title: Genome-wide histone modifications of secondary hair follicle stem cell during cashmere growth [ChIP-Seq]

first: Huiling

last: Xue

summary: To investigate the regulatory role of histone modifications in cashmere growth and development, we performed ChIP-seq targeting four key histone marks—H3K4me3, H3K27me3, H3K36me3 and H3K79me2 in isolated and cultured secondary hair follicle stem cells (SHFSCs) collected during early anagen and mid anagen phases. In parallel, RNA-seq was conducted on the same samples to profile transcriptomic changes. This study provides a genome-wide landscape of histone modifications in SHFSCs and identifies distinct epigenetic signatures associated with the transition from early to mid anagen.

overall_design: To investigate histone modifications in secondary hair follicle stem cells (SHFSCs), we performed ChIP-seq targeting H3K4me3, H3K36me3, H3K27me3 and H3K79me2 in SHFSCs collected during early anagen (April) and mid anagen (October) phases. ChIP-seq was conducted according to established protocols.

first: Xinyue

last: Liang

first: Bohan

last: Liu

first: Yanlei

first: Shengda

last: Sheng


title: An Epigenetetic Signature for Classifying Pancreatic Ductal Adenocarcinoma Based on their Cellular Origin

status: Public on Feb 24 2026

city: Brussels

first: Patrick

last: Jacquemin

address: Avenue Hippocrate 75

country: Belgium

institute: de Duve Institute, Université catholique de Louvain

type: Methylation profiling by genome tiling array

summary: Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest cancers, characterized by significant heterogeneity that complicates treatment and diagnosis. While acinar and ductal cells can serve as the origins of PDAC in mice, shaping differently tumor biology, no practical method exists to predict the cell of origin in PDAC models. Here, we leveraged DNA methylation as a powerful tool to trace the cellular origins of PDAC. We identified a cell-of-origin DNA methylation signature comprising 178 CpG sites. This signature remains preserved during tumorigenesis and robustly differentiates acinar-origin from ductal-origin PDAC samples across different experimental settings. It also predicted the cell of origin of PDAC samples from KPC mice, the most commonly used preclinical PDAC model, and revealed the influence of oncogenic mutations on tumor fate. A logistic regression model further confirmed the origin of most tumor samples. Notably, cell of origin influences PDAC characteristics and treatment response, underscoring its potential role in patient stratification, origin-informed molecular subtyping, and development of novel therapies. Our findings also raise important questions about the relevance of KPC mice as a preclinical model and the mechanisms driving PDAC heterogeneity.

overall_design: The Illumina Infinium Mouse MethylationEPIC array BeadChip (285K) was carried out by the Epigenomic Service from Diagenode (G02160004) to generate DNA methylation data. Processing of the data was done with the R Package (version 2.18.0)  RnBeads. All probes located on sex chromosomes, overlapping with single nucleotide polymorphisms (SNPs), missing value, or low variability were removed from subsequent analysis. Beta values were normalized using the wm.dasen method, with no background subtraction.

first: Ilianna

last: Zoi


title: The emergence of multiple testicular cell lineages in human stem cell-derived testis-like organoids [scRNA-Seq]

city: Parkville, Melbourne

first: Svenja

last: Pachernegg

state: VIC

address: 50 Flemington Road

department: Genomic Medicine

country: Australia

institute: Murdoch Children's Research Institute

type: Expression profiling by high throughput sequencing

summary: Reproductive development is a complex process orchestrated by precise gene expression and cellular interactions. Disruption to this process can result in Differences of Sex Development (DSDs) which occur in approximately 1-2% of live births. We have previously developed a protocol to differentiate human induced pluripotent stem cells (hiPSCs) into testis-like organoids as a model to study the molecular mechanisms underlying reproductive development and DSD. Here, we performed bulk and single-cell RNA sequencing on testis-like organoids to investigate their transcriptional landscape. Transcriptomic analysis revealed six cell clusters expressing markers associated with bipotential, early Sertoli, and testicular interstitial cells. To address the limited emergence of mature cell types, we generated a doxycycline-inducible NR5A1/SF1 hiPSC line, which successfully triggered the expression of Leydig cell markers upon overexpression. Our findings provide a comprehensive transcriptional profile of hiPSC-derived testis-like organoids, offering insights into human fetal gonadal development and a novel disease modelling system for DSDs.

overall_design: single cell RNA-seq of hiPSC-derived testis-like organoids at day 21 of differentiation

first: Gorjana

last: Robevska

first: Lucas

middle: G

last: Ferreira

first: Natalie

last: Charitakis

first: Jinchao

last: Gu

first: Eliza

last: Martin

first: Jan

last: Terhag

first: Denis

last: Bienroth

first: Jocelyn

last: van den Bergen

first: Sean

last: Wilson

first: Ben

last: Rollo

first: Melissa

middle: H

last: Little

first: Mirana

last: Ramialison

first: Andrew

last: Sinclair

first: Katie

middle: L

last: Ayers


title: FGFR Inhibition Overcomes Therapeutic Resistance and Immune Evasion in Oncogenic PIK3CA-Driven Serous Endometrial Cancers

city: Boston

first: Jean

last: Zhao

state: MA

address: 450 Brookline Ave, SM936

department: Cancer Biology

country: USA

institute: Dana Farber Cancer Institute

summary: We developed the first clinically relevant, immunocompetent SEC mouse model incorporating PIK3CA mutation, TP53 loss, and MYC overexpression. Through comprehensive analysis integrating mouse models, human cell lines, xenografts, and clinical samples, we investigated mechanisms of PIK3CA-targeted therapy resistance. Single-cell transcriptional profiling identified FGFR1/2 association with intrinsic resistance and FGFR3 with acquired resistance. Dual inhibition of FGFR and PI3Ka achieved enhanced tumor suppression. Additionally, we discovered that FGFR signaling promotes immune evasion by downregulating MHC-I/HLA-mediated antigen processing and presentation. Importantly, FGFR inhibition not only reversed immune suppression by restoring antigen presentation but also demonstrated a synergistic effect with anti-PD-1 therapy, enhancing immunotherapy response and anti-tumor immune memory. Our findings reveal FGFR's dual role in therapy resistance and immune evasion, supporting FGFR inhibition as a promising strategy to enhance treatment outcome in SEC patients.

overall_design: In this study, we developed the first clinically relevant, immunocompetent transgenic mouse model of SEC driven by PIK3CA mutation, P53 loss, and C-MYC overexpression. To model tumor recurrence, we withdrew doxycycline from a cohort of tumor-bearing mice and monitored them for several months. We then collected primary and recurrent tumors for both snRNA-seq and RNA-seq analysis.

first: Xin

last: Cheng


title: A viral transcriptional regulator from a dsRNA virus antagonizes the innate immune response by manipulating the host co-transcription factor DHX9 [ChIP-Seq]

city: Tianjin

first: Xueyang

last: Pang

state: Tianjin

address: 22 Meteorological Observatory Road, Heping District, Tianjin

country: China

institute: TMU

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Viral transcriptional regulators (vTRs) have emerged as potent factors that shape the host anti-viral gene expression programs. Delineating the molecular mechanisms by which vTRs inhibit or promote transcription would provide fundamental insights for developing anti-viral strategies. Using Mammalian orthoreovirus (REOV) as a model system, we identified a new viral mechanism by which viruses antagonize the host innate immune response. We found that the REOV outer capsid protein sigma3 functions as a vTR that limits RNA polymerase II (Pol II) recruitment to the promoter regions of NF-κB-dependent genes via its direct interaction with the host helicase DHX9. sigma3 competes with DHX9 for its interaction with Pol II, which led to marked attenuation of Pol II loading onto chromatin. More interestingly, sigma3 also suppresses DHX9 helicase activity, leading to aberrant accumulation of R-loops at promoter-proximal regions and a decrease in NF-κB-dependent gene expression. Together, our findings uncover an unprecedented strategy of a viral protein that regulates anti-viral gene expression by directly manipulating host transcription factor DHX9.

overall_design: RNA Pol II/R-Loop/H3K4me3 occupancy on chromatin upon TNFa treatment in sigma3 overexpressing cells were assessed by Cut&Tag assay.

first: Shiyu

last: Liu

first: Yixiao

last: Zhu

first: Meleana

last: Hinchman

last: Qiao

first: Xuejun

last: Li

first: Weiqian

last: Dai

first: Yingying

last: Tong

first: Man

last: Xing

first: Jiling

last: Ren

first: John

last: Parker

last: Guo

first: Dongming

last: Zhou


title: Characterization of cellular miRNA transcriptome during KSHV lytic reactivation

first: Soo Mi

last: Lee

address: 3 BLACKFAN CIRCLE, CLS 417

department: Pathology

institute: BIDMC/Harvard Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To characterize genome-wide microRNA (miRNA) expression profiles in the context of Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation.

Methods: We utilized a well-established model of KSHV reactivation, the doxycycline (Dox)-inducible KSHV producer cell line iSLK.219, which contains a latent KSHV genome and a Dox-inducible KSHV lytic switch protein RTA (replication and transcription activator) to mediate efficient reactivation upon Dox treatment. We performed small-RNA sequencing of RNA isolated from latent KSHV-infected iSLK.219 cells at 0 h or lytic iSLK.219 cells at 72 h post Dox-induced KSHV lytic reactivation using Illumina HiSeq 2500. To rule out the possibility that Dox itself can affect miRNA expression, we also performed small-RNA sequencing of RNA isolated from KSHV-negative iSLK cells, which lacks the KSHV genome but harbors the Dox-inducible RTA transgene, without Dox treatment at 0 h or at 72 h post Dox treatment. The mappable reads were aligned to the human genome and miRBase using Bowtie.

Results: Global cellular miRNA transcriptome analysis has identified changes in the host miRNA expression landscape during the switch from latent to lytic KSHV replication. The top down-regulated miRNAs included miR-31-5p, miR-29a-3p, miR-181a-3p, miR-194-5p, and miR-449c-5p and the top up-regulated miRNAs included miR-139-5p, miR-7-5p, miR-210-3p and miR-3065-5p. We confirmed that Dox treatment in KSHV-negative iSLK cells did not significantly down-regulate or up-regulate these cellular miRNAs, indicating that Dox itself or RTA transgene expression alone does not affect the levels of these miRNAs. In addition, 8 KSHV-encoded miRNAs, including pre-miR-K12-12, were significantly up-regulated upon lytic reactivation in iSLK.219 cells. Notably, the top four up-regulated host miRNAs have been implicated in inflammatory signaling pathways involved in a productive or lytic cycle of infection, suggesting that KSHV exploits these immunomodulatory miRNAs to facilitate lytic reactivation. On the contrary, four out of the top five down-regulated host miRNAs, miR-29a-3p, miR-181a-3p, miR-194-5p, and 449c-5p have been implicated in restricting the infection and replication of RNA and DNA viruses. Taken together with our small-RNA sequencing analysis, these findings suggest that KSHV lytic reactivation impacts the cellular miRNA expression landscape as a strategy to evade or subvert host antiviral responses and ensure efficient lytic replication and persistence.

