title: Menstrual Fluid-Derived Small Extracellular Vesicles: A Novel Reservoir with Distinct Molecular Signatures and Implications for Endometriosis Etiopathology

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

summary: STUDY QUESTION: Can the transcriptomic profile of small extracellular vesicles (sEV) derived from menstrual fluid (MF) provide insight into their potential roles as biomarkers and mediators in endometriosis (EM) development? SUMMARY ANSWER: MF-derived sEV from EM patients display altered molecular signatures reflective of EM pathophysiology and exhibit enhanced proangiogenic activity in vitro. WHAT IS KNOWN ALREADY: EM is a chronic gynecological disorder affecting approximately 10% of reproductive-age women, associated with pain, infertility, and delayed diagnosis. Small extracellular vesicles carry cargo that resembles their cellular origin, making them promising biomarkers for various diseases. While sEV have previously been isolated from MF and their protein content analyzed, their transcriptomic profile and angiogenic potential remain unexplored. STUDY DESIGN, SIZE, DURATION: The two cross-sectional study involved cohorts of nulliparous (n = 10) and multiparous (n = 12) women, EM (n = 10) and control (n = 11) patients, recruited at the Obstetrics and Gynecology Unit of Clínica Universidad de los Andes, Santiago, Chile. Peripheral blood was collected by a trained midwife and MF was self-collected using a menstrual cup on the second day of menses. PARTICIPANTS/MATERIALS, SETTING, METHODS: sEV were isolated from the plasma fraction of MF and from peripheral blood plasma. Nanoparticle tracking analysis, transmission electron microscopy, and FACS were used to assess sEV concentration, size, morphology, and tetraspanin expression. Next-generation sequencing was performed to analyze sEV transcriptomic profiles, and proangiogenic function was assessed through endothelial tubule formation assays using human umbilical vein endothelial cells (HUVECs). MAIN RESULTS AND THE ROLE OF CHANCE: MF-sEV exhibited canonical sEV characteristics and were significantly more abundant than those isolated from peripheral blood (P = 0.008). Neither parity nor disease affected MF-sEV concentration or size; however, CD63 expression was significantly reduced in sEV from nulliparous women and EM patients (P =0.02). Transcriptomic analysis revealed unique mRNAs and long noncoding RNAs (lncRNAs) signatures that reflect their contribution to disease etiopathology. Functionally, EM-derived sEV, significantly enhanced tubule formation in vitro (P < 0.05), supporting their proangiogenic role in EM. LARGE SCALE DATA: Raw sequencing data has been submitted to GEO. LIMITATIONS, REASONS FOR CAUTION: While sample size was sufficient for initial characterization and the in vitro validation, larger cohorts and in vivo studies are necessary to confirm these findings and clarify the molecular mechanisms underlying sEV proangiogenic effects. WIDER IMPLICATIONS OF THE FINDINGS: The non-invasive isolation and disease-associated transcriptomic signatures of MF-sEV highlights their potential as biomarkers for EM. The current gold-standard for EM diagnosis is invasive laparoscopic surgery, resulting in delayed identification and staging of the disease. The proangiogenic effect of MF-sEV observed in vitro suggest that their cargo may offer relevant insights into disease progression and response to treatment. These findings are in line with a recent report that explored the proteome of MF-sEV from EM patients, demonstrating their involvement in mesothelial barrier disruption, which reinforces the role of MF-sEV in EM progression.

overall_design: RNA was isolated from menstrual fluid plasma-derived sEV using TRIzol LS (Invitrogen, USA) on a 60 uL sEV sample volume. RNA concentration was assessed with a NanoDrop One (Thermo Fisher Scientific, USA). A minimum of 250 ng RNA was used for RNA sequencing (RNA-Seq). RNA-Seq was performed by Azenta Life Sciences (South Plainfield, NJ, USA). Briefly, library preparation was performed without rRNA depletion, and sequencing was carried out on an Illumina next generation sequencing platform with paired-end 150 bp reads. DESeq2 (Love et al. 2014) normalized counts were used for downstream analyses. Genes with a log2(Fold Change) ≥ 0.5 and a -log10(p value) ≥ 1.301 were considered differentially enriched (DE) in sEV. Data analysis was conducted using R (v4.2.3) (Team 2023), and graphs and heatmaps were generated using ggplot2 (v3.4.4) (Wickham 2016) package. Gene Ontology (GO) enrichment analysis was performed using the clusterProfiler (v4.6.2) (Yu et al. 2012) package.

first: Vicente

last: Peragallo-Papic

first: Paz

last: Cerda-Castro

first: Aliosha

last: I Figueroa-Valdés

first: Hugo

last: E Tobar

first: Patricia

last: Valdebenito

first: Manuel

last: B Donoso

first: Benjamín

last: Bustos

first: Javiera

last: Yakcich

first: Reyna

last: Peñailillo

first: Stephanie

last: Acuña-Gallardo

first: Sebastián

last: E Illanes

first: Francisca

last: Alcayaga-Miranda

first: Lara

last: J Monteiro


title: MicroRNA Differential Expression Analysis for Identification of Diagnostic Biomarkers for Canine Visceral Hemangiosarcoma

status: Public on Apr 08 2026

city: West Lafayette

first: Andrea

last: Pires dos Santos

address: 625 Harrison St.

country: USA

institute: Purdue University

type: Non-coding RNA profiling by high throughput sequencing

summary: Canine visceral hemangiosarcoma (HSA) is a highly aggressive malignancy of endothelial cells    with a poor prognosis and limited diagnostic tools. MicroRNAs (miRNAs) are small non-coding RNAs with emerging utility as diagnostic and prognostic biomarkers due to their stability and disease-specific expression profiles. This study aimed to identify and validate miRNA biomarkers for canine splenic and cardiac HSA using small RNA sequencing and quantitative PCR. Formalin-fixed, paraffin-embedded (FFPE) tissues were analyzed from 24 dogs with histologically confirmed HSA (18 splenic, 6 cardiac) and six non-neoplastic controls  (six cardiac and six splenic). A total of 67 and 71 miRNAs were differentially expressed (DE) in splenic and cardiac HSA, respectively, with 18 miRNAs shared between both tumor types. Forty candidate diagnostic miRNAs were selected for validation by RT-qPCR using customized panels. Thirteen miRNAs were validated as DE in each tissue type, showing strong concordance with sequencing results. Pathway enrichment analysis of validated miRNAs revealed significant involvement in oncogenic signaling pathways, including the PI3K-Akt, MAPK, HIF-1, and Ras  pathways. These results highlight miRNA signatures with potential diagnostic relevance in visceral HSA and support their utility as biomarkers in archival tissues, with possible future application to liquid biopsy approaches.

overall_design: Small RNAseq of dog cardiac and splenic formalin-fixed, paraffin-embedded tissues with visceral hemangiosarcoma and control counterparts from healthy animals.

first: Laura

last: Machado Ribas

first: Luis

last: Neves dos Santos

first: Kerstin

last: Muner

first: Francisco

last: Conrado

first: Elizabeth

last: Rozanski


title: A conserved enhancer cluster controls efnb2 expression in the vertebrate dorsal retina [ATAC-Seq-Aa]

city: Baton Rouge

last: Schneider

state: Louisiana

address: LSU 131 Life Sciences Building

department: Biological Sciences

institute: Louisiana State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The vertebrate retina is patterned along its dorsal-ventral (DV) axis by signaling centers that provide each domain with distinct molecular and functional properties, including differential photoreceptor composition and opsin expression. Although the key DV patterning genes are well studied, the cisregulatory mechanisms that establish and maintain these territories remain poorly understood. To explore this regulatory landscape, we turned to the four-eyed fish Anableps anableps, whose large, protruding eyes and expanded ventral retina facilitate precise dissection of dorsal and ventral halves for spatially resolved genomics. Bulk RNA-seq of the Anableps dorsal and ventral retina regions recovered canonical DV markers, while bulk ATAC-seq revealed dorsally enriched ATAC-seq peaks residing within a low-genedensity region between efnb2a and gtpbp8. These putative cis-regulatory elements located to a 29 kb interval forming a contiguous enhancer cluster. Via Hi-C analysis, we identified a topologically associating domain (TAD) encompassing efnb2a, gtpbp8, and slc10a2, with a dorsal-enriched chromatin contact linking the enhancer cluster to the efnb2a promoter. Comparative genomics showed that this architecture is deeply conserved: the efnb2-slc10a2 synteny and TAD boundaries are maintained from human to zebrafish. To enable functional testing of this long regulatory interval, we strategically turned to Tetraodon nigroviridis, a species with one of the most compact vertebrate genomes, allowing nearly the entire orthologous enhancer cluster (~13 kb) to be cloned intact. Transgenic assays in both zebrafish and mouse demonstrated that this Tetraodon enhancer cluster drives dorsal retina-specific eGFP expression, underscoring the deep conservation of its regulatory function across vast phylogenetic distances. Together, these results highlight how a multi-species approach leveraging complementary strengths of model and non-model organisms can illuminate ancient regulatory mechanisms underlying vertebrate eye patterning.

overall_design: ATAC-Seq profiling of Anableps anableps dorsal and ventral retina.

first: Lina

last: Shi

first: Louise

last: Perez

first: Gabriela

last: Lima

first: Josane

middle: F

last: Sousa

first: Zhuoxin

last: Chen

first: Dorota

last: Skowronska-Krawczyk

first: Evgeny

last: Kvon

first: Igor


title: Inhibiting Glycan Degradation Prevents HIV-Induced Inflammaging and Cognitive Impairment

city: New York

first: Alejandra

last: Borjabad

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

type: Expression profiling by high throughput sequencing

summary: Cognitive impairment is a frequent outcome of chronic viral infections linked to premature aging, including HIV. The mechanisms underlying this decline remain poorly understood. Here, we identify pro-inflammatory glycan degradation, characterized by loss of sialic acid and galactose, alterations that are hallmarks of premature aging, as key contributors to HIV-associated cognitive impairment (HIV-CI). In two independent cohorts of people living with HIV, these degradative changes were enriched in individuals with cognitive impairment, particularly women, and correlated with worse neurocognitive performance. In both a humanized mouse model of HIV and Eco-HIV, a complementary model that allows behavioral testing, pharmacological inhibition of glycan degradation with sialidase inhibitors prevented virally induced inflammation, immune activation, accelerated aging, and memory deficits. These findings implicate glycan degradation as a contributor to inflammation and neurocognitive impairment in HIV and highlight glycan-preserving therapies as a promising strategy to mitigate inflammation, premature aging, and cognitive decline during viral infections.

overall_design: RNAseq profiling of brain tissue of mice infecteced with EcoHIV or uninfected controls and treated or not with sialidase inhibitors.

first: Leila

middle: B

last: Giron

first: Mohamed

last: Abdel Mohsen

first: David

middle: J

last: Volsky


title: Looking up: eye remodeling supports aerial vision in the four-eyed fish Anableps anableps

first: Patricia

summary: The four-eyed fish Anableps anableps exhibits a unique visual system adapted for simultaneous aerial and aquatic vision, making it an exceptional model for investigating evolutionary innovations in vertebrate eye development. This dual vision capability is supported by specialized adaptations to the eye, including a thicker dorsal (aerial) cornea and asymmetric expression of visual opsins: opn1mw1 in the ventral retina, and opn1lw1 in the dorsal retina. To investigate the molecular and spatial basis of this asymmetry, we used single-nucleus RNA sequencing (snRNAseq) of the retina in combination with spatial transcriptomics of the whole eye. Our findings reveal that the asymmetric opsin distribution results from a developmental expansion of the ventral retina, which is adapted for detecting aerial light, alongside a reduction in the dorsal retinal domain responsible for aquatic vision. These results highlight a novel mechanism of regional specialization in the vertebrate retina and provide insights into the evolutionary innovations in the vertebrate visual system.

