title: Small RNA sequencing in NMD mutant and CHX-treated WT cells of N. castellii

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

summary: In order to determine whether RNAs that accumulate upon NMD inactivation and translation elongation inhibition in N. castellii can be processed into small RNAs by Dcr1, we performed small RNA-Seq.

overall_design: Small RNA-seq in NMD mutant and CHX-treated WT cells of N. castellii.

first: Ugo

last: Szachnowski

first: Constance

last: Creux

first: Quentin

last: Fouilleul

first: Marina

last: Lefrère

first: Antonin

last: Morillon


title: Translational landscape of cytoplasmic lncRNAs in N. castellii

status: Public on Oct 01 2025

country: France

summary: To define the translational landscape of cytoplasmic lncRNAs in N. castellii, we performed Ribo-Seq in WT and upf1 mutant cells treated with  translation elongation inhibitor (CHX).

overall_design: Ribo-seq in WT and upf1 mutant yeast cells, treated with CHX, including 3 biological replicates per condition.


title: High-resolution of NMD targets in N. castellii using RNA-Seq

type: Expression profiling by high throughput sequencing

summary: Profiling of NMD targets in Naumovozyma castellii, a budding yeast endowed with cytoplasmic RNAi. The sensitivity of cytoplasmic lncRNAs and mRNAs to Upf1 (NMD core factor), translation elongation inhibition (CHX) and Dcr1 (ribonuclease III Dicer) was analyzed using RNA-Seq.

overall_design: Strand-specific total RNA-seq in WT, dcr1, upf1 and CHX-treated WT cells.


title: 3D imaging and single-cells analysis reveal cellular heterogeneity of lymphatic valve endothelial cell types

city: Toulouse

first: Florence

last: Tatin

address: 1 avenue Jean Poulhès

summary: We have used single-cells transcriptomics to analyse the identity of lymphatic endothelial cells in adult dorsal skin. Lymphatic endothelial cells played an important role in skin homeostasis and protection. We showed that lymphatic vasculature has a highly organized architecture dependent to skin microenvironment. Our 3D imaging data associated to single-cells analysis revealed the importance of lymphatic valves in dermal lymphatic vascular network.

overall_design: Lymphatic endothelial cells have been isolated by cell sorting as CD45 negative, CD31 positive and GFP positive from Prox1creERT2; mTmG reporter mouse model and analysed by single-cells

first: F

first: E

last: Marchaud


title: Early life MES exposure inhibits testosterone production by upregulating TGF-β1 expression in mesenchymal cells by direct binding to GATA2

city: Jiang Su

first: ke

last: Ren

address: 608A, Chemistry Building, Northwest Gate, Gulou Campus, Nanjing University, Gulou District, Nanjing City, Jiangsu Province

department: medical college

country: China

institute: Nanjing University

summary: In this study, we investigated the effects of early life exposure to C18-MES on the reproductive system of mice, and by measuring semen quality, testicular structure, blood-testicular barrier integrity, and sex hormone levels, we clarified the reproductive toxicity of C18-MES and revealed its specific molecular regulatory mechanism.

overall_design: RNA-seq analysis was performed on testicular tissues of mice in the control group and MES-exposed group

first: Ke

first: Liehai

last: Hu

first: Juhan

last: Chen

first: Guijuan


title: Tandem duplications in UBTF create XPO1-dependent nuclear export signals necessary for leukemic progression [RNA-seq]

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

country: USA

institute: St Jude Children's Research Hospital

summary: UBTF tandem duplications (UBTF-TD) define a high-risk molecular subtype of acute myeloid leukemia (AML) characterized by poor clinical outcomes. While menin inhibitors have shown therapeutic promise, acquired resistance remains a significant challenge. Here, we use proteomic, genomic, and functional analyses to uncover mechanisms underlying UBTF-TD mediated leukemogenesis. We show that TDs create nuclear export signal (NES) motifs, which mediate interactions with Exportin-1 (XPO1) and chromatin-associated partners. These interactions drive aberrant chromatin binding and transcriptional activation of genes commonly dysregulated in UBTF-TD tumors, including the HOXA/HOXB clusters. We demonstrate that these NES motifs are critical for mislocalization of UBTF-TD proteins, cellular transformation, and transcriptional dysregulation. Importantly, we identify the XPO1 inhibitor eltanexor as a potential therapeutic strategy. Eltanexor treatment disrupts UBTF-TD chromatin localization, reduces tumor burden, and promotes differentiation in preclinical models. These findings provide mechanistic insights into UBTF-TD-driven leukemogenesis and highlight XPO1 inhibition as a promising therapy for UBTF-TD AMLs.

overall_design: RNA-seq in cbCD34+ cells expressing FKBP12-F36V-UBTF-TD54 via lentiviral tansduction. Data was collected in triplicates (n=3)/Condition. The three conditions include DMSO (control), Eltanexor treated (25nM), and dTAG-13 (1uM) treated for 24 hours.

middle: M

first: Juan

last: Barajas


title: Group 2 Innate lymphoid cells promote allograft survival by constraining and inducing anergy in  alloreactive CD4+ T cells

city: shanghai

first: Jifu

last: Ge

state: Shanghai

address: Wujin Road

institute: Shanghai General Hospital

summary: Despite significant improvements in solid organ transplant outcomes over the past several decades, our limited understanding of the immune interface between donor organs and recipient immune systems has hindered the development of strategies to expand immunoregulatory cell populations and induce immune tolerance in transplant recipients. Given that group 2 innate lymphoid cells (ILC2s) are resident in transplanted solid organs, play a role in wound healing, and coordinate immunoregulatory cell populations, we sought to investigate their function in the alloimmune response. Using a murine heterotopic cardiac transplant model, we demonstrate that recipient ILC2s replace donor ILC2s and upregulate MHC class II (MHCII) without expressing costimulatory molecules. These recipient-derived ILC2s process and present alloantigens, inducing CD4+ T cell anergy through the Caspase-3-dependent pathway. In the absence of recipient-derived ILC2s, we observed a marked increase in infiltrating donor-reactive CD4+ T cells and significantly reduced allograft survival. Furthermore, in vivo expansion of ILC2s via IL-33 administration prolonged murine heart allograft survival. Collectively, these findings reveal a critical and previously unrecognized immunoregulatory role of host-derived ILC2s in solid organ transplantation, where they promote alloimmune tolerance by inducing anergy in alloreactive CD4+ T cells.

overall_design: The study aims to compare the transcriptomic profiles of naive and graft-infiltrating ILC2 populations in cardiac transplantation. The overall design of this study includes SmartSeq sequencing of ILC2s isolated from mouse hearts. The dataset comprises 3 biological replicates of naive heart ILC2s and 4 biological replicates of graft-infiltrating ILC2s. Each sequencing replicate represents a pool of ILC2s isolated from 4-7 mouse hearts. Balb/C to C57BL/6 (B6) mouse heart transplant model, which develops acute rejection, was employed in this study. At 7 days post-transplantation, cardiac allografts were harvested and subjected to mechanical dissociation and enzymatic digestion. Single-cell suspensions were obtained, and CD45+ Lineage-ST2+ ILC2s were isolated using fluorescence-activated cell sorting (FACS) for RNA extraction.

first: Zijie

last: Xu

first: Zetao

last: Ding

first: Alex

last: Cuenca


title: RNA-seq analysis of BMSCs differentiated into osteoblasts treated with Hepa 1-6-derived CM and control medium

city: Shanghai

first: Yazhuo

last: Zhang

address: 320 Yueyang Road, Xuhui District

department: CAS Center for Excellence in Molecular Cell Science

institute: Chinese Academy of Sciences

summary: In certain pathological conditions, there exists a liver-bone axis. However, the intricacies of liver-bone communication in HCC growth and metastasis has so far remained incompletely understood. The conditioned medium from Hepa 1-6 cells (Hepa 1-6-derived CM), compared with the control medium, could enhance osteoblast differentiation of Bone Marrow Mesenchymal Stromal Cells (BMSCs). To investigate the mechanism by which remote HCC cells mediate the osteogenic activity of tumor-bearing mice, we performed bulk RNA-seq on BMSCs differentiated into osteoblasts treated with Hepa 1-6-derived CM and control medium. Following the analysis of upregulated genes analysis, we identified a significant elevation in C-X-C chemokine motif ligand 5 (Cxcl5), which encodes CXCL5 and could mediate osteogenic activity.

overall_design: RNA-seq profiling of BMSCs differentiated into osteoblasts treated with Hepa 1-6-derived CM and control medium at Day 7

first: Bo

last: Jiang

first: Shuqin

first: Weiguo

last: Zou


title: Antibiotic resistance in Aeromonas hydrophila associated with exposure to low levels of oxytetracycline

city: Hong Kong

first: Sophie

middle: Natasha

last: ST-HILAIRE

address: Kowloon Tong, Hong Kong SAR, PR China

institute: City University of Hong Kong

summary: Antibiotic resistance (AMR) in aquatic bacteria affecting aquaculture has been a growing concern given the potential for mixing of bacterial populations in the aquatic environment and exposure to different pharmaceuticals from drugs used in aquaculture, as well as wastewater effluent and agricultural run-off.  To better understand the mechanism for AMR in a common aquatic fish pathogen exposed to low dose antibiotics we monitored the genetic changes, as well as gene expression, in Aeromonas hydrophila as the bacteria was exposed to incremental doses of oxytetracycline (OTC), a commonly used drug in aquaculture.  We were able to render all three isolates of our original A. hydrophila resistant to therapeutic levels of OTC (i.e.  ≥100ppm). The relatively quick phenotypic adaptation (often less than 3 days) to different OTC concentrations was very similar across our replicates.  Our whole genome sequencing data and transcriptome results suggested several genes underwent point mutations across all replicates.  Further differential gene expression was observed and likely impacted several pathways which may explain the progressive resistance to OTC associated with incremental exposure to the drug.  The specific mutations consistently identified in isolates exposed to OTC were on AHA_ 2785 (associated with an outer membrane protein), AHA_2910 (involved in the efflux pump mechanism), and AHA_0308 (associated with the small ribosomal subunit protein S10). The pathways involved in the differential gene expression included efflux- pump mechanisms, outer membrane proteins, and ribosomal protein OTC target.  Our findings support the notion that AMR can occur via genetic regulation of several intrinsic mechanisms within a bacterial population. This finding could have implications in aquaculture where bacteria such as A. hydrophila can be exposed to varying levels of antibiotics during in-feed treatments.

overall_design: We trained  original Aeromonas hydrophila ATCC9766 to get resistance to different levels of oxytetracycline (i.e., 5ppm, 20ppm, 50ppm, 100ppm, and 200ppm). The data contains all RNAseq samples from original Aeromonas hydrophila ATCC9766 (R0), and all the resistant Aeromonas hydrophila (i.e., R5, R20, R50, R100, and R200).

first: Ju

first: Liqing

last: Huang

first: Liang

first: Zhaogyang

last: Wang

first: Celia

last: Schunter

last: St-Hilaire


title: Integrative Single-Cell RNA-Seq and ATAC-Seq Identifies Transcriptional and Epigenetic Blueprint Guiding Osteoclastogenic Trajectory [scATAC-seq]

