title: Mitochondrial Ca2+ homeostasis controls inter-compartmental proteostasis in Arabidopsis plants [Ribo-seq]

summary:
Purpose: The goals of this study are to determine the effects of mitochondrial Ca2+ homeostasis on cytosolic translation
Methods: The monosomal and polysomal mRNA profiles of 10-day-old WT, MCU2 overexpression and mcu sextuple mutation plants were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks
Results: Using an optimized data analysis workflow, we mapped a minimum of 23 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified more than 23,000 transcripts. Data analysis revealed that perturbation of mitochondrial Ca2+ altered specifically the translational efficiency of RNA modification genes
Conclusions: Our study represents the first detailed analysis of Arabidopsis monosomal and polysomal RNA transcriptomes in response to impaired mitochondrial Ca2+, with biologic replicates, generated by RNA-seq technology. Our results showed that perturbation of mitochondrial Ca2+ triggered cytosolic translation response. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses of inter-compartmental communication

overall_design:
The monosomal and ploysomal mRNA profiles of 10-day old wild type (WT) and MCU2 overexpression and sextuple mutant plants were generated by deep sequencing, in triplicate, using Illumina HiSeq2500
AA ttreatment = 50uM antimycin for 5 hours, CK treatment = DMSO control

first: Jian-Kang


title: Mitochondrial Ca2+ homeostasis controls inter-compartmental proteostasis in Arabidopsis plants [mRNA]

status: Public on Jun 03 2026

city: Kaifeng

first: Xiaohong

last: Zhu

address: Jinming Street

country: China

institute: Henan University

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goals of this study are to determine the effects of mitochondrial Ca2+ homeostasis on nuclear gene expression.
Methods: The mRNA profiles of 10-day-old WT, MCU2, MCU4, MCU6 overexpression and mcu sextuple mutation plants were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped a minimum of 14 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified more than 33,000 transcripts. Data analysis revealed that perturbation of mitochondrial Ca2+ altered nuclear gene expression.
Conclusions: Our study represents the first detailed analysis of Arabidopsis RNA transcriptomes in response to impaired mitochondrial Ca2+, with biologic replicates, generated by RNA-seq technology. Our results showed that perturbation of mitochondrial Ca2+ triggered nuclear gene expression response. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses of inter-compartmental communication at transcriptional level.

overall_design: mRNA profiles of 10-day old WT, MCU2, MCU4 and MCU6 overexpression and sextuple mutant plants were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.  AA ttreatment = 50uM antimycin for 5 hours, CK treatment = DMSO control


title: Ketogenic diet mediates intestinal tumorigenesis through lipids not ketones

status: Public on Jun 02 2026

city: Cambridge

first: Constantine

last: Tzouanas

address: 77 Massachusetts Avenue

country: USA

institute: Massachusetts Institute of Technology

summary: We used scRNA-seq to evaluate intestinal responses to ketogenic diet in mice

overall_design: Intestines were dissociated for scRNA-seq

first: Constantine N.

first: Jessica E.S.

last: Shay

first: Fangtao

last: Chi

first: Ömer H.

last: Yilmaz


title: A strain-specific role for the UDP-glucose 4-epimerase Uge3 in Aspergillus fumigatus virulence

city: Hanover

first: Nicole

last: Kordana

state: NH

address: 74 College Street, Hinman Box 7550

department: Microbiology and Immunology

institute: Dartmouth College

summary: Expression of a fungal-specific sub-telomeric gene, hrmA, in Aspergillus fumigatus is important for hypoxia fitness, a colony biofilm morphology termed H-MORPH, and virulence in a murine model of invasive pulmonary aspergillosis (IPA). How expression of hrmA contributes to virulence and worse disease progression is ill-defined. Surprisingly, increased hrmA expression results in loose attachment of the extracellular matrix (ECM) from the fungal cell wall resulting in decreased strain adherence. Fungal strains that are less adherent in vitro are typically less virulent as the ECM aids in adhesion to host cells and confers protection from host responses. Here we report that the UDP-glucose 4-epimerase encoding gene, uge3, that is required for GAG biosynthesis is necessary for virulence of the H-MORPH strain, hrmAREV (AF293::hrmAD304G) in contrast to its parent strain AF293. We leverage an isogenic set of A. fumigatus strains to identify a role for uge3 in central carbon metabolism that promotes disease progression complementing its essential role in GAG biosynthesis in a strain specific context.

overall_design: RNASeq profiling of A. fumigatus strains AF293, AF293∆uge3, hrmA-REV and hrmA-REV∆uge3 submerged biofilm tissue harvested after 24-hours development in four biological replicates.

middle: E

first: Charles

last: Puerner

first: Angus

last: Johnson

first: Jane

middle: T

last: Jones

first: Caitlin

middle: H

last: Kowalski

first: Katherine

middle: G

last: Quinn

first: Ko-wei

last: Liu

first: François

last: Le Mauff

first: Robert

middle: A

last: Cramer


title: Raw RNA-seq data for Characterization of the biosynthetic enzymes of the anticancer cephalotaxine and homoerythrina alkaloids

city: Beijing

first: Feifan

last: Lin

address: Tsinghua University,beijing,China

institute: 清华大学

summary: for doing gene-expression network analysis and selecting the candidate sequences

overall_design: sampled and extract RNA from Cephalotaxus fortunei across root, leaf, stem and then doing gene-expression network analysis and selecting the candidate sequences


title: Specification of the interstitial cell lineage in the fetal mouse ovary requires balanced Notch signaling

city: Research Triangle Park

first: Yu-Ying

last: Chen

address: 111 TW Alexander Dr

institute: National Institute of Environmental Health Sciences

summary: The ovary contains two major somatic lineages, granulosa cells and interstitial cells, that arise from progenitors within the coelomic epithelium. However, how these two lineages diverge during ovarian development remains unclear. By analyzing joint single-nucleus transcriptomic and chromatin accessibility profiles of murine ovarian cells at the onset of ovary formation, we identified two somatic progenitor populations from the coelomic epithelium distinguished by expression of the nuclear receptors Nr5a1 and Nr2f2. Based on their transcriptomic trajectories, the Nr5a1+ epithelial cells preferentially transitioned toward the granulosa lineage whereas the Nr2f2+ epithelial cells differentiated into mesenchymal populations. This lineage relationship was supported by Nr2f2 lineage tracing experiments that fetal Nr2f2+ progenitors contribute to ovarian interstitial cells postnatally. To define the molecular features underlying this divergence, we performed differential gene expression and chromatin accessibility analyses and found that Nr2f2+ epithelial cells, but not Nr5a1+ cells, were enriched for Notch pathway components and Notch effector motifs. Consistently, lineage tracing of Notch-responsive cells marked Nr2f2+ interstitial cells in postnatal ovaries, whereas ectopic Notch activation in Nr5a1+ cells promoted expansion of the interstitial population accompanied by reduced granulosa cells. By integrating motif analysis with accessible chromatin-gene linkage, we also identified downstream targets regulated by Notch effectors in Nr2f2+ cells, which showed concordant changes upon ectopic Notch activation. These findings demonstrate that somatic cell fate is established early during ovarian development, with active Notch signaling specifying the interstitial lineage and a balanced Notch activity required for proper somatic lineage establishment.

overall_design: scRNA-seq of embryonic day (E) 16.5 ovairan cells from Hes1+/CreERT2; ROSA+/Sun1-sfGFP mice that were lineage-labeled with tamoxifen at E10.5, and bulk RNA-seq of E13.5 Notch-induced (Tg(Nr5a1-cre)+; ROSA+/Notch) and control (Tg(Nr5a1-cre)+; ROSA+/+) mouse ovarian samples

first: Saniya

last: Rattan

first: Chang

first: Xin

last: Xu

first: Humphrey

last: Yao


title: Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [ATAC-seq]

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Estrogen receptor alpha (ER) is an established oncogenic transcription factor in breast and endometrial cancer; however, more is known about the mechanisms controlling ER behavior in breast cancer, and therapies targeting ER have been much more successful in breast cancer. To address this disparity, we seek to identify genomic features that control ER in endometrial cancer and determine to what extent these factors differ from those in breast cancer. We focus on the locations of estrogen response elements (EREs), ER’s preferred DNA binding motif, throughout the human genome. To identify factors that predict ER genomic binding and effects on target gene expression, we apply machine learning to genomic data for each ERE in Ishikawa cells (ER+ endometrial cancer) and T-47D cells (ER+ breast cancer). Many of these factors, such as chromatin accessibility and histone modifications, are predictive of ER activity in both cell lines. However, the transcription factors that predict ER activity are found to be cell type-specific, including FOXA1 and GATA3 in T-47D cells, and ETV4 and SOX17 in Ishikawa cells. In addition, the features that predict ER binding and effects on gene expression differ, with transcription at EREs in the absence of estrogen being predictive of regulatory activity.  To verify our findings in the Ishikawa cells, we perform a CRISPR knockout screen, which confirms the discovery that SOX17 controls ER activity in endometrial cancer cells. These results identify important genomic features of ER binding and regulatory activity and how these features differ between endometrial cancer and breast cancer cells.

overall_design: ATAC-seq on wild-type HCI-EC-23 cells with DMSO treatment

first: Alexandra

last: Richey

first: Noel

last: Kitchen


title: Glia underlies brain wide activation and sleep behavior during sickness through adrenergic-glutamatergic axis

city: Philadelphia

first: Jianing

last: Yang

state: Pennsylvania

address: 3400 Civic Blvd

department: Neuroscience

institute: University of Pennsylvania

summary: Sickness induces coordinated changes in physiology and behavior, including increased sleep, and despite specific circuits responsible for some of them have been recently described, how the brain orchestrates this global state shift remains unclear. Whole-brain-single-cell RNA sequencing in a Drosophila model of sickness revealed that glia, rather than neurons, undergo the most extensive transcriptional remodeling and follow up experiments uncovered a neuron-glia axis that drives sickness sleep behavior. Specifically, the process requires octopaminergic signaling in ensheathing glia (EG) and it is required for a coupled wave of glial and neuronal activation across the brain. EG gap junction functional coupling facilitates brain wide activation, which ultimately promotes sickness behavior through glutamatergic signaling. Altogether, these findings elevate glia from passive supporters to active coordinators of sickness behavior, opening new avenues for understanding the neuromodulatory basis of behavioral state drifts sleep, fatigue, and malaise.

overall_design: CantonS female flies (7-10 day old) were kept in 12:12 LD cycles. 6h after Lights on, flies were injected with an sterile PBS solution. This protocol induces sleep and can be observed as an increase in total time sleep versus handled control flies for 4 h after lights on (during the morning activity peak). For single cell, brains (100 control and 100 injured) were dissected at ZT0 and processed for library prep within five hours after dissection.

first: Sara

last: B Noya

first: Amita

last: Sehgal

first: Zhifeng

last: Yue

first: Andrew

last: Nguyen


title: MERFISH spatial transcriptomic profiling of extracellular matrix and vascular-associated populations in the adult human pancreas

city: San Francisco

first: Zev

middle: Jordan

last: Gartner

state: CA

department: PhramChem

institute: UCSF

summary: The extracellular matrix (ECM) and basement membrane (BM) are critical structural and signaling components of the human pancreatic endocrine niche. To define the cellular sources and spatial organization of vascular ECM programs in the adult human pancreas, we performed MERFISH spatial transcriptomics on FFPE pancreatic tissue sections from non-diabetic (ND) and type 2 diabetic (T2D) donors using the Vizgen MERSCOPE platform with a custom 300-gene panel enriched for extracellular matrix, vascular, endocrine, and stromal-associated genes.

