated anti-tumor activity. To investigate the clinical relevance, EVs were isolated from melanoma patient tumors, and fractioned into subpopulations, including B cell-derived EVs. MiRNA profiling of CD19+ EVs identifies miR-99a-5p as a top candidate, significantly upregulated in responder EVs. In downstream assays, we observed a B cell-dependent phenotype of miR-99a-5p, where its silencing impaired T cell-mediated anti-tumor cytotoxicity in an in vitro tumor-killing assay. Mechanistically, miR-99a-5p appears to regulate B cell cell-cycle, favoring non-homologous end joining DNA repair pathway, and promoting class-switch recombination. Collectively, data reported herein emphasizes the indispensable role of B cells and their derived EVs in shaping cancer immunotherapy outcome.

overall_design: To investigte the role of B cell-derived EVs in melanoma immunotherapy response

first: Ala'a

last: Hrout


title: Anti-Müllerian Hormone Reduces Uterine DNA Damage and Pregnancy Complications in Doxorubicin-Treated Mice [RNA-seq]

first: Ngoc Minh Phuong

last: Nguyen

first: David

last: Pepin


title: Trans-generational adaptation to maternal climate through hormone transport in plants

city: Norwich

first: Xiaochao

last: Chen

address: Norwich Research Park, Colney Ln

department: Crop Genetics

institute: John Innes Centre

summary: Whether and how organisms can inherit environmental information from their parents is a major question in evolutionary theory. Plants have evolved to link reproductive development to seasonal environmental cues and seed dormancy is highly contingent on the environmental temperature during seed set, although the mechanism by which seeds acquire seasonal timing information is unclear. Here we show that loss of maternal like heterochromatin protein 1 (LHP1) causes an inability of progeny seeds to sense temperature and that this is linked mechanistically to reduced ABA levels in seeds and hyperaccumulation of free nitrate. Remarkably, single cell transcriptomics reveals that in both maternal fruit and seed tissues, the effect of small changes in temperature closely phenocopies the lhp1 mutant phenotype and ABA biosensor imaging reveal large fluxes of maternal ABA into seeds is modulated by temperature cues. We show that temperature activates ABA production in leaves and that maternal ABA is necessary and sufficient for progeny seeds to acquire seed dormancy. Thus, we reveal that the climate experience of mother plants causes adaptation of progeny behaviour via hormone transport during seed set.

overall_design: Col-0 plants were grown at 22°C till bolting, then half plants were transferred to 16°C. At bent stage, siliques from 2 different temperature were dissected to separate fruit tissue and seed tissue which were sequenced seperately.

first: William

last: Bezodis

first: Steven

last: Penfield


title: Distinct 5′ and 3′ Coverage Biases Shape Transcriptome Interpretation in Nanopore Direct RNA versus PCR-cDNA Sequencing

status: Public on Aug 27 2025

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

summary: Long-read RNA sequencing enables isoform-resolved transcriptomics, but library preparation introduces systematic biases that shape biological interpretation. We benchmarked Oxford Nanopore’s two protocols—PCR-cDNA and direct RNA—using SKMM2 myeloma cells stimulated with interleukin-6 (IL-6) and ERCC synthetic spike-ins. Direct RNA produced longer, higher-quality reads and more high-confidence isoforms, but showed pronounced 5′ coverage loss. PCR-cDNA yielded shorter fragments with 3′ underrepresentation, detecting more low-abundance transcripts at reduced confidence. Protocol-specific biases had major consequences: differential expression analysis revealed limited overlap in IL-6–responsive genes, and pathway enrichment was broader in direct RNA. At the isoform level, differential transcript usage was almost entirely protocol-specific, with case studies (e.g. RPL22L1, GRB2, RNF220) illustrating concordance and divergence. ERCC controls confirmed these biases as technical rather than biological. Together, our results show that while both methods provide accurate gene-level quantification, transcript-level conclusions depend critically on protocol choice, highlighting the need for careful selection in long-read transcriptomics.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: SKMM2 multiple myeloma cells were cultured and treated in biological triplicates with either interleukin-6 (IL-6, 1 ng/mL, 18 h) or vehicle control (0.2% BSA). Total RNA was extracted and used to prepare sequencing libraries with two Oxford Nanopore Technologies (ONT) protocols: (i) PCR-cDNA sequencing (SQK-PCB111.24, 14 PCR cycles for SKMM2 RNA, 16 cycles for ERCC spike-ins) and (ii) direct RNA sequencing (SQK-RNA004). Each protocol was applied to both IL-6–treated and control samples, enabling direct benchmarking of protocol-specific biases. ERCC synthetic RNA spike-ins were sequenced in parallel as external controls. Libraries were sequenced on ONT PromethION flow cells (R9.4.1 for PCR-cDNA, RNA flow cells for direct RNA) with live base-calling. Downstream analyses included gene- and isoform-level quantification, differential expression, pathway enrichment, and differential transcript usage.

