title: A Proteostasis Checkpoint Governs EGFR Stability and Cell Fitness, Defined by an lncRNA [RNA-seq]

status: Public on Feb 27 2026

city: Shenzhen

first: Diansheng

last: Zhou

address: 1066 Xueyuan Road, Nanshan District

country: China

institute: Shenzhen University

type: Expression profiling by high throughput sequencing

summary: The protein abundance of receptor tyrosine kinases such as EGFR is actively maintained under basal conditions by mechanisms that are distinct from ligand-induced signaling and degradation, yet the molecular basis of this regulation remains poorly understood. Here, we identify the long noncoding RNA ERBBride as a critical regulator of EGFR proteostasis. ERBBride binds the EGFR intracellular domain and prevents K48-linked ubiquitination and proteasomal degradation via a UBAP2L-PSMD1 axis. Loss of ERBBride triggers rapid EGFR degradation, robustly reversed by proteasome inhibition, establishing ERBBride as a determinant of receptor stability. This regulation occurs across diverse cancer contexts, irrespective of EGFR mutation, demonstrating mutation-agnostic control of EGFR proteostasis. Despite preserved or even enhanced canonical EGFR signaling outputs, ERBBride depletion selectively impairs EGFR-driven cellular proliferation, including in EGFR-expressing models with oncogenic KRAS backgrounds, revealing that EGFR abundance sustains cell fitness independently of acute canonical signaling. Both genetic depletion and steric-blocking antisense oligonucleotides targeting the ERBBride-EGFR interface reduce tumor growth, providing mechanistic validation and potential therapeutic modulation. Together, these findings define an lncRNA-governed proteostasis checkpoint that controls EGFR stability and cellular fitness, uncovering a previously unappreciated layer of receptor regulation with broad implications for cancer biology and therapy.

overall_design: RNA-seq profiling of MDA-MB-231 cells transfected with control siRNA (siCTRL, n=3) or ERBBride-targeting siRNA-1(n=3)

first: Taewan

last: Kim


title: CLIPPER Regulates LPIN1-Mediated Mitochondrial Biogenesis and Heart Regeneration [RNAseq_differentiation]

city: Singapore

first: Roger

last: Foo

address: 14 Medical Drive, MD6

country: Singapore

institute: National University of Singapore

summary: The adult mammalian heart lacks the significant regenerative potential needed to cope with the massive loss of cardiomyocytes following myocardial infarction. Ultimately, irreversible cardiac damage leads to heart failure, which is associated with a very poor prognosis. Given this, reactivating dormant regenerative processes in the injured heart represents an attractive therapeutic approach. When regeneration does occur, newly formed cardiomyocytes are derived from preexisting ones.  We aimed to identify novel regulators of cardiomyocyte proliferation. In this context, the genome is transcribed for a large part into RNAs with little or no protein-coding potential. Among noncoding RNAs, long noncoding (lnc)RNAs represent the most diverse class of molecules, and are implicated in numerous epigenetic mechanisms, making them ideal targets for controlling cell identity and behavior. In this project, we developed a high-throughput screening assay to identify lncRNAs that promote cardiomyocyte proliferation upon knockdown. Using a stringent selection pipeline, we identified Clipper, an enhancer-associated lncRNA regulating the expression of its cognate protein-coding gene Lpin1 in cis.  Clipper was found to control mitochondrial biogenesis via LPIN1. Specifically, productive mitochondrial division, characterized by fission site positioning at the midzone of the mitochondrion, was stimulated by Clipper or Lpin1 silencing. The process was associated with a change in mitochondrial bioenergetics, particularly decreased oxidative metabolism, reduced production of reactive oxygen species, and dampened DNA damage, creating favorable conditions for cardiomyocyte proliferation. Importantly, Clipper knockdown in vivo following myocardial infarction stimulated cardiac regeneration in the damaged myocardium leading to the restoration of heart function. Importantly, CLIPPER is positionally and functionally conserved in humans.  Our data identify CLIPPER as a promising therapeutic target for heart regeneration, acting through control of LPIN1-dependent mitochondrial biogenesis and cardiomyocyte proliferation.

overall_design: Human ESCs were grown to 80% confluency before being seeded for differentiation. Directed differentiation into cardiomyocytes were performed and Total RNA were isolated at Day 0, 1, 3, 5, 7, 10, 14, and 28. Total RNA was extracted using Trizol Reagent (15596026, ThermoFisher) and Direct-Zol RNA miniprep Kit (Zymo Research, R2050) according to manufacturer’s protocol. RNA quality and yield was accessed using Agilent RNA 6000 pico kit (50167-1513, Agilent) for quality. Bulk RNA-seq library preparations were prepared using TruSeq Stranded Total RNA library Prep HMR kit (20020596, Illumina). cDNA libraries were quantified using the Agilent DNA1000 kit (5067-1505, Agilent), prior to sequencing on Illumina NextSeq Sequencing platform by Macrogen Asia Pacific Pte. Ltd. Raw Fastq files were trimmed using the trim-galore tool (v0.65) from Babraham Bioinformatics, to sequence length of 50. Paired-end reads were mapped and aligned to the human reference genome GrCh38/hg38 using STAR aligner (v2.7.0) as per default settings, and using gene annotations from GENCODE v38. Aligned gene counts were mapped using Htseq-count, and normalized to Counts per Million (CPM) by sequencing depth. The normalized gene expression count matrix was normalized by gene length.

first: Chang Jie Mick

last: Lee

first: Roger SY

first: Francesco

last: Ruberto

first: Thierry

last: Pedrazzini


title: Reinforced immunotherapy of M1 macrophage-derived exosomes with CEL on TNBC via regulating macrophage functions

city: Beijing

first: Xinyi

last: Luo

address: No. 11, North 3rd Ring East Road

department: School of Materia Medica

institute: Beijing University of Chinese Medicine

summary: Triple-negative breast cancer (TNBC) demonstrates poor prognosis due to its heterogeneity-related biological barrier, immunosuppressive tumor microenvironment (TME) and escape of cancer cells on immune surveillance. Exosomes are membrane-encased vehicles with properties of inter- and intra-cellular communication and regulation for therapeutic use, even as drug vehicles. M1 macrophage-derived exosomes (M1-Exos) can communicate with adjacent M2 macrophages and reprogram them to M1 subtypes to reshape TME. Celastrol (CEL) is a highly promising natural antitumor drug and plays an important role in immunotherapy but with high toxicity and low water solubility.

overall_design: MDA-MB-231 cells were inoculated in medium, then incubated for 24 h with different treatments. Total RNA was extracted by the TRIzol method (Invitrogen, CA, USA). NanoDrop spectrophotometer (Thermo Scientific, DE, USA) was used to evaluate its quality and integrity. Sequencing libraries were generated using NEBNext UltraTM RNA Library Preparation Kit for Illumina (NEB, USA). After that, the library was sequenced on Illumina Novaseq 6000 platform at Allwegene Technology Company Limited (Beijing, China).


title: scRNAseq analysis of human brochial epithelial cell air liquid interface cultures infected with the A/Perth/16/2009 H3N2 with and without PA-X

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

country: USA

institute: University of Wisconsin Madison

summary: The goal of this analysis was to examine the impact of PA-X activity during infection in a model of the human airway epithelium, using primary airway cells from two different donors. We profiled the effects of infection and PA-X activity in various airway epithelial cell types. Donor H1: Male, 21, Caucasian, no health issues noted. Donor H2: Male, 55, Caucasian, no health issues noted.

overall_design: Air liquid interface culture models of the human airway epithelium were differentiated for 3-4 weeks post air lift. Then they were either mock-infected or infected at an MOI of 0.1 with wild type or PA-X deficient A/Perth/16/2009 H3N2. Basal media was replaced and apical surfaces were washed every 24 hours post infection. At 1 and 3 days post infection, cells were trypsinized and dead cells were depleted using an Annexin V binding kit (Stemcell). Viable single cell suspensions were collected and fixed using the Parse Evercode Fixation Kit v3. Library preparation was performed with Parse Evercode WT kit and sequenced on a NovaSeq X Plus 100 cycle 10B flow cell. About 69,000 cells were detected, with a depth of approximately 20,000 reads/cell.

first: Marta Maria

first: Alessandra

last: Setaro


title: Paeonia delavayi seed oil alleviates UVB-induced inflammation, oxidative stress and photoaging in keratinocytes through inhibition of PI3K/Akt/mTOR and NF-κB signaling pathways

city: Kunming

first: Liping

last: Qu

state: Yunnan

address: No. 53 Keyi Road, Kunming City

institute: Yunnan Botanee Bio-technology Group Co., Ltd.

summary: UVB is one of the external stimuli posing a significant threat to the skin. Excessive exposure to UVB may trigger intracellular effects including inflammatory responses and oxidative stress, leading to severe skin issues. Peony seed oil is a nut oil unique to China, rich in unsaturated fatty acids, and reported to possess anti-inflammatory and antioxidant properties. Paeonia delavayi is a distinctive subspecies within the peony family, primarily distributed in southwestern China and high-altitude regions. This study aims to investigate the roles and underlying mechanisms of P. delavayi seed oil (PDSO) in protecting skin from UVB-induced damage. We found that treatment with PDSO effectively mitigated the adverse effects of UVB exposure on NHEK cells, including reduced viability and impaired migratory capacity. Additionally, PDSO significantly suppressed the upregulation of pro-inflammatory genes such as TNF, IL6, CXCL8 and PTGS2 in keratinocytes induced by UVB. Subsequent studies indicated that PDSO also alleviated UVB-induced oxidative stress and photoaging in NHEK cells, manifested by reducing ROS and MDA levels, upregulating antioxidant-related genes expression, and suppressing the expression of genes associated with cellular senescence. RNA-sequencing analysis and western blot assay revealed that PDSO exerts an inhibitory effect on the PI3K/Akt/mTOR pathway. We also found that PDSO suppressed the activation of the NF-κB pathway in UVB-irradiated NHEK cells. Thus, this study demonstrates that PDSO holds significant potential in protecting skin from UVB-induced damage and reveals that its mechanism of action involves the PI3K/Akt/mTOR and NF-κB signaling pathways.

overall_design: UVB irradiation of normal human epidermal keratinocytes (NHEK) cells was performed to establish a model for detecting UVB-induced cellular damage. The study evaluated the efficacy of PDSO in improving physiological processes such as cell survival rate, migration capacity, oxidative stress response, inflammatory response, and photoaging within this model. The mechanism of action of PDSO was explored and validated through transcriptome sequencing (RNA-seq) and western blot (WB) assays.

first: Rencong

last: Wang

first: Peng

last: Xu

first: Yindi

last: Zhang

first: Xiaoli

last: Jin

first: Ziyan

last: Zhao

first: Feifei


title: Effect of IL6 depletion on gene expression in Arid1a/Pik3ca Co-mutant mouse Ovarian Tumor Cell Lines

city: Sakai

first: Noriomi

last: Matsumura

state: Osaka

address: 1-14-1, Miharadai, Minami-ku

department: Gynecology and Obstetrics

country: Japan

institute: Kindai University

summary: Ovarian clear cell carcinoma is a refractory gynecological malignancy resistant to chemotherapy, with 50% exhibiting Arid1a/Pik3ca co-mutations and known to be IL6-high-producing tumors. Despite possessing an immunosuppressive tumor microenvironment, some cases have been reported to respond remarkably well to immune checkpoint inhibitors, though the molecular mechanisms underlying these responses remain unclear. Therefore, to confirm the role of IL6 in tumor immunity, we established cell lines from mouse model tumors with Arid1a/Pik3ca co-mutations that develop ovarian tumors. We created IL6 knockdown cell lines and compared gene expression.