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Osteoclasts (OCs) are multinucleated bone resorbing cells essential for skeletal development and remodeling. In adulthood, OCs originate from the serial fusion of monocytes, yet the transcriptional and epigenetic mechanisms shaping their osteoclastogenic potential at a single cell resolution remain poorly understood. Here, we employed an integrative multi-omics approach, combining single-cell (sc) RNA-seq, scATAC-seq, bulk RNA-seq, and ChIP-seq, to comprehensively define the regulatory landscape of osteoclastogenesis in wild-type (WT) and Irf8 conditional knockout (cKO) mice.

overall_design: 10x Genomics scATAC-seq platform comparing WT and Irf8floxCsf1rCre bone marrow cells (Irf8cKO)

first: Amitabh

last: Das

first: Stefania

last: Dell'Orso

first: Xiaobei

first: Joseph

last: Stains

first: Ryan

last: Riddle

first: Keiko

last: Ozato

first: Hong-Wen

last: Deng

first: Vivek

last: Thumbigere-Math


title: Multi-omics Analysis of Skeletal Muscle Identifies Dysregulation of Hypoxia-Induced Genes in Peripheral Artery Disease [RRBS]

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

type: Methylation profiling by high throughput sequencing

summary: Epigenetic modifications such as DNA methylation play a critical role in hypoxic cell programs. However, no previous studies have investigated the epigenetic regulation of gene expression in peripheral artery disease (PAD), a condition characterized by intermittent ischemia. In this study, we used reduced representation bisulphite sequencing (RRBS) to investigate how PAD affects the DNA methylome in skeletal muscle of PAD patients with intermittent claudication (IC) or critical limb ischemia (CLI) compared to non-PAD controls. We also used small and bulk RNA-sequencing (RNA-seq), which allowed for data integration. This multi-omics approach identified metabolic and hypoxia-related genes in PAD skeletal muscle that are regulated at the level of methylation and by various microRNAs. Specifically, binding and expression target analysis (BETA) revealed that epigenetic modifications to the DNA methylome contribute to modulation of the mRNA expression of family with sequence similarity 20, member C (FAM20C) and endothelial PAS domain-containing protein 1 (EPAS1), also known as hypoxia-inducible factor-2alpha (HIF-2α). Finally, we explored the effect of revascularization on the skeletal muscle DNA methylome and transcriptome, which identified the activator protein-1 (AP-1) early response transcription factor Fos proto-oncogene (FOS) as the primary gene influenced by revascularization. These results identify novel hypoxia-related genes regulated by DNA methylation in PAD skeletal muscle, which may provide potential new therapeutic targets.

overall_design: Gastrocnemius muscle specimens were collected from the anteromedial segment of the gastrocnemius, approximately 10 cm distal to the tibial tuberosity yielding a total sample of ~250 mg, from 10 non-PAD controls (Control), 10 patients with symptomatic intermittent claudication, both at baseline (pre-revascularization, IC) and 6 months after revascularization treatment (IC-post), and 10 patients with critical limb ischemia (CLI). Reduced representation bisulphite sequencing (RRBS) was performed on genomic DNA.

first: A

first: P

last: Koutakis


title: Tandem duplications in UBTF create XPO1-dependent nuclear export signals necessary for leukemic progression [CUT&Run]

first: Jeffery

last: Klco

overall_design: CUT&RUN Genomic Occupancy Analysis of UBTF-TD in hematopoeitic cells and actue myeloid leukemia samples

first: Juan

last: Barajas


title: The role of Nonsense-Mediated mRNA Decay in restricting long noncoding RNAs expression has been conserved in RNAi-capable budding yeast

first: Maxime

last: Wery

type: Non-coding RNA profiling by high throughput sequencing

summary: In most Eukaryotes, sense/antisense RNA duplexes can be processed into small interfering RNAs by the ribonuclease III Dicer, a key component of the RNA interference (RNAi) machinery, which has been lost by the budding yeast Saccharomyces cerevisiae. Previous studies in this species revealed the pervasive formation of double-stranded (ds)RNA involving antisense Xrn1-sensitive long noncoding (lnc)RNAs, which interferes with their degradation through translation-dependent Nonsense-Mediated mRNA decay (NMD). However, apart from S. cerevisiae, little is known about the post-transcriptional metabolism of lncRNAs, in particular the functional impact of RNAi. Herein, we profiled NMD targets in Naumovozyma castellii, a budding yeast endowed with cytoplasmic RNAi. We identified 592 lncRNAs accumulating in a mutant of the NMD core factor Upf1. Most of them also accumulate in other NMD mutants and upon translation elongation inhibition, indicating a translation-dependent degradation mechanism. Consistently, Ribo-Seq analyses confirmed ribosomes binding for a fraction of them. Within the coding transcriptome, we found that the Dicer-coding mRNA is also regulated by NMD. The resulting upregulation of DCR1 in NMD-deficient cells correlates with an increased production of small RNAs from dsRNA-forming NMD-sensitive lncRNAs and mRNAs. Finally, we observed that Dicer inactivation in Upf1-lacking cells attenuates the accumulation of dsRNA-forming NMD targets. Together, our data highlight the conserved roles of NMD and translation in the post-transcriptional metabolism of lncRNAs, and provide insight into the functional impact of endogenous RNAi on the transcriptome.

overall_design: Refer to individual Series.

first: Ugo

last: Szachnowski

first: Constance

last: Creux

first: Quentin

last: Fouilleul

first: Marina

last: Lefrère

first: Antonin

last: Morillon


title: Multi-omics Analysis of Skeletal Muscle Identifies Dysregulation of Hypoxia-Induced Genes in Peripheral Artery Disease [RNA-seq]

overall_design: Gastrocnemius muscle specimens were collected from the anteromedial segment of the gastrocnemius, approximately 10 cm distal to the tibial tuberosity yielding a total sample of ~250 mg, from 10 non-PAD controls (Control), 10 patients with symptomatic intermittent claudication, both at baseline (pre-revascularization, IC) and 6 months after revascularization treatment (IC-post), and 10 patients with critical limb ischemia (CLI). RNA-sequencing was performed on purified total RNA.


title: Integrative Single-Cell RNA-Seq and ATAC-Seq Identifies Transcriptional and Epigenetic Blueprint Guiding Osteoclastogenic Trajectory [scRNA-seq]

first: Keita

last: Saeki

overall_design: 10x Genomics scRNA-seq platform comparing WT and Irf8floxCsf1rCre bone marrow cells (Irf8cKO)

first: Amitabh

last: Das

first: Stefania

first: Xiaobei

last: Wang


title: Tandem duplications in UBTF create XPO1-dependent nuclear export signals necessary for leukemic progression [scRNA-seq]

overall_design: scRNA-seq data


title: Mislocalisation of MED12L in the nucleolus of female MED12 p.Arg1138Trp patients leads to temporal changes in neural development and dysregulation of the pre-ribosome complex [RNA-seq]

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

country: Australia

institute: The Kids Research Institute Australia

summary:
Background: A genetic variant MED12 c.3423C>T,p.Arg1138Trp, classified as a variant of uncertain significance, was identified in a female patient with multiple congenital anomalies and developmental delay. MED12, located on the X chromosome, is a subunit of the Mediator complex which is involved in regulation of transcription and RNA polymerase II activity. The functional consequence of these MED12 genetic variants in disease is undetermined, and insight into disease mechanism is required.
Method: We compare disease in seven female MED12 p.Arg1138Trp patients with a disease phenotype including  Blepharophimosis – intellectual disability syndrome, Maat-Kievet-Brunner MKB type, Choleostasis-pigmentary retinopathy-cleft palate syndrome, and non-syndromic MED12-related condition. Inducible pluripotent stem cells were derived from patient PBMCs, followed by neural disease modelling for transcriptomics and functional protein analysis.
Results: The phenotype for female patients with the MED12 c.3423C>T, p.Arg1138Trp genetic variant, indicated overlapping and divergent clinical features. In comparison of MED12 genetic variant neural cells, derived from patient induced pluripotent stem cells (iPSCs), identified altered expression levels for genes that regulate RNA polymerase II activity (ZNF558, ZIM2, ZFP3, TBR1, PEG3, EMX1, DMRTA2), transcription and pre-mRNA processing (ZIM2, and SNRPN) and neural development (BMP3, CNP, EBF2, EMX1, EOMES, LXH5, NHLH1, UNCX). Transcriptomics analysis further revealed a reduction in pathways related to axon development, forebrain differentiation, and cell specification (neural cell specification); and significant upregulation of pathway gene sets related to pre-ribosome complex (nucleolus) in the MED12 genetic variant cells. Comparison of MED12 wild-type and MED12 p.Arg1138Trp neural progenitor cells indicated similar MED12 transcript and protein expression. However, there was a decrease in MED12L expression, at the transcript and protein level, and significantly reduced MED12L localisation to the nucleolus in the MED12 p.Arg1138Trp cells.
Conclusion: Patient iPSC derived stimulated for neural cell differentiation indicate delayed neural development in MED112 p.Arg1138Trp expressing cells providing functional evidence of disease aetiology. Disease mechanism in genetic variant neural cells was linked to decreased localisation of MED12L to the nucleolus and dysregulation of the pre-ribosome complex.

overall_design: To investigate the functional consequences of a variant of unknown significance (VUS), we generated iPSC lines from PBMCs derived from the patient. We then studied two clonal lineages: one of which expressed the MED12 VUS, and one of which expressed the WT MED12 transcript. We compared the transcriptomic profile of both lineages at days 0, 18, and 24.

first: Nicole

middle: C

last: Shaw

first: Saraya

middle: H

last: Harrison

middle: G

first: Catherine

middle: A

last: Forbes

first: Emma

last: Kuzminski

first: Mitchell

last: Hedges

first: Kathryn

middle: O

last: Farley

first: Michelle

last: Ward

first: Lily

last: Loughman

first: Cathryn

last: Poulton

first: Gareth

last: Baynam

first: Timo

last: Lassmann

first: Vanessa

middle: S

last: Fear


title: Mislocalisation of MED12L in the nucleolus of female MED12 p.Arg1138Trp patients leads to temporal changes in neural development and dysregulation of the pre-ribosome complex [Amp-seq]


title: Mislocalisation of MED12L in the nucleolus of female MED12 p.Arg1138Trp patients leads to temporal changes in neural development and dysregulation of the pre-ribosome complex

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

overall_design: Refer to individual Series


title: Differential response of patient-derived intestinal organoids to site-specific mucosal bacteria in pediatric inflammatory bowel disease

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

institute: Monash University

summary: Objective: Inflammatory bowel disease (IBD) is secondary to an abnormal immune response to the microbiota. There is evidence of impaired stem cell signatures in IBD contributing to impaired epithelial repair. We therefore aimed to study the role of the microbiome in the intestinal stem cell population in paediatric IBD cases, a group without confounding treatments or comorbidities, by directly studying the interaction between patient-isolated bacteria and the epithelium. Design: We established a unique biobank with matched intestinal organoids and cultured mucosally adherent bacteria from 36 paediatric patients. To determine the bacterial effect on host epithelial cells, closely related bacterial isolates from control and IBD patients were selected for microinjection into their corresponding organoid line. Results: Whilst no differences were observed between control and IBD-derived organoids following injury, transcriptional profiling revealed differential gene expression between uninjured control and IBD- derived organoids. Furthermore, following microinjection of an isolate originating from a control patient, there was upregulation of inflammatory signalling pathways, whereas this was not observed with a closely related isolate originating from an IBD patient. Conclusion: This demonstrates the feasibility of isolating bacteria and generating organoids from the same biopsy tissue, to explore personalised host-microbe interactions. The microinjections show the individual nature of responses, with closely related bacteria inducing very different epithelial responses, with downstream implications for immune response. This highlights the importance of understanding host-microbe interactions in a strain and site-specific manner, and developing techniques for personalised microbiome-based therapeutics.

overall_design:
Organoids from intestinal biopsies from an IBD patient were compared to those from a healthy individual. In addition, organoids were microinjected with a bacterial isolate that was specific to IBD patients or a closely related bacterial isolate from healthy individual and transcriptomes were compared. Controls included mock-injected organoids, or organoids that were externally exposed to the relevant bacteria rather than injected.

