title: Single-cell RNA-sequencing reveals enrichment of different macrophage subsets following radiation or anti-CD47 therapy in Diffuse Midline Glioma and Glioblastoma

city: Aurora

first: Andrew

last: Donson

state: CO

institute: CU Anschutz Medical Campus

summary: Pediatric diffuse midline gliomas (DMGs), previously known as diffuse intrinsic pontine glioma (DIPG), is one of the most common malignant, fatal brain tumors of childhood arising in the ventral pons.  Currently, radiation therapy (RT) is the mainstay treatment for DIPG. However, RT is not a curative treatment and provides only temporary relief in most patients. Therefore, new, and effective therapies are desperately needed for children with these tumors, but decades of clinical trials have so far failed to improve outcomes. Recent advances in immunotherapy have yielded some fantastic opportunities to effectively treat patients with high-grade pediatric brain tumors. The goal of the current study is to perform scRNA-seq on macrophages that either phagocytose-or not. Briefly, a DMG cell line, BT245 was mock-treated or exposed to fractionated RT and co-incubated with macrophages-derived from human peripheral blood mononuclear cells for 24 hrs in the presence of anti-CD47 mAb. Macrophages that either phagocytosed tumor cells- or not were sorted using flow cytometry and scRNA-seq was performed.

overall_design: 10x Genomics single cell RNA sequencing of tumor-derived phagocytosing and non-phagocytosing macrophage populations.

first: Senthilnath

last: Lakshmanachetty

first: Kent

middle: A

last: Riemondy

first: Siddhartha

last: Mitra


title: Effect of Arg2 deletion on murine liver gene expression profiles in aging mice

status: Public on May 01 2025

city: St. Louis

first: Brian

middle: Jesse

last: DeBosch

state: MO

address: 660 S. Euclid Ave, Box 8208

department: Pediatrics and Cell Biology & Physiology

country: USA

institute: Washington University School of Medicine

type: Expression profiling by high throughput sequencing

summary: We demonstrate the long term physiologic consequences of hepatocyte-specific Arg2 deficiency on murine liver gene expression in chow-fed mice at 22-month of age by high-throughput RNA sequencing

overall_design: Examination of transcriptome changes in hepatocyte-specific Arg2 deficient murine livers compared to their Arg2 floxed WT littermates at 22-month-old.

first: Yiming

last: Zhang

middle: J


title: ApoE-dependent reprogramming of glioma-associated microglia into a tumor-promoting phenotype

city: Charlestown

first: Erik

last: Abels

state: Massachusetts

address: 149 13th Street

department: Neurology

institute: Massachusetts General Hospital

summary:
Method: Analysis of the transcriptomal changes in different sets of microglia, ApoE KO, ApoE wildtype
Result: Microglia transcriptional changes as detected in tumor are driven through an ApoE dependent pathway

overall_design: mRNA expression of microglia from  APOE KO mice injected with rAPOE or PBS  and uninjected APOE KO and APOE WT samples

middle: R

first: Sybren

middle: L

last: Maas

first: Liza

last: Morsett

first: Pike-See

last: Cheah

first: Lisa

last: Nieland

first: Marike

last: Broekman

first: Xandra

middle: O

last: Breakefield

first: Joseph

last: El Khoury


title: Mapping Immune Responses In Acute Infection Across Multiple Pathogens by Proteomics and CITESeq

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

summary: We used two novel, and previously optimized, analytical approaches, CITE-Seq and Quantitative Phopho-Proteomics, to perform detailed and cohesive characterization of the same paired PBMC and sera samples collected from patients at the acute and convalescent phases of infection with different microbial pathogens.

overall_design:
Samples were processed in four batches of 20-24 samples, each of which contained sets of all longitudinal samples for a given subject and subjects sampled from each infection cohort to minimize any coinciding batch effects between time points and infection groups. Each batch also contained replicate aliquots of two healthy donor PBMC samples to bridge across batches.
Please note that each processed data was generated from a set of three samples (*_A, *_G, and *_H) and is linked to the corresponding [ADT-derived cDNA] sample records.

first: Adeeb

last: Rahman

last: D’Souza


title: GRNsmile: gene regulatory network inference with a single-cell multi-layer omics approach [Micro-C]

city: Beijing

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology

summary: scRNA-seq and 10X scATAC-seq performed on mixed hESC-dreived cardiomyocyte on day 0, 2, 4, 6, 8 and 15. And MicroC performed on hESC-dreived cardiomyocyte on day 0 and 15.

overall_design: We present an integrated framework GRN-smile to infer gene regulatory networks from multiple layers of regulatory information. We tested this framework with a well-studied biological process: differentiation of hESC to cardiomyocyte. Cells were collected and mixed to mimic a complex tissue sample during in vitro cardiac differentiation of human ESCs (day 0, 2, 4, 6, 8 and 15). This artificial sample was profiled by 10X scRNA-seq and 10X scATAC-seq. And MicroC performed on hESC-dreived cardiomyocyte on day 0 and 15. To detect long-range cis-linkages, we generated 4 replicates of Micro-C in day 0 hESC-dreived cardiomyocyte and 2 replicates of Micro-C in day 15 hESC-dreived cardiomyocyte.

first: Qiang

last: Tu


title: RNA m6A reader IGF2BP3 promotes metastasis of triple-negative breast cancer via SLIT2 repression

city: xi'an

first: tongtong

last: jiang

address: changle western load

institute: Fourth Military Medical University

summary: Triple-negative breast cancer (TNBC) is a group of fatal malignancies characterized by high metastatic capacity, the underlying mechanisms of which remain largely elusive. We found here that insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) is highly expressed in breast cancer and correlated clinically with TNBC metastasis and patient prognosis. To investigate the downstream mechanism of IGF2BP3 regulation of TNBC, we performed RNA-seq on three repeated siNC and siIGF2BP3-treated MDA-MB-231 cells.

overall_design: Total RNA was extracted from MDA-MB-231 cells transfected with siIGF2BP3 or siNC after 48 hours. Three repeated siNC and siIGF2BP3-treated cells were conducted for RNA-seq.

first: Tongtong

last: Jiang

first: Lintao

last: Jia


title: Effect of miR-9-3p on gene expression in neurons

city: Nanjing

first: jin

last: wang

address: No. 321 Zhongshan Road

department: Department of Endocrinology

institute: Drum Tower hospital affiliated to Nanjing university medical school

summary: To further understand the mechanisms underlying the effects of miR-9-3p on synaptic damage, we analyzed the transcriptome of primary neurons infected with AAV-hsyn-miR-9-3p or AAV-hsyn-mCherry using RNA sequencing

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of primary neurons infected with AAV-hsyn-miR-9-3p or AAV-hsyn-mCherry

first: Wang

last: Jin


title: GRNsmile: gene regulatory network inference with a single-cell multi-layer omics approach [scATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We present an integrated framework GRN-smile to infer gene regulatory networks from multiple layers of regulatory information. We tested this framework with a well-studied biological process: differentiation of hESC to cardiomyocyte. Cells were collected and mixed to mimic a complex tissue sample during in vitro cardiac differentiation of human ESCs(day 0, 2, 4, 6, 8 and 15). This artificial sample was profiled by 10X scRNA-seq and 10X scATAC-seq. And MicroC performed on hESC-dreived cardiomyocyte on day 0 and 15. To detect long-range cis-linkages, we generated 4 replicates of Micro-C in day 0 hESC-dreived cardiomyocyte and 2 replicates of Micro-C in day 15 hESC-dreived cardiomyocyte.


title: GRNsmile: gene regulatory network inference with a single-cell multi-layer omics approach [scRNA-seq]


title: GRNsmile: gene regulatory network inference with a single-cell multi-layer omics approach

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

overall_design: Refer to individual Series


title: ENG upregulation transcriptomic profile in TC71 ES cell line

city: Seville

first: Pilar

last: Puerto-Camacho

state: Seville

address: Avda. Manuel Siurot s/n

department: Oncohematology

country: Spain

institute: Institute of Biomedicine of Seville

summary: Endoglin (ENG) is a mesenchymal stem cell (MSC) marker highly expressed  mainly in active endothelium and certain cancer types. This transmembrane protein is shed to the extracellular compartment by the matrix metalloproteinase 14 (MMP14). Previously, ENG was identified in patient samples from Ewing sarcoma (ES), a bone/soft tissue neoplasia with a putative MSC origin. ES is a predominant paediatric malignancy with high incidence of metastasis at diagnosis, around 30% patients, associated with poor prognosis. This scenario is worsened by the fact that current chemotherapeutic treatments fail to achieve a significant impact on advanced disease. On-target therapies emerge  strongly  appealing in the clinical setting of ES. Given that a high percentage of patients presented ENG expression at the cell surface, antibody-drug conjugates (ADCs) against ENG were studied. ,. Anti-ENG ADCs exerted an ENG-dependent and dose-dependent anti-proliferative effect in , both in vivo and in vitro ES models. These results suggest that the use of ENG-ADC  might have  potential benefits in  in ES . As the expression of ENG and MMP14 was variable amongst ES patients, a survival study was assessed in a cohort of 82 patients categorised according to their clinical stage (primary, post chemotherapy primary, metastasis and relapse). Both ENG and MMP14 were associated with worse prognosis. Functional assays revealed that ENG regulates migration, probably through the correct assembly of actin in stress fibres and filopodia, with a concomitant effect on the adhesive capacity of the cell. Furthermore, ENG was confirmed to be important in the activation of focal adhesion signalling, by favouring focal adhesion kinase phosphorylation and protein kinase C expression. verall, these results suggest that ENG exerts a main role as an adaptor protein in the correct migration machinery of ES cells.

overall_design: 12 samples were used in this study. 6 samples correspond to ENG-upregulated samples (pENG, two clones, n = 3 each). 3 samples correspond to the control group of the study, empty vector, which was used to compared results obtained from pENG group. Finally, 3 samples correspond to the reference wild type cell line, TC71.


title: Transcriptome regulated by ENG and MMP14 in Ewing sarcoma cells


title: ENG downregulation transcriptomic profile in SKNMC ES cell line

overall_design: 9 samples were used in this study. 6 samples correspond to ENG-downregulated samples, shENG1 and shENG2 (n = 3 each). 3 samples correspond to the control group of the study, shNT, which was used to compared results obtained from shENG group.


title: MMP14 downregulation transcriptomic profile in SKNMC ES cell line

overall_design: 8 samples were used in this study. 4 samples correspond to MMP14-knockout samples, shMMP141 and shMMP142 (n = 2 each). 4 samples correspond to the control group of the study, sgNT, which was used to compared results obtained from sgMMP14 group.


title: MMP14 downregulation transcriptomic profile in RM82 ES cell line

overall_design: 12 samples were used in this study. 6 samples correspond to MMP14-knockout samples, sgMMP141 and sgMMP142 (n = 3 each). 3 samples correspond to the control group of the study, sgNT, which was used to compared results obtained from sgMMP14 group. Finally, 3 samples correspond to the reference wild type cell line, RM82.