overall_design: Spatial transcriptomics of the adult Fundulus heteroclitus eye using Visium Spatial Transcriptomics technology (10x Genomics).

last: N. Perez

last: de Freitas Sousa


title: Therapeutic Synergy Overcomes Carboplatin Resistance in Triple-Negative Breast Cancer [bulk RNA-seq]

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: Background: Triple-negative breast cancer (TNBC) is an aggressive subtype lacking targeted therapeutic options, where platinum-based chemotherapy such as carboplatin serves as a cornerstone of treatment. Despite initial responses, the rapid emergence of acquired resistance remains a major clinical barrier. Understanding the molecular adaptations that drive platinum resistance is essential to develop strategies to restore sensitivity and identify alternative vulnerabilities. Methods: We generated four isogenic patient-derived xenograft (PDX) pairs (WHIM30, BCM‑2147, BCM‑3887, BCM‑7482) through serial carboplatin exposure to model acquired resistance in TNBC. Bulk RNA sequencing, immunohistochemistry, and histopathological analyses were performed to define transcriptomic and phenotypic changes associated with resistance. Synergistic therapeutic combinations were identified using high-throughput drug screening in carboplatin-resistant (CR) PDX-derived models, followed by in vivo validation in NSG mice. Tumor growth and survival were assessed using mixed-effects modeling, two-way ANOVA, and Welch’s student t-test. Results: The resulting isogenic PDX pairs captured both convergent and model-specific adaptations to carboplatin. CR tumors demonstrated heterogeneous activation of DNA damage repair pathways, including restoration of BRCA1-dependent homologous recombination (BCM‑2147, WHIM30) and compensatory upregulation of mismatch repair (BCM‑3887). In the BRCA1-mutant BCM‑7482 model, resistance correlated with HORMAD1 upregulation, suggesting an alternative HRD-associated mechanism. Morphologically, BCM‑7482CR tumors exhibited a significant increase in nuclear size compared to their sensitive counterpart (p < 0.0001). Drug screening identified mTOR pathway inhibition as a recurrent vulnerability across CR models. Sacituzumab govitecan (SG) combined with Everolimus produced robust synergy in vitro and superior tumor control in vivo compared to single agents in both WHIM30CR and BCM‑2147CR. A second combination, Everolimus + Selinexor (KPT‑330), also reduced tumor burden, achieving statistical significance in an expanded WHIM30CR cohort and suppressing metastatic progression in the intrinsically resistant WHIM2 model. Conclusions: Isogenic PDX models of TNBC provide a powerful platform to define molecular mechanisms of acquired carboplatin resistance and uncover actionable therapeutic strategies. Our findings reveal multiple adaptive routes to platinum resistance, including restoration of homologous recombination and activation of alternative DNA repair programs. Synergistic interactions between SG and mTOR inhibition offer a promising avenue for overcoming resistance, supporting further clinical investigation of these combinations in TNBC.

overall_design: Bulk RNA sequencing was performed on matched carboplatin-resistant (CR) and carboplatin-sensitive (CS) tumors from four TNBC PDX models (WHIM30, BCM-2147, BCM-3887, BCM-7482) to identify gene expression changes associated with acquired carboplatin resistance.

first: Julia

middle: E

last: Altman

first: Emily

middle: K

last: Zboril

first: Aaron

last: Valentine

first: Nina

last: Dashti-Gibson

middle: C

last: Boyd

first: Rachel

last: Myrick

first: Amy

middle: L

last: Olex

first: Mikhail

middle: G

last: Dozmorov

first: Joshua

last: Harrell


title: Therapeutic Synergy Overcomes Carboplatin Resistance in Triple-Negative Breast Cancer [scRNA-seq]

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on matched carboplatin-resistant (CR) and carboplatin-sensitive (CS) tumors generated from BCM-3887 TNBC PDX model


title: NAT10-Dependent N4-acetylcytidine (ac4C) on R-loops Drive Glioblastoma Tumorigenesis and Stemness [RRCHIP]

city: Chapel Hill

first: DONGHAI

last: WANG

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

summary: R-loop remodelling dynamically regulates chromatin states and gene expression; however, its exploitation by cancer stem cells to sustain self-renewal and malignancy remains poorly understood. In this study, we found that glioblastoma stem cells (GSCs) maintain a highly active R-loop state compared to their differentiated progeny and normal human stem cells. Genome-wide mapping via RR-ChIP-seq revealed cell-specific enrichment and spatial accumulation of R-loops at promoter-proximal regions in GSCs, correlating with active transcription and open chromatin states. To identify key regulators, we profiled the R-loop interactome and identified N-Acetyltransferase 10 (NAT10), an established RNA ac4C-modifying enzyme, as a high-affinity R-loop-binding protein in GSCs. Driven by transcriptional activation via OLIG1, NAT10 is overexpressed in both GSCs and GBM. ac4C RIP-seq on R-loop RNA revealed abundant ac4C-modified R-loops that regulated the GSC genome. Mechanistically, NAT10 catalyzes widespread ac4C deposition on the RNA stand of R-loops, stabilizing promoter-associated R-loops, and facilitating an open chromatin state to sustain GSC self-renewal through controlling key stemness regulators such as the transcription factor EGR1. NAT10 knockdown suppressed GSC proliferation and maintenance in vitro and attenuated GBM progression in orthotopic xenograft models in vivo. Pharmacological inhibition of NAT10/ac4C-modified R-loops using the small-molecule inhibitor Remodelin phenocopied NAT10 genetic targeting, demonstrating therapeutic promise for targeting this axis in GBM.

overall_design: Briefly, NLS-RNaseH1-D210N-V5 was expressed in GSC, DGC, and NSC cells. Approximately 1×10⁷ cells were harvested and crosslinked with 1% formaldehyde at 37 °C for 15 minutes, followed by RRChIP-seq using an anti-V5 antibody.

first: Xujia

last: Wu

first: Donghai

last: Wang

first: Jeremy

last: Rich


title: The vesicle trafficking R-SNARE VAMP714 connects auxin responses, ROS and ion homeostasis in Arabidopsis under salt stress

city: Durham

first: Jialei

last: Sun

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

summary:
•Plant responses to salt stress include an altered root architecture mediated by ion imbalances, reactive oxygen species (ROS) accumulation, and altered hormonal responses. Auxin is implicated in these processes, and to understand better the molecular network we investigated the role of VAMP714, a R-SNARE essential for correct trafficking of the auxin efflux carrier PIN-FORMED (PIN) proteins (implicated in the salt stress response), but also with a reported role in ROS vesicular transport in Arabidopsis.
•We show that under salt stress the VAMP714 gene shows a rapid transient increase in expression but subsequent perturbed localisation of VAMP714 and PIN proteins and altered auxin-responsive gene expression. RNA-seq analysis revealed that pathways related to oxygen signaling, SALT OVERLY SENSITIVE (SOS) pathway activation and ROS response are influenced by salt stress in a VAMP714-dependent manner. Low levels of transgenic overexpression of VAMP714 enhanced root salt tolerance, an effect enhanced by exogenous auxin, showing that maintenance of VAMP714 expression under salt stress allows auxin-mediated maintenance of root growth.
•We conclude that VAMP714 contributes to the coordinated regulation of auxin signaling and the SOS pathway during salt stress via distinct roles in vesicle trafficking to the plasma membrane (for auxin) and vacuole (for SOS).

overall_design: WT (Col-0) and vamp714 mutant (GABI) seedlings (5 dpg) were grown on half-strength MS medium with or without 150 mM NaCl for 0, 3, 9, or 24 h. Roots were collected for RNA extraction, and sequencing and bioinformatics analysis was performed by Novogene (UK) (Cambridge, UK).

first: Julien

last: Agneessens

first: Jennifer

last: Topping

first: Keith

last: Lindsey


title: NAT10-Dependent N4-acetylcytidine (ac4C) on R-loops Drive Glioblastoma Tumorigenesis and Stemness [ac4C-RIP-seq]

overall_design: Following NAT10 knockdown in GSC23 or GSC387 cells, R-loop RNA (collected by precipitation method) was extracted as input for RIP using an ac4C-specific antibody, followed by sequencing.


title: Alternative End-Joining Activation by miR-21-5p Confers Radiation Resistance in Oral Squamous Cell Carcinoma [miRNA-seq of radoresistant or sensitive OSCC cells]

city: ShenZhen

first: Lin

last: Ma

state: Guangdong Province

address: Lihu Campus: Xueyuan Avenue, Nanshan District, Shenzhen

department: Medical School

country: China

institute: ShenZhen University

summary: Marked heterogeneity in radiosensitivity is a major challenge in the treatment of oral squamous cell carcinoma (OSCC), often resulting in poor outcomes for radioresistant tumors. The underlying molecular drivers of this resistance remain elusive. Here, we identify a novel mechanism in which miR-21-5p promotes radiation resistance by selectively activating the error-prone DNA double-strand break (DSB) repair pathway alternative end-joining (Alt-EJ). Integrative miRNA profiling, multi-omic analyses, and functional assays demonstrate that miR-21-5p upregulation coupled with suppression of its target gene signature increases Alt-EJ dependence for DSB repair. This Alt-EJ reliance enhances genomic instability, increases tumor mutational burden and microhomology-mediated indels, and confers pronounced radiation resistance in OSCC models, while correlating with poor radiotherapy response in patients. Importantly, pharmacological or genetic inhibition of Alt-EJ components, including PARP1 and POLQ, restores radiosensitivity in vitro and in vivo, with PARP1 inhibition specifically reversing miR-21-5p-mediated resistance in a syngeneic mouse model. Further RNA-seq analyses of these mice tumors confirmed that PARP inhibitor induced selective radiosensitization effects for miR-21-5p-overexpressing tumors were accompanied by a pronounced reduction in alt-EJ expression. Collectively, these findings establish the miR-21-5p/Alt-EJ axis as a key driver of radiation resistance in OSCC and support Alt-EJ targeting as a promising approach for precision radiosensitization.

overall_design: Radioresistant (RR) clones were developed by repeatingly exposing CAL27 cells to 2 Gy X-ray daily for two cycles of five days. Each cycle was followed by a two-week recovery. Single-cell clones were isolated after the final recovery. Parallel mock-treated (single 2 Gy X-ray) and untreated control clones (CC) were established from parental CAL27 cells. Total RNA from CAL27 clones was extracted with TRIzol (Invitrogen) and quantified with a NanoDrop 2000 (Thermo Fisher). Libraries were prepared using the NEBNext® Small RNA Library Prep Set (NEB, E7330S) and quality assessed by Agilent 2100 Bioanalyzer. Sequencing was performed on an Illumina NovaSeq 6000 platform.


title: NAT10-Dependent N4-acetylcytidine (ac4C) on R-loops Drive Glioblastoma Tumorigenesis and Stemness [RNA-Seq]

overall_design: NAT10 was knocked down using shRNA, and total RNA was extracted with Trizol reagent, followed by next-generation sequencing to investigate the molecular mechanism of NAT10 regulation in GSC23 and GSC387 cells.


title: NAT10-Dependent N4-acetylcytidine (ac4C) on R-loops Drive Glioblastoma Tumorigenesis and Stemness