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

middle: K

first: Eva

last: Chan

first: Wing

first: Genevieve

last: Kerr

first: Thierry

last: Jardé

first: Helen

middle: E

last: Abud


title: Ablation of CD38 on Multiple Myeloma Cells Leads to an Aggressive Phenotype

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

summary: Multiple myeloma (MM), the second most common hematological cancer in the United States, is characterized by the proliferation of malignant clonal plasma cells primarily within the bone marrow. The multifunctional cell surface glycoprotein CD38 is expressed in majority of MM cells, making it a key biomarker. Since the FDA approval of daratumumab in 2015, CD38-targeted immunotherapies have significantly advanced the treatment of MM; albeit nonuniform patient response and relapse. The role of CD38 in the complex bone microenvironment remains under investigation. This study examined the effect of CD38 on tumor cells by evaluating a CD38 knock-out (KO) clone of a human MM cell line xenografted into immunodeficient mice. CRISPR/Cas9 gene editing was used to KO CD38 expression in the wild-type (WT) MM.1S human MM cell line (MM.1S-CBR-GFP), confirmed with RNA sequencing and flow cytometry. After tumor implantation in mice, bioluminescence imaging (BLI) was employed to track tumor cells. Small animal Positron Emission Tomography (PET) was performed with the metabolic tracer, fluorodeoxyglucose ([18F]-FDG), and CD38-targeted [89Zr]-Daratumumab, respectively. Post-PET tissue biodistribution and leg bone autoradiography was performed to evaluate tracer distribution. Computed Tomography (CT), dual-energy X-ray (DEXA), and immunohistochemistry were used to evaluate changes in bone mineral density and osteolytic disease. Differences in blood composition, cytokine production, and RNA sequencing between WT and KO mice were analyzed for characterizing the new CD38 KO phenotype. BLI showed significantly increased tumor burden in the CD38 KO MM models compared to WT mice after implantation: 1-week (P=0.0011), 2-weeks (P=0.0066), 3-weeks (P=0.0046), and 4 weeks (P<0.0001). CT and DEXA imaging revealed that the KO mice had significantly decreased bone density, and similarly, planar X-ray imaging indicated severe myeloma bone disease characterized by cortical and trabecular osteolytic lesions in the femur and tibia. Bone histology further confirmed the KO tumor more aggressively invading the bone and muscle tissue. [89Zr]-Daratumumab accumulated in the spine, femur, and tibia in WT MM mice, with minimal bone uptake in the CD38 KO MM mice. [18F]-FDG PET revealed an increased metabolic activity of CD38 KO MM, with an aggressive kinetic uptake of the tracer (P < 0.001). Bilateral kidney metastases were observed in nearly all CD38 KO MM mice, while remaining undetected in WT mice. Blood analysis indicated elevated markers of disease progression and renal dysfunction, with reduced leukocyte and thrombocyte production in the CD38 KO MM xenografts. Cytokine profiling revealed altered levels of pro-inflammatory cytokines, including IL-13, IL-6, RANKL, and VEGF-α in the bone microenvironment of MM with depleted CD38. RNA sequencing showed significant transcriptional changes in CD38 KO cells, suggesting that the observed enhanced aggressiveness is predominantly fueled by the activation of key pathways that promote accelerated cell proliferation, pathways that enhance osteoclast activity, and pathways that enhance metastatic potential.

overall_design: The human MM cell line, MM.1S, was obtained from Professor Katherine N. Weilbaecher in the Department of Medicine at Washington University School of Medicine (WUSM) and has been previously used to develop MM models.12, 13 The cell line was transduced with a lentivirus encoding green fluorescent protein (GFP), to enable visualization of cellular localization, and click beetle red (CBR), luciferase for bioluminescence-based tumor burden quantification and real-time monitoring of disease progression. The WT MM.1S cell line (MM.1S-WT-GFP-CBR) was genetically modified using CRISPR/Cas9 gene editing, performed by the McDonnel Genome Institute at WUSM, to create a CD38 KO clone (MM.1S-CD38 KO-GFP-CBR). The CD38 KO clone was expanded in bulk culture until sufficient cell aliquots were available for cryopreservation in liquid nitrogen. Similar to the WT MM.1S cell line, the CD38 KO clone cell line was tagged with GFP and CBR for visualization and bioluminescence analysis. RNA sequencing between WT and KO cells was performed to characterize the new CD38 KO phenotype. There were 6 RNA samples, 3 WT MM.1S cells and 3 CD38 KO cells.

first: Michael Riley

last: Dyer

first: Alex

last: Zheleznyak

first: Erin

last: Teubner

first: Julie

last: Prior

first: Brad

last: Manion

first: Han

last: Jing

first: Amit Kumar

last: Sharma

first: Junwei

last: Du

first: Deborah

last: Veis

first: John

middle: F

last: DiPersio

first: Rui

last: Tang

last: O’Neal

middle: Y

first: Monica

last: Shokeen


title: Super-Omics and PCAS Reveal Rheumatoid Arthritis as a Tumor-like Disease

city: Hangzhou

first: Feiyang

last: Ji

state: None Selected

address: 3 Qingchun East Road

institute: zhejiang university

summary: Rheumatoid arthritis (RA) is a debilitating systemic autoimmune disorder that significantly impairs quality of life. To elucidate the molecular alterations driving RA progression, we performed comprehensive super-omics analyses on synovial tissues from patients with joint trauma, arthritis, and RA. These analyses included transcriptomics, proteomics, metabolomics, microbiomics, and fourteen PTMs (phosphorylation, acetylation, lactylation, O-GlcNAc glycosylation, arginine monomethylation, lysine monomethylation, lysine dimethylation, lysine trimethylation, succinylation, malonylation, glutarylation, tyrosine nitration, N-glycosylation, and O-glycosylation). Additionally, we developed a protein-centered association study (PCAS) method to integrate these complex datasets. Using this approach, we identified key proteins, such as STK17B, and its interactors, which may be crucial in RA pathogenesis. Tumor-like features, including aberrant angiogenesis and epithelial-mesenchymal transition, were observed in RA, alongside the potential involvement of oncogenes and tumor suppressor genes. Finally, we constructed a molecular interaction map of RA, providing a comprehensive framework for advancing RA pathogenesis, diagnosis, and therapy.

overall_design: We selected 6 cases each of trauma patients, arthritis patients, and rheumatoid arthritis patients. Synovial tissue was obtained by removing the fat tissue from the joint capsule samples surgically excised from the patients. RNA was then extracted from the synovial tissue for gene expression sequencing, and the differences in gene expression among the three types of synovial tissue were analyzed.

first: Lanlan

last: Xiao

first: Shiwei

last: Ju

first: Xiaoxi

last: Ouyang


title: Bile duct ligation (BDL)-induced changes on the gene expression of different primary cells in mice liver.

city: Beijing

first: Runping

last: Liu

state: Beijing

address: 11 Beisanhuandonglu

institute: Beijing University of Chinese Medicine

summary: Cholestatic liver disease encompasses any condition characterized by impaired bile flow, culminating in excessive accumulation of toxic bile acids in the liver or systemic circulation, which can lead to liver fibrosis and even progress to liver failure. There is a notable lack of accurate and effective therapeutic drugs, highlighting the urgent need for new therapeutic targets. To identify the specific liver cell type that was damaged and contributed to liver injury following  bile duct ligation (BDL), primary hepatocytes (MPH), biliary epithelial cells (BECs), and Kupffer-like cells are isolated and subjected to bulk RNA-seq analysis.

overall_design: Biliary epithelial cells (BECs), Kupffer-like cells (Kupffer), hepatocytes (MPH), and hepatic stellate cells (HSC) are isolated from Sham and bile duct ligation (BDL) mice liver. Then total RNA of different primary cells is extracted and RNA sequencing analysis is performed.


title: Enhancing PARP inhibitor treatment efficacy for urothelial carcinoma by new biomarkers and synergistic combination treatment with bromodomain protein inhibitor PLX51107

city: Duesseldorf

first: Michèle

middle: J

last: Hoffmann

state: NRW

address: Moorenstr. 5

department: Urology

country: Germany

institute: Heinrich Heine University, Medical Faculty

summary: We characterized cellular and molecular effects of the PARP inhibitor (PARPi) Olaparib compared to Talazoparib in bladder cancer cell lines and their Cisplatin pre-treated sublines. We aimed to identify common target genes of both PARPi and differences in mechanism of action to understand resistance mechanisms and identify new PARPi response marker for bladder cancer. RNA was submitted to RNA sequencing analysis on the NextSeq2000 system (Illumina).

overall_design: Total RNA from urothelial carcinoma (UC) cell lines T24, T24 Cisplatin resistant cells (LTT), J82, J82LTT and RT112 cells treated with PARPI Olaparib or Talazoparib for 72h and compared to solvent control (DMSO). Triplicates were analysed for each condition.

first: Jutta

last: Schmitz

first: Anna L.

last: Bartkowiak

first: Patrick

last: Petzsch

first: Michael

last: Rose

first: Leandra

last: Lepping

first: Julka

last: Volkamer

first: Karl

last: Köhrer

first: Günter

last: Niegisch

first: Michèle J.

first: Tahlita C.M.

last: Zuiverloon

first: Tokameh

last: Mahmoudi

first: Vandana

last: Solanki

first: Nora

last: Kolks

first: Anne

last: Stoffel

first: Bianca

last: Faßbender

first: Marc

last: Seifert


title: Genome-wide maps of deaminated CPDs (dCPDs) in yeast, biological replicates 2 and 3.

