title: Whole-Transcriptome Profiling Reveals RNA Expression Dynamics and ceRNA Network Remodeling across Health, Sepsis, and Sepsis-Associated Acute Respiratory Distress Syndrome [RNA-Seq]

overall_design: 12 participants were enrolled, comprising four healthy controls (HC group), 4 patients with sepsis without ARDS (SWA group), and 4 patients with sepsis-associated ARDS (SA group). Peripheral blood samples were obtained and subjected to whole-transcriptome sequencing. Trend analysis was performed to identify transcripts exhibiting monotonic increases or decreases across the HC–SWA–SA sequence. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were subsequently performed. Target-gene prediction and expression-correlation analyses were also performed to construct a competing endogenous RNA (ceRNA) regulatory network.


title: MDM2 binds and suppresses RNA polymerase III to restrain the innate immune response to cytosolic DNA

status: Public on Aug 06 2026

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

type: Non-coding RNA profiling by high throughput sequencing

summary: The oncoprotein MDM2 is widely recognized as the principal negative regulator of p53, thereby controlling the expression of numerous RNA polymerase II (Pol II)-dependent genes involved in cell cycle arrest and apoptosis. Beyond this canonical role, MDM2 also engages in transcriptional regulation independently of p53, for instance through interactions with polycomb repressor complexes. Here, we identify RNA polymerase III (Pol III) as an additional target of MDM2 function. Using two complementary chemical tools – a small-molecule MDM2 antagonist (MI-1061) that releases p53 and augments MDM2 expression, and a PROTAC degrader (MD-224) that simultaneously activates p53 and promotes MDM2 ubiquitination and proteasomal destruction – we dissected the role of MDM2 in cells with amplified MDM2. Elevated MDM2 suppressed the transcription of Pol III-dependent genes encoding tRNA or 5S ribosomal RNA. Mechanistically, we found the aminoterminal domain of MDM2 associated with the catalytic subunit of Pol III, revealing a molecular link between MDM2 and the Pol III machinery. Because Pol III also acts as a cytosolic DNA sensor that converts DNA into double-stranded RNA to trigger RIG-I–TBK1–IRF3–dependent signaling, we asked whether MDM2 modulates this pathway. Indeed, enhanced MDM2 expression markedly attenuated the induction of innate immunity genes such as CXCL10, OAS1, and MX1 following transfection with Poly(dA:dT). Similarly, DNA damage induced by a radiomimetic agent activated Pol III–dependent innate signaling, and this was again blunted by high MDM2 levels, resulting in enhanced cell survival. Taken together, our findings establish MDM2 as a previously unrecognized suppressor of Pol III–dependent transcription in response to cytosolic DNA. This expands the repertoire of MDM2 functions beyond repression of p53 and Pol II activity, positioning MDM2 as a broad regulator of transcription and innate immunity.

overall_design: SJSA-1 cells treated for 12 h with DMSO, MI-1061 (1µM), MD-224 (1µM) and Nutlin-3a (20 µM).

first: Sabrina

last: Weber

first: Matthias

last: Dobbelstein

first: Emre Taylan

last: Duman

first: Nhu Quang

last: Vu


title: Long Reads RNAseq reveals an isoform switching pattern in healthy microglial cell lines exposed to radiotherapy.

city: Catania

first: Giuseppe

middle: Nicolò

last: Conti

state: CT

address: Via San Sofia, 97

department: Department of Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

type: Expression profiling by high throughput sequencing

summary: Background/Objectives: Radiotherapy (RT) is a fundamental treatment for brain tumors but often leads to long-term neurotoxicity, partly caused by microglial dysfunction. In this study, we used long-read RNA sequencing (LR-RNA-seq) to map the isoform-specific transcriptome of human microglial HMC3 cells after RT exposure Methods: HMC3 Microglial cell line was treated with standard radiotherapy and, after RNA extraction and library preparation, long reads RNAseq has been carried out. Further bioinformatic analyses allowed to investigate on the isoform switching pattern after radiation therapy exposure. Results: Gene-level analysis found 591 differentially expressed genes, with increased activity in PI3K/AKT signaling pathways and decreased translation-related processes. Isoform-level analysis uncovered 827 significant isoform switching events across 420 genes, often involving shifts from protein-coding transcripts to non-coding variants. Functional annotation showed that most isoform switches resulted in the loss of open reading frames and protein domains, especially in ribosomal proteins and translation machinery components

overall_design: Long Reads RNAseq profiling transcriptome of HMC-3 microglial cell line after acute exposure to canonical radiotherapy

middle: N

first: Tatiana

last: Zuppelli

first: Laura

last: Orlando

first: Enrico

last: La Spina

first: Lucia

last: Longhitano

first: Daniele

last: Tibullo

first: Giovanni

last: Li Volti


title: Sympathetic Neurons Restrain Pancreatic Cancer Lung Metastatic seeding through NPY-NPY1R Signaling [barcode]

city: STANFORD

first: Xiaochen

last: Xiong

state: CA

address: 327 Campus Drive

country: USA

institute: Stanford University

summary: The sympathetic nervous system regulates physiological homeostasis, but is increasingly recognized as a context dependent modulator of carcinogenesis. Here, we investigate the function of sympathetic innervation on pancreatic ductal adenocarcinoma (PDAC) metastasis. Although sympathetic signaling has been shown to promote primary PDAC growth, its contribution to metastatic progression remains poorly defined. Using a pool of barcoded Kras;Trp53-driven mouse PDAC cell lines that allows quantitative analysis of metastatic seeding and growth, we found that sympathetic innervation restrains metastatic seeding but promotes metastatic outgrowth. In vivo pharmacologic screening showed that inhibition of the Neuropeptide Y (NPY) receptor NPY1R phenocopied the effect of sympathetic ablation on metastatic seeding, indicating sympathetic release of NPY restrains metastatic seeding through NPY1R signaling, likely in lung stromal cells including alveolar fibroblasts. Single-cell transcriptional analyses revealed that NPY1R signaling affects alveolar fibroblasts and intermediate gCap endothelial cells, providing a mechanism for restraining vascular permeability and cancer cell seeding. Together, these findings uncover an unexpected metastasis-protective function of sympathetic innervation, distinct from its effect on metastatic growth, and identify a novel sympathetic-stromal signaling axis that regulates the vascular niche during PDAC lung metastasis.

overall_design: barcoded PDAC cell line pool was injected intravenously into syngeneic 6-OHDA and vehicle pre-treated 129/Bl6 F1 mice to establish lung metastases and analyzed 3 weeks after transplantation.


title: Sympathetic Neurons Restrain Pancreatic Cancer Lung Metastatic seeding through NPY-NPY1R Signaling [scRNA-seq]

overall_design: We performed single-cell RNA sequencing on whole-lung cell suspensions from mice treated with vehicle, 6-OHDA, or BIBO3304, both in the presence and absence of seeded PDAC cells.


city: Göttingen

state: Lower Saxony

address: Justus-von-Liebig Weg 11

department: Molecular Oncology

institute: University Medical Center

overall_design: RNA-Squencing of SJSA-1 cells treated for 72 h with DMSO or neocarcinostatin (NCS, 1 µg/mL). The last 24 h before harvesting the cells were either treated with DMSO, MI-1061 or MD-224 (1 µM)together with a refreshment of Neocarzinostatin treatment (1 µg/mL).


title: Bulk RNA Sequencing Reveals Differential Gene Expression Between Mesothelial Cells (MCs) and Cancer Associated Mesothelial Cells (CAMCs)

city: Boston

first: Maeva

middle: general

last: Chauvin

state: MA

address: 55 fruit st

institute: general hosp corp d/b/a mass general hosp

summary: This study presents a bulk RNA-sequencing analysis comparing mouse primary mesothelial cells (MCs) and cancer-associated mesothelial cells (CAMCs). MCs were treated for 72 hours with conditioned media derived from KPCA cancer cells or with vehicle control to induce CAMC-like reprogramming. RNA was extracted and subjected to bulk transcriptomic profiling to identify differentially expressed genes and associated biological pathways.

overall_design: Mouse primary mesothelial cells (MCs) were isolated and cultured in vitro. To generate cancer-associated mesothelial cells (CAMCs), MCs were treated for 72 hours with conditioned media derived from KPCA cancer cells. Vehicle-treated MCs served as controls. After treatment, total RNA was extracted from both MCs and CAMCs using the Qiagen RNA extraction kit following the manufacturer’s instructions. RNA quality and concentration were assessed prior to library preparation and sequencing.

first: David

last: Pepin


title: SET7-mediated methylation of IRF3 at Lysine 98 attenuates antiviral innate immunity

city: Wuhan

first: Hongyan

last: Deng

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

country: China

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: SET7 is a member of the SET domain (SETD) methyltransferase family that catalyzes the monomethylation of lysine residues in histones and nonhistone proteins. This process either enhances or suppresses gene activation. Interferon regulatory factor 3 (IRF3) is a key transcription factor in the type I interferon (IFN) signaling pathway. This pathway is controlled by multiple post-translational modifications that finely tune IRF3's function. Here, we identify SET7 as a negative regulator of IRF3. SET7 interacts with IRF3 and catalyzes the monomethylation of IRF3 at lysine 98. This modification decreases IRF3 phosphorylation, dimerization, and subsequent nuclear translocation, thereby inhibiting the production of downstream type I interferons. Furthermore, zebrafish lacking set7, as well as those treated with the inhibitor (R)-PFI-2, are more resistant to viral infection. Set7-deficient mice also exhibit greater resistance to RNA and DNA viral infections. Our findings reveal a role for SET7 in regulating antiviral innate immunity and provide insight into the IRF3 monomethylation that affects its activation.

first: Xueyi

last: Sun

first: Huangyuan

last: Zha

first: Zixuan

last: Wang

first: Jinhua

last: Tang

first: Xiaoyun

last: Chen

first: Chunchun

last: Zhu

first: Jiale

last: Hua

first: Wen

last: Liu

first: Shuke

last: Jia

first: Yiman

last: Luo

first: Yuhan

last: Xiang

first: Wenhua

last: Li

first: Xing

first: Wuhan

last: Xiao


title: mRNA-seq analysis of S100A16-mediated alternative splicing in lung adenocarcinoma under oxidative stress

city: Shenyang

first: Xu

last: Yang

state: Liaoning Province

address: No. 77, Puhe Road, Shenbei New District

institute: China Medical University

summary: Lung adenocarcinoma (LUAD) cells develop adaptive mechanisms to survive high oxidative stress in the tumor microenvironment. This study aims to elucidate the role of S100A16, a calcium-binding protein, in regulating mitochondrial quality control and oxidative stress resistance. We performed polyA-enriched mRNA sequencing on human lung adenocarcinoma A549 cells with stable knockdown of S100A16, hnRNPM (a splicing factor identified as S100A16 interactor) or MagoHB (a negative control interactor), with or without 100μM H₂O₂ treatment for 2 hours (3 biological replicates per group). Transcriptomic analysis revealed that S100A16 translocates to the nucleus under oxidative stress and interacts with hnRNPM to modulate alternative splicing of mitochondrial genes (e.g., LETMD1), thereby maintaining mitochondrial morphology, membrane potential and respiratory function. These data provide mechanistic insights into S100A16 as a potential therapeutic target for LUAD.