Conclusions: Our study represents the first detailed analysis of genome-wide miRNA transcriptomes during KSHV lytic reactivation, with biological replicates, generated by miRNA-seq technology. Our study provides crucial insights into the impact of lytic KSHV infection on the host and viral miRNA expression landscapes. Moreover, our results identify a previously unappreciated role for miR-31-5p in regulating KSHV lytic reactivation by modulating KHDRBS3 expression.

first: SooMi

first: Frank

middle: J

last: Slack


title: ERV-Derived RNA-DNA Hybrids Upregulate C4b to Induce Microglial Synaptic Pruning in autism [ChIP-seq]

city: Xiamen

first: Boxin

last: Zhang

address: 良渚实验室1369号

institute: 良渚实验室

summary: Microglia-mediated neuroinflammation has been identified as pathogenic in autism spectrum disorders (ASD). Pathogenic factors for microglial activation remain unclear. In our study, we discovered that complement C4b is highly expressed in the prefrontal cortex (PFC) neurons with SETDB1 deficiency, a high-risk gene of ASD, or by maternal inflammation (MI). Exposure to C4b led microglia to perform excessive synaptic pruning, which in turn manifested ASD-like phenotypes. Furthermore, we observed that removing microglia could improve synaptic functions, while the complete knockout of C4b could rescue all observed autistic phenotypes. The expression of C4b was contingent upon RNA-DNA hybrids formed by the reactivation of Endogenous Retroviruses (ERVs). Interestingly, the pharmacological reversal of this retrotranscriptional process with FDA-approved HIV medications significantly reduced C4b levels and ameliorated the symptoms of ASD. Our findings illuminate the pivotal role of C4b in microglia-driven synaptic pruning linked to ASD and suggest that targeting ERV reactivation could be a promising therapeutic strategy with existing FDA-approved HIV drugs.

overall_design: ChIP-seq for histone modifications H3K9me3 and H3K27ac in cortex.


title: ERV-Derived RNA-DNA Hybrids Upregulate C4b to Induce Microglial Synaptic Pruning in autism [RNA]

summary: Microglia-mediated neuroinflammation has been identified as pathogenic in autism spectrum disorders (ASD). Pathogenic factors for microglial activation remain unclear. In our study, we discovered that complement C4b is highly expressed in the prefrontal cortex (PFC) neurons with SETDB1 deficiency, a high-risk gene of ASD, or by maternal inflammation (MI). Exposure to C4b led microglia to perform excessive synaptic pruning, which in turn manifested ASD-like phenotypes. Furthermore, we observed that removing microglia could improve synaptic functions, while the complete knockout of C4b could rescue all observed autistic phenotypes. The expression of C4b was contingent upon RNA-DNA hybrids formed by the reactivation of Endogenous Retroviruses (ERVs).Interestingly, the pharmacological reversal of this retrotranscriptional process with FDA-approved HIV medications significantly reduced C4b levels and ameliorated the symptoms of ASD. Our findings illuminate the pivotal role of C4b in microglia-driven synaptic pruning linked to ASD and suggest that targeting ERV reactivation could be a promising therapeutic strategy with existing FDA-approved HIV drugs.

overall_design: The gene expression profiling analysis for the cortex of Ctrl and mG-cKO mice at P1,P7,P14,P45 and Ctrl，mG-cKD，mG-cKO，mG-cKD-RTI，mG-cKO-RTI mice at P21

first: Shaoxuan

last: Chen


title: The emergence of multiple testicular cell lineages in human stem cell-derived testis-like organoids [RNA-Seq]

first: Svenja

last: Pachernegg

overall_design: RNA seq profiling of hiPSCs (day -1 of differentiation) and hiPSC-derived testisl-like organoids at day 18 of differentiation

first: Gorjana

last: Robevska

first: Lucas

last: Ferreira

first: Natalie

last: Charitakis

first: Jinchao

last: Gu

first: Eliza

last: Martin

first: Jan

last: Terhag

first: Denis

last: Bienroth

first: Jocelyn

last: van den Bergen

first: Sean

last: Wilson

first: Ben

last: Rollo

first: Melissa

last: Little

first: Mirana

last: Ramialison

first: Andrew

last: Sinclair

first: Katie

last: Ayers


title: RNA-seq Profiling of Response to Cisplatin and Gemcitabine Chemotherapy in Advanced Urothelial Carcinoma: An External Validation Cohort

city: Incheon

first: Juwon

last: Kang

address: 85, Songdogwahak-ro

department: College of Pharmacy

country: South Korea

institute: Yonsei University

summary: This dataset includes RNA sequencing data from formalin-fixed paraffin-embedded (FFPE) tumor samples of advanced urothelial carcinoma patients treated with cisplatin and gemcitabine combination chemotherapy at Pusan National University Yangsan Hospital (PNUYH). RNA was extracted using the RNeasy FFPE kit (Qiagen) and sequenced on the Illumina platform using the SureSelectXT RNA Direct Reagent Kit (Agilent) for paired-end sequencing. Raw sequencing data underwent quality control and trimming using Trimmomatic-0.39-1, followed by sequence alignment using STAR 2.7.8a and expression quantification using RSEM 1.3.3. Treatment responses were evaluated according to RECIST v1.1 criteria. This dataset serves as an external validation cohort for a deep learning-based chemotherapy response prediction model in urothelial carcinoma.

overall_design: RNA-seq analysis of pre-treatment FFPE tumor samples from 10 stage IV bladder cancer patients who received palliative gemcitabine-cisplatin chemotherapy (3 non-responders and 7 responders, as determined by RECIST v1.1 criteria).

first: Kwonoh

last: Park

first: Sang-Bo

last: Oh

first: Jong Kil

last: Nam

first: Tae Un

last: Kim

first: Hwaseong

last: Ryu

first: Yong Kan

last: Ki


title: Genome-wide transcriptome analysis upon KSHV lytic reactivation

first: Soo Mi

last: Lee

summary:
Purpose: To characterize genome-wide mRNA expression profiles in the context of Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation.
Methods: We utilized a well-established model of KSHV reactivation, the doxycycline (Dox)-inducible KSHV producer cell line iSLK.219, which contains a latent KSHV genome and a Dox-inducible KSHV lytic switch protein RTA (replication and transcription activator) to mediate efficient reactivation and entry into the lytic cycle upon Dox treatment. We performed mRNA-sequencing (mRNA-seq) of RNA isolated from latent KSHV-infected iSLK.219 cells at 0 h or lytic iSLK.219 cells at 72 h post Dox-induced KSHV lytic reactivation using Illumina. The mappable reads were aligned to the human genome or the KSHV genome using Bowtie.
Results: We analyzed global transcriptome changes in iSLK.219 cells during the latency to lytic transition and found that reactivated lytic iSLK.219 cells exhibited an increased abundance of cellular genes involved in cell cycle, DNA replication, and nuclear division, consistent with lytic infection activating mitogenic signaling to support viral DNA replication. In addition, expression of key viral lytic genes with strong mitogenic activities, including vIL-6 (K2), K1, and the KSHV-encoded chemokines, vCCL1 (K6), vCCL2 (K4) and vCCL3 (K4.1), were markedly induced during lytic KSHV replication.
Conclusions: These results confirm that the gene expression profile of reactivated lytic iSLK.219 cells exhibit some key hallmark features of KSHV lytic reactivation.

first: SooMi

first: Frank

last: Slack


title: Phosphorylation of SF3B1 by CDK11 1 orchestrates spliceosome activation via SNIP1 dependent RES complex recruitment

city: Pamplona

first: Igor

last: Ruiz de los Mozos

state: Nyp

address: C. del Sadar s/n

department: Department of Personalized Medicine

country: Spain

institute: NASERTIC

summary: Splicing Factor 3b Subunit 1 (SF3B1), a core component of the spliceosome, undergoes dynamic phosphorylation and dephosphorylation during the splicing cycle to regulate pre-mRNA splicing. Twenty-eight threonine/proline repeats are phosphorylated by CDK11 during spliceosome activation and remain phosphorylated in the catalytically active spliceosomes. The function of phosphorylated SF3B1 (P-SF3B1), and the identity of spliceosomes stalled by CDK11 inhibition remain unclear. Using quantitative proteomics of chromatin-associated spliceosomes, we identify a previously uncharacterized intermediate complex BOTS964, arrested by CDK11 inhibitor OTS964, that incorporates the nineteen-related (NTR) but not nineteen (NTC) complex. iCLIP-seq revealed that P-SF3B1 engages with the U6 snRNA internal stem-loop (ISL), suggesting a potential role in stabilizing the RNA catalytic core. We further demonstrate that P-SF3B1 is recognized by forkhead-associated (FHA) domain of SNIP1, which promotes recruitment of retention and splicing (RES) complex during spliceosome activation. Acute SNIP1 depletion disrupts RES incorporation, causes widespread splicing defects, and promotes hyperphosphorylation of SF3B1 by CDK11. Mutations in SNIP1 FHA domain, including the neurodevelopmental disorder associated E366G variant, impair P-SF3B1 binding, pre-mRNA splicing, and cell viability. Together, these findings uncover the phosphorylation-dependent CDK11/P-SF3B1/SNIP1 signaling axis that is critical for pre-mRNA splicing and cellular proliferation and provide a mechanistic insight into its dysregulation in disease.

overall_design: Examination of P-T211-SF3B1 and P-T235-SF3B1 iCLIP in the presence or absence of OTS964 inhibitor on HCT116 cells

first: Pavla

last: Gajduskova

last: Ruiz de Los Mozos

first: Milan

last: Hluchy

first: Antonina

last: Myskova

first: Katerina

last: Zabrady

first: Peter

last: Manik

first: Neda

last: Dragisic

last: Hanakova

first: David

last: Potesil

first: Sara

last: Bologna

first: Jiri

last: Novacek

first: Caroline

middle: C

last: Friedel

first: Konstantinos

last: Tripsianes

first: Zbynek

last: Zdrahal

first: Dalibor

last: Blazek


title: The host-adapted commensal fungus provides cross-kingdom protection

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

summary: Fungi are ubiquitous in the environment and, like bacteria, are an integral part of the gut microbiome. However, unlike bacteria, fungal species that can stably colonize the murine gut and model commensal behavior remain elusive. Here, we show that Kazachstania pintolopesii, a dominant fungus found in pet store mice from geographically distinct regions, stably colonized laboratory mice. K. pintolopesii outcompeted other fungi and maintained stable colonization independent of gut bacteria. We find that K. pintolopesii does not induce a typical antifungal response in murine hosts locally in the gut or upon systemic challenge. Accordingly, K. pintolopesii colonization did not afford protection against systemic fungal infection by Candida albicans. Instead, K.pintolopessii colonization increased type 2 immune responses in the intestine and protected mice against helminth infection.

overall_design: To investigate the role of commensal fungus in the small intestine, murine-derived fungus was treated to mice via oral route. After two weeks, the small intestine of mice were harvested and processed for bulk RNA -seq.

