title: SGLT2 Inhibitor Empagliflozin Enhances Metabolic Efficiency and Ameliorates Left Ventricular Hypertrophy in Myosin R403Q Mutant Hypertrophic Cardiomyopathy Mice

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

summary: Background: Hypertrophic cardiomyopathy (HCM) is a genetic cardiac disorder characterized by left ventricular hypertrophy (LVH), diastolic dysfunction, and impaired metabolic efficiency. This study investigates the therapeutic potential of the sodium-glucose cotransporter 2 inhibitor empagliflozin (EMPA) in ameliorating these pathological features in a mouse model carrying the myosin R403Q mutation. Methods: Male mice harboring the R403Q mutation were treated with EMPA for 16 weeks. We utilized multinuclear magnetic resonance spectroscopy (31P, 13C, 23Na MRS), alongside echocardiography, transcriptomic, proteomic, and phosphoproteomic profiling to assess metabolic, structural, and functional changes. Results: EMPA facilitated the coupling of glycolysis with glucose oxidation and normalized elevated intracellular sodium levels. Treatment resulted in a significant reduction in LVH and myocardial fibrosis as evidenced by echocardiography and histopathology. These structural improvements correlated with enhancements in mitochondrial ATP synthesis, fatty acid oxidation (FAO), and branched-chain amino acid (BCAA) catabolism. Furthermore, empagliflozin improved left ventricular diastolic function and contractile reserve, underscored by improved ATP production and reduced energy cost of contraction. Notably, these benefits were linked to downregulation of the mTOR signaling pathway and normalization of myocardial substrate metabolic fluxes. Conclusion: EMPA significantly mitigates structural and metabolic dysfunctions in a mouse model of HCM, underscoring its potential as a therapeutic agent for managing this condition. These findings suggest broader applicability of SGLT2 inhibitors in cardiovascular diseases, including those due to myocardial-specific mutations, warranting further clinical investigation.

overall_design: We hypothesized that treatment with EMPA would improve cardiac energetics, contractile function and structure in HCM. To test this hypothesis, we studied mice carrying the myosin R403Q mutation treated with EMPA for 16 weeks. Through the application of multinuclear MR spectroscopy (31P, 13C, and 23Na MRS), alongside transcriptomic, proteomic, and phosphoproteomic profiling, we determined that EMPA treatment facilitates the coupling of glycolysis with glucose oxidation and normalizes the elevated intracellular sodium levels observed in HCM myocardium. Nine-to-ten-week-old male mice harboring R403Q mutation in cardiac myosin heavy chain or wild-type littermates were fed ad libitum a control diet or the same diet enriched with EMPA for 16 weeks. Single-nucleus RNA sequencing analysis was conducted in 12-week-old R403Q hearts prior to the onset of left ventricular hypertrophy.

first: Tomas

last: Baka

first: Ivan

last: Luptak


title: The impact of oligodendroglial Serpina3n depeletion on brain aging in mice

status: Public on Dec 01 2025

city: Sacramento

first: Hyun Kyu

last: Kim

state: CA

address: 2425 Stockton Blvd

department: Neurology

country: USA

institute: UCDAVIS

type: Expression profiling by high throughput sequencing

summary: This study investigates the role of oligodendroglial Serpina3n in brain aging by examining its depletion using Olig2-Cre Serpina3n flox/flox mice model. To assess the molecular impact of oligodendroglial Serpina3n depletion on brain aging, RNA-seq was performed on forebrain samples from three experimental groups: 1) Young Wild-Type Mice (2-month-old): Representing baseline gene expression in a young, healthy brain; 2) Aged Wild-Type Mice (22-month-old): Serving as a control group to analyze age-related changes in gene expression without genetic modifications. 3) Aged Olig2-Cre Serpina3n flox/flox mice (22-month-old): Assessing the effects of oligodendroglial Serpina3n depletion on the transcriptomic profile of aged brains. The experiment aims to identify gene expression changes associated with normal brain aging by comparing young and aged wild-type mice, determine the specific impact of oligodendroglial Serpina3n depletion on the aged brain by comparing aged wild-type mice to aged knockout mice, and highlight molecular mechanisms influenced by Serpina3n in the context of brain aging. This design allows for a comparative analysis of aging-related transcriptional changes and the specific contribution of Serpina3n depletion in this process.

overall_design: RNA-seq profiling of forebrains from 2-month-old young wild-type mice, 22-month-old aged wild-type mice, and 22-month-old aged oligodendroglial Serpina3n knockout mice.

first: Yan

last: Wang

first: Meina

last: Zhu

first: Fuzheng

last: Guo


title: Astrocytes enhance the synaptic transmission between VTA GABASST and DA neurins to induce depression in chronic neuropathic pain

city: Chengdu

first: Cheng

last: Zhou

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

country: China

institute: West China Hospital of Sichuan University

summary: Background: As pain persists, it is often accompanied by the development of negative emotional states, such as depression. Approximately 50%-85% of patients with chronic pain experience depressive symptoms. Ventral tegmental area (VTA) γ--aminobutyric acid (GABA) neurons play a crucial role in regulating emotions. VTA GABA neurons can be mainly classified into those expressing somatostatin (SST) and parvalbumin (PV) neurons. The subtypes of VTA GABA neurons exhibit significant heterogeneity, but it remains unclear whether these subtypes mediate different functions in the development of chronic pain and depression. Inward rectifying potassium channel 4.1 (Kir4.1) is an important potassium channel mainly expressed in astrocytes and plays an important role in regulating neural activity. In lipopolysaccharide (LPS)-induced depression, Kir4.1 in lateral habenula (LHb) was upregulated. Lys05 (an inhibitor of Kir4.1) reversed the Kir4.1-driven depression-like phenotype. However, there was no study has reported the changes of Kir4.1 in chronic pain-induced depression or verified the therapeutic effects of Lys05 on it. Methods: We established chronic constriction injury (CCI) model to induce chronic pain in mice, and used the sugar preference test (SPT), tail suspension test (TST), and open field test (OFT) to detect depressive behavior in mice. Lys05 was injected to investigate the effect of Kir4.1 inhibitors on depression caused by chronic neuropathic pain. The adeno-associated virus (AAV) was designed to knockdown or overexpress the expression of Kir4.1 in VTA astrocytes.  Using optogenetic manipulations and transgenic mice, specific activation of VTA GABASST neurons or VTA GABAPV neurons was used to explore which types of VTA GABA neurons Kir4.1 has effects on.  Patch-clamp recording was applied to explore the effects of Kir4.1 on the excitability of different types of VTA neurons. Results: Lys05 could reverse the depressive behaviors induced by LPS. In detail, mice treated with 10 mg/kg Lys05 showed increased sucrose preference, decreased immobility durations in TST and increased percent center time in OFT. However, Lys05 didn’t show any specific response to depression behavior in CCI-induced depression mice. Then we found Kir4.1 expression decreased in VTA and LHb of CCI-induced depression mice. Next, we found knockdown of Kir4.1 in the VTA resulted mice became depression but with no hyperalgesia. Correspondingly, overexpress Kir4.1 in VTA astrocytes could reverse the chronic pain-induced depression like states. In the patch clamp, when knocked down Kir4.1 in VTA astrocytes, the excitability of dopamine neurons decreased, GABASST neurons increased, but GABAPV neurons did not change significantly. Specifically excitable VTA GABASST neurons could cause depression in mice, while excitable GABAPV neurons did not. Conclusion: Chronic pain decreases the expression of Kir4.1 in VTA astrocytes, which activates GABASST neurons and in turns inhibits DA neurons, then leads depression.

overall_design: The VTA of wide type and chronic neuropathic pain adult mice were analyzed by single-nucleus RNA sequencing.

first: Yali

last: Chen

first: Mengchan

last: Ou

first: Xialian

last: Hu

first: Jin

last: Liu

first: Xuechao

last: Hao


title: RNA-Seq analysis of islets from Akita mice treated with the SGLT2 inhibitor Dapagliflozin and wild-type controls