overall_design: mRNA-seq of human lung adenocarcinoma A549 cells: 6 groups × 3 biological replicates. Groups: (1) Wild type control (untreated); (2) Wild type treated with 100μM H₂O₂ for 2h; (3) S100A16 stable knockdown (untreated); (4) S100A16 stable knockdown + 100μM H₂O₂ for 2h; (5) hnRNPM stable knockdown (untreated); (6) MagoHB stable knockdown (untreated).

first: Bo

first: Yangyuwei


title: Dual Roles of SBSN in Renal Cell Carcinoma Progression and Tumor Thrombus Formation: Cell-Autonomous NF-κB-CD44 Activation and Paracrine Angiogenesis via IFI6

city: Guangzhou

first: Jinming

last: Di

address: No. 600, Zhongshan Avenue, Tianhe District

department: Urology

institute: The Third Affiliated Hospital, Sun Yat-sen University

summary: Renal cell carcinoma (RCC) is a highly vascularized malignancy with a propensity for venous invasion and tumor thrombus (TT) formation, yet the molecular mechanisms linking vascular aggression to tumor progression remain incompletely understood. In this study, we identify suprabasin (SBSN) as a key oncogenic mediator that is consistently upregulated in RCC tissues and further enriched in TT, correlating with poor patient prognosis. Functional assays demonstrate that SBSN promotes RCC cell proliferation, migration, and invasion in vitro. Transcriptomic analysis reveals activation of the NF-κB signaling pathway in SBSN-overexpressing cells, with CD44 emerging as a critical downstream effector. We further delineate a novel SBSN-NF-κB-CD44 axis that drives malignant phenotypes in RCC cells. In vivo, SBSN knockdown attenuates tumor growth and induces a shift in epithelial-mesenchymal transition (EMT) markers. Clinically, SBSN expression in RCC tissue positively correlates with microvessel density (MVD). Mechanistically, tumor-secreted SBSN enhances angiogenesis through a paracrine pathway by upregulating the anti-apoptotic protein IFI6 in endothelial cells, thereby suppressing cleaved caspase-3 and Bax activation and promoting endothelial survival and tube formation. Collectively, our findings uncover a dual role for SBSN in RCC progression: intrinsically via the NF-κB-CD44 axis to drive tumor cell aggressiveness, and extrinsically via the SBSN-IFI6 axis to promote angiogenesis and TT formation. This study positions SBSN as a potential prognostic biomarker and therapeutic target to disrupt both tumor growth and vascular support in advanced RCC.

overall_design: RNA-seq profiling of OS-RC-2 cells (vector control vs. SBSN overexpression) and HUVECs treated with conditioned medium from OS-RC-2 cells (vector control vs. SBSN overexpression), each with n=3 biological replicates.

first: Yuedian

last: Ye

first: Jinbin

last: Xu

first: Weihao

first: Zhansen

last: Huang

first: Xiaoming

first: Jiang


title: In vivo genome editing of human hematopoietic stem cells for treatment of blood disorders using mRNA delivery

status: Public on Aug 13 2026

city: shanghai

first: xu

middle: sai

last: juan

address: DongchuanRoad

institute: East china normal university

summary: Ex vivo autologous hematopoietic stem cell (HSC) gene therapy provides a promising treatment option for hematological disorders. However, current methods involve complex processes and chemotherapeutic conditioning, leading to limited accessibility for treatment and significant side effects. Here, we develop antibody-free targeted lipid nanoparticles (LNPs) for mRNA delivery to HSCs in vivo, enabling efficient base editing of the γ-globin gene (HBG1/2) promoters target in human HSCs to reactivate fetal hemoglobin in derived erythroid cells. Delivery of ABE8e/sgRNA mRNA with optimized LNPs achieves efficient in vivo base editing of HBG1/2 in transfusion-dependent β-thalassemia (TDT) patients-derived HSCs engrafted in immunodeficient NCG-X mice, showing restored globin chain balance in erythroid cells. Our research indicates that using LNPs for genome editor delivery achieves efficient editing of endogenous genes of human HSCs. This non-viral delivery system eliminates the need for harvesting or mobilizing HSCs, providing a potent and one-time treatment potential for blood disorders like sickle cell disease (SCD) and TDT.

overall_design: In this study, the efficiency and applicability of ABE8e-mediated gene editing were evaluated in human CD34+ hematopoietic stem cell-engrafted mouse models through both ex vivo and in vivo approaches. For ex vivo editing (Figures 2g and 2h), healthy donor-derived CD34+ cells were electroporated with ABE8e protein and sgRNAs targeting either the BCL11A enhancer (Figure 2g) or the HBG promoter (Figure 2h). Edited cells were then co-transplanted with unedited CD34+ cells into severely immunodeficient NCG-X mice. After 16 weeks, bone marrow (BM) cells were harvested, and DNA was extracted for PCR amplification of the target regions followed by deep sequencing to assess editing efficiency and stability in vivo. For in vivo editing (Figures 3i, k, l and Extended Figures 6d, i), healthy human CD34+ cells were first transplanted into moderately immunodeficient mice. Sixteen weeks post-transplantation, when human cell engraftment was established, lipid nanoparticle (LNP)-encapsulated ABE8e mRNA and HBG-targeting sgRNA were delivered via multiple intravenous injections. At various time points post-injection, BM cells were collected, human cells were sorted, and genomic DNA was analyzed by PCR and deep sequencing to editing efficiency . Additionally, in a disease-relevant model (Figure 5b), patient-derived CD34+ cells (e.g., from individuals with β-hemoglobinopathies) were transplanted into immunodeficient mice. Following engraftment, similar LNP-based in vivo editing was performed, and editing outcomes were assessed using deep sequencing .


title: Divergent Cytotoxic and Inflammatory Functions of Intratumoral Vd2+ gdT Cells in Renal Cell Carcinoma

city: Suwon

first: WonJoon

last: Oh

address: 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do

country: South Korea

institute: Sunkyunkwan university

summary: We characterized Vd2+ gdT cell subsets in paired peripheral blood and tumor samples from three treatment-naive clear cell renal cell carcinoma (ccRCC) patients using flow cytometry and single-cell RNA sequencing. Two major subsets distinguished by CD16 expression exhibited divergent cytotoxic and inflammatory effector programs within the tumor microenvironment. Single-cell RNA sequencing identified four transcriptional clusters with a TOX+ progenitor-like cluster giving rise to divergent effector states.

overall_design: Single-cell RNA sequencing of tumor-infiltrating gdT cells and B cells sorted from fresh tumor tissues of three treatment-naive ccRCC patients (pT1a, pT2b, pT3a) undergoing nephrectomy. 5' gene expression libraries prepared using 10x Genomics Chromium Controller and sequenced on Illumina NovaSeq 6000.

first: Oh

last: Won Joon

first: Park

last: Jaeyoun

first: Dahanayake

last: Tilanka Kalanapriya

first: Yeom

last: Seon Yong

first: Ryu

last: Heeju

first: Seo

last: Seong Il

first: Kim

last: Tae Jin


title: Halofantrine protects photoreceptors in multiple models of retinal degeneration [rd10]

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Inherited retinal degenerative diseases (IRDs), including retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA), cause progressive vision impairment due to photoreceptor degeneration. We previously demonstrated the protective effects of reserpine in models of CEP290-LCA and in the female Rhodopsin-P23H rat model of autosomal dominant RP. Given that reserpine is limited by side effects, we expanded our compound screen using retinal organoids from the rd16 mouse model of CEP290-LCA to include structurally diverse small molecules that may converge on proteostasis pathways. Follow-up evaluations in Rhodopsin-P23H rats, human CEP290-LCA retinal organoids, and rd10 mice (a model of PDE6B-RP) identified halofantrine as the most promising molecule, conferring strong protection on both rod and cone photoreceptors and demonstrating therapeutic potential across the divergent IRD models tested. Transcriptome analysis revealed a convergent molecular response to halofantrine across these models, primarily through upregulation of oxidative phosphorylation and ribosomal processes. Notably, halofantrine elicited significant improvements in retinal function, as assessed by electroretinography, despite pharmacokinetically limited and transient retinal exposure after subconjunctival injection in Rhodopsin-P23H rats. Our studies highlight the potential of halofantrine as a gene-independent therapy and suggest that it may be developed for ocular delivery via eye drops for the treatment of IRDs.

overall_design: Wild-type treated with DMSO and rd10 mice treated with DMSO or halofantrine were used for retina RNA-seq analysis.

first: Minji

last: Kim

first: Anupam

middle: K

last: Mondal

first: Holly

middle: Y

last: Chen

first: Dheeraj

last: Agrohia

first: Milton

middle: A

last: English

first: Philip

last: Vanlandingham

first: Florian

last: Regent

first: Raja Muhammad Nasser

last: Khan

first: Yi

last: Zeng

first: Oluwatobi

middle: T

last: Arisa

first: William

middle: D

last: Figg

first: Manju

last: Swaroop

first: Wei

last: Zheng

first: Wenwei

first: Rafal

last: Farjo

first: Hyun Beom

last: Song

first: Anand


title: Halofantrine protects photoreceptors in multiple models of retinal degeneration [organoids]

first: Matthew

overall_design: Control or LCA donor iPSCs were derived to retinal organoids. LCA organoids were treated with DMSO or Halofantrine prior to RNA-seq.

first: Minji

last: Huang


title: Oxygen gradients shape cross-feeding, leading to emergent spatial organization in gut commensal bacteria

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

institute: Helmholtz Insitute

summary: Microbial interactions unfold within environments structured by physical transport, and chemical gradients, yet most mechanistic studies rely on well-mixed systems that mask the reciprocal influences of ecology and metabolism. Here, we dissected the interactions between the mammalian gut commensal Bacteroides thetaiotaomicron, a primary degrader of dietary polysaccharides, and Escherichia coli, a facultative intestinal anaerobe. In anoxic liquid culture, B. thetaiotaomicron extracellularly hydrolyzes amylopectin and releases diffusible breakdown products that E. coli assimilates, as confirmed by C¹³-starch tracing and sugar utilzation-impaired mutants. In a microfluidic system engineered to mimic intestinal crypt-like oxygen gradients, this same pair of species no longer behaves as in bulk culture, but self-organizes into complementary spatial niches. B. thetaiotaomicron colonizes anoxic regions where it degrades polysaccharides, while E. coli occupies oxygenated zones where it consumes the released sugars. Through aerobic respiration, E. coli locally reduces oxygen, widening the anoxic region that B. thetaiotaomicron subsequently invades. Disrupting sugar uptake in E. coli collapses this organization, whereas increasing oxygen availability reverses it. A reaction–transport model shows that these patterns arise from coupled feedbacks between resource release, resource consumption, and oxygen modification. Together, our results reveal how spatial structure and physicochemical gradients convert a cross-feeding interaction into a dynamic niche-construction process that stabilizes coexistence and generates emergent ecological organization.

sample_organism:
Escherichia coli
Bacteroides thetaiotaomicron

overall_design: Bacterial RNA-seq samples. RNA extracted using the MATQ-seq protocol from E.coli and B.thetaiotaomicron grown either in liquid culture or in a microfluidic device under an oxygen gradient.