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Here, we describe a genome-wide map of uracil lesions arising form deaminated UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast (Saccharomyces cerevisiae). Deaminated CPDs (dCPDs) were mapped at single nucleotide resolution across the yeast genome using the new dCPD-seq method in repair-deficient (rad14∆), G2/M-arrested (cdc13-1) yeast cells immediately after UV irradiation (0 hour) and following 6 hour (6hr), 24hr, or 48hr of deamination in arrested, repair-deficient yeast cells. We also generated a full deamination control, in which genomic DNA from a 48h cellular deamination sample was incubated in vitro for an additional 16h at 67C. We used these data to analyze CPD deamination in different trinucleotide sequence contexts, yeast genes, transcription factor binding sites, and nucleosomes.

overall_design: We used the new dCPD-seq method to map cytosine-containing UV-induced cyclobutane pyrimidine dimers (CPDs) that had undergone deamination to uracil. Deaminated CPDs were mapped at single nucleotide resolution across the yeast genome, both immediately after UV-irradiation of yeast cells (0 hour) and following 6 hour (6hr), 24hr or 48hr of deamination in arrested, repair-deficient yeast cells. We also mapped deamination in unirradiated cells (No UV control) and in genomic DNA from a 48h cellular deamination sample was incubated in vitro for an additional 16h at 67C, as a full deamination control.

first: Marian

last: Laughery


title: Deciphering Spatial Transcriptomic Signatures Reveals Insights into Perifascicular Atrophy in Dermatomyositis

city: Jinan

first: FUCHEN

last: Liu

state: 山东省

address: No 107, West Wenhua Road, Lixia District

institute: Qilu Hospital

summary: Dermatomyositis is an autoimmune disease that primarily affects the skin and muscles. Perifascicular atrophy is a characteristic feature of dermatomyositis, yet its underlying mechanisms remain unclear. Hereby we conducted spatial transcriptomics to study the changes in the RNA expression in the muscle fibers with perifascicular atrophy from patients with juvenile and adult dermatomyositis, compared with muscles with non-atrophic areas. Our findings provide new insights into the molecular mechanisms underlying perifascicular atrophy and highlight potential pathways for future investigation.

overall_design: We used the muscles of 1 patient with juvenile dermatomyositis and 1 patient with adult dermatomyositis. Both patients had perifascicular atrophy. The gene expression in the frozen section of muscles from both patients were tested with spatial transcriptomics.

first: Fuchen


title: Transcriptional differences in nasopharyngeal carcinoma cell lines induced to reactivate EBV lysis

city: 广州

first: 清双

last: 罗

address: 南方医科大学

institute: 第三附属医院

summary: We report transcriptional differences in the nasopharyngeal carcinoma cell line NPC43 following induction of EBV lysis and reactivation

overall_design: NPC43 cells (2.5*106 cells/well) were suspended in 1640 complete medium containing 10% fetal bovine serum and 1% penicillin/streptomycin, cultured at 37°C, 5% CO2, and seeded in each well of a 6-well culture plate (BiolandTM, CCP06-006). The pcDNA3.1-BZLF1(+) and empty vector pcDNA3.1 plasmid were transfected into NPC43 cells, respectively, and cultured for 48 h. It was verified that BZLF1 had been successfully induced to be expressed by RT-qPCR and Western Blot. The extracted RNA was used for library preparation, RNA sequencing and preliminary analysis.

first: Lyu

middle: X

last: Ming

first: Luo

middle: Q

last: Shuang

first: Long

last: Yi


title: TCR signal–enhancing mutation alters lipid metabolism of thymocytes and impairs antitumor immunity of mature T cells

first: Wenhua

last: Liang

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: The T cell receptor (TCR), a master regulator of adaptive immunity, serves as a molecular transducer that converts antigen recognition into precisely modulated intracellular signals, orchestrating both T cell development and effector functions. In this study, we leveraged a germline CD3εI173A mutation, a previously characterized alteration that amplifies TCR signaling through the disruption of inhibitory lipid interactions, to dissect how thymocyte-intrinsic TCR signaling amplification influences the fate of mature T cells. Remarkably, thymic double-positive cells in CD3εI173A mice with altered TCR repertoires demonstrated a significant downregulation of the phosphatidylserine decarboxylase homolog gene AC149090.1. This modulation triggered a comprehensive rewiring of lipid metabolic pathways, establishing a systemic compensatory mechanism to counterbalance excessive TCR signaling. These metabolic adaptations culminated in functionally compromised mature T cells, characterized by diminished activation potential, reduced proliferative capacity, and impaired antitumor efficacy in CD3εI173A mice. Our results underscore the critical role of thymic TCR signaling in T cell development for sustaining immune homeostasis and orchestrating mature T cell functionality, unveiling the lipid metabolic plasticity during thymocyte development that acts as a critical regulatory checkpoint for maintaining immune homeostasis.

overall_design: Thymic T cells from WT and I173A mice were isolated by Fluorescent cell sorting according to the CD4+CD8-, CD4-CD8+ and CD4+CD8+, and submitted for 10x genomics single-cell multiome sequencing.

first: Feng

last: Wang


title: Genome-wide maps of deaminated CPDs (dCPDs) following UV-irradiation in cells and deamination as naked DNA in vitro

summary: Here, we describe a genome-wide map of uracil lesions arising from deaminated UV-induced cyclobutane pyrimidine dimers (CPDs) that arose from UV irradiation of yeast cells (Saccharomyces cerevisiae) and deamination in vitro as isolated yeast genomic DNA (i.e., naked DNA control). Deaminated CPDs (dCPDs) were mapped at single nucleotide resolution across the yeast genome using the new dCPD-seq method in repair-deficient (rad14∆), G2/M-arrested (cdc13-1) yeast cells immediately after UV irradiation (0 hour) and following 6 hour (6hr), 24hr, or 48hr of deamination in solution in vitro. We also generated a full deamination control, in which genomic DNA from a 48h deamination sample was incubated in vitro for an additional 16h at 67C. We used these data to analyze CPD deamination in different trinucleotide sequence contexts, yeast genes, transcription factor binding sites, and nucleosomes.

overall_design: We used the new dCPD-seq method to map cytosine-containing UV-induced cyclobutane pyrimidine dimers (CPDs) that had undergone deamination to uracil. Deaminated CPDs were mapped at single nucleotide resolution across the yeast genome, both immediately after UV-irradiation of yeast cells (0 hour) and following 6 hour (6hr), 24hr, or 48hr deamination in vitro. We also mapped deamination in genomic DNA from a 48h deamination sample was incubated in vitro for an additional 16h at 67C, as a full deamination control.


title: The effect of STING knockout on gene expression in cholestatic mice

first: Runping

summary: STING has been identified to play a role in the onset and progression of various liver diseases.We aim to investigate whether STING mediates cholestatic liver injury. We here report that STING knockout significantly reversed cholestatic liver injury induced by bile duct ligation (BDL) and Mdr2 deficiency. Mechanistically, BDL induced the enrichment of several signaling pathways, including those associated with programmed cell death in the liver, type I interferon, innate immune response, chemotaxis, inflammation, senescence, and extracellular matrix assembly, which were significantly reversed by STING knockdown.

overall_design: Total liver RNA is extracted from mice, which are subjected to  bile duct ligation (BDL) for seven days or 60-day-old Abcb4 deficiency. Then, RNA sequencing analysis is performed.


title: N6-Methyladenosine reader YTHDF3 regulate Sindbis virus release by incomplete selective autophagy flux maintenance through SQSTM1

city: xi'an

first: yajing

last: zhao

address: No. 169, Changle West Road, Xincheng District

institute: Department of Oral & Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University

summary: N6-methyladenosine (m6A) is vital for RNA metabolism and function and is one of the most abundant internal RNA modiﬁcations. Recently, m6A has been indicated in regulating replication of multiple viruses; however, the role of m6A in typical arbovirus-alphavirus, is mainly elusive. Alphavirus containing several emerging and re-emerging pathogens that poses great threat to human health. Here, we show that the prototype alphavirus, Sindbis virus (SINV), its replication is regulated by m6A readers. Of which, depleting YTHDF3 results in reduced SINV release but increased viral capsid within the cell. Mechanically, YTHDF3 bind and regulate the mRNA stability of SQSTM1, the major selective autophagy receptor, which targeting of capsid into autophagosomes. Furthermore, we found interaction between YTHDF3, SQSTM1 and capsid in pairs. K27 ubiquitination is the dominant modification for SINV capsid. Besides ubiquitin-associated (UBA) domain, the N-terminal domain of SQSTM1 has stronger interaction with capsid, highlighted the role of RL peptide mimic within the capsid. Further experiments revealed that the interaction between YTHDF3 and SQSTM1 protein relies on their YTH-domain and ZZ-type Zinc finger domain respectively. Together, these results highlight the role of m6A modification reader YTHDF3 in regulating selective autophagy during virus infection and provide new insights into alphavirus replication cycle.

overall_design: To investigate the role of YTHDF3 in the regulation of cellular functionn, we established A549 cell lines in which  target gene YTHDF3 has been knocked down by shRNA. Then infected with SINV.

first: Wei

last: Ye

first: Yajing

last: Zhao


title: The effect of HDCA on gene expression in cholestatic mice

summary: HDCA has been reported to exhibit liver protective effects against chronic liver diseases, including MAFLD; however, its effect on cholestatic liver disease remains unclear. In this study, we elucidate the mechanism by which HDCA improves cholestatic liver fibrosis through the modulation of extracellular matrix.

overall_design: Mice subjected to  7-day bile duct ligation (BDL) were administered HDCA (100 mg/kg) for 4 days following a 3-day post-surgery period. Additionally, 60-day-old Abcb4-/- mice received 100 mg/kg of HDCA for a duration of 21 days. Total liver RNA was extracted, and RNA sequencing was subsequently performed.


title: LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

summary: In most eukaryotic cells, euchromatin is localized in the nuclear interior, whereas heterochromatin is enriched at the nuclear envelope (NE). This conventional chromatin organization is established by heterochromatin tethering to the NE, however its importance for cellular homeostasis is largely unexplored. Peripheral heterochromatin localization relies on redundant NE-tethering systems. One tether is constituted by the lamin B receptor (LBR) in mammals, but the enigmatic nature of the other tethers has hampered functional analyses. Here we demonstrate that the downregulation of abundant, ubiquitous NE proteins can induce the global detachment of heterochromatin from the NE. Among these factors, we identify LBR and LAP2 as major players in bulk heterochromatin attachment to the NE in pluripotent and differentiated mammalian cells. Their loss leads to repositioning of heterochromatin to the nuclear interior, changes in chromatin accessibility, deregulation of gene expression including activation of antiviral innate immunity, and defects in cell fate determination.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HCT116 and mESCs cells depleted of specific nuclear envelop proteins were subjected to RNA-, ATAC-, ChIP- and HiC-sequencing to decipher transcriptional and accessibility changes in these cells.

first: Renard

last: Lewis

first: Virginia

last: Sinigiani

first: Noura

last: Maziak

first: Krisztian

last: Koos

first: Cristiana

last: Bersaglieri

first: Ivo

last: Zemp

first: Caroline

last: Ashiono

first: Constance

last: Ciaudo

first: Peter

last: Horvath

first: Juanma

last: Vaquerizas

first: Raffaella

last: Santoro

first: Ulrike

last: Kutay


title: Human Primary Airway Epithelium Response to HCoV-229E Infection in the Presence and Absence of Human Macrophages

city: Richland

first: Lindsey

middle: N

last: Anderson

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary: The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection in the presence and absence of macrophages. Sample data was obtained for mock and infected (MOI 3) primary human airway epithelial cells with and without macrophages and grown in air-liquid interface conditions, processed for RNA sequencing (RNA-Seq) expression analysis.