overall_design: RNA-seq profiling of tumors in a subcutaneous tumor model derived from ovarian tumor cell lines. Wildtype APC245 cellline drived from Arid1a/Pik3ca co-mutated tumor and their  knockdown deriverties (shRNA1; TRCN000067551 and MISSION® pLKO.1-puro Non-Mammalian shRNA Control Transduction Particles, Sigma)

first: Chiho

last: Miyagawa

first: Yukari

last: Kobayashi


title: Integrating copy number, methylation, and fusion detection in one assay: A Nanopore sequencing approach for pediatric and adults’ rare tumors diagnosis

city: Paris

first: Mathilde

last: Filser

address: 26 rue d'Ulm

department: Genetics Department

country: France

institute: Institut Curie

type: Methylation profiling by high throughput sequencing

summary: Recent advances in sequencing technologies have significantly refined tumor characterization by enabling detailed analysis of genetic alterations, transcriptomic profiles, and DNA methylation patterns. Combined with pathological data, these molecular insights have become essential for accurate tumor classification at diagnosis, allowing for more precise prognostic assessment and the implementation of the most appropriate therapeutic strategies. Currently, obtaining this comprehensive molecular information requires the use of multiple techniques, often leading to extended turnaround times and high cost. A key challenge is therefore the development of an integrated method capable of simultaneously detecting copy number variations, structural rearrangements, and methylation-based classifications in a time-efficient manner. In this study, we applied Nanopore long-read sequencing combined with adaptive sampling to a series of 20 pediatric and rare tumors previously characterized using conventional short-read panels and RNA sequencing. Our approach successfully detected all clinically relevant and classifying structural variants, including gene fusions and internal tandem duplications, previously identified by traditional short read sequencing. In addition, we generated high-quality genome-wide copy number profiles and methylation data from the same DNA sample, enabling integrated molecular classification. These findings demonstrate the strong concordance of this unified method with standard approaches and highlight the value of Nanopore sequencing as a powerful and time-efficient tool for comprehensive tumor profiling. Requiring only a single sample and offering rapid technical processing, this approach aligns with the clinical objective of accelerating diagnostic workflows and improving patient care.

overall_design: Nanopore adaptive sequencing of 20 fresh frozen tumor samples. DNA libraries were prepared using the SKQ-LSK114 kit (Oxford Nanopore Technologies), according to the manufacturer's instructions.


title: CLIPPER Regulates LPIN1-Mediated Mitochondrial Biogenesis and Heart Regeneration

first: Roger

last: Foo

overall_design: Human ESCs were grown to 80% confluency before being seeded for differentiation.  Beating hESC-CMs were transfected 9 days after the initiation of differentiation with 50 nM of either Control or CLIPPER-GapmeRs using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher #13778150), and harvested 48 hours later for transcriptomic analysis.   Total RNA was extracted using Trizol Reagent (15596026, ThermoFisher) and Direct-Zol RNA miniprep Kit (Zymo Research, R2050) according to manufacturer’s protocol. RNA quality and yield was accessed using Agilent RNA 6000 pico kit (50167-1513, Agilent) for quality. Bulk RNA-seq library preparations were prepared using TruSeq Stranded Total RNA library Prep HMR kit (20020596, Illumina). cDNA libraries were quantified using the Agilent DNA1000 kit (5067-1505, Agilent), prior to sequencing on Illumina NextSeq Sequencing platform by Macrogen Asia Pacific Pte. Ltd. Raw Fastq files were trimmed using the trim-galore tool (v0.65) from Babraham Bioinformatics, to sequence length of 50. Paired-end reads were mapped and aligned to the human reference genome GrCh38/hg38 using STAR aligner (v2.7.0) as per default settings, and using gene annotations from GENCODE v38. Aligned gene counts were mapped using Htseq-count, and normalized to Counts per Million (CPM) by sequencing depth. The normalized gene expression count matrix was normalized by gene length.

first: Chang Jie Mick

first: Roger SY

first: Francesco


title: SynNotch-iNOS CAR-Macrophages Remodel the Tumor Immune Microenvironment and Exhibit Antitumor Efficacy via a CD4+ T Cell-Dependent Mechanism

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

institute: xiamen university

summary: Background: Chimeric antigen receptor T-cell (CAR-T) therapy shows limited efficacy against solid tumors due to the immunosuppressive tumor microenvironment (TIME). Macrophages possess superior infiltration capabilities, yet their therapeutic potential remains under-realized. Methods: We engineered a synNotch-iNOS CAR-macrophage (CAR iNOS-M) that releases nitric oxide (NO) upon CD19 recognition. Its efficacy was evaluated in syngeneic, immunocompetent murine models of metastatic melanoma. Results: CAR iNOS-M therapy effectively reprogrammed the pulmonary TIME, inducing potent antitumor responses independent of CD8+ T cells but strictly dependent on CD4+ T cells. Mechanistically, CAR iNOS-M treatment led to a significant reduction in pro-tumorigenic lung interstitial macrophages (IMs), subsequently decreasing platelet factor 4 (PF4) levels. This disruption of the PF4 signaling axis inhibited the polarization of immunosuppressive Th1-Tregs, alleviating T-cell exhaustion. Conclusions: This study delineates a novel indirect mechanism for CAR-M, shifting the focus from direct phagocytosis to strategic TIME remodeling, providing a foundation for treating solid tumors.

overall_design: B16F10 lung metastases tissues were taken from the ECD group and the CAR group, CD45-positive immune cells were isolated by FACS, then 10x Genomic scRNA-seq library construction was performed

first: Yuling

last: Hong

first: Buyun

last: Dang

first: Shih-Chin

last: Cheng


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [ChIP-Seq 2]

city: Mainz

first: Aarón

last: Gallego Crespo

state: Rhineland-palatinate

address: Langenbeckstraße 1

department: III. Medical Department

country: Germany

institute: University Medical Center of the Johannes Gutenberg University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The lysine acetyltransferase (KAT) activity of p300/CREBBP has traditionally been linked to transcriptional activation. This has been attributed largely to acetylation of histone residues such as H3K27ac, a defining hallmark of active regulatory elements. Here we show that, in acute myeloid leukemia (AML), inhibition of p300/CREBBP catalysis can paradoxically increase transcription. We combined time-resolved dynamics of nascent and total transcription with chromatin binding dynamics of p300/CREBBP and their associated TFs/co-regulators (inferred from chromatin pull-down proteomics, acetyl-proteomics and motif enrichment) to uncover mechanisms of transcriptional rewiring after p300/CREBBP catalytic inhibition. In parallel, we dissected the functional contribution of individual p300/CREBBP acetyl-interactome members to KAT inhibition using genome-wide CRISPR-Cas9 dropout and focused Perturb-seq screens. Together, these approaches revealed that KAT inhibition paradoxically retains p300/CREBBP and promotes cooperative TF assembly and increased H3K27 acetylation at a subset of regulatory elements. The effect was most pronounced at IRF motif-enriched loci, including interferon-stimulated genes (ISGs), where KAT inhibition triggered p300/CREBBP accumulation and enhanced combinatorial TF binding, enabling recruitment of the ISG activator STAT1. Consequently, ISG loci were converted into transcriptionally active states that induced cell-cycle arrest, differentiation and apoptosis. Therapeutically, combining KAT inhibition with interferon-alpha augmented ISG expression, synergistically drove AML cell death in vitro and significantly extended survival in both AML xenografts and murine models. These findings refine our understanding of p300/CREBBP KAT activity, demonstrating that cooperative TF assembly can reconfigure p300/CREBBP-containing complexes under catalytic inhibition to induce transcription, with translational implications for reprogramming interferon-driven programs through catalytic inhibition in AML and beyond.

overall_design: ChIP-Seq performed on multiple transcription factors and co-regulators associated with p300/CREBBP in two monocytic leukemia cell lines (MOLM-13 and OCI-AML3) under two conditions (DMSO control and 24h of A-485 treatment)

first: Markus

last: Meyerhöfer

first: Yawen

last: Zhou

last: Gallego-Crespo

first: Malte

last: Behrendt


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML

summary:
The lysine acetyltransferase (KAT) activity of p300/CREBBP has traditionally been linked to transcriptional activation. This has been attributed largely to acetylation of histone residues such as H3K27ac, a defining hallmark of active regulatory elements. Here we show that, in acute myeloid leukemia (AML), inhibition of p300/CREBBP catalysis can paradoxically increase transcription. We combined time-resolved dynamics of nascent and total transcription with chromatin binding dynamics of p300/CREBBP and their associated TFs/co-regulators (inferred from chromatin pull-down proteomics, acetyl-proteomics and motif enrichment) to uncover mechanisms of transcriptional rewiring after p300/CREBBP catalytic inhibition. In parallel, we dissected the functional contribution of individual p300/CREBBP acetyl-interactome members to KAT inhibition using genome-wide CRISPR-Cas9 dropout and focused Perturb-seq screens. Together, these approaches revealed that KAT inhibition paradoxically retains p300/CREBBP and promotes cooperative TF assembly and increased H3K27 acetylation at a subset of regulatory elements. The effect was most pronounced at IRF motif-enriched loci, including interferon-stimulated genes (ISGs), where KAT inhibition triggered p300/CREBBP accumulation and enhanced combinatorial TF binding, enabling recruitment of the ISG activator STAT1. Consequently, ISG loci were converted into transcriptionally active states that induced cell-cycle arrest, differentiation and apoptosis. Therapeutically, combining KAT inhibition with interferon-alpha augmented ISG expression, synergistically drove AML cell death in vitro and significantly extended survival in both AML xenografts and murine models. These findings refine our understanding of p300/CREBBP KAT activity, demonstrating that cooperative TF assembly can reconfigure p300/CREBBP-containing complexes under catalytic inhibition to induce transcription, with translational implications for reprogramming interferon-driven programs through catalytic inhibition in AML and beyond.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

last: Zhow

first: Viral

last: Shah

first: Daniel

last: Sasca


title: Ataxin-2 regulates the synaptonemal complex to ensure chromosome pairing during female meiosis

city: Toronto

first: Thomas

last: Hurd

state: Ontario

address: 661 University Avenue

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: Sexual reproduction relies on meiotic recombination and the accurate segregation of homologous chromosomes to generate viable, genetically diverse gametes. While the molecular mechanisms of recombination and chromosome segregation are well studied, the upstream regulatory cues that drive expression of key meiotic genes remain poorly understood, especially in metazoans. Emerging evidence suggests that post-transcriptional regulation plays a central role in initiating and coordinating the meiotic program in both fruit flies and mammals. Here, we identify the RNA-binding protein Ataxin-2 (Atx2) as a crucial regulator of meiosis in Drosophila melanogaster. We show that Atx2 positively regulates critical meiotic factors, especially components of the synaptonemal complex (SC), a structure essential for pairing, recombination and segregation of homologous chromosomes. In Atx2-depleted germ cells, SC component mRNA and protein levels are markedly reduced, leading to defective SC assembly and maintenance. Consequently, homologous chromosomes fail to pair properly, which is essential to ensure homolog segregation and prevent aneuploidy. These findings uncover Atx2 as a key regulator of the SC and highlight an underappreciated layer of gene regulation essential for accurate meiotic chromosome segregation and fertility.