first: David

last: Scheidweiler

first: Hannah

last: Ochner

first: Sonja

last: Blascher

first: Stanislas

last: Thiriet-Rupert

first: Louis

last: Dorison

first: Cristophe

last: Beloin

first: Yohan

last: Davit

first: Tanmay

last: A. M. Bharat

first: Samy

last: Gobaa

first: Alexander

last: J. Westermann

first: Kiran

last: R. Patil

first: Jean-Marc

last: Ghigo


title: Halofantrine protects photoreceptors in multiple models of retinal degeneration [P23H]

last: Brooks

overall_design: Control no treatment and P23H rat retinas treated with DMSO or Halofantrine prior to RNA-seq of the retina.

last: Kim

first: Anupam

last: Mondal

first: Holly

last: Chen

first: Dheeraj

last: Agrohia

first: Milton

last: English

first: Philip

last: Vanlandingham

first: Florian

last: Regent

first: Raja Muhammad Nasser

last: Khan

first: Yi

last: Zeng

first: Oluwatobi

last: Arisa

first: William

last: Figg

first: Manju

last: Swaroop

first: Wei

last: Zheng

first: Wenwei

first: Rafal

first: Hyun Beom


title: CXXC Finger Protein 1 drives BMP signaling and progenitor cell differentiation during limb development

first: Diana

middle: L

last: Carlone

address: 300 Longwood Avenue

department: Endocrinology

institute: Boston Children's Hospital

summary: The mechanisms mediating endochondral bone formation remain incompletely understood. Here, we show that CXXC Finger Protein 1 (CFP1) is required for the onset of chondrogenesis during forelimb development. CFP1-deficient mesenchymal progenitor cells (LMPs) retain an immature molecular signature with elevated FGF and SHH signaling and repressed BMP signaling, in part, due to (1) reduced expression of type I BMP receptors, (2) reduced Smad1 protein levels and (3) an altered extracellular niche. Moreover, the addition of exogenous BMP ligand or antagonism of heparan sulfate restores LMP differentiation toward a chondrogenic fate and enhances BMP signaling, suggesting a defect in BMP ligand bioavailability mediates the CFP1-deficient LMP phenotype. Together, these findings define CFP1 as a gatekeeper between the undifferentiated and differentiated state of LMPs during endochondral bone formation and as a physiological regulator of BMP signaling.

overall_design: Expression profiling by high throughput sequencing of control and Cxxc1 conditional knockout forelimb buds from E11.5-12 embryos.


title: Mycobacterium tuberculosis acid growth arrest on priopionate or lactate

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

summary: We have examined the transcriptional adaptations of WT Mtb when cultured on propionate or lactate as sole carbon sources at pH 5.7 as compared to pH 7.0. We have also examined the role of a phoR transposon mutant when cultured on priopionate at acidic and neutral pH and a phoT transposon mutant when cultured on lactate at acidic and neutral pH.

overall_design: Mtb cultures were grown at 37 degrees celsius in T-75 vented flasks standing tissue culture flasks at 40ml of a defined minimal media and seeded at an OD of .1.  8 conditions conditions, and three strains,WTERDMAN, phoR::Tn and phoT::Tn were examined with two biological replicates. The conditions examined include: 1)WT, 2mM propionate acidic, pH 7.0; 2) WT, 2mM propionate acidic, pH 5.7, 3) phoR::TN, 2mM propionate, pH 7.0, 4) phoR::TN, 2mM propionate, pH 5.7; 5) WT, 4 mM lacate,  pH7.0, 6) WT, 4 mM lactate, pH 5.7; 7) phoT::Tn 4 mM lactate, pH 7.0, 8) phoT::Tn, 4 mM lacate, pH 5.7.   Following, a 3 day incubation, total bacterial RNA was extracted.

first: Shelby

last: Dechow

first: Heather

last: Murdoch

first: Adam

last: Kibiloski


title: Exercise Training Attenuates the Monocyte Transcriptome Response to Acute Exercise in Adolescents: Evidence for Sex-Specific Molecular Adaptations

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

summary: Background: Atherosclerosis is tied to functional characteristics of circulating monocytes, the disease in adults likely begins in childhood and adolescence, and clinical heart disease differs substantially between women and men. Since monocyte function is influenced by exercise, we measured monocyte gene and noncoding RNA [ncRNA] responses to acute exercise before and after an 8-week endurance training intervention in adolescents. We identified pathways related to cardiovascular disease risk and explored sex differences in the exercise response. Methods: Twelve males and 9 females (14-17 years) completed an acute exercise protocol consisting of ten 2-min cycling bouts at 70% of maximal work rate, interspersed with 1-min rest performed before and after training intervention. Blood was collected before and immediately after each acute exercise. Peripheral blood monocytes were isolated and total RNAseq was performed. Results: Exercise training did not alter baseline (pre-acute exercise) monocyte transcriptomic profiles in either sex (FDR>0.1). Prior to training, acute exercise induced a markedly greater monocyte transcriptomic response in females compared with males (5,148 vs. 571 differentially expressed molecules, FDR < 0.1), with 315 transcripts demonstrating sex-specific responses. Pathway analyses identified vascular-function-related pathways only in males, whereas pathways related to adipose tissue crosstalk and oxidative metabolism were identified only in females. Following training, the acute transcriptomic response was markedly attenuated in both sexes (165 molecules in males and 94 in females, FDR < 0.1), representing an approximately 98% reduction in females and a ~70% reduction in males compared with pre-training responses. Twenty-six molecules exhibited sex-specific post-training response patterns, with minimal residual pathway activation. Conclusion: This study provides new insight into sex-specific monocyte transcriptomic responses to acute exercise in adolescents and demonstrates that training markedly attenuates monocyte molecular responsiveness to acute exercise. These immune adaptations may contribute to the cardioprotective effects of regular physical activity in both sexes.

overall_design: 12 healthy males and 9 females (14-17 years) completed 8-week endurance exercise intervention program (1 hour/session, 3 days/week). V̇O2 peak was assessed, before and after the intervention program by ramp-type progressive cycle ergometer until exhaustion. On a separate laboratory visit, blood was collected at baseline and immediately after 10, 2-min bouts of cycle ergometer exercise interspersed with 1-min rest at 70% of maximum work rate, equivalent to ~75% of V̇O2peak. We included 20 participants with 4 blood time points and 1 participant with 3 time points. In total, 83 samples.

first: Abel

last: Plaza Florido

first: Fadia

last: Haddad

first: Dan

middle: M

last: Cooper

first: Shlomit

last: Radom Aizik


title: Interferon-λ-Neutralizing Autoantibodies and Common Autoimmune Disease Autoantibodies in Pediatric Acute-Onset Neuropsychiatric Syndrome [CTD-CC]

city: Stanford

first: Paul

middle: Joseph

last: Utz

address: 269 Campus Dr

institute: Stanford University School of Medicine

summary: We measured IgG autoantibodies associated with Connective Tissue Disease (CTD) and Cytokine & Chemokine (CC) antigens in pediatric patients with Pediatric Acute-Onset Neuropsychiatric Syndrome (PANS) and healthy controls.

overall_design: We constructed protein arrays by coupling recombinant protein antigens to fluorescent carboxylated magnetic beads. We then used the protein arrays to probe patient plasma samples and healthy control samples for IgG autoantibodies. A Luminex FLEXMAP 3D® system was used to quantitatively measure autoantibody reactivity in units of median flourescent intensity (MFI).

first: Xihui

last: Yin

first: Jennifer

last: Frankovich

first: Muge

last: Kalaycioglu

first: Ananya

last: Choudhury

first: Michael

last: Burry Jr

first: Woo Joo

last: Kwon

first: Lu

last: Tian

first: Meiqian

last: Ma

first: Bahare

last: Farhadian

first: Cindy

last: Manko

first: Melissa

last: Silverman

first: Yuhuan

last: Xie

first: Paula

last: Tran

first: Noelle

last: Schlenk

first: Tyler

middle: R

last: Prestwood


title: Transcriptomic profiling of blood neutrophils from preterm infants with bronchopulmonary dysplasia

first: Sen

last: Li

address: 9 Jinsui Road, Tianhe District

institute: Guangzhou Women and Children's Medical Center

summary: Bronchopulmonary dysplasia (BPD) is a major complication of preterm birth, yet its immune mechanisms remains poorly understood. To explore the role of neutrophils in the pathogenesis of BPD, a prospective study was conducted in the Neonatal Intensive Care Unit of Guangzhou Women and Children’s Medical Center from June to September 2024. Inclusion criteria were: (1) preterm birth at <32 weeks of gestational age, and (2) admission within 6 hours after birth. Peripheral blood samples were collected on day 14 after birth. Infants with major congenital anomalies or acute infections were excluded. A total of 22 preterm infants were enrolled, of whom 12 developed BPD. Neutrophils were isolated from peripheral blood, and bulk RNA sequencing was performed.

overall_design: RNA-seq profiling of blood neutrophils from infants who later developed BPD and preterm controls at postnatal day 14

first: Wenhao

last: Zhou

first: Huayan

last: Zhang

first: Xiaohui

last: Wang


title: MEF2C controls lysosomal and lipid clearance programs linked to Alzheimer’s disease risk in macrophagesm [scRNAseq_WTC11_iMGL_ReN]

city: New York

first: Anna

last: Podlesny-Drabiniok

state: NY

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Risk alleles for late-onset Alzheimer’s disease (AD) are enriched in myeloid cis-regulatory elements, implicating myeloid gene-regulatory networks in disease susceptibility. A conserved lipid-associated transcriptional signature—spanning disease-associated microglia and peripheral lipid-associated macrophages (DLAM)—emerges across neurodegenerative and metabolic diseases, yet the transcriptional regulators of this gene expression program remain incompletely defined. Here, we show that MEF2C—a candidate AD risk gene—is a master DLAM regulator. Using MEF2C knockout and knockdown in human iPSC-derived microglia and macrophages, we found that total or partial MEF2C loss is sufficient to induce DLAM-associated transcriptional, epigenomic, and functional remodeling, including enhanced lysosomal activity and cholesterol efflux. Integration of chromatin accessibility and regulatory epigenetic profiles with functionally informed fine-mapping linked AD causal variants in other loci to MEF2C-regulated regulatory regions and downstream risk genes. In a triculture model of AD, microglial MEF2C loss is associated with an increased DLAM population and a reduced Aβ42/40 ratio, supporting context-dependent reprogramming of microglia as a mechanism to modulate AD-relevant pathology.

overall_design: scRNAseq profiling of mature iPSC-derived microglia (iMGLs) lacking myocyte enhancer factor 2C (MEF2C) and wild-type (WT) controlsco-cultured with control (CTRL) or AD ReN-derived neurons/astrocytes

first: Edoardo

last: Marcora

first: Alison

last: Goate

first: Tulsi

last: Patel


title: Halofantrine protects photoreceptors in multiple models of retinal degeneration

first: Matthew

last: Brooks

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

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Helicobacter pylori infection causes gastric mucosal reprogramming into a fetal-like antimicrobial state