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

overall_design: Refer to individual Series


title: Global Gene Expression  profiling of Whole Blood RNA of  Type 2 Diabetes (T2D) and Azlzheimr's Disease (AD) Patient

city: Washington

first: Somiranjan

last: Ghosh

state: DC

address: 415 College Street EE JUST HALL BIOLOGY EE JUST HALL BIOLOGY

department: Biology

institute: Howard University

summary:
Type 2 diabetes mellitus (T2D) and Alzheimer’s disease (AD) are a growing concern in low- and middle-income countries, including Pakistan. The relationship between T2DM and AD is complex and concerning, as more older adults with T2DM are experiencing cognitive impairment.
The study aimed to investigate the relationship between T2D and AD in a Pakistani population. Through transcriptomic analysis, this research explored shared molecular mechanisms, genes, and pathways between T2DM and AD.

overall_design: Our microarray studies of global gene expression were conducted on the Affymetrix platform using HuGene-2_0-st Array along with Ingenuity Pathway Analysis (IPA) were implemented in a subgroup of participants to identify overlapping gene networks and canonical pathways implicated in both diseases. Blood samples were collected in PAXgene® Blood RNA Tubes (BD, Cat # 762164). RNA was extracted using the PAXgene Blood RNA kit (Qiagen, Cat. # 762164, PreAnalytiX GmbH, Germany) following the manufacturer's instructions. Total RNA was reverse-transcribed to cDNA by using High-Capacity cDNA Reverse Transcription Kits (Part # 4387406; Applied Biosystems, CA, USA) according to manufacturer’s instruction.  Oligonucleotide microarray experiments were performed by using the Affymetrix U133 Plus 2.0 Array platform, which provides comprehensive coverage of the entire transcribed human genome on a single array. Differentially expressed gene sets were analyzed with microarray results using Transcriptome Analysis Console (V 4.0, ThermoFisher, CA, USA).

first: Tanmoy

last: Mondal


title: Nickel exposure disrupts epigenetic repression of developmental genes in mouse embryonic stem cells

first: Suresh

last: Cuddapah

address: 341 East 25th Street

institute: NYU School of Medicine

summary: Nickel (Ni) is a naturally occurring heavy metal widely found in the environment, but anthropogenic activities such as industrial processes and the widespread use of Ni-containing products have elevated its environmental levels. Ni exposure poses significant health risks, and both vertebrate models and epidemiological studies link it to developmental toxicity. However, the mechanisms underlying Ni-induced developmental toxicity remain poorly understood.  In this study, we investigated how Ni exposure affects pluripotency in mouse embryonic stem cells (mESCs). Ni exposure led to aberrant activation of genes associated with mesodermal and endodermal lineages, while ectodermal genes remained largely unaffected. Despite this induction of lineage-associated genes, key pluripotency genes were not downregulated, suggesting a metastable or incomplete differentiation state. Examination of the underlying mechanisms revealed that Ni exposure induced a loss of the repressive histone modification H3K27me3 at bivalent mesodermal gene promoters, without altering its global levels. Pharmacological inhibition of H3K27me3 demethylases attenuated Ni-induced gene activation, confirming that H3K27me3 loss contributes to this process. ESCs are known to naturally exist as heterogeneous populations that fluctuate between naïve and lineage-primed pluripotent states. Maintaining this balance is essential for proper differentiation. Our findings suggest that Ni exposure disrupts this equilibrium by prematurely inducing mesodermal and endodermal programs. Such dysregulation of early pluripotent states may bias cell-fate decisions and contribute to Ni-induced developmental toxicity, providing a mechanistic link between Ni exposure and developmental toxicity.

overall_design: RNA-seq of E14Tg2A mouse embryonic stem cells maintained in LIF-containing media and treated with 0, 100, 150, 200 uM nickel for 4 or 6 days

first: David

last: Filipovic


title: Transcriptomic profiling of brain tissues from HIV-1 gp120 transgenic mice reveals insights into neuropathogenesis

city: Guangzhou

first: Jinhu

last: Zou

state: Guangdong

address: No. 1023-1063, Shatai South Road, Guangzhou City, Guangdong Province, China

department: Department of Microbiology, School of Public Health

institute: Southern Medical University

summary: Despite tremendous progress with antiretroviral therapy, HIV-associated neurocognitive disorders (HAND) remain prevalent, underscoring the need for effective treatments. Sustained immune activation induced by the HIV-1 glycoprotein gp120 is a proposed mechanism leading to neuronal damage in the central nervous system (CNS). To investigate the gp120-mediated transcriptional changes underlying neuropathogenesis, we performed RNA-sequencing (RNA-seq) analysis on brain tissue samples from HIV-1 gp120 transgenic mice and wild-type (WT) control mice to identify differentially expressed genes (DEGs) in the gp120-expressing brains compared to controls.

overall_design: We performed high-throughput RNA-seq analysis using Illumina NovaSeq 6000 on brain tissues from five 12-month-old HIV-1 gp120 transgenic mice and five age-matched wild-type controls.

first: Xuefeng

last: Gao

first: Hong

last: Cao


title: Alternative End-Joining Activation by miR-21-5p Confers Radiation Resistance in Oral Squamous Cell Carcinoma [RNA-seq of SUGH-OSCC patient tumors]

overall_design: OSCC samples and adjacent normal tissues from patients were collected in operating room or pathology core for FFPE samples at Shenzhen University General Hospital (SUGH). The study was approved by the ethics committee of Shenzhen University General Hospital, and written informed consents were obtained from all patients.Fresh tissue samples were snap-frozen in liquid nitrogen and stored at –80°C. Total RNA was extracted (TRIzol) from these samples using Qiagen's protocol and assessed for quality and quantity. Ribosomal RNA was depleted, and sequencing libraries were prepared (Vazyme). SUGH-OSCC samples were sent for RNA-seq with Illumina platform.


title: Effect of endostatin administration on epididymal white adipose tissue gene expression in female mice during the day.

city: San Antonio, TX 78229

first: Christopher

last: Litwin

state: TX

address: 4939 Charles Katz Dr, San Antonio, TX 78229

department: Biochemistry and Structural Biology

institute: University of Texas Health Science Center San Antonio

summary: Endostatin is an endogenous cleavage product of Collagen 18 type a 1, an extracellular matrix protein that has anti-angiogenic properties. Increasing evidence suggests that endostatin has metabolic benefits in obesity models independently from its anti-angiogenic effects. Furthermore, multiple reports have shown drastic reduction in weight gain with endostatin treatment with high fat diet, and cell -autonomous effects of endostatin on adipocytes. The pathways that regulate endostatin 's effects on adipocytes are elusive. We have determined that there is a sex- and time-dependent effect of endostatin on adipose tissue gene expression. Therefore, we treated female mice with endostatin, collected adipose tissue and performed Total RNA-seq on RNA extracted from the tissue.

overall_design: 4 Female mice were treated with 50 mg/kg endostatin or pbs vehicle and tissue was collected 2 hours post-tail vein injection. Food was removed during the post-injection period to account for effects of acute food intake.

first: Kevin

last: Koronowski


title: Generation of expandable hepatocyte organoids with multipolar organization from human embryonic stem cells

first: Wu

last: Haibin

address: Waihuan east road

institute: South china university of technology

summary: In this study, we successfully generated mature grape-like heporgs (G-heporg) from human embryonic stem cells (hESCs) using a modified hepatocyte organoid culture system. Within this differentiation platform, spherical hepatocyte organoids (S-heporg) spontaneously emerged alongside G-heporgs. Similar to primary heporgs, differentiated G-heporgs exhibited high ALB expression and expansion capability, whereas the S-heporgs lacked both characteristics. Comparative analysis revealed that IGF2 stimulates G-heporg formation. Moreover, we found that targeted modulation of the Hippo-YAP pathway overcame long-term expansion limitations in G-heporgs. Crucially, the differentiated and expandable G-heporgs developed multipolar architectures with functional BC networks, recapitulating the polarity characteristic of primary hepatocytes. Finally, we modeled copper ion metabolism using G-heporgs, demonstrating their utility for investigating polarized trafficking processes of hepatocyte metabolites

overall_design: RNA-seq profiling of G-heporgs, S-heporgs and G-heporgs treated with IL6/OSM or maturation differentiation.

first: Yuyou

last: Duan

first: Haibin

last: Wu


title: Trisomy 21 drives ADARB1 overexpression and premature RNA recoding in the developing fetal brain

city: New York City

first: Michael

middle: S

last: Breen

department: Depts. of Psychiatry, Genetics and Genomic Sciences

summary: Understanding how chromosome 21 gene dosage contributes to neurodevelopmental and systemic phenotypes in trisomy 21 (T21) remains a fundamental challenge. We performed transcriptome-wide RNA sequencing on fetal cortical and hippocampal tissues from 20 T21 cases and 27 euploid controls collected between 13–22weeks post-conception—a critical period for human brain development. Differential expression analysis revealed 572 dysregulated genes in the cortex and 519 in the hippocampus (FDR < 5%), with significant enrichment for chromosome 21 genes. Functional enrichment analyses highlighted disruptions in neurodevelopmental, synaptic, and immune-related pathways. Among the most strongly dysregulated genes was ADARB1, a chromosome 21–encoded RNA editing enzyme, whose overexpression in T21 fetal brain was associated with increased adenosine-to-inosine (A-to-I) editing, including key recoding events in GRIA2 (p.R764G), GRIA3 (p.R775G), and GRIK2 (p.Y571C, p.Q621R). A meta-analysis incorporating nine independent transcriptomic datasets spanning early embryonic and progenitor cell types validated robust chromosome 21 dosage effects, including consistent ADARB1 overexpression. Extending these findings, a meta-analysis of A-to-I editing across datasets revealed widespread over-editing at 3′UTRs and at GRIA3 (p.R775G), a site critical for AMPA receptor desensitization. Together, these results implicate dysregulated RNA editing—driven by ADARB1 overexpression—as a novel post-transcriptional mechanism contributing to fetal neuropathology in T21 and provide a framework for understanding the broader molecular consequences of chromosome 21 dosage sensitivity during brain development.

overall_design: Transcriptome-wide RNA sequencing was performed on fetal cortical and hippocampal tissues from 21 T21 and 27 euploid controls collected between 13 and 22 weeks post-conception.

first: Andy

last: Yang

first: Xuran

last: Wang

first: Miguel

last: Rodriguez de los Santos

first: Ran

last: Tao

first: Daniel

middle: R

last: Weinberger

first: Joel

last: Kleinman

first: Kalina

last: Mihova

first: Gergana

last: Stancheva

first: Radka

last: Kaneva

first: Violeta

last: Dimitrova

first: Vladimir

last: Vladimirov

first: Thomas

middle: M

last: Hyde

first: Joseph

middle: D

last: Buxbaum


title: Circulating Epigenetic Signatures Classifying Brain Insulin Resistance in humans

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

type: Methylation profiling by genome tiling array


title: Alternative End-Joining Activation by miR-21-5p Confers Radiation Resistance in Oral Squamous Cell Carcinoma [RNA-seq of SCC7 mice tumors]

first: Lin

last: Ma

overall_design: Female C3H mice (aged 6-8 weeks; Shanghai Model Organisms Center, Inc., China; Catalog No. SM-008) were subcutaneously injected into the posterior flank region with primary SCC7 cells, SCC7 cells overexpressing miR-21-5p (OE) or negative control (NC) cells with empty vector. Each mice was seeded with about 1000000 cells. Tumor sizes were measured with calipers twice a week. When average volum of tumors reached about 300 mm³, mice were randomly assigned into different treatment groups. Mice were anesthetized with isoflurane and positioned within a lead-shielded apparatus to expose only the tumor to irradiation (8Gy X-ray/fraction/day for 3 days). Olaparib was administrated to mice by intraperitoneal injection (50mg/Kg) at 2 hours before irradiation every day and with an additional boost at the day after last irradiation. Tumors were collected when mice were sacrificed. Three tumor for each treatment group were sent for RNA-seq with Illumina platform.