first: Rebecca

last: Yunker

first: Mohammad

last: Hasan

first: Alex

last: Bruce

first: Kellie

last: Baldaro

first: Jessica

last: Pacia

first: Nicholas

middle: N

last: Jarjour

first: Lalit

middle: K

last: Beura

first: Shipra

last: Vaishnava


title: Histone acetylation-dependent clustering of BRD2 instructs transcription dynamics

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Bromodomain (BD) and extra-terminal domain (BET) proteins are key regulators of RNA polymerase II (Pol II)-mediated transcription and their BDs represent promising drug targets. Yet, the interplay between histone acetylation and the chromatin dynamics of individual BET proteins with respect to transcriptional regulation is not fully understood. Here in mouse embryonic stem cells, we uncover an essential role of BRD2 in maintaining RNA Pol II recruitment at promoters through its interaction with TFIID, which becomes particularly critical under the conditions of impaired pause release. Combining rapid protein degradation, chemogenomics and super-resolution microscopy, we show that MOF-mediated histone H4 acetylation promotes BRD2 chromatin association, which in turn enables BRD2 clustering. Accordingly, MOF depletion or deletion of the BRD2’s intrinsically disordered region largely recapitulates defects in promoter enrichment and clustering of the transcription machinery observed upon BRD2 loss. Thus, these findings support a model in which histone acetylation-dependent spatiotemporal dynamics of BRD2 coordinate the transcription machinery to regulate transcription initiation.

overall_design: ChIP-Seq, TT-Seq, Pro-seq and micro-C experiments were performed upon acute depletion of targeted factors using degron systems and/or PROTAC reagents.

first: Niyazi Umut

last: Erdogdu

first: Ronald

last: Oellers


title: Cytoplasmic competition between separate parental pronuclei in zygotes.

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

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

overall_design: Refer to individual Series


title: Co-cultivation of Schizosaccharomyces japonicus-Fusarium graminearum revealed the biocontrol effect of the yeast and the Fusarium-induced transcriptomic changes

city: Debrecen

first: Laszlo Attila

last: Papp

state: Hajdú-Bihar Vármegye

address: Egyetem tér 1.

department: Department of Genetics and Applied Microbiology

country: Hungary

institute: University of Debrecen

summary: The growth control of Fusarium species and modification of their harmful mycotoxins are of paramount importance. In this study, we used an in silico approach to find yeast species containing trichothecene-3-O-acetyltransferase homologous genes. Many species, including S. japonicus, whose genome contained seven copies of a gene putatively coding for such enzyme, were identified. Several of these paralogous genes could be induced by deoxynivalenol (DON). Toxin tolerance tests also revealed that S. japonicus had a stronger DON tolerance than the closely related S. pombe, whose genome did not contain such a gene. Growth and metabolome analysis showed that S. japonicus was able to inhibit F. graminearum and thus reduce the mycotoxin concentration of supernatant in the co-culture. The transcriptomic analysis of the yeast cells highlighted that several transport and membrane-associated genes, and genes putatively encoding oxidoreductases, transferases, or hydrolases had altered mRNA levels after co-culturing with F. graminearum. Although the exact role of these genes requires further investigation, our data can contribute to a better understanding of the mycotoxin-caused molecular changes and the identification of potential genes involved in defense and biological detoxification.

sample_organism:
Fusarium graminearum
Schizosaccharomyces japonicus yFS275

overall_design:
To investigate the changes in gene expression in Schizosaccharomyces japonicus during co-cultivation with Fusarium graminearum using RNA sequencing.
Samples:
Control S. japonicus (SJG - S. japonicus control)
Co-cultured S. japonicus with F. graminearum (FgSj - S. japonicus co-cultured)
Each samples have 3 technical replicates.
Control Groups: S. japonicus was grown in MXGB media.
Co-cultivation Groups: S. japonicus and F. graminearum were grown together to assess the impact of co-cultivation on gene expression.

first: Laszló

last: Attila Papp

first: Lajos

last: Ács-Szabó

first: Gyula

last: Batta

first: Ida

last: Miklós


title: Serological type I interferon promotes AIM2 inflammasome dysregulation in lupus patients

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: The Absent in Melanoma 2 (AIM2) inflammasome is a crucial producer of IL-1beta and IL-18 upon double-stranded (ds)DNA sensing but its role in SLE remains ambiguous. We aimed to investigate the involvement and underlying mechanism leading to AIM2 inflammasome dysregulation in lupus patients. Serological factors leading to the perturbed AIM2 inflammasome response was tested by in vitro culture of primary monocytes. SLE patients’ sera and recombinant interferon (IFN)-alpha could promote AIM2 inflammasome activity by augmenting AIM2 expression. We compared the transcriptome profile changes in primary human monocytes upon exposure to SLE serum and type I interferon by RNA-seq. Our findings revealed a novel pathway by which serological type I IFN propagates innate immune dysfunction in SLE via the STAT1-STAT2/AIM2 inflammasome axis in monocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in healthy human monocytes upon SLE serum stimulation (vs. HC serum stimulation) and type I IFN stimulation (vs. untreated control). Each treatment group consists of three biological replicates.

first: Jia

last: Chow

first: Vera

last: Chan


title: The effect of temporal BCAT1 inhibition on activated human CD8+ T cells

city: Washington

first: Adonia

middle: Evangelos

last: Papathanassiu

state: DC

address: 416 Marietta PL, NW

institute: Ergon Pharmaceuticals LLC

summary: Branched chain amino acid transaminase 1 (BCAT1) moderates iron balance during CD8+ T cell activation by limiting the conversion of iron regulatory protein 1 (IRP1) to aconitase 1 (ACO1). BCAT1 inhibition (BCAT1i) increases ACO1 activity, prevents iron uptake by activated CD8+ T cells, increases iron-sulfur (Fe-S) clusters in the mitochondria, arrests the timely degradation of nuclear ACO1, and inhibits CD8+ T cell differentiation in vitro and in vivo. The effects of BCAT1i on CD8+ T  cell activation are reversible and temporal BCAT1i yields CD8+ T cells with increased effector functions. CD8+ T cells, which were activated in the presence of ERG245 (BCAT1 inhibitor) for 24h and cultured for an additional 48h without it, upregulated genes that support bioenergetics processes such as OXPHOS, glycolysis, FA metabolism.

overall_design: CD8+ T cells were isolated from the peripheral blood of 3 individual donors. Approximately 3x106 cells were activated with anti-CD3/anti-CD28 Dynabeads for 24h in the presence or absence of 100 mM ERG245. The beads were subsequently removed, media were replenished with complete RPMI media, and the cells were cultured for and additional 48h. The cells were collected 72 hrs after initiation of activation.

middle: E


title: The nBAF complex subunit CREST/SS18L1 regulates hippocampal memory processes via tyrosine 397 and histone acetyltransferase CBP

city: Irvine

first: Kousha

last: Changizi

state: CA

address: 4038 Donald Bren Hall

department: Computer Science

institute: University of California, Irvine

summary: Chromatin modifying/remodeling machinery are important for learning-induced transcriptional activity, yet it remains unclear how they coordinate to drive de novo gene expression for memory formation. Here, we examine the transcription factor known as calcium-responsive transactivator (CREST) in memory formation, synaptic plasticity and learning-induced gene expression. CREST is known to bind major chromatin modifying and remodeling machinery via interaction with CREB-binding protein (CBP) and brahma-related gene 1 (BRG1), respectively. In silico modeling of CREST identified tyrosine 397 (Y397) within the CBP binding domain. Expression of a CREST Y397F point-mutant impairs long-term potentiation and memory. Conversely, expression of a CREST Y397D point-mutant enhances memory in a CBP-dependent manner. Differential gene expression analysis reveals distinct CREST Y397-regulated signatures during memory consolidation. CBP acts through CREB and post-translation modifications to affect memory, but the findings of this study argue for the consideration of the CREST-CBP interaction and Y397 accessibility as factors for memory processes.

overall_design:
To investigate the contribution of CREST to long-term memory formation, we designed condtions for expressing a phospho-null and -mimetic in the adult dorsal hippocampus.
We performed differential gene expression analysis to examine learning-induced gene profiles across 5 distinct conditions consisting of homecage, vehicle and CREST phospho-mutants in 2 different training periods of OLM.

first: Franklin

last: Garcia

first: Maria Farias

last: De Albuquerque

first: Vanessa

last: Johnson

first: Enikö

last: Kramár

last: Changizi Ashtiani

first: Sherif

last: Abdelkarim

first: Agatha

middle: S

last: Augustynski

first: Dina

middle: P

last: Matheos

first: Joseph

last: Picone

first: Tracy

last: Fetterly

first: Alyssa

last: Rodriguez

first: Jessica

last: Childs

first: Angela

last: Gomez-Arboledas

first: Julia

last: Winter

first: Elizabeth

last: Heller

first: Pierre

last: Baldi

first: Marcelo

middle: A

last: Wood


title: Rapid disassembly and Piwi-independent reassembly of Drosophila piRNA cluster heterochromatin following acute heat shock

city: Worcester

first: Samantha

last: Ho

address: 373 Plantation St.

department: Department of Molecular Medicine

institute: University of Massachusetts Chan Medical School

summary: Environmental stress activates transposons and is proposed to generate genetic diversity that facilitates adaptive evolution. piRNAs guide germline transposon silencing, but the impact of stress on the piRNA pathway is not well understood. In Drosophila, the Rhino-Deadlock-Cuff complex (RDC) drives transcription of clusters composed of nested transposon fragments, generating precursors that are processed into mature piRNAs in the cytoplasm. We show that acute heat shock triggers rapid, reversible loss of RDC localization and cluster transcript expression with coordinate changes in the cytoplasmic processing machinery. Maternal piRNAs bound to Piwi are proposed to guide Rhino localization to clusters during early embryogenesis. However, RDC relocalization after heat shock is accelerated in piwi mutants and delayed in thoc7 mutants, which disrupt piRNA precursor binding to THO complex, and we show that maternally deposited piRNAs are dispensable for RDC localization to the major 42AB cluster. Cluster specification is reconsidered in light of these findings.


title: Rapid disassembly and Piwi-independent reassembly of Drosophila piRNA cluster heterochromatin following acute heat shock [RNA-seq]

summary: Environmental stress activates transposons and is proposed to generate genetic diversity that facilitates adaptive evolution. piRNAs guide germline transposon silencing, but the impact of stress on the piRNA pathway is not well understood. In Drosophila, the Rhino-Deadlock-Cuff complex (RDC) drives transcription of clusters composed of nested transposon fragments, generating precursors that are processed into mature piRNAs in the cytoplasm. We show that acute heat shock triggers rapid, reversable loss of RDC localization and cluster transcript expression with coordinate changes in the cytoplasmic processing machinery. Maternal piRNAs bound to Piwi are proposed to guide Rhino localization to clusters during early embryogenesis. However, RDC re-localization after heat shock is accelerated in piwi mutants and delayed in thoc7 mutants, which disrupt piRNA precursor binding to THO complex, and we show that maternally deposited piRNAs are dispensable for RDC localization to the major 42AB cluster. Cluster specification is reconsidered in light of these findings.