overall_design: FFPE adult human pancreatic tissue sections from ND and T2D donors were profiled using MERFISH spatial transcriptomics with the Vizgen MERSCOPE platform. Spatial datasets were integrated using CONCORD and analyzed using Scanpy and Squidpy to characterize vascular-associated stromal populations, extracellular matrix programs, and spatial niche organization across endocrine and exocrine compartments.

first: Luisa

middle: K

last: Meneses

middle: J

first: Julie

middle: B

last: Sneddon


title: Scutellarein accelerates diabetic wound healing by inhibiting P2RX1 and rescuing mitochondrial dysfunction and oxidative stress in fibroblasts

city: shanghai

first: Fei

last: Liu

address: No. 1908, Gaoke West Road

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Background: Diabetic wounds are a major complication of diabetes mellitus and heal poorly due to persistent inflammation, fibroblast dysfunction, oxidative stress, mitochondrial injury, and impaired angiogenesis. Scutellarein (SCU) is a natural flavonoid with demonstrated anti-inflammatory, antioxidant, and fibroblast-relevant bioactivities, but its effects on diabetic wound repair and the underlying molecular mechanisms remain poorly defined. Methods: A streptozotocin-induced diabetic mouse cutaneous wound model was used to evaluate the effects of topical SCU treatment on wound closure, epithelial repair, and collagen deposition. In vitro, an H₂O₂-induced oxidative injury model in fibroblasts was employed to assess SCU-mediated protection on migration, viability, redox balance, and mitochondrial structure and function. Transcriptomics (RNA-seq) was performed to identify SCU-responsive molecular pathways, and SCU-P2RX1 molecular docking combined with ATP rescue experiments was used to interrogate a P2RX1–calcium axis. Results: SCU accelerated diabetic wound closure and improved epithelial gap, collagen deposition, fibroblast-like cell proliferation, and angiogenesis in vivo. In vitro, SCU promoted fibroblast migration, suppressed H₂O₂-induced cell death, reduced intracellular ROS, restored mitochondrial morphology and membrane potential, and preserved ATP production. RNA-seq revealed that SCU downregulated P2rx1 and enriched calcium-transport, mitochondrial, and wound-healing pathways. Molecular docking predicted SCU binding to P2RX1 with a docking score of ΔG = −9.2 kcal/mol, and ATP addition reversed the SCU-mediated suppression of calcium overload, mitochondrial depolarization, and inflammatory gene expression.

overall_design: RNA-seq profiling of L929 fibroblasts treated with H2O2 or H2O2 plus scutellarein (SCU), with three biological replicates per condition.

first: Huang

last: Yizhuo

first: Shan

last: Shengzhou

last: Mengling

first: Yang

last: Jun

first: Liu

last: Fei


title: CD40 agonism in renal cell carcinoma enhances immune checkpoint activity through myeloid cells

city: NEW HAVEN

first: Dijana

last: Djureinovic

state: CT

address: 333 Cedar street

institute: Yale University

summary: Immune checkpoint blockade (ICB) has improved survival for patients with metastatic renal cell carcinoma (RCC) but there remains a need to overcome resistance mechanisms. CD40 agonists increase anti-tumoral immunity, but limited data are available on their activity in RCC. We evaluated CD40 agonism in combination with ICB in preclinical RCC models. Adding CD40 agonism to anti-CTLA-4, but not anti-PD1, improved survival in Renca-bearing mice. CD40 agonism and anti-CTLA-4 upregulated CCL2, increased intra-tumoral macrophages and type 1 conventional dendritic cells (cDC1), whereas polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) decreased compared to control. Neutralizing CCL2 with CD40 agonism and CTLA-4 blockade partially abrogated the anti-tumoral effect and led to less increase of cDC1 and less decrease of PMN-MDSCs populations. Our studies suggest that CCL2 at least partially mediates the anti-tumoral effects of CD40 agonism, and more importantly, that the addition of CD40 agonism to ICB, particularly anti-CTLA-4, might be beneficial in RCC.

overall_design: Renca cells were implanted subcutaneously in Balb/c mice. After tumor formation, mice were treated for two cycles with PBS, αPD-1+αCTLA-4, α-PD-1+ αCD40, αCD40+αCTLA-4  and αPD-1+ αCD40+αCTLA-4 (n=3 mice/group), and 24 hours after the second treatment, tumors were collected and processed for sc-RNA-seq on Illumina  NovaSeq 6000.


title: Single-cell mapping portrays the distinct expression features between chronic phase and B-lymphoblastic crisis samples from patients with CML

city: Dalian

first: Xuehong

last: Zhang

state: Liaoning

address: No. 9 West Section Lvshun South Road, Dalian 116044, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Background: Chronic myeloid leukemia (CML) is a biphasic clonal hematopoietic stem cell disorder driven by the Philadelphia chromosome (Ph)-encoded BCR::ABL1 oncogene. The blast phase (BP) in CML progressed from indolent chronic phase (CP), usually has a dismal outcome. Single-cell RNA sequencing (scRNA-seq) have identified the pretreatment features linked to therapy resistance and disease progression. However, data on CML in B-cell lymphoblastic crisis (BLBC) remain limited. Methods: We performed the scRNA-seq on bone marrow cells derived from paired CML-CP and CML-BLBC samples to evaluate their underlying cellular heterogeneity. and. Additionally, we also unveil the distinct gene expression signatures of BLBC samples by comparing with CP samples and de novo Ph-positive (Ph+) B-cell acute lymphoblastic leukemia (B-ALL) samples. Results: By constructing a single-cell atlas, we delineated that the hematopoietic lineage of different patients skewed towards to erythroid or myeloid progenitors at their CP diagnosis respectively, which was consistent with the enrichment of gene sets related to canonical erythroid regulator GATA1 and myeloid regulator EVI1. Patient-specific B-cell progenitor types including PreB, ProB, and ImmatureB cells further illustrated the clear inter-tumor heterogeneity within CML-BLBC samples. Comparative analysis revealed that CP cells presented strong proliferation and oxidative phosphorylation characteristics, and BLBC cell populations had a series of unique expression features encompassing elevated stemness and relative quiescence, enhanced inflammatory (interferon gamma [IFN-γ], IFN-α, IL12, and IL6) and apoptotic signaling pathways, as well as ed previously unreported augmentation in ERBB2 and epithelial to mesenchymal transition (EMT) pathways. In single-cell data of CML-BLBC, we also confirmed a remarkably increased expression of DNTT which has been shown to predict BLBC transformation at diagnosis. Importantly, CD24 displayed a striking upregulation in CML-BLBC samples when compared with both the CML-CP and Ph+ B-ALL samples, suggesting the potential as a target in the future therapy of patients with CML-BLBC. Conclusion: In summary, our study presents a single-cell atlas which portrays the cellular heterogeneity and distinct cell state of CML-CP and CML-BLBC samples, as well as abnormal high expression of CD24 in patients with CML-BLBC. These findings may imply unique functional behaviors and therapeutic vulnerabilities of CML-BLBC, and thereby facilitating the development of detection methods, further enabling the identification of high-risk CP patients at diagnosis, and preventing the progression to BP through further early intervention.

overall_design: We profiled CP-BLBC pairs of samples from patients with CML using sc-RNA-Seq technology.

first: Shuheng

last: Yan


title: Transcriptomic analysis of U-373MG exposed to synthetic ShK-like peptide from the Jellyfish

city: Incheon

first: Jeong-In

last: Park

address: 119, Academy-ro

country: South Korea

institute: Incheon National University

summary: Jellyfish-derived ShK-like peptides are potent blockers of the voltage-gated potassium channel Kv1.3, which plays key roles in immune cell activation and glioblastoma cell physiology. In this study, we investigated the transcriptomic responses of U-373MG human glioblastoma cells exposed to two synthetic ShK-like peptides, NnK-1 (derived from Nemopilema nomurai) and CBRV1-10493 (derived from Carybdea brevipedalia), at 200 nM for 48 h (n = 3 per group). Since neither peptide affected cell viability at this concentration, 200 nM was selected as the treatment dose. Gene expression profiling was performed using QuantSeq 3' mRNA-Seq on an Illumina NextSeq 550 platform. Differentially expressed genes (DEGs) were identified using EdgeR with TMM+CPM normalization (fold change ≥ 1.5, p-value < 0.05). Exposure to NnK-1 resulted in 149 DEGs, with GO and IPA analyses indicating significant alterations in cell signaling and immune-related functions, including predicted inhibition of neuroinflammatory and immune response pathways associated with neurodegenerative diseases. Exposure to CBRV1-10493 identified 107 DEGs, with GO analysis revealing categories related to neurotransmission. These findings provide insights into the neuro-modulatory and immunological mechanisms of jellyfish ShK-like peptides in glioblastoma cells, and suggest their potential as candidates for therapeutic research in neurodegenerative and immune diseases.

overall_design: U-373MG human glioblastoma cells were exposed to two synthetic ShK-like peptides derived from jellyfish, NnK-1 and CBRV1-10493, at 200 nM for 48 h (three biological replicates per treatment). A shared set of three untreated control replicates was used for both comparisons. Total RNA was extracted using TRIzol reagent and purified with Rneasy Mini Kit (RIN ≥ 9 for all samples). Gene expression profiling was performed using Quantseq 3’ mRNA-Seq (Lexogen). Libraries were sequenced on an Illumina NextSeq 550 platform (single-end, 75 bp). Reads were aligned to the human genome using Bowtie2, and differentially expressed genes (DEGs) were identified using EdgeR with TMM + CPM normalization.

first: Seungshic

last: Yum

first: Youn-Jung

last: Kim


title: Identification of genes to predict optimal T cell receptor function in single cells

city: Houston

first: Cliona

last: Rooney

state: TX

address: 1102 Bates Ave

institute: Baylor College of Medicine

summary: Antigen-specific T cells can be effective for the treatment of viral infections and malignancies; however, the in vitro expansion of tumor antigen-specific T-cells is often difficult due to the low frequency of circulating antigen-specific T-cells that are rendered anergic in the immunosuppressive tumor microenvironment.  Hence the frequency of tumor antigen-specific T-cells within an infusion product may be low. This problem has been overcome by using recombinant tumor antigen-specific T cell receptors (TCRs) identified from patients. However, the identification of TCRs with optimal binding affinities among potentially thousands of TCRs has not been described. Therefore, to selectively rank TCRs, we identified a gene signature transiently expressed during viral antigen specific T cell activation that we associate with the mechanism of control governing an optimal T cell response. Using this gene signature and a scoring metric against a reference dataset we could predict the specificity of low frequency TCRs and their functional avidity with greater accuracy than predictions made using the canonical marker IFN-γ. We conclude that single cell RNA sequencing ofthe use of single gene expression following single cell RNA sequencing vastly underestimates TCR repertoire specificity and suggest using a multidimensional approach. Using our method, it is possible to rank single cells against any reference and gene set chosen to define optimal response.