overall_design: Mock infected and human coronavirus 229E infected samples in the presence or absence of macrophages were collected in primary human airway epithelial cells at 24 hours post infection. Cultures were first washed, inoculated with human coronavirus 229E for 2 hours and the inoculum removed and the cultures washed twice.  Freshly harvested primary human macrophages (isolated from PBMC) were then incubated on the apical surface for 4 hours prior to removal and two additional washes of the cultures.

first: Amy C

last: Sims

first: Hugh D

last: Mitchell

first: Lindsey N


title: The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [Embryo_RNA-seq]

city: Westmead

first: Riley

last: McMahon

address: 214 Hawkesbury Road

institute: Children's Medical Research Institute

summary: The development of the embryonic head in mice relies on the activity of the transcription factor LIM homeobox 1 (LHX1) in the anterior epiblast.  In this study, we sought to unravel the molecular role of LHX1 during and immediately following gastrulation. We utilized  CRISPR-Cas9 gene editing in embryo models as well as DamID-seq, RNA-seq, and ATAC-seq in mouse embryos. These techniques enabled us to reveal the genome wide targets of LHX1 for the first time in gastrulation stage mouse embryos. Integrated analysis of the omics datasets uncovered that LHX1 is instrumental in decommissioning the pluripotency network and determining the anterior fate of the precursor tissue of the embryonic head. We found that LHX1 directly binds to and regulates genes involved in WNT and FGF signaling pathway inhibition. We also identified a downstream target of LHX1, Kctd1, expressed in the anterior tissue, which acts to modulate canonical WNT activity. These findings identified a component of the gene regulatory network anchored by LHX1 that governs the development of the embryonic head.

overall_design: RNA-seq was run on day six embryoid bodies derived from wild type (R1 ESC), Lhx1-knockout or Kctd1-knockout mouse embryonic stem cells. RNA-seq was run on chimeric mouse embryos with high contribution of doxycycline inducible FLAG-Lhx1 or FLAG-Lhx1-Δ ESCs. Following 24 hours of doxycycline treatment in utero, E7.25 or E7.75 chimeric embryos were dissected and RNA was extracted from individual embryos. DamID-seq peaks were called for LHX1 from ESC and XEN derived neuruloids as well as, E7.75 chimeric mouse embryos. ATAC-seq was run on E7.25 and E7.75 embryos from wild-type (control) or Lhx1-epiCKO embryos.

first: Tennille

last: Sibbritt


title: The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [Embryo DamID-seq]


title: Disrupted Brain Progenitor Development and Signaling as a New Mechanism Underlying Microcephaly

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: Brain development relies on precise temporal and spatial patterning of progenitors, which form distinct brain regions. Mutations in the NDE1 gene cause severe developmental disorders like microlissencephaly and microhydranencephaly, characterized by abnormal brain morphology. To explore how NDE1 mutations disrupt brain development, we used human-derived models and validated findings in a mouse model. We applied advanced techniques, including microfluidic devices, live imaging, brain organoids, and RNA sequencing, to identify shifts in progenitor identity and extended mitosis duration. The NDE1 knockout altered the rostrocaudal axis, reducing forebrain size and affecting the dorsoventral axis by elevating ventral markers. Mechanistically, abnormal FGF and ERK signaling pathways were implicated. These findings reveal critical insights into the molecular mechanisms driving brain malformations linked to NDE1 mutations, suggesting a novel mechanism for microcephaly.

overall_design: Rostrocaudally patterned neural tube models were derived from wild type and NDE1 knock-out human pluripotent stem cells. On day 9 of culture, the tissues were cut in half and dissociated to perform scRNA-seq.

first: Orly

last: Reiner

first: Jianping

last: Fu

first: Jeyoon

last: Bok

first: Rami

last: Tshuva

first: Mio

last: Nonaka

first: Tamar

last: Sapir

first: Xuefeng

last: Xue

first: Bidisha

last: Bhattacharya

first: Aditya

last: Kshirsagar

first: Miri

last: Danan-Gotthold


title: Inferring differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data

city: Ann Arbor

first: Joshua

last: Welch

state: MI

address: 500 S State St

department: DCMB

institute: University of Michigan

summary: Understanding the gene regulatory mechanisms that establish and maintain cell type identities is a central goal in cellular and developmental biology. Single-cell RNA sequencing and multi-omic profiling have revolutionized this field, enabling high-resolution investigation of gene expression dynamics across differentiation stages. RNA velocity, which estimates gene expression changes using mechanistic models, has emerged as a powerful approach for trajectory inference. Recent advances in RNA velocity methods address key limitations such as steady-state assumptions and lack of support for multi-omic data but still fall short in multi-sample integration and differential testing. To overcome these challenges, we introduce MultiVeloVAE, a probabilistic framework for multi-sample RNA velocity inference that integrates single-cell RNA and multi-omic data. MultiVeloVAE models gene expression on a shared time scale, accounts for lineage bifurcations, and enables statistical testing of velocity parameters. Our approach achieves a good balance between batch correction and biological variance conservation and outperforms existing methods in trajectory reconstruction. Using newly generated 10X Multiome datasets from human embryoid bodies and hematopoietic cells, we demonstrate that MultiVeloVAE provides novel insights into chromatin accessibility and gene expression dynamics during development. These results highlight the potential of MultiVeloVAE as a comprehensive tool for de novo multi-omic trajectory analysis and biological discovery.

overall_design:
Human EB, HSPC, and macrophage multi-omic sequences on 10X Genomics platform.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************

**Raw data for HSPC and Macrophage samples has been deposited to dbGAP phs002915.v2.p1**

first: Chen

last: Li

first: Yichen

last: Gu

first: Maria

last: Virgilio

first: Kun

last: Lee

first: Kathleen

middle: L

last: Collins

middle: D


title: Single cell RNA sequencing of TSCM predominnant allogeneic anti-BCMA CAR-T cells

city: San Diego

first: Hubert

last: Tseng

state: CA

address: 9390 Towne Centre Drive Suite 200

institute: Poseida Therapeutics

summary: We characterize the phenotype and heterogeneity of P-BCMA-ALLO1, a TSCM-predominant allogeneic CAR-T therapy targeting BCMA in heavily pretreated relapsed/refractory multiple myeloma. Our analyses showed that P-BCMA-ALLO1 has a high frequency of memory CD8+ T cells, and their abundance correlates with antitumor potency. This finding matches our other observations that memory phenotype and functionality correlates with antitumor efficacy, along with viability and cytotoxicity.

overall_design: 18 different lots of research-grade P-BCMA-ALLO1 from 15 different healthy donors were run for scRNAseq to find correlates of antitumor potency

first: Andrew

last: Bacong


title: The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [Neuruloid_DamID-seq]

first: Riley

last: McMahon

first: Tennille

last: Sibbritt


title: Human Primary Airway Epithelium Response to HCoV-229E Infection

first: Lindsey

last: Anderson

summary: The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected (MOI 3) primary human airway epithelial cells grown in air-liquid interface conditions, processed for RNA sequencing (RNA-Seq) expression analysis.

overall_design: Mock infected and human coronavirus 229E infected samples were collected in primary human airway epithelial cells at 24 hours post infection

first: Amy

middle: C

last: Sims

first: Hugh

last: Mitchell


title: The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [EB_RNA-seq]


title: The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [Embryo_ATAC-seq]


title: Human A549 and MRC5 Cell Response to HCoV-229E Infection

summary: The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected (MOI 5) immortalized human lung epithelial cells (A549) and immortalized human lung fibroblasts cells (MRC5) processed for RNA sequencing (RNA-Seq) expression analysis.

overall_design: Mock infected and human coronavirus 229E infected samples were collected in A549 and MRC5 cells at 24 hours post infection

first: Sims

last: Amy C.

first: Mitchell

last: Hugh D.

first: Anderson

last: Lindsey N.


title: Genome-wide repetitive element expression associated with the tumor suppressor gene p53

city: Rochester

first: Julia

last: Freewoman

state: NY

address: 1 Lomb Memorial Dr

department: Thomas H. Gosnell School of Life Sciences

institute: Rochester Institute of Technology

summary: Using newly created RNA-seq data and previously published data the DE RE expression patterns were investigated for patterns in expression.

overall_design: Eighteen samples of IMR90 derived total RNA.  These samples include 2 none-treatment control, 8 DMSO control 2 associated with each time point and drug treatment, 6 5-FU treatments 2 for 6 hours, 12 hours and 24 hours, and 2 Nutlin at 6 hours.

last: Rosato

first: Rajiv

last: Snape

first: Feng

last: Cui


title: S-nitrosylation of IRF7 induced by NOS1 expression in Melanoma suppresses anti-tumor immunity [scRNA-seq]

city: Guangzhou

first: Yuxin

last: Dai

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

summary: Endogenous nitric oxide (NO) produced by nitric oxide synthases (NOSs) plays an important immunosuppressive role in the tumor microenvironment. In melanoma, NOS1 expression was increased with tumor progression and correlated with tumor immune escape through inhibition on type I interferon (IFN) signaling. However, the immune regulatory role and its related mechanism of NOS1 and its impacts on immune therapy such as immune checkpoint blockade (ICB) in melanoma is unclear. Here, we found that NOS1 expression induced IRF7 modification by s-nitrosylation at C435 site in mouse (C481 in human), which functionally promotes tumor growth in mouse models. Mechanically, IRF7-C435-SNO inhibited IFNβ transcription under PRR signal activation, leading to disorder in initiation of type I interferons response in melanoma cell. In melanoma mouse model, IRF7-C435-SNO decreased infiltration and activation of CD8 T cells  in tumor microenvironment, by reducing antigen presentation processes in tumor cells and inhibits the maturation of DC1. Clinically, high expression of NOS1 correlated with poor survival prognosis and resistance with to ICB anti-tumor therapies in melanoma cases  with less immune cell infiltration.  Our study  suggested that NOS1 expression in melanoma characterizes IFN-I signal disorders in response to innate immune stimulation by IRF7 s-nitrosylation. Targeting NOS1 signaling might benefit for overcome of immune therapeutically resistance particularly in immune cold melanoma phenotype.

overall_design: Live CD45+ immune cells from melanoma lung metastasis tissue in C57 mice were isolated by Fluorescence-Activated Cell Sorting (FACS) based on the presence or absence of IRF7 mutations and subsequently analyzed using scRNA-seq.

first: Sisi

last: Zeng

first: Keyi

last: Li

first: Qiuzhen

last: Liu


title: Bifidobacterium lactis Derived Vesicles Attenuates Hippocampal Neuroinflammation via Targeting IL-33 to Regulate FoxO6/P53 Signaling

city: beijing

first: Haina

last: Gao

address: fucheng road

institute: beijing technology and business university

summary: Hippocampal Neuroinflammation (HNF) is a critical driver of cognitive impairment. The lipo-polysaccharide (LPS) accumulate amyloid beta (Aβ) and lead to HNF. The Bifidobacterium lactis (BL) 99 have anti-inflammatory ability. However, the whether BL99-derived microbiota-derived vesi-cles (MV) could alleviate LPS induced HNF remain unclear.