overall_design: RNA-seq profiling of FACS isolated bamP-GFP Drosophila ovarian cells either expressing a control shRNA (mCherry, RRID:BDSC_35785) or Atx2 shRNA (RRID:BDSC_36114) under nos-GAL4::VP16.

first: Vernon

middle: L

last: Monteiro

first: Zhuyi

last: Wang

first: Jose

middle: F

last: Santé

first: Camilla

last: Roselli

first: Baskar

last: Bakthavachalu

first: Mani

last: Ramaswami

first: Craig

last: Smibert

middle: R


title: Hdac11 promotes idiopathic pulmonary fibrosis through macrophage M2-type polarization and myofibroblast differentiation by inhibiting Parkin-dependent mitophagy

city: Wuxi

first: yunjuan

last: Nie

state: Jiangsu

address: 1800 Lihu Avenue

department: Wuxi School of Medicine

institute: Jiangnan University

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease in which macrophages play a central role in driving fibrogenesis. In this study, we observed marked upregulation of histone deacetylase 11 (Hdac11) in lung tissues from IPF patients, lung organoid models, and bleomycin‑induced fibrotic mouse lungs, with predominant expression in alveolar macrophages. Genetic deletion of Hdac11 or adoptive transfer of Hdac11‑deficient macrophages significantly reduced fibrotic progression. Hdac11 loss impaired M2 macrophage polarization and macrophage‑to‑myofibroblast transition, leading to decreased myofibroblast accumulation and reduced profibrotic gene expression. Mechanistically, Hdac11 directly deacetylates Parkin at lysine 76, promoting its ubiquitination and proteasomal degradation, thereby suppressing Parkin‑mediated mitophagy. Impaired mitophagy resulted in mitochondrial dysfunction that enhanced profibrotic macrophage activation. Pharmacological inhibition of Hdac11 alleviated bleomycin‑induced lung fibrosis. These findings identify Hdac11 as a regulator of Parkin‑dependent mitophagy in macrophages and suggest Hdac11 inhibition as a potential therapeutic strategy for IPF.

overall_design: Alveolar macrophages (AMs) from C57BL/6 mice were stimulated with IL‑33 (10 ng/mL) at 0, 3, 6, 12, 24, 48, 72, and 96 h — with three biological replicates at 0 and 24 h and one replicate at each other time point. In parallel, lung-derived primary fibroblasts were treated with TGF‑β1 (10 ng/mL) for 24 h. Transcriptomic profiles for all samples were generated via Illumina RNA‑seq.

first: Yunjuan

first: Li

last: Xu

first: Yanyan

last: Liu

first: Jiao

last: Li

first: Manjula

last: Karpurapu

first: Huaqi

last: Guo

first: Gaoshang

last: Chai


title: Pyelonephritis decreases serum cholesterol and mitigates atherosclerosis severity despite systemic inflammation

city: Bonn

first: Georg

last: Sendtner

address: Venusberg Campus 1a

department: Medical Clinic 1, Nephrology Section

institute: University Hospital Bonn

summary: Urinary tract infections are common and often recur. Using a pyelonephritis mouse model, we investigated the interplay between renal and systemic inflammation. Bulk RNA sequencing analysis of kidneys collected 16 hours post-infection was performed to identify novel regulators and modulators of inflammatory pathways. Our results highlight key molecular signatures involved in both local and systemic immune responses, providing new insights into the regulatory networks underlying the pathophysiology of pyelonephritis.

overall_design: Female C57BL/6J mice were infected with uropathogenic E. coli strain 536, which was instilled into the bladder twice at a 3-hour interval. Kidneys were harvested 16 hours after the second infection. Control mice received urethral instillation with PBS.

first: Lena

last: Possenriede

first: Peyman

last: Falahat

first: Uta

last: Scheidt

first: Julia

last: Miranda

first: Jessica

last: Schmitz

first: Jan Hinrich

last: Braesen

first: Sibylle

last: von Vietinghoff


title: DKC1 promotes colorectal cancer progression and therapy resistance by dysregulating sphingolipid biosynthesis

city: Kanpur

first: Bushra

last: Ateeq

state: Uttar Pradesh

address: Lab-4, BSBE, Indian Institute of Technology Kanpur, Kalyanpur

department: Department of Biological Sciences and Bioengineering

country: India

institute: Indian Institute of Technology Kanpur

summary: Higher expression of Dyskerin Pseudouridine Synthase 1 (DKC1) associates with poor prognosis in colorectal cancer (CRC) patients. However, the mechanism associated with DKC1 upregulation, and its functional significance in disease pathogenesis and therapeutic resistance remains largely unexplored. Here, we performed global transcriptome sequencing outlining the molecular mechanism associated with DKC1 depletion in CRC. We show a positive feedback loop between canonical WNT signaling and DKC1, which orchestrates DKC1 expression.  Moreover, we show the role of altered sphingolipid metabolism upon DKC1 abrogation in imparting CRC oncogenicity and first-line chemotherapeutic resistance.

overall_design: RNA-seq was performed on scramble (shSCRM) control and DKC1 knockdown (shDKC1-2 and shDKC1-3) SW620 cells using two distinct lentiviral shRNAs stably silencing DKC1 gene.

first: Ateeq

last: Bushra

first: Khan

last: Umar

first: Goel

last: Ayush

first: Nigam

last: Shivansh


title: Effects of a temporary period on pasture on the transcriptomic signature of horses housed in individual boxes.

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

institute: INRAE

summary: Over the past two decades, improving horse welfare through better housing conditions has emerged as a major concern. Different studies suggest that group living on pasture supports a higher welfare state compared with individual stabling. However, it remains unclear whether short-term access to pasture confers similar benefits for horses that are normally housed alone. To address this question, we monitored a population of horses accustomed to year-round individual stabling before and after a 1.5-month period on pasture, and compared them with a control group of individually housed horses that remained in their boxes. Blood transcriptome analyses were conducted to complete the behavioural assessments. Our results showed that acces to pasture didn’t have the same effet on the different behavioural indicators and that aggressiveness toward humans was the behavioural trait most strongly correlated with alterations in blood gene expression. The associated molecular pathways were predominantly linked to systemic inflammatory processes.

overall_design: The study population consisted of 22 sport horses. RNA was extracted from blood and gene expression profiles were performed using Agilent microarrays before and after a pasture period (2 samples par horse).

last: Foury

first: Alice

last: Ruet

first: Nuria

last: Mach

first: Léa

last: Lansade

first: Marie-Pierre

last: Moisan


title: HFD-inducued metabolic syndrome is promoted by JNK7b isoform.

city: Worcester

first: Sithara Raju

last: Ponny

state: MA

address: 55 N Lake Ave

department: Program in Molecular Medicine

institute: UMass Chan Medical School

summary: JNK7b isoform promotes metabolic syndrome in a mouse model of obesity

overall_design: Livers were harvested from HFD-fed hepatocyte-specific JNK spliceoform mice over the course of a 24h period every 3 hours to analyze changes in circadian gene expression between groups:: LJ1J2control (GFP),  LJ1J27a (CRE) and LJ1J27b (FLPO). Liver mRNA was isolated and sequenced.

first: Alexandra

last: Lee

first: Autumn

last: Gentzler

first: Declan

last: Fitzpatrick

first: Sithara

last: RajuPonny

first: Myoung

last: SookHan

first: Roger

middle: J

last: Davis


title: HFD-induced metabolic syndrome is promoted by JNK7b isoform

overall_design: To elucidate liver cell heterogeneity and the changes in immune cell types by HFD, we perforemd ScRNA Seq on isolated liver leukocytes.

first: Myoung Sook

last: Han


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [Perturb-Seq]

first: Aarón

last: Gallego Crespo

overall_design: Cells were transduced with a targeted sgRNA library (186 sgRNAs). After selection cells were treated with either A-485 or DMSO. Cell Fixation performed directly 24 hours after treatment. Subsequent barcoding performed with Kits from ParseBiosciences (Mini/Mega v3) plus CRISPR Detect.

first: Markus

last: Meyerhöfer

first: Yawen

last: Zhou

last: Gallego-Crespo

first: Viral

last: Shah

first: Malte

last: Behrendt

first: Daniel

last: Sasca


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [ChIP-seq]


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [SLAM-Seq]

overall_design: SLAM-Seq performed in monocytic leukemia cell line MOLM-13 at three timepoints (2h, 12h and 24h). At each timepoint, the cells were studied under four conditions (DMSO control, A-485 treatment, Inobrodib treatment (bromodomain inhbitor for p300/CREBBP) and dCBP-1 treatment (p300/CREBBP degradation).


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [CRISPR-Screens]

overall_design: Dropout Screens using either Inobrodib or A-485, Treatment performed for 48 Hours, total screen duration 14 days


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [PRO-Seq]

overall_design: PRO-Seq performed in monocytic leukemia cell line MOLM-13 in DMSO controls and after 12h of A-485 treatment


title: IFN-α Induces Heterogenous ROS Production in Human β-Cells

city: Indianapolis

first: Amelia

middle: K

last: Linnemann

state: IN

address: 1210 Waterway Blvd. Suite 4000

department: Pediatrics

institute: Indiana University School of Medicine

summary: Type 1 diabetes (T1D) is a multifactorial disease involving genetic and environmental factors, including viral infection. We investigated the impact of interferon alpha (IFN-α), a cytokine produced during the immune response to viral infection or the presence of un-edited endogenous double-stranded RNAs, on human beta cell physiology. Intravital microscopy on transplanted human islets using a beta cell-selective reactive oxygen species (ROS) biosensor (RIP1-GRX1-roGFP2), revealed a subset of human beta cells that acutely produce ROS in response to IFN-α. Comparison to Integrated Islet Distribution Program (IIDP) phenotypic data revealed that while all donors had functional islets, donors with lower BMI and HbA1c had more ROS accumulating cells. In vitro IFN-α treatment of human islets similarly elicited a heterogenous increase in superoxide production that originated in the mitochondria. To determine the unique molecular signature predisposing cells to IFN-α stimulated ROS production, we flow sorted human islets treated with IFN-α. RNA sequencing identified genes involved in inflammatory and immune response in the ROS-producing cells. Importantly, rapid stimulation of key antiviral response genes by IFN-α was dependent on mitochondrial ROS elevation. Comparison with single cell RNA-Seq datasets available through the Human Pancreas Analysis Program (HPAP) showed that genes upregulated in ROS-producing cells are enriched in beta cells from nondiabetic and autoantibody positive donors rather than T1D donors. Combined, these data suggest that IFN-α stimulates mitochondrial ROS production in healthy human beta cells, potentially predicting a more efficient antiviral response if the processes to respond to the ROS elevation are intact.

overall_design: Human islets were obtained from organ donors and procured through either the Integrated Islet Distribution Program (IIDP) or the Alberta Diabetes Institute (ADI) then treated acutely with recombinant human IFN-⍺ for 1h in the presence of dihydroethidium (DHE) to detect reactive oxygen species (ROS). Dispersed cells were flow sorted into ROS-positive and ROS-negative populations then RNA-sequencing was performed on the populations.