title: ENG downregulation transcriptomic profile in RM82 ES cell line

overall_design: 12 samples were used in this study. 6 samples correspond to ENG-downregulated samples, shENG1 and shENG2 (n = 3 each). 3 samples correspond to the control group of the study, shNT, which was used to compared results obtained from shENG group. Finally, 3 samples correspond to the reference wild type cell line, RM82.


title: Transcriptome sequencing of Anopheles darlingi mosquitoes using RNA-seq

city: Lisbon

first: Henrique

last: Silveira

address: Rua da Junqueira, 100

department: Global Health and Tropical Medicine

country: Portugal

institute: Instituto de Higiene e Medicina Tropical, IHMT, UNL

summary: Anopheles darlingi transcriptome in response to Plasmodium vivax invasion of midgut

overall_design: A. darlingi mosquitoes  were: i) membrane-fed on P. vivax infected blood, ii) membrane-fed on blood with inactivated gametocytes or iii) fed on 10 % sugar solution. 18-24 hours after feeding, mosquitoes were dissected and pools of 30 midguts were collected from each group. Three independent biological replicates of each experiment were performed.

first: Rosa

middle: G

last: Santana

first: Patrícia

last: Abrantes

first: Maria

middle: B

last: Guerra


title: Investigation of genomic imprinting in cattle

city: Sendai

first: Hiroaki

last: Okae

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Informative Genetics

country: Japan

institute: Tohoku University Graduate School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Genomic imprinting is an epigenetic mechanism whereby a subset of genes, called imprinted genes, show parent-of-origin-dependent monoallelic expression. Most imprinted genes are regulated by allele-specific DNA methylation at differentially methylated regions (DMRs). Although major imprinted genes and DMRs have already been identified in human and mouse, information on genomic imprinting is sporadic and limited in other mammalian species due to the cost and technical difficulties of genome-wide allele-specific gene expression and DNA methylation analyses. Here we propose two strategies to predict DMRs from whole-genome bisulfite sequencing (WGBS) data: one is based on conservation and the other is on germline DNA methylation patterns. Both strategies do not require genotype information and predict DMRs with high sensitivity and low background. We applied these strategies to human, rhesus, mouse and cow and estimated the evolutionary trajectory of individual DMRs. These analyses suggest that various factors, including CpG density, germline methylation and sequence-specific DNA binding proteins, may contribute to species-specific differences in genomic imprinting. Our strategies will facilitate cross-species comparison of genomic imprinting and identification of novel DMRs.

overall_design: Genomic DNA was purified with phenol/chloroform extraction and ethanol precipitation. WGBS libraries were constructed using the post-bisulfite adapter-tagging (PBAT) method. The PBAT libraries were sequenced on the HiSeq 2500 platform (Illumina, CA, USA) with 101-bp single-end reads.

first: Takahiro

last: Arima


title: H3F3A K27M Mutations Drive a Repressive Transcriptome by Modulating Chromatin Accessibility, Independent of H3K27me3 in Diffuse Midline Glioma [ATAC-seq]

status: Public on Apr 30 2025

city: Austin

first: James

last: Robinson

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

institute: University of Minnesota

summary: Heterozygous histone H3.3K27M mutation is a primary oncogenic driver of Diffuse Midline Glioma (DMG). H3.3K27M inhibits the Polycomb Repressive Complex 2 (PRC2) methyltransferase complex, leading to a global reduction and redistributing of the repressive H3 lysine 27 tri-methylation.  This rewiring of the epigenome is thought to promote gliomagenesis. We established novel, isogenic DMG patient-derived cell lines that have been CRISPR-Cas9 edited to H3.3 WT or H3.3K27M alone and in combination with EZH2 and EZH1 co-deletion, inactivating PRC2 methyltransferase activity of PRC2 and eliminating H3K27me3. RNA-seq and ATAC-seq analysis of these cells revealed that K27M has a novel epigenetic effect that appears entirely independent of its effects on PRC2 function.  While the loss of the PRC2 complex led to a systemic induction of gene expression (including HOX gene clusters) and upregulation of biological pathways, K27M led to a balanced gene deregulation but having an overall repressive effect on the biological pathways. Importantly, the genes uniquely deregulated by the K27M mutation, independent of methylation loss, are closely associated with changes in chromatin accessibility, with upregulated genes becoming more accessible. Notably, the PRC2-independent function of K27M appears necessary for tumorigenesis as xenografts of our H3.3K27M/EZH1/2 WT cells developed into tumors, while H3.3/EZH1/2 KO cells did not. We demonstrate that K27M mutation alters chromatin accessibility and uniquely deregulates genes, independent of K27 methylation. We further show the mutation's role in altering biological pathways and its necessity for tumor development.

overall_design: We established novel, isogenic DMG patient-derived cell lines including SF8628 cell line that have been CRISPR-Cas9 edited to H3.3 WT or H3.3K27M alone and in combination with EZH2 and EZH1 co-deletion, inactivating PRC2 methyltransferase activity of PRC2 and eliminating H3K27me3. RNA-seq and ATAC-seq analysis were carried out in these modified cell lines.

first: Suraj

last: Bhattarai

middle: P


title: Obesity accelerates age-related memory deficits and alters white matter tract integrity in Ldlr-/-.Leiden mice

city: Leiden

first: Robert

last: Kleemann

address: Sylviusweg 71

country: Netherlands

institute: The Netherlands Organisation for Applied Scientific Research

summary: - Background: Obesity in mid-adulthood has been suggested to promote brain aging and is associated with progressive cognitive impairment later in life. However, the structural and functional alterations that underlie obesity-related cognitive dysfunction are still poorly understood, partly owing to the lack of translational models replicating age- and obesity-related brain pathology.  - Methods: The effect of age and high-fat diet (HFD)-induced obesity was investigated in adult Ldlr-/-.Leiden mice, an established translational model for obesity and its comorbidities. During mid-adulthood, from three to eight months of age, brain structure and function (hippocampal volume, cortical thickness, white matter integrity, cerebral blood flow (CBF), resting-state functional connectivity) were monitored with brain magnetic resonance imaging, and cognitive function was evaluated using cognitive tests. Brain pathology was further examined with histopathological and gene expression analyses.  - Results: Ldlr-/-.Leiden mice showed age-related decreases in cortical thickness, CBF, brain connectivity, and neurogenesis along with the development of neuroinflammation and (short-term) memory impairments. On HFD feeding, Ldlr-/-.Leiden mice exhibited similar features, but memory deficits started at a younger age than in chow-fed mice. HFD-fed mice additionally showed a rise in CBF with concomitant decline in fractional anisotropy in white matter tracts. Analyses of hippocampal gene expression further revealed an age-related suppression of processes related to metabolic and neuronal function while HFD feeding strongly activated neuroinflammatory pathways.  - Conclusions:  Ldlr-/-.Leiden mice show similar critical age-related changes in brain structure and function as observed in humans. In this mouse model, HFD feeding particularly trigger disturbances in brain blood perfusion and white matter tract integrity, which may underlie an accelerated cognitive decline in obesity.

overall_design: At the start of the experiment the animals were 10-12 weeks old (corresponding to young adults). One group of chow-fed mice (Young-Chow, n=15) was euthanized at 3 months of age as a younger lean (healthy) reference. Then, from 2.5 to 8 months of age, one aging group (Aging-Chow, n=15) remained on the standardized chow diet and another aging group (HFD, n=17) was fed an obesity-inducing energy-dense high-fat diet (HFD). These 2 groups were sacrificed around 8 months of age. RNAseq analysis was performed on Hippocampi isolated from the right hemispheres of fresh brains at sacrifice.

first: Florine

last: Seidel

first: Martine

middle: C

last: Morrison

first: Ilse

last: Arnoldussen

first: Vivienne

last: Verweij

first: Joline

last: Attema

first: Christa

last: de Ruiter

first: Wim

last: van Duyvenvoorde

first: Jessica

last: Snabel

first: Bram

last: Geenen

first: Ayla

last: Franco

first: Maximilian

last: Wiesmann

first: Amanda

last: Kiliaan


title: Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant

city: Baltimore

first: Jennifer

last: Elisseeff

state: MD

address: 1800 Orleans St

institute: Johns Hopkins

summary: The gut microbiota influences systemic immunity and the function of distal tissues, including the brain, liver, skin, lung, and muscle. However, the role of the gut microbiota in the foreign body response (FBR) and fibrosis is largely unexplored. To investigate this connection, we perturbed the homeostasis of the murine gut microbiota via infection with the pathogenic bacterial species enterotoxigenic Bacteroides fragilis (ETBF) and implanted particulate material (mean particle size <600 μm) of the synthetic polymer polycaprolactone (PCL) into a distal muscle injury. ETBF infection in mice led to increased neutrophil and γδ T cell infiltration into the PCL implant site. ETBF infection alone promoted systemic inflammation, increased levels of neutrophils in lymphoid tissues, and altered skeletal muscle gene expression. At the PCL implant site, we found significant changes in the transcriptome of sorted stromal cells between infected and control mice, including differences related to ECM components such as proteoglycans and glycosaminoglycans. However, we did not observe ETBF-induced differences in fibrosis levels. These results demonstrate the ability of the gut microbiota to mediate long-distance effects such as immune and stromal responses to a distal biomaterial implant.

overall_design: Bulk RNA sequencing of sorted stromal cells from PCL implant site in mice with and without ETBF infection. On Day -11, both groups were treated with antibiotics. On Day -7, antibiotics were removed; the control group was inoculated with DPBS and the experimental group was inoculated with ETBF. On Day 0, both groups underwent volumetric muscle loss surgery with PCL implantation in the defect space. Data was collected 6 weeks after implantation.

first: Brenda

last: Yang

first: Kavita

last: Krishnan

first: Natalie

last: Rutkowski

first: Anna

last: Ruta

middle: H


title: Integrated transcriptomic and epigenomic analysis demonstrates apple mango leaf extract induced maturation and functional activation of BMDCs

city: Daejeon

first: Suyoung

last: Choi

address: 266, Munhwa-ro, Jung-gu

department: Department of Medical Science

country: South Korea

institute: Chungnam National University

summary: The apple mango (Mangifera indica L.) is primarily consumed for its fruit, and the other components of the plant, including the leaves, are often discarded as agricultural by-products. This study investigated the immunomodulatory properties of apple mango leaf extract (AMLE) using transcriptomic and chromatin accessibility analyses, focusing on gene regulation and signaling pathways in bone marrow-derived dendritic cells (BMDCs). Weighted gene co-expression network analysis (WGCNA) revealed two inversely regulated gene network modules. The upregulated module following AMLE treatment included pathways essential for dendritic cell (DC) activation, while the downregulated module was enriched in cell cycle and metabolic pathways. Assay for Transposase Accessible Chromatin with Sequencing (ATAC-seq) analysis revealed increased promoter accessibility in AMLE-treated BMDCs, suggesting increased transcriptional activity. By integrating RNA-seq and ATAC-seq data, we identified 33 commonly regulated genes, with 25 upregulated genes forming a protein-protein interaction network centered on IL1b. These genes were associated with pathways related to cytokine signaling, T cell differentiation and extracellular matrix interactions. AMLE treatment enhanced DC chemotaxis, antigen presentation and promoted T cell differentiation signaling. Specifically, flow cytometric analysis shows that AMLE increased the expression of major histocompatibility complex class II (MHCII) and the co-stimulatory molecules CD40 and CD80, leading to BMDC maturation and expansion of the CD11c+MHCIIhi and CD11c+CD11blo subsets. These findings suggest that AMLE induces potent maturation responses through multiple pathways within DC subpopulations. By elucidating the transcriptional and epigenetic effects of AMLE on BMDCs, this study contributes to a broader understanding of plant-derived compounds in immune modulation.