overall_design: Long and small RNA sequencing to evaluate the effect of heat stress or the loss of maternal piRNAs on gene/transposon expression and small RNA production.

first: Nicholas

last: Rice

first: Zhiping

last: Weng

first: William

last: Theurkauf


title: Targeting RNase H2: A Dual Mechanism Strategy to Elevate Replication Stress, DNA Damage, and Antitumor Immunity in Triple-Negative Breast Cancer

status: Public on Feb 23 2026

city: Houston

first: Thai Quynh Anh

last: Nguyen

state: TX

address: 6565 MD Anderson Blvd

department: Systems Biology

institute: The University of Texas MD Anderson Cancer Center

summary: Triple-negative breast cancer (TNBC) lacks effective targeted therapies and carries a poor prognosis. TNBC cells escape oncogene-induced senescence and adapt to elevated replication stress. Here, we show that cells escaping senescence depend on overexpression of RNase H2, which removes misincorporated ribonucleotides from genomic DNA. RNASEH2A, the catalytic subunit of RNase H2, is overexpressed in TNBC tumors and correlates with poor survival. Genetic silencing or pharmacological inhibition of RNase H2 selectively impairs TNBC viability while sparing non-tumorigenic mammary epithelial cells and suppresses tumor growth in vivo. Mechanistically, RNase H2 inhibition increases replication stress, DNA damage, and cytosolic single-stranded DNA accumulation, triggering innate immune activation and upregulation of T cell–recruiting chemokines. RNase H2 inhibition synergizes with ATR and PARP inhibitors and enhances immune checkpoint blockade efficacy. Together, these findings identify RNase H2 as a therapeutic vulnerability in TNBC and support combined strategies integrating DNA damage modulation and immunotherapy.

overall_design: RNAseq profile of wildtype MDA-MB-231 and their knockout derivatives of RNASEH2A

first: Jing

last: Zhang

first: Hui

last: Dai

first: Aysegul

last: Murat

first: Yong

last: Du

first: Daniel J

last: McGrail

first: Funda

last: Meric-Bernstam

first: Shiaw-Yih

last: Lin


title: Rapid disassembly and Piwi-independent reassembly of Drosophila piRNA cluster heterochromatin following acute heat shock [CUT&RUN]

overall_design: Cut and Run sequencing to evaluate Rhino binding in response to heat stress or loss of 42AB maternal piRNAs.


title: Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

institute: Tsinghua University

summary: Advancing CRISPR/Cas9 genome editing demands a thorough understanding of its associated risks.Yet, most of risk assessments have focused on the mutagenic effects stemming from off-target cleavage in gene-coding regions, largely neglecting the implications of cleavage within the extensive non-coding genome. We observed that CRISPR/Cas9-induced DNA cleavage, even at sites several kilobases away from the nearest regulatory elements, can trigger premature differentiation of somatic neural stem cell in vivo.Leveraging a refined multi-omics technology, we delved into the consequences of CRISPR/Cas9-induced DNA cleavage in these non-coding regions. Our findings reveal an impact, especially pronounced in cells with high stemness, where cleavage-induced disruptions can span long ranges, potentially culminating in the loss of stemness. These effects are tied to extensive chromatin perturbations. Building on this understanding, we used chromatin perturbation as a key marker to refine gene editing technologies that could minimize such disruptions.This key finding illuminates the path towards the development of safer and more broadly applicable genome editing technologies.

overall_design: See individual sub-series.

first: Ming

last: Zhu

first: Junsong

last: Yuan

first: Qiuchen

last: Meng


title: Aub, Vasa and Armi concentration in phase separated nuage is dispensable for piRNA biogenesis and transposon silencing

summary: The piRNA biogenesis machinery localizes to phase-separated nuage granules, but nuage function is not well understood. We therefore assayed nuage composition, piRNA expression, and transposon silencing in Drosophila mutants that disrupt piRNA precursor production and nuclear export, ping-pong amplification, and phased piRNA biogenesis. These mutations destabilize the genome and activate Chk2 signaling, and chk2/mnk double mutants were therefore analyzed in parallel. Aub and Vasa are required for ping-pong amplification, and Armi promotes phased piRNA processing. We show that Chk2 activation releases Aub and Vasa from nuage and that piRNA precursors are required for nuage localization of the ping-pong and phased biogenesis machinery. However, this analysis also indicates that Vasa, Aub, and Armi concentration in nuage is dispensable for piRNA production and transposon silencing, indicating that dispersed cytoplasmic proteins can drive these processes. We speculate that nuage sequesters silencing effectors, which are released by Chk2 in response to transposon mobilization.

overall_design: We evaluated long RNA transcript expression and small RNA expression patterns in various piRNA pathway mutants and corresponding mnk (Chk2) double mutants.

first: Tianxiong


title: Lethal Mtb dissemination occurre in the combined absence of lymhocytes and is independent of innate immune response

city: Cairns

first: Andreas

last: Kupz

state: Queensland

address: McGregor Road, Smithfield

department: Australian Institute of Tropical Health and Medicine

institute: James Cook University

summary: About two billion people are latently infected with Mycobacterium tuberculosis (Mtb), which can reside in multiple organs, including the lymphatics. The risk of latent Mtb infection (LTBI) reactivation increases with immunosuppression, such as HIV coinfection, yet the immunological correlates that maintain LTBI remain largely elusive. Using a mouse model of contained lymphatic Mtb infection we dissect the drivers of containment versus reactivation. We show that immunosuppression-induced dissemination of lymphatic Mtb and ensuing progressive disease can be prevented by vaccination with BCG or recombinant BCG even in the absence of CD4+ T cells. Multi-parameter imaging, spatial transcriptomics and network analysis reveal that anti-CD4-mediated immunosuppression triggers distinct repositioning of non-CD4 immune cells at the edge of TB lesions in cervical lymph nodes. Although B cell numbers increase, they prove dispensable for Mtb containment during CD4+ T cell loss. Using immune cell-deficient mice, cell depletion and adoptive transfers, we reveal that CD8+ T cells mediate vaccination-induced prevention of Mtb dissemination in the absence of CD4+ T cells, informing LTBI management in immunocompromised individuals.

overall_design: To experimentally address the role of these cells for lymphatic LTBI containment, we induced lymphatic Mtb infection in a variety of genetically modified mouse strains with and without vaccination. First, we infected wild-type C57BL/6 mice, B6.muMT-/- mice that lack mature B cells 48, B6.Rag1-/- mice that lack mature B and T cells 49 and B6.Rag2-/-Il2rg-/- mice that lack mature B, T and NK cells 50 i.d. with Mtb. Two groups of C57BL/6 mice received anti-CD4 mAb treatment either alone or in addition to Mtb infection and naïve mice were also included as controls.3- 5 mice per group.


title: Unraveling linc00645: A Wnt-regulated lncRNA driving epithelial-mesenchymal transition through the linc00645/miR-452-5p/vimentin axis in triple-negative breast cancer

city: Gandhinagar

first: Amit Kumar

last: Pandey

state: Gujarat

address: NIPER-Ahmedabad, Palaj

department: Biotechnology

country: India

institute: National Institute of Pharmaceutical Education and Research

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis and high recurrence rates. Wnt signaling plays a critical role in the pathogenesis of TNBC, with aberrant activation of this pathway observed in many cases. Emerging evidence suggests that long non-coding RNAs (lncRNAs) may modulate key signaling pathways, including Wnt signaling, in TNBC. In this study, we investigated the interplay between lncRNAs and Wnt pathway activation in TNBC. RNA-Seq analysis comparing Wnt-positive and Wnt-negative cell lines derived from MDA-MB-231 identified linc00645 as a highly upregulated lncRNA in Wnt-activated cells. Further gene ontology analysis revealed that the differentially expressed lncRNAs, including linc00645, were enriched in pathways related to epithelial-to-mesenchymal transition (EMT), a key process in cancer metastasis. To validate these findings, recombinant human Wnt3A was used to activate the Wnt pathway in MDA-MB-231 cells. RT-qPCR confirmed the upregulation of linc00645 in Wnt-activated cells. Functional studies demonstrated that knockdown of linc00645 led to a significant reduction in cell proliferation and migration in TNBC cells, suggesting its oncogenic role. Moreover, mechanistic investigations revealed that linc00645 directly interacts with miR-452-5p, leading to the downregulation of this microRNA and the upregulation of the mesenchymal marker vimentin, further promoting EMT. These findings suggest that linc00645 functions as an oncogenic lncRNA in Wnt-activated TNBC by regulating the linc00645/miR-452-5p/vimentin signaling axis. Targeting this axis could represent a novel therapeutic strategy for treating TNBC. This study highlights the potential of linc00645 as a promising target for interventions aimed at inhibiting TNBC progression.

overall_design: The 7TGP vector, which has an EGFP encoding sequence downstream of an inducible promoter with seven Tcf repeats (7xTcf-eGFP) 27 was stably transfected into low passage MDA-MB-231 cells. Fluorescence-activated cell sorting (FACS) was then employed to enrich for EGFP-positive (EGFP+) or EGFP-negative (EGFP-) cells from the MDA-MB-231 cells stably transfected with the 7TGP vector. The expanded EGFP+ and EGFP- cells were then again subjected to FACS. After eight rounds of expansion followed by FACS, the resultant MDA-MB-2317TGP-POS cell line was greater than 80% EGFP+, while the MDA-MB-2317TGP-NEG cell line was greater than 95% EGFP-.

first: Samarth

last: Kansara

first: Manoj

last: Garg

first: Ramón

last: García-Areas

first: Thierry

last: Dubois


title: A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements [CLIP]

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: How piRNA-mediated genome defense achieves specificity against transposons while sampling a complex transcriptome has remained unresolved. Here we show that piRNA biogenesis operates through pervasive, non-specific sampling of cytoplasmic RNAs, with specificity imposed by tissue-specific molecular modules that exploit intrinsic vulnerabilities of transposons. In Drosophila somatic cells, the specificity factor Yb steers basal processing towards uridine-rich RNAs—automatically capturing antisense retrotransposon transcripts due to their intrinsically adenosine-biased genomes. In germline cells lacking Yb, basal sampling generates naïve piRNAs loaded into catalytically active Argonaute proteins, which trigger autocatalytic ping-pong amplification upon encountering complementary targets. In both contexts, transposon mobility facilitates the production of antisense RNAs that enable either biased processing or amplification. Thus, piRNA clusters, long associated with pathway specificity, act as sources of transposon antisense sequences, while specificity arises from layering distinct molecular mechanisms onto a shared foundation of indiscriminate transcript sampling, enabling robust and adaptable genome defense without predefined templates.