title: HFD-inducued metabolic syndrome is promoted by JNK7b isoform

overall_design: mRNA expression analysis of livers from male control and Rxra S65A mutant mice under HFD condition


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [RNA-seq]

overall_design: RNA-Seq performed in two monocytic leukemia cell lines (MOLM-13 and OCI-AML3) under three conditions (DMSO control, 24h of A-485 treatment and 24h of Inobrodib treatment (bromodomain inhibition of p300/CREBBP).


title: Lisinopril Activates BI1 to Reprogram Lipid Metabolism and Restore Autophagy in ALS

city: Changchun

first: Hanlan

last: Yin

state: Jilin

address: 2699, Qianjin street

institute: Jilin University

summary:
Background
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder. Abnormal lipid metabolism represents a critical pathogenic determinant and key therapeutic target in ALS. Bax inhibitor 1 (BI1), an endoplasmic reticulum membrane protein, is downregulated in ALS and exhibits neuroprotective properties. However, due to incomplete understanding of its metabolic regulatory mechanisms, targeting BI1 for ALS therapy remains an area requiring further investigation.
Methods
Skeletal muscles from ALS mice pre- and post-BI1 treatment underwent transcriptomic analysis to identify BI1-regulated target genes and signaling pathways. Subsequently, we performed a structure-based virtual screening of FDA-approved compounds to identify potential BI1 activators. Lisinopril was selected as a lead candidate, and its effects were validated in SOD1G93A-transfected NSC34 cells and an ALS mouse model. Mechanistic studies explored its impact on autophagy regulation, lipid metabolism, and TGF-β1signaling pathways.
Results
Lisinopril upregulated BI1 protein expression, stabilizing mitochondrial membrane potential and conferring resistance to SOD1G93A-induced apoptosis. Concurrently, it regulated TGF-β1/PI3K/AKT/mTOR-dependent autophagy, maintained neuromuscular junction (NMJ) integrity, and reshaped triglyceride/sphingolipid/glycerophospholipid metabolism to attenuate spinal cord pathology in ALS mice, promoting energy metabolism shift toward glucose oxidation. Additionally, lisinopril inhibited the TGF-β1/Smad2/3 pathway to alleviate muscle fibrosis, downregulate Acp5/FN expression, and reduce type I collagen deposition.
Conclusions
Our study elucidated the molecular mechanism by which BI1 remodels lipid metabolism via the TGF-β1 pathway to influence ALS pathogenesis. These findings provided the first evidence that pharmacological activation of BI1 suppresses TGF-β1 expression and modulates triglyceride/sphingolipid/glycerophospholipid metabolism, thereby ameliorating ALS-related pathological phenotypes. Notably, repurposing lisinopril (an FDA-approved drug for hypertension) held promise for ALS therapy.

overall_design: Skeletal muscle tissue samples (100 mg) from ALS CON, and ALS BI1 mice were homogenized in TRIzol reagent for total RNA extraction, with RNA quality verified using an Agilent 2100 Bioanalyzer. Pooled libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads, with base calling and demultiplexing performed using CASAVA software.

first: Zhichao

last: Ren

first: Yan

last: Zhang

first: Yuxiang

last: Wang

first: Yiyang

last: Sun

first: Fuqiang

first: Linlin

last: Zeng


title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle [A549_cell_lines_RNAseq]

city: New York

first: Abigail

last: Xie

state: New York

address: 430 E 67th St

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-sequencing of A549 cell lines with CRISPR/Cas9-mediated editing of AAVS1, ACO2, or both ACO2 and CS treated with vehicle (water) or pyruvate 5mM for 24 h.

first: Julia

middle: S

last: Brunner

first: Lydia

middle: W

last: Finley


title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle [ACO2_citrate_kidney_RNAseq]

overall_design: RNA-sequencing of kidneys harvested from Aco2 floxed UBC-CreERT2 mice 10-12 days after tamoxifen recombination. Mice were supplied either normal drinking water or 3% sodium citrate water for 7 days prior to start of tamoxifen administration. First 3-digit numbers of each data file corresponds to individual mouse identifiers.


title: RNA-seq analysis of E18.5 mouse embryonic lungs reveals impaired saccular maturation and airway differentiation in Svep1 knockout embryos

city: Boston

first: Maria

last: Loscertales

address: 185 Cambridge st

institute: MGH

summary: Loss of Svep1, an extracellular matrix protein, leads to severe defects in airway patterning and alveolar differentiation during lung development. To investigate transcriptional changes associated with impaired saccular maturation, we performed bulk RNA sequencing of whole lungs isolated from wild-type (Svep1+/+) and homozygous knockout (Svep1-/-) mouse embryos at embryonic day 18.5 (E18.5), corresponding to the saccular stage of lung development. Differential gene expression analysis revealed dysregulation of pathways related to extracellular matrix organization, smooth muscle differentiation, epithelial maturation, and FGF signaling. These data provide insight into how loss of Svep1 disrupts coordinated epithelial–mesenchymal interactions required for normal distal lung development.

overall_design: Whole lungs were dissected from E18.5 mouse embryos generated from heterozygous Svep1 intercrosses. Genotypes were determined by PCR and embryos were grouped as wild-type (Svep1+/+) or knockout (Svep1-/-). Total RNA was extracted from individual whole lungs. Poly(A)-selected RNA-seq libraries were prepared and sequenced on an Illumina platform. Differential gene expression analysis was performed comparing Svep1-/- versus Svep1+/+ lungs.


title: A Functional Cell Model using Basophil Activation Test to Study Molecular Mechanisms and Biomarkers of Response to Omalizumab Treatment in Patients with Asthma

city: Maribor

first: Mario

middle: Smode

last: Gorenjak

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine, University of Maribor

summary: Patients with severe asthma may benefit from targeted biological therapies. However, personalized therapy in children and adolescents with asthma, based on individual susceptibility to molecular mechanisms addressed by different biologicals is underdeveloped. Here we established a functional in vitro model to study the differential responses of asthma patients to omalizumab (an IgE targeting biological) therapy. White blood cells isolated from asthmatic children and adolescents were pre-treated with omalizumab. Next, basophil activation and degradation were used to assess the in vitro patient’s response to omalizumab after exposure to patient-specific allergens. In parallel, basophils-specific whole RNA sequencing was used to screen for differentially expressed genes associated with in vitro response to omalizumab. The results of the screen were first confirmed in an independent cohort of patients and finally compared to the clinically relevant data. The in vitro basophil activation + degradation test may be used to study the differential response to omalizumab in patients. The differentially expressed genes in the basophils of the better vs. the poor / non-responders are predominantly associated with defense against viruses and apoptosis. The low RSAD2 expression correlates with poor response to omalizumab in vitro and with high FeNO levels (an indicator of lung inflammation) in the omalizumab-treated juvenile asthmatics. We describe an in vitro test to study the differential response to omalizumab in patients. RSAD2 may be a biomarker for response to omalizumab in asthma.

first: Boris

last: Gole

first: Larisa

last: Goričan

first: Gregor

last: Jezernik

first: Uroš

last: Potočnik

first: Anja

last: Bizjak

first: Vojko

last: Berce


title: Targeting Keap1/Nrf2/ARE Signaling Pathway by Esculin in Zebrafish Larvae

city: Coimbatore

first: Ekambaram

last: Perumal

address: Maruthamalai Main Road

institute: Bharathiar University

summary: Nuclear factor E2-related factor 2 (Nrf2) is a basic leucine zipper (bZIP) transcription factor that plays a crucial role in cellular defense mechanisms by regulating the expression of phase II detoxification enzymes and antioxidant proteins. Nrf2 exerts its protective effects by binding to antioxidant response elements (AREs), which are cis-acting regulatory sequences located upstream of the transcription start site (TSS) of cytoprotective genes. This study aims to identify and characterize AREs in the whole genome of zebrafish larvae exposed to esculin, a bioactive coumarin compound with antioxidant properties. Therefore, a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) was employed using an Nrf2-specific polyclonal antibody to map genome-wide Nrf2 binding sites. Our findings reveal that Nrf2 interacts with ARE sequences in promoter-proximal and distal regions, highlighting the intricate and dynamic nature of Nrf2-mediated transcriptional regulation. These results provide novel insights into the genome-wide regulatory landscape of Nrf2 in response to esculin exposure, further elucidating its role in modulating oxidative stress-related gene expression.

overall_design: Control and Esculin exposed Zebrafish larvae were immunoprecipitated with Nrf2 polyclonal antibody and precipitated with magnetic G beads, followed by downstream sequencing.

first: Srija

last: Babu


title: A pig model of human radiation-induced veno-occlusive liver disease reveals ferroptosis as a therapeutic target

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: Radiation-induced liver disease (RILD) is a significant complication of radiotherapy and radiation-based preconditioning for cell transplantation. Despite its importance, understanding its pathogenesis and developing effective therapies have been challenging due to the lack of an appropriate animal model that faithfully reproduces the pathological hallmarks of RILD. In this study, given their anatomical and physiological similarities to humans, we used Bama miniature pigs to establish a reliable large-animal model of RILD through a dose-escalation study using hypofractionated stereotactic body radiation therapy. Pigs receiving 40 Gy radiation developed RILD symptoms and exhibited significant liver dysfunction within 4 weeks, closely resembling human disease progression. Moreover, the pigs developed key pathological RILD hallmarks, including hepatic veno-occlusive disease, centrilobular necrosis, liver fibrosis, and compromised liver regeneration. Through single-nucleus RNA sequencing (snRNA-seq) and histological analyses, we found that hepatocytes in the RILD pig model underwent ferroptosis. Notably, treating these pigs with the ferroptosis inhibitor Liproxstatin-1 after irradiation significantly reversed the symptoms and pathological features of RILD and enhanced liver regeneration, particularly by promoting the proliferation of hepatocytes and endothelial cells. These results underscore the role of hepatocyte ferroptosis as a pivotal driver of RILD and highlight its potential as a therapeutic target. Our study provides a valuable large-animal platform for advancing the understanding and treatment of RILD, as well as optimizing radiation-based therapies and preconditioning strategies.

overall_design: To comprehensively understand the pathogenesis and molecular mechanisms underlying RILD in the early stages, we performed snRNA-seq on liver biopsy samples from the 40 Gy group on day 14 and non-irradiated controls (0 Gy).  To further investigate the therapeutic mechanism of Lip-1 in preventing RILD, we performed snRNA-seq analysis on liver biopsy samples from pigs in the control group (40 Gy) and Lip-1 treatment group (Lip-1) 14 days post-irradiation.

first: Zhen

first: Ludi

last: Zhang

first: Baihua

last: Wu

first: Chandan

last: Guha


title: Targeting mitochondrial stress responses: Terbinafine and Miglustat as novel lifespan and healthspan modulators

city: LAUSANNE

first: Johan

last: Auwerx

address: Station 15

department: SV-IBI

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne EPFL

summary: Mitochondria are key regulators of cellular homeostasis, aging, and age-related diseases. This study investigates the mitochondrial stress response (MSR) and its role in longevity by identifying Terbinafine and Miglustat as novel mitochondrial stress inducers in Caenorhabditis elegans. Using a two-step screening approach, we found that both compounds activate MSR pathways, including the mitochondrial unfolded protein response (UPRmt) via ATFS-1, and modulate mitochondrial function across species, similarly to Doxycycline. To further explore the molecular mechanisms, we performed RNA sequencing (RNA-seq) analysis on C. elegans treated with Terbinafine and Miglustat, as well as controls, to assess transcriptomic changes associated with mitochondrial stress. Gene expression analysis revealed activation of MSR pathways and an interplay between the ATFS-1 and DAF-16 signaling networks. Additionally, validation studies in human HEK293T cells confirmed mitochondrial stress induction and functional modulation, demonstrating the translational potential of these compounds. This dataset provides gene expression profiles of C. elegans under mitochondrial stress conditions, offering insights into the regulatory mechanisms of mitochondrial stress responses and their role in aging.