overall_design: RNA and ATAC sequencing of bone marrow-derived dendritic cells (BMDCs) from female C57BL/6 mice (8-10 weeks old) were cultured in cRPMI medium (RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin, 50 μM 2-mercaptoethanol and 20 ng/mL GM-CSF) for 7 days. Non-adherent cells were collected as immature BMDCs on day 6, treated with AMLE (400 μg/mL) or 0.04% DMSO for 24 hours and used for next-generation sequencing.

first: Jaeyul

last: Kwon


title: Transcriptomic Validation of ALS-Derived Motor Neurons Following m6A Hypomethylation Restoration

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

summary: In this experiment, we investigated transcriptomic alterations in iPSC-derived motor neurons from ALS patients following the restoration of m6A hypomethylation to mitigate neurodegenerative processes.

overall_design: To explore whether the transcriptomic level rescued upon restoring the m6A level in degenrated ALS iPSC~MNs. We differentiated two fALS patient (C9ORF72exp~800 G4C2 and SOD1+/L144F) iPSC~MN lines and one sALS iPSC~MN line under defined conditions to cause MN degeneration through a selective ER stressor, CPA. Subsequently, we applied FB23-2 to determine if doing so could elevate m6A levels and thereby restore the m6A repertoire to rescue MN degeneration in different contexts of ALS. Finally thtoal RNA were harvest and performed the Illumina NextSeq 500.

first: Jun-An

last: Chen


title: Din oversees MSC homeostasis in mouse incisors

city: College Station

first: James

last: Cai

state: TX

address: 4458 TAMU

department: Veterinary Intergrative Biosciences

institute: Texas A&M University

summary: The murine incisor presents an excellent model for investigating stem cell homeostasis due to its regenerative capacity and continuous growth throughout the lifetime. Proper homeostasis of the dental mesenchymal stem cells (MSCs) is pivotal for the continuous growth, tissue turnover and injury healing in murine incisors. By employing a newly developed knockout mouse model, we revealed that a predicted gene, Din (4930453N24Rik), plays pivotal roles in the homeostasis of MSCs in murine incisors. This study represents the first transcriptomic analysis of Din role in mouse incisors.

overall_design: The proximal tissues of the lower incisors of P15 Din-KO mice and WT mice were obtained and minced into 0.5 mm pieces and dissociated into single-cell suspension.

first: Dong

last: Changchun

first: Lamichhane

last: Bikash

first: Wang

last: Xiaofang


title: Atf4 protects islet beta-cell identity and function under acute glucose-induced stress but promotes beta-cell failure in the presence of free fatty acid

city: Nashville

first: Guoqiang

last: Gu

state: TN

address: 2213 Garland Avenue, MRB4, Rm 9415

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Glucolipotoxicity is known to cause beta-cell failure and type 2 diabetes (T2D) via stress response-related mechanisms. Yet the detailed mechanisms are not known. This study examine the roles of activating transcription factor 4 (Atf4) in glucolipotoxicity. Using beta-cell specific gene knockout in mice, we show here that Atf4 is dispensable in young mice for glucose homeostasis. But it is required for beta-cell function during aging and under long-term obesity-related metabolic stress. Henceforth, aged Atf4-deficient beta-cells display compromised function under acute hyperglycemia. In contrast, these mutant beta-cells are resistant to acute free fatty acid-induced dysfunction. Corresponding to these phenotypes, Atf4-deficient beta-cells down-regulate genes involved in protein translation, reducing beta-cell identity gene products under high glucose. They also upregulate several genes involved in lipid metabolism or signaling, likely contributing to their resistance to free fatty acid-induced dysfunction. These results suggest that although Atf4 activation is required for beta-cell identity and function under high glucose, this activation induces beta-cell failure in the presence of high levels of free fatty acids.

overall_design: Atf4 mutant (Atf4F/f; Ins1Cre) and contol (Atf4F/F) iselts were isolated from 2-month-old mice (2 males and 2 females for each individual sample) follow routine collagenase perfusion. Islets were immediately washed with Ca2+/Mg2+ free HBSS 3-times anddissociated into single cells (5 minutes). The smaple were then used for TrueDrop-seq and processing following routine pipeline.

first: Mahircan

last: Yagan

first: Sadia

last: Najam

first: Ruiying

last: Hu

first: Aisha

last: Nour

first: Yu

last: Wang

first: Prasanna

last: Dadi

first: Yanwen

last: Xu

first: Alan

last: Simmons

first: Roland

last: Stein

first: Christopher

middle: M

last: Adams

first: David

last: Jacobson

first: Ken

last: Lau

first: Qi

last: Liu


title: SAMHD1 Knockout iPSC model enables high lenti-viral transduction in myeloid cell types [barcode_count]

city: San Francisco

first: Scot

last: Federman

state: CA

address: 499 Illinois St

department: Biochemistry

institute: UCSF

summary: Recent advances in functional genomics tools have ushered in a new era of genetic editing to identify molecular pathways relevant to developmental and disease biology. However, limited model systems are available that adequately mimic cell states and phenotypes associated with human disease pathways. Here, we quantitatively analyzed the founder population bottleneck effect and demonstrated how the population changes from induced pluripotent stem cells (iPSCs) to hematopoietic stem cells and to the final induced macrophage population. We then engineered SAMHD1 knockout (KO) iPSC and characterized the iPSC line with RNA Seq, and induced macrophages from two distinct protocols with functional analysis. We then generated SAMHD1 KO CRISPR-dCAS9 KRAB iPSC through lenti-viral transduction aiming to increase the efficiency of lentiviral mediated gene transfer. We demonstrated increased lenti-viral transduction efficiency in induced macrophage, as well as microglia induced with two distinct protocols. This model allows for efficient gene knock down, as well as large-scale functional genomics screens in mature iPSC-derived macrophages or microglia with applications in innate immunity and chronic inflammatory disease biology. These experiments highlight the broad applicability of this platform for disease-relevant target identification and may improve our ability to run large-scale screens in iPSC-derived myeloid model systems.

overall_design: To investigate how founder cell population diversity changes during the macrophage induction process of different protocols, we barcoded founder cell population, then each stage during the induction was sampled, as well as the final mature macrophage. With the barcode sequence diversity, we were about to quantitatively identify the bottleneck effect of the induction process.

first: Huinan

last: Li

first: Maliha

last: Afroze

first: Gunisha

last: Arora

first: Kaivalya

last: Shevade

first: Yeqing

last: Yang

first: Phuong

last: Nguyen

first: Rustam

last: Esanov

first: Laralynne

last: Przybyla

first: Adam

last: Litterman

first: Shawn

last: Shafer


title: The Motor Neuron m6A Repertoire Governs Neuronal Homeostasis and Augmented m6A Production Mitigates ALS Symptom Manifestation [snMultiome-seq]

first: Ya-Ping

last: Yen

summary: Amyotrophic lateral sclerosis (ALS) is a swiftly progressive and fatal neurodegenerative ailment marked by the degenerative motor neurons (MNs). Why MNs are specifically susceptible in predominantly sporadic cases remains enigmatic. Here, we demonstrated N6-methyladenosine (m6A), an RNA modification catalyzed by the METTL3/METTL14 methyltransferase complex, as a pivotal contributor to ALS pathogenesis. By conditional knockout Mettl14 in murine MNs, we recapitulate almost the full spectrum of ALS disease characteristics. Mechanistically, pervasive m6A hypomethylation triggers dysregulated expression of high-risk genes associated with ALS and an unforeseen reduction of chromatin accessibility in MNs. Additionally, we observed diminished m6A levels in induced pluripotent stem cell (iPSC)-derived MNs from familial and sporadic ALS patients. Restoring m6A equilibrium via a small molecule or gene therapy significantly preserves MNs from degeneration and mitigates motor impairments in ALS iPSC-derived MNs and murine models. Our study presents a substantial stride towards identifying pioneering efficacious ALS therapies via RNA modifications.

overall_design: snMultiome-seq: Single nuclei were extracted from P100~P120 Sun1sfGFP; ChAT-Cre; Mettl14floxed (cKO) and Sun1sfGFP; ChAT-Cre (control) lumbar spinal cord. Cholinergic neurons were labeled in GFP and sorted via FACS, and loaded onto 10x Genomics Chromium Next GEM Chip J Single Cell Kit. Join snRNA and scATAV libaries were prepared using 10x Genomics plateform.

first: Jun-An

last: Chen

first: Ee Shan

last: Liau


title: Lung disease in relation to unique monocyte-macrophage subpopulations induced by combined inhalant endotoxin and collagen-induced arthritis

city: Omaha

first: Aaron

middle: D

last: Schwab

state: NE

address: 42nd and Emile St.

institute: University of Nebraska Medical Center

summary: Lung disease is the most overrepresented cause of death in rheumatoid arthritis (RA). Animal studies have demonstrated potentiated autoimmunity, arthritis, and profibrotic/inflammatory lung disease with a combination of airborne exposures and collagen-induced arthritis (CIA), a model that recapitulates features of RA-associated interstitial lung disease (RA-ILD). As patients with RA-ILD demonstrate unique circulating monocyte subpopulations, this study aims to characterize lung infiltrating monocytes/macrophages in a mouse model of RA-ILD and determine whether reducing these cells mitigates the development of lung disease. Autoimmune-prone DBA/1J mice received intranasal inhalation of lipopolysaccharide (LPS) daily for up to 5 weeks and CIA induction. Experimental groups included Sham (saline injection/saline inhalation), CIA (CIA/saline), LPS (saline/LPS), and CIA+LPS (CIA/LPS). Lung disease was assessed by longitudinal imaging, lung function measurements, bronchoalveolar lavage fluid, lung tissues, and lung histopathology. Cell subpopulations were analyzed by single cell RNA-sequencing. Unsupervised clustering revealed 16 discrete clusters among the experimental groups with 2 robust clusters characterized as infiltrating inflammatory monocytes/macrophages for both CIA+LPS and CIA. The interaction of inhalation-induced airway inflammation and autoimmune arthritis results in lung disease associated with uniquely activated infiltrating inflammatory monocytes-macrophages that mediate adverse lung consequences. Whereas the induced monocyte/Mɸ immunophenotype is more aligned to CIA than endotoxin exposure, co-exposure modeling renders unique features that potentially inform the pathogenesis and treatment of RA-ILD.