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: In diabetes, hyperglycemia drives the progression of b-cell failure and multi-organ complications. Prolonged exposure to high glucose stimulates mTORC1, resulting in impaired glucose metabolism and exacerbation of ER stress and inflammation. However, the precise mechanism by which glucose regulates mTORC1 activity in diabetes remains unclear. We performed metabolic labeling with 13C6- glucose in diabetic animals treated with or without the SGLT2 inhibitor (SGLT2i) dapagliflozin or insulin, followed by targeted metabolomics and metabolic flux analysis. We found that tissue glucose concentrations strongly correlate with glucosamine, rather than with other glucose or amino acid metabolites. Plasma glucosamine levels are increased in patients with impaired fasting glucose (IFG) and type 2 diabetes (T2D) and are inversely correlated with b-cell function. Glucosamine is synthesized by amine group transfer from glutamine to glucose, which enhances O-GlcNAcylation (O-GlcN) of mTORC1- regulating proteins, including Raptor, via O-GlcNAc transferase (OGT), subsequently activating mTORC1. Genetic inhibition of b-cell mTORC1 by heterozygous Raptor KO and inhibition of the glucosamine-mTORC1 pathway by SGLT2i improved diabetes and b-cell function. We propose that the glucosamine-mTORC1 pathway is a key mediator of glucose toxicity in diabetes.

overall_design: To investigate the molecular mechanisms underlying glucotoxicity in beta cells, we performed RNA-seq analysis on whole islets from wild-type (WT) and Akita mice, a model of endoplasmic reticulum (ER) stress-mediated diabetes. Akita mice were treated with or without a glucose-lowering sodium-glucose cotransporter 2 inhibitor (SGLT2i). SGLT2i-treated Akita mice received the drug in their drinking water for two weeks immediately after weaning. Islets were subsequently collected from all groups and processed for RNA-seq analysis. Each experimental group included three biological replicates, with each replicate consisting of pooled islets (50 islets pooled) from 2–3 mice.

first: Yael

last: Riahi

first: Elisheva

last: Zemelman


title: The FAM53C/DYRK1A axis regulates the G1/S transition of the cell cycle

city: Palo Alto

first: Debadrita

last: Bhattacharya

state: California

address: Lorey Lokey Stem Cell Research Building,265 Campus Drive

department: Pediatrics

institute: Stanford University

summary: A growing number of therapies are being developed to target the cell cycle machinery for the treatment of cancer and other human diseases. Consequently, a greater understanding of the factors regulating cell cycle progression becomes essential to help enhance to response to these new therapies. Here, using data from the Cancer Dependency Map, we identified the poorly-studied factor FAM53C as a new regulator of the G1/S transition. We found that FAM53C is necessary and sufficient for this cell cycle transition and that it acts upstream of the CyclinD-CDK4/6-RB axis in the regulation of the G1/S transition. By mass spectrometry, biochemical, and cellular assays, we identified and validated DYRK1A as a cell cycle kinase inhibited by and directly interacting with FAM53C. DYRK1A kinase inhibition rescues the G1 arrest induced by FAM53C knock-down. Fam53C knockout human cortical organoids also display increased cell cycle arrest and growth defects. Fam53C knockout mice are viable but show defects in body growth, as would be expected for a promoter of cell proliferation. Because DYRK1A dysregulation contributes to tumorigenesis and developmental disorders such as Down syndrome, future strategies aiming at regulating FAM53C activity may benefit a broad range of patients.

overall_design: To investigate changes in gene expression of RPE-1 cell lines upon siRNA-mediated knockdown of FAM53C, 48 hours post transfection.

first: Taylar

last: Hammond

first: Julien

last: Sage


title: Transcriptional Hallmarks of Drug Tolerance in Hormone-Dependent Cancers

city: London

first: Heena

last: Dhiman

address: 72 Du Cane Road

country: United Kingdom

institute: Imperial College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Drug tolerance is a key step allowing the development of drug resistance in hormone-dependent breast cancer. While transcriptional heterogeneity has been correlated with tolerance, the transcriptional programs specifically driving it remain poorly understood. To address this, we profile and computationally mine 300’000 single-cell transcriptomes following drug adaptation in models of breast and prostate cancer, spanning seven different treatments (endocrine therapies and CDK-inhibitors), and validate these via integration with novel and published profiles of lesions treated with neo-adjuvant endocrine therapies. We identify a comprehensive spectrum of transcriptional programs and upstream regulators, correlated to different stages of drug tolerance, and conserved across first- and second-line therapies, and therapeutic approaches. Pre-existing programs cooperate with adaptive ones, with the former being more conserved across therapies. These newly identified programs suggest fine-tuning of existing cell states, rather than cell-type or lineage switches, as a main driver of tolerance and resistance. Notably, JAK-STAT signalling emerges as one of the critical regulators of these programs in both the early and late stages of drug tolerance and serves as a predictor of progression in primary hormone-dependent tumours treated with endocrine therapies.

overall_design: ATAC-seq profiling of FACS-sorted subpopulations of MCF7 and MCF-LTED (LTED) cell lines, in depulicates or triplicates.

first: Stephan

last: Gruener

last: Dhinam

first: Daniele

last: Generali

first: Giacomo

last: Corleone

first: Ali

last: Simak

first: Sung Pil

last: Hong

first: Luca

last: Magnani

first: Iros

last: Barozzi


title: Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [short-read RNAseq ]

city: Madison

first: anthony

middle: shawn

last: abrantes

state: WI

address: 402 Paunack st apt 1

department: genetic medicine

institute: unc-chapel hill

summary: Over the past 15+ years, genetic studies have been notably successful in revealing the architecture of multiple psychiatric disorders, including schizophrenia. It is now widely acknowledged that schizophrenia is highly polygenic, consisting of both common variants of unknown significance, identified through genome-wide association studies (GWAS), and rare CNVs and coding variants. Despite these advances, the underlying mechanisms of specific genes implicated by GWAS are not well understood. Multiple lines of evidence implicate alternative splicing in the pathophysiology of schizophrenia. Single-nucleotide polymorphisms (SNPs) within implicated schizophrenia loci could alter isoform diversity and abundances which may not be reflected in a typical differential expression study. Hence, we generated a comprehensive isoform survey of postmortem human dorsolateral prefrontal cortex (DLPFC) from schizophrenia cases and neurotypical controls to identify case-control isoform-level differences. We developed an analysis pipeline that combines the strengths of PacBio SMRT long-read RNA sequencing in conducting a detailed isoform census with the capacity of short-read RNA sequencing for the quantification of isoform abundances. From several hundred thousand discovered long-read isoforms we curated a transcriptome with tens of thousands of high confidence novel isoforms. We then identified differential isoform usage (DIU) genes using a combination of established and in-house pipelines that enables case-control comparisons. Many of these novel isoforms are differentially expressed in schizophrenia DLPFC vs neurotypical controls. Differentially expressed genes are enriched in gene sets related to synaptic structure and function, RNA binding and splicing, as well as cell types previously implicated in schizophrenia, including cortical excitatory neurons, medium spiny neurons, and pyramidal CA1 neurons. Publicly available splicing data, genotyping, proteomics, and single nucleus sequencing results verify and support our results.

overall_design: bulk RNA-seq data from human post mortem DLPFC tissue in schizophrenic and healthy control subjects

first: Anthony

last: Abrantes

first: Lisa

last: Bast

first: Fatima

last: Memic

first: Shuyang

last: Yao

first: NaEshia

last: Ancalade

first: Shadia

last: Sekle

first: Anke A.

last: Dijkstra

first: Elizabeth

last: Tseng

first: George

last: Jurjus

first: James

last: Overholser

first: Gouri

last: Mahajan

first: Craig A.

last: Stockmeier

first: Gloria

last: Sheynkman

first: Jens

last: Hjerling-Leffler

first: Guus

last: Smit

first: Patrick F.