overall_design: To define transcriptome-wide RNA binding sites of the piRNA-pathway factor Yb in Drosophila melanogaster ovarian somatic cells (OSCs), we performed UV crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) using a monoclonal anti‑Yb antibody. OSCs were washed with PBS and UV‑crosslinked on ice at 254 nm (200 mJ/cm² twice with 90° rotation). Crosslinked cells were lysed, clarified, and treated with RNase I to fragment RNA, and Yb–RNA complexes were isolated by immunoprecipitation on antibody-coupled magnetic beads under stringent high-salt wash conditions. Protein–RNA complexes were resolved by SDS–PAGE, transferred to nitrocellulose, excised based on radiolabeled signal, and recovered RNA was used to generate gel-based small RNA libraries for Illumina sequencing (single-end 50 bp). The experiment includes two biological replicates of Yb CLIP (CLIP_YB_Rep1, CLIP_YB_Rep2) and an input control (CLIP_INPUT). Processed data include strand-specific bigWig coverage tracks for all reads and uniquely mapped reads (sense and antisense) to enable comparison of Yb-bound RNA profiles across replicates and relative to input.

first: W. Y. Wylan

last: Wong

first: Alexander

last: Tsarev

first: Rippei

last: Hayashi

first: Julius

last: Brennecke


title: A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements [smallRNA]

overall_design: Sequencing of total or Argonaut bound small RNAs from wildtype and piRNA factor depleted cell lines. In addition, small RNA data from cell lines harboring reporter constructs to test piRNA biogenesis precursorSequencing of total and Argonaute-bound small RNAs from wild-type and piRNA factor–depleted cell lines. In addition, sequencing of small RNAs from cell lines harboring reporter constructs to test piRNA precursor specificity and biogenesis. specificity.


title: A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements [RNA]

overall_design: RNA-seq and TT-SLAM-seq profiling of cultured Drosophila ovarian somatic cells (OSCs) to investigate the molecular logic of piRNA biogenesis and specificity. The experimental design includes: (1) RNA-seq analysis of wildtype OSCs and their derivatives following siRNA-mediated knockdown of key piRNA pathway factors, including Yb (siYB) and Armitage (siARMI), compared to control (siLUC) to determine their impact on steady-state transcript levels and piRNA precursor selection. (2) TT-SLAM-seq (Transient Transcriptome Sequencing with SLAM-seq) using 10-minute 4-thiouridine (4sU) labeling to measure nascent transcriptional output and RNA turnover rates in OSCs.


title: A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements


title: Erk3 deletion drives oxidative adaptations in skeletal muscle

city: Warsaw

first: Grzegorz

last: Sumara

address: L Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology PAS

summary: Skeletal muscle plays a central role in whole-body energy expenditure and metabolic homeostasis, and improving its mitochondrial function and oxidative fiber profile is considered an effective strategy to counteract diet-induced metabolic impairments, although the molecular regulators of these adaptations are not yet fully understood. Erk3 has been implicated in myotube differentiation and in skeletal muscle adaptations to aerobic exercise; however, its potential role in skeletal muscle during diet-induced metabolic dysfunction remains to be determined.

overall_design: In this study, we used mice with striated muscle-specific Erk3 deletion alongside in vitro cultured C2C12

first: Angel

last: Loza Valdes

first: Carlos

last: Acosta-Gallo

first: Toufic

last: Kassouf

first: Andrei

last: Belykh

first: Dominika

last: Malińska

first: Katia

last: El Ghoz

first: Rabih

last: El-Merahbi

first: Filip

last: Dziaczkowski

first: Kasia

last: Kolczyńska-Matysiak


title: Quiescent neural stem cells transiently become neuronal-like to coordinate long-range reactivation

city: New York

first: Jocelyn L.Y.

last: Tang

address: 540 1st Avenue

country: United Kingdom

institute: NYU School of Medicine

summary: Reactivation of quiescent neural stem cells (qNSCs) is a coordinated process that generates new neurons and glia to maintain homeostasis or enable repair post-injury. Here, we discovered that NSC reactivation in Drosophila follows a hierarchical sequence, whereby anterior qNSCs in the brain lobes control the timely reactivation of more posterior qNSCs in the ventral nerve cord. To achieve this, qNSCs transiently activate neuronal genes and contact neurons to relay reactivation. This transient neuronal state is specific to qNSCs, as neuronal genes are switched off after stem cells resume proliferation. Our results reveal long-range communication between qNSCs to coordinate reactivation across the entire CNS, enabled by a transient, remarkably plastic, neuronal state that allows direct interaction with axons.

overall_design: Aim of the experiment is to identify differentially expressed genes between quiescent and reactivated NSCs, The CNS from stage 17 embryos (representing quiescence) and from larval 24 ALH (representing reactivated) were isolated, dissociated and NSCs were enriched by FACS.

first: Andrea H.

last: Brand


title: Persistent Activation of Monocytes/Macrophages and Cell Senescence in SIV-Infected Macaques on ART

city: New Orleans

first: Xuebin

last: Qin

state: LA

address: 1430 Tulane Avenue

institute: Tulane University

summary: Despite effective viral suppression with antiretroviral therapy (ART), people living with HIV (PLWH) experience persistent inflammation, immune dysfunction, and premature onset of cardiovascular and aging-related comorbidities. To define the underlying mechanisms, we performed longitudinal transcriptomic profiling in peripheral blood mononuclear cells (PBMCs) from a cohort of simian immunodeficiency virus (SIV)-infected rhesus macaques spanning four key stages: pre-infection, acute infection, short-term ART, and long-term ART. Bulk RNA sequencing revealed dynamic immune remodeling across infection and treatment. Acute SIV infection induced robust antiviral and inflammatory programs, with upregulation of interferon-stimulated genes (ISGs), IL-27, JAK/STAT, and NF-κB signaling, coupled with suppression of T- and B-cell activation pathways. Short-term ART effectively reversed these transcriptional perturbations, restoring adaptive immune gene expression and reducing innate antiviral responses to near-baseline levels. In contrast, chronic SIV infection on long-term ART maintained viral suppression but was characterized by reactivation of innate immune pathways, including TLR2/TLR4/MYD88, NF-κB, and inflammasome (NLRP3/NLRP12, caspase-1) signaling, along with sustained macrophage activation, platelet/coagulation signaling, and senescence-associated secretory phenotype. Protein analyses confirmed persistent CASPASE-1 and NF-κB activation in spleen tissue. Pathologic evaluation of a carotid artery from an SIV-infected, long-term ART–treated macaque revealed macrophage-rich plaques with p21⁺ senescent cells with intraluminal thrombus formation, recapitulating key features of HIV-associated atherogenesis. Together, these findings demonstrate that while ART normalizes acute infection–induced immune dysregulation, chronic SIV infection sustains a chronic, macrophage- and TLR-driven inflammatory state linked to vascular injury and aging process regardless of long-term suppression of viremia. Targeting inflammasome, NF-κB, and senescence pathways may mitigate non-AIDS comorbidities in PLWH.

overall_design: We randomly selected 4 animals from a previous cohort that had longitudinal PBMC samples collected at four key time-points: pre-SIV infection (day 0), 6 weeks post-SIV infection (acute SIV infection), after 2 months of short-term ART, and after one year (12 months and 20 months) of long-term ART, for RNA-seq analyses. This cohort effectively models the major stages of HIV infection in humans: 1) pre-infection, 2) acute HIV infection, 3) HIV infection on short-term ART treatment, and 4) chronic HIV infection on long-term ART treatment as seen in PLWH. Of note, the plasma samples from two of the animals in group 4 chronic HIV infection on long-term ART treatment were collected at two time points (12 months and 20 months), hence adding to 6 samples in that group. To comprehensively profile the dynamic transcriptomic changes in the PBMCs collected before and after SIV infection, with or without ART treatment, we conducted the bulk RNA-seq and performed six pairwise comparisons: 1) acute SIV-infection vs. baseline, 2) acute SIV-infection on short-term ART vs. acute SIV-infection, 3) acute SIV-infection on short-term ART vs baseline, 4) chronic SIV-infection on long-term ART vs acute SIV-infection, 5) chronic SIV-infection on long-term ART vs baseline, and 6) chronic SIV-infection on long-term ART vs chronic SIV-infection on short-term ART.

first: Yilin

last: Chen

first: Xiaofeng

last: Ding

first: Sonalika

last: Ray

first: Siva

last: Thirugnanam

first: Robert

last: Blair

first: Ahmad

last: Saied

first: Sergiy

last: Sukhanov

first: Jay

last: Kolls

first: Woong-Ki

last: Kim

first: Patrice

last: Delafontaine

last: Rappaport

first: Namita

last: Rout


title: Listerine® attenuates cytokine-induced inflammation and activates zinc–metallothionein responses in gingival fibroblasts

first: Reinhard

last: Gruber

address: Sensengasse 2a

institute: Medical University Vienna

summary: Gingival fibroblasts amplify periodontal inflammation by producing chemokines in response to pro-inflammatory cytokines. Mouth rinses directly contact the gingival tissues, yet their effects on host inflammatory signaling remain incompletely defined. This study investigated how a zinc-containing Listerine® formulation modulates IL-1β/TNF-α–induced responses in human gingival fibroblasts and compared these effects with zinc alone. Primary human gingival fibroblasts were stimulated with IL-1β and TNF-α in the presence or absence of Listerine®. Global transcriptional changes were analyzed by RNA sequencing and validated by quantitative PCR. CXCL8 secretion was quantified by immunoassay. Zinc ions and individual essential oil components were tested separately. Metal content was determined by inductively coupled plasma–mass spectrometry. IL-1β/TNF-α induced a broad inflammatory transcriptional program, including chemokines and innate immune–associated genes. Co-treatment with Listerine® consistently reduced the magnitude of cytokine-induced gene expression while preserving inducibility, indicating quantitative attenuation rather than suppression. Listerine® significantly decreased cytokine-induced CXCL1, CXCL2, and CXCL8 mRNA levels and reduced CXCL8 protein release. Transcriptomic profiling revealed strong induction of metallothionein family members. Zinc was identified as the predominant metal at biologically relevant concentrations. Zinc alone robustly induced metallothioneins but did not significantly reduce cytokine-induced chemokine expression. Individual essential oil components did not reproduce the inhibitory effect. Taken together, Listerine® constrains cytokine-driven inflammatory output in gingival fibroblasts while activating a zinc-associated metallothionein stress response. Zinc alone is insufficient to explain the anti-inflammatory phenotype, supporting a formulation-dependent host-modulating effect.

overall_design: We exposed gingival fibroblasts to IL-1β and TNF-α in the presence or absence of Listerine®. Global transcriptional changes were analyzed by RNA sequencing and validated by quantitative PCR. CXCL8 secretion was quantified by immunoassay. Zinc ions and individual essential oil components were tested separately. Metal content was determined by inductively coupled plasma–mass spectrometry.