overall_design: An established 5-week exposure model was utilized whereby mice were randomized to 1 of 4 experimental groups including Sham (saline injection/saline inhalation), LPS alone (saline injection/LPS inhalation), collagen-induced arthritis (CIA) alone (CIA induction/saline inhalation), and CIA+LPS co-exposure (CIA injection/LPS inhalation). DBA/1J mice (age 6-8 weeks) were purchased from Envigo and allowed to acclimate for one week prior to initiation of experiments. Male mice were utilized for all studies because we have previously demonstrated that female mice were profoundly less susceptible to development of lung disease in the setting of arthritis induction. CIA was induced as per the Chondrex protocol (Chondrex, Inc, Redmond, WA). Airway inflammation was induced using an established model of repetitive intranasal LPS inhalation. Under light sedation with isoflurane, mice received 100 ng of LPS from gram-negative Escherichia coli (O55:B5; Sigma, St. Louis, MO) in 50 μl of sterile saline or saline alone daily for up to 5 weeks (weekends excluded). Animals were euthanized 1 day after the final LPS exposure by isoflurane. 4-5 mice per treatment group were euthanized with whole lungs harvested after removal of blood from the pulmonary vasculature. Lungs were dissociated with gentleMACS Dissociator (Miltenyi Biotech, Gaithersburg (MD)) in a digestion solution (collagenase I, 0.2 μg/μl + DNase I, 75 U/ml + heparin, 1.5 U/ml, in Dulbecco’s Modified Eagle’s Media; DMEM) and incubated for 30 minutes at 37°C in a shaking incubator. Digestion solution activity was neutralized with PBS containing 4 mM EDTA. Red blood cells were lysed with 1 ml ammonium-chloride-potassium (ACK) lysis buffer (Quality Biological, Gaithersburg, MD) for 1 minute and neutralized with ice-cold DMEM (Gibco). Sample were then pooled by treatment group.

first: Jill

last: Poole


title: The Inflammaging Microenvironment Induces Dysfunctional Rewiring of Tfh Cell Differentiation

city: Boston

first: Cody

last: Nelson

state: MA

address: 221 Longwood Ave

institute: Brigham and Women's Hospital

summary: Humoral immunity is orchestrated by follicular helper T (Tfh) cells, which promote cognate B cells to produce high-affinity, protective antibodies. In aged individuals, humoral immunity after vaccination is diminished despite the presence of Tfh cells, suggesting defects after initial Tfh formation. In this study, we utilized both murine and human systems to investigate how aging alters Tfh cell differentiation after influenza vaccination. We found that young Tfh cells underwent progressive differentiation after influenza vaccination, culminating in clonal expansion of effector-like cells in both draining lymph nodes and blood. In aging, early stages of Tfh development occurred normally. However, aging rewired the later stages of progressive development in Tfh cells, resulting in a transcriptional program reflective of cellular senescence, sustained pro-inflammatory cytokine production, and metabolic reprogramming. We investigated the extent to which this rewiring of aged Tfh cells is due to the age-associated inflammatory (“inflammaging”) microenvironment and found that this setting was sufficient to both block the transition of Tfh cells to a post-effector resting state and to skew Tfh cells towards a hyperinflammatory phenotype. Together, these data suggest that aging dampens humoral immunity by cytokine-mediated rewiring of late effector Tfh cell differentiation into an activated, yet dysfunctional, cellular state.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: T follicular helper cells/duplicates or triplicates

first: Peter

middle: T

last: Sage

middle: S


title: Peptide Driven Identification of TCRs (PDI-TCR) reveals dynamics and phenotypes of CD4 T cells in tuberculosis

city: La Jolla

first: Bjoern

last: Peters

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: Accurately assigning antigen specificity to T cell receptor (TCR) sequences is challenging due to the complexity of the TCR-antigen recognition process in humans. We developed the Peptide-Driven Identification of TCRs (PDI-TCR) assay, a novel method combining in vitro expansion with peptide pools, bulk TCR sequencing, and statistical analysis to identify antigen-specific TCRs from human blood. A key feature of PDI-TCR is its ability to account for bystander T cell expansion using both antigen-specific and non-specific peptide pools, distinguishing true antigen-specific TCRs from the unspecific ones. We applied PDI-TCR to Tuberculosis (TB) patients, sampling blood at diagnosis and throughout therapy, and Mycobacterium tuberculosis (Mtb)-sensitized healthy individuals (IGRA+). We identified hundreds of Mtb-specific and unspecific TCRs, and in combination with single-cell mRNA and TCR sequencing of CD4 T cells, we characterized the transcriptome of Mtb-specific and unspecific T cells in each cohort. Mtb-specific T cells were highly diverse, with the presence of short-lived effector phenotypes only in TB at diagnosis and memory phenotypes maintained through treatment. In contrast, unspecific T cells were more clonally restricted and expanded, cytotoxic, and maintained through treatment. Thus, PDI-TCR is a powerful tool for identifying antigen-specific TCRs. Combined with single-cell sequencing of T cell populations, it enables direct ex vivo monitoring of antigen-specific T cells.

overall_design:
HLA-DR+CD4+CD8- T cells, HLA-DR-CD4+CD8-  T cells and CD3+CD4-CD8- T cells were sorted ex vivo and subjected to single-cell mRNA and TCR sequencing.

Please note that the records have been updated with additional *airr_rearrangement.tsv files on May 16, 2025.

***************************************************************
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.
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title: PELP1 regulate medulloblastoma progression via NF-κB pathway

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We examined the transcriptional changes modulated by Proline Glutamic acid and Leucine rich Protein 1 (PELP1) by performing global transcriptome analysis. Daoy medulloblastoma cells were transduced with control shRNA or PELP1 shRNA lentiviral particles and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that PELP1 modulated genes were related to inflammatory processes and extra cellular matrix such as inhibition of matrix metalloproteases, toll like receptor signaling, TNFR2 signaling, IL-8 signaling and NF-kB signaling.

overall_design: Total RNA was isolated from Daoy cells expressing either control shRNA or PELP1 shRNA. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

last: Sareddy

first: Yidong

first: Ratna

middle: K

last: Vadlamudi


title: Identification of Keratin 5 expression lineage fibroblasts in hair follicles

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

summary: We investigated epidermis derived fibroblasts in neonatal skin at single cell-transcriptomic levels. We found that keratin 5 lineage mesenchymal cells mainly showed the transcriptomic signatures as dermal papilla and dermal sheath cells. Our data suggested that hair follicle dermal cells were originally derived from epidermis via epithelial to mesenchymal transition.

overall_design: Neonatal skins from head, back and abdomen of Krt5-Cre; R26-stop-tdTomato; Pdgfra-H2B-eGFP mice were hervested. Each specimens were dissociated enzymatically, and then the cell suspensions were sorted by fluorescence-activated cell sorting (FACS) according to eGFP+ and tdTomato+/-. The sorted cells were analyzed using single cell RNA sequencing.

first: Tomomi

last: Kitayama

first: Yuya

last: Ouchi

first: Asaka

last: Miura

first: Yoshikazu

last: Hirose


title: LSD1 inhibition attenuates targeted therapy-induced lineage plasticity in BRAFV600E colorectal cancer

city: Bloomington

first: Heather

last: O'Hagan

state: IN

address: 1001 E. 3rd St. Bloomington, IN 47405

institute: Indiana University

summary: Background: BRAF activating mutations occur in approximately 10% of metastatic colorectal cancer (CRCs) and are associated with worse prognosis in part due to an inferior response to standard chemotherapy. Standard of care for patients with refractory metastatic BRAFV600E CRC is treatment with BRAF and EGFR inhibitors and recent FDA approval was given to use these inhibitors in combination with chemotherapy for patients with treatment naïve metastatic BRAFV600E CRC. Lineage plasticity to neuroendocrine cancer is an emerging mechanism of targeted therapy resistance in several cancer types. Enteroendocrine cells (EECs), the neuroendocrine cell of the intestine, are uniquely present in BRAFV600E CRC as compared to BRAF wildtype CRC. Methods: BRAF plus EGFR inhibitor treatment induced changes in cell composition were determined by gene expression, imaging and single cell approaches in multiple models of BRAF mutant CRC. Furthermore, multiple clinically relevant inhibitors of the lysine demethylase LSD1 were tested to determine which inhibitor blocked the changes in cell composition. Results: Combined BRAF and EGFR inhibition enriched for EECs in all BRAF mutant CRC models tested. Additionally, EECs and other secretory cell types were enriched in a subset of BRAFV600E CRC patient samples following targeted therapy. Importantly, inhibition of LSD1 with a clinically relevant inhibitor attenuated targeted therapy-induced EEC enrichment through blocking the interaction of LSD1, CoREST2 and STAT3. Conclusions: Our findings that BRAF plus EGFR inhibition induces lineage plasticity in BRAFV600E CRC represents a new paradigm for how resistance to BRAF plus EGFR inhibition occurs. Additionally, our finding that LSD1 inhibition blocks lineage plasticity has the potential to improve responses to BRAF plus EGFR inhibitor therapy in patients.

overall_design: Patient derived xenograft colon organoids were emplanted into the colons of NSG mice and tumors were allowed to grow. Resulting tumors were then treated with vehicle or a combination of encorafenib and cetuximab for three weeks and 10X Flex single cell RNA sequencing was performed. For the mouse syngenic model, TPKO organoids were emplanted into the colons of wild type C57Bl/6 mice and tumors were allowed to form. Tumors were then treated for 3 weeks with vehicle or a combination of encorafenib and gefitinib for three weeks and 10X Flex single cell RNA sequencing was performed

first: Christopher

last: Ladaika

first: Averi

last: Chakraborty

first: Ashiq

last: Masood

first: Galen

last: Hostetter

first: Joo Mi

last: Yi

last: O’Hagan


title: Expression data from Lean and Obese Rat Mammary Glands, with and without treatment with bazedoxifene + conjugated estrogens (BZA/CE)

city: Ann Arbor

first: Erin

last: Giles

state: MI

address: 830 N University Ave

department: School of Kinesiology

institute: University of Michigan

summary:
Many risk-eligible women refuse tamoxifen for primary prevention of breast cancer due to concerns about common side effects such as vasomotor symptoms. Tamoxifen may also induce or worsen insulin resistance and hypertriglyceridemia, especially in women with obesity. Bazedoxifene/conjugated estrogens (BZA/CE) reduces vasomotor symptoms and is currently undergoing evaluation for breast cancer risk reduction. However, the impact of BZA/CE on insulin resistance and metabolic health, particularly in those with excess adiposity, is understudied. Here, we examined the effects of obesity on response to BZA/CE in a rat model of breast cancer risk using older ovary-intact rats. Female Wistar rats received carcinogen to increase mammary cancer risk and were fed a high-fat diet to promote obesity. Lean and obese rats were selected based on adiposity, then randomized to BZA/CE or vehicle for 8 weeks. BZA/CE reduced adiposity, enriched small (insulin-sensitive) mammary adipocytes, increased the abundance of beneficial metabolic gut microbes (Faecalbaculum rodentium and Odoribacter laneus), and reversed obesity-associated changes in lipids and adipokines. BZA/CE also reversed obesity-induced mammary enrichment of cell proliferation pathways, consistent with risk-reducing effects. Together, these data support the use of BZA/CE to improve metabolic health and reduce breast cancer risk in individuals with obesity.
RNA from mammary glands  was analyzed by gene expression microarray.