overall_design: To investigate, we used ultrafiltration with ultracentrifuge to extract BL99-derived-MV (BL99-MV). We used hippocampal neuronal HT22 cells (HT22) to establish LPS induced HNF model, and ex-plored BL99-MV alleviate LPS induced HNF. The confocal microscopy showed that BL99-MV were taken up by HT22 and reduced oxidative stress (ROS) level. The PCR showed that BL99-MV up-regulate IL-10 level, down-regulate TNF-α, IL-1β and IL-6. Transcriptomic analysis revealed that 4,127 differentially expressed genes, with 2,549 genes upregulated and 1,578 genes down-regulated in BL99-MV group than LPS group. Compared to LPS group, BL99-MV decreased FoxO6, IL-33, P53 and NFκB expression, while increased FoxO1 and Bcl2 expression. The WB showed that BL99-MV modulated NFκB, FoxO6, P53, Caspase9 and Caspase3 protein expression via reducing IL-33 expression in HT22. The findings demonstrated that IL-33 as a regulator for FoxO6/P53 signaling.

first: Xiaoyu

last: Du


title: PROM1/CD133 MARKS A PROLIFERATIVE STEM CELL LIKE POPULATION OF BLASTS IN KMT2A REARRANGED INFANT ALL

city: Oxford

first: Joe

middle: Wilson

last: Cross

address: Wellington Square

country: United Kingdom

institute: University of Oxford

summary: Among pediatric acute lymphoblastic leukemias (ALL), KMT2A-rearranged infant ALL (KMT2Ar iALL) carries a particularly poor prognosis due to high rates of treatment-refractory or relapsing disease.  Mechanistically, KMT2Ar drives aggressive disease through epigenetic dysregulation of multiple genes as a direct effect of expression of KMT2A-fusion proteins, most commonly KMT2A::AFF1, in leukemic cells. We previously showed that one of the top 2 most dysregulated genes, PROM1 (Prominin-1), encodes the cell surface protein prominin-1/CD133 and that this is essential for proliferation of KMT2A::AFF1+ cell lines.  Here we show that PROM1 gene expression and cell surface CD133 expression specifically mark a highly proliferative subset of KMT2A::AFF1 blasts both in primary patient samples and in our highly physiologically relevant, primary human fetal liver HSPC-derived KMT2A::AFF1 ALL model (CRISPRKMT2A::AFF1 ALL). CD133+ CRISPRKMT2A::AFF1 blasts, but not CD133- CRISPRKMT2A::AFF1 blasts, exhibit a stem-cell gene expression profile and drive more aggressive disease in vivo. Furthermore, CRISPR-mediated inactivation of PROM1 reduces leukemic proliferation and prolongs survival of mice transplanted with CRISPRKMT2A::AFF1 blasts. These data show that PROM1/CD133 expression has an important functional role in CRISPRKMT2A::AFF1 ALL, and supports targeting PROM1/CD133 by pharmacological or immunotherapy-based approaches in KMT2A::AFF1 iALL.

overall_design: CRISPR-KMT2A::AF4 leukaemias were generated as previously described (Rice et al. doi:10.1038/s41467-021-27270-z). Up to 300,000 CD19+CD133+ and CD19+CD133- blasts were sorted from CRISPR-KMT2A::AF4 leukaemias (n = 3)  and RNAseq libraries generated as previously described (O'Byrne et al. doi:10.1182/blood.2019001289).


title: Enhanced T cell-monocyte interation allievates malaria-associated acute respiratory distress syndrome : Bulk RNA-seq

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

summary: Malaria-associated acute respiratory distress syndrome (MA-ARDS) is a severe manifestation of malaria with high mortality and no effective treatment. IFN-γ, a key regulator of immunity, plays a role in both promoting and suppressing malaria infection, though its effects on specific cell types remain unclear. In this study, we show that IFN-γ directly enhances CD8+ T cell proliferation, cytotoxicity, and cytokine production in a MA-ARDS mouse model. In IFNGR1-deficient T cells, IFN-γ deficiency led to increased CD8+ expression on Ly6c+ monocytes, enhancing their phagocytic ability. These findings highlight the role of T cell IFN-γ signaling in modulating monocyte function and suggest targeting this pathway could improve T cell-based therapies for MA-ARDS

overall_design: To investigate the mechanisms underlying the lung adaptive immune response during malaria-associated acute respiratory distress syndrome (MA-ARDS), we performed a comprehensive transcriptomic analysis of lung tissues collected from infected mice at multiple time points. A total of 28 lung samples were analyzed, representing six critical time points during the infection: 3, 5, 7, 9, 11, and 13 days post-infection (dpi). As a control, we included lung samples from naïve, uninfected mice to provide baseline comparisons. This design enables us to capture dynamic changes in gene expression associated with the progression and resolution of MA-ARDS, thereby providing insight into the immune responses involved at various stages of the disease

first: Jingwen

last: Lin

first: Shasha

last: Chen

first: Qingxin

last: Yang


title: The glial cells missing 1 triggers gliosis and vasculogenesis after neonatal brain injury [ChIP-Seq]

city: Setagaya

first: Kazuhiko

last: Nakabayashi

country: Japan

institute: NCCHD

summary: The glial cells missing (gcm) protein in Drosophila plays a crucial role in the cell fate switch in the nervous system and in induction of glial cell differentiation. However, the functions of the mammalian homologue Gcm1 in normal neural development and pathological conditions remain elusive. Here, we report that Gcm1 was upregulated in Nestin+ cells immediately after neonatal brain injury, followed by accumulation of GFAP+ and Olig2+ cells in the penumbra region. In addition, Gcm1 strongly induced vasculogenesis in the injury lesion as well as in the developing brain via the actions of VEGF-A and VEGF-C. Lack of Gcm1-mediated vasculogenesis could be a major cause of the dysplasia in placental labyrinths found in Gcm1–/– embryos, leading to embryonic lethality. Our data suggest that Gcm1 triggers both gliosis and vasculogenesis after brain injury and could be a target for therapeutic intervention.

overall_design: ChIP-seq for HA was performed for mouse neuroblastoma Neuro2a cells.

first: Naoko

last: Morimura

first: Seiji

last: Hitoshi


title: Anti-Glycan Reactivity in Humans is Driven by the Selection of B cells Utilizing Private Antibody Gene Rearrangements that are Affinity Maturated in Germinal Centers

city: Birmingham

first: Rodney

middle: Glenn

last: King

state: AL

address: 411 Shelby Interdisciplinary Biomedical Research Building 1825 University Boulevard

department: Microbiology

institute: University of Alabama at Birmingham

summary: The human antibody repertoire is broadly reactive with carbohydrate antigens represented in the universe of all living things, including both the host/self- as well as the commensal microflora-derived glycomes. Here we have used BCR receptor cloning and expression together with single-cell transcriptomics to analyze the B cell repertoire to the ubiquitous N-acetyl-D-glucosamine (GlcNAc) epitope in human cohorts and dissect the evolutionary history of this predominant class of antibodies. We find that circulating anti-GlcNAc B cells exhibiting canonical BMem phenotypes emerge rapidly after birth and couple this observation with evidence for germinal center-dependent affinity maturation of carbohydrate-specific B cell receptors in situ during early childhood. Direct analysis of individual B cell clonotypes reveals they exhibit strikingly distinct fine-specificity profiles for palettes of GlcNAc containing moieties. These results suggest that a generalized, exposure to complex environmental glycans drives the steady state anti-glycan repertoire.

overall_design: CD19 expressing B cells and Group A Carbohydrate binding B cells were facs sorted and subjected to scRNAseq and BCR seq

first: James

last: New

first: Christopher

last: Fucile

first: Amanda

middle: R

last: Callahan

first: Julia

last: Burke

first: Wayne

last: Duck

first: Alexander

last: Rosenberg

first: John

last: Kearney

middle: G


title: Fluoxetine promotes recovery from noise-induced cochlear neural degeneration

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

country: South Korea

institute: CHA university

summary: Fluoxetine treatment after noise exposure restored cochlear synaptic expression of brevican and decreased low-frequency hearing thresholds. In cochlear nuclei, fluoxetine treatment decreased the expression of PNN and was predicted to upregulate the neuropeptide signaling pathway

first: Hyunju


title: TOR1-Mediated Control of Lifespan Genes: Insights from Saccharomyces cerevisiae

city: Canakkale

first: Melih

last: GUNAY

address: Izmir Street, Terzioglu Campus,

country: Turkey

institute: Canakkale Onsekiz Mart University

summary: This study investigated the effects of TOR1 gene deletion on Saccharomyces cerevisiae through transcriptome analysis of wild-type and tor1Δ mutant cells during exponential development under non-stress circumstances. A significant number of differentially expressed genes (DEGs) were identified in the absence of TOR1, comprising 1665 upregulated genes and 1425 downregulated genes. These findings demonstrate the extensive impact of TOR signaling on several biological processes, including metabolism, stress response, and lifespan regulation. A significant number of differentially expressed genes (DEGs) were identified in the absence of TOR1, comprising 1665 upregulated genes and 1425 downregulated genes. These findings demonstrate the extensive impact of TOR signaling on several biological processes, including metabolism, stress response, and lifespan regulation. A total of 736 DEGs were associated with either replicative lifespan or chronological lifespan, further emphasizing the significance of TOR1 in aging. Although genes associated with glucose transporters and storage were upregulated, glycolytic genes remained unchanged, indicating a metabolic shift towards alternative pathways such as gluconeogenesis and the pentose phosphate pathway. Among these, HXK1 exhibited the highest upregulation in tor1Δ cells, contrasting with HXK2, whose expression remained stable. This suggests that HXK1, typically active under low glucose or caloric restriction, plays a crucial role in reregulating glucose metabolism in the absence of TOR1. The research also identified specific transcription factors, including ADR1, HAP4, and their paralogs, which were upregulated and bound only to the HXK1 promoter, pointing to their regulatory role in this metabolic shift. The findings indicate that TOR1 inactivation triggers nutrient- and energy-sensing mechanisms that redirect cellular resources towards stress adaptation and longevity, highlighting Tor1's crucial function in aging and proposing that modulation of the TOR pathway could be a potential strategy for anti-aging therapies.

overall_design:
For the investigation of the effect of tor1Δ on the wild type S. cerevisiae, yeast strains were growth on the minimal growth medium until the exponential stage. Samples in the exponential stage were collected, the RNA extraction was carried out, and cDNA libraries were constructed, and cDNA samples were sequenced by the Ion Torrent Sequencing platform.
Gene expression profiles of wild type and mutant yeast cells were determined utilizing RNA-Seq data from yeast samples. After, lifespan related genes retrieved from Sachharomyces Genome Database (SGD) and analysed with our general transcriptom datasets.

first: Tülay

last: Turgut Genç

last: Günay


title: Inhibition of PfCLK3 directly affects RNA splicing and influence the splicing machinery.