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

institute: Charité Universitätsmedizin

summary: During gastrointestinal homeostasis, Wnt/R-spondin and BMP signaling regulate the proliferation and differentiation of Lgr5+ cells. Injuries trigger transient epithelial reprogramming into a highly proliferative fetal-like regenerative state, which is Lgr5 signaling-independent and is instead fueled by alternative pathways such as Hippo/YAP signaling. Mechanisms that drive tissue reprogramming are not well understood. In the stomach, infection with the gastric pathogen Helicobacter pylori triggers gland hyperplasia and causes premalignant development. While infection is associated with alterations of homeostatic signals such as enhanced R-spondin signaling and reduced BMP signaling, the development of gastric pathology has also been linked to YAP activation. The exact interplay between these signaling molecules and their contribution to H. pylori-driven pathology remains unclear.  Here, we demonstrate that H. pylori-driven gland hyperplasia is fueled by fetal-like regenerative reprogramming, which is mechanistically linked to reduced BMP signaling. The loss of epithelial BMP signaling is sufficient to induce the fetal-like state in vivo but not in organoids, indicating the involvement of cell-extrinsic mechanisms. We discover that epithelial cells that lack BMP signaling are primed to respond to microbes by producing proinflammatory chemokines, which drive tissue infiltration by macrophages and neutrophils. These immune cells in turn trigger stromal remodeling and production of pro-regenerative factors such as prostaglandin E via IL-1β signaling, thus promoting epithelial fetal-like regenerative state. Depletion of the IL-1 receptor in the stroma is sufficient to prevent H. pylori-driven tissue reprogramming and pathology. Our data provide mechanistic insights into fetal-like mucosal reprogramming and demonstrate how this epithelial-immune-stromal cascade is highjacked in the context of H. pylori-driven gastric pathology.

overall_design: Axin2CreErt2-Bmpr1afl/fl mice were used to generate KO of Bmpr1a in stomach epithelial cells, and 2 replicates were generated for each of the WT and KO conditions. Uninduced Col1a2CreErt2-Il1r1 fl/fl mice with or without infection with H.pylori were used for infection experiments, with 2 replicates in each group. 10x Genomics scRNA profiliing was applied to combined epithelial and stromal cells from each replicate.

first: Giulia

last: Beccaceci

first: Stefanie

last: Müllerke

first: Manqiang

last: Lin

first: Hilmar

last: Berger


title: Endothelial PERK Impairs Post-transplant Lymphoid Regeneration by Reducing DLL4-NOTCH3 Signaling at the Pre-B Niche

city: Houston

first: Junjun

last: Zheng

state: TX

address: 6670 Bertner Ave, Houston, TX 77030

department: Houston Methodist Neal Cancer Center

institute: Houston Methodist Research Institute

summary: This study addresses how ER stress impacts hematopoietic regeneration in the bone marrow microenvironment. We evaluated how endothelial PERK-DLL4 axis regulates early HSC and B progenitor regeneration by using single-cell analysis of regenerating bone marrow cells collected from mice with endothelial-specific deletion of Perk (EP), Dll4 (ED), or combined (DKO). Through bone marrow transplantation and single cell analysis, we revealed that perturbation of PERK or DLL4 resulted in opposite changes in B and granulomonocytic progenitor recovery. Further, PERK-DLL4 axis orchestrates the regenerative network by regulating endothelial DLL4 signaling to NOTCH3 on MSCs, lymphoid commitment of hematopoietic stem cells, IL7 expression in MSCs, and coordinated interferon response. These findings establish that ER stress regulates a regenerative pre-B niche through PERK-regulated endothelial DLL4 signaling to NOTCH3 on MSCs.

overall_design: Floxed mice (PerkF/F and Dll4F/F) and VE-cadherinERT2-Cre mice were crossed to generate inducible endothelial-specific knockout of Perk, Dll4, or Perk/Dll4 (DKO) by five consecutive doses of tamoxifen. Mice were then irradiated one week after the last dose of tamoxifen injection.

first: Lan


title: MEF2C controls lysosomal and lipid clearance programs linked to Alzheimer’s disease risk in macrophages [scRNA-seq]

overall_design: scRNAseq profiling of mature iPSC-derived microglia (iMGLs) lacking myocyte enhancer factor 2C (MEF2C) and wild-type (WT) controls treated with myelin fragments (20ug/ml, 24h)


title: MEF2C controls lysosomal and lipid clearance programs linked to Alzheimer’s disease risk in macrophages [bulkRNAseq_WTC11_iMGL]

overall_design: RNA-seq profiling of mature iPSC-derived microglia (iMGLs) lacking myocyte enhancer factor 2C (MEF2C) and wild-type (WT) controls following treatment with myelin fragments (20 µg/mL, 24 h) or lipopolysaccharide (LPS; 50 ng/mL, 24 h).


title: Clonal Hematopoiesis Drives Fibrotic Remodeling of the Bone Marrow Microenvironment [dataset 1]

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: Clonal hematopoiesis of indeterminate potential (CHIP) is associated with aging, inflammation, and increased risk of hematologic malignancy, yet its impact on the human bone marrow (BM) microenvironment remains unclear. Using single-cell transcriptomic and histologic profiling of freshly isolated human BM, we show that CHIP profoundly remodels the niche through fibroblast expansion and early fibrotic transformation. CHIP carriers exhibited myeloid-biased hematopoiesis, broad enrichment of inflammatory signaling, and metabolic reprogramming of CD4⁺ and CD8⁺ T cells, with CD8⁺ T cells emerging as key sources of TNFα. Strikingly, fibroblast expansion occurred irrespective of mutational subtype and was characterized by transcriptional programs analogous to cancer-associated fibroblasts (CAFs). These cells demonstrated signaling interactions with hematopoietic and immune compartments through collagen-integrin adhesion pathways as well as IL-6 and TGFβ cytokine networks. Histologic validation confirmed reticulin and collagen deposition, establishing a pre-fibrotic niche state. These findings position fibroblast-driven remodeling as an early hallmark of CHIP, linking inflammation, fibrosis, and clonal persistence, and highlight antifibrotic strategies as potential avenues to intercept malignant evolution.

overall_design:
Bone marrow samples were collected from patients undergoing elective total hip replacement surgery and

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

first: Alicia G.

last: Aguilar-Navarro

first: Gibran

last: Edun


title: Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss [RNA-seq P199-6]

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Rationale: Bronchopulmonary Dysplasia (BPD) arises from disrupted lung development after preterm birth and produces structural deficits at every level of the respiratory tree. Lower airway disease is emerging as a clinically significant BPD phenotype with increased mortality, yet the molecular mechanisms whereby preterm birth disrupts airway development remain poorly defined. Objectives: To develop a human model of lower airway disease following preterm birth and to define a molecular endotype of evolving BPD (eBPD) at baseline and in response to injury.  Methods: An ex vivo organotypic Airway Epithelial Cell (AEC) model was combined with well-characterized pathologic and transcriptomic patient samples for quantitative immunohistochemistry and RNA sequencing analyses. Measurements and Main Results: Compared to AECs from healthy controls, eBPD-derived AECs exhibited reduced proliferation, impaired differentiation to ciliated epithelium, and expansion of a vimentin-positive population with a transcriptional profile associated with impaired AEC differentiation. Following hyperoxia exposure, eBPD-derived AECs mounted a robust vimentin response ex vivo, paralleling increased vimentin expression observed in airway cells from lung tissue from human infants with BPD. Conclusions: Using an organotypic model of neonatal airway differentiation, we demonstrate eBPD is associated with impaired AEC differentiation, increased vimentin-expression and concomitant loss of ciliated cells, and an exaggerated vimentin response to hyperoxic injury. These findings mimic the effects of prematurity in airway cells in human patients. These data support a mechanism whereby hyperoxia leads to impaired epithelial differentiation and associated lower airway dysfunction in BPD and inform future mechanistic studies interrogating the role of intermediate filaments in evolving BPD.

overall_design: This study compares airway epithelial cell cultures from BPD patients with and without hyperoxic injury. Included 2 BPD donors.

first: Laurie

last: Eldredge

first: Stephan

last: Pribitzer

first: Steven

last: Ziegler

first: Scott

last: Presnell


title: MEF2C controls lysosomal and lipid clearance programs linked to Alzheimer’s disease risk in macrophages [ATAC-seq]

first: Anna

last: Podlesny-Drabiniok

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATAC-seq profiling of mature iPSC-derived microglia (iMGLs) lacking myocyte enhancer factor 2C (MEF2C) and wild-type (WT) controls

first: Edoardo

last: Marcora

first: Alison

last: Goate

first: Tulsi


title: Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss [RNA-Seq P199-8]

overall_design: This study compares airway epithelial cell cultures established from tracheal aspirates of patients with BPD with airway brushings from pediatric patients without BPD undergoing airway procedures. Samples were cultured in room air or cultured in hyperoxia conditions for 72 or 96 hours. 15 samples total from 5 donors (2 BPD, 3 controls)


title: Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss [RNA-Seq P199-7]

overall_design: This study compares airway epithelial cell cultures established from tracheal aspirates from patients with BPD with airway brushings from pediatric patients without BPD undergoing airway procedures. It includes 49 samples total  from 7 BPD donors and 7 controls cultured in room air or hyperoxia exposure


title: Next-GenerationPediatric Cancer Models: Patient-Matched Orthotopic Xenografts, 3D Organoids, 2D Cultures, and Cell Lines for Identification of Therapeutic Vulnerabilities in Pediatric Solid Tumors [scRNAseq]

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

summary: Most pediatric solid tumor cell lines were established decades ago, so patient-matched organoids and xenografts are not available, limiting their translational utility. Here, we present a new approach to generate triads of patient-matched xenografts, 3-dimensional (3D) organoids, and 2D cultures. We have generated 3D organoids from 135 pediatric tumors, including rhabdomyosarcoma, osteosarcoma, neuroblastoma, Ewing sarcoma, Wilms tumor, and retinoblastoma. We have also generated patient-matched 2D cultures (n=82) and cell lines (n=20). When these 3D organoids, 2D cultures, or cell lines were orthotopically implanted into immunocompromised mice, they replicated the molecular and cellular features of the original patient tumor and xenograft. We have completed 352 single-cell and single-nucleus RNA-sequencing experiments (>2.2 million cells) to confirm that our patient-matched triads preserve tumor cell heterogeneity. All samples are renewable and >3,000 vials have been cryopreserved for unrestricted distribution through the Childhood Solid Tumor Network. We demonstrate the utility of patient-matched triads for identifying therapeutic vulnerabilities, providing a powerful tool for advancing pediatric cancer research.

overall_design: Using patient derivired orthotopic xenografts (PDX), we generated organoids (3D), cell cultures (2D) and established cell culture (CCLF) to model different solid tumors. We were able to validate these models by comparing to patient samples.