first: Anna

last: Podesser

first: Xiaoyu

last: Huang

first: Panahipour

last: Layla


title: Synergistic role of riboflavin-auxotrophic Enterococcus for MR1 expression and in-tra-tumoral mucosal associated invariant T (MAIT) cell activation

city: Baltimore

first: Franck

last: Housseau

state: MD

address: 1651 E.Jefferson St

institute: Johns Hopkins University School of Medicine

summary: The role of mucosal invariant T (MAIT) cells in the lung tumor microenvironment re-mains poorly understood, especially in the setting of immune checkpoint inhibitors. We identified intratumoral MAIT cells from paired single cell RNA and TCR sequencing datasets of tumor infil-trating CD3 T cells isolated from non-small cell lung cancer tumors in patients receiving neoadju-vant PD-1 blockade therapy. MAIT cells were subclustered to identify conventional MAIT-associ-ated TCR clonotypes, which were then tested for the recognition of bacteria using a MAIT TCR capture functional assay. Strikingly, surveillance of intratumoral bacteria in lung cancer patients revealed Enterococcus spp. that are not directly recognized by MAIT cells but, nevertheless can synergize with exogenous riboflavin biosynthesis-derived metabolites to induce expression of MR1 by antigen presenting cells (APC, dendritic cells, B cells and mononuclear phagocytes). Enhanced MR1 cell surface expression resulted from enterococcal-mediated perturbation of an endo-lysosomal vacuolar pathway with recycling of early endosomal MR1 to the APC cytoplasmic membrane. Riboflavin auxotrophic Enterococcus spp may therefore exercise their beneficial im-munomodulatory functions upon immune checkpoint blockade treatment, at least in part, by pro-moting intratumoral MR1 expression and innate-like T cell activation. Our results indicate that composition of the intratumoral microbiome during immune checkpoint inhibitor treatment has the potential to impact the function of human intratumoral MAIT cells.

overall_design: RNA seq profiling of U266 cells incubated with PFA fixed 125 MOI of E.fecalis and E. coli alone or in combination with 6.25uM 5-A-RU

first: Pakhi

last: Birla


title: Transcriptional regulation by TES and TEAD1 in SNB19 glioblastoma cells: Cut&Tag

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

summary: This study uses Cleavage Under Targets and Tagmentation (Cut&Tag) chromatin profiling to map genome-wide binding sites of TES (TEAD1 Epigenetic Silencer, an engineered epigenetic silencer factor consisting of KRAB-hTEAD1(1-166)-DNMT3A/3L with V5 tag) and overexpressed wild-type TEAD1 (HA-tagged) in SNB19 glioblastoma cells. Cut&Tag was performed using the CUTANA protocol (EpiCypher). Three biological replicates were prepared for TES (detected via anti-V5) and TEAD1 (detected via anti-HA), with mouse IgG and rabbit IgG as negative controls. Peak calling identified binding sites for both factors, showing that TES largely preserves the DNA-binding specificity of wild-type TEAD1 while converting it into a transcriptional repressor.

overall_design: Cut&Tag chromatin profiling of SNB19 glioblastoma cells following the CUTANA CUT&Tag Protocol (EpiCypher): 3 TES replicates (anti-V5, detecting V5-tagged TES construct), 3 TEAD1 replicates (anti-HA, detecting HA-tagged overexpressed TEAD1), 1 mouse IgG control, 1 rabbit IgG control (8 samples total).

first: Eva

last: Baronchelli

first: Silvia

last: Ferretti

first: Antonella

last: Covino

first: Valerio

last: Benedetti

first: Edoardo

last: Bellini

first: Serena

last: Giannelli

first: Mirko

last: Luoni

first: Elisa

last: Ventura

first: Federica

last: Banfi

first: Gaia

last: Colasante

last: Ungaro

first: Vania

last: Broccoli

first: Alessandro

last: Sessa


title: Comprehensive molecular profiling of regenerated retinal neurons in the adult zebrafish

city: Ann arbor

first: Thanh

last: Hoang

state: Michigan

address: 1000 wall street

institute: University of Michigan ann arbor

summary: Unlike mammals, zebrafish possess a remarkable capacity to regenerate ablated retinal neurons. In response to cellular injury and death, Müller glia dedifferentiate into a stem cell state, and each gives rise to a single Müller glia-derived progenitor. Progenitors then proliferate and differentiate into to replace the ablated retinal neurons. This study aimed to determine if the injury context influences the quantity of regenerated neurons and to comprehensively identify the cellular and molecular characteristics and diversity of newly born regenerated neurons during regenerative neurogenesis. To definitely label Muller glia-derived regenerated neurons, we utilized a genetic lineage tracing line, Tg(mmp9:creERt2;Ola.actb2:loxp-dsRed-loxp-eGFP). By integrating this approach with scRNAseq and morphological profiling, we characterize quantity, molecular and morphological identity, and diversity of regenerated neurons across two distinct injury models, an intense light photolytic lesion or an intraocular injection of the excitotoxin, NMDA which procedures selective damage to photoreceptors or inner retinal neurons, respectively. Our data show that while regenerated neurons are biased toward the cell type originally ablated, both lesion modes consistently generate other cell types. This suggests a robust intrinsic neurogenic program present among Muller glia-derived progenitors. Transcriptome analysis demonstrates a high degree of similarity between regenerated and endogenous populations, indicating successful restoration of homeostatic molecular signitures. Finally, subtype analysis of amacrine cells show generation of diverse subtype and successful reestablishment of their neurochemical and morphological identities equivalent to their original counterparts. These findings demonstrate that regenerative neurogenesis in the zebrafish retina can faithfully reconstitute the specialized cellular diversity and molecular and structural complexity of the mature retina.

overall_design: The transgenic line, Tg(mmp9:creERt2;Ola.actb2:loxp-dsRed-loxp-eGFP), was utilized to perform lineage tracing of Müller glia-derived, regenerated neurons. Animals were subjected either to an intense light photolytic lesion or an intraocular injection of the excitotoxin, NMDA. Regenerated, eGFP+ retinal neurons at 14 days post lesion were collected via FACS. eGFP+ cells were loaded into the 10x Genomics Chromium Single Cell System and libraries were generated using V4 chemistry following the manufacturer’s instructions. Libraries were sequenced on the Illumina NovaSeq platform.

first: Hoang

last: Thanh

first: Nagashima

last: Mikiko

first: Awad

last: Sherine


title: Transcriptional regulation by TES and TEAD1 in SNB19 glioblastoma cells: RNA-seq

first: Michal

last: Kubacki

summary: This study investigates transcriptional regulation by TES (TEAD1 Epigenetic Silencer, an engineered epigenetic silencer factor targeting the YAP/TAZ-TEAD axis) in SNB19 glioblastoma cells using RNA-seq. TES was engineered by fusing the KRAB domain, the catalytic domain of DNMT3A together with DNMT3L, and the N-terminal 166 amino acids of TEAD1. RNA-seq was performed 48 hours after lentiviral transduction to identify differentially expressed genes upon TES expression compared to GFP control in three biological replicates per condition. TES expression induced widespread transcriptional repression of YAP/TAZ-dependent gene programs, with downregulated genes enriched for cell-cycle regulation and TEAD family transcription factor binding sites.

overall_design: RNA-seq profiling of SNB19 glioblastoma cells expressing TES (a synthetic TEAD1-targeting transcriptional silencer) versus GFP control. Three biological replicates per condition (6 samples total).

last: Baronchelli


title: Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from  SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

institute: Medical University of Vienna

summary: Respiratory viral infections caused by SARS-CoV-2 and Influenza virus pose significant public health concerns, with severe outcomes for at-risk and even healthy patients. While disease severity is often associated with dysregulated monocyte-macrophage activities in patients, emerging evidence highlights the active role of infected epithelial cells in early viral defense with subsequent implications on disease severity. We assessed the contribution of monocytes to host defense against respiratory viral infections and discovered that Ccr2-/-  mice exhibited a markedly worsened outcome, increased viral load and more severe lung damage following SARS-CoV-2 infection, whereas we found similar disease severity upon Influenza A virus (IAV) infection. Both viral infections prompted early monocyte infiltration in wild-type mice, and longitudinal RNA sequencing of sorted lung monocytes and monocyte-derived macrophages in SARS-CoV-2 and IAV infection revealed transcriptionally similar yet temporally distinct gene expression patterns, including an induction of Interferon (IFN) type I and type II dependent genes. Interestingly, epithelial cell transcriptional responses differed significantly between SARS-CoV-2 and IAV infection. Our findings emphasize the significant role of epithelial cells in shaping the immune response during respiratory viral infections. The distinct interactions between epithelial cells, monocytes, and macrophages can lead to varying antiviral immune outcomes, as observed in SARS-CoV-2 and IAV infections.

overall_design: bulk RNA seq (Quantseq) of 2x 94 samples with RNA from 4 different cell types (Alveolar macrophages "trAM", Ly6C+ Monocytes "Mono", bone marrow derived alveolar macrophages "bmAM", Epithelial cells "EC"), 4 replicates/group,  from infected (SARS-CoV-2 "SC2", Influenza A Virus "IAV") and non-infected (PBS, timepoint 0Dpi) mouse lungs on different timepoints after the infection (2, 4, 8, 28 Days post infection - Dpi). Cells were FACS sorted directly into RLT buffer + 2-Mercaptoethanol. RNA was isolated with the micro RNA kit (Qiagen), frozen with liquid nitrogen and stored at -80 for at least 1 week.

first: Lisabeth

last: Pimenov

first: Riem

last: Gawish

first: Florian

last: Deckert


title: 10x 16plex flex scRNAseq with either uninfected or SARS-CoV-2 infected mouse lungs from WT or Ccr2-/- mice

summary: Respiratory viral infections caused by SARS-CoV-2 and Influenza virus pose significant public health concerns, with severe outcomes for at-risk and even healthy patients. While disease severity is often associated with dysregulated monocyte-macrophage activities in patients, emerging evidence highlights the active role of infected epithelial cells in early viral defense with subsequent implications on disease severity. We assessed the contribution of monocytes to host defense against respiratory viral infections and discovered that Ccr2-/-  mice exhibited a markedly worsened outcome, increased viral load and more severe lung damage following SARS-CoV-2 infection compared to WT animals. WT bone marrow transplanted in Ccr2-/-  mice could not mitigate disease severity upon SARS-CoV-2 infection. To assess cell type specific responses to SARS-CoV-2  in the presence and absence of monocyte recruitment, we sorted viable CD45+ and CD45- cells from uninfected and SC2-infected WT and Ccr2-/- lungs and performed single-cell RNA sequencing (scRNAseq) at day 1 post infection at a time point when monocyte recruitment is still limited even in WT mice. We found that Ccr2-/- mice mount an exaggerated inflammatory response as early as day 1 post SC2 infection in all cell types, with limited changes at baseline.

overall_design: 8 samples for 10x Chromium Flex scRNAseq for 16plex containing pooled  FACS sorted lung cells (sorted. CD45+, CD45-, Epithelial cells) to enrich for Epithelial cells and remove dead cells, from 2 different genotypes ("WT", "CCR2 KO"), in mock ("PBS"), or SARS-CoV-2 infection


title: Gene expression profile at single cell level of human bronchial epithelium cells cultured at the air-liquid interface (ALI) treated with CdCl2 (10µM) or DMSO (0,1%)

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: We use scRNA-seq to identify the  signature of CdCl2 expsosure of ALI culture. CdCl2 was dissolved in DMSO (0,1%) and the effect of DMSO is also reported.

overall_design:
ALI cultures from three healthy donnors were incubated for 6 hours (basal and apical sides) in medium, DMSO  0,1% or CdCl2 (10µM) in 0,1% DMSO.