overall_design: We report analysis on the actvation of T cells that have been stimulated with viral antigens. Experiment #1: Single cell mRNA were extracted from healthy donor samples from one multivirus specific (MVST) T cell line with specificity towards the CMV, EBV, BKV and Adv antigens.Three samples were sequenced in total. One control, a CMV stimulated sample and an EBV stmulated sample. Samples were stimulated with viral pepmix and sequenced 3 hours after stimulation. Experiment #2: Single cell mRNA were extracted from healthy donor samples from one multivirus specific (MVST) T cell line with specificity towards the CMV, EBV, BKV and Adv antigens.Three samples were sequenced in total. One control co-culture with monocytes, a CMV stimulated sample and an EBV stmulated sample. Samples were stimulated with viral pepmix presented by monocytes and sequenced 6 hours after stimulation. Experiment #3: Single cell mRNA were extracted from healthy donor samples from one Epstein Barr virus specific T cell line. Four samples were sequenced in total. Whole PBMC manufactured EBVSTs 3 hours after stimulation with EBV pepmix and LMP2 peptides TYG and PYL, EBVSTs mnaufactured from CD45RA-depleated PBMCs stimulated with EBV pepmix and LMP2 paptides TYG and PYL. EBVSTs manufactured from whole PBMCs tetramer sorted with a PYL and TYG specifc tetramer 3 hours after stimulation with EBV pepmix and the peptides TYL and PYG. EBVSTs manufactured from CD45RA depleted PBMCs 3 hours after stimulation with EBV pepmix and LMP2 specific peptides TYG and PYL.

first: Mae

last: Woods

first: Sandhya

last: Sharma

first: Paul

last: Shafer

first: Rafael

last: Fracasso

first: Noah

last: Crooks

first: Valentina

last: Hoyos

first: Malcolm

last: Brenner


title: A Universal 6iL/E4 Culture System for Deriving and Maintaining Embryonic Stem Cells Across Mammalian Species [EM-seq]

city: Ann Arbor

first: Duo

last: Wang

state: MI

address: 2800 Plymouth Road

department: Center for Advanced Models Translational Sciences and Therapeutics

institute: University of Michigan

type: Methylation profiling by high throughput sequencing

summary: The derivation of authentic embryonic stem cells (ESCs) across mammalian species remains a major challenge. Here, we report the development of a defined, serum-free culture system, termed 6iL/E4, that enables the derivation and long-term self-renewal of ESCs across diverse mammalian species. To further characterize the state of 6iL-hiPSCs, we performed whole-genome bisulfite sequencing (WGBS) to compare 6iL-hiPSCs with hESCs cultured under mTeSR1 and t2iL/Go conditions. Library PCR amplification was performed for five cycles using NEBNext Multiplex Oligos for Enzymatic Methyl-seq. Equimolar amounts of each library were then pooled and quantified by qPCR before paired-end 150-bp sequencing on a 10B 300-cycle shared flow cell using the NovaSeq X Plus platform at the Advanced Genomics Core.

overall_design: Integration-free human induced pluripotent stem cells (hiPSCs) were generated from cord blood cells by plasmid-based reprogramming with SOX2, KLF4, OCT4, L-MYC, and LIN28A. After electroporation, the cells were plated on feeder layers and switched to 6iL/E4 medium on day 3. To further characterize their cellular state, WGBS was performed on long-term passaged 6iL-hiPSCs and compared with two reference cell types:WIBR3 hESCs carrying a doxycycline-inducible KLF2/NANOG cassette, in which DOX-induced resetting was maintained in t2iL/Go; and WT hiPSCs cultured in mTeSR1 on Matrigel.

first: Jie

last: Xu

first: Y Eugene

last: Chen

first: Qilong

last: Ying


title: Sustained Yap/Taz activation promotes aberrant alveolar epithelial cell differentiation and drives persistent fibrotic remodeling

city: Nashville

first: Jason

last: Gokey

state: TN

department: Medicine - Allergy, Pulmonary and Critical Care

institute: Vanderbilt University Medical Center

summary: YAP/TAZ signaling is required for initiation of lung alveolar repair, yet previous studies in idiopathic pulmonary fibrosis (IPF) predicted increased YAP/TAZ signaling in alveolar epithelial cells (AECs). We investigated whether persistent YAP/TAZ AEC signaling contributes to failed epithelial repair and persistent fibrotic remodeling. In IPF lungs, we identified increased YAP+/TAZ+ AECs and increased transcriptional target expression. Pharmacological YAP/TAZ activation in human AEC organoids and in murine AT2 cell organoids generated with genetic Yap/Taz activation (YTactive) (via deletion of Hippo-kinases Stk3/4), resulted in phenotype shifts into aberrant transitional and airway-like states. Bleomycin injury of YTactive mice resulted in persistent fibrotic remodeling at 28- and 56-days post-bleomycin injury. Gene promoter activity associated with transitional cell markers (Krt19, Hopx, and Runx2) was increased in YTactive AT2 cells. Immunofluorescent staining showed a loss of AT2 associated Cebpa and increased Krt19 in YTactive lineage traced AT2 cells 28 days post-injury. Inhibition of Yap/Taz using Verteporfin resulted in improved lung repair in YTactive mouse lungs, including restored Cebpa and decreased Krt19+ transitional cells. These findings demonstrate sustained Yap/Taz activation drives abnormal alveolar repair and persistent fibrotic remodeling. Blocking aberrant persistent Yap/Taz activity promotes adaptive repair and has potential as a therapeutic strategy for pulmonary fibrosis.

overall_design: Cultured CD326+ epithelial cells from wild-type and Yap/Taz active (driven by Stk3/4 deletion in Sftpc+ AT2 cells) with Tomato lineage trace. After Passage 1, cells were flow sorted for Tomato+ to isalate only lineage traced cells. Cells were then cultured an additional 10 days in SFFFM media then either continued in SFFFM or switched to alveolar differentiation media (ADM) for 7 days. Cells were then bulk RNA sequenced.

first: Isabella

middle: P

last: Gaona

first: A

middle: S

last: McCall

first: Natalie

middle: M

last: Geis

first: Arlo

middle: C

last: Colvard

first: Gianluca

last: DiGiovanni

first: Taylor

last: Sherrill

first: Ujjal

last: Singha

first: David

last: Nichols

first: Ana

last: Serezani

first: Holly

last: David

first: Jean-Philippe

last: Cartailler

first: Shristi

last: Shrestha

first: Sergey

last: Gutor

first: Timothy

last: Blackwell

first: Jonathan

last: Kropski


title: Sustained Yap/Taz activation promotes aberrant alveolar epithelial cell differentiation and drives persistent fibrotic remodeling [Multi-omics]


title: Broad therapeutic benefit of myosin inhibition in hypertrophic cardiomyopathy [RNASeq_LSM]

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Myosin inhibitor mavacamten is the first targeted treatment available for hypertrophic cardiomyopathy (HCM), a disease caused by hundreds of genetic variants that affect mainly sarcomeric myosin and its negative regulator cardiac myosin-binding protein C (cMyBP-C, encoded by MYBPC3). Here, we have examined whether the reported limited efficacy of mavacamten in a fraction of HCM patients can result from dissimilar HCM pathomechanisms triggered by different genetic variants, a scenario particularly relevant for MYBPC3-associated HCM. To this aim, we have generated knock-in mice including missense pathogenic variant cMyBP-C p.R502W, which, different from patients who carry truncations in the protein, develop progressive pathogenic myocardial remodeling in the absence of alterations of cMyBP-C levels and localization. Mechanistically, mutation R502W reduces the binding affinity of cMyBP-C for myosin, increases Ca2+ sensitivity and promotes the ON structural state of myosin heads without inducing a shift towards more active myosin conformations as observed when cMyBP-C levels are reduced. Despite these differences, we demonstrate that mavacamten blunts myocardial remodeling both in R502W and cMyBP-C-deficient, knock-out hearts, correlating with its ability to normalize the levels of ON myosins in R502W sarcomeres. These beneficial effects are accompanied by improved tolerance to exercise in R502W animals. In human engineered heart tissues carrying R502W, we show that mavacamten opposes hypercontractility induced by the mutation. Hence, in combination our results indicate that myosin inhibition is effective to treat HCM caused by both truncating and missense variants in MYBPC3 regardless of the primary pathomechanisms they elicit.

overall_design: Bulk RNA-seq profiling was conducted in WT and R502W cMyBP-C mouse models at 3 and 18 weeks of age to evaluate gene expression changes associated with genotype and age

first: Laura

last: Sen Martín

first: Lucía

last: Sánchez García

first: Jon

last: Sicilia

first: Fàtima

last: Sánchez Cabo


title: Broad therapeutic benefit of myosin inhibition in hypertrophic cardiomyopathy [RNASeq_MAVA]

overall_design: Bulk RNA-seq profiling was conducted in WT and R502W cMyBP-C mouse models. The study included three groups: WT control (n=5), R502W control (n=4), and R502W treated with mavacamten (2.5 mg/kg/day) administered in drinking water for 21 weeks (n=4). Mice were 24 weeks old at the time of sequencing. Gene expression profiles were compared across genotype and treatment conditions.


title: Anti-PD-1 Treatment in an HFD/CCl4-Accelerated MASH-Fibrosis Mouse Model

city: Hirataka

first: Takashi

last: Yamaguchi

state: Osaka

address: Shinmachi 2-3-1

department: Gastroenterology and Hepatology

country: Japan

institute: Kansai Medical University

summary: Immune checkpoint inhibitors (ICIs) show variable efficacy in hepatocellular carcinoma (HCC) depending on etiology. In metabolic dysfunction-associated steatohepatitis (MASH), PD-1+ CD8+ T cells may paradoxically drive liver injury. We investigated whether PD-1 blockade exacerbates liver fibrosis in a non-neoplastic MASH environment. Male C57BL/6J mice were fed a high-fat diet (HFD) for 18 weeks, with weekly carbon tetrachloride (CCl4) during the final 12 weeks. Mice received anti-PD-1 antibody or isotype control every 3 days during the HFD/CCl4 phase. Liver injury, immune cell accumulation, and fibrosis were evaluated via biochemistry, histology, flow cytometry, and transcriptomic analysis. The HFD/CCl4 model exhibited significant hepatic accumulation of PD-1+ CD8+ T cells. PD-1 blockade increased AST/ALT and LDH levels, alongside heightened necroinflammation. Transcriptomic analysis showed upregulation of exhaustion-associated and cytotoxicity-related genes. Histologically, anti-PD-1 treatment was associated with periportal accumulation of F4/80+ macrophages and increased collagen deposition. Notably, we observed close spatial proximity between F4/80+ macrophages and α-smooth muscle actin+ myofibroblasts, suggesting a pro-fibrotic immune-stromal axis. PD-1 inhibition aggravates liver injury and accelerates fibrosis in this MASH model. These findings suggest that PD-1 blockade may provoke unintended pathological consequences in the context of chronic metabolic liver injury.

overall_design: Mice fed a high-fat diet (HFD) and treated with CCl₄ were administered anti-PD-1 antibody (n = 3) or a isotype control (n = 3) every three days during the 12-week HFD/CCl4 treatment period. To compare the anti-PD-1 antibody group with the control group, gene expression analysis was performed using whole-liver bulk RNA-seq.

first: Panuwat

last: Promsorn

first: Eriko

last: Yamamoto

first: Syunsuke

last: Shiba

first: Katsunori

last: Yoshida

first: Noriyo

last: Yamashiki

first: Koichi

last: Tsuneyama

first: Shinji

last: Shimoda

first: Makoto

last: Naganuma


title: A Universal 6iL/E4 Culture System for Deriving and Maintaining Embryonic Stem Cells Across Mammalian Species

first: Duo

last: Wang

summary: The derivation of authentic embryonic stem cells (ESCs) across mammalian species remains a major challenge. Here, we report the development of a defined, serum-free culture system, termed 6iL/E4, that enables the derivation and long-term self-renewal of ESCs across diverse mammalian species. To further characterize the cellular states, we performed single-cell RNA sequencing (scRNA-seq) on 6iL-hiPSCs and 6iL-mESCs. Library preparation was carried out using the Single Cell 3′ RNA Prep T2 kit (Illumina). For indexing, the Mix 7 index set was used for 6iL-hiPSC samples and the Mix 8 index set for 6iL-mESC samples. Sequencing was performed on a NovaSeq X Plus platform using paired-end 150 bp reads (2 × 150 bp), generating approximately 200 million reads per sample (100 million reads per direction).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Integration-free human induced pluripotent stem cells (hiPSCs) were generated by plasmid-based reprogramming of cord blood cells using SOX2, KLF4, OCT4, L-MYC, and LIN28A. Following electroporation, the cells were plated onto feeder layers and switched to 6iL/E4 medium on day 3. To further characterize the cellular states, single-cell RNA sequencing (scRNA-seq) was performed on 6iL-hiPSCs after long-term passaging. In addition, mESCs maintained under 6iL conditions for extended passages were also subjected to single-cell RNA sequencing.