overall_design: Total RNA samples were extracted from C. elegans day 1 adults worms that had been exposed to the compounds-RNAi of interest from the L1 larval stage.

first: Amélia

last: Lalou

first: Sandra

last: Rodríguez-López

first: Jean-David

last: Morel

first: Giorgia

last: Benegiamo

first: Adrien

last: Faure

first: Arwen

last: Gao

first: Joaquim

last: Barmaz

first: Qi

last: Wang

first: Terytty

last: Yang Li

first: Feng

first: Danaé

last: Broustail

first: Kristina

last: Schoonjans


title: BCR::ABL1-induced enhancer reprogramming uncovers hypersensitivity of Ph+B-ALL cells to enhancer-targeting drugs [ChIP-Seq]

city: London

first: Niklas

last: Feldhahn

address: The Commonwealth Building, Hammersmith Hospital, Du Cane Road

department: Department of Medicine

country: United Kingdom

institute: Imperial College London

summary: To better understand how BCR::ABL1 establishes the Ph+B-ALL-defining transcriptional program, we adopted an integrative multi-omics approach to study the transcriptome, enhancer activities, and 3-dimensional interactions of enhancers with target genes in Ph+B-ALL cells. We performed an in-depth analysis of cells from human Ph+B-ALL patients and a murine Ph+B-ALL model using ChIP-Seq, RNA-Seq, and Hi-C-based methods to link enhancers to the promoters they regulate. We further interfered with enhancer function to explore their role in Ph+B-ALL and investigated BCR::ABL1-regulated TFs that are recruited to them using targeted proteasomal degradation and RNA interference (RNAi).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
This dataset contains several different experimental designs:

(1) Monitoring of enhancer activation during BCR::ABL1-induced malignant transformation using murine primary B-cell precursors from Trp53bp1-/- mice: H3K27ac ChIP-Seq was done on primary B-cell precursors from Trp53bp1-/- mice cultured for 7 or ~60 days and either transduced with BCR::ABL1(p210)-encoding retrovirus or empty vector (EV) as controls. Culture was done in presence of mIL3 throughout.

(2) Monitoring of enhancer activation during BCR::ABL1-induced malignant transformation using murine primary B-cell precursors from C57BL/6 mice: H3K27ac ChIP-Seq was done on primary B-cell precursors from C57BL/6 mice cultured for 3 or ~60 days and either transduced with BCR::ABL1(p190)-encoding retrovirus or empty vector (EV) as controls. Culture was done in presence of mIL3 throughout. For successfully transformed BCR::ABL1(p190) expressing cells (at ~D60), cells were additionally treated with 10nM Ponatinib or DMSO as control for analysis of BCR::ABL1 kinase-dependent enhancer activation.

(3) Comparison of enhancer activation in human Ph+B-ALL cells vs normal bone marrow B-cell precursors: H3K27ac ChIP-Seq was done on Ph+B-ALL cell lines (SUP-B15, TOM-1, BV-173) or primary leukaemia cells (BAL05, BAL08, BAL11), and bone marrow B-cells purified from healthy mononuclear bone marrow cells (obtained from Cambridge Bioscience).

(4) Analysis of the effect of BCR::ABL1 kinase inhibition by Ponatinib on enhancer activation in human Ph+B-ALL cells for comparison to PCHI-C and RNA-Seq data: H3K27ac ChIP-Seq was done on Ph+B-ALL cell lines and primary cells (SUP-B15, TOM-1, BAL08) treated for 24h with DMSO or 100nM Ponatinib. IgG ChIP-Seq and/or Input libraries were generated as controls for peak calling. Primary BAL08 cells were co-cultured on mitotically-inactivated OP9 feeder cells for 3 weeks before experiment.

(5) Analysis of the effect of BCR::ABL1 kinase inhibition on enhancer activation in human Ph+B-ALL cells for using Asciminib: H3K27ac ChIP-Seq was done on Ph+B-ALL cell lines (SUP-B15, TOM-1, BV-173) treated for 24h with DMSO or 1uM Asciminib.

(6) Analysis of the effect of BCR::ABL1 kinase inhibition by Ponatinib on enhancer activation in human CML cells: H3K27ac ChIP-Seq was done on CML cell lines (K562, KCL-22, LAMA-84) treated for 24h with DMSO or 100nM Ponatinib.

(7) Comparison of the effect of the BCR::ABL1-induced TFs MYC, STAT5, ETV5 on enhancer activation vs BCR::ABL1-induced enhancer activation in human Ph+B-ALL cells: H3K27ac ChIP-Seq was done on Ph+B-ALL cell lines (SUP-B15 and BV-173) that were either treated with Ponatinib (24h, 100nM), the STAT5 degrader AK-2292 (24h, 2.5uM), the MYC degrader A80.2HCl/MYC degrader 1 (24h, 25nM), and/or expressing shRNAs against ETV5 or respective C911 negative control shRNAs.

Please note: H3K27ac and respective IgG ChIP‐Seq were performed on 15 mio or 1 mio cells depending on cell availability but with consistency within each experimental comparison. ChIP-Seq for MYC, STAT5 and respective IgG controls were performed using 50 mio cells throughout. Specifically, ChIP-Seq libraries for GSM9037533-GSM9037555, GSM9447961-GSM9447967, GSM9447971-GSM9447974 and GSM9447978-GSM9447983 were generated using 1 mio cells, GSM8577378-GSM8577427 and GSM9447984-GSM9447989 using 15 mio cells, and GSM9447968-GSM9447970 and GSM9447975-GSM9447977 using 50 mio cells.

first: Han

last: Ng

first: Trudy

last: Glaser


title: Targeted genes of Isl1 in E13.5 mouse retina with CUT&Tag

city: Augusta

first: Lin

last: Gan

state: Geogia

address: 1120 15th Street

department: Department of Neuroscience & Regenerative Medicine

institute: Augusta University

summary: The transcription factor ISL1 regulates a unique set of genes in retinal ganglion cells. KEGG Pathway analysis of differentially expressed genes in Isl1 cKO retina revealed multiple genes involved in axon guidance, extracellular matrix-receptor interactions, and cell adhesion molecules.

overall_design: To determine if ISL1 directly regulates these downstream genes, we performed CUT&Tag of ISL1 in wildtype E13.5 retina. The identity of the peaks were characterized and big chromatin profiles were obtained.

first: Li

last: Shuchun

first: Gan

last: Lin

first: Biswas

last: Shiona


title: RNA-Seq of E13.5  control and Isl1 cKO retinae

overall_design: To get an overall picture of the transcriptomic changes upon loss of Isl1, we performed RNA-Seq on control and Isl1-null retina at E13.5. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 control and 2 Isl1cKO retina at E13.5.


title: Chronic replication stress-mediated genomic instability disrupts placenta development in mice

city: Ithaca

first: Mumingjiang

last: Munisha

state: NY

address: 618 Tower Rd, CVM 14 T1-010 VRT

institute: Cornell University

summary: Abnormal placentation drives many pregnancy-related pathologies and poor fetal outcomes, but the underlying molecular causes are understudied. Here, we show that persistent replication stress due to mutations in the MCM2-7 replicative helicase disrupts placentation and reduces embryo viability in mice. MCM-deficient embryos exhibited normal morphology but their placentae had a drastically diminished junctional zone (JZ). Whereas cell proliferation in the labyrinth zone (LZ) remained unaffected, JZ cell proliferation was reduced, independent of cell death during early development. Mouse trophoblast stem cells (TSCs) with high genomic instability failed to maintain stemness, suggesting that replication stress affects the initial trophoblast progenitor pool in a manner that preferentially impacts the developing JZ. Genetically increasing chromatin-bound MCM levels in the mutants rescued placental defects and embryo viability. Developing female mice deficient for FANCM, a protein involved in replication-associated DNA repair, also had placentae with a diminished JZ. These findings indicate that replication stress-induced genomic instability compromises embryo outcomes by impairing placentation.

overall_design: Transcriptomic profiles of E13.5 male and female placentae from control and mutants

first: John

last: Schimenti

first: Jen

last: Grenier


title: Effete and Cullin 4 affect nuclear organization of the gypsy chromatin insulator [ChIP-Seq]

city: Bethesda

first: Elissa

middle: P

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

summary: Chromatin insulators demarcate the genome into distinct transcriptional domains and contribute to higher-order genome organization. In Drosophila, Su(Hw), CP190, and Mod(mdg4)67.2 are core protein components of the gypsy insulator complex. Multimerization of these core components contributes to formation of large structures within the nucleus termed insulator bodies. Post-translational modifications of insulator proteins appear to affect insulator body localization and be required for full insulator activity, but few factors involved in these processes have been identified. To address this gap in understanding, we performed a high-throughput visual screen for Mod(mdg4)67.2-GFP localization using a ubiquitination-related RNAi library. We identified ubiquitination pathway proteins Effete (Eff) and Cullin 4 (Cul4), as novel regulators of CP190 localization and function. Both Eff and Cul4 physically associate with gypsy insulator proteins and promote gypsy-dependent insulator barrier activity. Moreover, Cul4 extensively colocalizes with CP190 on chromatin and assists in the recruitment of CP190 to gypsy sites. Both Eff and Cul4 affect transcription near topologically associating domain (TAD) borders, with Eff specifically altering the 3D nuclear positioning of gypsy insulator sites. Overall, our findings reveal a novel role for ubiquitination pathway-related enzymes in chromatin insulator activity, 3D genome organization, and gene expression.

overall_design: To determine the interaction of Effete and Cul4 with gypsy insulator complex in chromatin association, we performed ChIP-seq analysis for Effete, Cul4, CP190 and Su(Hw) in Kc cell. We performed ChIP-seq to detect core gypsy components after RNAi to verify whether Effete and Cul4 promote the recruitment of gypsy insulator proteins to chromatin.

first: Shue

last: Chen

first: Dagyeong

last: Yang


title: Depletion of the E3 ubiquitin ligase HUWE1 impairs Kras-induced lung adenocarcinoma tumorigenesis and induces a senescent phenotype

city: Manchester

first: Carlos

last: Lopez Garcia

state: Greater Manchester

address: Paterson Building, Wilmslow Rd

department: TLCB

institute: CRUK-MI

summary: The E3 ubiquitin ligase HUWE1 modifies a diverse network of substrate proteins by ubiquitination, through which it regulates various intracellular processes and contributes to both oncogenic and tumour suppressor mechanisms in different cancer contexts. Here, by analysing human lung adenocarcinoma (LUAD) patient samples we reveal that HUWE1 protein expression is commonly upregulated in LUAD tumours compared to normal adjacent lung tissue and that this increase is associated with tumour stage. Using multiple, independent murine models of LUAD initiation and growth, we identify that Huwe1 is essential for mutant Kras-induced lung tumour development and reveal a novel, p53-independent requirement for Huwe1 in LUAD. Mechanistically, we demonstrate induction of a senescent phenotype following HUWE1 depletion - characterised by impaired proliferation, an atypical cell cycle distribution, emergence of morphologically abnormal enlarged cells, and transcriptional reprogramming associated with inflammatory SASP signalling and NFkB activation. Together, these data highlight a crucial role for HUWE1 in mutant Kras-induced LUAD tumorigenesis and in the continued growth and proliferation of established LUAD cells, confirming HUWE1 as a rational therapeutic target for LUAD.