last: Sullivan

first: Paola

last: Giusti-Rodriguez


title: Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [long-read RNAseq ]

first: anthony

last: abrantes

overall_design: pacbio long read RNA-seq data from human post mortem DLPFC tissue in schizophrenic and healthy control subjects

first: Anthony

last: Abrantes


title: Plasma small extracellular vesicles of ischemic cardiomyopathy aggravate ventricular remodeling post-myocardial infarction through miR-223-3p-mediated dysfunction in regulatory T cells

city: guangzhou

first: bifang

last: mai

address: yanjiang Road107

institute: sun yat sen memorial hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Ischemic cardiomyopathy (ICM), caused by acute myocardial infarction (AMI), is the most common type of chronic heart failure (HF). Treg cells, maintaining peripheral immune tolerance, are dysfunctional in ICM mice. The mechanism of dysfunctional Treg cells in ICM remains unclear. Furthermore, small extracellular vesicles (sEVs) are significant in intracellular communication and tissue homeostasis. This study tends to illustrate whether plasma sEVs of ICM promote the dysfunctional state of Treg cells through miRNA and thus aggravate cardiac remodeling.In ICM patients, the number of Treg cells was increased while Foxp3 mean fluorescence intensity (MFI) was decreased in peripheral blood, indicating a dysfunctional phenotype of Treg cells. miR-223-3p, identified by sequencing using plasma sEVs of ICM patients, was upregulated and negatively correlated with blood Treg cell number. Additionally, the number of cardiac Treg cells of ICM mice was increased while Foxp3 MFI was decreased. Furthermore, plasma sEVs from ICM mice aggravate ventricular remodeling in mice post-AMI. Besides, ICM-sEVs decreased the number of Treg cells while miR-223-3p knockdown increased the number of them and promoted the expression of Foxp3 in vitro.Plasma sEVs of ICM aggravate ventricular remodeling post-AMI through miR-223-3p-mediated Treg cells dysfunction in ICM.

overall_design: ICM-sEVs from patients, isolated using ultrafiltration, and the control group were used for miRNA sequencing to find out miRNAs relevant to Treg cells and ischemic injury

first: Bifang

last: Mai

first: Jing

last: Yang

first: Shuanglun

last: Xie


title: Childhood brain tumors instructs cranial haematopoiesis and immunotolerance

city: Cambridge

last: Cooper

address: Li Ka Shing Centre, Robinson Way

institute: CRUK Cambridge Institute

summary: ZFTA-RELA ependymoma poses a formidable challenge due to limited treatment avenues, prompting exploration into immunotherapeutic approaches. Recent investigations have shed light on the calvaria bone marrow as a source of meningeal immune cells crucial for central nervous system (CNS) immunity. Whether or not cues from the tumour microenvironment can instruct local haematopoiesis within the skull is unknown. We used single cell RNA sequencing (snRNAseq + snATAC) to analyze the dynamic transcriptional regulation of skull, peripheral bone marrow  from tumour-bearing and non-tumour bearing ZFTA-RELA fusion driven ependymoma mice.

overall_design: Age-matched 6-8 week-old EPZFTA-RELA and NestinCreERT2 mice were intravenously injected with CD45-PE 3 minutes prior to schedule 1. For skulls the dura was peeled and removed with fine forceps. The skull were then cut into small pieces using sterile scissors and mechanically dissociated in FACS buffer with a pestle, followed by a filtration step through a 70-μm cell strainer. Samples were centrifuged for 5 minutes at 420 x g. For peripheral bone marrow, both tibia were flushed with 0.05% BSA PBS with 0.05% EDTA, filtered through 7- µm meshes and washed with 2% fetal bovine serum in RPMI and resuspended on 0.05% BSA PBS solution. Samples were stained with DAPI (0.2 µg/ml). Samples were centrifuged, resuspended in FACS buffer with anti-CD16/32 (FC block; Biolegend) diluted 1:50 in FACS buffer and fluorescently conjugated antibodies (anti-CD45 APC and anti-Ter 119 FITC)  at 4°C, followed by for 20 minutes. Cells were sorted using the Influx Cell Sorter (BD Biosciences) or FACsAria II (BD Biosciences) into 1% BSA coated 1.5 mL Eppendorf tubes with 500 μL of DMEM


title: The ROS/AKT/S6K axis induces corneal epithelial dysfunctions under LED blue light exposure

city: Hangzhou

first: KUANGQI

last: Chen

state: Zhejiang

address: Qingchun Road 79th

institute: Zhejiang University School of Medicine First Affiliated Hospital

summary: In recent years, concerns have escalated regarding eye health problems arising from Light-emitting diode (LED), which emits high-energy blue light (BL), potentially causing corneal epithelial dysfunctions (CEpD). Nevertheless, the mechanisms underlying this damage remain poorly comprehended. This study endeavors to explore the specific mechanisms through which BL exposure induces CEpD. The study carried out diverse assays and treatments to investigate the toxicological effects of BL exposure. 48 hours (h) of 440 nm of BL exposure decreased the migration of human corneal epithelial cells (hCEpCs) while augmenting reactive oxygen species (ROS) production and apoptosis. RNA-Sequencing and bioinformatic analysis indicated that cellular oxidation and reduction equilibrium, wound healing, the positive regulation of the apoptotic process, and the Phosphoinositide 3-kinase (PI3K)/AKT pathway were significantly influenced by BL exposure. Treatment with N-acetylcysteine (NAC), a ROS scavenger, restored cell viability and AKT/S6 kinase (S6K) activation, suggesting the involvement of ROS in BL-induced damage. NAC also reversed BL-induced apoptosis and migration. Blocking AKT/S6K replicated detrimental effects, while pre-treatment with SC79 (SC), an AKT activator, alleviated the changes caused by BL exposure in hCEpCs. Furthermore, in mice, the combination of AKT inhibition and BL exposure led to CEpD. However, treatment with SC and NAC restored CEpD caused by BL exposure. These results imply that the regulation of the ROS/PI3K/AKT/S6K axis is implicated in BL-induced CEpD. Collectively, this study offers insights into the molecular mechanisms of BL-induced CEpD and proposes targeting the ROS/PI3K/AKT/S6K cascade as a potential therapeutic approach. The findings contribute to ocular health knowledge and establish the basis for developing interventions to safeguard the cornea from the detrimental effects of excessive BL exposure.

first: Le

last: Jin

first: Qianjie

first: Ye

last: Shen

first: Kuangqi


title: Rab2B promotes chaperonin-mediated actin folding and prevents developmental transcription reprogramming and quiescence in trypanosomes

city: Singapore

first: Fengjun

last: Li

address: S1A, #06-04, 14 Sicence Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: The Rab family of small GTPases are regulators of intracellular membrane trafficking. Rab2B, a Golgi-resident Rab GTPase, has been shown to function in ER-Golgi transport and autophagosome-lysosome fusion in mammalian cells and Drosophila. In T. brucei, the autophagy-related function of Rab2B was conserved and depletion of Rab2B blocked autophagosome-lysosome fusion. Intriguingly, depletion of Rab2B induced differentiation of T. brucei from a proliferative slender form to a quiescent stumpy form, a step crucial for parasite transmission.

overall_design: To investigate the mechanism of Rab2B and actin depletion in slender-to-stumpy differentiation, the RNA-SEQ was performed to check the transcriptome change in these cells and the procyclic cell differentiated from the stumpy cells triggered by Rab2B knockdown.

first: Feng-Jun

first: Cynthia

middle: Y

last: He


title: U2AF1 mutation causes an oxidative stress and DNA repair defect in hematopoietic and leukemic cells

city: Tianjin

first: Yishuang

address: 288 Nanjing Road, Tianjin 300020, P. R. China

institute: State Key Laboratory of Experimental Hematology

summary: U2AF1 is a core component of spliceosome and controls cell-fate specific alternative splicing. U2AF1 mutations have been frequently identified in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) patients, and mutations in U2AF1 are associated with poor prognosis in hematopoietic malignant diseases. To investigate the effects of U2af1 S34F in hematopoietic cells, we performed global gene expression profiling by RNA sequencing on U2af1-WT and U2af1 S34F 32D cells. We find that U2AF1 S34F causes increased reactive oxygen species (ROS) production. In hematopoietic cell line, a defect in mitochondrial function and DNA damage response deficiency are found in U2AF1 S34F expressing 32D cells.