city: Glasgow

first: Katarzyna

middle: Kinga

last: Modrzynska

state: Glasgow (City of)

address: B627 Sir Graeme Davies Building, 120 University Place

institute: Wellcome Trust Centre for Molecular Parasitology

summary: Next generation antimalarials are required to be active across different Plasmodium species, offering cure and transmission blocking capability. Previously, we employed an extensive array of approaches (chemo-genetics, adaptive evolution followed by whole genome sequencing and mosquito membrane feeding assays) to validate the protein kinase PfCLK3 as an antimalarial target with these properties. Due to the close relationship of PfCLK3 to human kinases PRPF4B and CLK2 involved in key phosphorylation events that drive the assembly of the spliceosome, we hypothesise that the malaria kinase plays a role in splicing and RNA processing in Plasmodium parasites. However, no direct investigation has been carried out to confirm this postulation. Here, we present evidence that PfCLK3 inhibition by our tool compound TMCDC-135051 results in disruption of RNA-splicing. Following 1-hour exposure of 30-hours post invasion trophozoites to TCMDC-135051, RNA-sequencing revealed that RNA-splicing was extensively affected. In these experiments, multiple splice-junctions were mis-spliced in treated parasites compared to untreated controls. This effect was not seen in parasites expressing a mutant form of PfCLK3 (PfCLK3_G449P) insensitive to TCMDC-135051 – indicating the impact of the inhibitor on RNA-splicing in wild type parasites is via PfCLK3 inhibition. Importantly, analysis of the function of mis-spliced transcripts showed that the effected genes were involved in several essential parasite processes. In summary we established the role of PfCLK3 as a master regulator of spliceosome activity and RNA splicing in P. falciparum parasites and confirmed the mechanism of action of TMCDC-135051. This system can now be used to further investigate the mechanism of splicing in Apicomplexa and optimise CLK3 selective inhibitors.

overall_design:
To investigate the effect of PfCLK3 inhibition on P falciparum 3D7 parasites, tightly synchronised wild type 3D7 and mutant parasites expressing mutant PfCLK3 (G449P) resistant to the PfCLK3 inhibitor were grown to a parasitaemia of 2-4% and 2% haematocrit upto 30-hours post invasion (30-hpi). Parasites were then treated with 1µM of TCMDC-135051, the selective  PfCLK3 inhibitor for 1-hour under standard cultire conditions. The culture was spun down to pellet the cells and TRiZol was added as RNA preservative and stored at -80 until RNA purification.
Using the purified RNA, we then prepare poly-A RNA librabry and proceed to sequencing using Illumina sequencing with upto 30-million paired-end reads.
The RNA-sequencing data was used to investigate differential expression and differential splicing comparing resistant mutant and wild type parasites.

first: Omar

last: Jaha

first: Andrew

middle: B

last: Tobin


title: ATAC-seq analysis of WT and Pik3cdE1020K/+ in vitro polarizaed mouse Th2 cells

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

summary: Activating mutations in the PI3K-delta gene result in a primary immunodeficiency called Activated PI3K delta syndrome. Using a mouse model of APDS (Pik3cdE1020K/+) we sought to understand the role of PI3K-delta hyperactivation in regulating chromatin accessibility. Here we performed ATAC-seq analysis of in vitro polarized WT and Pik3cdE1020K/+ Th2 cells.

overall_design: ATAC-seq for in vitro polarizaed mouse Th2 cells

first: Kan

last: Jiang

first: Hong-Wei

last: Sun

first: Hiroyuki

last: Nagashima

first: Dominic

last: Golec

first: Pamela

last: Schwartzberg


title: Effect of knockdown of ACSS2 on H3K27ac in the HepAD38

city: Wuhan

first: jie

last: yang

address: No. 888 Gaoxin Avenue, Wuhan

institute: Wuhan IGENEBOOK Biotechnology Co.,Ltd

summary: Our study identified ACSS2 as the epigenetic regulators in HBV-related HCC and was essential in cellular proliferation. ACSS2 promoted HBV-related HCC proliferation mainly depended on the accumulation of acetyl-CoA via tis enzymatic activity. Through the joint analysis of RNA-seq and CTU&TAG-seq, we found ACSS2 promoted HBV-related HCC proliferation by mitophagy via the upregulation of H3K27ac.

overall_design: To investigate the downstream of ACSS2, ACSS2 knockdown in HepAD38 cells was established by shRNA.


title: The effect of leptin on the genome wide enrichment of cJun in OVCAR8 cells

first: jingtao

last: wang

address: No. 299, Bayi Road, Wuchang District, Wuhan City, Hubei Province

institute: Wuhan University

summary: Studies have shown that leptin activates several signaling pathways and stimulates the expression of numerous downstream genes and that the key transcription factor that exerts this effect might serve as a promising therapeutic target in leptin-driven ovarian cancer. cJun is a widely recognized transcription factor that is located downstream of MAPK signaling pathways, and encodes a nuclear protein that regulates various aspects of cell growth and differentiation. c-Jun is activated by JNK through phosphorylation at Ser63, Ser73, Thr91, and Thr93, and by ERK and p38 via increased gene expression. However, whether c-Jun is involved in leptin-mediated stemness maintenance in ovarian cancer remains mostly unknown.

overall_design: We examined the genome-wide enrichment of c-Jun after leptin treatment in the OVCAR8 cell line. OVCAR8 cells were serum starved overnight and then treated with 100 ng/ml leptin for 24 h. Chromatin immunoprecipitation DNA sequencing (ChlPseq) for cJun and H3K27ac in OVCAR8 cells.

first: J

middle: T

last: Wang

first: F

last: Yang

last: Li

first: W

last: Zhang


title: ICAM1 mRNA Functions Independently of Protein Coding to Inhibit Translation via a dsRNA-ILF2/ILF3 Pathway in Lung Cancer [CUT&Tag]

city: Nanjing

first: siyuan

last: jiang

state: Jiangsu

address: sipailou NO2

department: Zhongda Hospital

institute: Southeast University

summary: This study investigates the role of Intercellular Adhesion Molecule 1 (ICAM1) in lung cancer using RNA-seq and CUT&Tag sequencing. We performed ICAM1 knockout and knockout&knockdown experiments in CALU-1 lung cancer cells to examine changes in gene expression and chromatin accessibility. Our findings provide insights into ICAM1's regulatory mechanisms and its potential as a therapeutic target in lung cancer.

overall_design: RNA-seq was performed on ICAM1 knockout and knockout&knockdown CALU-1 cells, along with control samples. CUT&Tag sequencing was conducted on ICAM1 knockdown in Calu-1 knockout cells and corresponding controls to assess changes in chromatin accessibility.

first: Siyuan

first: Jinghan

first: Ya

last: Gao

first: Haifeng

first: Ying

last: He

first: Yibi

first: Zhiyuan

last: Xu

first: Shuwen

last: Cheng

first: Hong

last: Yan

first: Liqiang

last: Duan

first: Peng

first: Shan


title: Loss of ribosomal RNA methyltransferase Nsun5 Leads to Hypomyelination and Reduced Sleep Amount [BS-seq]

city: Shanghai

first: Huali

last: Shen

address: 130 Dongan Road

institute: Fudan University

summary: Sleep is regulated by intricate homeostatic and circadian systems and is influenced by genetic, environmental, and lifestyle factors. However, the roles of the epitranscriptome in sleep-wake regulation remain to be clarified. Here, we find that mice lacking the rRNA methyltransferase Nsun5 exhibit prolonged wakefulness. The absence of Nsun5 decreases 28S rRNA m5C levels, impairing the translational efficiency of nascent proteins associated with myelination, microtubule-based movement, and ribosome binding. This leads to a decreased number of oligodendrocytes and hypomyelination. These deficits result in increased excitability, particularly within the cortex. Notably, restoring myelination properties with clemastine or blocking the abnormally exposed voltage-gated potassium channels rescues the sleep phenotype, suggesting that reduced sleep is associated with hypomyelination. These findings highlight the significant role of epigenetic modifications in sleep regulation and offer broad mechanistic and therapeutic implications for brain disorders involving both myelin and sleep disturbances.

overall_design: To elucidate the role of Nsun5-mediated m5C modification in the brain and its impact on sleep phenotypes, we conducted a multi-omics analysis comparing Nsun5-KO mice to WT mice. This analysis included bisulfite sequencing (BS-seq) analysis of m5C methylation in mRNA in the CC, rRNA m5C methylation detection in the whole brain, transcriptome sequencing of the whole brain, ribosome profiling (Ribo-seq) of the whole brain.

first: Peipei

last: Chen

first: Zhi-li

last: Huang


title: Identification of miR-34c-5p as a potential regulatory molecule associated with testicular development of black goat

city: Nanning

first: Zhiqiang

address: No. 6 TaoYuan Rd.

institute: Guangxi Academy of Medical Sciences and the People’s Hospital of Guangxi Zhuang Autonomous Region

summary: The growth and mature of Sertoli cells (SCs) are important part of testicular development and miRNAs are considered as novel regulatory molecules involved in it. Here we systematically screened and analyzed the key miRNAs participating in testicular development of black goat, as well as identifying underlying mechanism of candidate mRNAs contributes to spermatogenesis. The miRNA transcriptional profiles of testicular tissues at 3 days old (D3), 30 days old (D30), 90 days old (D90) and 180 days old (D180) were constructed and comparative analyzed. Results showed that the most differentially expressed (DE) miRNAs were found between the testicular tissues of D30 and D90 black goats. Moreover, the predicted target genes of DE miRNAs are mainly enriched in biological processes including cell proliferation, cell composition and enriched in signaling pathways including p53, FoxO and PI3K-Akt. The top one DE miRNA (miR-34c-5p), which significantly highly expressed in the testis of D90 when compared to that of D30, was mainly located within SCs and targeted to IGF1R. By performing miR-34c-5p overexpression and RNA interference, we found that the function of miR-34c-5p in SCs was inhibited cell proliferation, increased apoptosis rate, and significantly reduced the expression of growth factors (CXCL12, BMP4, GDNF and IGF1). In summary, our study suggests that miR-34c-5p can serve as a potential target for regulation of testicular development and a reference marker of sex maturation applicated in black goat genetic breeding.

overall_design: To investigate the roles of miRNAs in the regulation of black goat testicular development, twelve cDNA libraries of neonatal (D3-1, D3-2, D3-3), prepuberty (D30-1, D30-2, D30-3), puberty (D90-1, D90-2, D90-3) and postpuberty (D180-1, D180-2, D180-3) testes were constructed. Then performed comparative gene expression profiling analysis of RNA-seq data and identified key DE miRNAs. Finally,  the location and function of  key miRNA (miR-34c-5p ) in Sertoli cells  were confirmed.

first: Chan

last: Luo

first: Deshun

last: Shi


title: Loss of ribosomal RNA methyltransferase Nsun5 Leads to Hypomyelination and Reduced Sleep Amount [Ribo-seq]


title: S-nitrosylation of IRF7 induced by NOS1 expression in Melanoma suppresses anti-tumor immunity

first: Yuxin

last: Dai

overall_design: Examination of IRF7-C435A mutant versus wild-type B16F10 mouse melanoma cells with and without IFNα stimulation.