overall_design: Transcriptomic analysis of H358 LUAD cells -/+ treatment with doxycycline to induce expression of control (shCTRL) or HUWE1 targeting (shHUWE1) shRNA constructs. Three biological replicates of each condition.

first: Joshua

last: Searle

first: Matteo

last: Menotti

first: Martin

last: Baker

first: Anshuman

last: Chaturvedi

first: Mathew

last: Carter

first: Fiona

last: Blackhall

first: Angeliki

last: Malliri

first: Colin

last: Lindsay


title: Effect of L-leucine uptake inhibitor on whole-genome transcriptomic profile of Mtb mc2 6206

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

institute: Translational Health Science and Technology Institute

summary: The main objective of this study is to analyze changes in whole-genome transcriptomic profile of mc2 6206 strain of Mycobacterium tuberculosis H37Rv after treatment with a drug which blocks L-leucine uptake. By RNASeq, it was observed that total 482 transcripts are differentially regulated by >2-fold in three biological replicates with p value of <0.05 (FDR of 1%). While 251 genes were downregulated, expression of 231 genes was induced.

overall_design: mRNA profile of M. tuberculosis H37Rv mc2 6206 after treatment with 50nM drug for 24hrs.

first: Agarwal

last: Nisheeth


title: BCR::ABL1-induced enhancer reprogramming uncovers hypersensitivity of Ph+B-ALL cells to enhancer-targeting drugs [PCHiC]

first: Niklas

last: Feldhahn

summary: To better understand how BCR::ABL1 establishes the Ph+B-ALL-defining transcriptional program, we adopted an integrative multi-omics approach to study the transcriptome, enhancer activities, and 3-dimensional interactions of enhancers with target genes in Ph+B-ALL cells. We performed an in-depth analysis of cells from human Ph+B-ALL patients and a murine Ph+B-ALL model using ChIP-Seq, RNA-Seq, and Hi-C-based methods to link enhancers to the promoters they regulate.

overall_design: Ph+B-ALL leukaemia cell lines (TOM-1 and SUP-B15) were treated in cell culture with DMSO or 100nM Ponatinib for 24h and then harvested for PCHi-C. In addition, primary leukaemia cells from a Ph+B-ALL patient (BAL08) were ex vivo cultured on OP9 feeder cells for 3 weeks and then treated with DMSO or 100nM Ponatinib for 24h and harvested for PCHi-C. For comparison, Ph+ CML cells (K562) were processed as Ph+B-ALL cells and subjected to PCHI-C. In addition, primary B-cell precursors (bone marrow CD19+CD10+) were directly subjected to PCHi-C.

first: Han

last: Ng


title: Periodontal ligament stem cell-derived exosomal miR-378a programs osteogenic commitment via DAZAP2/SMAD signaling

status: Public on Feb 26 2026

city: Tokyo

first: Jingyi

last: Gao

state: Tokyo

address: Yushima, Bunkyo District

department: Periodontology

institute: Institute of Science Tokyo

summary: Functional recovery of the periodontium remains a major clinical challenge. To harness the therapeutic potential of extracellular vesicles (EVs) derived from human periodontal ligament mesenchymal stem cells (hPDL-MSC), we identified and characterized the encapsulated miR-378a as a pivotal regulator associated with osteogenic commitment. hPDL-MSC and derivative EVs were dynamically examined throughout osteogenesis, revealing a temporal and progressive enrichment pattern. Mechanistically, integrative microarray, RNA sequencing, bioinformatic analysis, and functional assays established PIM2 and DAZAP2 as direct targets of miR-378a. Overexpression of miR-378a post-transcriptionally suppressed DAZAP2, leading to enhanced nuclear translocation of phosphorylated-SMAD1/5/9 and subsequent activation of canonical BMP signaling. Rescue experiments reinforced the essential role of the miR-378a–DAZAP2–SMAD axis in osteogenic differentiation. Collectively, our findings delineate the molecular pathway triggered by hPDL-MSC-derived exosomal miR-378a and provide new mechanistic insights into EV-mediated modulation of stem cell fate.

overall_design: Bulk RNA-seq were performed to screen the potential target genes of miR-378a-3p.

first: Anhao

last: Liu

first: Takanori

last: Iwata


title: Single-Cell RNA Sequencing Analysis of Proliferative and Differentiated Hepatic Organoids Generated from hPSC-Derived Hepatocyte-Like Cells, using STEMdiff™ Hepatic Organoid Growth Medium and STEMdiff™ Hepatic Organoid Differentiation Medium

city: Vancouver

first: STEMCELL

last: Technologies

state: BC

address: 1618 Station st

department: RND

institute: STEMCELL Technologies

summary: Functionally relevant in vitro human hepatocyte models are critical for drug safety and efficacy screening, and liver research. However, currently available models, such as primary human hepatocytes and immortalized cell lines, often either rapidly de-differentiate or lack metabolic maturity. Human pluripotent stem cell (hPSC)-derived hepatocyte-like cells (HLCs) and hepatic organoids represent scalable and patient-representative alternatives to conventional models, particularly for long-term cell-based assays. STEMdiff™ Hepatic Organoid media are designed to support the establishment, expansion, and differentiation of proliferative and differentiated hepatic organoids, derived from HLCs generated using the STEMdiff™ Hepatocyte Kit. Here, we compare the composition of proliferative and differentiated HLC-derived hepatic organoids, cultured in STEMdiff™ Hepatic Organoid Growth Medium and STEMdiff™ Hepatic Organoid Differentiation Medium, respectively.

overall_design: Hepatocyte-like cells were generated from induced pluripotent stem cell line WLS-1C using STEMdiff™ Hepatocyte Kit, and then embedded into Matrigel domes to generate proliferative hepatic organoids using STEMdiff™ Hepatic Organoid Growth Medium (OGM). Once established, organoids were fragmented and cryopreserved using CryoStor10. To generate samples for sequencing, cryopreserved organoid fragments were recovered and cultured in OGM and passaged twice using a 7-day passaging schedule, seeding ~1000 fragments per 30uL Matrigel dome per passage. Organoids were passaged a third time in OGM and on day 7, they were either harvested for characterization of proliferative hepatic organoids, or switched to STEMdiff™ Hepatic Organoid Differentiation Medium (ODM) for a further 10 days for maturation in 3D before harvest for characterization. To harvest both proliferative and differentiated organoid conditions, Gentle Cell Dissociation Reagent was added to Matrigel domes for organoid recovery, followed by dissociation to single cells using the Animal Component-Free Cell Dissociation Kit. Cell concentration was determined using a Nucleocounter NC-250. Single cell capture and library preparation was performed using the 10X Genomics Chromium platform.

first: Claire

last: Haston

first: Ryan

last: Bailey

first: Eloi

last: Mercier

first: Aishwariya

last: Sharma

first: Emma

last: Nolan


title: Dosage compensation defects due to roX RNA deletion are rescued by recalibration of X/autosome stoichiometry [ChIP-seq]

city: Planegg-Martinsried

first: Fotios

last: Gkountromichos

address: Großhaderner Strasse 9

department: Molecular Biology

institute: Biomedical Center, Ludwig-Maximilians-Universität München

summary: Metazoa evolved regulatory networks to balance the expression of their sex chromosomes. In Drosophila, males have a single gene-rich X chromosome, whereas females have two. Balanced X/autosome expression is essential for viability, and in male flies is achieved by activation of genes on the X through the male-specific-lethal (MSL) dosage compensation complex (DCC). This ribonucleoprotein assembly contains long, non-coding roX RNAs. To dissect the functional requirements of roX in a cell-based system, we deleted the roX2 gene in male S2 cells and selected two independent lines lacking detectable roX RNA. In the absence of roX, the remaining MSL protein complex was unable to associate with known or newly identified binding sites and thus failed to activate transcription. Surprisingly, the X/autosome expression ratio appeared nevertheless compensated. Cytogenetic and genomic analyses revealed that both roX-deficient cell populations had acquired additional X chromosomes. Apparently, chromosome gains due to mis-segregation made up for the loss of DCC-mediated dosage compensation. Interestingly, ectopic expression of full-length roX2, but not of shortened derivatives, fully restored DCC binding and normalized the karyotype. These findings illustrate that X chromosome dosage compensation is critical for viability even in cultured cells and provide a striking example of rapid evolution under stringent selection.

overall_design: ChIP-seq of MSL2 and H4K16ac in wild-type and roX2-KO Drosophila Schneider S2 cells.

first: George

last: Yankson

first: Muhunden

last: Jayakrishnan

first: Aline

last: Campos Sparr

first: Marisa

last: Müller

first: Patrick

last: Heun

first: Peter

middle: B

last: Becker


title: Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation

city: Richland

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

summary: Microbially induced calcium carbonate precipitation (MICP) holds potential for soil stabilization and carbon sequestration efforts. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such processes remain poorly characterized. To address this gap, we interrogated a MICP-capable four-member consortium of soil bacteria termed carbon storing consortium - A (CSC-A). Prior work shows that CSC-A yields carbonate at a higher quantity compared to the sum of carbonate individually produced by each member, suggesting MICP is driven by consortium dynamics.Thus, we applied a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of specialization by two members, while metatranscriptomic perturbation suggested that R. qingshengii is a keystone species when grown in urea, a key molecule to the MICP process. By comparing individual species’ metabolomes to the metabolic profile of a shared well, we identified over 200 metabolites predicted to be produced or consumed by CSC-A. Integrating both data types and mapping them to the KEGG reactome highlighted over 20 different enriched pathways with reactions related to glutamate metabolism, succinate metabolism, and branched chain amino acid biosynthesis. As succinate metabolism was a major node in this network we applied laboratory assays to confirm that succinate led to increased carbonate precipitation by CSC-A, a critical validation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortium to carbonate precipitation.

sample_organism:
Curtobacterium flaccumfaciens
Microbacterium foliorum
Bacillus toyonensis
Rhodococcus qingshengii

overall_design: RNA-seq profiling of CSC-A as well as CSC-A lacking   C. flaccumfaciens in the presence and absence of urea-enriched media, with samples taken at time points of 0 hours, 24 hours, and 48 hours and CSC-A lacking R. qingshengii in urea enriched media with samples taken at time points of 24 hours and 48 hours.

first: Lin

last: Tesia T.

first: Anthony

last: Winston

first: McClure

last: Ryan

first: Mitchell

last: Hugh


title: BCR::ABL1-induced enhancer reprogramming uncovers hypersensitivity of Ph+B-ALL cells to enhancer-targeting drugs [RNA-Seq]

first: Niklas

last: Feldhahn

overall_design:
This dataset contains several different experimental designs:

(1) Monitoring of transcriptional deregulation during BCR::ABL1-induced malignant transformation using murine primary B-cell precursors from Trp53bp1-/- mice: RNA-Seq was done on primary B-cell precursors from Trp53bp1-/- mice cultured for 7 or ~60 days and either transduced with BCR::ABL1(p210)-encoding retrovirus or empty vector (EV) as controls. Culture was done in presence of mIL3 throughout.