first: Justina

last: McEvoy

first: Melody

last: Allensworth

first: Mariajose

last: Franco

first: Shannon

last: Sweeney

first: Natalie

last: Geiger

first: Juliette

last: Kippen

first: Asha

last: Jannu

first: Stefan

last: Atkinson

first: Ayush

last: Attery

first: Chen

last: Hu

first: Shay

last: Sneed

first: Asa

last: Karlstrom

first: Cynthia

last: Cline

first: Cody

last: Ramirez

first: Antonia

last: Chroni

first: Hongjian

last: Jin

first: Yiping

last: Fan

first: Gang

last: Wu

first: Beisi

last: Xu

first: Abbas

last: Shirinifard

first: Jackie

last: Norrie

first: Brittney

last: Gordon

first: Kaitlin

last: Lord

first: Jakayla

last: Johnson

first: Madison

last: Parks

first: Heather

last: Sheppard

first: George

last: Campbell

first: Jennifer

last: Peters

first: Cam

last: Robinson

first: Carmen

last: Rios

first: Ruvimbo

last: Dzurumi

first: Hannah

last: Golding

first: Lindsey

last: Sheft

first: Anang

last: Shelat

first: Yuen-Yi

last: Tseng

first: Anand

last: Patel

first: Elizabeth

last: Stewart


title: Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss

first: Stephanie

last: Osmond


title: Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss [RNA-seq P199-4Data]

overall_design: This study is comparing transcriptomes between neonatal (N=12) and school-age (N=10) human airway epithelial cultures. We have noticed that neonatal airway epithelial cultures, grown at air-liquid interface, do not polarize normally and have a disorganized cellular structure. In this study, we will be investigating unique molecular mechanisms associated with epithelial growth and differentiation that differ between 1) the neonatal and school-age cultures, and 2) between submerged and ALI conditions.

first: Laurie

last: Eldredge

first: Stephan

last: Pribitzer

first: Steven

last: Ziegler

first: Scott

last: Presnell


title: SLF2 and SMC5 dysfunction drives HSC aging and predisposes to MDS, defining a new inherited bone marrow failure syndrome  [ATAC-seq]

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

summary: Pathogenic variants in SLF2 and SMC5 cause a developmental disorder known as Atelis Syndrome, characterized by microcephaly, short stature, and hematological abnormalities, most notably anemia and lymphopenia. However, its clinical relevance to hematology has not yet been established, and the underlying pathogenic mechanisms remain largely unknown. Prompted by our longitudinal follow-up and re-evaluation revealing that some patients with Atelis Syndrome developed myelodysplastic syndromes (MDS) or MDS-like features, we elucidated the hematopoietic defects using hematopoietic stem and progenitor cells (HSPCs) derived from patient-specific induced pluripotent stem cells carrying compound heterozygous SLF2 mutations (mutant HSPCs) and gene-corrected isogenic controls. Mutant HSPCs exhibited impaired colony-forming capacity and defective erythroid differentiation with a myeloid bias. Crucially, in vivo xenotransplantation revealed that mutant HSPCs had significantly reduced long-term engraftment capacity. Knockdown of SMC5 in human cord blood CD34+ cells similarly impaired colony formation. Mechanistically, disruption of the SLF2–SMC5 axis induces increased genomic instability, p53/p21 activation, and transcriptional signatures of  senescence. Furthermore, ATAC sequencing uncovered epigenetic features of hematopoietic stem cell (HSC) aging, including increased accessibility at PU.1 motifs, driving myeloid bias. In conclusion, we establish that SLF2 and SMC5 dysfunction drives premature HSC aging and predisposes to MDS, defining Atelis Syndrome as a distinct entity within the inherited bone marrow failure syndromes (IBMFS). These findings highlight the need to incorporate Atelis Syndrome into the diagnostic framework of IBMFS, improving genetic diagnosis and guiding clinical management of hematological abnormalities.

overall_design: Chromatin accessibility were compared between hematopoietic stem and progenitor cells derived from human induced pluripotent stem cells with SLF2 variant and gene-corrected isogenic controls.

first: Sho

last: Shibata

first: Kazuhisa

last: Chonabayashi

first: Yasuko

last: Matsumura


title: Infants who develop BPD have an airway endotype defined by vimentin expression and ciliary loss [RNA-Seq P199-9Data]

overall_design: This study compares airway epithelial cell cultures established from airway brushings from pediatric patients without BPD undergoing airway procedures. 18 samples total from 7 donors (2 BPD, 5 controls)


title: High throughput sequencing data of equol aptamers obtained through Capture-SELEX after 15 rounds of selection

city: Kobe

first: Tamai

last: Endoh

address: 7-1-20, Minatojima-minamimachi, Chuo-ku

department: FIRST/FIBER

institute: Konan University

summary: Expanding healthy life expectancy requires technologies for continuous and non-invasive health monitoring. Sensors detecting health-related biomarkers in urine can be used for such applications. DNA aptamers targeting equol, a gut microbiota–derived metabolite with various health benefits, were obtained by Capture-SELEX to construct the aptamer-based equol sensors.

overall_design: After 15 rounds of selection, single stranded DNA fragments consisting of equol aptamer candidates were amplified by PCR. Sequences of the DNA fragments obtained were analyzed using the IonS5 Next Generation Sequencing (NGS) System.

first: Tamaki

first: Hidenobu

last: Yaku

first: Peter

last: Podbevsek

first: Janez

last: Plavec

first: Naoki

last: Sugimoto


title: SLF2 and SMC5 dysfunction drives HSC aging and predisposes to MDS, defining a new inherited bone marrow failure syndrome  [RNA-seq]

overall_design: Transcriptome profiles were compared between hematopoietic stem and progenitor cells derived from human induced pluripotent stem cells with pathogenic SLF2 variant and gene-corrected isogenic controls.


title: Resolvin E1 limits cyclosporine-induced toxicity and drives durable recovery in autoimmune bone marrow failure

city: Albany

first: Katherine

middle: C

last: MacNamara

address: 47 New Scotland Avenue

department: Immunology and Microbial Disease

institute: Albany Medical College

summary: Chronic inflammatory diseases are among the leading causes of morbidity and mortality worldwide, yet conventional immunosuppressive therapies (IST) often fail to achieve durable remission and can cause systemic toxicity. Severe aplastic anemia (SAA), a lethal autoimmune disease and bone marrow failure disorder, exemplifies this challenge with its first-line therapy Cyclosporine A (CsA). CsA suppresses pathogenic T cells and partially restores hematopoiesis in the context of murine SAA, but is associated with nephrotoxicity, hepatotoxicity, and increased Th17 cells one month post-treatment. Conversely, the pro-resolving lipid mediator Resolvin E1 (RvE1) prevents SAA-induced mortality, while also reducing inflammatory immune activation and preserving tissue homeostasis. Treatment with both CsA and RvE1 achieved 100% survival, restored hematopoietic and immune homeostasis, and mitigated CsA-induced toxicity. Mechanistically, RvE1 required the GPCR ChemR23 on immune cells to reverse CsA-induced inflammation and immune dysregulation. To better understand the mechanisms by which CsA drives long-term toxicity and immune dysfunction, and how RvE1 reverses such, we performed single-cell RNA sequencing on total bone marrow from SAA-induced mice one-month post therapy with 10mg/kg CsA and/or 0.00125mg/kg RvE1.

overall_design: Hybrid F1 (C57BL/6;Balb/c) mice, at 7- to 8 weeks of age, were exposed to sub-lethal radiation (350 RADs,137Cs source) and received 6.5x106 C57BL/6 splenocytes from age- and gender-matched donors via intraperitoneal injection 3-4 hours post radiation. SAA-induced mice were then treated with 10mg/kg Cyclosporine A (CsA) and/or 0.00125 mg/kg Resolvin E1 (RvE1) every other day by intraperitoneal injection starting on day 7 post-irradiation, for a total of five treatments. Healthy mice received no treatment. Mice were then monitored for 30 days and total bone marrow (BM) collected 45 days post-irradiation. BM cells from 3-6 mice per experimental group (5 healthy, 3 SAA+RvE1, 6 SAA+CsA, and 6 SAA+CsA+RvE1) were pooled for single-cell RNA sequencing. Libraries were prepared using the Next GEM-X Single Cell 5’ GEM Kit v3 (10x Genomics) and sequenced at the Rensselaer Polytechnic Institute Genomic Core Facility.

first: Rachel

last: Grazda


title: Reprogramming lineage features promotes epithelial behavior in carcinoma cells [ChIP-Seq]

city: Dallas

first: Lance

last: Terada

address: 5323 Harry Hines Blvd, MC 8448

institute: University of Texas Southwestern

summary: Cancer cells distort epigenetic control of gene expression, allowing for a remarkable degree of plasticity and loss of cell type identity.  At the same time, expression of identity-discordant lineage determinants can significantly shift cell phenotype by creating lineage hybrid states.  One example is the misexpression of IKZF3, encoding the lymphocyte restricted transcription factor Aiolos, by roughly half of non-small cell lung carcinomas (NSCLC) and the majority of small cell lung carcinomas [1].  During normal lymphocyte development, pre-B progenitors enter a proliferative phase dependent on survival cues from bone marrow stroma.  To progress, Aiolos and its paralog Ikaros (IKZF1) repress multiple adhesion-related genes, releasing cells from this epithelial-type dependence on solid matrix in preparation for their release as mature lymphocytes into the circulation [2, 3].  In lung cancers, unlicensed expression of Aiolos initiates a similar shift from an epithelial to a lymphocyte-like state by repression of multiple adhesion-related genes, resulting in loss of anoikis and consequent metastatic spread [1].  To reverse these lymphoid traits, we created a chimeric epigenetic editor designed to specifically retrieve Aiolos-repressed epithelial adhesion properties.  Here, we demonstrate proof of principle for epithelial lineage restoration by exploiting a lymphocyte developmental pathway.

overall_design:
ChIP-seq of Aiolos in control H1155 cells
ChIP-seq of HA in chimera expressing cells
ChIP-seq of H3K27ac in control and chimera-expressing cells H1155 cells
ChIP-seq of H3K27me3 in control and chimera-expressing cells H1155 cells


title: Modification of the transcription factor FOXL2 at serines 101 and 107 disables DNA binding, leads to nucleolar relocalization, and rewires granulosa-cell programs

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

summary: We demonstrate that FOXL2 is phosphorylated by PKC in vitro on several residues and that these modifications alter FOXL2 localization and activity. Specifically, phosphorylation of the FHD residues Ser101 and Ser107 by PKC are expected to lead to major changes in FOXL2 properties. Consistently, the phosphomimetic substitutions S101D and S107D abolish DNA binding and drives nucleolar enrichment. RNA-seq shows that S101D and a C-terminal truncation (ΔC) produce broad loss-of-function (LOF) indicating that DNA engagement and the C-terminus are required for full transcriptional output. We also observed variant-specific gain-of-function (GOF) effects. By contrast, S101A perturbs few transcripts.

overall_design: Transcriptomes of transduced FOXL2WT/WT KGN cells (human granulosa cells) expressing the WT form of FOXL2 or different variants (S101A, S101D, deltaCter). Cells were treated with 500 ng/ml doxycycline for 24 h in order to express the different FOXL2 forms. We used KGN transduced with WT FOXL2 without doxycycline induction as a control.Doxycycline-inducible FOXL2 cells were generated using the Lenti-X TetOne Inducible Expression System (Clonetech, 631844).

first: Mousseron

last: Ludovic

first: Chousianiti

last: Despoina

first: Poulat

last: Francis

first: Legois

last: Bérangère

first: Veitia

last: Reiner

first: Todeschini

last: Anne Laure


title: Reprogramming lineage features promotes epithelial behavior in carcinoma cells [ATAC-seq]

overall_design:
ATAC-seq in control H1155 cells, biological triplicates
ATAC-seq in chimera-expressing H1155 cells, biological triplicates

first: Terada

last: Lance


title: Maternal exposure to air pollution alters the postnatal metabolic response to ozone in peri-adolescent offspring.