overall_design: Transcriptome sequencing of U2af1-WT and U2af1 S34F 32D cells.

first: Jianxiang

last: Wang

first: Qing

last: Rao


title: Depression and Anxiety-Induced Metabolic Reprogramming Promotes Hepatocellular Carcinoma Progression through CBX5 Lactylation: Involvement of Taurocholate and PHGDH-Mediated Ferroptosis

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

summary: Traditional Chinese medicine posits that emotional disorders like depression and anxiety can lead to liver qi stagnation, promoting the occurrence and progression of hepatocellular carcinoma (HCC). However, the specific mechanisms remain unclear. This study investigated the association between depression and HCC risk through large-scale epidemiological analyses, and the underlying biological mechanisms were explored. Data were analyzed from the China Health and Retirement Longitudinal Study (CHARLS; n = 14,770) and the National Health and Nutrition Examination Survey (NHANES; n = 29,983), assessing depression levels and HCC risk. Participants with moderate to severe depression had a significantly increased risk of HCC compared to those without depression in both CHARLS (adjusted hazard ratio [HR] = 2.27; 95% confidence interval [CI]: 1.05–4.91) and NHANES (adjusted odds ratio [OR] = 5.96; 95% CI: 2.42–14.04). A meta-analysis indicated an overall 3.59-fold increased risk of HCC (95% CI: 1.40–9.24) among depressed participants. These findings remained robust across sensitivity analyses. Building on these results, a social isolation (SI) model was employed to study the impact of depression on HCC progression. SI significantly accelerated HCC progression in a spontaneous tumor mouse model. Mechanistically, social isolation drove metabolic reprogramming in HCC, characterized by elevated lactate levels, which in turn led to increased protein expression and lactylation of one of the key transcriptional regulators, CBX5. Knockout of Cbx5 attenuated the progression of HCC associated with social isolation in the transgenic mouse model. Then, it was shown that lactylation of CBX5 at the K91 site enhances its nuclear translocation, promoting tumor proliferation through enhancing the accumulation of taurocholate and upregulating PHGDH via forming a complex with c-Myc to inhibit ferroptosis. The elevated taurocholate disrupted the interaction between RNF123 and CBX5, stabilizing CBX5 in HCC. To target this pathway, a novel H-PROTAC molecule was developed that effectively degrades CBX5, enhances ferroptosis, and inhibits HCC proliferation, demonstrating potential therapeutic value. In conclusion, the study reveals the critical role of depression and anxiety-induced CBX5 lactylation in HCC occurrence and progression within a social isolation model. These findings provide new insights into HCC prevention and treatment, suggesting that CBX5-targeted therapies hold significant potential for HCC treatment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Sequencing analysis of social isolation and the role of CBX5 in liver cancer tissues and cells

first: Ruijiang


title: Effect of Vitamin D Receptor Knockout on the Transcriptomic Landscape of Th2 Cells

city: Boston

first: Vrushali

middle: Dipak

last: Fangal

state: MA

address: 181 Longwood Avenue

department: Brigham and Women's Hospital

institute: Harvard Medical School

summary: This dataset examines the transcriptional effects of VDR-KO in TH2 cells isolated from Mus musculus (C57BL/6 strain). TH2 cells from these mice (N=7) were compared to TH2 cells from wild-type mice (N=3) to assess the impact of vitamin D deficiency on gene expression. RNA-seq was used to generate raw gene-level counts.

overall_design: This study explores transcriptional changes in TH2 cells from VDR-KOt versus wild-type mice. Naïve CD4+ T cells were isolated, polarized into TH2 cells, and analyzed using RNA-seq. Differential expression analysis was performed to identify genes and pathways affected by vitamin D deficiency.

middle: D

first: Ayşe

last: Kiliç

first: Hooman

last: Mirzakani

first: Augusto

middle: A

last: Litonjua

first: Marie

middle: B

last: Damey

first: Bruce

last: Levy

first: Scott

middle: T

last: Weiss


title: Early onset and average onset colorectal cancer with matched normal colon tissues

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: To dissect the contributions of the epithelia, immune, and non-immune stromal populations in 3 early onset vs. 3 average onset colorectal cancers and their matched normal tissues using the GEOMx spatial transcriptomics platform.

overall_design: Three early onset and three average onset colorectal cancers with their matched normal tissues were selected. Epithelia (panCK), immune (CD45), and non-immune stroma (vimentin) targeted antibodies were used to define these populations in the chosen tissues. Regions of interest were chosen containing at least 30 nuclei, delimited by the markers and the accompanying fluorochrome. Regions of interest were then subjected to bulk RNA-sequencing.

first: Emina

last: Huang


title: Regulation of heterochromatin formation and tumor suppression in leukemia by IKAROS, HDAC1 and EZH2 [Molt4_CT]

city: Hershey

first: Bing

state: PA

address: 500 University Dr

institute: Penn State University

summary: The IKZF1 gene encodes IKAROS – a DNA binding protein that acts as a tumor suppressor in  T-cell acute lymphoblastic leukemia (T-ALL). IKAROS can act as a transcriptional repressor via chromatin remodeling, however the mechanisms through which Ikaros exerts its tumor suppressor function via heterochromatin in T-ALL are largely unknown. We studied human and mouse T-ALL using loss-of-function and Ikzf1 re-expression approach, along with Ikzf1-wildtype primary human and mouse T-ALL and thymocytes to establish the role of  Ikaros and Ikaros-associated protein histone deacetylase 1 (HDAC1)  in global regulation of facultative heterochromatin and transcriptional repression in T-ALL.   Results identified novel Ikaros and HDAC1 functions in T-ALL: Ikaros and HDAC1 are essential for EZH2 histone methyltransferase activity, and formation of facultative heterochromatin; Recruitment of HDAC1 by Ikaros is critical for establishment of H3K27me3 and repression of active enhancers; and Ikaros-HDAC1 complexes promote formation and expansion of H3K27me3 large organized chromatin lysine domains (LOCKs) and broad genic repression domains (BGRDs) in T-ALL.  Our results establish that Ikaros’ tumor suppressor function in T-ALL occurs via activation of EZH2 and HDAC1 function, global regulation of the facultative heterochromatin landscape and silencing of active enhancers that regulate oncogene expression.

overall_design: The IKZF1 gene was deleted in human T-ALL cells MOLT4 using the CRISPR-Cas system to create MOLT-4 IKZF1-null cells

first: Sinisa

last: Dovat

first: Yali

last: Ding


title: Development and validation of a high-throughput screening pipeline of compound libraries to target EMT

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

summary: Epithelial to Mesenchymal transitions (EMT) drive cell plasticity and are associated with cell features such as invasiveness, migration and stemness. They are orchestrated by select families of EMT-associated transcription factors, which exhibit pleiotropic roles in the malignant progression of various cancer types, such as breast and colorectal cancer (CRC). This has spurred interest in EMT as a promising target for the development of novel therapeutic strategies. In this study, we developed a phenotypic dual EMT Sensor screening assay, amendable to efficient high-throughput identification of small molecules interfering with EMT. In a proof-of-concept screening we identified anti-EMT repurposing drugs. From these, we validated RepSox, a selective inhibitor of the TGF-β type I receptor ALK5, and demonstrated that it is potently blocking EMT in both breast and colorectal cancer cell lines in vitro.

overall_design: We performed RNA-seq on both untreated SW620 and HT-29 +iZEB1 (a DOX-inducible ZEB1 expression system) and  samples treated with RepSox. For HT-29 iZEB1, we treated cells with DOX for 48 hours.