(2) Monitoring of transcriptional deregulation during BCR::ABL1-induced malignant transformation using murine primary B-cell precursors from C57BL/6 mice: RNA-Seq was done on primary B-cell precursors from C57BL/6 mice cultured for 3 or ~60 days and either transduced with BCR::ABL1(p190)-encoding retrovirus or empty vector (EV) as controls. Culture was done in presence of mIL3 throughout. For successfully transformed BCR::ABL1(p190) expressing cells (at ~D60), cells were additionally treated with 10nM Ponatinib or DMSO as control for analysis of BCR::ABL1 kinase-dependent enhancer activation.

(3) Monitoring of transcriptional differences between human Ph+B-ALL cells and normal bone marrow B-cell precursors: RNA-Seq was done on Ph+B-ALL cell lines (SUP-B15, TOM-1, BV-173) or primary leukaemia cells (BAL08), and bone marrow B-cells purified from healthy mononuclear bone marrow cells (obtained from The John Goldman Centre for Cellular Therapy of Hammersmith Hospital/Imperial College London).

(4) Analysis of the effect of BCR::ABL1 kinase inhibition by Ponatinib on transcription in human Ph+B-ALL cells for comparison to PCHI-C and H3K27ac ChIP-Seq data: RNA-Seq was done on Ph+B-ALL cell lines (SUP-B15, TOM-1, BV-173) or primary leukaemia cells (BAL08) treated for 24h with DMSO or 100nM Ponatinib. Primary BAL08 cells were co-cultured on mitotically-inactivated OP9 feeder cells for 3 weeks before experiment.

(5) Analysis of the effect of global enhancer inhibition on transcription in human Ph+B-ALL cells for comparison to PCHI-C, H3K27ac ChIP-Seq and RNA-Seq data: RNA-Seq was done on the Ph+B-ALL cell lines SUP-B15 and TOM-1 treated for 24h with DMSO or 250nM dCBP-1, or for 48h with DMSO or 0.5uM A-485.

first: Han

last: Ng

first: Trudy

last: Glaser


title: Implication of FOXD2 loss of function in renal hypo(dys)plasia

city: Freiburg

first: Gwang-Jin

last: Kim

address: Albertstrasse 25

institute: University of Freiburg

summary: FOXD2 loss of function causes renal hypodysplasia/CAKUT  in mice, however the underlying mechanism has not been understood. Aim of the study was to identify differentially regulated genes in Foxd2 mutant metanephric mesenchyme cells compared to control cells.

overall_design: We used CRISPR/Cas technology to generate an mk4 cell clones carryinga  homozygous frameshift mutations. Mutant clones were compared to wildtype clones using RNAseq, qPCR and western blot techniques.We observed a change in the expression pattern of a number of genes implicated in early renal development, inlcuding PAX2.

first: Miriam

last: Schmidts

first: Sebastian

last: Arnold

first: Minh

last: Nguyen


title: BCR::ABL1-induced enhancer reprogramming uncovers hypersensitivity of Ph+B-ALL cells to enhancer-targeting drugs

overall_design: ATAC-Seq was performed on primary leukaemia cells from a Ph+B-ALL patient and on two Ph+B-ALL cell lines (TOM-1 and SUP-B15) according to the Omni-ATAC-seq protocol (https://doi.org/10.1038/protex.2017.096). Cells were kept in cell culture under standard conditions and treated for 24h with 100nM Ponatinib or DMSO as control. Primary BAL08 cells were cultured on irradiated OP9 feeeder cells for 3 weeks before experiment.

first: Ozgen

last: Deniz


title: Minimizing far-extending chromatin perturbation in genome editing  preserves stem cell identity [ATAC-Seq]

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

institute: Tsinghua University

summary: While CRISPR/Cas9 holds therapeutic promise, broader application demands understanding complications in vast non-coding regions. We found that CRISPR/Cas9 can cause premature differentiation of neural stem cells in vivo and mouse embryonic stem cells in vitro, even when cleavage occurred at distant sites tens of kilobases away from the nearest regulatory elements. To investigate this, we employed an integrated ATAC/RNA approach (AR-seq) and identified editing-induced chromatin accessibility change, with its scale varying by cell types. Cells with stemness are most affected, experiencing perturbations that extend over a hundred kilobases. Furthermore, even local DNA perturbations can disrupt CTCF- and condensate-associated chromatin architecture, causing distal transcriptional rewiring and ultimately loss of stemness identity. To minimize chromatin perturbations and preserve cell identity we refined gene editing strategies, including distance-aware sgRNA design, pharmacological attenuation of DNA resection, and alternative editing systems. This work paves the way for safer and broader application of genome editing technologies.

overall_design: To characterize how genome editing reshapes chromatin state at and beyond the cleavage locus, we implemented an ATAC-centered design that emphasizes spatial extent and mechanistic interpretability rather than peak-level changes alone. Using the ATAC arm of AR-seq, we quantified editing-associated accessibility shifts as a distance-resolved signal (ΔATAC/ΔATAC span), enabling direct evaluation of whether chromatin perturbation decays with increasing genomic distance from the edit site. The framework was structured to distinguish local DNA damage effects from broad regulatory remodeling by integrating matched RNA outputs, repair-pathway perturbations, and orthogonal chromatin assays. In particular, the design tested whether pathway bias toward resection-prone non-cNHEJ states is linked to broader accessibility propagation, and whether these accessibility changes align with disruption of higher-order regulatory architecture.

first: Zhu

last: Ming

first: Yuan

last: Junsong

first: Meng

last: Qiuchen

first: Yu

last: Jiawei


title: Whole-blood rna-seq of cattle metaphylactically treated with tulathromycin

city: Canyon

first: Bradly

middle: Isaiah

last: Ramirez

state: Texas

address: 3201 Russel Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

summary: To elucidate the connection between tulathromycin metaphylaxis and gene expression over time, eighty-eight commercial steers were enrolled in a study with treatment groups consisting of metaphylaxis at arrival, or a control receiving no drug. Whole blood was collected at various timepoints with Tempus blood RNA collection tubes, and total RNA was extracted and sequenced for differential expression.

overall_design: Of cattle which did not present symptoms of bovine respiratory disease (BRD) for the duration of the study, seven of each treatment group were selected for sequencing of whole blood samples collected at days 0 (pre-treatment), 7, 14, and 21. Of cattle which did present for BRD, blood from three tulathromycin and seven control were sequenced from samples taken at day 0 and time of treatment for symptoms.

first: Matthew

last: Scott

first: William

last: Crosby

first: Amelia

last: Woolumns


title: Gene expression profiles of NSCLC cells treated with almonertinib, paclitaxel, and their combination

city: Dalian

first: Hai-long

last: Piao

state: Liaoning

address: No.457 Zhongshan Road

institute: Dalian Institute of chemical physics

summary: Transcriptomic profiling revealed that the combination therapy elicits an unique molecular signature distinct from either monotherapy alone. We identified a specific gene cluster (C8) that was suppressed only by the drug combination, and mainly enriched in cell cycle, DNA replication and mitochondrial function in PC9 cells. The downregulation of these processes was validated in H1975 cells, and key genes (e.g., XRCC2, SKA3, TOMM40) also exhibited prognostic relevance.

overall_design: The PC9 or H1975 cell lines treated under control, paclitaxel alone (0.3 nM for PC9; 1 nM for H1975), almonertinib (2 nM for PC9; 1 nM for H1975), and thepaclitaxel+almonertinib combination for 24 hours were collected and their RNAs were isolated using TRIzol reagent.


title: Minimizing far-extending chromatin perturbation in genome editing  preserves stem cell identity [Cut&Tag]

overall_design: To investigate whether editing-induced chromatin effects involved changes in active regulatory marks, we performed histone CUT&Tag profiling after genome editing as an orthogonal epigenomic readout. In this study, histone CUT&Tag was used to evaluate how active chromatin signatures around edited loci and nearby regulatory elements changed in relation to the observed accessibility and transcriptional shifts. To investigate whether editing could alter higher-order regulatory architecture through boundary-associated factors, we performed CTCF CUT&Tag after genome editing. Here, CTCF CUT&Tag was designed to measure the extent and direction of CTCF occupancy changes around edited sites, and to test whether these changes were consistent with the chromatin and transcriptional patterns observed in matched samples. We used this assay conservatively as an architectural readout, together with other datasets, to assess whether displacement or reduction of CTCF-linked regulation was a plausible contributor to distal expression changes.


title: Macrophages restrict tumor immune infiltration 3 by controlling collagen topography through a Tcf4-Col3 axis

city: Geneva

first: Zoe

last: Fusilier

address: Michel servet 1

institute: UNIGE

summary: During tumorigenesis, the extracellular matrix is profoundly remodeled. While the impact of such remodeling on tumor growth and invasion is well-described, less is known on its consequences on immune infiltration. Combining tissue imaging and machine-learning, we show that immune cell localization in tumors can be predicted by the local topography of fibrillar collagens. Such topographies are dictated by a fibrotic pathway driven by the transcription factor Tcf4 in both cancer and stromal cells, which promotes collagen 3 deposition, resulting in intermingled collagen networks that favor intra-tumoral infiltration of T cells and neutrophils. Macrophages inhibit this pathway, highlighting their key structural role in shaping the tumor extracellular matrix. Human database analyses revealed a strong correlation between Tcf4, collagen 3, and tumor infiltration by T cells and neutrophils in different solid tumors, attesting the clinical relevance of our findings. Collagen network topographies thus emerge as a major regulator of antitumor immunity .

overall_design: D14 MC38 tumors from CD64DTR and CD64WT were harvested at day 14 d.p.i., digested in Liberase TL 0,25mg/ml (Roche, #5401020001) DNAse 0,5mg/ml (Sigma, DN25-100MG) in CO2 independent medium (Gibco, 18045088) using GentleMacs Octo dissociator pre-set program (37C_m_TDK1, 41min at 37° under agitation). Cells were filtered on a 100 μm cell strainer and red blood cells were lysed using red blood cells lysis bufer 1X (Biolegend, 420301) diluted in water. After centrifugation (5min, 1500rpm), cells were incubated 10 min with Fcblock solution diluted in FACS bufer (BD, 553142, 1:100) and stained either with (1) DAPI (Invitrogen, 11534886, 1:10000) for the first experiment (batch #1), or (2) with DAPI, anti-CD45 APC-Cy7 (BD, 557659, 1:200) and anti-CD64 APC (Biolegend,139306, 1:200) (for the second experiment (batch #2) diluted in FACS bufer (PBS 1X, 0,5%BSA, 2mM EDTA). For batch#1, DAPI- cells were sorted while for batch#2, DAPI-CD45-, DAPI-CD45+CD64+, DAPI- CD45+CD64- populations were sorted separately. For batch #1, 15 000 cells form CD64WT and CD64DTR tumors were loaded. For Batch #2, 10000 cells form CD64WT and CD64DTR tumors were loaded. Sequencing was performed on a Novaseq 6000, with the Single Cell 3’ V3.1 Next-GEM kits. Batch #1 and DAPI-CD45- from batch #2 were sequenced at 50,000 reads / cell, DAPI-CD45+CD64+, DAPI- CD45+CD64- from batch #2 were sequenced at 100,000 reads / cell. ScRNAseq data were analyzed with R using the Seurat suite (v4). Cells were then filtered out when expressing less than 1000 genes, or when expressing more than 10% of mitochondrial genes. Doublets were identified using the DoubletFinder package. Clusters containing less than 100 cells were excluded from the analysis.