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

institute: U.S. Environmental Protection Agency

summary: Exposure to environmental pollutants during key stages of development increases the risk of disease later in life. One such toxicant with growing evidence of this response is the air pollutant, ozone. Exposure to ozone during the implantation receptivity period in rats affects the metabolic status of offspring at adolescence, which may increase their susceptibility to subsequent environmental exposures. Herein, we studied the impacts of maternal ozone exposure on postnatal systemic responses to ozone in male and female offspring. Following peri-implantation ozone exposure (0.8 ppm for 4 hours/day on gestation days 5 and 6), offspring were exposed to ozone for 1 day/week on postnatal weeks 5–7. After the final exposure, metabolic effects were analyzed by circulating hormones and clinical chemistries, as well as hepatic lipid status and transcriptomic alterations. By and large, male offspring from ozone-exposed dams were more greatly impacted than those from air-exposed dams. This included increased hepatic lipid mobilization, increased circulating glucose, and a robust number of differentially expressed genes (2,348). Interestingly, many of these transcriptomic differences were attributed to maternal ozone exposure, with 1,741 of these genes sharing directional similarity with postnatally exposed air littermates. Females, on the other hand, reported minimal baseline effects of maternal ozone exposure (108). However, postnatal ozone exposure in female offspring substantially increased these differences to 947 genes. Collectively, this work supports the growing evidence that early pregnancy exposure to ozone alters the metabolic development of the offspring. Furthermore, postnatal exposure to environmental stressors reveals hepatic susceptibilities that are sexually dimorphic.

overall_design: Liver sections were collected from ~PND 48 offspring from dams exposed to either filtered air or 0.8ppm ozone at GD 5 and 6, then exposed postnatally to ozone through adolescence. Samples were sequenced using the Illumina NextSeq 500 platform.


title: RNA sequencing of HeLa cells with scramble control and CNOT11 knockdown

city: Onna

first: Saori

last: Nishijima

state: Okinawa

address: 1919-1 Tahncha

department: cell signal unit

institute: OIST

summary: HeLa cells were transfected with scramble siRNA or siRNA targeting the CCR4-NOT subunit CNOT11. After 72 hours, total RNA was extracted and subjected to polyA-selected RNA sequencing.

overall_design: Comparative transcriptome profiling of HeLa cells transfected with scramble siRNA versus CNOT11-siRNA to investigate transcriptional changes induced by CNOT11 knockdown.

first: Toru

last: Suzuki

first: Tadashi

last: Yamamoto


title: Functional anaylsis of IRF9 in the chicken innate antiviral immune response

city: University Park

first: Grace

last: Schmidt

state: PA

address: 323 AVBS Bldg

institute: Penn State University

summary: The chicken immune system is distinct from many mammalian models due to its reduced immune gene repertoire yet retained ability to mount a highly effective immune response. In mammals, interferon regulatory factor 9 (IRF9) is a key transcriptional regulator of the type I interferon pathway, stimulating the expression of hundreds of antiviral genes. Although IRF9 was previously thought to be absent in chickens, recent genomic reannotation suggests the presence of a putative IRF9 ortholog. To learn about the function of this gene in chickens, we utilized chicken embryonic fibroblast cell lines constitutively expressing clustered regularly interspaced short palindromic repeats interference (CRISPRi) to repress endogenous IRF9 gene expression. We induced an anti-viral immune response in IRF9 repressed cell lines by stimulation with double stranded RNA and analyzed the transcriptomes at 0 hours, 30 minutes, 1 hour and 6 hours post-stimulation. Transcriptomic analysis revealed that IRF9 repression resulted in the enrichment of pathways associated with regulating the innate anti-viral immune response, including the retinoic acid inducible gene I like (RIG-I like) receptor pathway and the Toll-like receptor pathway. Interestingly, suppressor of cytokine signaling 1 (SOCS1) and SOCS3, Major Histocompatibility Complex transactivator (CIITA) and tumor necrosis factor (TNF) receptor associated factor 2 (TRAF2) expression kinetics changed during the immune response as a result of IRF9 repression. Our preliminary findings provide a molecular basis to elucidate the functional role of IRF9 in the innate anti-viral immune response in chickens.

overall_design: Total RNA isolated from chicken DF1 (embryonic fibroblast) cells with wildtype and IRF9 knockdown phenotypes, stimulated with poly(I:C). Total RNA was collected at 0 hours, 30  minutes, 1 hour and 6 hours post poly(I:C) stimulation.

first: Tae Hyun

last: Kim


title: Systematic discovery of potential regulators of transcriptional variability reveals NAP1L1 as a transcriptional stabilizer in mouse ESCs [scRNA-seq]

city: Jerusalem

first: Tamar

last: Segal

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: Embryonic stem cells (ESCs) maintain their capacity to generate all different cell types of the developing embryo. When grown in serum, ESCs display transcriptional heterogeneity of several key pluripotency-related genes (e.g. Nanog). This transcriptional variability was suggested to support ESC pluripotency by enabling them to differentiate along different lineages simultaneously. We hypothesized that expression heterogeneity is a regulated process, mediated by transcriptional (de)stabilizers. To test this systematically, and to identify potential ESC regulators of transcriptional variability, we compared single-cell RNA-seq (scRNA-seq) with ChIP-seq datasets to identify variable and stable genes in ESCs. One of the potential ‘stabilizer’ proteins we identified is Nucleosome Assembly Protein 1-Like 1 (NAP1L1), a member of the NAP1 family. NAP1L1 participates in many cellular functions, including nucleosome maintenance, chromatin remodeling, cell division, and transcription. To test its potential ‘stabilizer’ function, we recruited NAP1L1 to the Nanog promoter via fusion with dCAS9. Immunofluorescence (IF) and single-molecule fluorescence in situ hybridization (smFISH) analyses of Nanog expression revealed that NAP1L1 directly stabilizes both RNA and protein expression levels. To further explore NAP1L1’s function genome-wide, we generated Nap1l1-knock-out (KO) ESCs. scRNA-seq experiments comparing Nap1l1-KO and WT ESCs, revealed increased gene expression variability in Nap1l1-KO cells. To reveal the potential mechanism by which NAP1L1 exerts its stabilizing activity we identified NAP1L1-interacting partners by co-IP followed by Mass-Spectrometry experiments, revealing DPPA3 as a key interacting partner. Taken together, we provide a systematic discovery platform for regulators of transcriptional variability and identify NAP1L1 as a transcriptional stabilizer in ESCs.

overall_design: To investigate transcriptional heterogeneity in WT and the two NAP1L1-KO ESC lines, we performed single-cell RNA sequencing (scRNA-seq) using the inDrop method (Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells, 2015).

first: Elad

last: Dvir

first: Xue

last: Sun

first: Oren

last: Ram

first: Eran

last: Meshorer


title: Tubulin hyperglutamylation causes retinal degeneration by impairing the structural integrity of cilia and protein mistrafficking

city: zhengzhou

first: Fang yuan

last: Zhen

state: henan

address: 河南省郑州市

institute: Sichuan Provincial People's Hospital

summary: Tubulins undergo various posttranslational modifications (PTMs) that confer diverse functions to microtubules. Tubulin polyglutamylation is dynamically regulated by glutamylation and deglutamylation. AGBL5 is a deglutamylase that specifically removes glutamate at the branching point. Mutations in AGBL5 in humans are associated with retinitis pigmentosa, but the underlying mechanism remains undefined. Here, we generated an Aglb5 knockout mouse that showed tubulin hyperglutamylation in photoreceptors, resulting in progressive retinal degeneration. RNA-seq analysis revealed the altered ciliary function in the Agbl5 knockout. Transmission electron microscopy indicated an impaired inner scaffold in the connecting cilium (CC). Consequently, phototransduction proteins were mislocalized or downregulated in mutant rod and cone photoreceptors. Disk membranes in photoreceptor outer segments were disorganized. Immunofluorescence revealed that the recruitment of IFT88, kinesin-II, and dynein-2 to the CC was affected, implicating defective intraflagellar transport (IFT). Collectively, these findings demonstrate that tubulin glutamylation homeostasis regulated by AGBL5 is critical for photoreceptor survival by maintaining the structural integrity of the CC and normal protein trafficking through IFT.

overall_design: This study utilizes an Agbl5 knockout mouse model to explore the gene’s function in retinal photoreceptors. The study includes a wild-type control group and an Agbl5 knockout experimental group. Key methods employed are RNA sequencing to analyze gene expression changes, transmission electron microscopy to assess ciliary structural integrity, and immunofluorescence to examine the recruitment of proteins involved in intraflagellar transport.

first: Tongdan

last: Zou

first: Ting

last: Wang

first: Fangyuan


title: Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma

city: Boston

first: Prathyusha

last: Konda

state: Massachusetts

address: 450 BROOKLINE AVENUE

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Renal cell carcinomas comprise multiple molecularly distinct cancers but most are treated empirically with therapies designed for clear cell RCC (ccRCC), the most common subtype, due to incomplete understanding of subtype-specific biology. We analyzed single-cell transcriptomes and chromatin accessibility profiles from translocation renal cell carcinoma (tRCC), an aggressive RCC defined by oncogenic TFE3 gene fusions.

overall_design: We performed single-nucleus RNA sequencing and single-nucleus ATAC sequencing on a cohort of translocation renal cell carcinoma tumors.

first: Srinivas

last: Viswanathan


title: Deficiency of pnkp in zebrafish causes microcephaly, seizures and developmental delay through mitochondrial dysfunction

city: wuhan

first: guihua

last: wang

address: hubei

institute: Huazhong University of Science and Technology

summary: Variants in the polynucleotide kinase-phosphatase (PNKP) gene leads to a severe neurological disease characterized by microcephaly, intractable seizures, and developmental delay (MCSZ). Despite its clinical impact, the underlying pathological mechanisms remain unclear. In this work, we utilized CRISPR/Cas9 technology to generate a zebrafish model with a pnkp knockout (pnkp-/-), overcoming limitations seen in prior mouse models that suffered from postpartum death. This zebrafish model faithfully recapitulated phenotypic traits observed in human PNKP deficiency, facilitating an in-depth exploration of the molecular mechanisms involved. The study revealed that pnkp deficiency disrupts mitochondria function, leading to mitochondrial apoptosis and inhibition of autophagy. Notably, the anti-seizure drug lamotrigine (LTG) demonstrated particularly promising efficacy in rescuing the hyperactive behavior. RNA-seq data analysis revealed downregulation of Gamma-aminobutyric acid (GABA) receptor-related gene, with the GABAA receptor agonist muscimol (MUSC) partially rescuing the hyperactive behavior in pnkp-/- zebrafish, suggesting potential link between GABAergic signaling and seizure. This work provides evidence supporting the role of damaged mitochondrial function, increased apoptosis and reduced autophagy as potential pathological mechanisms associated with PNKP variants. Furthermore, we propose this zebrafish-based model as a valuable platform for drug screening, holding promise for potential therapeutic interventions in MCSZ caused by PNKP variants.