first: Sven

last: Jonckheere

first: Joachim

last: Taminau

first: Jamie

last: Adams

first: Jef

last: Haerinck

first: Jeroen

last: Verstappe

first: Evelien

last: Peeters

first: Aurélie

last: Candi

first: Matthias

last: Versele

first: Kyra

last: Campbell

first: Steven

last: Goossens

first: Geert

last: Berx


title: De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes [RNA-Seq]

city: San Francisco

first: Katherine

middle: S

last: Pollard

address: 1650 Owens St

institute: Gladstone Institutes

summary: Three-dimensional genome organization plays a critical role in gene regulation, and disruption of chromatin structure has been shown to lead to developmental disorders through the changed contact between key genes and their distal regulatory elements. Structural variants (SVs) have the ability to disrupt local genome organization, such as the joining of topologically associated domains upon deletion of a boundary. Unfortunately, testing large numbers of SVs for their effects on chromatin structure and gene expression is time and cost prohibitive. To overcome these experimental limitations, we previously developed SuPreMo, a convolutional neural network based method that accurately predicts how sequence variants change genome structure. Here, we extended the tool to specifically measure changed contact at regions of interest, such as cell type specific regulatory elements. Using this updated SuPreMo, we tested hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings and predicted how nearby genes’ regulatory interactions were affected in neurons. We found that putative cis-regulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings, allowing us to prioritize proband CREints of genes involved in neuronal development. We experimentally validated our top locus using induced pluripotent stem cell-derived excitatory neurons with and without the dnSV and found that the variant resulted in mis-regulation of 1102 genes. This in vitro characterization of a candidate causal variant is important, because most ASD patients do not carry a damaging protein-coding variant that alters neurodevelopment or neuronal function. This study establishes disrupted genome folding as a new genetic mechanism for ASD and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions in any tissue.

overall_design: To investigate the effect of the full and CTCF deletions on gene expression, RNAseq was performed on two WT cell lines, two CTCF deletion cell lines, and two full deletion cell lines.

first: Ketrin

last: Gjoni

first: Xingjie

last: Ren

first: Amanda

last: Everitt

first: Yin

last: Shen


title: IGF2 deficiency induces sarcopenia and muscle functional decline

first: Xihua

last: Lin

address: 3 East Qingchun Road

department: Department of Endocrinology and Metabolism

institute: Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University

summary: Background and aims: Insulin-like growth factor 2 (IGF2) is closely associated with the occurrence and development of primary and secondary muscle atrophy. This study investigates the role of IGF2 deficiency in inducing muscle atrophy using muscle-specific Igf2 knockout mice, aiming to provide theoretical basis and new concepts for growth hormone supplementation therapy in muscle atrophy.  Methods: We analyzed Igf2 expression using the Tabula Muris single-cell database and generated muscle-specific Igf2 knockout mice using the Cre/LoxP system with Mck-cre transgenic mice. We characterized the phenotype and assessed muscle size and mass through external observation, dissection, H&E staining, and microCT scanning. Muscle function was evaluated using the Md3000 grip strength meter, treadmill tests for endurance and electromyography (EMG) for contraction force. Transcriptome sequencing was performed on muscle tissues to analyze the impact of Igf2 deletion on gene expression and pathways.  Results: The Tabula Muris database confirmed high Igf2 expression in limb muscles, and we successfully developed muscle-specific Igf2 knockout (Igf2 cKO) mice. Analyses using MicroCT and H&E staining showed reduced muscle size, weight, and density in the gastrocnemius of Igf2 cKO mice versus controls. Grip strength tests using the Md3000 animal grip strength meter and treadmill tests assessing running endurance both indicated reduced physical performance in the Igf2 cKO group, with weakened grip strength and decreased running endurance distance and time. Electromyography (EMG) measurements disclosed a decrease in gastrocnemius muscle contraction force in the Igf2 cKO group. Transcriptome sequencing highlighted significant functional changes in muscle-related processes, RNA polymerase II transcription, and the PI3K pathway in the Igf2 cKO mice.  Conclusions: Igf2 is highly expressed in skeletal muscle tissue. Muscle-specific Igf2 knockout mice exhibited reduced muscle size, weight, and density, weakened grip strength, decreased gastrocnemius muscle contraction force, and reduced running endurance distance and time. These findings suggest that IGF2 supplementation may be a potentially effective strategy for treating muscle atrophy.

overall_design: Global transcriptome profiling was performed by RNA-Seq using muscle tissues of Control Igf2f/f and Igf2 cKO mice (n=3). RNA was extracted, sequenced, and analyzed by a custom service provided by Novogene using an Illumina NovaSeq 6000. Bioinformatics analysis was performed using the OmicStudio tools at https://www.omicstudio.cn/tool. The cut-off for differential expression threshold was based on | (log2FC) |> 1 and p-value < 0.05.

first: Weiwei

last: Gui


title: De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes [Hi-C]

overall_design: To investigate the effect of the full and CTCF deletions on 3D genome contacts, HiC was performed on two WT cell lines, two CTCF deletion cell lines, and two full deletion cell lines.


title: Regulation of heterochromatin formation and tumor suppression in leukemia by IKAROS, HDAC1 and EZH2 [Molt4_RNA]

first: Bing

last: He

first: Sinisa

last: Dovat

first: Yali

last: Ding


title: Molecular Features of Congenital Cytomegalovirus Infection in Neonatal Mouse Brain at Single-cell Resolution

city: WUHAN

first: Meng-Jie

last: MEI

address: Golden Dragon Street

institute: Wuhan Institute of Virology, Chinese Academy of Sciences

summary: Cytomegalovirus (CMV) is the leading viral cause of congenital infection, posing a significant risk to fetal brain development with neurodevelopmental sequelae. Effective medical treatments are limited due to an inadequate understanding of the interactions between CMV and the developing brain. Here, we applied single-cell transcriptomics to characterize the molecular features of neonatal mouse brains congenitally infected with murine CMV.

overall_design: 100 pfu MCMV-K181 with GFP was intracranially injected at embryonic day 13.5 (E13.5). At postnatal 7 days (P7), the cerebrum part from Mock- and MCMV- infected neunatal mouse brain was isolated for single-cell RNA sequencing (scRNA-seq) to characterize the molecular features at single-cell resolution.

last: Mei

first: Xuan

last: Jiang

first: Simon

last: Rayner

first: Han

last: Cheng

first: Min-Hua

last: Luo


title: Poly(I:C) offers a therapeutic opportunity to redirect immunosuppressed colorectal tumour landscapes towards a proinflammatory and CMS1-like regenerative state

city: Belfast

first: Shania

middle: M

last: Corry

address: Queen's University

institute: Patrick G Johnston Centre for Cancer Research

summary: Investigating cell-lineage specific repsonses to poly(I:C) in epithelial and macrophages.

overall_design: HCT116 epithelial cell lines and THP-1 derived macrophages were treated with poly(I:C) and transcriptionally profiled 24 hours later using microarray.

first: Svetlana

last: Sakhnevych

first: Keara

last: Redmond

first: Philip

last: Dunne


title: The inflamed cauda epididymidis: a hub for ectopic lymphoid organ genesis

city: GLEN IRIS

first: Claire

last: Sun

state: VIC

address: 27-31 wright street

country: Australia

institute: hudson institute of medical research

summary: Infection and inflammation of the male reproductive tract are major factors leading to infertility. Insults targeting the epididymis are of concern as they can impair fertility. A considerable number of patients with epididymitis, even after antibiotic treatment, exhibit the presence of an epididymal infiltrate specifically in the cauda epididymidis and even suffer from infertility. For this reason, this study focused on investigating the cauda epididymidis at later time points from the infection in a well-established model of acute bacterial epididymitis as well as in an autoimmune model – experimental autoimmune epididymo-orchitis. We show that multiple elements associated with tertiary lymphoid organs formation, organization and maintenance are present in UPEC-infected as well as EAEO epididymidis compared to control cauda epididymidis.