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

first: Fadi

last: Abou Choucha

first: Rafaël

last: Lopes Goncalves

first: Thomas

last: Hermet

first: Jessica

last: Mille

first: Laetitia

last: Guardini

first: Mariem

last: Benkhedher

first: Caroline

last: Lacoux

first: Marine

last: Gautier-Isola

first: Baharia

last: Mograbi

first: Jérémie

last: Roux

first: Françoise

last: Cottrez

first: Bernard

last: Mari

first: Hervé

last: Groux

first: Claude

last: Pasquier

first: Roger

last: Rezzonico

first: Georges

last: Vassaux


title: Directed Differentiation of Trophoblast Stem Cells Provides a Useful In Vitro Model of Placenta Development in Cattle [RNA-Seq]

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

summary: By utilizing a previously established bovine trophoblast stem cell (bTSC) model, we developed an optimized differentiation strategy to capture the complete developmental trajectory of placental binucleate cells (BNCs). This study provides new insights, demonstrating that extending the culture duration allows bTSCs to overcome previous developmental bottlenecks and faithfully recapitulate the in vivo BNC program, including the expression of late-stage secretory markers. Furthermore, we have shown that this tractable in vitro system serves as a robust platform for functional genomics, as evidenced by our validation of the transcription factor GCM1 as a driver of BNC differentiation.

overall_design: The trophoblast cells from undifferentiated, day 4 of differentiation and day 10 of differentiation were collected and RNA was extracted using RNAsy microkit and sequenced by Azenta Life Sciences using three replicates each time point. Libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina and sequenced (2 x 150 bp paired end) using Illumina instrument (4000 or equivalent). Raw sequence data (.bcl files) generated from Illumina Hiseq was converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software.

first: Abdallah

last: Abdelhady

first: Sarayut

last: Winuthayanon

first: Sofia

middle: M

last: Ortega

last: Spencer


title: HDAC1/2 -mediated repression of Wnt receptors controls polarity orientation in epidermal stem cells in C. elegans.

city: London

first: Mar

last: Ferrando Marco

address: Imperial College Road

institute: Imperial College London

summary: In this study we employ TargetedDamID  to identify targets within the epidermis for the histone deacetylase HDA-1 that we identified as a key epidermal development regulator.

overall_design: Identification of HDA-1 genome-wide binding by epidermis-specific expression of HDA-1:Dam fusion in C. elegans. Samples containing the NLS-GFP:dam fusion only constitute control samples.

last: Ferrando-Marco

first: Bea

last: Garcia del Valle

first: Mark

last: Hintze

first: Lucy

last: Narunsky

first: Amelia

last: Lin

first: Junyue

last: Huang

first: Shannon

last: Edwards

first: Michalis

last: Barkoulas


title: Directed Differentiation of Trophoblast Stem Cells Provides a Useful In Vitro Model of Placenta Development in Cattle [scRNA-seq]

overall_design: To assess cellular heterogeneity and differentiation dynamics in day-10 differentiated trophoblast cells, nuceli were extracted from snap frozen cells and submitted to the Genomics core at the university of Missouri for Multi-omoic analysis. Only transcriptomic data is included in this manuscript.

first: Thomas


title: Maternal antibodies orchestrate the establishment of salivary and oral mucosal immunity_Gingiva

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: The establishment of mucosal homeostasis after birth involves mutual development of the microbiota and the immune system, with each mucosal barrier has specific mechanisms. Here, we show that in utero-delivered maternal IgG antibodies are translocated to the salivary glands and secreted to the neonatal saliva. As a result, the microbial burden of the neonate oral cavity and salivary glands is reduced. In the absence of maternal antibodies, oral dendritic cells migrate in higher frequencies to the salivary glands resulting in elevated activation of T and B cells, while dampening T regulatory cells. The IgG/IgA balance in the adult saliva was also dysregulated. The absence of maternal antibodies further regulates the adult gingival immunity, a key oral barrier, increasing alveolar bone loss during experimental periodontitis. This work reveals the importance of the salivary-oral axis during neonatal life via maternal antibodies, orchestrating local mucosal immunity and protecting against pathological damage in adulthood.

overall_design: B cell-deficient (JhT-/- ) females were crossed with wild-type (WT) males to generate offspring with intact B cells that were not exposed to mIg.

first: Reem

last: Naamneh

first: Avi-Hai

last: Hovav

first: Yasmin

last: Netanely

first: Shahd

last: Yacoub

last: Jaber


title: CITE-seq profiling of human splenic dendritic cells

city: Wuhan

first: Harris

last: Han

state: Hubei

address: No. 115, East Lake Road, Wuchang District

department: Medical Research Institute

institute: Wuhan University

summary: To depict a comprehensive atlas of human splenic DCs and investigate DC2hm in a broad context, we performed Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) using a panel of 151 oligo-conjugated antibodies recognizing surface proteins on Lin [CD3/CD19/NKp46]⁻CD66b⁻ CD88⁻CD89⁻HLA-DR⁺ splenocytes from two donors. This dataset identified nearly all currently recognized human splenic DC subsets. Integrated transcriptomic- and protein-level analyses support the conclusion that DC2hm represents a homeostatic maturation state originating from cDC2 and is distinct from other DC lineages.

overall_design: Lin[CD3/CD19/CD56]⁻CD89⁻CD66b⁻CD88⁻HLA-DR⁺ splenocytes from non-diseased adult human donors (trauma-induced splenectomy cases)

first: Meng-Meng

last: Lu

first: Runpeng

first: Liang

last: Cheng


title: EWSR1::FLI1 Suppresses Ribosome Biogenesis and Creates a Targetable Vulnerability in Ewing Sarcoma

city: Wien

first: Christoph

last: Dotter

address: Zimmermannplatz 10

institute: St. Anna Children’s Cancer Research Institute (St. Anna CCRI)

overall_design: RNA extracted from polysome fraction (fractionated on 10-50% sucrose gradient) and matched total RNA seq of Ewing sarcoma (A-673, TC-32, SK-N-MC, CHLA-9), rhabdomyosarcoma (RH-30, RD), osteosarcoma (U2OS), and fibroblasts (IMR90) cell lines. Primary human mesenchymal stem cells (hMSCs) are also included in the analysis, as well as A-673/TR/shEF before and after administration of doxycycline for 7 days. 3 biological replicates for each sample.

first: Jason

last: Sims

first: Matteo

last: Colombo

first: Eleni

last: Tomazou


title: Technical and biological sources of noise confound multiplexed enhancer AAV screening [dataset4]

city: Seattle

first: John

middle: Kenneth

last: Mich

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

summary: Cis-acting regulatory enhancer elements are valuable tools for gaining cell type-specific genetic access. Leveraging large chromatin accessibility atlases, putative enhancer sequences can be identified and deployed in adeno-associated virus (AAV) delivery platforms. However, a significant bottleneck in enhancer AAV discovery is charting their detailed expression patterns in vivo, a process that currently requires gold-standard one-by-one testing. Here we perform barcoded multiplexed screening of enhancer AAVs at cell type resolution using single cell RNA sequencing and taxonomy mapping. We executed a proof-of-concept study using small pools of well-validated enhancer-AAVs expressing in a variety of neuronal and non-neuronal cell types across the mouse brain. Unexpectedly, we encountered substantial technical and biological noise including chimeric packaging products, necessitating development of novel techniques to accurately deconvolve enhancer expression patterns. These results underscore the need for improved methods to mitigate noise and highlight the complexity of enhancer AAV biology in vivo.

overall_design: We injected young adult C57Bl/6J mice with various cell type-specific PHP.eB-encapsidated barcoded enhancer-AAV vectors, either alone or as pools.  Three to four weeks later, we profiled YFP-expressing whole cells [or nuclei] from C57Bl/6 cell suspensions using fluorescence activated cell sorting (FACS). These sorted cells were then prepared for scRNA-seq using the 10X Chromium NextGEM v3.1 3' GEX droplet-based sc/snRNA-seq platform. cDNA and sequencing libraries were prepared according to the manufacturer's protocols, and then sequenced to a depth of approx 125k read pairs per cell (cDNA libraries). Additionally, in some experiments cDNA libraries were amplified with custom indexed PCR primers to maximize detection of AAV-encoded mRNA barcodes (mBCs). Furthermore, in some experiments low-molecular weight supernatant from cDNA bead purification was amplified with different custom indexed PCR primers to detect AAV-encoded Tornado barcodes (oBCs). GEX and mBC and oBC libraries were each sequenced.

first: Avery

last: Hunker

first: Jean-Benoît

last: Lalanne


title: Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis

city: Seongnam-si

first: Clementine

last: Charton

state: Gyeonggi-do

address: 82 Gumi-ro-173-beon-gil Bundang-gu

institute: Seoul National University Bundang Hospital

summary: Gastric cancer peritoneal metastasis (GCPM) is a distinct clinical entity with a poor prognosis, characterized by aggressive features and limited treatment options. Understanding its molecular biology is critical for developing effective therapies. We performed whole genome and transcriptome sequencing on GCPM samples and paired primary gastric cancer (GC) tissues from 14 and 26 patients, respectively. Our analysis revealed substantial intra-patient heterogeneity between GCPM and primary tumors at both genetic and functional levels. Inter-patient variability was observed in mutational overlaps, with some signatures unique to either GCPM or primary tumors. Tumor evolution analysis suggested divergent clonal evolution, with distinct clones specific to GCPM or primary tumors in most patients. The tumor microenvironment (TME) was poorly conserved between primary GC and GCPM, with desert-type primary tumors often transitioning to immune-enriched TMEs in metastases. These findings suggest that immunotherapy resistance in GCPM may arise from factors beyond intrinsic TME characteristics, such as limited drug delivery due to the peritoneal-plasma barrier. Collectively, our results highlight significant molecular and TME heterogeneity between GCPM and primary tumors, emphasizing the need for GCPM-specific stratification and innovative treatment strategies to improve outcomes.