overall_design: We conducted RNA-seq analysis using three biological replicates for both WT and pnkp-/- zebrafish. For each replicate, 30 fishes each replicate (5 dpf larvae) was dissected. The tail tissue was used for genotyping, and the heads of homozygote mutant were selected for RNA extraction. Total RNA of WT and pnkp-/- zebrafish heads was isolated and subsequently used for cDNA synthesis. Illumina sequencing, with library construction from Novogene (China), was used for the RNA-seq process.


title: Caspase-3 Control of RNA Splicing and Mitochondrial Dynamics in Microglia during Parkinson’s Disease [RNA-Seq]

city: Seville

first: Miguel

last: Burguillos

address: Antonio Maura Montaner

country: Spain

institute: IBiS-CSIC

summary: Caspase-3, a cysteine-aspartic protease canonically known for its role in apoptotic cell death, has been implicated in several non-apoptotic functions, particularly in microglia, the brain-resident macrophages. These novel functions appear to depend on distinct levels of caspase-3 activation; however, the role of basal caspase-3 activity remains unclear. Here, we show that basal caspase-3 regulates RNA splicing in microglia, and its inhibition in a Parkinson´s disease (PD) model leads to splicing dysregulation. Loss of basal caspase-3 activity also increases double-stranded RNA (dsRNA) accumulation, inducing a type I interferon response. Additionally, caspase-3 deficiency impairs mitochondrial respiration, reduces ATP production, and causes sex-specific mitochondrial abnormalities, predominantly in female microglia. Together, our findings uncover a non-apoptotic, homeostatic role for basal caspase-3 activity in microglia. Its disruption, such as in PD, may drive key molecular features of neuroinflammation and neurodegeneration, positioning caspase-3 as a critical regulator of microglial function in health and disease.

overall_design:
RAN-seq profiling of wildtype primary microglia origianted from postnatal day 1 to  postnatal day 4 BALB/c mice treated with vehicle or 40 uM Caspase-3/7 Inhibitor I (Cayman Chemical; Cat# 14464) for two hours.
RAN-seq profiling of wildtype primary microglia origianted from postnatal day 1 to  postnatal day 4 BALB/c mice treated with vehicle or 20 uM DEVDfmk (MedChemExpress; Cat# HY-12466)  for two hours.

first: Rafael

last: Medina-Guzman

first: Bazhena

last: Bahatyrevich-Kharitonik

first: Marie-Kim

last: St-Pierre

first: Sara

last: Marquéz-Perez

first: Elena

last: Gavilán

first: Alicia

last: Flores-Cortes

first: Cristóbal

last: Coronel-Guisado

first: Rodrigo

last: García-Valiente

first: Sandro

last: Argüelles

first: Edel

last: Kavanagh

first: Yiyi

last: Yang

first: Tomas

last: Deierborg

first: José

last: Venero

first: Cristina

last: González-Aguilera

first: Bertrand

last: Joseph


title: A TROP2-targeting ADC synergizes with oxidative phosphorylation inhibitor to enhance apoptosis in ESCC by suppressing the PI3K-AKT-mTOR signaling pathway

city: Ganzhou

first: zhou

last: dongdong

address: hexie avenue

institute: Gannan Medical University

summary: Currently, there are no effective targeted therapies for advanced esophageal squamous cell carcinoma (ESCC). Trophoblast cell surface antigen-2 (TROP2) are considered robust therapeutic targets which leverages antibody-drug conjugates (ADCs) to control solid tumors. Mitochondrial oxidative phosphorylation (OXPHOS) influences the growth of cancer cells, metastasis and drug resistance. However, whether inhibiting OXPHOS can potentiate the efficacy of TROP2-targeting ADCs is not well understood. Here, we investigated the therapeutic efficacy of IMMU132 (IMMU), an ADC targeting TROP2, either alone or in combination with IACS010759 (IACS), a selective OXPHOS inhibitor, through clinically ESCC models. Immunohistochemical analysis was performed on a cohort of 222 patients, which revealed that 94.6% of all specimens tested positive for TROP2. Among them, moderate and strong staining were observed in 29.3% and 27.0% of cases, respectively. Co-administration of IMMU and IACS synergistically inhibited the growth of tumors in human ESCC cell lines, PDXO and PDX models. Mechanistically, we found that the combination treatment achieved tumor suppression in ESCC cells via inducing apoptosis and oxidative stress, as well as preventing cell motility. Results of the RNA-seq analysis demonstrated that the combined treatment of IMMU and IACS downregulated the expression level of several cancer-related pathways, such as the PI3K-AKT-mTOR pathway, OXPHOS and apoptosis. Moreover, the data confirmed that inhibition of the PI3K-AKT-mTOR pathway significantly suppressed ESCC tumor growth following administration of the combination therapy. Based on these findings, we present a novel therapeutic strategy that enhances the efficacy of TROP2-targeting ADCs via concurrent inhibition of OXPHOS, which is likely to improve clinical outcomes of patients with TROP2-positive ESCC.

overall_design: In this study, we aimed to systematically explore the feasibility of combining TROP2-targeting ADC (IMMU) and OXPHOS inhibitor (IACS) to treat patients with advanced ESCC. The data uncovered that the combination of IMMU and IACS synergistically induced apoptosis in vitro in TROP2-positive ESCC cells. It also inhibited the growth of ESCC organoids ex vivo and PDX tumors in vivo. Further analysis RNA-seq confirmed that the combination suppressed the ESCC growth by targeting the PI3K-AKT-mTOR signaling pathway. In summary, these findings provide robust preclinical evidence to support the therapeutic benefits of OXPHOS inhibitors in potentiating the efficacy of TROP2-targeting ADCs in patients with ESCC.

first: Xinxin

last: Liu

first: Jie

first: Yi’an

last: Zhou

first: Mei

last: Li


title: Caspase-3 Control of RNA Splicing and Mitochondrial Dynamics in Microglia during Parkinson’s Disease

first: Miguel

last: Burguillos

overall_design: 24 samples in total; 3 biological replicates per treatment. Groups include microglia isolated from the sustantia nigra using cd11b beads (Miltenyi) from male/female, caspase-3flox/ caspase-3floxcx3cr1 mice treated with saline or MPTP for 96h. All animales were treated with tamoxifen to induce teh recombinase activity in the caspase-3flox/ caspase-3floxcx3cr1 mice.

first: Rafael

last: Medina-Guzman

first: Bazhena

last: Bahatyrevich-Kharitonik

first: Marie-Kim

last: St-Pierre

first: Sara

middle: Ã


title: Il1b signaling in mouse gastric stromal cells

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

institute: Charité Universitätsmedizin

summary: IL-1b is a proinflammatory cytokine which is involved in gastric diseases development. Stromal cells are known to respond to pro-inflammatory stimuli, and they express the IL-1b receptor IL1r1. We therefore wanted to investigate which genes are regulated upon IL-1b signaling activation in stromal cells.

overall_design: Stromal stomach cells from mice were treated with or without Il1beta in two independent biological replicates.

first: Giulia

last: Beccaceci

first: Sigal

last: Michael

first: Mollenkopf

last: Hans

first: Berger

last: Hilmar


title: Transcriptional control of Sulf1 by WT1 primes epicardial signalling and fate by modifying extracellular heparan sulfate status [CUT&Run]

city: Oxford

first: Andia

middle: Nicole

last: Redpath

address: IDRM IMS-Tetsuya Nakamura Building, Roosevelt Dr, Headington

country: United Kingdom

institute: University of Oxford

summary: Considering the transcriptional correlations we observed between WT1 and 6-O-endosulfatases in the epicardium, we sought to elucidate whether WT1 regulates 6-O-endosulfatase expression directly and how its binding may differ between Sulf1 and Sulf2 in the epicardium.  We employed CUT&RUN-seq experiments that mapped genome-wide binding sites of WT1 and histone modifications in cultured epicardial cells (MEC1). We identified weak, although variable, binding of WT1 to the Sulf1 promoter and significant WT1 binding to an intronic enhancer, marked by active chromatin modification H3K27ac, located in intron 1 of the Sulf1 gene. Interestingly, the CUT&RUN-seq experiments also revealed significant binding of WT1 to the third intron of the Sulf2 gene, displaying chromatin accessibility without any histone marks or gene activity.

overall_design: CUT&RUN-seq of MEC1 epicardial cells.

first: Nicola

last: Smart


title: Transcriptional control of Sulf1 by WT1 primes epicardial signalling and fate by modifying extracellular heparan sulfate status [scRNA-Seq]

summary: Despite their decisive influence over the signalling that underlies cardiac morphogenesis, the expression of core HSPGs and the enzymes that give rise to distinct spatiotemporal sulfation patterning have not been well documented in the developing heart. In the present study, we systematically profiled 6-O-endosulfatases and target HSPGs expression in the embryonic mouse heart. We found that HSPGs are dynamically expressed, with cell-type specific expression, and changing tissue composition contributing to HSPG diversity in the developing embryonic heart. We identified cell type-specific expression patterns for Sulf1 and Sulf2, that changed over the course of development, unrelated to lineage or embryonic origin. We reveal Sulf1 as the major 6-O-endosulfatase expressed in the epicardium.

overall_design: A whole embryonic heart was isolated from Rosa26tdTomato;Wt1CreERT2/+ embryo at E17.5, to define the transcriptional profile of all cardiac cells, including epicardial lineage cells (tdTomato labelled) at that developmental stage. Epicardial lineage labelling was achieved in embryos by administering tamoxifen to pregnant females by oral gavage at E9.5 and E11.5. Single-cell RNA sequencing was performed using the Chromium Single Cell 3' Reagent Kit (v3 chemistry, 10x Genomics). Libraries were sequenced in three runs on the Illumina NextSeq 500 platform using the NextSeq® 500/550 High Output Kit v2 (150 cycles, Illumina), generating 400 million reads, with a target of 8,000 cells per sample. Sequencing reads were processed with CellRanger (10x Genomics).


title: SPLEVs, a new therapeutic modality for cytokine storm syndromes

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

summary: Since cytokine storm syndromes such as sepsis, acute respiratory distress syndrome (ARDS) and coagulopathy, including those seen in COVID-19, are fatal, development of highly effective therapeutics is urgently needed. We previously reported that the hydrolysis of extracellular vesicles (EVs) by secreted phospholipase A2 (sPLA2) leads to production of immunomodulatory lipid mediators in lymphoproliferative diseases. We aimed to apply this phenomenon technically using sPLA2-reacted EVs — here in designated as “SPLEVs”, which showed high therapeutic efficacies against various disease. Mechanistically, SPLEVs bind to type II alveolar epithelial cells and elicit “lipid counterstorm”, drastically increasing the production of tissue-protective and anti-inflammatory lipid mediators through the phosphoinositide 3-kinase and sterol regulatory element-binding protein 1 pathways. And these effects showed an important role of PG in hep-EVs, and Lyso-PG hydrolyzed by sPLA2 was involved in the regulation of inflammation. Also, hep-SPLEVs injection showed increased lipid mediators and anti-inflammatory effects in inflammatory diseases other than ARDS, prolonged survival and reduced tissue damage. Thus, SPLEVs are expected to be an effective therapeutic tool for treatment of broad ranges of inflammatory diseases including COVID-19 and other new pandemic diseases.