overall_design: Female Wistar rats received carcinogen to simulate increased mammary cancer risk and were fed a high-fat diet to promote obesity. Lean and obese rats were selected based on adiposity, then  randomized to BZA/CE or vehicle-control for 8 weeks. 5 samples from each group (Lean Control, Lean + BZA/CE, Obese Control,and  Obese + BZA/CE) were analyzed.

first: Ramsey

last: Jenshcke

first: Katherine

last: Cook

first: Karen

last: Corleto

first: Danilo

last: Landrock

first: Tara

middle: N

last: Mahmood

middle: E

last: Sanchez

first: Alina

last: Levin

first: Stephen

last: Hursting

first: Bruce

middle: F

last: Kimler

first: Barry

last: Komm

first: Carol

last: Fabian


title: The detecting of m6A RNA modifications upon Oxford Nanopore direct-RNA sequencing [Nanopore]

first: Ya-Ping

last: Yen

summary: To investigate the potential mechanisms by which m6A contributes to ALS disease degeneration, we utilized a direct RNA sequencing platform, allowing for the identification of the m6A modification sites at single-nucleotide resolution. With the croreference of the ALS risk genes and transcriptomic RNA-seq data in ALS, we could further indntify the m6A-dependent potential genes and pathways in ALS.

overall_design: We employed an optimized method using mouse ESC-derived motor neurons (MNs), matured with conditioned medium. This approach successfully generated MNs expressing mature neuronal markers and exhibiting longer, more developed neurite structures, as indicated by discrete Syn1-positive puncta. We then subjected these mature MNs to the ONT Nanopore platform, which leverages advanced machine-learning algorithms to detect RNA modifications through sequencing metrics.

first: Fang-Yu

last: Hsu

first: Jun-An

last: Chen


title: Hexokinase 2 Exacerbates Mitochondrial Damage, Neuroinflammation, and Lipid accumulation by promoting ACSL4 ISGylation in Sepsis-Associated Encephalopathy

city: Wuhan

first: Jianmin

last: Ling

address: 1095 Jiefang Dadao, Wuhan 430000, China

department: Emergency

institute: Huazhong university of science and technology

summary: Metabolic reprogramming is often observed in sepsis-associated encephalopathy (SAE). However, little is known about the aberrant metabolic genes involved in mitochondrial damage, neuroinflammation, and lipid accumulation in microglial cells. Here, we show that hexokinase 2 (HK2) is upregulated and is strongly associated with the inflammatory response and lipid metabolism in lipopolysaccharide-induced BV2 cells. Genetic silencing or pharmacological inhibition of HK2 attenuates mitochondrial damage in vitro. Downregulation of HK2 lowered the NOD-like receptor signaling family pyrin domain containing three activations, both in BV2 cells and in the hippocampus of cecal ligation and puncture-induced male septic mice. Moreover, the inhibition of HK2 promoted lipid droplet reduction and activated mammalian target of rapamycin-mediated autophagy. Mechanistically, HK2 knockdown in microglial cells reduced the ISGylation of Acyl-CoA Synthetase Long-chain Family Member 4 (ACSL4) during lipid metabolism by interferon-stimulated gene 15 (ISG15). Notably, ISG15 eﬀectively down-regulated the expression of ACSL4 in vitro. Our findings provide new mechanistic insights of HK2 in microglial cells through regulation of ACSL4 ISGylation, suggesting a promising therapeutic strategy for treating SAE by targeting HK2.

overall_design: To investigate the expression of HK2 in vitro, RNA-Seq was performed to compare the transcriptomic profiles of BV2 cells under control and LPS conditions.


title: ATF2 phosphorylation is essential for neuronal apoptosis, linking the DLK/LZK kinase cascade to JUN upregulation

city: Bethesda

first: Pedro

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

summary: Apoptotic neuron death is a common feature of many neurodegenerative diseases. Perhaps surprisingly, the exact mechanisms by which neurons undergo apoptosis have yet to be elucidated. We conducted an unbiased whole genome screen in human neurons to discover genes required for apoptotic neuron death, and found ATF2, MAP3K12 and JUN among top hits. We demonstrate that ATF2 is a previously unappreciated master regulator of neuron death. ATF2 is phosphorylated downstream of MAP3K12 (dual leucine zipper kinase) and MAP3K13 (leucine zipper kinase) and its phosphorylation is essential for transcriptional upregulation of JUN. We show that JUN upregulation is essential for apoptosis – but not its phosphorylation. Contrary to previous assumptions, cJun phosphorylation is therefore simply a correlate of JUN upregulation. In this study, we identify phosphorylation of ATF2 as a key event in the mechanism of neuronal apoptosis, linking the MAP3K12/13 kinase cascade to transcriptional upregulation of JUN. Since targeting members of this signaling pathway to block neuronal death has proved difficult, ATF2 offers a novel and promising alternative.

overall_design: ChIP-seq was performed in iNeurons differentiated from human iPSCs with and without vincristine treatment.

first: Jorge

last: Gomez-Deza

first: Claire

last: LePichon

first: Zhenyu

last: Zuo


title: Transcriptional Dynamics of HuES-derived spinal motor neurons

department: Institute of Molecular Biology

summary: We take advantage of in vitro-derived motor neurons as a paradigm to investigate the cellular level during motor neuron differentiation. In this study, to uncover the abundantly expressed gene in the development of spinal motor neuron, we characterize transcriptomic signatures of HuES (human embryonic stem cell) derived motor neuron .

overall_design: To investigate motor neuron maturation in a human context, we used HuES lines to differentiate into spinal motor neurons and performed strand-specific RNA-seq at indicated time points. Specifically, we profile motor neuron transcriptome at Day 8, Day 16, and Day 31, referring to motor neuron progenitor (pMN), postmitotic motor neuron, and mature motor neuron.


title: HDAC5, an early osimertinib-responsive gene, is a novel therapeutic target for the drug resistance in EGFR-mutant lung adenocarcinoma cells.

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: Aberrant epigenetic regulation is closely associated with drug tolerance, an early step in the acquisition of drug resistance. We previously reported that a pioneer transcriptional factor (also called an epigenetic initiator) rapidly induced by osimertinib, a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor, plays a pivotal role in promoting the formation of osimertinib-tolerant cells. In this study, to identify novel epigenetic factors associated with osimertinib-tolerance, we performed a comprehensive screening of epigenetic factors whose expression is rapidly induced by osimertinib. Our results revealed that HDAC5, a class IIa histone deacetylase (HDAC), is the most prominently induced epigenetic factor in EGFR-mutant non-small cell lung cancer (NSCLC) cell lines during the early response to osimertinib. Knockdown of HDAC5 significantly reduced the emergence of osimertinib-resistant cells. Furthermore, treatment with LMK235, a selective HDAC5 inhibitor, significantly increased global histone acetylation and enhanced osimertinib-induced apoptosis. These findings underscore the potential of HDAC5 as a novel therapeutic target to overcome osimertinib-resistance and propose LMK235 as a promising compound to provide significant therapeutic benefits for EGFR-mutant NSCLC patients undergoing osimertinib treatment.

overall_design: Comaprison between HCC827 cells expressing control shRNA (Scr) treated with or without 50 nM osimertinib for 6 hours.

first: Hanbing

last: Lyu

first: Akihiko

last: Ishimura

first: Ryusuke

last: Suzuki

first: Khurelsukh

last: Buyanbat

first: Gerelsuren

last: Batbayar

first: Makiko

last: Meguro-Horike

first: Takeshi


title: Clinical utility and biological function of Transfer RNA-derived small RNAs in Patients with Acute Coronary Syndrome [ncRNA-seq]

city: 武汉

first: yi

last: he

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院

type: Non-coding RNA profiling by high throughput sequencing

summary: Acute coronary syndrome (ACS) is one of the leading causes of death worldwide. Aberrant expression of Transfer RNA-derived small RNAs  (tsRNA)  contributed to various human disease. However, the clincal utility and biological function of tsRNA in ACS are largely unknown. High throughput sequencing revealed a landscape of novel sncRNAs in the human PBMCs. tsRNAs represented a characteristic expression pattern in responding to acute coronary syndrome;  tRF-Gly-GCC-06 and tRF-Lys-CTT-02 were significantly up-regulated in patients with unstable angina(UA) and acute myocardial infarction(AMI). Both of the two tRFs demonstrated reasonable diagnostic accuracy for ACS detection. tRF-Gly-GCC-06 and tRF-Lys-CTT-02 upregulation were independent predictors of an increased risk of ACS. Both of the two tRFs expression levels show a significantly positive correlation with Gensini score.Our study identified novel tsRNA alterations  associated with ACS and provided potential clinical  biomarkers and therapeutic targets.

overall_design: We performed high throughput small RNA-sequencing for circulating peripheral blood monocyte cells (PBMCs)samples from 12 acute myocardial infarction patients, 12 unstable angina patients and 12 healthy controls.


title: Circulating eosinophil cell-free DNA as a noninvasive biomarker for perforated appendicitis in pediatric patients-a proof-of-concept study

city: Jerusalem

first: Ilana

last: Fox-Fisher

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

type: Methylation profiling by genome tiling array

summary: Appendicitis is the most common condition necessitating emergency abdominal surgery. While most cases are localized, 20% are complicated and result in appendix perforation. The management of non-complicated appendicitis varies across different medical centers, encompassing both surgical and non-surgical options, whereas complicated appendicitis is predominantly managed surgically. Differentiating them poses a clinical challenge, especially in pediatric patients, crucial for guiding appropriate treatment strategies. Therefore, there is an unmet need for biomarkers to distinguish the two entities. Here we examined the utility of epigenetic liquid biopsies in appendicitis. We used DNA methylation markers specific to immune and gastrointestinal epithelial cells to assess the tissue origins of plasma cell-free DNA (cfDNA) in patients with appendicitis. Appendix epithelium cfDNA was not detected in plasma samples from children with appendicitis relative to patients with abdominal pain and controls. In contrast, neutrophil and regulatory T-cell cfDNA were elevated in appendicitis enhancing the specificity and sensitivity of appendicitis diagnosis beyond the information provided by neutrophil counts. Notably, eosinophil cfDNA was most significantly elevated in children with perforated compared with non-perforated appendicitis. This finding was cross-validated using a machine-learning approach. In conclusion, eosinophil cfDNA can serve as a non-invasive biomarker for diagnosing perforated appendicitis.