first: Cribbs

last: Adam


title: Preadipocyte uncoupling protein 1 expression invoked by fibroblast growth factors imprints on post-differentiation white and brown adipocyte function [iBAT]

first: Katharina

last: Küllmer

state: Bavaria

overall_design: Immortalized brown preadipocytes (Gantert et al., 2021) were cultured in DMEM supplemented with 10% FBS and treated with 5.5 nM FGF8 or vehicle control at ~80% confluency for 48 h. Following pretreatment, cells were either harvested directly or subjected to adipogenic differentiation using the established protocol described in Gantert et al. (2021) (2 days induction followed by 7 days differentiation). Samples were collected after pretreatment, or on day 3 or day 7 of differentiation. Total RNA was isolated using the Promega kit. Library preparation was performed usigng the Illumina kit, and sequencing was carried out at Novogene.

last: Kuellmer

first: Tobias

last: Fromme


title: Coxsackievirus B infection invokes unique cell-type-specific responses in primary human pancreatic islets

city: St. Louis

first: Daniel

middle: Andre

last: Veronese-Paniagua

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University in St. Louis

summary: Coxsackievirus B (CVB) infection has long been considered an environmental factor precipitating Type 1 diabetes (T1D), an autoimmune disease marked by loss of insulin-producing b cells within pancreatic islets. Previous studies have shown CVB infection negatively impacts islet function and viability but do not report on how virus infection individually affects the multiple cell types present in human primary islets. Therefore, we hypothesized that the various islet cell populations have unique transcriptional responses to CVB infection. Here, we performed single-cell RNA sequencing on human cadaveric islets treated with either CVB or poly(I:C), a viral mimic, for 24 and 48 hours. Our global analysis reveals CVB differentially induces dynamic transcriptional changes associated with multiple cell processes and functions over time whereas poly(I:C) promotes an immune response that progressively increases with treatment duration. At the single-cell resolution, we find CVB infects all islet cell types at similar rates yet induces unique cell-type specific transcriptional responses with b, a, and ductal cells having the strongest response. Sequencing and functional data suggest that CVB negatively impacts mitochondrial respiration and morphology in distinct ways in b and a cells, while also promoting the generation of reactive oxygen species. We also observe an increase in the expression of the long-noncoding RNA MIR7-3HG in b cells with high viral titers and reveal its knockdown reduces gene expression of viral proteins as well as apoptosis in stem cell-derived islets. Together, these findings demonstrate a cell-specific transcriptional, temporal, and functional response to CVB infection and provide new insights into the relationship between CVB infection and T1D.

overall_design: Cadaveric islets from four donors were treated with either poly(I:C) or GFP-tagged coxsackievirus B3 for 24 hr and 48 hr. Endotoxin-free water served as a negative control. Cells from patients 1-3 were multiplexed for single-cell RNA sequencing. Cells from patient 4 were processed indepedently for single-cell RNA sequencing.

first: Marlie

last: Maestas

first: Diana

last: Hernandez-Rincon

first: Kate

middle: E

last: Hinshaw

first: Matthew

last: Ishahak

first: Jared

last: Taylor

first: Hubert

last: Tse

first: Jeffrey

middle: R

last: Millman


title: DNase I alleviates renal inflammatory injury in MRL/lpr mice by inhibiting NETs formation

city: Hohhot

first: yong

last: jin

address: 1 North Passage Road, Hohhot, Inner Mongolia, China

institute: Inner Mongolia Medical University

summary: Neutrophil extracellular traps (NETs) formation has been closely associated with renal inflammatory injury. We administered DNase I to MRL/lpr mice, monitored signs and renal pathology, quantified gene expression levels, and conducted flow cytometry and RNA-seq analysis. Following DNase I treatment, the lupus-related manifestations, renal pathology, and renal function were significantly improved in the LN mouse model. The expression levels of MPO and CitH3 were reduced, and the expression of inflammatory damage molecules, including IL-1β, TNF-α, and Kim1, was down-regulated. RNA-seq analysis revealed that the neutrophil and T cell activation and chemotaxis pathways were suppressed, and the infiltration of cytotoxic immune cells in the kidneys was decreased in the DNase I-treated group compared to MRL/lpr mice. In conclusion, DNase I alleviates renal inflammatory injury by inhibiting the NETs/TLR4/MYD88 cell signaling axis, reducing the formation of NETs and the infiltration of immune inflammatory cells such as T cells and macrophages. These findings may provide a novel clinical prevention and treatment strategy for LN.

overall_design: To further investigate the potential molecular mechanisms underlying DNase I-targeted NETs in the treatment of LN in a mouse model, we conducted RNA sequencing on kidney tissues from four 21-week-old MRL/lpr mice (Lpr), four MRL/lpr mice treated with DNase I (DNase), and three sex- and age-matched healthy control mice (Ctr).