overall_design: Each mouse was anesthetized with isoflurane and the abdomen was opened. The apical 1/3 of the cecum was ligated with silk thread and punctured with a 21G needle (CLP; cecum pancture and ligation). Then closed, kept warm at 38°C. Two hours after recovery, each mouse received 100 μL each of EVs (30 μg), SPLEVs (30 μg), and PBS from tail vein. Ten days after the operation, the mice was dissected and the spleen removed.

first: Shunya

last: Nakayama

first: Akane

last: Kanamori

first: Takeshi

last: Kamakura

first: Ai

last: Kotani


title: Matrix Stiffness-Sensitive LDHA Drives Autophagy of Pancreatic Ductal Adenocarcinoma via Lactate-Induced FOXO3 Expression and Lactylation

city: Shanghai

first: Tiancheng

last: Gong

address: No. 366 Longchuan North Road, Xuhui District, Shanghai

institute: Shanghai Xuhui Central Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC), a highly aggressive tumor within the digestive system, is characterized by the high stiffness of the extracellular matrix (ECM), which has fundamental influences on biological processes and malignant phenotypes of PDAC. Autophagy, as a key process of PDAC, significantly accelerates malignant progression and ultimately leads to adverse prognosis. Consequently, it is crucial to comprehend the underlying mechanisms of the interplay between matrix stiffness and PDAC autophagy. To serve the intent, Polyacrylamide (PA) hydrogels with adjustable stiffness were utilized to cultivate MIA PaCa-2 and PANC-1 cells. The outcomes established that high stiffness induced lactate production via the activation of lactate dehydrogenase A (LDHA), resulting in the upregulation of transcription factor FOXO3 and subsequent induction of autophagy. Interestingly, in vivo experiments, the MIA PaCa-2 cells educated by stiff PA hydrogels exhibited not only higher tumorigenicity, but also persistent phenotype maintenance and gene expression, which implied the potential epigenetic modulation of matrix stiffness. Through DeepKla analysis, Co-Immunoprecipitation (Co-IP) and Western Blot (WB), we identified that matrix stiffness drives FOXO3 lysine lactylation (Kla) modification by promoting LDHA-dependent lactate production, thereby sustaining the persistent activation of autophagy. In conclusion, we revealed the key role of matrix stiffness in lactate metabolism, lactylation modification and autophagy activation of PDAC, offering both foundational theory and potential therapeutic targets for precision medicine in PDAC.

overall_design: Pancreatic Ductal Adenocarcinoma cell lines (MIA  PaCa-2) cultured respectively on the Polyacrylamide hydrogels with low (2.55 kPa) and high (40.40 kPa) stiffness for 5 days were prepared for RNA-seq analysis

first: Yidan

last: Ma

first: Shulong

last: Zhang

first: Qi

last: Han

first: Yuanzhi


title: Epithelial BMP signaling regulates gastric tissue responses upon H. pylori infection

first: Michael

summary: In the gastric mucosa, BMP signaling is known to regulate the differentiation of progenitor epithelial cells into differentiated pit secretory mucous cells thanks to BMP ligands production in stromal cells located at the gland pit and to BMP antagonists secretion at the gland base. Upon Helicobacter pylori infection there is an alteration of ligands and antagonists production which ultimately results in BMP signaling downregulation in the gastric epithelium. We investigate the correlation of BMP signaling downregulation with the development of hyperplasia and inflammation exploiting a conditional mouse model that allows the inhibition of BMP signaling in gastric glands via Axin2CreErt2:Bmpr1a fl/fl.

overall_design: Stomach cells from Bmpr1a KO mice were compared to WT mice in two independent biological replicates.


title: Il1r1 signaling induces stromal cells reprogramming upon H. pylori infection

summary: Helicobacter pylori infection leads to influx of immune cells in the gastric mucosa, causing chronic inflammation. Since the mesenchymal niche is known to play a crucial role in the development of infection-associated gastric pathology, we investigate how stromal cells respond to inflammatory triggers, founding that they respond to Il1b and promote epithelial regeneration. To characterize the function of Il1 signaling in stromal cells, we exploit a conditional mouse model that allows the knockout of Il1r1 receptor in the gastric mesenchyme via Col1a2CreErt2:Il1r1 fl/fl.

overall_design: Stomach cells from Il1r1 KO mice were compared to WT mice in two independent biological replicates.

first: Giulia


title: Transcriptional control of Sulf1 by WT1 primes epicardial signalling and fate by modifying extracellular heparan sulfate status [ATAC-Seq]

summary: Considering the transcriptional correlations we observed between WT1 and 6-O-endosulfatases in the epicardium, we sought to elucidate whether WT1 regulates 6-O-endosulfatase expression directly and how its binding may differ between Sulf1 and Sulf2 in the epicardium.  We first assessed the landscape of chromatin accessibility in FACS sorted epicardial cells at E13.5 (CD31-tdTomato+PDPN+), and employed TOBIAS footprinting to identify candidate WT1 binding sites in the Sulf1 and Sulf2 loci. This analysis predicted WT1 binding to the highly accessible Sulf1 promoter but no binding was predicted for Sulf2. As expected, there was lower accessibility in this locus which reflected reduced Sulf2 gene activity in the epicardial layer.

overall_design: Whole embryonic hearts were isolated from Rosa26tdTomato;Wt1CreERT2/+ embryos at E12.5 and E13.5, to define the chromatin landscape in FACS sorted epicardial cells (tdTomato labelled) at those developmental stages using bulk ATAC-seq. Epicardial lineage labelling was achieved in embryos by administering tamoxifen to pregnant females by oral gavage at E9.5. Live epicardial cells (CD31-tdTomato+PDPN+) isolated by FACS were subjected to the ATAC-seq protocol as previously described.


title: The impact of TRF2 deletion on gene expression profile of muscle stem cells

city: Philadelphia

first: Ji-Hyung

last: Lee

state: Pennsylvania

address: 3450 Hamilton Walk, Stemmler Hall

department: Department of Orthopaedic surgery

institute: University of Pennsylvania

summary: Telomeric proteins are present in all mammalian cells protecting chromosomal ends and ensuring organismal homeostasis. However, it was also suggested that they have additional roles in certain tissues. Muscle stem cells (MuSCs), expressing a pivotal transcription factor Pax7, are fundamental to preserve regenerative capacity of muscle tissue. Yet, the cell autonomous mechanism that regulates Pax7 expression to maintain MuSC identity is unclear. Here, we uncover that the telomeric protein TRF2 is critical to sustain stem cell identity in adult muscles and is dynamically regulated upon injury. MuSC-specific TRF2 ablation in mice aggravates muscular dystrophy, mimicking closely the severity of the human disease. Mechanistically, TRF2 directly binds to the regulatory regions of Pax7 gene and affects its expression. These findings identify a unique non-telomeric TRF2 function essential for transcribing Pax7 gene, a master stem cell regulator of the myogenic lineage, to modulate cellular properties indispensable for stem cell maintenance.

overall_design: To investigate the role of TRF2 in muscle stem cell function, we generated muscle stem cell specific TRF2 knockout mice. Muscle stem cells were FACs-isolated from control and TRF2 deleted skeletal muscles of uninjured and 3 days post-injured mice. 4 biological replicates per groups (total 16 samples) were subjected to RNA-seq. Gene expression profiles of control and TRF2-deleted muscle stem cells were analyzed.

first: Ji-hyung

first: Ryan

middle: P

last: Calhoun

first: Patrick

last: Seale

first: Foteini

last: Mourkioti


title: Changes in sites of open chromatin in muscle stem cells that occur upon knockout of TRF2

city: Madison

first: Jeffrey

last: Dilworth

email: jdilworth@ohri.ca, fdilworth@wisc.edu

state: WI

address: 1111 Highland Ave - WIMR II 4518

department: Cell and Regenerative Biology

institute: University of Wisconsin - Madison

overall_design: To investigate the role of TRF2 in muscle stem cell function, we generated muscle stem cell specific TRF2 knockout mice. Muscle stem cells were FACs-isolated from skeletal muscles of uninjured mice. Two biological replicates per groups (total 4 samples) were subjected to ATAC-Seq analysis. ATAC-Seq profiles of control and TRF2-deleted muscle stem cells were analyzed.

first: Sarah

last: Hachmer

first: Eric

last: Arezza


title: Effect of the depletion of YAP1 in adult spinal cord neural stem cells

city: montpellier

first: Jean-Philippe

last: Hugnot

address: 141 rue de la Cardonille

institute: Institut de génomique fonctionnelle

summary: Mouse spinal cord neural stem cells are know to be multipotent in vitro but mainly produce astrocytes in vivo. RNA sequencing and proteomic analysis showed that neural stem cells downregulate the Hippo/YAP1 pathway during OPC formation. To understand the implication of YAP1 in the oligodendrogliogenesis, we used transgenic cells expressing a truncated form of YAP1 and analyzed their mRNA expression in proliferation and differentiation

overall_design: To investigate the effect of YAP1, we use a transgenic mouse model YAP1 KO were the exon3 can be deleted under the cre recombinase. RNA sequencing were realized on cells maintained in proliferative condition or during differentiation

first: Sandra

last: Joppe

first: Robert

last: Chevreau


title: Increasing TET expression and 5-hydroxymethylcytosine formation by a carbocyclic 5-aza-2’-deoxy-cytidine antimetabolite [RNA-seq]

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

institute: Saarland University

summary: Ten-eleven translocation (TET) enzymes are critical epigenetic regulators, which oxidize the methylated cytosine nucleobase 5-methyl-dC (5mdC) in the genome to 5-hydroxymethyl-dC (5hmdC) in an α-ketoglutarate-dependent manner. Because the presence of 5mdC in the promoter region of a given gene silences its expression, this oxidation goes in hand with the reactivation of such silenced genes. In different highly aggressive cancers such as acute myeloid leukemia (AML) and glioblastoma, loss of TET enzyme function and therefore reduced 5hmdC levels pave the way for tumor development. Impairment of TET activity can occur through metabolic inhibition, through loss-of-function mutations in TET genes themselves, and finally through suppression of TET-expression via epigenetic silencing. Reactivation of TET enzyme expression represents a major aim of epigenetic cancer therapy. Here we show that the carbocyclic antimetabolite 5-aza-2’deoxycytidine (cAzadC), which is supposed to suppress the methylation of DNA during replication, leads to a substantial increase of TET2 expression and strongly increasing 5hmdC levels. We show that the treatment with cAzadC goes in hand with the broad reactivation of the cellular anti-tumor responses. With patient-derived xenograft AML-mouse models, we show that this translates into a strongly improved anti-cancer effect in vivo.

overall_design: MOLM-13 cell line was treated with 5-Aza-2’-deoxycytidine (0.5uM) or with carbocyclic AzadC derivative (0.5uM). Cells treated with DMSO only were used as a control. All treatments were performed in triplicates.

first: Maike

last: Däther

first: Elsa

last: Peev

first: Annika

last: Fröhlich

first: Binje

last: Vick

first: Sogol

last: Fatourechi

first: Matthias

last: Heiss

first: Corinna

last: Pleintinger

first: Emmanuel

last: Bisong

first: Hans

last: Hurmitz

first: Davide

last: Guglielminotti

first: Yasmin

middle: V

last: Gärtner

first: Tina

last: Aumer

first: Kartsen

last: Spiekermann

first: Jörn

last: Walter

first: Irmela

last: Jeremias

first: Franziska

last: Traube

first: Thomas

last: Carell