title: Circulating Epigenetic Signatures Classifying Brain Insulin Resistance in humans [2]

summary: Brain insulin action plays an important role in metabolic and cognitive health but so far, there is no biomarker available to assess brain insulin resistance in humans. Here, we developed a machine learning framework based on blood DNA methylation profiles of participants who did not have Type 2 Diabetes with and without brain insulin resistance and detailed metabolic phenotyping.

overall_design: We identified 540 DNA methylation sites (CpGs) as classifiers of brain insulin resistance in a discovery cohort (n = 167), results that were validated in two replication cohorts (n = 33 & 24) with high accuracy (83%-94%). All 540 CpGs were differentially methylated and annotated to 445 genes mapping to neuronal development and axonogenesis processes. Of note, methylation patterns of 98 out of 540 CpGs exhibited a strong and significant (p < 0.05)  blood-brain correlation, indicating that blood cells are a reliable proxy to capture brain-specific DNA methylation changes.

first: Stephanie

last: Kullmann

first: Amandeep

last: Singh

first: Britta

last: Wilms

first: Markus

last: Jähnert

first: Svenja

last: Meyhöfer

first: Hubert

last: Preissl

first: Martin

last: Heni

first: Andreas

last: Birkenfeld

first: Annette

last: Schürmann

first: Meriem

last: Ouni


title: Loss of Pum2 Exacerbates Colitis by Disrupting Macrophage–Epithelial Crosstalk and Promoting Epithelial Necroptosis

city: wuhan

first: Xuefei

last: Wang

state: hubei

address: tongji

institute: Huazhong University of Science and Technology Tongji Medical College Union Hospital

summary: Ulcerative colitis (UC) is a chronic and relapsing inflammatory disease marked by sustained mucosal immune activation and impaired epithelial barrier integrity. Here, we identify the RNA-binding protein PUMILIO2 (Pum2) as a previously unrecognized regulator of intestinal inflammation.

overall_design: Pum2-knockout (Pum2-/-) mice and WT mice colon RNA-seq


title: NAT10-Dependent N4-acetylcytidine (ac4C) on R-loops Drive Glioblastoma Tumorigenesis and Stemness [H3K27ac]

first: DONGHAI

last: WANG

overall_design: NAT10 was knocked down using shRNA, followed by ChIP-seq analysis in GSC23 and GSC387 glioma stem cells.

first: Xujia

last: Wu

first: Donghai

first: Jeremy

last: Rich


title: Circulating Epigenetic Signatures Classifying Brain Insulin Resistance in humans [1]

first: Heike


title: Multiplex organoid mutagenesis reveals gene combinations driving transformation, pathology and chemosensitivity in ovarian carcinoma

city: Ithaca

first: Coulter

last: Ralston

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

summary: High-grade serous ovarian carcinoma (HGSC) is the sixth leading cause of cancer-related death among women. Many cases arise from the Fallopian tubal epithelium (TE), exhibit numerous mutations, and present heterogenous pathological features. However, the contribution of specific mutation combinations to cellular transformation, pathological phenotype and chemotherapeutic response remains poorly understood. Here, we used a Trp53-deficient mouse TE-derived organoid platform to perform combinatorial CRISPR mutagenesis of 20 candidate HGSC driver genes. Mutations in Nf1, Cdkn2a and Map2k4 were most frequently observed in transformed organoids. Upon transplantation into mice, those containing Map2k4 mutations predominantly gave rise to papillary-glandular histology, whereas those containing Nf1 mutations formed more mesenchymal-like carcinomas. Transcriptomic analysis revealed that tumors bearing Nf1 mutations overexpressed the long non-coding RNA Pvt1, a marker associated with poor prognosis in HGSC patients, regardless of pathological phenotype Map2k4-mutant organoids were more sensitive to paclitaxel and niraparib, while Nf1-mutant combinations responded better to trametinib. Notably, the removal of Rho kinase inhibitor (ROCKi) reduced trametinib sensitivity in both Map2k4- and Nf1-mutant organoids, underscoring the importance of culture conditions and potential antagonistic drug interactions in organoid-based drug screens. Collectively, our results demonstrate that TE-derived organoids coupled with combinatorial CRISPR mutagenesis provide a powerful system to unravel the genetic and phenotypic complexity of HGSC. In particular, we found that Map2k4 functions as a tumor suppressor that shapes distinct tumor histology and chemosensitivity, suggesting it as a potential therapeutic target in select HGSC cases.

overall_design: RNA-seq analysis to explore how mutation combinations in tubal epithelial organoids drive papillary and mesenchymal tumors after subcutaneous flank injections in mice.

first: Daryl

last: Phuong

first: Alexander

middle: Y

last: Nikitin

first: John

last: Schimenti


title: Succinate Modulation as a Novel Mechanism Underlying the Effects of Intermittent Fasting on Brain Function and Metabolism in Diet-Induced Obesity

city: Pisa

first: Paola

last: Tognini

address: 33 Piazza Martiri della Libertà

department: Health Science Interdisciplinary Center

country: Italy

institute: Scuola Superiore Sant’Anna

summary: Obesity significantly impacts the central nervous system (CNS), increasing risks of neuropsychiatric disorders and dementia. Intermittent fasting (IF) shows promise for improving peripheral and CNS health, but its mechanisms are unclear. Using a diet-induced obesity mouse model (10 weeks high fat diet (HFD), then 4 weeks intervention), we compared HFD, HFD-IF, ad libitum control chow (CC), and CC-IF groups. Switching to CC or IF reduced body weight, fat mass, and improved glucose tolerance. Notably, CC-IF uniquely enhanced exploration and reduced anxiety-like behavior. Transcriptomics revealed HFD-induced hippocampal neuroinflammation, while metabolomics identified a specific succinate signature in CC-IF mice: plasma concentration decreased while liver and brown adipose tissue (BAT) levels increased. Succinate supplementation mimicked CC-IF metabolic and behavioral benefits and reduced hippocampal inflammation. These findings suggest that regulating plasma succinate and its metabolism in liver and BAT may represent a novel mechanism underlying the metabolic, neuroinflammatory, and behavioral improvements induced by IF.

overall_design: RNA-seq profiling of liver and hippocampus from diet-induced-obese male C57BL/6J mice after a 10-week high-fat diet, followed by 4 weeks on one of four regimens: (i) HFD (high-fat ad libitum), (ii) HFD-IF (high-fat intermittent-fasting every other day), (iii) CC (control chow ad libitum), and (iv) CC-IF (control chow intermittent-fasting). Four biological replicates per group (total = 32 samples) were sequenced (2 × 125 bp, Illumina HiSeq 2500) to examine transcriptional changes driven by diet switch and intermittent fasting.

first: Andrea

last: Tognozzi

first: Fabrizia

last: Carli

first: Sherif

last: Abdelkarim

first: Sara

last: Cornuti

first: Francesca

last: Damiani

first: Maria

last: Giuliano

first: Alice

last: Miniati

first: Martina

last: Nasisi

first: Lia

last: De Benedictis

first: Kousha

last: Ashtiani

first: Gaia

last: Scabia

first: Margherita

last: Maffei

first: Pierre

last: Baldi

first: Amalia

last: Gastaldelli


title: Neuroblastoma tumors are sensitive to ferroptosis inducers – GPX4 inhibitors

city: Woolloongabba

first: Fernando

last: Guimaraes

state: QLD

address: 37 Kent Street

country: Australia

institute: Frazer Institute - University of Queensland

summary: We aim to look at the GPX4 inhibitor affect human neuroblastoma cell lines.

overall_design: We cultured MYCN-amplified (SK-N-BE(2)) and MYCN-nonamplified (SK-N-AS) human neuroblastoma cell lines in the presence of GPX4 inhibitor ML210 for overnight culture and followed by bulk RNAseq analysis.

first: Cui

last: Tu


title: Small regulatory RNAs modulate Lactococcal susceptibility to cell wall-targeting antimicrobials

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Life sciences center

country: Lithuania

institute: Vilnius Universitye

sample_organism: Lactococcus cremoris subsp. cremoris MG1363


title: Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [RNA-seq]

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

summary: NF-κB signaling in pancreatic ductal adenocarcinoma (PDAC) operates through canonical and noncanonical pathways mediated by RELA and RELB, respectively. We show that TNFα selectively activates the canonical RELA pathway, while TWEAK induces noncanonical signaling through RELB. Through integrated transcriptomic, epigenomic, and transcription factor binding analyses, we reveal distinct temporal dynamics and binding patterns, with RELB preferentially occupying AP1-rich, epigenetically active regions. Single-cell RNA-seq and tissue staining highlight pathway-specific crosstalk with the tumor microenvironment. These findings uncover fundamental differences in RELA and RELB regulatory mechanisms and their distinct contributions to PDAC gene regulation.

overall_design: To dissect the roles of canonical and noncanonical NF-κB signaling in pancreatic ductal adenocarcinoma (PDAC), we used a combination of time-resolved stimulation experiments, transcriptomic profiling, and chromatin immunoprecipitation. PDAC cell lines were treated with TNFα (a canonical NF-κB activator) and TWEAK (a noncanonical activator) across multiple time points to capture early and late signaling dynamics. We performed bulk RNA-seq and ChIP-seq for RELA and RELB to compare transcriptional output and DNA binding activity of each pathway. Additionally, single-cell RNA-seq was employed to explore cell state heterogeneity and pathway-specific gene expression in response to each stimulus, highlighting potential roles in tumor microenvironment crosstalk.

first: Joana

last: Aggrey-Fynn


title: Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [Hi-C]

city: Basel

first: Filippo

address: Fabrikstrasse 24,

country: Switzerland

institute: FMI

summary: Little is known about how three-dimensional chromatin topology shapes mammalian craniofacial development. In mouse cranial neural crest cells, a Polycomb Repressive Complex 2 (PRC2)-dependent chromatin architecture is established before migration. This configuration maintains craniofacial gene promoters poised and connects them with distal Polycomb tethering elements, positioning promoters in spatial proximity to future long-range enhancers. Deletion of Ezh2 disrupts this early topology, causing inappropriate gene derepression in post-migratory craniofacial subpopulations where these genes are normally silenced, and failure of long-range enhancer recruitment where activation is required, thereby impairing proper gene expression. We further identify a distal Polycomb tethering element essential for Hoxa2 enhancer recruitment across topologically associating domains. Thus, Polycomb acts not only as a transcriptional repressor, but also as a chromatin-folding organizer that prepares developmental genes for later activation, by facilitating subsequent recruitment of distal active enhancers previously not in contact. Polycomb-mediated topology therefore orchestrates the transition from progenitor plasticity to precise spatiotemporal control of morphogenetic gene programs during neural crest development and face formation.