first: Manling

last: Zhang

first: Xinran

last: Xie

first: Gula

last: Da

first: Hongbin

last: Li

first: Yong

last: Jin


title: The antisense RNA CDH3-AS1 regulates expression of the melanoma suppressor P-cadherin

city: Tampa

first: Alex

last: Jaeger

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: Moffitt Cancer Center

summary: Thousands of regulatory noncoding RNAs (ncRNAs) have been annotated; however, their functions in gene regulation and contributions to cancer formation remain poorly understood. To gain a better understanding of the influence of ncRNAs on gene regulation during melanoma progression, we mapped the landscape of ncRNAs in melanocytes and melanoma cells. Nearly half of deregulated genes in melanoma are ncRNAs, with antisense RNAs (asRNAs) comprising a large portion of deregulated ncRNAs. CDH3-AS1, the most significantly downregulated asRNA, overlaps the CDH3 gene, which encodes P-cadherin, a transmembrane glycoprotein   involved in cell adhesion that was also reduced in melanoma. Overexpression of CDH3-AS1 increased cell aggregation and reduced xenograft tumor growth, mimicking the tumor-suppressive effects of CDH3. CDH3-AS1 interacted with CDH3 mRNA and enhanced P-cadherin protein levels. Interestingly, secondary structures at the CDH3 5’ end regulated P-cadherin translation, and ribosome profiling revealed that CDH3-AS1 promotes ribosome occupancy at the CDH3 5’UTR. Notably, 5’UTR ribosome occupancy was generally increased in mRNAs having cognate asRNA. Taken together, this study revealed the CDH3-AS1-mediated enhancement of P-cadherin translation, underscoring the broader potential of asRNAs as regulators of protein-coding genes and their role in diseases like melanoma.

overall_design: Comparison of Ribosome density in Hermes melanocytes treated with either control siRNA or siRNA targeting CDH3-AS1.

first: Manon

last: Chadourne

first: Emily

last: Brennan

first: Florian

last: Karreth


title: PRDM16 controls smooth muscle cell fate in atherosclerosis [RNA-Seq]

first: Ryan

last: Calhoun

first: Josephine

last: Tan

first: Patrick

last: Seale


title: Myocardial Reprogramming by HMGN1 Underlies Heart Defects in Trisomy 21 [scRNA-seq]

first: Angelo

last: Pelonero

overall_design: We used human pluripotent stem cells (hIPSCs) from an individual who was mosaic for Down Syndrome. Thus we compare cells that are trisomic for Ch21 with cells that are isogenically similar and disomic for Ch21. As well, we generated a CRISPR-activation knock-in to disomic cells and used sgRNAs directed to chromosome 21 genes. Sample replicates are defined and all single cell samples were processed with 10X Genomics pipelines. Cut&Run samples were processed with Epicypher reagents. All samples were isolated with Accutase or Trypsin reagents.

first: Sanjeev

last: Ranade

first: Deepak

last: Srivastava


title: PRDM16 controls smooth muscle cell fate in atherosclerosis [ChIP-Seq]

overall_design: All mice for this study were male C57BL6/J WT mice obtained from Jackson Laboratory. Animals were raised at room temperature on standard chow (LabDiet, 5010) with a 12-h light–dark cycle at room temperature (22 °C). 12 mice were pooled and divided over the three ChIPs

first: Angela

last: Weller


title: RNA-seq Analysis of Drosophila melanogaster Heads Harvested 4-Hours Post-PenetratingTraumatic Brain Injury

city: Madison

first: Grace

last: Boekhoff-Falk

state: WI

address: 1111 Highland Ave.

department: Cell and Regenerative Biology

institute: UW-Madison

summary: We are utilizing an adult penetrating traumatic brain injury (PTBI) model in Drosophila to investigate early regenerative mechanisms after damage to the central brain. Here we incorporate RNA-seq analyses to identify candidate pathways that may trigger cell proliferation following PTBI. We find that transcript levels for components of both Toll and Immune Deficiency (Imd) innate immunity pathways are rapidly and highly upregulated post-PTBI. We then tested mutants for the NF-κB transcription factors of the Toll and Imd pathways, Dorsal-related immunity factor (Dif) and Relish (Rel) respectively. Induction of transcripts for antimicrobial peptide (AMP) levels are substantially elevated after PTBI, however their levels revert to near baseline within 24 hours. These results indicate that the innate immunity pathways play an integral role in the regenerative response. Innate immunity previously has been implicated as both a potentiator and an inhibitor of regeneration. Our work suggests that modulation of innate immunity may be essential to prevent adverse outcomes.

overall_design: RNA-Seq analysis from isolated from heads of young male Drosophila melanogaster collected within 6 hrs of eclosion generated by our 'standard cross' =  w; UAS-mCD8-GFP;; OK107-GAL4 X yw  at four hours after PTBI to both hemispheres of the central brain and from the heads of age- and sex-matched controls without injury. Samples are divided into 3 biological replicas, each from ~100-120 heads.  w; UAS-mCD8-GFP;; OK107-GAL4 X yw  at four hours after PTBI to both hemispheres of the central brain and from the heads of age- and sex-matched controls without injury. Samples are divided into 3 biological replicas, each from ~100-120 heads.

first: Khailee

last: Marischuk

first: Shawn

last: Ahern-Djamali

first: Kassi

last: Crocker