first: Jie

last: Xu

first: Qilong

last: Ying

first: Hao

last: Ming

first: Brian

last: Bennett

first: Guang

last: Hu


title: Transcriptomic evidence that lignolytic fungi deconstruct fungal necromass and plant litter via similar pathways

city: Saint Paul

first: Jonathan

last: Schilling

state: Minnesota

address: 1445 Gortner Avenue

department: Plant and Microbial Biology

institute: University of Minnesota

summary: Fungal necromass in soil is one of the major carbon stocks. A wide range of fungi are associated with necromass decomposition in soil, however, wood rot fungi have not be tested to determine how they might be utilizing carbon and nitrogen embedded in the fungal necromass. Given their saprotrophic capabilities of brown and white rot fungi, we characterized genes and pathways that might be involved in the decomposition of melanized and non-melanized necromass from Hyaloscypha bicolor.

sample_organism:
Trametes versicolor
Gloeophyllum trabeum

overall_design: We grew Gloeophyllum trabeum and Trametes versicolor in liquid cultures with glucose, low melanin, and high melanin fungal necromass and determined their gene expression patterns on each carbon source.

first: Irshad Ul

last: Haq

first: Peter

last: Kennedy


title: Rapamycin Fly Cell Atlas Reveals Sex-Specific Pro-longevity Impacts at cellular resolution

first: Hongjie

last: Li

address: One Baylor Plaza

department: Huffington Center on Aging

summary: Aging is the dominant risk factor for chronic disease, yet the cell-type–resolved consequences of pro-longevity interventions remain insufficiently defined. Rapamycin, a pharmacological inhibitor of mechanistic target of rapamycin (mTOR) signaling, robustly extends lifespan across taxa and is now being evaluated in human clinical studies. However, how its benefits and liabilities are distributed across distinct cell types in a whole organism is still unclear. Here, we introduce the Rapamycin pro-longevity Fly Cell Atlas (Rapa-FCA), generated using whole-organism single-nucleus transcriptomic profiling in Drosophila melanogaster. Rapamycin elicits the most pronounced transcriptional remodeling in the reproductive system, adipose- and hepatocyte-like metabolic cells, and muscle, whereas neuronal populations show comparatively modest responses. Notably, rapamycin modulates male and female cell types and associated functions in a sex-dependent manner, including effects on reproductive tissues and the neuromuscular junction. We further identify a convergent aging trajectory (CAT) shared across multiple cell types, characterized by elevated mTOR activity, and show that rapamycin suppresses CAT-associated cell states more strongly in females than in males. Finally, we develop cell type–specific aging clock models that uncover divergent geroprotective outcomes between sexes. Collectively, Rapa-FCA provides an organism-wide, sex-resolved cellular map of rapamycin action, delineating tissue-specific benefits and vulnerabilities and informing opportunities for precision longevity interventions.

overall_design: F1 progeny generated from two wild-type Drosophila strains (virgin w^1118 females crossed to Oregon R males) were collected 3 days after eclosion and maintained on standard cornmeal–molasses medium at 25 °C under a 12 h light/12 h dark photoperiod for an additional 3 days to allow mating. Flies were then sex-separated and transferred to aging cages (110 individuals per cage). For lifespan assays, food was replaced and mortality was recorded every 2–3 days. Beginning on day 7, cohorts were maintained on either control food containing 0.1% DMSO (dimethyl sulfoxide) or rapamycin-supplemented food. Rapamycin (LC Laboratories) was prepared as a 20 mM stock solution in DMSO and incorporated into the diet to a final concentration of 20 μM. At designated ages, fly heads and bodies were collected into 1.5 mL RNase-free tubes, snap-frozen in liquid nitrogen, and stored at −80 °C until further processing.

first: Tzu-Chiao

last: Lu

first: Chung-Yi

last: Liang


title: Nuclear class 3 PI3K co-activates fasting-specific chromatin remodeling

city: Paris

first: Ganna

last: Panasyuk

address: 156-160 Rue Vaugirard, Faculté de Médecine Paris Descartes,, 4th Floor - Lab-408/Office-404,, 4th Floor - Lab-408/Office-404,

country: France

institute: Inserm U1151/CNRS UMR 8253, Necker Enfants Malades Institute (INEM)

summary: Transcriptional remodeling in fasting assures metabolic adaptation that provides health benefits across species1-5. While the regulators of transcription and chromatin organization in fasting are known6-10, how lack of nutrients impacts RNA Pol II (RNAPII) and epigenetic writers remains unclear. Surprisingly, we find that class 3 Phosphatidyl inositol-3 kinase (PI3K-3) lipid kinase, a master regulator of autophagy11, is present at chromatin where it co-activates epigenetic writers for transcriptional activation. To this end, the chromatin distribution of PI3K-3 largely overlapped with transcriptionally engaged RNAPII phosphorylated on Ser5 (RNAPII-S5p) and Setd1a/COMPASS, the transcription activating H3K4me3 methyltransferase complex12. Mechanistically, nuclear PI3K-3 interacted with RNAPII and the Set1a/COMPASS transcriptional complexes and facilitated their binding. Accordingly, PI3K-3 deletion resulted in lower H3K4me3 and RNAPII-S5p enrichment at selective loci. Conversely, PI3K-3 overexpression co-activated acetyltransferase p300/CBP while chromatin targeting of PI3K-3 promoted H3K4me3 deposition. In starved cells, PI3K-3 was needed for the transcriptional induction of autophagy-related genes, and in fasted liver, it was critical for metabolic shift, such as ketogenesis and lipid degradation. Thus, PI3K-3 couples nutrient availability to chromatin remodeling enabling adaptive transcriptional activation during nutrient stress.

overall_design: Poly-A enriched paired-end RNA sequencing HEK293T cells transfected with NLS-Methionase construct for indicated times, and treated with either DMSO or Vps34-IN1 (Vps34 lipid kinase inhibitor, 5uM, 12h)

first: Nathaniel

middle: F

last: Henneman

first: Genki

last: Kawamura

first: Ying

last: Luo

first: Catia

last: Dias

first: Jiaqi

last: Su

first: Arianna

last: Segaloni

first: Ivan

last: Nemazanyy

first: Samuel le

last: Cam

first: Calvin Steve

last: Rodrigues

first: Nicolas

last: Kuperwasser

last: Cagnard

first: Karim

last: Hnia

first: Raphaël

last: Margueron

first: Dominik

last: Lutter

first: Takeaki

last: Ozawa


title: Endoplasmic Reticulum Associated Lipolysis Regulates Hepatic Fat Synthesis and Turnover [Microarray]

city: Edmonton

first: Richard

last: Lehner

state: Alberta

address: 315 Heritage Medical Research Centre, 11207 - 87 Ave

department: Pediatrics

country: Canada

institute: University of Alberta

summary: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is characterized and initiated by the excessive accumulation of triacylglycerols (TG) and cholesteryl esters (CE) in the liver. Hepatic TG and CE synthesis, lipolysis and transport are tightly regulated by nutritional status, and disruption of this homeostasis contributes to MASLD pathogenesis. We have found that an endoplasmic reticulum-localized arylacetamide deacetylase (AADAC) catalyzes hepatic TG/CE turnover, and suppresses SREBP- and LXR-regulated lipogenesis and fatty acid esterification. Consequently, AADAC deficiency in mice leads to increased hepatic lipid synthesis, exacerbated steatosis, and impaired whole-body metabolism during Western-type diet feeding. These findings implicate AADAC as an important regulator of hepatic neutral lipid metabolism, linking endoplasmic reticulum cholesteryl ester hydrolysis as a modulator of lipid synthesis, and suggest its potential role in limiting MASLD pathogenesis under conditions of chronic overnutrition.

overall_design: Intestinal mucosa was collected from male WT and AADAC KO mice in the 12-hour fasted or 2-hour refed states after one week of western-type diet feeding.

first: Jihong

last: Lian

first: Russell

last: Watts

first: Randal

last: Nelson

first: John

last: Kennelly

first: Aducio

last: Thiesen

first: Ariel

middle: D

last: Quiroga

first: Donna

last: Vine

first: Robin

last: Clugston

first: René

middle: L

last: Jacobs


first: Ganna

last: Panasyuk

overall_design: Poly-A enriched paired-end RNA sequencing Vps15f/f MEFs transduced with either adeno-GFP (WT) or adeno-CRE (Vps15KO) vectors. Cells treated with either basal growth media (Control) or with EBSS amino-acid free medium for 2h.

first: Nathaniel

last: Henneman

first: Genki

last: Kawamura

first: Ying

last: Luo

first: Catia

last: Dias

first: Jiaqi

last: Su

first: Arianna

last: Segaloni

first: Ivan

last: Nemazanyy

first: Samuel le

last: Cam

last: Rodrigues


title: Molecular therapeutic insights of lidocaine in human oral cells

city: Taipei

first: Zih-Syuan

last: Wu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114201, Taiwan

country: Taiwan

institute: National defense medical center

summary: Local anesthesia is commonly used in various dental treatments, including extractions, implants, gum grafts, and jaw surgery. Recently, there has been growing interest in studying the potential impact of anesthetics such as lidocaine on postoperative outcomes in cancer patients. In the present study, to further understand the potential mechanisms of lidocaine, we conducted experiments using oral epidermoid carcinoma OECM-1 cells and gingival epithelial SG cells. Our results revealed contrasting working mechanisms of lidocaine in these two types of oral cells. In OECM-1 cells, we observed that lidocaine had various effects, including suppression of metabolic activity (above 4 mM), cellular proliferation, S phase population, and late apoptosis (below 4 mM). We also observed that lidocaine induced changes in mitochondrial membrane potential, endoplasmic reticulum stress, hypoxia, and autophagy, as well as alterations in the expression of specific proteins and mRNAs. Conversely, in SG cells, lidocaine had different effects, such as inducing changes in cell cycle profiles, apoptotic cells, cytosolic reactive oxygen species (ROS), JC-1 aggregates, and the expression of certain proteins and mRNAs. In addition, our combination index analysis demonstrated that lidocaine acted synergistically with cisplatin and 5-fluorouracil in both OECM-1 and SG cells. Moreover, in both cell types, impedance patterns indicated similarities between the effects of lidocaine and the effects of a combination of lidocaine and cisplatin. In summary, our findings highlighted three major differences between OECM-1 and SG cells in terms of the effects of lidocaine, specifically with respect to cell cycle profiles, cytosolic ROS, and mitochondrial membrane potential. These findings demonstrate that local anesthetics such as lidocaine may have important roles to play in potential combination therapies for oral cancers, and in the wound healing process following gum grafts, in addition to their established usage for pain management in oral surgery.