overall_design: Induction of experimental autoimmune epididymo-orchitis (EAEO) was performed as previously described (Nicolas et al., 2017). In brief, the mice were actively immunised with testicular homogenate prepared from decapsulated testes obtained from adult syngeneic mice, combined with adjuvant. The testicular homogenate was administered subcutaneously, 3 times, two weeks apart, together with an intraperitoneal injection of 100 ng Bordetella pertussis toxin (Calbiochem, Darmstadt, Germany). Complete Freund’s adjuvant (Sigma-Aldrich, Saint Louis, USA) was used for the first immunisation, while incomplete Freund’s adjuvant (Sigma-Aldrich) was used for subsequent immunisations. Control animals received either the respective adjuvant injections instead of testicular homogenate, or were left untreated. Animals were euthanized using carbon dioxide overdose, and tissues were collected at 30 and 50 days after the first immunisation. For RNA sequencing, the cauda epididymis from 4 mice from the experimental autoimmune orchitis group (E), and 4 mice from the Adjuvant treated group (A), and 3 mice from the control group (C) were selected.

first: Hiba

last: Hasan

first: Rukmali

last: Wijayarathna

first: Monika

last: Fijak


title: Low-intensity Pulsed Ultrasound regulates osteoclasts mitochondrial function in the treatment of diabetic periodontitis.

city: Chongqing

first: Li

last: houxuan

address: Medical College Road, Yuzhong District,

institute: Chongqing Medical University

summary: Periodontitis and type Ⅱ diabetes mellitus (T2D) have emerged as prevalent global chronic diseases, with a bidirectional relationship existing between them.  Individuals with periodontitis and T2D are susceptible to tooth loss, primarily attributed to alveolar bone resorption resulting from excessive osteoclasts (OC) differentiation.  Although low-intensity pulsed ultrasound (LIPUS) is an established treatment method for bone-related conditions, its mechanism of action on OC remains unclear.  The aim of this research is to examine the effects and mechanism of on OC within a diabetic inflammatory environment.  In summary, our data explored how LIPUS affects OC in the inflammatory environment of diabetes.

overall_design: The gene expression of db/db OC was compared using RNA sequencing in inflammatory settings, with or without LIPUS treatment.

first: Houxuan

last: Li

first: Shuhong

first: Jie

first: Jinlin

last: Song


title: Derepression of a single microRNA target causes female infertility in mice [smallRNA-Seq]

first: David

middle: P

last: Bartel

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute / MIT

summary: The miR-200a and miR-200b families control mouse ovulation and are essential for female fertility. The ZEB1  transcription factor is a conserved target of both families and has been implicated as a key player in female fertility at multiple levels. Using gene-edited mice that express a miR-200a/b-resistant form of Zeb1, we found that derepression of Zeb1 in the female pituitary caused decreased production of luteinizing hormone and anovulatory infertility. These phenotypes were accompanied by widespread changes in pituitary gene expression characterized by decreased levels of ZEB1 targets, which include the miR-200a/b miRNAs, as expected from the miR-200a/b–ZEB1 double-negative feedback loop. Also observed were increased levels of mesenchymal genes, neuronal genes, and miR-200a/b targets. These results show that a double-negative feedback loop centered on the miRNA regulation of a single transcription factor can significantly influence the expression of thousands of genes and have dramatic phenotypic consequences.

overall_design: To investigate the physiological importance of the miR-200a/b–ZEB1 double-negative feedback loop, we generated miR-200a/b-resistant Zeb1 mice. We performed miRNA expression profiling analyses using data obtained from small RNA-seq of pituitary tissue from adult female wild-type (WT), heterozygous (Zeb1_200H), and homozygous (Zeb1_200M) mice.

first: Benjamin

last: Kleaveland

first: Lara E

last: Elcavage


title: scRNAseq on skin-draining LN migratory DC in steady state and TSLP-overexpression mouse model

city: ILLKIRCH

first: Mei

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire

summary: Characterization of OX40L-expressing migratory DC in skin-draining lymph nodes

overall_design: We performed multiplexing scRNAseq to characterize the BFP+ migDC and BFP- migDC sorted from non-treated (NT) or MC903-treated (MC903; where TSLP is overexpressed) OX40L-BFP reporter Tnfsf4KI/+ mice. We used Hashtag oligos (HTO) to label 4 populations  NT_BFP+; NT_BFP-; MC903_BFP+ and MC903_BFP- for multiplexing.

first: Pierre

last: Meyer

last: Marschall

first: Marine

last: Guivarch

first: Antoine

last: Braud

first: Matthieu

last: Jung


title: PDX1 Phosphorylation Mediates Amino Acid-mTORC1 Signaling in Pancreatic β-Cells [RNA-seq]

city: New Brunswick

first: Jialin

last: Fan

state: NJ

address: 195 Little Albany St, Room 3527

institute: The Cancer Institute of New Jersey (CINJ)

summary: PDX1 is known as the insulin transcription factor that regulates insulin expression in pancreatic β-cells in response to circulating glucose levels. Our previous study showed PDX1 also acts as a downstream effector that mediates β-cell mTORC1 signaling in the control of whole-body glucose homeostasis in response to stimulation by amino acids (AAs). Here we report that PDX1 has a broad role in AA-mTORC1-regulated transcriptome in β-cells, especially in processes related to β-cell proliferation and function. Mechanistically, mTORC1 phosphorylates PDX1 at S61 in an AA-dependent and rapamycin-sensitive manner. S61 phosphorylation promotes PDX1 protein levels and transcriptional activity. Interestingly, S61 is located within the transactivation domain targeted by monogenic diabetes mutations, which interfere with S61 phosphorylation and PDX1's transcriptional activity. To help understand the role of S61 phosphorylation in vivo, we generated S61A and S61E genomic mutations in mice, mimicking the unphosphorylated and phosphorylated states, respectively. Our results indicate that S61 phosphorylation positively regulates insulin expression and β-cell proliferation, promoting Western diet-induced hyperinsulinemia, obesity, and liver steatosis. These findings reveal the mechanism and roles of AA-mTORC1-PDX1 signaling in the control of pancreatic β-cell proliferation and function under physiological and pathological conditions.

overall_design: RNA-seq for Pdx1 in MIN6 cells under different amino acid treatment.

first: Steven

last: Zheng


title: Generation of an EHE Extended Primary Cell Culutre

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Epithelioid hemangioendothelioma (EHE) is a difficult to treat vascular sarcoma defined by mutually exclusive TAZ-CAMTA1 (TC) or YAP-TFE3 (YT) fusion proteins. Human cell line systems are needed to dissect the mechanisms underpinning this cancer and evaluate new therapeutic approaches, however human EHE cell lines have yet to be developed.  We have developed a method to generate EHE extended primary cell cultures from human samples and have characterized them. Important aspects are conserved between the tumors and cell cultures including detection of the fusion protein by RT-PCR, expression of CAMTA1 by single cell RNA-Seq, and western blot. The cell cultures display many established characteristics of EHE including proliferation, the ability to grow in an anchorage independent manner and susceptibility to TEAD inhibition. Whole genome sequencing (WGS) showed links to epigenetic modifying complexes known to be recruited by the fusion proteins. RNA-Seq demonstrated upregulation of pathways known to be involved in the progression of the disease including PI3K-Akt signaling, ECM receptor interaction, Hippo signaling pathway, focal adhesion, and proteoglycans in cancer. Continued efforts to generate EHE cultures will aid in the mechanistic understanding of the disease and serve as a platform for testing new therapeutic avenues.

overall_design: Early passage number and late passage number EHE 001 cells to asses heterogeneity as well as what might be contributing to the senescence of the cells

first: Nicholas

last: Scalora

first: Gillian

last: DeWane

first: Lullia

last: Drebot

first: Ali

last: Khan

first: Souradip

last: Sinha

first: Denise

last: Robinson

first: Patricia

last: Cogswell

first: Munir

middle: R

last: Tanas


title: Derepression of a single microRNA target causes female infertility in mice [RNA-Seq]

city: Cambridge

first: David

last: Bartel

overall_design: To investigate the physiological importance of the miR-200a/b–ZEB1 double-negative feedback loop, we generated miR-200a/b-resistant Zeb1 mice. We performed gene expression profiling analyses using data obtained from RNA-seq of pituitary, hypothalamus, and ovary tissue from adult female wild-type (WT), heterozygous (Zeb1_200H), and homozygous (Zeb1_200M) mice.