overall_design: Our aim was to analyze the methylome of human appendix epithelial cells and identify specific methylation markers unique to the appendix, which could be applied to cfDNA. We extracted genomic DNA from three different appendix epithelial cell preparations (n=3) and assessed their methylome using Illumina 450k BeadChip arrays.

first: Ruth

last: Shemer


title: AAV-mediated silencing of Sox4 leads to long-term amelioration of liver phenotypes in mouse models of Alagille syndrome (scRNA-Seq)

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: BACKGROUND & AIMS: In patients with Alagille syndrome (ALGS), bile duct paucity often leads to severe cholestatic phenotypes that can only be cured with liver transplantation. However, no mechanism-based strategies exist to enhance biliary development in ALGS or other diseases associated with bile duct paucity. We aimed to identify a therapeutic target to address this unmet clinical need. METHODS: Preclinical mouse models of ALGS lacking one copy of Jag1 in germline with or without conditional deletion of one or both copies of Sox9 with Albumin-Cre were used. Sox4 levels were reduced in these models genetically or by using adeno-associated virus serotype 8 (AAV8) vectors driving a Sox4-silencing sequence. Liver histology, biliary tree ink injection, serum chemistry, RNAscope, and single-cell RNA-sequencing (scRNA-Seq) were performed for phenotypic characterization and gene expression analysis. RESULTS: Conditional removal of one copy of Sox4 in the liver significantly improved the liver phenotypes in ALGS mouse models in a Sox9-dependent manner. RNAscope experiments showed an increase in Sox4 expression level and relative abundance of Sox4-Sox9 double-positive cells in early postnatal livers of Jag1-heterozygous mice. scRNA-Seq revealed the appearance of an intermediate hepatobiliary cluster co-expressing Sox4 and Sox9 in Jag1-heterozygous livers. AAV8-mediated Sox4 knockdown, ubiquitously or driven by the hepatocyte-specific TBG promoter, led to long-term improvement of ALGS liver phenotypes upon one injection at postnatal day 1 (P1). An AAV8 injection at P15, when the liver damage response is activated, also led to phenotypic improvement. CONCLUSIONS: Our preclinical studies provide proof of principle for AAV-mediated Sox4 knockdown in TBG+ cells as a therapeutic approach for ALGS liver disease.

overall_design: Single-cell RNA sequencing studies of preclinical mouse models of ALGS lacking one copy of Jag1 in germline compared to wild-type provide evidence of differences in cell-type distribution and differentially activated pathways.

first: Duncan

last: Fox

first: Jun

last: Xie

first: Jennifer

last: Burwinkel

first: Josh

last: Adams

first: Kashish

last: Chetal

first: Marzieh

last: Keivandarian

first: Yaniv

last: Faingelernt

first: Sanjay

last: Subramanian

first: Mario

last: Lopez

first: Neda

last: Zarrin-Khameh

first: Guangping

last: Gao

first: Stacey

last: Huppert

first: Hamed

last: Jafar-Nejad


title: Soluble epoxide hydrolase inhibition confers neuroprotective and anti-inflammatory effect in a tauopathy mouse model

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

summary: Inhibition of soluble epoxide hydrolase (sEH) has been shown to suppress neuroinflammation through stabilizing epoxy fatty acids. Here we examined the role of sEH inhibitor TPPU in PS19 tauopathy mouse model by treating the 6-month-old wild-type and PS19 mice with vehicle or TPPU via drinking water continuously for 12 weeks, followed by performing single nucleus RNA-sequencing of the hippocampal tissues of the treated mice.

overall_design: single nuclear RNA sequencing (snRNA-seq) of hippocampus of wild-type and PS19 tau transgenic mice with or without TPPU treatment  at 9.5 month-of-age

first: Hui

last: Zheng


title: Coilin Mutation in Zebrafish Impairs the Innate Immune Zebrafish

city: Jackson

first: Lavanya

last: Challagundla

state: MS

address: 2500 North State Street

department: Cell and Molecular Biology

institute: University of Mississippi Medical Center

summary: Coilin is a nuclear protein known for its roles in assembling the Cajal Body and participating in the biogenesis of ribonucleoproteins. We have uncovered novel functions for coilin in promoting microRNA biogenesis and the phosphorylation/SUMOylation of various proteins, through which we have observed a role for coilin in responding to stress signals. Coilin has also been found to participate in the stress response in plants through the regulated expression of immunity genes and activation of defense mechanisms. In this study, we further investigated this role of coilin in regulating the immune response by applying transcriptomic analyses to examine the response to lipopolysaccharide-mediated stress in coilin-depleted human cells and coilin mutant zebrafish embryos. Our results indicate a vital function for coilin in regulating the expression of immunity-related genes and establish a conserved role for vertebrate coilin in the promotion of the innate immune response across humans and zebrafish.

overall_design: RNA was isolated by TRIzol Reagent (Invitrogen Life Technologies, Grand Island, NY, USA) and purified with RNeasy Mini Kit (QIAGEN; Hilden, Germany) according to manufacturer’s instructions. RNAseq was used to analyze differential expression between the following groups. RNA was evaluated for quality (Qubit fluorimeter) and fidelity using Qiagen QIAxcel Advanced System, with all sample demonstrating and RIS > 8. Libraries were generated with TruSeq stranded mRNA kit (Illumina; San Diego, CA, USA), indexed with TruSeq RNA CD indexes (Illumina; San Diego, CA, USA), and sequenced with NextSeq 2000 P3 (PE200) flow cell (Illumina; San Diego, CA, USA)

first: Douglas

last: McLaurin

first: Shanzida

middle: J

last: Siddique

first: Michael

last: Hebert


title: SAS cell line KDM4C-CUT&Tag sequencing

city: Hsinchu

first: Wen-Ching

last: Wang

address: NO.101, Sec. 2, Kuang-Fu Road, Hsinchu 300044, Taiwan (R.O.C)

department: Insitute of Molecular & Cellular Biology

institute: National Tsing Hua University

summary: This study explores the role of KDM4C, a histone lysine demethylase, in the development of head and neck squamous cell carcinoma (HNSCC). KDM4C is responsible for removing methyl groups from H3K9me3/2, a modification of histone proteins that can influence gene expression. To examine the distribution of KDM4C across the genome, we performed KDM4C-CUT&Tag sequencing analysis on SAS cells. Our study revealed that KDM4C binding was mainly concentrated around the transcription start site.

overall_design: We used KDM4C-CUT&Tag sequencing analysis on SAS cells to investigate the distribution of KDM4C across the genome.

first: Menjen

last: Wu

first: Shanmin

last: Yang


title: Plasma cell-free DNA methylation profile of patients with non-small cell lung cancer (NSCLC).

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

department: Pathology

institute: Keio University School of Medicine

summary: Genome-wide DNA methylation analysis using the Infinium MethylationEPIC BeadChip (Illumina) in 185 cell-free DNA samples.

overall_design: Blood samples were taken from the patients with NSCLC. Five ml of plasma was subjected into cfDNA extraction. All amount of extracted cfDNA minus that required for genomic analysis was subjected to bisulfite conversion. DNA methylation status at 865,918 CpG loci was examined by Infinium assay.

first: Eri

last: Arai

first: Mao

last: Fujimoto

first: Hiroyuki

last: Yasuda

first: Noriyuki

last: Matsutani

first: Nobuhiko

last: Seki

first: Akira

last: Togashi


title: The chromatin reader DIDO3 is a regulator of the gene network that controls B cell differentiation.

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

institute: Centro Nacional de Biotecnologia

summary: The development of hematopoietic cell lineages is a highly complex process that is governed by a delicate interplay of various transcription factors. The expression of these factors is influenced, in part, by epigenetic signatures that define each stage of cell differentiation. In particular, the formation of B lymphocytes depends on the sequential silencing of stemness genes and the balanced expression of interdependent transcription factors, along with DNA rearrangement. We have investigated the impact that the deficiency of DIDO3, a protein involved in chromatin status readout, has on B cell differentiation within the hematopoietic compartment of mice. Our findings revealed significant impairments in the successive stages of B cell development. The absence of DIDO3 resulted in remarkable alterations in the expression of essential transcription factors and differentiation markers, which are crucial for orchestrating the differentiation process. In addition, the somatic recombination process, which is responsible for generation of antigen receptor diversity, was also adversely affected. These observations highlight the vital role of epigenetic regulation, in particular the involvement of DIDO3, in ensuring proper B cell differentiation. Further research into the mechanisms underlying these disruptive alterations will deepen our understanding of hematopoiesis and may potentially lead to insights that aid in the development of therapeutic interventions for disorders involving aberrant B cell development.

overall_design: ChIP-Seq analysis of DIDO3 wild-type and E16 mutant in hematopoietic precursors (LSK, lin-Kit+Sca1+) cells.

first: Fernando

last: Gutiérrez del Burgo

first: María

middle: A

last: García-López

first: Carlos

last: Martinez-A

first: Ricardo

last: Villares


title: A secretome CRISPR screen identifies SFRP1 as a regulator of epidermal self-renewal [ATAC-seq]

city: Irvine

first: Bryan

last: Sun

state: California

address: 829 Medical Sciences Ct

institute: University of California Irvine

summary: Secreted epidermal proteins play pivotal roles in cell-cell communication, extracellular matrix remodeling, and antimicrobial defense. However, the complete spectrum of secreted proteins in the epidermis has not been experimentally defined. In this study, we performed mass spectrometry on conditioned media from primary human keratinocytes, identifying 406 proteins that constitute the keratinocyte secretome. To assess functional impacts of uncharacterized secreted proteins on epidermal stem cell behavior, we devised a colony formation assay-based CRISPR screen. The screen identified six candidate proteins that promoted proliferation of epidermal progenitors and two proteins that inhibited it. Secreted frizzled related protein-1 (SFRP1), an inhibitor of Wnt signaling, was the most potent inhibitor of progenitor proliferation in the screen. We discovered that in addition to regulating Wnt activity, SFRP1 restrained epidermal stem cell proliferation by inhibiting ectopic expression of leukemia inhibitory factor (LIF). Collectively, our study defines the keratinocyte secretome, demonstrates the application of a CRISPR screen to assess the function of non-cell autonomous factors, and highlights SFRP1’s role in regulating epidermal balance.

overall_design: To investigate the regulation on chromatin accessibility  of SFRP1 in human epidermal keratinocytes, we knocked SFRP1 gene by shRNA in primary kerationcytes, with SCR as a control.