overall_design: In the present study, we investigated the effects of lidocaine on oral epidermoid carcinoma meng-1 (OECM-1) cells24 and Smulow–Glickman (SG) gingival epithelial cells25 to elucidate the molecular mechanisms of its cytotoxicity and its potential antitumor function. Furthermore, we assessed the combination index of lidocaine with cisplatin, to support its potential role in chemotherapy for oral cancer.

first: WeiZhi

last: Huang

first: GunngShinng

last: Chen

first: ShuTing

last: Liu

first: ShiaoPieng

last: Lee

first: ShihMing

first: JiaLin


title: The RNA-binding protein Imp1 promotes a Spdef transcriptional program and mucus fucosylation during necrotizing enterocolitis

city: Portland

first: Sarah

last: Andres

state: Oregon

address: 3181 S.W. Sam Jackson Park Road

department: Department of Pediatrics

institute: Oregon Health and Science University

summary: Background: In the United States over 10% of all neonates are born premature (less than 37 weeks gestational age), and many face complications, including necrotizing enterocolitis (NEC). NEC is the most deadly gastrointestinal disease in preterm neonates with up to 50% mortality. Since there is no cure for NEC, prevention is the best strategy. Enhancing our understanding of intestinal epithelial cell (IEC) responses to NEC damage will provide novel therapeutic targets to prevent NEC. Published evidence suggests that the RNA-binding protein insulin-like growth factor 2 mRNA binding protein 1 (IMP1) plays roles in intestinal development, barrier function, and intestinal repair. Notably, however, roles for IMP1 in NEC are not defined. Goblet cells produce protective mucus in the intestine, and their mature function is dependent on the transcription factor Spdef. Emerging evidence suggests that goblet cell mucus complexity impacts barrier function and inflammation susceptibility. This study aimed to define the role of IMP1 in NEC pathogenesis using neonatal human enteroids and a model of NEC-like intestinal injury in mice with IEC-specific Imp1 overexpression and loss. Hypothesis: IMP1 expression is protective in a mouse model of NEC. Methods: This study used mice with intestinal epithelial Imp1 overexpression or loss and corresponding wildtype controls. At post-natal day 3, mice of both sexes were randomly assigned to control or NEC groups. NEC was induced with the well-established experimental NEC-like intestinal injury model, including stress, formula feeding, and hypoxia. Effects were assessed using RNA sequencing, western blotting, and immunostaining. Results: Inflammatory bacteria induced IMP1 expression in neonatal human enteroids. Mice with Imp1 overexpression incur worse intestinal damage during NEC. Pathway analysis of RNA sequencing data revealed a significant enrichment of the Spdef transcriptional network in Imp1IEC-OE during NEC. This included significant upregulation of Spdef target genes such as Agr2 and Fut2. In silico analysis predicted Imp1 binding to Spdef and mucus glycosylation mediator mRNAs. Although genotype did not affect goblet cell number, Imp1IEC-OE mice with NEC exhibited significant increases (p<0.05) in Spdef protein, genes responsible for goblet cell function (Spink4, Klk1, Tspg1) and mucus glycosylation (Gcnt3, B3gnt7, Qsox1). Ultimately, Imp1 overexpression led to increased mucus fucosylation during NEC. Conclusion: Our data indicate that during NEC, upregulation of Imp1 promotes goblet cell function via Spdef, including enhanced goblet cell maturation and mucus fucosylation.

overall_design: RNA seq of terminal 0.5 cm whole thickness illium in 6 conditions. P6 mice with modified IEC-Imp1 genotypes: WT, OE, and KO. In two treatment conditions: model NEC (formula fed) or control (dam fed).

first: Kevin

last: Swift

first: Alexandria

last: Shumway

first: Molly

last: Aloia

first: Madeline

last: Hedges

first: Rachel

last: Pung

first: Moqing

first: Cariam

last: Rodriguez Santiago

first: Michael

last: Shanahan

first: Alex

last: Drake

first: Hakar

last: Melanie

first: Leigh

last: Selesner

last: Kuhn

first: Claire

last: Yung

first: Praveen

last: Sethupathy


title: AI digital pathology as a key tool providing in-depth understanding of the progression and regression of MASH and fibrosis in male mouse models

city: South San Francisco

first: ashmita

last: Saigal

state: California

address: 213 E Grand Ave, South San Francisco, CA-94080, USA

institute: Merck & Co., Inc.

summary: Bulk RNA sequencing (RNA-seq) was performed on mouse liver samples to characterize transcriptomic changes that occur over time when mice are fed the GAN (Gubra-Amylin NASH) diet. The aim was to compare molecular signatures between mice housed under standard vivarium conditions (TA) and those housed under thermoneutral (TN) conditions, and to use these data as an initial validation of our diet-induced disease model.

overall_design: Male C57BL/6J mice (7–8 weeks old) were obtained from Jackson Laboratories and maintained on a 12-hour light/dark cycle (lights on at 06:00). Animals were housed either at ambient temperature (TA; 21 ± 1°C) or at thermoneutrality (TN; 29 ± 1°C) and given ad libitum access to water and food (normal chow, NC Lab5001, or GAN diet D09100310, Research Diets) for up to 32 weeks. For bulk RNA-seq, mice were euthanized by cardiac puncture under isoflurane anesthesia after a 5-hour fast, and livers were collected at weeks 12, 16, 23, and 32. Group sizes were up to n = 8 per condition; an additional normal-chow–fed control group was included at the 23-week time point.

first: Ashmita

first: Wendy

last: Blumenschein

first: Yang

first: Saswata

last: Talukdar


title: Endoplasmic Reticulum Associated Lipolysis Regulates Hepatic Fat Synthesis and Turnover [RNA-seq]

first: Richard

last: Lehner

summary: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is characterized and initiated by the excessive accumulation of triacylglycerols (TG) and cholesteryl esters (CE) in the liver. Hepatic TG and CE synthesis, lipolysis and transport are tightly regulated by nutritional status, and disruption of this homeostasis contributes to MASLD pathogenesis. We have found that an endoplasmic reticulum-localized arylacetamide deacetylase (AADAC) catalyzes hepatic TG/CE turnover and suppresses SREBP- and LXR-regulated lipogenesis and fatty acid esterification. Consequently, AADAC deficiency in mice leads to increased hepatic lipid synthesis, exacerbated  steatosis, and impaired whole-body metabolism during Western-type diet feeding. These findings implicate AADAC as an important regulator of hepatic neutral lipid metabolism, linking endoplasmic reticulum cholesteryl ester hydrolysis as a modulator of lipid synthesis, and suggest its potential role in limiting MASLD pathogenesis under conditions of chronic overnutrition.

overall_design: RNA-seq profiling of livers harvested from male and female wildtype (WT) and global AADAC KO mice after one week of western-type diet feeding at fed state.

first: Jihong

last: Lian

first: Russell

last: Watts

first: Randal

last: Nelson

first: John

last: Kennelly

first: Aducio

last: Thiesen

first: Ariel

last: Quiroga

first: Donna

last: Vine

first: Robin

last: Clugston

first: René

last: Jacobs


title: In vitro PI3Kδ inhibition skews CD8 T cell differentiation towards progenitor exhaustion in vivo and reprograms tumor microenvironment metabolism, immune composition, and inflammation [scRNA-seq]

city: Lebanon

first: Edward

last: Usherwood

address: Rubin Building, Level 7, 710-53

institute: Geisel School of Medicine at Dartmouth College

summary: In vitro PI3Kδ inhibition using Idelalisib (CAL-101) drives CD8 T cells toward a progenitor exhausted (Tpex) phenotype while resisting terminal exhaustion in vitro. We performed single-cell RNA sequencing and spatial transcriptomics on B16-melanoma tumors and show that CAL-101-treated T cells enhance oxidative phosphorylation, proliferation, and Ifnγ responsiveness. The CAL-101 treated cells deeply infiltrate tumors and upregulate the CXCR3-CXCL10 axis, coinciding with reduced tumor-associated macrophage signatures and increased pro-inflammatory signaling in the tumor microenvironment. CAL-101 reprograms T cell fate and remodels the TME, offering insight into how to improve immunotherapeutic efficacy for solid tumors.

overall_design: Six RAG-KO mice bearing B16-F10 melanoma were given adoptively transferred Pmel Thy1.1 CD8+ T cells. Three mice each received T cells with in vitro CAL-101 treatment or control treatment. Live CD45.2+ cells were collected for sequencing.

first: Alexandrea

last: Turnquist

first: Owen

last: Wilkins


title: FGFR3-driven gene regulatory network analysis reveals a pro-tumoral role for p63 in luminal bladder tumors.

city: Gif-sur-Yvette

first: Lilia

last: Estrada Virrueta

address: 1, Avenue de la Terrasse

summary: FGFR3 (Fibroblast Growth Factor Receptor 3) is one of the most frequently altered genes in bladder cancer, primarily through activating mutations that drive oncogenesis and are enriched in luminal tumors. However, the underlying gene regulatory network (GRN) remains poorly characterized. Here, we inferred an FGFR3-mutated GRN using a bottom-up bioinformatics approach, integrating transcriptomic data from bladder cancer cell lines, FGFR3-mutated tumors, and FGFR3-perturbation experiments in human and mouse models. Using CRISPR-Cas9 screen public data, we identified transcription factors (TFs) from this GRN that regulate the viability of FGFR3-mutated cells, with a focus on p63 (TP63). We showed that FGFR3 activation upregulates p63 in patient-derived xenografts and cell lines, while single-cell RNA sequencing revealed heterogeneous p63 activation associated with basal differentiation. Functional studies, including TP63 knock-down in FGFR3-dependent in vitro and in vivo models and RNA-seq along with p63 ChIP-seq, demonstrated that p63 directly promotes cell proliferation and migration, and uncovered a positive feedback loop between FGFR3 and p63. Together, these findings identified p63 as a pro-tumorigenic regulator in FGFR3 mutated tumors despite their luminal differentiation and provide a detailed FGFR3-driven GRN, offering insights into FGFR3-induced oncogenic dependency and potential strategies to circumvent resistance to FGFR inhibitors.

overall_design: 3'RNAseq of bladder cancer cell lines MGHU3 and VMCBU1 upon TP63 knockdown or control after 48h of treatment

first: Isabelle

last: Bernard-Pierrot

first: Xiang-Yu

last: Meng

last: Estrada-Virrueta

first: Guerric

last: Gilbert

first: Helene

last: Neyret-Kahn


title: Systematic transcriptomic analysis enables targeted drug repurposing for neurotropic flavivirus infections

first: Miguel A.

last: Martín-Acebes

address: Ctra. de La Coruña, km 7, 5

institute: INIA-CSIC

summary: Emerging mosquito-borne orthoflaviviruses like WNV and USUV pose global health risks due to rapid spread, severe neurological effects, and the lack of approved antivirals. This study used transcriptomic and bioinformatic analyses to uncover host–virus interactions and key molecular pathways. Based on these findings, approved drugs with potential antiviral activity were prioritized, and two were selected for experimental validation. The results highlight how integrating transcriptomic profiling with drug repurposing can accelerate the discovery of antiviral strategies against emerging viruses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for USUV SAAR (GenBank: KU760915.1) infected and mock-infected Vero CCL-81 cells

first: Patricia

last: Mingo-Casas

first: Ana-Belén

last: Blázquez


title: Protective effects of metformin against ponatinib-induced toxicity in iPSC-derived cardiomyocytes

city: Maastricht

first: Brigitta

middle: Rita

last: Szabo

address: Minderbroedersberg 4-6

department: CARIM

country: Netherlands

institute: Maastricht University

summary: Aims: Ponatinib is currently considered the most effective treatment for patients with chronic myeloid leukemia (CML) or Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL), who develop resistance or intolerance to first- and second-line therapy, particularly those with T315I "gatekeeper" mutation in BCR-ABL. However, ponatinib is also one of the most cardiotoxic tyrosine kinase inhibitors (TKIs), with toxicity stemming from a combination of contractile dysfunction and inflammatory effects. Our goal was to model and investigate this toxicity in human-induced pluripotent stem-cell derived cardiomyocytes (hiPSC-CMs) and to evaluate whether metformin, a clinically well-tolerated antidiabetic drug with known cardioprotective potential via AMPK pathway activation in various pathologies, can mitigate the damage.