overall_design: Hi-C analysis of the 3D chromatin structure in Cranial Neural Crest Cells at developmental stages E10.5 and E11.5 (Md and PA2) WT, Ezh2cKO and Hoxa2-PTE-36kb-del

first: Yousra

last: Ben Zouari

first: Onkar

last: Joshi

first: Adwait

last: Salvi

first: Sandra

last: Kessler

first: Sebastien

last: Ducret

first: Fiona

last: Ross

first: Sojoerd

last: Holwerda

first: Nathalie

last: Vilain

first: Soujanya

last: Mamilla-Sanivaram

last: Smallwood

first: Hubertus

last: Kohler

first: Michael

last: Stadler

first: Maryline

last: Minoux

last: Rijli


title: Autophagy activators normalize aberrant Tau proteostasis and rescue synapses in human familial Alzheimer’s disease iPSC-derived cortical organoids

city: La Jolla

first: Jeffery

last: Kelly

state: California

address: 10550 North Torrey Pines Road

department: Chemistry

institute: The Scripps Research Institute

summary: Alzheimer’s disease (AD) is the most common form of dementia worldwide. Despite extensive progress, the cellular and molecular mechanisms of AD remain incompletely understood, partially due to inadequate disease models. To illuminate the earliest changes in hereditary (familial) Alzheimer’s disease, we developed an isogenic AD cerebrocortical organoid (CO) model. Our refined methodology produces COs containing excitatory and inhibitory neurons alongside glial cells, utilizing established isogenic wild-type and diseased human induced pluripotent stem cells (hiPSCs) carrying heterozygous familial AD mutations, namely PSEN1ΔE9/WT, PSEN1M146V/WT, or APPswe/WT. Our CO model reveals time-progressive accumulation of amyloid beta (Aβ) species, loss of monomeric Tau, and accumulation of aggregated high-molecular-weight (HMW) phospho(p)-Tau. This is accompanied by neuronal hyperexcitability, as observed in early human AD cases on electroencephalography (EEG), and synapse loss. Single-cell RNA-sequencing analyses reveal significant differences in molecular abnormalities in excitatory vs. inhibitory neurons, helping explain AD clinical phenotypes. Finally, we show that chronic dosing with autophagy activators, including a novel CNS-penetrant mTOR inhibitor-independent drug candidate, normalizes pathologic accumulation of Aβ and HMW p-Tau, normalizes hyperexcitability, and rescues synaptic loss in COs. Collectively, our results demonstrate these COs are a useful human AD model suitable for assessing early features of familial AD etiology and for testing drug candidates that ameliorate or prevent molecular AD phenotypes.

overall_design: Individual familial AD and isogenic WT control COs at ~2- and 3-month timepoints were dissociated and single cell-sequenced using 10x Genomics' Cellplex kits. Multiple replicates from two different genetic backgrounds were used.

first: Sergio

last: Labra

first: Jadon

last: Compher

first: Christine

last: Baal

first: Lynee

last: Massey

first: Wei

last: Lin

first: Nicholas

last: Schork

first: Tony

last: Mondala

last: Head

middle: W

first: Stuart

last: Lipton


title: HNRNPH1 regulates cell cycle-associate genes in glioblastoma

city: Boston

first: Marco

last: Mineo

state: MA

address: 60 Fenwood Rd, BTM 8016N

institute: Brigham and Women's Hospital

summary: Glioblastoma (GBM) is an aggressive and deadly brain tumor with a poor prognosis despite advances in therapeutic intervention. Clinical trials of targeted therapy, anti-angiogenic agents, gene therapy, and immunotherapy have led to some extension of the length of GBM patient survival. However, a cure for GBM remains elusive, and almost all tumors recur in a more aggressive form for which there is no standard of care. One critical reason for GBM resistance to current therapies can be attributed to the tumor’s extensive heterogeneity and the presence of different mechanisms that promote GBM progression. Post-transcriptional regulation of messenger RNAs participates in many cancer processes, and it is usually controlled by several different RNA-binding proteins. Dysregulation of RNA-binding protein expression alters RNA metabolism and results in the production of abnormal proteins that promote cancer development. In this study, we performed transcriptome analysis of HNRNPH1 knockout cells and showed that silencing HNRNPH1 reduced the expression of genes involved in cell cycle regulation. Our findings suggest RNA-binding proteins as novel targets for the development of more effective therapies for GBM.

overall_design: Tumor cell lines were transfected with a control siRNA control or siRNAs targeting HNRNPH1. RNA expression profiles were generated by RNA-seq in duplicate using Illumina NovaSeqX.

first: Genaro

last: Villa

first: Antonio

last: Chiocca


title: Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [PCHi-C]

first: Filippo

overall_design: PCHi-C analysis of the 3D chromatin structure in Cranial Neural Crest Cells at developmental stages E8.5, E10.5 and E11.5 (WT, Ezh2cKO, Hoxa2PTE-36kb-del and Hoxa2PTE-42kb-del)

first: Yousra

last: Ben Zouari

first: Onkar

last: Joshi

first: Adwait

last: Salvi

first: Sandra

last: Kessler

first: Sebastien

last: Ducret

first: Fiona

last: Ross

first: Sojoerd J.B.

last: Holwerda

first: Nathalie

last: Vilain

last: Mamilla-Sanivaram

last: Smallwood

last: Kohler


title: Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [ChIP-Seq]

first: Steven

last: Johnsen

first: Joana

last: Aggrey-Fynn


title: Effects of HNRNPH1 silencing on global transcriptomic changes in glioblastoma

overall_design: Tumor cell lines were nucleofected with a control sgRNA control or sgRNAs targeting HNRNPH1. RNA expression profiles were generated by RNA-seq in triplicate using Illumina NovaSeqX.


title: Hes1 regulates bone marrow mesenchymal stromal cell function through suppressing NFATc2-mediated inflammation

city: Pittsburgh

first: Wei

last: Du

state: Pennsylvania

address: 5051 Centre Ave

department: Division of Oncology

institute: University of Pittsburgh

summary: Transcriptome analysis reveals that disruption of Hes1 in BM microenvironment alters expression of genes critical for cellular metabolism and inflammation. Our study unveils a pivotal role of Hes1 in maintaining bone marrow mesenchymal stromal cell hemostasis and regulating their hematopoiesis supportive function.

overall_design: We used the standard procedure of Qiagen RNeasy kit to extract total RNA from the bone marrow MSC of the heterozygous Hes1fl/+ mice in a C57BL/6 background. We calculated total RNA concentration and assessed the integrity. A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101). We then compare gene expressions between the Hes1 KO and control MSC to the resistant cell lines to look for changes in drug-resistance associated pathways with and without NFA treatment.

first: Sanghoon

last: Lee


title: Delta-catenin is required for cell proliferation in virus positive Merkel cell carcinoma cell lines but not in human fibroblasts

city: Seattle

first: Joselyn

last: Landazuri Vinueza

state: WA

address: 4131 11th Ave NE

department: Microbiology

institute: University of Washington

summary: Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine skin cancer often driven by the integration of Merkel cell polyomavirus (MCPyV) into the host genome and the persistent expression of its viral oncoproteins, small tumor (ST) antigen and truncated large tumor (t-LT) antigen. While human fibroblasts support MCPyV replication, the cell of origin for MCC remains unknown. We hypothesized that MCPyV initially replicates in fibroblasts but, in rare cases, infects Merkel cell progenitors, contributing to MCC development. Using TurboID mass spectrometry, we identified δ-catenin as a novel ST interactor in fibroblasts. However, while ST binds δ-catenin in fibroblasts, this interaction is absent in virus-positive (VP)-MCC cell lines. Despite this, δ-catenin is essential for VP-MCC, but not for fibroblast, cell proliferation. We found that fibroblasts predominantly express δ-catenin isoform 1, whereas VP-MCC cells mainly express isoform 3. Overexpression of isoform 1 in VP-MCC failed to restore ST binding. δ-catenin promotes VP-MCC proliferation by regulating cell cycle gene expression through its interaction with Kaiso, a transcriptional repressor. Additionally, we found that LSD1 (KDM1A) regulates δ-catenin isoform 3 expression by modulating ESRP1, a δ-catenin splicing factor. Our findings reveal novel host factors involved in MCPyV infection and MCC tumorigenesis, suggesting that the host cell supporting viral replication and the MCC cell of origin may be distinct cell types.

overall_design: MKL-2 cells were transduced with two doxycycline-inducible lentiviral vectors encoding shRNA targeting δ-catenin or non-tragetting control for 6 days. Cells were collected, RNA extracted and send for bulk RNA sequencing.

first: Denise

last: Galloway


title: Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development

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

overall_design: Refer to individual Series


title: TCR Signaling Induced Kdm6b Antagonizes Ezh2 to Sustain Tissue Regulatory T Cells [CUT&Run]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: Regulatory T cells (Tregs) expressing Forkhead Box P3 (Foxp3) play crucial roles in maintaining immune tolerance and tissue integrity. Ezh2, a Histone H3 lysine 27 (H3K27) methyltransferase, is known as a crucial regulator of Treg cell identity and suppressive function upon activation, raising a question about whether overactivation of this pathway would further boost Treg cell function. Here, we demonstrate that lysine demethylase Kdm6b catalyzing the reverse reaction to Ezh2 is also required for Treg cell identity and function after activation. Treg-specific deletion of Kdm6b impairs tissue Treg cell fate and function, such as in the lung after injury or adipose tissue during animal aging. Mechanistically, T cell receptor (TCR) signaling upregulates Kdm6b expression and recruits it to Foxp3-bound chromatin to restrict H3K27me3. This antagonism helps suppress the expression of inflammatory cytokines and promote the expression of Treg functional genes, thus supporting tissue Treg cells.

overall_design: Cut&Run protocol were performed to detect Kdm6b chromatin binding in Treg cells. Each have 2 replicates.

first: Minghong

last: He

first: Yongqiang

last: Feng

first: Jason

last: Mock


title: Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq]

first: Filippo

overall_design: ChIP-seq (H3K27me3, H3K4me2, H3K27ac and CTCF) profiling of cranial neural crest cell (NCC) progenitors (E8.5) and post-migratory subpopulations (FNP, Mx, Md, PA2; E10.5 and E11.5) of wildtype, Ezh2-conditional knockout, HIRE1 knockout and Hoxa2PTE-36kb-del knockout genotypes.

first: Yousra

last: Ben Zouari

first: Onkar

last: Joshi

last: Salvi

last: Kessler

last: Ducret

first: Sojoerd

first: Soujanya

first: Hubertus

first: Michael

last: Stadler

first: Maryline

last: Minoux

last: Rijli


title: Application of spatial transcriptomics across organoids for a high-resolution spatial whole-transcriptome benchmarking dataset

city: Melbourne

first: Maria Rosaria

last: Nucera

state: VICTORIA

address: 50, Flemington road

department: Paediatrics

institute: University of Melbourne

summary: Stem cell-derived organoids hold promise to model tissue-specific disease. To enable this, it is crucial to assess how transcriptional signatures, cellular organisation and composition of organoids compare to in vivo counterparts. However, spatial transcriptomics has been challenging to apply to organoids to elucidate regional molecular identity. This study presents the first systematic profiling of multiple stem cell derived organoid models (brain, heart muscle, heart valve, kidney, lung, cartilage, and haematopoietic) with Stereo-seq, a full transcriptome, spatial assay using on-chip in situ RNA capture. It describes assay optimisation for characterisation, use of multiple organoid samples on a single chip, assesses limitations in RNA capture efficiency compared to reference tissues. Furthermore, it introduces a bespoke analysis method that partitions samples into regions for characterisation. These findings inform future works to characterise organoids using spatial transcriptomics, providing insights in optimising RNA capture of multiple organoids across a chip and regional analysis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We profiled brain, heart, kidney, lung, cartilage, haematopoietic, and engineered heart valve organoids in comparison to mouse E13.5 head and 21 postconceptional weeks (PCW) mouse heart tissue. In addition to multi-organoid placement on a single chip, organoids of the same tissue type cultured under different conditions were co-embedded and profiled on the same Stereo-seq chip.