first: Benjamin

last: Kleaveland

first: Lara E

last: Elcavage


title: Ependymoma instructs cranial haematopoiesis and immunotolerance

first: Elizabeth

last: Cooper

address: Li Ka Shing Centre, Robinson Way

institute: CRUK Cambridge Institute

summary: ZFTA-RELA ependymoma presents a significant clinical challenge due to the lack of effective treatments, driving the need to explore novel immunotherapeutic strategies. Recent studies have identified the skull bone marrow as a source of meningeal immune cells critical for central nervous system (CNS) immunity, yet the role of these cells in childhood CNS tumor surveillance and pathology remains unclear. Here, we demonstrate that intracranial childhood ependymoma tumors harbour a unique myeloid cell population, including hematopoietic stem cells (HSCs) not from the blood, but supplied by adjacent skull bone marrow, ontogenetically distinct from their blood-derived counterparts. Our findings challenge the conventional view of HSCs as passive players in the CNS, revealing that antigen-specific interactions between skull bone marrow-derived HSCs and CD4+ T cells actively promote immunotolerance in childhood brain tumors by enhancing local myelopoiesis and inducing regulatory T cell polarization. This work uncovers a previously unrecognized cellular network linking the skull to brain tumors in children and underscores the therapeutic potential of modulating skull bone marrow haematopoiesis to shift the local immune environment. Targeting this skull-specific immune pathway offers a promising avenue for developing localized immunotherapies to improve treatment outcomes.

overall_design: Age-matched 6-8 week-old EPZFTA-RELA and NestinCreERT2 mice were intravenously injected with CD45-PE 3 minutes prior to schedule 1. For skulls the dura was peeled and removed with fine forceps. Both the tibia and skull were then cut into small pieces using sterile scissors and mechanically dissociated in FACS buffer with a pestle, followed by a filtration step through a 70-μm cell strainer. Samples were centrifuged for 5 minutes at 420 x g. For peripheral bone marrow, both tibia were flushed with 0.05% BSA PBS with 0.05% EDTA, filtered through 7- µm meshes and washed with 2% fetal bovine serum in RPMI and resuspended on 0.05% BSA PBS solution. The whole intact deep cervical lymph nodes were mashed through a 70 μm cell strainer, using a sterile syringe plunger, and washed with 5 mL of FACS buffer. Deep cervical lymph node samples were then filtered through 70 µm meshes. Samples were centrifuged for 5 minutes at 420 x g.. Brains were macrodissected based on TdTomato fluorescent signal to harvest the tumor and region-matched brain in non-tumor bearing animals. Tumor/brain samples were mechanically dissociated using sterile surgical scalpels into ∼1 mm3 cubes, and dissociated using the mouse tumor dissociation kit (Miltenyi Biotec) using the gentleMACS Octo Dissociator (Miltenyi Biotec). After dissociation, the samples were then filtered through 100 µm meshes and washed with 2% fetal bovine serum in RPMI, spun down 420 g for 5 minutes. Samples were resuspended in 40% percoll and centrifuged at 600 x g for 10 minutes. Samples were stained with DAPI (0.2 µg/ml). Samples were centrifuged, resuspended in FACS buffer with anti-CD16/32 (FC block; Biolegend) diluted 1:50 in FACS buffer and fluorescently conjugated antibodies (anti-CD45 APC and anti-Ter 119 FITC)  at 4°C, followed by for 20 minutes. Cells were sorted using the Influx Cell Sorter (BD Biosciences) or FACsAria II (BD Biosciences) into 1% BSA coated 1.5 mL Eppendorf tubes with 500 μL of DMEM.


title: PDX1 Phosphorylation Mediates Amino Acid-mTORC1 Signaling in Pancreatic β-Cells [ChIP-seq]

overall_design: ChIP-seq for Pdx1 in MIN6 cells under different amino acid treatment.


title: NKG2D-mediated cytotoxicity of CD4 cytotoxic T cells in multiple myeloma

city: Seoul

first: Sojeong

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Blood Cancer Research Institute

country: South Korea

institute: Yonsei University College of Medicine

summary: Emerging evidence indicates that CD4+ T cells contribute to antitumor immunity beyond their traditional roles as helpers or regulators. However, the specific subset of CD4+ T cells mediating beneficial outcomes in patients with multiple myeloma remains unclear. Here, we performed single-cell RNA sequencing and T cell receptor sequencing on CD4+ T cells sorted from the bone marrow of patients across the stages of myeloma progression. We identified several distinct states of CD4+ cytotoxic T lymphocytes (CTLs) that were significantly increased and clonally expanded in myeloma patients. CD4+ CTLs displayed transcriptional and phenotypic characteristics indicative of cytotoxicity, demonstrating their ability to directly kill myeloma cells. This cytotoxicity, however, was abrogated by NKG2D blockade. Notably, the abundance of NKG2D+CD4+ CTLs correlated with improved survival in myeloma patients. Our findings suggest that harnessing CD4+ CTLs could lead to novel strategies for enhancing immunotherapy outcomes in multiple myeloma.

overall_design: CD4+ T cells sorted from bone marrow mononuclear cells (BMMCs) isolated from healthy donors and patients with MUGS, SMM, and MM at diagnosis were processed for scRNA-seq alongside scTCR-seq. Each GEM contained four BM samples which were demultiplexed using the Demuxlet package

first: Jeong-Eun

last: Kwak

first: June-Young

last: Koh

first: Ji Eun

last: Le

first: Hye Won

last: Kook

first: Minchae

first: Haerim

last: Chung

first: Yu Ri

first: Soo Jeong

first: Jin Seok

first: June-Won

last: Cheong

first: Min Goo

last: Lee

first: Hoyoung

first: Su-Hyung

last: Park

first: Eui-Cheol

last: Shin

first: Saeam

first: Sun Ock

last: Yoon

first: Kihyun

first: Il-Kyu

last: Choi

first: Jeong Seok

first: Hyunsoo

last: Cho


title: PTPRZ1 dephosphorylates and stabilizes RNF26 to decrease the efficacy of TKIs and PD-1 blockade in ccRCC

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

summary: Background: ccRCC, the most prevalent pathological subtype of renal cell carcinoma, has demonstrated a proclivity for drug resistance when treated with TKIs as a monotherapy. Notably, the integration of PD-1 blockade with TKIs has significantly enhanced patient survival, thereby emerging as a frontline therapeutic approach for ccRCC. However, the efficacy of this combined therapy still holds room for improvement. Consequently, there is a pressing need to delve deeper into the regulatory mechanisms that govern the effectiveness of TKIs/PD-1 blockade combination therapy in ccRCC. Methods: By mass spectrometry, RNA sequencing, lipidomic analysis, immunohistochemical staining and ex vivo experiments, we investigated the interaction between PTPRZ1 and RNF26 and their effects on the biological behavior of ccRCC cells. Results: Our findings revealed a distinct interaction between PTPRZ1 and RNF26 in ccRCC cells, wherein PTPRZ1 stabilized RNF26's protein expression by dephosphorylating it at the Y432 site. Notably, the overexpression or knockdown of PTPRZ1 significantly modulated the protein level of RNF26, and this phenomenon was linked to the proteasome pathway. Furthermore, PTPRZ1, through its interaction with RNF26, activated the TNF/NF-κB signaling pathway, ultimately promoting proliferation, angiogenesis, and regulating lipid metabolism in ccRCC cells. Crucially, inhibiting PTPRZ1 enhanced the sensitivity of ccRCC to TKIs and PD-1 blockade, an effect that was mitigated when RNF26 was co-knocked down. Conclusion: Our study underscores the significant role of the PTPRZ1-RNF26 axis in ccRCC, indicating that a combined approach utilizing PTPRZ1 inhibitors alongside existing TKIs and PD-1 blockade therapies could potentially enhance the therapeutic outcomes for ccRCC patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the A498 cells. PTPRZ_Si vs. PTPRZ_nc

first: Yongkang

last: Ma

first: Wei

last: li

first: Xinlin

last: Liu


title: ZEB1-mediated Epithelial to Mesenchymal Transition in Colorectal cancer HT-29 cell line

first: Jordy

last: De Coninck

summary: We report the induction of epithelial-mesenchymal transition (EMT) in the epithelial colorectal cancer (CRC) cell line HT-29. ZEB1 expression is sufficient to induce the downregulation of epithelial markers such as E-cadherin, claudins, keratins and occludin, while upregulating the expression of several mesenchymal markers such as vimentin and fibronectin.