first: Sisi

last: Zeng

first: Keyi

first: Qiuzhen

last: Liu


title: Loss of ribosomal RNA methyltransferase Nsun5 Leads to Hypomyelination and Reduced Sleep Amount [RNA-seq]


title: HMGA2 overexpression drives a leiomyoma-like phenotype by modulating the epigenomic environment in primary myometrial cells [RNA-Seq]

city: Chicago

first: Debabrata

last: Chakravarti

state: IL

address: 303 E Superior St.

department: Obstetrics and Gynecology

institute: Northwestern University

summary: High-mobility group AT-hook 2 is a non-histone chromatin binding nuclear protein that belongs to the high-mobility group A family, which are known as "architectural transcription factors". Overexpression of HMGA2, resulting primarily due to chromosomal rearrangements of 12q15 loci, is considered a driver event in approximately 10% of uterine leiomyoma cases. To better understand how HMGA2 overexpression contributes to the formation of uterine leiomyoma, we generated primary myometrial cells engineered to overexpress HMGA2 (n=3) and determined the effect of HMGA2-overexpression on genome-wide mRNA levels, H3K27ac deposition, and chromatin accessibility.

overall_design: Primary myometrial cells were obtained from three patients and treated with empty or V5-tagged HMGA2 vector using lentiviral transduction. RNA was harvested from these cells and used for next generation sequencing.

first: Priyanka

last: Saini

first: Austin

last: Holmes

first: Jian-Jun

last: Wei

first: J

last: Parker


title: Targeted delivery of viridicatol from deep-sea-derived fungus for ameliorate bone loss through the SHN3/SLIT3 pathway

city: Xiamen

first: Chunlan

last: Xie

address: Daxue

summary: The adaptor protein Schnurri-3 (SHN3) is an attractive target for osteoporosis, fractures, and osteogenesis imperfecta, as short-term inhibition of SHN3 resulted in a high–bone mass due to augmented osteoblasts activity. However, there have been no reports of natural small molecules targeting SHN3 inhibition. Here, we report a screening strategy for the discovery of marine compounds that promoted osteoblast differentiation by targeting silencing SHN3. One lead quinolinone alkaloid named viridicatol (VDC), isolated from deep-sea-derived fungus, strongly promoted osteogenic differentiation and angiogenesis. Mechanistically, VDC promotes osteogenic activity and H-type angiogenesis through the SHN3/SLIT3 signaling pathway, ultimately achieving treatment for osteoporosis and fracture repair. These results firstly develop a promising marine natural product, VDC, that targets the SHN3/SLIT3 pathway for the treatment of osteoporosis and fractures, highlighting its translational potential in clinical applications.

overall_design: To gain mechanistic insight into how HB-1(VDC) was influenced in osteogenesis, we performed RNA-sequencing (RNA-seq) transcriptional profiling.


title: Distinct Autoreactive CD19– Plasma Cell Subsets Accumulate in Lupus

city: Berlin

first: Andreia

middle: C.

last: Lino

address: Charitéplatz 1

institute: Charité – Universitätsmedizin Berlin

summary: Plasma cells (PCs) play a pathogenic role in autoimmune diseases by secreting autoantibodies and inflammatory cytokines. While PC elimination therapies exist, they risk depleting protective long-lived plasma cells. Using single cell RNA sequencing, including B cell receptor repertoire analysis, and genetic models, we identified disease- and organ-specific PC subsets in systemic lupus erythematosus (SLE) mice. We uncovered a substantial expansion of autoreactive CD19– PCs, particularly switched CXCR3+ and phosphatidylcholine-specific B-1-derived subsets, which exhibit unique gene expression profiles in SLE. Notably, our findings suggest that CD19– PCs originate from CD19+ PCs in a unidirectional manner, complicating the effectiveness of CD19-targeted therapies in advanced disease stages. This study highlights the crucial role of timing in anti-CD19 therapy and the necessity to broaden therapeutic targets beyond CD19+ PCs. The emergence of CD19– subpopulations underscore the need for novel therapeutic strategies that target these elusive PCs, offering new avenues for intervention in SLE treatment.

overall_design: BM (healthy/sick: each n= 6), spleen (healthy/sick: each n= 6) and kidney (sick: n= 13)  of SLE123 mice were collected and pooled. PCs from those tissues were enriched using anti-CD138 magnetic beads followed by cell sorting. Mice without proteinuria (9-12 weeks) were included as healthy control compared to mice with proteinuria (>24 weeks). Sequencing was performed using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit v1.1 (single index) and Illumina NextSeq2000.

first: Van

last: Dang

first: Franziska

last: Szelinski

first: Marta

last: Ferreira-Gomes

first: Gabriela

middle: M

last: Guerra

first: Pawel

last: Durek

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi


title: Integrative identification of non-coding regulatory regions driving metastatic prostate cancer

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

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

overall_design: Refer to individual Series


title: Integrative identification of non-coding regulatory regions driving metastatic prostate cancer [CLIP-seq]

summary: Large-scale sequencing efforts have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of variants occur within non-coding genomic regions. We designed an integrative computational and experimental framework to identify recurrently mutated non-coding regulatory regions that drive tumor progression. Applying this framework to sequencing data from a large prostate cancer patient cohort revealed a large set of candidate drivers. We used (i) in silico analyses, (ii) massively parallel reporter assays, and (iii) in vivo CRISPR interference screens to systematically validate mCRPC drivers. One found enhancer region, GH22I030351, acts on a bidirectional promoter to simultaneously modulate expression of U2-associated splicing factor SF3A1 and chromosomal protein CCDC157. SF3A1 and CCDC157 promote tumor growth in vivo. We nominated a number of transcription factors, notably SOX6, to regulate expression of SF3A1 and CCDC157. Our integrative approach enables the systematic detection of non-coding regulatory regions that drive human cancers.

overall_design: CLIP-seq data was generated in C4-2B CRISPRi-ready cell lines using anti-SF3A1 antibody to understand SF3A1 RBP binding landscape.

first: Brian

middle: J

last: Woo

first: Ruhollah

last: Moussavi-Baygi

first: Heather

last: Karner

first: Mehran

last: Karimzadeh


title: Nanoparticle immunoadjuvant complexes augment antigen-specific germinal center responses and enhance humoral immunity

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: An alluring strategy for improving protective humoral immunity against infectious diseases would be to directly target the germinal center (GC). There remains a critical need for next generation vaccine approaches to elicit more potent GC responses and durable humoral immunity. Here, we investigated whether cytokines could be scaffolded on nanoparticles to further enhance antigen-specific GC responses. We designed a chimeric nanoparticle using the GT8-60mer, a germline-targeting HIV immunogen, as a model to scaffold IL-21. Nanoparticle immunoadjuvant complexes (NICs) scaffolding GT8 and IL-21 (GT8-IL-21-NIC) drove improved serum antibody titers, antigen-specific GC B cells, and functional Tfh cell responses relative to antigen-only nanoparticles and to co-delivery of IL-21 monomer. Single-cell RNA sequencing of antigen-specific GC B cells from GT8-IL-21-NIC immunized mice demonstrated upregulation of LZ and selection-associated gene signatures. The NIC platform was versatile and could support changes to both the antigen and cytokine domains utilizing numerous GC-associated cytokines. Thus, NICs may provide value as a tool to improve antigen-specific vaccine-induced immunity.

overall_design: Single Cell RNA-Seq of antigen-specific germinal center B cells sorted from lymph nodes of mice immunized with a DNA-launched nanoparticle vaccine or DNA-launched nanoparticle immunoadjvuant complex (NIC)

first: Nicholas

last: Tursi

first: Daniel

last: Kulp

first: David

last: Weiner


title: Effect of knockdown of ACSS2 on H3K27ac in the HepAD38 [RNA-Seq]

first: jie

last: yang


title: Integrative identification of non-coding regulatory regions driving metastatic prostate cancer [CRISPR]

overall_design: We harvested tumors from xenograft mouse models resulting from subcutaneous injections with C4-2B CRISPRi-ready cells transduced with a targeted validation library. This library contained sequences of interest as well as non-targeting control sgRNAs. An amplicon sgRNA library was then generated from extracted tumor gDNA.


title: PHF6 regulates stress susceptibility in the pituitary intermediate lobe [CUT&Tag]

first: Bing

last: Liu

address: No. 280, South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: We revealed that stress triggers PHF6 to bind to the promoters of various stress-regulated genes in IL-melanotrophic cells and regulate their expression levels.

overall_design: CUT&Tag assays were conducted using a PHF6 antibody on enriched pituitary tissue obtained within 3 hours (8 AM - 11 AM) from 100 control and 100 RS-treated wild-type mice (6-7 weeks old), followed by high-throughput sequencing.

first: Jingjie

last: Wang

first: Xiaohua

last: Wu

first: Linhua

last: Gan

first: Jingjing

last: Sun

first: Guangzhong

first: Qian

last: Li

first: Ju

last: Huang


title: 3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer

city: Beijing

first: Ruifeng

address: haidian

institute: Tsinghua University

summary: CD8+ T cell responses are essential for anti-tumor immunity, but chronic antigen exposure in cancer can lead to T cell exhaustion, marked by high PD-1 expression. Recent studies have identified progenitor-like CD8+ T cells (Tprog cells) within tumor-infiltrating lymphocytes (TILs) that sustain antitumor responses. These cells can differentiate into terminally exhausted cells (Tterm cells), losing their proliferative and effector functions. Immunotherapy aims to enhance CD8+ TILs functionality, promoting their transition from Tprog to Tterm cells. However, the mechanisms behind this exhaustion remain unclear. Single-cell RNA sequencing and ATAC-seq have revealed distinct profiles and chromatin accessibility between progenitor and terminally exhausted states. Histone modifications predict a loss of enhancer-promoter contacts during this transition. Chromatin structure plays a crucial role in T cell differentiation. We constructed a high-resolution 3D genome map of CD8+ T cell subsets and, through multi-omics integration, identified chromatin structure changes linked to T cell exhaustion, including alterations in topologically associating domains (TADs) and chromatin loops, providing new insights into the genetic basis of CD8+ T cell exhaustion in cancer.

overall_design: Hi-C experiment of naïve, effector,memory, progenitor exhausted, terminal exhausted CD8 T cells in E.G7 tumor and LCMV clone 13 models. Hi-C for cotransferred WT and Irf8-/- OT-I TILs from E.G7 tumors

first: Chen

last: Dong


city: Chengdu

first: Xinyi

last: Fang

address: Guoxue alley

institute: Lab for Aging Research and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University

summary: A polyphenol-mediated redox-active algin/gelatin hydrogel encapsulating a conductive poly(3,4-ethylenedioxythiopene)-assembled polydopamine-mediated silk microfiber (PEDOT-PSF) network and a H2S sustained-release system utilizing bovine serum albumin nanoparticles (BNP) is developed. This hydrogel is found to reverse the hyperglycemic inflammatory microenvironment and promote functional tissue regeneration in periodontitis in diabetes. The RNA sequencing of PDLSCs on Polyphenol-Mediated Redox-Active Hydrogel with H2S Gaseous-Bioelectric Coupling was conducted to explore the underlying mechanism.

overall_design: To investigate the effect of the BNP-PEDOT-PSF-AG hydrogel,  we conducted RNA seq of PDLSCs cultured on various hydrogels.