overall_design: RNA-seq profiling of compound responses (ponatinib, metformin, combination of ponatinib and metformin treatment) in healthy control hiPSC-CMs

first: Brigitta R.

first: Leo

last: Smit

first: Georgios

last: Kosmidis

first: Paul

last: Volders

first: Elena

last: Matsa


title: Medial preoptic PNOC neurons constrain brown adipose tissue thermogenesis and energy expenditure

city: Leipzig

first: Alexander

last: Jais

address: Philipp-Rosenthal-Straße 27

country: Germany

institute: Helmholtz Institute for Metabolic, Obesity, and Vascular Research (HI-MAG)

summary: The preoptic area (POA) of the hypothalamus is a key neural hub for thermoregulation, yet its role in modulating energy expenditure during caloric excess remains poorly defined. Here, we characterize prepronociceptin (PNOC)-expressing neurons in the medial POA (PNOCmPOA) that inhibit brown adipose tissue (BAT) thermogenesis and systemic energy expenditure. Chemogenetic activation of PNOCmPOA neurons reduced BAT activity, core temperature, energy expenditure, and glucose tolerance through inhibitory projections to the dorsomedial hypothalamus (DMH). In contrast, silencing or ablation of PNOCmPOA neurons increased BAT thermogenesis. Furthermore, PNOCmPOA activation promoted non-REM sleep, coupling thermoregulatory and arousal states. These findings define a hypothalamic circuit that limits postprandial arousal, thermogenesis, and energy dissipation, contributing to the pathophysiology of obesity. Targeting the PNOCmPOA→DMH pathway may provide a new therapeutic strategy to enhance BAT function in metabolic disease.

overall_design: Translating ribosome affinity purification (BacTRAP) was performed on preoptic area (POA) tissue from 17-18-week-old female NuTRAP::Pnoc-Cre mice to isolate ribosome-bound mRNAs from PNOC-expressing neurons. POA punches were pooled (three animals per replicate, three replicates total), and immunoprecipitation was carried out using anti-GFP antibodies and magnetic beads. RNA was extracted, quality-controlled, and used for Illumina library preparation. Sequencing was performed on the NovaSeq X Plus platform (paired-end 2 × 75 bp). Raw reads were filtered, aligned to the mm39 mouse genome, and gene expression was quantified. Differential gene expression was assessed using DESeq2. Input (total) RNA from each sample was processed in parallel as control.

first: Dropmann

last: Lea


title: Antagonistic histone H2A variants and autonomous heterochromatin formation shape epigenomic patterns in Arabidopsis

city: Tokyo

first: Shoko

last: Oda

address: 7-3-1, Hongo, Bunkyo-ku

institute: The University of Tokyo

summary: Heterochromatin formation is pivotal in many eukaryotes with repetitive sequences, such as transposable elements (TEs). However, in plants, where the known de novo DNA methylation mechanism (RdDM) targets euchromatin, how heterochromatin is formed in a region-specific manner remains unclear. We previously reported an RdDM-independent de novo establishment of H3K9me and non-CpG methylation, both of which localize in heterochromatin. Here we show that the mutually exclusive histone H2A variants, H2A.W and H2A.Z, function as guides to initiate heterochromatin formation; H2A.W and H2A.Z promotes and inhibits heterochromatin establishment, respectively, especially in chromosomal arm regions with dispersed TEs. In contrast, pericentromeric TEs demonstrate autonomous heterochromatin formation, less dependently on these H2A variants. Furthermore, H2A.Z protects protein-coding genes from ectopic heterochromatin formation, possibly by preventing its spreading. We propose that the genome indexing mechanism driven by H2A variants, as well as the autonomous formation of pericentromeric heterochromatin, shapes proper epigenomic patterns in Arabidopsis.

overall_design: Examination of DNA methylation (WGBS) and histone variants (ChIP-seq) in Arabidopsis WT, several DNA methylase and histone modification mutants, and their genetic hybrids.

first: Sayaka

last: Tominaga

first: Shumpei

last: Takeuchi

first: Akihisa

last: Osakabe

first: Akira

last: Kawabe

first: Tetsuji

last: Kakutani

first: Taiko

last: To


title: Distinct interactions between pioneer factor Ascl1/E12a and nucleosomes drive cell fate transitions [ATAC-seq]

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

institute: University of Pennsylvania

summary: Understanding how pioneer transcription factors target nucleosomal DNA and initiate chromatin accessibility provides insight into the earliest events in cell fate control. We used structural, biophysical, biochemical approaches to assess how the neural pioneer factor Ascl1 heterodimerizing with E12a binds nucleosomes in vitro. The nucleosomal binding, but not free DNA binding, by Ascl1/E12 is enhanced by two types of interactions with core histones. We performed ChIP-seq and ATAC-seq to investigate how histone interaction mutants of Ascl12 (called AAA, allRs, and QA respecrively) affect its global chromatin targeting and chromatin opening.

overall_design: hBJ fibroblasts were transduced with doxycycline inducible lentiviral vectors expressing E12a with Ascl1 WT, or Ascl1 mutants, allRs, AAA and QA, at the MOI of 0.7 - 1.0. Cells with stable integration of the lentiviral vectors were selected with puromycin at final concentration of 1 μg/mL for 7 days, followed by expansion of at least 3 passages in puromycin. The puromycin resistant cells were pooled and plated at 100,000 cells per 6-well, and induced with 0.5 μg/mL dox for 0, 48, 96 and 168 hr of dox induction before being collected for ATACseq. All conditions were performed in three biological replicates.

first: Bing-Rui

last: Zhou

first: Edgar

last: Luzete-Monteiro

first: Jingchao

last: Zhang

first: Hsin-Yao

last: Tang

first: Meilin

last: Fernandez Garcia

first: Mariel

last: Coradin

first: Naomi

last: Takenaka

first: Megan

last: Frederick

first: Benjamin

last: Garcia

first: Yawen

last: Bai

first: Kenneth

last: Zaret


title: Distinct interactions between pioneer factor Ascl1/E12a and nucleosomes drive cell fate transitions

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

overall_design: Refer to individual Series


title: Distinct treatment-induced neuroendocrine prostate cancer subtypes predict prognosis

first: Pei-Ching

last: Chang

address: No. 155, Sec. 2, Linong Street, Beitou District

department: Institute of Microbiology and Immunology

institute: National Yang Ming Chiao Tung University

summary: Second-generation hormonal therapy inhibits castration-resistant prostate cancer (CRPC), but the tumor eventually recurs as neuroendocrine prostate cancer (NEPC) and turns lethal. With limited treatment options for advanced CRPC exhibiting an NEPC phenotype, we aimed to elucidate the mechanisms of adeno-to-neuroendocrine lineage transition to guide the development of effective therapeutic strategies. By integrating single-cell RNA sequencing data from fresh human CRPC cases, we identified three distinct neuroendocrine subtypes in CRPC: a REST-dependent subtype (NE I), an N-Myc-dependent subtype (NE II), and a combined N-Myc/REST subtype (NE I+II) among 5,797 neuroendocrine-like epithelial cells. These subtypes were validated through multiplex immunofluorescence staining. Single-cell trajectory analysis uncovered N-Myc and REST as key transcription factors driving these distinct neuroendocrine lineages, and multi-omics time course analysis of publicly available transcriptomic data further recapitulated the N-Myc and REST lineage progression. Notably, we observed PSMA loss in the N-Myc lineage and identified STMN1 as a biomarker for PSMA-negative NEPC. We further validated the prognostic value of STMN1 in the TCGA dataset and in 60 in-house CRPC tissues. Our analyses provide valuable insights into the adeno-to-neuroendocrine lineage transition in prostate cancer, offering a powerful tool for early detection of lethal NEPC phenotypes and guiding 177Lu-PSMA-617 therapy for advanced CRPC.

overall_design: Three metastatic castration-resistant prostate cancer (mCRPC) samples and one hormone-sensitive prostate cancer (HSPC) sample were collected at Taipei Veterans General Hospital (TVGH). The resulting cell suspensions were enriched for viable cells using Ficoll density gradient centrifugation and subsequently analyzed by single-cell RNA sequencing.

first: Tzu-Ping

last: Lin


title: Spatial gene expression and microenvironmental changes in the transition of nevus to melanoma

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

institute: Leiden University Medical Center

summary: Approximately one-third of melanomas arise from benign nevi, yet the transcriptional and microenvironmental changes accompanying this transition remain incompletely understood. To study the nevus-to-melanoma transition, we employed genome-wide spatial transcriptomics combined with imaging mass cytometry on adjacent nevus-melanoma lesions.

overall_design: Slides with both nevus and melanoma were used for 10X Visium spatial transcriptomics

first: Inger

last: Kreuger

first: Veerle

last: Merkus

first: Sanne

last: de Haan

first: Anne

last: Schrader

first: Ferenc

last: Scheeren

first: Sjoerd

last: van der Burg

first: Tim

last: van Groningen

first: Remco

last: van Doorn


title: Effect of depletion of p38α and p38β on gene expression in naïve CD8+ T cells

city: Xiamen

first: Lichen

last: Hu

state: Fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

department: School of Life Sciences

institute: Xiamen University

summary: p38 MAPK is activated during CD8+ T cell primary response. p38 activation promotes effector CD8+ T cell terminal differentiation but represses MPEC formation. p38α/β-deficient mice possess a similar number of virus-specific effector CD8+ T cells as wildtype counterparts. Meanwhile p38α/β deletion doesn’t influence the clearance of LCMV although it impairs the cytolytic activity of CD8+ T cells. Loss of p38α/β significantly enhances IL-2-producing Tcm accumulation in mouse spleen with no impact on total memory CD8+ T cell numbers yet. And in line with this, more robust proliferation of memory CD8+ T cells in the secondary response and stronger antigen-specific killing ability in rechallenged mice are resulted from p38α/β deficiency. These results establish a pivotal role for p38α/β in skewing MPEC formation toward SLEC differentiation, as well as in suppressing Tcm formation, and thus affecting the recall response. p38α was reported to be essential in CD8+ T cell maturation, and our mice were observed to be at loss of p38α/β expression in thymic T cells during development. So it's important to see the influence of p38α/β deletion on peripheral naive CD8+ T cells and its potential inborn impact on later events. This would help determining the exact role of p38 signaling in CD8+ T cell immune responses.

overall_design: To investigate the cooperative function of p38α and p38β in CD8+ T cell maturation, we purified naive CD8+ T cells from p38αfl/flp38βfl/fl and p38αfl/flp38βfl/flGzmBcre mice spleens. We then performed gene expression profiling analysis using data obtained from RNA-seq of 8 different mice. Comparative gene expression profiling analysis of RNA-seq data  for WT cells and its KO counterparts (p38α-/-p38β-/-).