first: Natalie

last: Charitakis

first: Ryan

last: Leung

first: Anna

last: Leichter

first: Natasha

last: Tuano

first: Marzena

last: Walkiewicz

first: Vallari

last: Sawant

first: Lynn

last: Rowley

first: Michelle

last: Scurr

first: Pei

middle: X

last: Er

first: Ker

last: Tan

first: Rebecca

last: Sutton

first: Feroz

last: Ahmad

first: Ritika

last: Saxena

first: Alexander

last: Maytum

first: Declan

last: Turner

first: Holly

last: Voges

first: Hieu

middle: T

last: Nim

first: Kira

last: Sun

first: Bicheng

last: Yang

first: Nick

last: Li

first: Gareth

last: Ball

first: Andrew

last: Elefanty

first: Shireen

last: Lamande'

first: Kynan

last: Lawlor

first: Jessica

last: Vanslambrouck

first: Richard

last: Mills

first: Elizabeth

last: Ng

first: Edouard

last: Stanley

first: Rhiannon

last: Werder

first: Melissa

middle: H

last: Little

first: David

last: Elliot

first: Enzo

last: Porrello

first: Maree

last: Faux


title: Metabolic reprogramming driven by impaired trophoblasts and decidual XCR1+PMN-MDSCs crosstalk controls adverse outcomes in advanced maternal age

city: Guangzhou

first: shuyi

last: kuang

address: ShaTai southern load

institute: Southern Medical Univercity

summary: Decidual polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) are crucial for maternal–fetal stability and accumulate to support fetal development. Although advanced maternal age (AMA) increases the risk of adverse outcomes, the regulatory role and mechanism of decidual PMN-MDSCs in these outcomes remain unclear. Herein, the XCL1–XCR1 interaction mediated specific crosstalk between trophoblast cells and decidual PMN-MDSCs in both humans and mice. Single-cell sequencing identified a decidual PMN-MDSCs subset highly expressing XCR1 markedly reduced in AMA. Impaired XCL1-stimulated decidual XCR1+PMN-MDSCs delayed fetal growth in AMA and Xcr1-/- pregnant mice. Perinatal XCL1 supplementation and oltipraz treatment rescued these functions by activating decidual XCR1+PMN-MDSCs in AMA mice, not Xcr1-/- pregnant mice. The XCL1–XCR1 axis induced FOXO1 nuclear localization, regulating oxidative phosphorylation-related targets and enabling metabolic processes. Hence, XCL1–XCR1 crosstalk between trophoblast cells and PMN-MDSCs is critical in driving metabolic reprogramming of decidual XCR1+PMN-MDSCs and controlling adverse outcomes caused by AMA.

overall_design: Single-cell RNA sequencing (ScRNA-seq) analysis of decidual PMN-MDSCs. Decidual LOX1+ immune cells were collected from healthy pregnancies and pregnancies with AMA and decidual PMN-MDSCs were idetified according to their specific signatures.

first: Meiqi

last: Chen

first: Yuxiong

last: Guo

first: Jingping

last: Liu

first: Shuyi

last: Kuang

first: Qing

last: Zhao

first: Zhengcong

last: Huang

first: Chenlin

last: Lv

first: Shuxiu

last: Xu

first: Zekai

last: Zhuang

first: Jing

first: Yumei

last: He


title: Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [RNA-seq]

first: Filippo

overall_design: RNA-Seq profiling of E11.5 (FNP, Mx, Md and PA2)  cranial neural crest cells WT and Ezh2cKO

first: Yousra

last: Ben Zouari

first: Onkar

last: Joshi

first: Adwait

last: Salvi

first: Sandra

last: Kessler

first: Sebastien

last: Ducret

first: Fiona

last: Ross

first: Sojoerd

last: Holwerda

first: Nathalie

last: Vilain

first: Soujanya

last: Mamilla-Sanivaram

last: Smallwood

first: Hubertus

last: Kohler

first: Michael

middle: B

last: Stadler

first: Maryline

last: Minoux

last: Rijli


title: Microarray-based transcriptome analysis of BMDMs from UBA3 myeloid knockout mice and control mice

city: Beijing

first: Wu

last: Meng yao

address: No.27 Taiping Road, Haidian District

institute: Beijing Institute of Basic Medical Sciences

summary: To investigate the effects on the DSS-induced colitis  of UBA3-myeloid-deletion mice, we sorted BMDMs from UBA3 myeloid deletion mice and control mice for transcriptome sequencing

overall_design: Comparative analysis of gene expression profiles of RNA-seq data from BMDMs of UBA3 myeloid knockout mice and control mice

first: Jiyan

last: Zhang

first: Zhenjie

last: Ye

first: Mengyao

last: Wu

first: Wenbin

last: Gai


title: CUT&Tag from KYSE150 and KYSE30

city: guangzhou

first: yong

last: she

address: Sun Yat-sen University Cancer Prevention and Treatment Center, No. 651 Dongfeng East Road, Guangzhou

institute: Sun Yat-sen University Cancer Center

summary: PRDM1CUT&Tag on human KYSE150 and KYSE30 cells

overall_design: In each cell line, three biological replicates were constructed using CUT&Tag for PRDM1 to identify differences.

first: Yuanyang

last: Huang

first: Ming

last: Cheng

first: Rui

last: Li

first: Yong

last: She


title: Activating locus coeruleus-hippocampus noradrenaline system alleviates sepsis-induced encephalopathy by promoting astrocyte AQP4 related autophagy through α2A-AR

city: hefei

first: mei

last: bin

state: anhui

address: Meishan Road Campus, No. 81, Meishan Road

institute: Anhui medical university

summary: Single-cell analysis of differential changes in astrocytes in the hippocampus of septic mice and sham-operated mice

overall_design: Sham surgery mice and septic mice were subjected to laparotomy under surgical anesthesia without cecal ligation and puncture(CLP) or CLP for 3 days respectively. Subsequently, the hippocampi were dissected and prepared for single cell RNA-sequencing.

first: Bin

last: Mei

first: Juntao

last: Weng

first: Yueyue

last: Yang

first: Chenyu

first: Sandong

last: Cao

first: Daqing

last: Ma

first: Xuesheng

last: Liu


title: Effect of in vitro dolutegravir exposure on transcriptome of oligodendrocyte precursor cells and oligodendrocytes

city: Philadelphia

first: Judith

middle: B.

last: Grinspan

state: PA

address: 3615 Civic Center Blvd., Abramson Research Center, 516D

department: Neurology

institute: Children's Hospital of Philadelphia

summary: In this study, we demonstrated that exposing primary rat oligodendrocyte precursor cells  and oligodendrocytes to dolutegravir during both proliferation and differentiation impaired oligodendrocyte maturation and myelin protein production. Bulk RNA sequencing revealed that dolutegravir exposure does not significantly alter the transcriptome of oligodendrocyte precursor cells compared to DMSO treatment. Conversely, we identified transcriptional changes after dolutegravir exposure in mature oligodendrocytes related to a variety of cellular mechanisms, including cellular responses to stress pathways, amino acid starvation, and mitochondrial dysfunction. In particular, differential gene expression analyses revealed 127 significantly altered transcripts in dolutegravir treated oligodendrocytes, with 3 of these being Trib3, Atf4, and Cebpb, which have interconnected roles in regulating the integrated stress response.

overall_design: RNA-seq profiling of untreated, DMSO-treated, and dolutegravir-treated primary rat oligodendrocyte precursor cells (24 hours of proliferation treatment) and oligodendrocytes (24 hours of proliferation treatment + 72 hours of differentiation treatment).

first: Marisa

last: Jeffries

first: Raj

last: Putatunda

first: Melanie

last: Cruz-Berríos

first: Micah

last: Romer

first: Kelly

last: Jordan-Sciutto


title: Metabolic reprogramming driven by impaired trophoblasts and decidual XCR1+PMN-MDSCs crosstalk controls adverse outcomes in advanced maternal age [CUT&Tag]

first: shuyi

last: kuang

overall_design: CUT&Tag analysis of decidual PMN-MDSCs from mouse samples. Decidual PMN-MDSCs were collected from the healthy pregnancy group and the advanced pregnancy group.

first: Meiqi

last: Chen

first: Yuxiong

last: Guo

first: Jingping

first: Shuyi

last: Kuang

first: Qing

last: Zhao

first: Zhengcong

last: Huang

first: Chenlin

last: Lv

first: Shuxiu

last: Xu

first: Zekai

last: Zhuang

first: Jing

first: Yumei

last: He


title: TCR Signaling Induced Kdm6b Antagonizes Ezh2 to Sustain Tissue Regulatory T Cells

first: Beisi


title: Inhibition of 5`- Cap Trimethylation Prevents Exosome Targeting of Telomerase RNA, Despite Promoting Increased 3`- end Oligoadenylation

city: Clayton

first: Luis

last: Batista

state: MO

address: 6329 San Bonita Avenue

institute: Washington University in St. Louis

summary: Mutations that impact maturation of human telomerase RNA (hTR) are common in telomere-biology disorders. Here, we describe sequential posttranscriptional modifications that coordinate hTR biogenesis and decay. Initially, TGS1-mediated 5`- cap trimethylation targets long genomically extended hTR precursors for degradation. Prevention of trimethylation results in accumulation of nucleolar 3`- end extended precursors, evading MTR4 recognition and degradation by the exosome, which in turn facilitates processing into mature hTR. In a second step, 3`- end oligoadenylation by PAPD5 promotes degradation of mature hTR, a process that remains dependent on 5`- cap modifications, as prevention of trimethylation inhibits decay of 3`- end oligoadenylated molecules. Combined inhibition of 5`- cap trimethylation and 3`- end oligoadenylation synergistically increases hTR in cells harboring pathogenic mutations in telomerase. These data reveal a precise interplay between 5`- and 3`- end posttranscriptional modifications that dictate hTR fate and highlight the potential of RNA therapeutics for treatment of telomere-biology disorders.

overall_design: RNA-ligase-mediated 3`- RACE sequencing of hTR from WT_hTERT cells and DKC1_DL37_hTERT cells treated with DMSO, sinefungin, RG7834, or a combination of both.

first: Aniruddha

last: Samajdar

first: Roberta

last: Amato

first: Seongmoon

last: Jo

first: Ethan

last: Cordes

first: Albert

last: Tai

first: Grazia

last: Raffa


title: Tofacitinib Repairs GM-CSF-induced RA Mitochondrial Dysfunction

city: Chicago

first: Shiva

last: Shahrara

address: 840 S. Wood St

institute: University of Illinois Chicago

summary: Rheumatoid arthritis (RA) is an autoimmune disease in which synovial tissue macrophages (MΦs) are the primary producer of inflammatory factors. RA synovial MΦ expansion is strongly linked to ultrasound-detected hypertrophy and pathology, and their frequency is 25-fold upregulated during a flare. Consequently, infiltrating MΦs sense and respond to the RA synovial tissue's high energy and oxygen demands. Thus, understanding how hypoxic RA MΦs experience changes in metabolic activity and mitochondrial remodeling will unravel novel therapeutic strategies. Intriguingly, we found that granulocyte-macrophage colony-stimulating factor (GM-CSF) stimulates an RA MΦ inflammatory profile associated with mitochondrial oxidative stress. This study utilized RNA-seq to investigate the effect of GM-CSF treatment on global gene expression changes in MΦs derived from the peripheral blood of rheumatoid arthritis patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GM-CSF-treated or untreated RA MΦs.