first: Binbin

last: Cheng


title: A secretome CRISPR screen identifies SFRP1 as a regulator of epidermal self-renewal [RNA-seq]

overall_design: To investigate the funciton and downstrem target of SFRP1 in the regulation of human epidermal keratinocyte self-renewal and differentiation, we knocked SFRP1 gene by shRNA in primary kerationcytes. We then performed gene expression profiling analysis data obtained from RNA-seq of 2 different cells at two time points. Comparative gene expressin profiling analysis of RNA-seq data for shSCR(shcontrol) and shSFRP1, at day0 and day2.


title: DYRK1B phosphorylates FOXO1 to promote hepatic gluconeogenesis

city: Shanghai

first: Hong

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: One of the causes of hyperglycemia in type 2 diabetes is elevated hepatic glucose production. AKT-FOXO1 pathway is primarily involved in the hormonal upregulation of this process, and pharmacological or genetic inhibition of this pathway prevents diabetes in animal models. Here we report that DYRK1B regulates FoxO1 function through phosphorylation to regulate hepatic glucose metabolism. DYRK1B expression is induced by fasting and in diabetic mice. DYRK1B promoted hepatic gluconeogenesis and glucose intolerance in in vivo and in vitro model systems. Liver-specific DYRK1B conditional knockout mice were protected from diet-induced hyperglycemia. Mechanistically, DYRK1B interacted with and phosphorylated FoxO1, primarily at T467S468, which is required for its nuclear localization. DYRK1B inhibited AKT mediated FoxO1 phosphorylation at T24 and S256 and enhanced its nuclear retention. DYRK1B mediated phosphorylation of FoxO1 enhanced the expression of gluconeogenic genes and promoted gluconeogenesis. Treatment with DYRK1B pharmacological inhibitor AZ191 significantly lowered blood glucose levels in diabetic mice. We conclude that DYRK1B is a regulator of glucose metabolism, and its pharmacological inhibition could serve as therapeutic target for treating diabetes.

overall_design: To illustrate the mechanism how DYRK1B regulates the expression of gluconeogenic genes and functions in the regulation of glucose homeostasis, we did gene-expression profiles of primary hepatocytes treated with AZ191 or vehicle in fed or fasted state were analyzed.

first: Shanshan

last: Li

first: Cheng

last: Hu


city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

overall_design: To determine the gluconeogenesis genes regulated by Dyrk1b, we investigated the genome-wide location analysis of Dyrk1b and FoxO1 in fasted primary hepatocytes, using CUT&TAG analysis.

first: Mohan

last: Man


title: Acute BRCAness Induction and AR Signaling Blockage through CDK12/7/9 Degradation Enhances PARP Inhibitor Sensitivity in Prostate Cancer

city: Boston

first: Li

last: Jia

state: Massachusetts

address: 20 Shattuck Street, Thorn 1529

department: Urology

institute: Brigham and Women's Hospital

summary: Current treatment strategies for advanced prostate cancer (PCa) primarily rely on androgen receptor (AR)-directed therapies. However, the emergence of castration-resistant prostate cancer (CRPC) and resistance to AR signaling inhibitors (ARSI) pose substantial challenges. This study introduces a triple degrader, BSJ-5-63, targeting CDK12, CDK7, and CDK9, which has the potential to transform CRPC therapy. BSJ-5-63 uniquely downregulates homologous recombination repair (HRR) genes, including BRCA1 and BRCA2, by degrading CDK12, and it also attenuates AR signaling by degrading CDK7 and CDK9, further enhancing BSJ-5-63's therapeutic impact. Importantly, BSJ-5-63 induces a 'BRCAness' state that persists for a significant duration, enabling rational combination therapy with PARP inhibitors (PARPis) while minimizing drug-related toxicity and resistance. In both in vitro and in vivo studies, potent anti-proliferative effects were observed in both AR-positive and -negative CRPC cells. This research presents a promising multi-pronged approach for CRPC treatment, addressing both DNA repair mechanisms and AR signaling, with the potential to benefit a wide range of patients, regardless of their BRCA1/2 mutational status.

overall_design:
22Rv1 cells were treated with DMSO, BSJ-5-63 (100 nM), or BSJ-5-63-NC (100 nM) for 8 hours.
Cells were harvested then RNA was extracted using Rneasy mini kit. Library preparations were conducted by GENEWIZ.

first: Fu

last: Gui

first: Takuya

last: Tsujino


title: Geographic variation in epigenetic responses to hypoxia in deer mice (Peromyscus maniculatus) distributed along an elevational gradient

city: Princeton

first: Dhriti

last: Tandon

state: New Jersey

address: 106A Guyot Hall

department: Ecology and Evolutionary Biology

institute: Princeton University

summary: Spatially varying environments can pose distinct costs and benefits on traits under selection, such that a beneficial trait in one environment may be counter-productive in another. As an example, lowland and highland Peromyscus maniculatus populations display divergent, locally adapted physiological mechanisms shaped by altitudinal differences in oxygen availability. Particularly, lowland mice leverage ancestral plasticity derived from acute episodic bouts of low internal oxygen triggered by causes such as blood loss, anemia or tissue ischemia. These responses can be maladaptive under persistent low-oxygen conditions, as they could lead to physiological complications such as pulmonary hypertension. Therefore, highland ancestry is associated with traits promoting chronic hypoxia tolerance. Given each population’s distinct adaptive histories and reliance on plasticity for hypoxia tolerance, we hypothesized that upon hypoxia exposure lowland mice would have a more robust epigenetic response, driving trait plasticity, than highland mice. Using DNA methylation data collected from left ventricle tissues, we show that upon hypoxia exposure, lowland mice can chemically modulate the epigenetic landscape to a greater extent than highland mice, especially at key hypoxia-relevant genes such as Egln3, a regulator of Epas1- a gene frequently targeted for positive selection at high elevation. In addition, lowland mice show greater enrichment of DNA methylation change concentrated at hypoxia-relevant biological pathways, particularly those related to Notch ligands. These findings exemplify each population’s distinct reliance on molecular plasticity driven by their unique evolutionary histories.

overall_design: To investigate population-specific DNA methylation changes in response to hypoxia among lowland and highland lineages.

first: Shane

last: Campbell

first: Zac

last: Cheviron

first: Bridgett

last: vonHoldt


title: Effect of Lactate dehydrogenase inhibitor (LDHi; GSK2837808A) on BCG vaccine induced trained immunity in vitro

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. This study examined the in vitro effect of an LDH inhibitor on BCG induced trained immunity in human primary monocytes.

overall_design: Monocytes from four donors were cultured in medium or stimulated with BCG  for 24h in the presence or absence of LDH inhibitor, followed by treatment with or without LDH inhibitor for 5 more days. At day 6 macrophages were washed and stimulated with LPS  or cultured in media for 4h followed by transcriptome analysis with RNA-seq.

first: Athanasios

last: Ziogas

first: Mihai

last: Netea


title: Remodeling of Histone lactylation, acetylation, and methylation in circulating monocytes by BCG vaccination

summary: The innate immune system can develop memory-like features, recalling past infections or vaccinations and enabling more efficient responses to future threats, a process known as trained immunity (cite). Trained innate immune cells triggered by various microbial components or vaccines such as Bacille Calmette-Guérin (BCG), can confer broad-spectrum, heterologous (non-specific) protection against diverse pathogens. Subjects were  vaccinated in with BCG vaccine and lood samples were obtained immediately before BCG vaccination (day 0) and subsequently on day 14 and day 90 post-vaccination

overall_design: Blood was collected using venapuncture and PBMCs were isolated at three time points following BCG vaccination: baseline, 1 month, and 3 months. Circulating monocytes were isolated and chromatin immunoprecipitation sequencing (ChIP-seq) was performed to map genome-wide distribution of H3K4me1, H3K27ac and H3K18lac.

first: Marijke

last: Baltissen

first: Joost

last: Martens

first: Musa

last: Mhlanga


title: Transcriptomes during monocyte-to-macrophage differentiation and BCG induced trained immunity in vitro

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. This study examined the transcriptional remodeling during  BCG induced trained immunity in human primary monocytes.

overall_design: Human monocytes from 3 donors were different iated  to naive or trained macrophages. Primary human monocytes were differentiated to macrophages after a 6 days in vitro culture.Trained immunity was induced by initial exposure of primary human monocytes to BCG vaccine for 24 hours, followed by removal of stimulus and differentiation to macrophages for an additional 5 days. Cells were collected at baseline (day 0), 24 hours, and 6 days, and RNA was extracted for RNA-seq analysis.


title: Remodeling of Histone 3 Lysine 18 lactylation (H3K18lac) in monocytes-to-macrophage differentiation and induction of Trained Immunity by BCG in vitro

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. This study profiled the distribution of the active histone modification (H3K18lac) in human monocytes responding to the BCG vaccine and during monocyte-to-macrophage differentiation.

overall_design: Human monocytes from 3 donors were differentiated  to naive or trained macrophages. Primary human monocytes were differentiated to macrophages after a 6 days in vitro culture.Trained immunity was induced by initial exposure of primary human monocytes to BCG vaccine for 24 hours, followed by removal of stimulus and differentiation to macrophages for an additional 5 days. Cells were fixed for chromatin collection at baseline (day 0), 24 hours, and 6 days.


title: Single-cell RNA sequencing of blood cells from patients with VEXAS syndrome.

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

summary: We performed single cell RNA sequencing, and VDJ sequencing of TCR and BCR of peripheral blood samples (Peripheral Blood Mononuclear Cells[PBMCs]) from 9 patients with VEXAS to understand disease pathogenesis.

overall_design: RNA profiles of single peripheral blood cells of 9 VEXAS patients and 5 healthy donors were generated by deep sequencing using Illumina NovaSeq.

first: Hiroki

last: Mizumaki


title: Arabidopsis thaliana: Control vs heat vs microwave irradiation

city: Tokyo

first: Nobuhiro

last: Suzuki

state: 東京都

address: 7-1, Kioicho, Chiyoda

institute: Sophia University

summary:
Arabidopsis plants (Col-0) were exposed to heat stress (40oC) or microwave irradiation (23W) for 1h.
Shoots were sampled and transcripts significantly up- or down-regulated by heat stress or microwave irradiation were investigated.

overall_design: Three conditions experiment: Control 4 replicates, heat stress 4 replicates, microwave irradiation 4 replicates

first: Satoshi

last: Horikoshi


title: Novel Plasma Cell developmental intermediates produce graded expression of IgM secretory transcripts

first: Yoseop

last: Yoon

state: CA

address: 1002 Health Sciences Rd

summary: Differentiation into plasma cells (PC) enables secretion of ~10,000 antibody molecules per second. This extraordinary capacity requires the upregulation of PC transcriptional determinants that increase immunoglobulin mRNA synthesis, coordinate alternative 3’end processing of the heavy chain transcript from the distal to proximal poly-adenylation site (PAS), and remodel the secretory pathway. Based on the difficulty of prospectively identifying secretory cells, we developed a dual-fluorescent protein reporter mouse to study the post-transcriptional-level transition from membrane-anchored to secretory immunoglobulin M (µM PAS and µS PAS, respectively), in single cells. We observed (i) dynamic acquisition of graded µS PAS usage during PC differentiation (ii) IRF4 and Blimp-1 functioned hierarchically to increase µ abundance as well as µS PAS usage and (iii) graded µS populations did or did not express Blimp-1. Interestingly, the low and high µS and Blimp-1-expressing populations arose from distinct developmental intermediates that exhibited dissimilar endoplasmic reticulum features revealing unpredicted complexity of PC differentiation. The novel cell and µS PAS fate trajectories may have implications for discrete specializations of the secretory pathway.