title: Glycosylation Orchestrates Megakaryocytic Fate of Hematopoietic Stem Cells via Wnt-Muc13 Signaling

city: Milwaukee

first: Karin

last: Hoffmeister

state: WI

address: 8727 Watertown Plank Road

institute: Versiti Blood Research Institute


title: The role and mechanism of METTL1 in regulating the phenotype and function of renal macrophages

city: Hefei

first: Chao

last: Hou

state: Anhui province

address: 81 Meishan Road

institute: Anhui Medical University

summary: Macrophages promote the progression of acute kidney injury (AKI), but the specific factor that regulates their phenotype and function remains unknown. Preliminary experimental results indicate the following: 1) The level of METTL1 and its mediated m7G modification were significantly up-regulated in macrophages in AKI; 2) The absence of METTL1 in macrophages alleviated renal injuries in AKI mice; 3) METTL1 deficiency suppressed the proportions of pro-inflammatory macrophages in renal tissues. Based on these findings, we hypothesize that AKI increases the level of METTL1 and m7G modification in macrophages, promoting their differentiation into a pro-inflammatory phenotype and ultimately worsening kidney damage. This study aims to investigate the expression of METTL1 in macrophages in patients and mice with AKI. Myeloid METTL1 conditional knockout mice were utilized to elucidate the regulatory role of m7G modification in macrophage differentiation. Additionally, target genes with immunoregulatory functions of m7G modification in macrophages were identified through m7G sequencing and transcriptomics. This study will elucidate the novel mechanism which METTL1-mediated m7G modification regulates macrophage plasticity to promote AKI, and also lays the foundation for using METTL1 as a drug target to treat inflammatory diseases.

overall_design: RNA sequencing (RNA-seq) and subsequent analyses were performed by SeqHealth Technology Co., Ltd. In this study, six samples were sequenced and clean reads from each sample were compared to the designated reference genome. The sequenced reads were aligned with the reference genome, allowing the reconstruction of transcripts.

first: Xinru

last: Zhang

first: Tong

last: Chen


title: Spatial Multi-Omics Landscape of Colorectal Cancer Macro- and Micrometastases

city: Houston

first: Yang

last: Liu

state: TEXAS

address: 1885 EL Paseo St

institute: MD anderson cancer center

summary: Colorectal cancer (CRC) metastases often recur due to minimal residual disease (MRD) and micrometastases that persist after therapy. Here, we analyzed 341,328 spatially resolved spots from 37 tumors, including liver (CLiM) and lung (CLuM) metastases, and primary CRC from 11 patients. Phylogenetic analysis of copy number variations revealed heterogeneous tumor evolution, with early dissemination and quiescence in liver micrometastases (CLiMi). Spatial analysis identified 10 conserved and 7 distinct metaprograms, highlighting stromal interactions in CLiM and CLuM, with macrophages enriched in CLiM and lymphocytes in CLuM. Micrometastases showed strong immunosuppressive signature and increased T cell exhaustion. Notably, we identified a CLiMi-specific six-gene signature associated with MRD status, disease-free survival, and chemotherapy resistance across multiple independent cohorts. These findings elucidate the spatial evolutionary landscape of CRC metastases and provide tissue-based spatially validated biomarkers for surveillance and therapeutic targeting.

overall_design: 37 Colorectal cancer metastasis samples


title: Extracellular stiffness regulates site-specific lung development [AWO]

city: Guangzhou

first: junjie

last: lv

address: haizhu

institute: GZLAB

summary: Extracellular matrix (ECM) stiffness plays a crucial role in regulating cell fate and maturation, but its influence on lung development is limited known. Here we utilized stiffness-tunable gelatin methacryloyl (GelMA) hydrogels to investigate how ECM stiffness influences site-specific lung development in a stem cell-derived lung organoid model. We found increased stiffness promoted NKX2-1+ lung progenitor cells (LPCs) generation. In airway organoids (hAWOs), stiff hydrogels directed proximal airway differentiation enriched with goblet, ciliated, and basal cells; whereas the decreased stiffness favored emergence of secretory cells in the proximal-distal transition zone and distal airway. In alveolar organoids (hALOs), increased stiffness enhanced AT2 and AT1 cells transition. Moreover, infection assays with Omicron BA.1.1 and Delta variants recapitulated the proximal-to-distal tropism of SARS-CoV-2 in the lung. Transcriptomic sequencing revealed ECM stiffness regulates lung development via Hippo, TGF-β, HIF and Wnt pathways. These findings advance mechanism understanding of ECM stiffness on lung development and provide a novel mechanical regulation for generating site-specific lung organoids.

overall_design: AWO organoid scRNA-seq data under G30,G60 and G90 conditions


title: Extracellular stiffness regulates site-specific lung development [ALO]

overall_design: ALV organoid scRNA-seq data under G30,G60 and G90 conditions


title: Targeting astrocytic CLC2(CLCN2) restores myelin regeneration through inhibition of SPP1/CD44 signaling pathway in leukoencephalopathy

first: Lu

last: Yang

state: Guangdong

address: No.600 Tianhe Road, Tianhe District, Guangzhou, China

institute: The Third Affiliated Hospital of Sun Yat sen University

summary: Accumulating myelin damage and impaired remyelination are central pathological features of leukoencephalopathies, including Multiple Sclerosis and Alexander Disease, where astrocytes play essential roles in maintaining central nervous system homeostasis and mediating astrocyte-oligodendrocyte interactions. Chloride Ion Channel 2 (ClC-2), encoded by CLCN2, is functionally expressed in astrocytes and is likely critical to white matter integrity; however, its precise roles and interactions remain unclear. Clarifying the mechanisms by which astrocytic ClC-2 influences white matter is essential for developing treatments for CLCN2-related leukoencephalopathy (CC2L) and potentially other white matter disorders. In this study, we demonstrate that dysfunctional ClC-2 in astrocytes—derived from both mouse models and human-induced pluripotent stem cells (hiPSCs)—impairs oligodendrocyte lineage cell development in vitro and delays remyelination in vivo. Transcriptomic analyses identified SPP1 as a key inhibitory factor on remyelination, secreted from ClC-2-deficient astrocytes. This inhibition was validated through astrocyte-specific modulation of SPP1 expression, where overexpression exacerbated, and downregulation alleviated, demyelination effects. Furthermore, we discovered that SPP1 upregulation in astrocytes with abnormal ClC-2 negatively impacts remyelination by interacting with CD44 on oligodendrocyte progenitor cells. Finally, we confirmed that increased SPP1 expression and the resulting suppression of oligodendrocyte lineage cell development were also present in hiPSC-derived astrocytes harboring a CLCN2 mutation from a CC2L patient. Collectively, these findings reveal that astrocytic ClC-2 is intricately linked to white matter integrity through SPP1 regulation, positioning it as a potential therapeutic target for CC2L and other leukoencephalopathies.

overall_design: RNA-seq profiling of astrocytes derived from induced pluripotent stem cells with (shCLCN2-1, shCLCN2-2, shCLCN2-3) or without (shCtrl-1, shCtrl-2, shCtrl-3) CLCN2 knockdown

first: Yubao

last: Lu

first: Jia

first: Fan

last: Zhu

first: Ying

last: Jiang

first: Tingting

first: Xiufeng

last: Zhong

first: Wei

last: Qiu

first: Changyong

last: Tang

first: Fuhua

last: Peng


title: Genome wide DNA methylation analysis in a prospective observational study identifies several epigenetically deregulated genes during renal replacement therapy at ESRD.

city: Valencia

first: Angela

middle: L.

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

institute: University of Valencia, and INCLIVA

type: Methylation profiling by genome tiling array

summary: Renal replacement therapy (RRT) can be initiated in the end-stage renal disease (ESRD). Over four million people worldwide receive RRT. Haemodialysis (HD) is the most frequently employed treatment, followed by peritoneal dialysis (PD), while conservative treatment (CT) is selected more frequently for elderly individuals, particularly women. The molecular mechanisms of ESRD-RRT, and its possible impact on cellular processes, are not yet fully understood, although recent evidence suggests a correlation between epigenetic regulation of chromatin dynamics, mainly DNA methylation, and control of gene transcription in this pathology. This investigation represents the first prospective study of epigenomic alterations during HD, PD and CT treatments in ESRD. Advanced Infinium EPIC array technology, capable of measuring levels of DNA methylation of over 850,000 CpG sites in the genome, was used in peripheral blood mononuclear cells. The results show an inverse relationship between the methylation levels of certain CpGs of significant genes and changes in gene expression during the different ESRD treatments. Namely, the genes FBXWD7, TMEM229B and MZF1 in CT group, NELL1, CBLN1 and EEF1D in HD group and COX11, TMCO and RSPO3 in PD group. These genes are linked to inflammation, oxidative stress, immune response, mitochondrial disorders, pericardial oedema, vascular congestion or metabolic diseases. The findings suggest that these genes may contribute to the differing prognoses observed between the different treatment groups. The epigenomic alterations identified could contribute to the pathophysiology and prognosis of ESRD and may represent important therapeutic targets for the improvement of future treatment options.

overall_design: This is a prospective cohort observational pilot study. The target population comprises patients who have recently been diagnosed with ESRD. Sampling was conducted in a consecutive manner from the outpatient nephrology consultation specifically for patients with advanced CKD. Participants in the study were categorised into the following groups: The Non-Renal Group (NRG) comprised patients without CKD who were recruited from the relatives of patients with ESRD in order to control for potential environmental biases. A blood and urine test was conducted to ascertain the absence of renal failure, albuminuria/proteinuria, or urinary sediment abnormalities. The Haemodialysis Group (HDG) comprises patients diagnosed with ESRD who initiated RRT via HD. The Peritoneal Dialysis Group (PDG) comprised patients diagnosed with ESRD who initiated RRT via PD.  The Conservative Treatment Group (CTG) comprised patients diagnosed with ESRD who had elected to refrain from undergoing RRT and would continue with CT. A baseline peripheral blood sample was obtained from the patients group at the time of ESRD diagnosis, with an estimated glomerular filtration rate by CKD-EPI equation equal to or less than 15 ml/min/1.73 m², and a second sample was taken at the six-month follow-up point for CTG or at the six-month point from the commencement of treatment for those undergoing RRT for HD and PD.

first: García Testal

last: Alicia

first: Riffo-Campos

last: Ángela L.

first: Sandoval del Amor

last: Juan

first: López-Rodas

last: Gerardo


first: Alexander

last: Jais

overall_design: Gene expression profiling analysis of RNA-seq data from brown adipose tissue (BAT).  Intrascapular BAT samples were collected one hour after activating PNOCmPOA neurons


title: Nuclear class 3 PI3K co-activates fasting-specific chromatin remodeling

city: Paris

first: Ganna

last: Panasyuk

address: 156-160 Rue Vaugirard, Faculté de Médecine Paris Descartes,, 4th Floor - Lab-408/Office-404,, 4th Floor - Lab-408/Office-404,

institute: Inserm U1151/CNRS UMR 8253, Necker Enfants Malades Institute (INEM)

summary: Transcriptional remodeling is essential for stress adaptation such as in fasting. While the core transcriptional machinery and its regulators are known, how information regarding energy availability is relayed to transcriptional complexes remains unclear. Surprisingly, we find that class 3 Phosphatidyl inositol-3 kinase (PI3K-3) lipid kinase, a master regulator of cytosolic autophagy, co-activates epigenetic writers for fasting-induced transcription. To this end, chromatin distribution of PI3K-3 significantly overlapped with transcriptionally engaged RNA Pol II phosphorylated on Ser5 (RNAPII-S5p) and transcriptionally permissive H3K4me3. Mechanistically, nuclear PI3K-3 interacted with both RNAPII and the Set1a/COMPASS methyltransferase of H4K4me3. Moreover, decreased binding between RNAPII and Set1a/COMPASS was found in PI3K-3 depleted cells. Accordingly, PI3K-3 deletion led to lower H3K4me3 and RNAPII-S5p enrichment at selective loci. Conversely, PI3K-3 overexpression co-activated acetyltransferase p300/CBP in luciferase assays while its chromatin targeting promoted H3K4me3 deposition. In starved cells, PI3K-3 induced transcription of autophagy-related genes, and in fasted liver, it was critical for transcriptional remodeling of metabolism, such as activation of lipid degradation. Thus, PI3K-3 couples nutrient availability to chromatin remodeling for transcriptional activation, enabling metabolic adaptation in fasting.