first: Zoé

first: Hélène

last: Moreau

first: Christel

last: Goudot

first: Ana-Maria

last: Lennon-Duménil


title: Chronic PFOA and PFOS Exposure Triggers Cellular Oxidative Stress and Alters Lipid Levels as Revealed through Multi-omics Analysis

city: Buffalo

first: G. Ekin

last: Atilla-Gokcumen

address: 120 Founders Promenade

department: Chemistry

institute: University at Buffalo

summary: Per- and polyfluoroalkyl substances (PFAS), or "forever chemicals," are linked to metabolic, immune, and neurotoxic disorders, yet their long-term cellular effects remain unclear. Using a 24-week chronic exposure model with non-transformed human epithelial cells, we examined responses to low, environmentally relevant concentrations of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS). Integrated transcriptomic and lipidomic analyses revealed that despite minimal cellular accumulation, molecular changes emerged around week 17, marked by transcriptional signatures indicative of oxidative stress responses, cell survival pathways, and lipid metabolism. Our data suggests a multi-faceted model in which long-term PFOA and PFOS exposure induces oxidative stress mediated by SESN2 and SOD3 , increases lipid biosynthesis via SREBP pathway, and causes compound-specific disruptions of membrane lipids. These findings highlight the importance of multi-omic, time-resolved approaches in uncovering the mechanisms of chronic low-dose chemical exposure and provide a foundation for future in vivo studies.

overall_design: hTERT RPE-1 cells were exposed to MeOH (vehicle control), perfluorooctanoic acid (PFOA), or perfluorooctane sulfonic acid (PFOS) for 24 hours or 7, 17, and 24 weeks . Each condition includes three independent biological replicates (n = 3). Total RNA was extracted from each sample and subjected to paired-end RNA sequencing. Gene-level expression counts were generated and differential expression analysis was performed using DESeq2 to compare treatment conditions across time points.

first: Paddayuman

middle: Z

last: Jenise

first: Cristobal

last: Judith

first: Landau

last: Luane J.

first: Ashleigh

last: Gagnon

first: Gokcumen

last: Omer

first: Aga

last: Diana S.

first: Atilla-Gokcumen

last: G. Ekin


title: Dosage compensation defects due to roX RNA deletion are rescued by recalibration of X/autosome stoichiometry [RNA-seq]

first: Fotios

last: Gkountromichos

overall_design: ChIP-seq and CUT&RUN of MSL2 and H4K16ac and RNA-seq profiling of wild-type and roX2-KO Drosophila Schneider S2 cells.

first: George

last: Yankson

first: Muhunden

last: Jayakrishnan

first: Aline

last: Campos Sparr

first: Marisa

last: Müller

first: Patrick

last: Heun

first: Peter

last: Becker


title: A Single-Cell Transcriptomic Atlas of Symmetry Breaking in Sheep

city: Madrid

first: Priscila

last: Ramos-Ibeas

address: Avda. Puerta de Hierro, 12, local 10

department: Animal Reproduction

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC

summary: The mammalian body plan is established during symmetry breaking and gastrulation. In ungulates and primates, these events occur within a flat embryonic disc and coincide with the developmental window most susceptible to pregnancy loss. Using the EvercodeTM Cell Fixation kit v2 (ECF2101, Parse Biosciences), we have  generated a single-cell RNA sequencing atlas of in vivo sheep embryos that defines the timing and molecular programs underlying lineage segregation, as well as the inter-lineage signalling mediating anterior visceral hypoblast specification (AVH) and primitive streak formation.

overall_design: We collected single cells cells from eight pooled samples, comprising 80 in vivo-derived embryos collected from superovulated ewes between embryonic day (E) 11, prior to symmetry breaking and onset of gastrulation, and 13.5, after gastrulation but before neural folding and somitogenesis. The dataset included E11 and E11.5 whole embryos (spherical and ovoid), as well as isolated embryonic discs (EDs) with surrounding extraembryonic membranes (EEMs) from E12.5 and E13.5 (tubular and filamentous) conceptuses. Sequencing was performed on Illumina NovaSeq 6000. Two sublibraries were generated.

first: Leopoldo

last: González-Brusi


title: Minimizing far-extending chromatin perturbation in genome editing  preserves stem cell identity [Long Read Amplicon Sequencing]

first: Jiawei

last: Yu

overall_design: To rigorously test whether CRISPR-induced phenotypic disruption near stemness-associated regulatory regions is driven by direct structural damage at the edited locus, we implemented an orthogonal validation strategy centered on long-read amplicon Nanopore sequencing. The design rationale was to overcome the resolution limits of conventional short-read assays and gel-based screening, and to quantify the full spectrum of local repair outcomes at single-molecule scale, with particular sensitivity to larger deletion classes. Conceptually, this assay was positioned as a mechanistic discriminator: if distal transcriptional and cell-state perturbations were primarily a consequence of extensive on-target sequence loss, a substantial burden of long deletions would be expected in edited populations.  Accordingly, we profiled locus-spanning long-read amplicons from edited and matched control samples, then quantified deletion-length distributions relative to the nuclease cut site. The analytical framework was designed to distinguish rare large-deletion events from the dominant indel background while controlling for amplification-related representation bias, enabling robust estimation of the structural contribution to phenotype. In parallel with PEM-seq and targeted off-target interrogation, this design provided convergent evidence for interpreting causality: structural lesions were detectable but limited in prevalence, supporting a model in which widespread chromatin/transcriptional rewiring cannot be explained solely by frequent large on-target deletions.

first: Zhu

last: Ming

first: Yuan

last: Junsong

first: Meng

last: Qiuchen

first: Yu

last: Jiawei


title: Charting the transition from in vitro gliogenesis to the in vivo maturation of transplanted human glial progenitor cells

city: Rochester

first: Steven

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Neither rodent models nor in vitro studies of human cells adequately describe the molecular ontogeny of human glial progenitor cells (hGPCs). Here, we used scRNA-seq together with scATAC-Seq and CUT&TAG assessment of chromatin availability to track the in vitro genesis and in vivo differentiation of hGPCs from pluripotent stem cells (PSCs). In vitro, the hGPC pool comprised 4 transcriptionally distinct subpopulations, each associated with a distinct pattern of chromatin accessibility and histone modification of stage-dependent genes. After the neonatal transplant of these cells into myelin-deficient shiverer mice, they differentiated further as astrocytes and oligodendrocytes. A combination of gene co-expression, motif enrichment, cell-trajectory, cell-cell interaction, and spatial transcriptomic analyses revealed that the host environment potentiated the context-dependent differentiation of the hGPCs, via their activation of distinct gene regulatory networks. Together, these data describe the process and pathways by which human PSC-derived GPCs are generated in vitro and diversify in vivo to mature as astrocytes and oligodendrocytes.

overall_design: To validate the expression of key GPC receptors driving in vivo maturation, we utilized the Xenium Prime 5K human gene panel (10X Genomics) on 16-19wk human glial chimeric shiverer mice (WA09, n=4; C27, n=2).

first: John

middle: N

last: Mariani

last: Schanz

first: Benjamin

last: Mansky

first: Xiaolu

last: Wei

first: Carter

middle: C

last: Long

first: Devin

last: Chandler-Militello

first: Hannah

middle: E

last: Aichelman

first: Nguyen

last: Huynh

middle: A


title: Destabilization of the noncanonical PRC1.1 complex via USP7 inhibition induces neuronal differentiation in neuroblastoma [CHIP-Seq, CUT&RUN, PCGF1KO]

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: Pediatric cancers are frequently driven by genomic alterations that result in impaired differentiation during tissue development.  To identify protein complex-level dependencies required for differentiation in neuroblastoma, a pediatric cancer of the developing peripheral nervous system, we curated a list of protein complexes using the CORUM database and mined the Dependency Map (DepMap) using single sample gene set enrichment analysis. This analysis identified the non-canonical PRC1.1 complex, which represses transcriptional activity through ubiquitination of histone 2A, lysine 119 (H2AK119Ub), as a selectively enriched dependency in neuroblastoma. Knockout of several PRC1.1 subunits reduced neuroblastoma growth, arrested the cell cycle, and induced a neuronal differentiation program. While no known direct inhibitors of PRC1.1 exist, co-dependency analysis of PRC1.1 subunits against all other genes in DepMap identified that the deubiquitinase USP7 strongly correlated with PRC1.1 dependency. Treatment with XL177A, a small molecule inhibitor of USP7, significantly reduced neuroblastoma growth in both cellular and animal models. Integrated RNA- and ChIP-sequencing showed that both PRC1.1 knockout and USP7 inhibition resulted in highly correlated transcriptional alterations and reduced H2AK119Ub deposition on chromatin, suggesting that USP7 inhibition reduced neuroblastoma growth through a PRC1.1-dependent mechanism. Mechanistically, global proteomics and ubiquitinomics revealed that USP7 inhibition disrupted non-canonical PRC1 complex assembly, resulting in destabilization of PRC1.1 and subsequent proteolysis. Our findings expand our understanding of the chromatin complexes required to maintain a de-differentiated state in neuroblastoma and suggest the therapeutic potential for USP7 inhibitors in the treatment of this disease.

overall_design: ChIPsequencing for H2AK119Ub at day 10 with 1 µM XL177A treatment in NGP cels.


title: Enhanced mitophagy promotes lung repair and regeneration by restoring epithelial metabolic fitness [RNA-Seq]

city: Shanghai

first: pei

last: wu

address: 393 Middle Huaxia Road

institute: ShanghaiTech University

summary: Alveolar Type II cells (AT2s) are the stem cells in the alveoli, responsible for both alveolar homeostasis and regeneration. Mitochondrial dysfunction has been reported in the AT2 cells from both chronic and acute injury induced alveolar diseases, including idiopathic pulmonary fibrosis (IPF) and viral pneumonia. Here, we demonstrate that genetic depletion of Ubiquitin Specific Peptidase 30 (USP30), a negative regulator of mitophagy, boosts mitophagy and restores mitochondrial function, leading to protection from injury induced AT2 apoptosis and increased AT2 stem cell activity. Both global Usp30 knockout (KO) and AT2-specific Usp30 KO protects the mice from bleomycin induced lung fibrosis and influenza puneumonia. Moreover, pharmaceutical inhibition of USP30 using a small molecule inhibitor effectively alleviates lung fibrosis and influenza pneumonia. Our study underscores a therapeutic potiential of USP30 inhibition for the treatment of injury induced alveolar diseases, offering a promising strategy for treating injury induced diseases

overall_design: RFP+ AT2 cells were flow-sorted from tamoxifen-treated WT-sftpc-creert2 and Usp30-Sftpc-creert2 mice at day 14 after saline or bleomycin treatment

first: Ying

last: Xi

first: Pei

last: Wu

last: Chen