first: Neha

last: Satoeya


title: Metabolic reprogramming driven by impaired trophoblasts and decidual XCR1+PMN-MDSCs crosstalk controls adverse outcomes in advanced maternal age [RNA-Seq]

first: shuyi

last: kuang

overall_design: RNA-seq analysis of decidual PMN-MDSCs,  peripheral PMN-MDSCs and extravillus trophoblast from human samples. Decidual PMN-MDSCs and peripheral PMN-MDSCs were collected from the healthy pregnancy group. Extravillus trophoblasts were collected from the healthy pregnancy group and the advanced pregnancy group.

first: Meiqi

last: Chen

first: Yuxiong

last: Guo

first: Jingping

last: Liu

first: Shuyi

first: Qing

last: Li


title: Leukemia aggressiveness is driven by chromatin remodeling and expression changes of core regulators [ChIP-seq]

first: Gracia

middle: M.

last: Bonilla

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Molecular mechanisms driving clonal aggressiveness in leukemia are not fully understood. We tracked and analyzed MLL-rearranged leukemic clones independently evolving towards higher aggressiveness. More aggressive subclones lost their growth differential ex vivo but restored it upon secondary transplantation, suggesting molecular memory of aggressiveness. Development of aggressiveness was associated with clone-specific gradual modulation of chromatin states and expression levels across the genome, with a surprising preferential trend of reversing the earlier changes between normal and leukemic progenitors. To focus on the core aggressiveness program, we identified genes with consistent changes of expression and chromatin marks that were maintained in vivo and ex vivo in both clones. Overexpressing selected core genes (Smad1 as aggressiveness driver, Irx5 and Plag1 as suppressors) affected leukemic progenitor growth in the predicted way and had convergent downstream effects on central transcription factors and repressive epigenetic modifiers, suggesting a broader regulatory network of leukemic aggressiveness.

overall_design: ChIP sequencing was performed for H3K4me3, H3K27me3, H3K4me1 and H3K27me3 samples for two clones

first: Ruslan

last: Sadreyev

first: Sharmistha

last: Kundu

first: Francois

last: Mercier


title: Leukemia aggressiveness is driven by chromatin remodeling and expression changes of core regulators [RNA-seq]

overall_design: RNA sequencing was performed for leukemic progenitors after overexpression of Irx5, Plag1, and Smad1 using lentiviral transduction.

first: Alexander

last: Morris


title: Generation of Stable Chambered Cardioids from human Pluripotent Stem Cells

city: Hangzhou

first: Tiancheng

last: Yu

state: Zhejiang

address: Dunyu Road

institute: Westlake University

summary: The human heart is a vital organ under intense investigation for the hope to improve health and longevity. Recent advances to generate cardiac organoids (cardioids) provide unprecedented opportunities to cardiac research. However, achieving stable chambered cardioids structures remains a challenge, thus limiting its application in disease modeling and drug screening. In this study, we address this challenge by orchestrating cardiac signaling pathways, including synergistic modulation of FGF and Wnt signaling via the HAND1 transcription factor. We have successfully demonstrated the formation of stable chambered cardioids structured with endocardium, myocardium, and epicardium, mimicking early cardiac development with well-organized structural components. Furthermore, we demonstrate the feasibility to leverage this platform for drug toxicity screening. Our findings provide a system to understand human heart development and generate models for cardiac tissue engineering and regenerative medicine.

overall_design: There are three groups in this study: 2D cultured tissue, stable chambered cardioids with PD173074 treatment, and stable chambered cardioids without PD173074 treatment. All samples were collected for single-cell sequencing on day 42.5.

first: XINLE

last: ZOU

first: FANWEN

last: WANG

first: HUILING

last: ZHENG

first: TIANCI

last: KONG


title: Deletion of immune regulatory factor Fgl2 affects the mouse spleen immune profile

city: Wuhan

first: Zhaohui

last: Tang

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

summary: Transcription profiles identified 18 cell types, including 9 B cell subsets, 5 T cell subsets, pc cells, monocytes, natural killer (NK) cells, and dc cells. Compared with WT group, the proportion of naive B cells, transitional B cells, marginal B cells, follicular B cells, CD4-T naive, CD8-T naive, CD4-T regulatory subsets, NKT, NK and DC subsets in Fgl2 KO group decreased. The proportion of PCs, CD4-Tem and monocyte subsets increased. Notably, we identified four new B cell subpopulations in the Fgl2 KO group that cannot be classified as classical B cell subpopulations and are therefore named B cell_sp1, B cell_sp2, B cell_sp3, and B cell_sp4.B cell_sp1 subgroup showed dominant clones of IGHA, IGHM and IGHD in the constant region, while the other 3 different subgroups and pc only showed dominant clones of IGHA in the constant region. This suggests that IGHA clones are most abundant and dominant in Fgl2 KO B cells. In addition, we analyzed in detail the number of different BCR heavy chain genes and related VH gene fragments in the Fgl2 KO-specific B cell subpopulation. At the same time, they also highly express Ccl5, Ccl4, Cxcl2, Cxcl10, Slpi, S100a8, S100a9, Fcer1g and IL-1b genes, which are involved in the regulation of immune process and molecular function. In addition, these specific B cells also highly express genes. Such as PDCD1, HAVCR2, CTLA4 and ICOS, suggesting that these B cells are more likely to fail and may not survive for long.

overall_design: To study the effects of Fgl2 gene deletion on spleen immune cells in mice under physiological conditions. We obtained spleens from a pair of SPF bred wild-type (WT) mice of the same age (8 weeks) and sex (male) and Fgl2 KO mice. The function and effect of Fgl2 in immune cells, especially B cells, were investigated by single cell sequencing and immune bank.

first: Jiang

last: Chang

first: Jingzhi

last: Yang


title: B-Type Lamins organize 3D chromatin architecture through associations with nuclear lamina and nuclear speckles [TSA]

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

summary: B-type lamins (Lamin B1 and B2) are key components of the nuclear lamina and play essential roles in three-dimensional (3D) chromatin organization by anchoring Lamina-Associated Domains (LADs). Recent studies have indicated that abnormal gene expression resulting from B-type lamin loss occurs in both LAD and non-LAD regions; however, the underlying molecular mechanisms remain unclear. In this study, we demonstrate that the majority of differentially expressed genes (DEGs) in B-type lamin-depleted cells are predominantly located in non-LAD regions, which are characterized by a constitutive association with nuclear speckles. Through RNA-Seq combined with SC35 Tyramide Signal Amplification Sequencing (TSA-Seq) analysis, we find that aberrant gene regulation is closely associated with the repositioning of chromatin either toward or away from nuclear speckles. The absence of B-type lamins causes a global reorganization of chromatin rather than changes in its fine structure, leading to the disruption of constitutive Speckle-Associated Domains (cSPADs). Additionally, the loss of B-type lamins results in euchromatin deactivation and heterochromatin de-repression, which impairs cell viability by increasing apoptotic signaling and causes defective mRNA splicing. Our data reveal a novel role for B-type lamins in regulating transcriptional activity by conserving genome architecture between the nuclear lamina and nuclear speckles.

overall_design: Each sgRNA target sequence for LMNB1, and LMNB2 was designed by using the sgRNA prediction program.


title: Mechanisms Underlying the Progression of Congenital Scoliosis Involving Bone Marrow Stromal Progenitors [BiSulfite-seq]

last: Sun

address: Datun road, No.15th

institute: Institute of Biophysics, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: The functional contributions of individual cellular components in the bone marrow and bone microenvironment to spinal deformities in patients with congenital scoliosis (CS) remain inadequately understood. Our objective was to construct a comprehensive map of the bone-marrow stromal progenitors  at a single-cell level in murine models of CS. And exploring mechanisms underlying the progression of scoliosis combining epigenomic and transcriptome analysis of bone in CS patients. Our analysis in  murine models identified bone-marrow stromal progenitors to be pro-scoliosis cells. During the spinal growth stage, specific precursor cells/MSCs underwent functional reprogramming, losing their progenitor status and initiating differentiation into gliogenic, fibrotic, and osteogenic phenotypes in the phase of spinal deformities. They perform tissue repair differentiation and anti-inflammatory effect. Meanwhile, scoliosis-inducing insults, such as proneurodegenerative and proinflammatory cytokines, influenced specific precursor cells/MSCs, leading to a fate switch toward gliogenesis, extracellular matrix synthesis, and osteogenesis. These processes, in turn, contributed to the development of scoliosis through neurodegeneration, fibrosis, and disruptions in bone homeostasis. we validated neurodegeneration, fibrosis, and disruptions in bone homeostasis  in clinical CS patient samples through epigenomic and transcriptome analysis and  histological testing. In addition, excessive differentiation during MSC injury repair marked scoliosis progression in murine models, indicating that inflammatory and neurodegeneration are two underlying pathogenic factors contributing to spinal deformities in CS. Meanwhile, the decreased expression of Hmox1 and  increased expression of SPP1 in murine models and clinical patients indicating perhaps they are potential diagnostic and therapeutic targets in CS early phase.

overall_design: To determine the epigenomical changes in the clinical patients bone tissues during CS progression, we conducted whole genome bisulfate sequencing of bone tissues obtained from seven clinical CS patients and six spinal health patients.

first: Sun

last: Qing

first: Wang

first: Hao

last: Yan

first: A

last: Jiancuo

first: Li


title: A new insight into Glutamine promoting tumor proliferation: The mitochondrial metabolic pathway - Gln/GGCT/GSH/ROS axis

city: Harbin

first: Lijun

address: yikuang street

institute: Harbin Institute of Technology

summary: γ-Glutamylcyclotransferase (GGCT) is a crucial enzyme for glutathione (GSH) metabolism. Little is known about its role in the process of glutamine (Gln) affecting tumor progression. The research found that Gln was significantly increased and promoted tumor growth. It promoted the proliferation of hepatocellular carcinoma and prostate cancer cells by reducing the production of reactive oxygen species (ROS) and increasing GSH levels. GGCT was correlated with Gln concentration. The depletion of GGCT inhibited cell proliferation, decreased GSH levels and promoted ROS production, while overexpression had the opposite effects. miR-29b-3p mediated the decrease in GGCT expression under Gln-deficient conditions. GGCT affected mitochondrial morphology and regulated oxidative phosphorylation. It also affected tricarboxylic acid (TCA) cycle metabolism.. GGCT knockdown significantly inhibited tumor growth and promoted ROS production, whereas N-acetylcysteine increased tumor growth and reduced ROS production in vivo. In conclusion, GGCT maintains mitochondrial metabolism through the Gln-GGCT-GSH-ROS axis, providing a promising therapeutic approach for cancer treatment.

overall_design: RNA-seq Profiling of the Human Hepatocellular Carcinoma Cell Line MHCC87H following Transfection with siRNA Targeting GGCT or Non-targeting Control siRNA. Three independent experiments were conducted, and the GGCT knockdown MHCC97H cells were compared against the control cells.

first: Huan

last: Nie


title: TCR Signaling Induced Kdm6b Antagonizes Ezh2 to Sustain Tissue Regulatory T Cells [RNA-seq]

first: Beisi

last: Xu

overall_design: Cut&Run protocol were performed to detect Kdm6b chromatin binding in Treg cells. Each have 2 replicates.

first: Minghong

last: He

first: Yongqiang

last: Feng

first: Jason

last: Mock


title: Super-enhancers reorganization controls re-sensitization of oxaliplatin-resistant FBXW7-mutated colorectal cancer