overall_design:
ChIP sequencing of RNA Pol II S5P, H3K4me3, and Vps15 in fed and fasted mouse liver.
ChIP sequencing of RNA Pol II S5P fed and fasted mouse liver.

first: Nathaniel

last: Henneman

first: Genki

last: Kawamura

last: Luo

first: Arianna

last: Segaloni

first: Ivan

last: Nemazanyy

first: Samuel le

last: Cam

first: Calvin Steve

last: Rodrigues

first: Nicolas

last: Kuperwasser

last: Cagnard

first: Raphaël

last: Margueron

first: Dominik

last: Lutter

first: Takeaki

last: Ozawa

first: Catia

middle: O

last: Dias

first: Karim

last: Hnia

first: Jiaqi

last: Su


overall_design:
Cut and Run sequencing Vps15 in mouse embryonic fibroblasts in conditions of basal DMEM media, methionine starvation for 4h, and methionine stimulation of 1h.
Cut and Run sequencing of H3K4me3 in HEK293T cells overexpressing either empty vector (ev) or Flag-Vps15 constructs.

first: Ying


title: Lycopene Ameliorates Ionizing Radiation-Induced Intestinal Injury

city: beijing

first: bio

last: xin

address: Cancer Hospital, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Lycopene, a carotenoid known for its potent anti-inflammatory, antioxidant, and immune-modulating properties, is widely utilized in food, nutraceuticals, and medicine. This study aimed to explore the protective and therapeutic effects of lycopene against ionizing radiation-induced intestinal injury. Using a C57BL/6 mouse model exposed to ionizing radiation, we assessed the protective effects of lycopene by analyzing intestinal histology and serological markers. Our findings reveal that ionizing radiation induces oxidative stress, inflammation, and apoptosis in the intestinal epithelium. Lycopene administration effectively mitigated these effects by reducing oxidative stress, decreasing inflammatory responses, and inhibiting apoptosis. Mechanistically, lycopene was found to regulate key metabolic pathways, including linoleic acid and arachidonic acid metabolism, thereby exerting its anti-inflammatory and immune-modulatory effects. These results highlight lycopene's potential as a therapeutic agent for managing radiation-induced intestinal injury, offering a promising strategy for improving the clinical outcomes of patients undergoing radiotherapy.

overall_design: mice were further divided into four groups: Control, IR, Lycopene (LYC, 10 mg/kg/day), and IR + Lycopene (IR+LYC, 10 mg/kg/day). Lycopene, dissolved in corn oil, was administered via gavage to the LYC and IR+LYC groups for 10 consecutive days, while the Control and IR groups received corn oil. On the fourth day, the IR and IR+LYC groups received 12 Gy of whole-abdominal irradiation to induce intestinal injury. Lycopene treatment continued for one week post-irradiation. The mice’s survival and body weight were monitored throughout the experiment. At the end of the experiment, mice were euthanized, and we collected mouse intestinal samples and performed rna-seq analysis (control group, ir group, and ir+lyc group)

first: Xin

last: Chen

first: Rongli

last: Xu

first: Min

last: Deng


title: Mechanosensing by T cells promotes a tissue-resident memory transcriptional program

city: Montreal

first: Judith

last: Mandl

state: QC

address: 3649 Promenade Sir William Osler

institute: McGill University

summary: Cell migration and strategic positioning within tissues is critical for the rapid mobilization of a T cell response. T cells must remain motile in both lymphoid and non-lymphoid tissues, which vary widely in mechanical properties such as stiffness. Here we showed that activated T cells sensed mechanical cues  and responded with changes in cell morphology, nuclear envelope composition and initiation of DNA repair to protect their genomic material from force-mediated damage. Increased mechanical input also drove the transcriptional reprogramming of activated T cells, including changes in many of the core genes shared by tissue resident memory T (TRM) cells across diverse tissues, by modulating the expression of the TRM cell-associated transcription factors Klf2, Runx3 and Hic1. Thus, mechanosensing by activated T cells impacted T cell fate, promoting a transcriptional program associated with tissue-residency.

overall_design: CD8+ T cells were isolated from the spleen and LNs of WT male mice (n=3 per group). A fraction of the naive cells was not activated and directly lysed to extract RNA for bulk RNA sequencing (fresh). The rest was activated and expanded in vitro for 3 days before being cultured in media or in collagen gels (2 mg/mL) for an additionnal 24h (Bv: bovine collagen; RT: rat tail collagen). Finally, the cells were recovered from the gels and RNA was extracted for bulk RNA sequencing.

first: Jérémy

last: Postat


title: The ERBB4 agonist JK07 Mitigates Atrial Remodeling and Inducibility of Atrial Fibrillation in Mice and Minipigs

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Gasthuisberg

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

summary: To establish changes in cardiomyocyte transcription profiles brought about by atrial fibrillation, we collected left atrial appendage samples from minipig induced by DOCA or DOCA and JK07 and from vehicle samples. The transcriptional profile of mRNA in these  samples will be measured with high throughput technology. Changes in transcriptional profiles can be correlated with the physiologic profile of atrial fibrillation acquired at the time of harverst.

overall_design: 10 minipig samples were analysed. 5 from control, 2 from DOCA and 3 from DOCA with JK07.

first: Jens

last: van Fraeyenhove

first: Michiel

middle: R

last: Tubeeckx

first: Bo

last: Govaerts

first: Yile

last: Fu

first: Juan

last: Zhang

first: Arthur

last: Bezerra

first: Tim

last: De Coster

first: Julie

last: Cools

first: Eike

last: Wülfers

first: Siel

last: Van den Bogaert

first: Samuel

last: Murphy

first: Antoine

last: de Vries

first: Erik

last: Fransen

first: Nele

last: Vandersickel

first: Daniel

last: Pijnappels

first: Guido

middle: Y

last: De Meyer

first: Hein

last: Heidbuchel

first: H.

last: Llewelyn Roderick

first: Vincent

last: Segers

first: Gilles

middle: W

last: De Keulenaer


title: Metabolic and Innate Immune Memory Alterations in Human Monocytes on Chiang-Mai-PM2.5 Stimulation

city: Khlong Luang

first: Naunpun

last: Sangphech

state: Prathumtani

address: Moo 18, Phahon Yothin Rd., Khlong Nueng

department: Medical Technology

country: Thailand

institute: Thammasat University

summary: The rise of PM2.5 in air pollution correlates with increased disease exacerbation, especially in asthma. This study aims to examine how Chiang-Mai, Thailand PM2.5 (CM-PM2.5) affects innate immune responses in primary human monocytes. A transcriptomic profile was obtained from cells that were stimulated with low and high doses of CM-PM2.5 (5 and 20 μg/ml) for 24 hr. The data indicated that primary human monocytes respond to CM-PM2.5 in a dose-dependent manner. The pyrimidine ribonucleotide metabolism was predominant in both datasets, but the suppression of glycolytic rate was found in high doses of CM-PM2.5 stimulation. The upregulation of the key metabolic genes was unable to compensate for the suppression. Moreover, CM-PM2.5 priming induced immune tolerance during subsequent LPS stimulation in primary human monocytes from asthma.

overall_design: Primary human monocytes were stimulated with PM2.5 collected from Chiang-Mai during March 2023, for 24 h. RNA were collected, extracted using RNAeasy kit (QIAGEN, Germany), and subjected to RNAseq analysis at at the Omics Sciences & Bioinformatics Center, Chulalongkorn University, Thailand. In brief, sample quality and quantity were measured by a Bioanalyzer (Aligent2Donor20 Bioanalyzer System, Canada). The sample library was prepared using a TruSeq mRNA library kit (Illumina, USA). RNA sequencing was performed using NextSeq500 (Illumina).

first: Tanapat

last: Palaga

first: Tassanee

last: Prueksasit

first: Jomkhwan

last: Meerak


first: Ganna

last: Panasyuk

overall_design:
Poly-A enriched paired-end RNA sequencing in fed and fasted mouse liver, in either WT or Vps15iLKO mice.
Poly-A enriched paired-end RNA sequencing Vps15f/f MEFs transduced with either adeno-GFP (WT) or adeno-CRE (Vps15KO) vectors. Cells treated in basal, 4h methionine deprivation, or 4h methionine deprivation followed by 1h or 4h methionine replenishment.

first: Nathaniel

last: Henneman

first: Genki

last: Kawamura

first: Ying

last: Luo

first: Arianna

last: Segaloni

first: Ivan

last: Nemazanyy

first: Samuel le

last: Cam

first: Calvin Steve

last: Rodrigues

first: Nicolas

last: Kuperwasser

last: Cagnard

first: Raphaël

last: Margueron

first: Dominik

last: Lutter

first: Takeaki

last: Ozawa

first: Catia

last: Dias

first: Karim

last: Hnia

first: Jiaqi

last: Su


title: Ribo-seq from cells with depletion of DIS3 from human cell lines

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

institute: Institut Curie

summary: DIS3 is a 3’ to 5’ exoribonuclease responsible for degradation of multiple RNA targets. Most reports in human cells focus on its function in RNA surveillance in the nucleus. However, a small fraction of DIS3 can be also found in cytoplasm. Thus, the focus of this experiment was to identify the cytoplasmic targets of DIS3 that can be translated. Using rapid, auxin inducible, degradation of DIS3 protein and ribosome profiling, we were able to identify RNA accumulated in cytoplasm containing non-canonical Open Reading Frames . The raw data and counts for from the experiment are provided.

overall_design: The Ribo-seq was performed on technical duplicates for from a control cell line and  CRISPR clone with introduced DIS3-AID  without treatement or after 1h with auxin for inducion of DIS3 depletion

first: Dominika

last: Foretek

first: Marina

last: Pinskaya

first: Marc

last: Gabriel


title: Depletion of XRN1 from human cell lines

summary: XRN1 is a cytoplasmic 5’-3’ exoribonuclease responsible for degradation of multiple types of RNA. Data obtained on yeast model described XRN1 function in degradation of messenger (m)RNA, Rapid transfer (t)RNA Decay (RTD) of hypomodified and unstable tRNA transcripts as well as maturation of 25S ribosomal (r)RNA and small nucleolar (sno)RNAs. Our group discovered previously that deletion of XRN1 gene results in stabilization of a group of long non-coding RNAs, which are often transcribed antisense to protein-coding genes and may regulate their expression on transcriptional level. However much less is known about human (h)XRN1 function. Data available from human cell lines confirm involvement of hXRN1 in degradation of mRNA, initiator tRNA methionine and some miRNA. The high sequence similarity of XRN1 between yeast and man suggests that also its function should be well conserved for hXRN1. To determine the cytoplasmic transcripts dependent on XRN1 activity we have constructed an auxin-degron system with inducible depletion of XRN1 protein in cell line, combined with subcellular fractionation followed by high-throughput sequencing. The raw data and counts for annotated and non-annotated transcripts resulting from this experiment are provided.

overall_design: The total RNA-seq was performed on technical triplicates for cytoplasmic and chromatin fractions from a control cell line and two CRISPR clones with introduced XRN1-AID  withouth treatement or after 24h with doxycycline and auxin for inducion of XRN1 depletion