overall_design: RNAseq profiling of 26 advanced gastric cancer patients, including 18 primary GC tumors, 26 GC peritoneal seeding tumors (GCPM), 6 Normal adjacent to the tumor, 2 omentum metastatic tumors and 2 lymph node metastatic tumors; paired primary-metastatic tumors were available for 20 patients

first: So Hyun

last: Kang

first: Stephanie

last: Kim

first: Young Suk

last: Park

first: Sang-Hoon

last: Ahn

first: Yun-Suhk

last: Suh

first: Nak Jung

last: Kwon

first: Kyoung Un

first: Jieun

last: Lee

first: Jinho

first: Hyung-Ho


title: Decoy Antibodies Block Extracellular HSP70, Prevent Self Signaling and Inhibit Melanoma Cell Survival

first: Inbar

last: Plaschkes

summary: Melanoma cells actively secrete melanosomes-large, extracellular vesicles (EVs) enriched with oncogenic factors that reprogram the tumor microenvironment, enhance self-signaling, and promote tumor growth. Despite their abundance and immunogenic potential, humoral responses to melanoma-derived melanosomes remain unexplored. Here, we identify a novel immune surveillance mechanism in which melanosome-elicited decoy antibodies target melanoma-derived melanosomes by binding to the extracellular form of heat shock protein 70 (HSP70), a chaperone broadly implicated in cancer cell survival and stress adaptation. Anti-HSP70 decoy antibodies potently and effector-independently inhibit growth and survival of both murine and human melanoma cells and suppress key transcriptional programs involved in proliferation, cytoskeletal dynamics, and metabolism. In a preclinical B16 melanoma model, prophylactic administration of decoy monoclonal antibodies Mel322-34 and Mel321-35 conferred significant survival benefits of 27% and 48%, respectively. Strikingly, anti-HSP70 antibodies were enriched in the sera of melanoma patients achieving complete responses to immune checkpoint blockade, in contrast to non-responders with progressive disease. Collectively, our findings uncover a novel EV-antibody axis as a promising avenue to block cancer-promoting signaling pathways. Decoy autoantibodies targeting the extracellular form of HSP70 advance the understanding of tumor-intrinsic vulnerability and promote biomarker-driven immunotherapy in melanoma.

overall_design: 4 antibodies were incubated (Mel321-31, Mel322-34, Mel321-35 and isotype control-MGO.53) with B16 cancer line and RNA was produced following 24 hours. Our goal is to understand the pathways, the different genes that are up or down-regulated following treatment with the antibodies.

first: Noam

last: Ben-Shalom

first: Shivang

last: Parikh

first: Lilach

last: Abramovitz

first: Ron

last: Yefet

first: Paulee

last: Manich

first: Dafna

last: Tussia-Cohen

first: Ori

last: Moskowitz

first: Roma

first: Stav

last: Melamed

first: Ksenia

last: Polonsky

first: Sebastien

last: Apcher

first: Tzachi

last: Hagai

first: Merav

last: Cohen

first: Yochai

last: Wolf

first: Ronnie

last: Shapira-Frommer

first: Carmit

last: Levy

first: Natalia

last: T Freund


title: Technical and biological sources of noise confound multiplexed enhancer AAV screening [dataset2]

first: John

last: Mich

overall_design: Single-cell RNA-seq of  flow cytometry-sorted H2B-YFP-expressing mouse brain nuclei. H2B-YFP expression was driven by cell type-specific enhancer-AAV PHP.eB vectors, injected at a moderate dose (5e11 vg/mouse) in young adulthood, and nuclei were prepared and sorted 3-4 weeks later. Nuclei from three regions were sorted: anterior lateral motor cortex (ALM) and striatum (STR) and primary visual cortex (VISp). Libraries were generated from one nucleus per library prep, performed using the SMART-Seq v4 procedure (Takara), and sequenced by paired-end sequencing at ~0.5M reads/nucleus on the Illumina platform.

first: Avery

last: Hunker

first: Jean-Benoît

last: Lalanne


title: Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [RNA-seq]

city: Washington

first: Sreejith

last: Nair

institute: Georgetown University

summary: Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. To accomplish this, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) .We found that the recruitment of cisplatin to rG4s partially contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent. RNA seq was performed to catalogue all non-ribosomal RNAs present in A2780 cells.

overall_design: A2780 cells were treated with 10 µM cisplatin 24  hours. RNA was collected and rRNA depleted library was constructed. The objective of the experiment was to identify non-ribosomal RNAs expressed in A2780 cells in basal and cisplatin-treated conditions.

first: Arun

last: Krishnaraj

first: Richi

last: Thakral


title: Mucosal vaccination transcends pathogen boundaries to protect from diverse respiratory threats

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: Traditional vaccines target specific pathogens, limiting their scope against diverse respiratory threats. We describe an intranasal liposomal formulation combining Toll-like receptor (TLR) 4 and 7/8 ligands with ovalbumin that provides broad, durable protection for nearly seven months against such threats. In mice, it protected against viruses (SARS-CoV-2, influenza, SARS, SCH014 coronavirus), bacteria (Staphylococcus aureus, Streptococcus pneumoniae), and allergen. Protection was mediated by persistent ovalbumin-specific CD4⁺ and CD8⁺ lung memory T cells that imprinted alveolar macrophages (AMs) via RANKL, enhancing antigen presentation and antiviral immunity; depletion of AMs, abolished protection, while their transfer restored it. Following infection, vaccinated mice mounted rapid pathogen-specific T-cell and antibody responses and formed ectopic lymphoid structures in the lung. These results reveal a   class of “universal vaccines,” against diverse respiratory threats.

overall_design: RNA-seq and ATAC-seq aboout lung cells from unvaccinated, vaccinated (21 days and 3 months after vaccinations). Spatial transcriptomic analysis about lung sections from unvaccinated, vaccinated (21 days after vaccination), vaccinated with blocking cd4cd8 cells (21 day after vaccinations) all the samples was from mouse lung. vaccinated means give four doses of GLA-3M052-LS+OVA intranasally (1 dose per week)

first: Zhang

last: Haibo

first: Fang

last: Zhuoqing


title: Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [CUT&TAG]

summary: Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. We developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay to map transcriptome-wide interaction of cisplatin. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s). To test the relationship with RNA-DNA hybrid R-loop structures and cisplatin-RNA interaction, we used CUT&Tag experiment using S9.6 R-loop specfic antibody. This result revealed an increased cisplatin interacitn on R-loop engaged RNAs.

overall_design: Cells were treated with Cisplatin (25 µM) or DMF for 6 hours. R-loops were pulldown and sequencing libraries were prepared using CUT&Tag-IT R-loop Assay Kit (Active Motif, 53167). The goal was to estimate R-loop enrichment in cisplatin-target RNA promoters.

first: Weiyi

last: Guo


title: Host-directed microRNA-based intervention against intracellular Staphylococcus aureus: High-throughput screening identifies miR-4430, miR-147a, and miR-1249-5p as multifunctional antimicrobial candidates

city: León

first: Pablo

last: Castañera

address: Cjón. Campus Vegazana, s/n

institute: Universidad de León

summary: The intracellular persistence of Staphylococcus aureus represents a major therapeutic challenge, as it facilitates immune evasion and limits the efficacy of antibiotics with poor intracellular activity. Host-directed therapies based on microRNAs (miRNAs) offer a promising alternative to overcome these limitations. We performed a high-throughput screen of 2,469 human miRNA mimics in S. aureus USA300–infected A549 epithelial cells, followed by network centrality–based prioritization and validation across multiple S. aureus strains and epithelial cell lines. This approach identified ten candidate miRNAs, among which miR-4430, miR-1249-5p, and miR-147a consistently reduced intracellular bacterial burden and improved host cell viability. Host transcriptomic profiling revealed distinct yet complementary mechanisms of action: miR-4430 enhanced innate immune responses, including STAT1- and PTAFR-associated signaling, whereas miR-1249-5p and miR-147a modulated extracellular matrix organization and integrin-mediated adhesion, thereby impairing bacterial entry. Collectively, these miRNAs impose convergent host-driven pressures that restrict intracellular S. aureus proliferation. Our findings highlight the therapeutic potential of miRNA-based host-directed interventions, which could be combined with conventional antibiotics to improve infection control and reduce the emergence of resistance.

overall_design: RNA-seq profiling of A549 cells transfected with cel-miR-231 (negative control) or with hsa-miR-4430, hsa-miR-147a, and hsa-miR-1249-5p (candidate treatments) to investigate host transcriptional responses associated with the control of intracellular Staphylococcus aureus.

first: Jesús

last: Llano Verdeja

first: Helena

last: Á. Ferrero

first: Sergio

last: Fernández Martínez

first: Blanca

last: Lorente Torres

last: F. Aparicio

first: Luis

last: M. Mateos

first: Álvaro

last: Mourenza

first: Michal

last: Letek


title: Technical and biological sources of noise confound multiplexed enhancer AAV screening [dataset1]

first: John

last: Mich

first: Avery

last: Hunker

last: Lalanne


title: Transcriptome analysis in skeletal muscle conditional Phf2 KO gastroceiumus muscle in male mice

city: Nagakute

first: Taku

last: Fukushima

state: Aichi

institute: Aichi Medical University

summary: To evaluate the role of PHF2 in  skeletal muscle, we generated  skeletal muscle conditional Phf2 KO mice and analyzed the transcriptome by CUT&RUN-sequencing.

overall_design: Examination of the role of PHF2 in skeletal muscle. the samples are to be added to GSE290665.

first: Iori

last: Sakakibara


title: Synthetic synovial fluid drives biofilm and virulence expression in Staphylococcus aureus

city: Gent

first: Amber

last: De Bleeckere

address: Ottergemsesteenweg 460

department: Laboratory of Pharmaceutical Microbiology

country: Belgium

institute: Ghent University

summary: Staphylococcus aureus is a leading cause of implant-associated infections, including periprosthetic joint infections (PJI). Its high virulence and ability to form biofilms make these infections particularly difficult to treat. Traditional in vitro studies rely on conventional growth media that lack key components of the infectious microenvironment, limiting their physiological relevance. To this end, a synthetic synovial fluid (SSF2) model was developed incorporating essential host compounds such as amino acids, hyaluronic acid, albumin and fibrinogen. However, how accurately this model reflects S. aureus behavior during PJI remains unclear.  To investigate this, RNA sequencing was performed on a PJI isolate of S. aureus grown in SSF2 and Luria-Bertani (LB) medium, followed by differential gene expression analysis. Functional classification using Clusters of Orthologous Groups (COG) and gene ontology (GO) enrichment was applied, and known and putative virulence and resistance genes were evaluated. To assess how closely SSF2 mimics in vivo conditions, transcriptomic profiles were compared with previously published in vivo gene expression data for the same strain.  Approximately half of the protein-coding genes were differentially expressed in SSF2 compared to LB (56.8%). Consistent with transcriptomic findings, growth in SSF2 resulted in reduced growth rates and enhanced biofilm formation. Furthermore, SSF2 induced a large fraction of virulence-associated genes (69.5%), including those encoding toxins, iron acquisition systems, adhesins and efflux pumps. These findings are in line with previously published in vivo data of the same strain. These results highlight the potential of the SSF2 medium to approximate in vivo conditions encountered by S. aureus during PJI. Nonetheless, more comprehensive in vivo transcriptomic datasets are needed to fully validate this model.

overall_design: 4 biological replicates of clinical S. aureus isolate SAU060112 grown in LB and in SSF2 (total 8 samples)

first: Filip

last: Van Nieuwerburgh

first: Tom

last: Coenye


title: Technical and biological sources of noise confound multiplexed enhancer AAV screening [dataset3]

first: Jean-Benoît