overall_design: To investigate the relationship between uS poly-adenylation site (PAS) usage and its relationship to Plasma cell (PC) differentiation, we created a mouse with an engineered allele of the u locus that reports on uS expression and bred that mouse to Blimp-1:YFP mice that marks PC. B cells from such mice were used to generate emergent PC using in vitro systems and we observed 4 populations of graded uS expression, uS INT and uS HI, that were Blimp-1:YFP negative (pre-PC) and uS INT and uS HI Blimp-1:YFP positive (PC). Comparative gene expression analysis of RNA-seq data was used to establish the transcriptomic states of the populations.

first: Evelyn

last: Sievert

first: Marissa

last: Franke

first: Yongsheng

last: Shi

first: Roger

last: Sciammas


title: Transcriptomic analysis reveals key pathways influenced by HIV-2 Vpx

city: Debrecen

first: József

last: Tőzsér

address: Egyetem tér 1., Life Science Building

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen, Faculty of Medicine

summary: Viral protein X (Vpx) is a unique accessory protein encoded by the genome of the Human immunodeficiency virus type 2 (HIV-2) and lineages of the simian immunodeficiency virus of sooty mangabeys. So far, counteracting the cellular restriction factor SAMHD1 and mediating efficient translocation of viral pre-integration complex have been recognized as key functions of Vpx, however, thorough exploration of its effects on the cellular transcriptome and cytokine milieu have not yet been explored.  In this study, we carried out transcriptomic analysis of THP-1 cells and determined differential gene expression induced by HIV-2 Vpx, additionally, we measured the effect of Vpx expression on secretion of key cytokines in the medium of transfected cells. Our findings revealed that wild-type HIV-2 Vpx can significantly alter the expression of genes coding for helicases, zinc finger proteins, chaperons, transcription factors and proteins involved in DNA methylation. Differentially altered genes were involved in negative regulation of viral process; type I interferon signaling pathway; DNA-templated transcription, elongation; positive regulation of interferon-beta production and negative regulation of innate immune response. Moreover, Vpx downregulated genes associated with negative regulation of TGF-β1, resulting in stimulation of its production. Importantly, Vpx was also found to decrease the expression of HIV-2 Tat, possibly through downregulation of a crucial splicing factor required for maturation of Tat.

overall_design:
To explore the impact of HIV-2 Vpx on the cellular transcriptome and cytokine environment, we utilized a THP-1 monocyte cell line exposed to three distinct transfection conditions: with plasmids coding for wild type (1) and mutant (2) Vpx in conjugation with GFP, and one devoid of Vpx but still with GFP as mock control (3). We performed experiments in duplicates.
We performed comparative gene expression profiling analysis using RNA-Seq data from the three distinct transfected cell variants, comprising a total of six samples.

first: Zsófia

middle: I

last: Szojka

first: Balázs

last: Kunkli

first: Irene

middle: W

last: Kiarie

first: Tamás

middle: R

last: Linkner

first: Aya

last: Al-Muffti

first: Hala

last: Ahmad

first: Szilvia

last: Benkő

first: Mohamed

last: Mahdi


title: L1-MET silencing induces cell apoptosis and impairs MET and EGFR protein expression in cancer cells

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

country: Italy

institute: University of Turin

summary: To address the role of L1-MET by investigating the effects of its selective silencing on cells expressing variable levels of L1-MET /MET mRNA

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq after gene silencing
RNA expression of triplicates obtained by L1-MET silencing in four cancer cell lines

first: Umberto

last: Miglio

first: Enrico

last: Berrino

first: Tiziana

last: Venesio


title: Identification of tRNA-derived Small RNAs and Their Potential Roles in Myocardial Infarction

city: Zhanjiang

first: Fanji

last: Meng

address: 12# Minyou Road, Xiashan District

department: Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University

institute: Guangdong Medical University

summary: tRNA-derived small RNAs (tsRNAs), as a novel type of non-coding RNAs are significantly involved in multiple cellular processes and biological functions in many diseases. Microarray analysis was used to evaluated the tsRNA expression profiles of myocardial tissue in myocardial infarction (MI) (n = 3)  and sham in mice (n = 3). Bioinformatics analysis and functional experiment indicated that tsRNAs potential biological functions involved in MI.

overall_design: We performed small RNA microarray to obtain a profile of small RNA in myocardium from myocardial infarction and sham groups

first: Can

last: Chen


title: Single cell RNA sequencing of spinal motor neurons and interneurons differentiated from isogenic FUS and TARDBP human induced pluripotent stem cell lines harbouring ALS-causative mutations

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

summary: Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disease that can be inherited with genetic mutations in > 25 different genes including e.g. FUS, TARDBP, and C9ORF72. It is currently unclear how these mutations lead to motor neuron degeneration and whether different gene mutations converge on similar pathogenic pathways early on, or if each mutation leads to motor neuron death in a unique manner. To address these questions in depth, we generated a number of isogenic iPSC (induced pluripotent stem cell) lines harbouring point mutations in FUS (R495X and P525L) or TARDBP (M337V) as well as a knock-out of FUS (FUS-KO), to discern loss-versus gain-of-function mechanisms in FUS. The use of isogenic lines enables identification of subtle early disturbances in the transcriptome which may be detrimental but impossible to detect when lines of different backgrounds are used. We conducted single cell RNA sequencing of motor neurons and interneurons derived from these lines using Smart-seq2. We show that ALS-causative mutations elicit a much larger transcriptional response in motor neurons than in interneurons. A large number of transcripts were coregulated across FUS R495X and P525L motor neurons and the majority of these were part of gain-of-function of FUS. Cross-comparison with isogenic ALS-linked TARDBP M337V identified an early dysfunctions shared across ALS-causative mutations unique to motor neurons that could have major implications for motor neuron survival and that might be targeted therapeutically.

overall_design: Smart-Seq2 single cell sequencing of spinal neurons derived in vitro according to two protocols from isogenic human induced pluripotent stem cell DF6-9-9T.B lines with unedited control or edited genotype harbouring FUS KO (homozygous) , FUS R495X (homozygous), FUS P525L (heterozygous and homozygous) or TARDBP M337V (homozygous) mutations.

first: Christoph

last: Schweingruber

first: Jik

last: Nijssen

last: Mei

first: Julio

last: Aguila


title: CDX1 and CDX2 suppress colon cancer stemness by inhibiting b-catenin-facilitated formation of Pol II–DSIF–PAF1C complex

status: Public on Apr 29 2025

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Gene expression profiles of DLD1-TetOff cells comparing control TetOff cells with TetOff cells expressing Cdx1 or Cdx2 for 12 and 24 hours.

overall_design: A two-condition experiment, DLD1-TetOff vs DLD1-TetOff expressing Cdx1 or Cdx2. Three sets of control and Cdx-induced TetOff cells were analyzed.

first: Koji

last: Aoki


title: CDX1 and CDX2 suppress colon cancer stemness by inhibiting beta-catenin-facilitated formation of Pol II-DSIF-PAF1C complex

city: Yoshida-gun

state: Fukui

address: 23-3 Matsuokashimoaizuki, Eiheiji-cho

department: Faculty of Medical Sciences

institute: University of Fukui

summary: Homeobox transcription factors CDX1 and CDX2 (hereafter, CDX1/2) play key roles in determining the identity of intestinal epithelial cells and regulating their stem cell functions. However, the role of CDX1/2 in regulating colon cancer stemness and the underlying mechanism have been unclear. Here, we show that the complete loss of Cdx1 or concurrent loss of Cdx1/2 increased the stemness and malignancy of intestinal tumors. Consistently, CDX1/2 reduced the expression levels of cancer stemness-related genes including LGR5. CDX1/2 bound to the downstream region of the LGR5 transcription start site (TSS), where b-catenin also binds. Despite increased H3 acetylation and an open chromatin structure, CDX1/2 reduced the levels of DRB sensitivity-inducing factor (DSIF), RNA polymerase II-associated factor 1 (PAF1), and Pol II complexes around the LGR5 TSS. Through a homeodomain, CDX1/2 cooperatively inhibited the b-catenin-promoted formation of the active Pol II complex containing DSIF and PAF1 complexes by preventing interactions between b-catenin and these complexes, in an additive manner. Our findings suggest that CDX1/2 cooperatively suppress colonic tumorigenesis and cancer stemness by antagonizing b-catenin through the DSIF and PAF1 complexes. Additionally, DSIF and PAF1 complexes act as transcriptional platforms that integrate both tumor-suppressive and oncogenic signals into the expression of genes that controls colonic tumorigenesis.

overall_design: ChIP-seq of flag-tagged Cdx1 or Cdx2 in DLD1-TetOff cells.


title: DNA methylation profiles of cKit positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

summary: Here we show that the combination of Idh1R132 plus Npm1c mutations cooperatively induced overt AML in vivo, using genetically engineered mouse model. In contrast, the combination of Idh1R132 plus Flt3ITD led to myeloid proliferation disease, but not AML. The mice harboring both of Idh1R132 and Npm1c mutations got fatal (median survival, 254 days) due to AML, which demonstrated rapid lethality on recipient mice in secondary transplantation experiments. We analyzed cKit-positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD. We isolated cKit positive BM cells from the mice of the two different ages (3 and 6 months old), and subjected to RNA-seq, bisulfite-seq, and ATAC-seq.

overall_design: Using Bisulfite-Seq, we profiled gene-wide DNA methylation patterns of cKit positive BM cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD, with 3-5 biological replicates for each genotype. We examined the cells from mice of the two different ages (3 and 6 months old).

first: Takashi

last: Sakamoto

first: Jonathan

last: Foox

first: Julie

last: Leca

first: Christopher

last: Mason

first: Ari

last: Melnick

first: Tak

last: Mak


title: Single cell RNA-seq of fetal thymus, bronchial, esophageal, and lung cells

city: Stanford

first: Andrew

last: Gentles

address: 1201 Welch Road

institute: Stanford University

summary: We performed scRNA-seq on epithelial and stromal cells isolated from fetal thymus, bronchus, esophageal and lung cells to identify drivers of lieage commitment.

overall_design: Single cell RNA-seq (10X Genomic 3' gene expression) from individual fetal cells.

first: Katja

last: Weinacht