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

institute: University of Udine

summary:
Epigenetic plasticity and large-scale chromatin remodeling characterize tumor evolution and the emergence of subclones resistant to conventional therapies. Catalytically inactive class IIa HDACs (HDAC4, HDAC5, HDAC7, HDAC9) act as acetyl-lysine readers that form the scaffold for the targeted recruitment of chromatin remodeling complexes, making them very attractive therapeutic targets in the field of oncology.
In this study, we found that HDAC4 is proteasomal degraded in cancer cells impaired in DNA repair by homologous recombination. Genetic screening identified FBXW7 as the E3 ligase responsible for this degradation. FBXW7 loss-of-function (LOF) mutations are frequently found in patients with colorectal cancer (CRC), and FBXW7 mutation status is associated with the development of resistance to oxaliplatin. Deletion of HDAC4 or its forced degradation with a PROTAC-based compound restored Oxaliplatin sensitivity in FBXW7-mutated CRC cells, patient-derived organoids (PDOs) and xenografts, with no effect on DNA damage response activation or DNA platination.
Mechanistically, forced removal of HDAC4 in FBXW7-mutant CRC cells and PDOs treated with Oxaliplatin resulted in a deep rearrangement of the super-enhancer landscape, with a dramatic loss of super-enhancers found in Oxaliplatin-resistant samples and restoration of defined super-enhancers found in Oxaliplatin-sensitive cells. The pharmacological disassembly of HDAC4 complexes partially recapitulated the effects obtained with the PROTAC-based HDAC4 compound, demonstrating the importance of the epigenetic function of HDAC4 in supporting drug resistance.
This study supports HDAC4 as a key mediator of Oxaliplatin resistance in FBXW7-mutated CRC and highlights the remodeling of a well-defined repertoire of super-enhancers as part of the process of successful re-sensitization.

overall_design: PDM-96 and PDM-257 CRC PDOs were treated for 48h with PROTAC compound #11 and Tsq (1µM) or DMSO as a control. For the last 24h samples were treated or not with OxPt (50 µM).

first: Vanessa

last: Tolotto

first: Ylenia

last: Cortolezzis

first: Eros

last: Di Giorgio


title: A human model of histiocyte associated neurodegeneration

city: Austin

first: Anna

last: Warden

address: 2500 Speedway

institute: University of Texas at Austin

summary: Neurodegenerative diseases are increasingly recognized as having an innate immune component to both disease onset and progression, but the extent and mechanisms are incompletely understood. Langerhans cell histiocytosis (LCH) is a highly heterogenous inflammatory mononuclear cell disorder caused by activating somatic mosaic mutations in the mitogen-activated protein kinase (MAPK) pathway, most commonly BRAFV600E. An unpredictable subset of LCH patients develop a heterogenous progressive and incurable neurodegenerative disease (LCH-ND). Here we generate a human induced pluripotent stem cell model from patients with somatic hematologic mosaicism for BRAFV600E. Brain macrophage/microglia from LCH iPSCs exhibit disease specific pathogenic features of MAPK activation. Stepwise differentiation identified hematopoietic progenitors as hyperproliferative, whereas brain macrophages were apoptosis resistant. Through application of cerebral organoids and a humanized murine xenotransplantation model we identify marked heterogeneity of differentiation potential within clonal BRAFV600E lines in vivo. This model phenocopied human specific phenotypes not found in murine models including dense basal ganglia foci of abnormal macrophages and caused marked neurodegeneration and astrogliosis due to BRAFV600E microglia. This approach will allow for human specific in vitro and preclinical testing of therapeutics in LCH-ND

overall_design: To query the effect of the Langerhans Cell Histiocytosis variant BRAF(600E) on brain macrophages/microglia, we generated a cohort of iPSCs from patients with somatic blood mosaicism for BRAFV600E, generating isogenic cell lines with and without the BRAFV600E mutation. For some patients where we did not isolate the BRAFV600E containing cell line we after reprogramming, we then induced the BRAFV600E mutation in the healthy patient iPSCs using CRISPR/Cas9 and homology directed repair. These were then differentiated in to iMGs, and we performed gene expression profiling analysis using data obtained from RNA-seq from both isogenic control and BRAFV600E lines (8 lines in total). Comparative gene expression profiling analysis of RNA-seq data in iPSC derived microglia from lines with and without the BRAFV600E variant was performed.

first: Shivakumar

last: Rajamanickam

first: Samantha

last: Trescott

last: Mak

first: Bing

last: Xia

first: Jennifer

last: Picarsic

first: Christopher

middle: K

last: Glass

first: Carl

middle: E

last: Allen

first: Nicole

last: Coufal


title: Co-targeting CDK7/CDK9 and CKIα exerts efficacious anticancer effects against TERT gene-rearranged neuroblastoma

city: Sydney

first: Jingwei

last: Chen

address: High Street

institute: Children's Cancer Institute

summary: TERT gene rearrangement with transcriptional super-enhancers leads to substantial TERT over-expression and neuroblastoma. No targeted therapy is available for clinical trials in patients. Here we show that the transcriptional kinases CDK7/CDK9 and the casein kinase CKIα were required for TERT gene over-expression and p53 protein degradation respectively in TERT-rearranged neuroblastoma cells. Co-knockdown of CDK7/CDK9 and CKIα or treatment with the CDK7/CDK9 and CKIα co-inhibitor A51 reduced TERT gene transcriptional initiation, elongation and expression, activated p53 protein expression, co-operatively induced apoptosis and suppressed tumor progression in mouse models. Screening of an approved oncology drug library identified Ceritinib as the agent exerting the best synergistic anticancer effects with A51. A51 and Ceritinib synergistically down-regulated mitochondrial complex I gene expression and induced oxidative stress and TERT-rearranged neuroblastoma cell apoptosis. In mice xenografted with TERT-rearranged patient-derived xenograft neuroblastoma cells, A51 and Ceritinib synergistically induced tumor cell apoptosis, suppressed tumor progression and improved mouse survival. A51 and Ceritinib combination therapy is therefore a good candidate for translation into the first clinical trial of a targeted therapy against TERT-rearranged neuroblastoma.

overall_design: To investigate the mechanisms through which A51 and Ceritinib combination therapy exerts synergistically anticancer effects against TERT-rearranged neuroblastoma. TERT-rearranged neuroblastoma cells were treated with vehicle control, 62.5nM A51, 1μM Ceritinib, or combination for 12 hours, followed by RNA sequencing analysis of differential gene expression. Gene Ontology and Gene Set Enrichment Assay (GSEA) analysis were performed to determine the terms and pathways were impacted by the A51 and Ceritinib combination treatment.

first: Jing

last: Wu

first: Nisitha

last: Jayatilleke

first: Tao

last: Liu


title: Single-cell transcriptional profiling of lung epithelial cells after naphthalene club cell injury in adult C57 Bl/6 mice with temporal resolution

city: Boston

first: margherita

last: paschini

address: 1 blackfan circle, Karp Building

department: Hem/Onc

institute: Boston Children's Hospital

summary:
The aim of this study was to study tissue-wide responses to club cell airway injury.

Keywords: Expression profiling by high throughput sequencing

overall_design: Examination of the transcriptional changes in lung epithelial cells at various timepoints after naphthalene-mediated airway injury.

first: Irene

last: Wong

first: Carla

middle: F

last: Kim

first: Margherita

last: Paschini


title: IL-17 signaling pathway and NMDAR1 antibodies shape NMDAR encephalitis

city: Hengyang

first: Hongye

last: Yan

state: Hunan

address: 69 Chuanshan Road

institute: The First Affiliated Hospital of University of South China

summary: Human forebrain organoids (hFOs, day 110) derived from U2F iPS cell line were exposed with or without 10 μg/mL anti-NMDAR1 antibody for 24 hours. Organoids were then randomly selected for RNA sequencing (RNA-seq). By performing RNA-seq analysis, we showed that anti-NMDAR1 antibody exposure in hFOs downregulated expression of genes enriched with multiple neuronal functions including the glutamatergic synapse.These downregulated genes were also enriched with neuropsychiatric disorder-related genes.

overall_design: We generated hFOs from U2F iPS cell lines. On day 110 of organoid culture, hFOs were exposed with or without 10 μg/mL anti-NMDAR1 antibody for 24 hours. Three organoids in each group were randomly pooled together as one mixed sample. At least three mixed samples in each group were then used for RNA-seq (BGI DNBseq-T7, paired-end 150 bp) to identify genes affected by anti-NMDAR1 antibody. Differentially expressed genes (adjusted P value < 0.05) that identified in hFOs were used for Gene Ontology and KEGG pathway analysis.

first: Qingtuan

last: Meng

first: Zhenhong

last: Xu


title: Spatial multiomics reveals the interplay between neuroblastoma and its immune environment

city: Woolloongabba

first: Fernando

last: Guimaraes

address: 37 Kent Street

institute: Frazer Institute - University of Queensland

summary: DSP RNA profling using the whole transcriptome atlas kit was performed on a cohort of neuroblastoma tumor samples from pediatric patients.

overall_design: Differential expression and geneset analysis were performed on the tumor and tumor microenvironment (TME) regions of a tumor microarray to identify differences between high-risk (22 cores, n=12) and low-risk (44 cores, n=11) neuroblastoma.

first: Cui

last: Tu

first: Chin

last: Wee Tan

first: Arutha

last: Kulasinghe


title: B-Type Lamins organize 3D chromatin architecture through associations with nuclear lamina and nuclear speckles [RNA-seq]

first: Jung-Woong


title: Targeting one-carbon metabolism in stem cell-like T cells to prevent chronic graft rejection [ChIP-seq]

city: wuhan

first: wang

last: yi

institute: Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Splenic CD4+ T cells were sorted and stimulated with anti-CD3/CD28 antibodies in the presence of MAPK13 inhibitors or DMSO for 72h. And then cells were collected for ChIP-seq.


title: Chromatin accessibility profile at single cell level of different phenotypic tumors derived from the human non-muscle invasive bladder carcinoma cell line, MGH-U3

status: Public on Apr 07 2026

city: Shenzhen

first: Zeqin

address: No. 1, Fuxin Road, Pinghu Street, Longgang District, Shenzhen, Guangdong Province, China

institute: Shenzhen University

summary: To understand the genetic mechanisms by which IGFBP5 regulates aggressive progression and squamous traits, we performed whole-exome sequencing (WES) on three distinct cell lines: CTR-MGH-U3-LT, UCSD-MGH-U3-LT, and MP-MGH-U3-LT. WES revealed no mutations in IGFBP5, suggesting that its regulatory role may involve epigenetic mechanisms. We next sought to perform single-cell ATAC-seq to investigate a potential epigenetic mechanism underlying IGFBP5 regulated squamous traits and aggressiveness.

overall_design: In this study, we performed single-cell assay for Transposase-Accessible Chromatin with high throughput sequencing on three phenotypically distinct tumors derived from the human non-muscle invasive bladder carcinoma cell line, MGH-U3 (i.e., urothelial carcinoma (UC), urothelial carcinoma with squamous differentiation (UCSD), and mixed phenotype (MP). All samples are processed immediately after collection, dissociated into high-viability single-cell suspensions using a standardized enzymatic protocol, and subjected to single-cell capture and library preparation on the 10x Genomics platform.

first: Yan

last: Zeqin


title: Targeting one-carbon metabolism in stem cell-like T cells to prevent chronic graft rejection

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

overall_design: Refer to individual Series