overall_design: We developed a DOX-inducible ZEB1 expression system in HT-29. Transcriptome analysis was performed by RNA-seq on three independent clones of HT-29+iZEB1 treated or non-treated with DOX for 48 hours.

first: Jonchkheere

last: Sven

first: Taminau

last: Joachim

first: De Coninck

last: Jordy

first: Goossens

last: Steven

first: Berx

last: Geert


title: CUT&RUN sequencing on wildtype HSCs, MPP3s, GMPs, and macrophages with four weeks M. avium infection

city: Houston

first: Brandon

last: Tran

email: Brandon.Tran@bcm.edu, brttran@gmail.com

state: Texas

address: 1 Moursund St

institute: Baylor College of Medicine

summary: Purpose: Central trained immunity is a phenomenom in which reprogrammed HSPCs differentiate into innate immune cells with heightened immune responses. To determine whether histone modifications are conserved and passed down to downstream lineage cells, we performed CUT&RUN sequencing on various HSPC subpopulations and macrophages in both M. avium infected and naive states. This was done to determine if there were conserved changes across all subpopulations, which would imply to us if specific gene signatures and genomic loci  could be conserved for eliciting central trained immunity.

overall_design: CUT&RUN-sequencing protocol was performed with slight modifications previously published work from the lab and others (Skene and Henikoff et al., Elife 2017 and Le et al., iScience 2023). Bone marrow from M. avium infected or sham-treated mice was isolated from tibias, femurs, and pelvic bones and pooled per group. After red blood cell lysis, cells were separated by cKit-enrichment and stained for specific cell surface markers. From cKit+ postivie fractions, 30,000 HSCs (Lin-,cKit-enriched, CD150+, CD48-), 200,000 MPP3s (Lin-, cKit-enriched, CD150-+, CD48+, Flk2-, CD34+), 200,000 GMPs (Lin-, cKit-enriched) were sorted per sample. 200,000 macrophages (CD3-, B220-, NK1.1-, CD11b+, Ly6g-, Ly6c+) were sorted per sample from the cKit- fractions. Samples were counted and washed with wash buffer (50 mL H2O with 20 mM HEPES (GIBCO 15630080)  three times. Cells were then incubated with activated concanavalin a beads (Bang Laboratories L2007231C) for fifteen minutes at room temperature. Sample slurries were then washed one more time and resuspended in wash buffer supplemented with 0.5% Digitonin (Dig-wash buffer). Dig-wash buffer was used for the remainder of the experimental method, with samples and buffers were kept on ice or at 4°C.  Samples were then incubated with histone modification antibodies overnight at 4°C on a rotator. Depending on the sample, the antibodies used were targeted for Rabbit anti-H3K27ac (Cell Signaling Technologies 8173, 1:50 concentration), Rabbit anti-H3K427me3 (Cell Signaling Technologies 9733, 1:50 concentration), and Rabbit-antimouse IgG (Jackson ImmunoResearch 315-005-003, 1:50 concentration) for negative controls. Samples were washed once again three times and incubated with pAG-MNase (Epicypher SKU:15-016 ) on a rotator for one hour in 4°C. After, samples were washed three times and then resuspended in 150uL Dig-wash buffer and 2uL of 100mM CaCl2 was added to catalyze MNase activity and cutting. Cell-bead homogenates were kept in 4°C for 40 minutes while the reaction occured. The reaction was quenched with 2X stopping buffer (5 mL total, H2O, NaCl 340mM, EDTA 20 mM, EGTA, 4 mM, Digitonin 0.05%, RNAse A 100ug/mL, Glycogen 50 ug/mL, and Spike-in DNA 1ng/mL), and samples were heated to 37 C for 20 minutes for MNase/Histone/DNA complex release from cells and out into the supernatant. Samples were placed on magnetic stands to separate the DNA supernatant from the bead slurry, and DNA purification was completed via phenol chloroform and ethanol precipitation extraction. Libraries were generated with the services of Admerahealth. Quantified DNA by Qubit 2.0 HS DNA (ThermoFisher, Massachusetts, USA) was assessed by Tapestation High on a D1000 High sensitivity DNA Assay (Agilent Technologies, California, USA). Library preparation was completed using the KAPA HyperPrep kit (Roche, Basel, Switzerland) per the manufacturer’s instructions. Library quality was assessed with Qubit 2.0 (ThermoFisher, Massachusetts, USA), Tapestation (Agilent Technologies, California, USA), and QuantStudio 5 System (Applied Biosystems, California, USA). Illumina 8-nt dual indices were used. Libraries were pooled equimolarly based on quality and sequenced on an Illumina NovaSeq (Illumina, California, USA) with a 150 paired-end (PE) read length.

first: Katherine

last: King


title: H4K16 acylations fine-tune transcriptional response during metabolic perturbations (ChIP-seq)

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

summary: We studied the combined effects of the H4K16 acylations in vivo using a mouse model of the metabolic disorder propionic acidemia (PA), which causes metabolic challenges and systemic shifts in acyl-CoA ratios. Our findings indicate that H4K16 acylations modulate transcriptional responses in a concerted manner, providing insights into an adaptive chromatin regulation in response to metabolic stress.

overall_design: H4K16ac, H4K16pr, H4K16bu, H4K5ac, H4K5pr, H4K12ac, H4K12pr, H3K27ac, H3K9ac ChIP-seq on WT and PA female mouse livers in 2 biological replicates.

first: Sandra

last: Nitsch

first: Eva

last: Richard

first: Lourdes

last: Desviat

first: Robert

last: Schneider


title: Oncogenic role of PMEPA1 and its association with immune exhaustion and TGF‑β activation in HCC

city: Barcelona

first: Ana

last: Hernández de Sande

address: C/ del Rosselló, 153

country: Spain

institute: IDIBAPS

summary: To explore the role of PMEPA1 in hepatocellular carcinoma (HCC) promoting TGF β oncogenic effects

overall_design: We generate genetically engineered mouse models overexpressing MYC+PMEPA1 and HCCs obtained were molecularly analysed.

first: Marta

last: Piqué-Gili

first: Roger

last: Esteban-Fabró

first: Amaia

last: Lujambio

first: Josep

last: Llovet


title: In vivo Spatial Perturb-Seq in the mouse brain

city: South San Francisco

first: Kimberle

last: Shen

address: 1 Dna way

institute: Genentech

summary: Functional genomics that knocks out individual genes is ideal for investigating gene functions. Examining these perturbations in vivo, within native tissue architecture and with spatial context, is crucial for accurately assessing the impact of genetic modifications both within the cell and on its microenvironment.

overall_design: We stereotaxically injected an AAV library targeting 18 genes directly into the mouse hippocampus to induce sparse perturbations, then performed Stereo-seq. The 18 loci that are targeted are: mSafe1, Trem2, Rraga, Flcn, Fasn, Olig2, Gfap, Clu, Dpp6, Tbk1, C9orf72, Cfap410, Stk39, Lrrk2, Ndufaf2, Sh3gl2, Srf, Rbfox3. The dataset here consists of 2 coronal hemisphere sections from 1 mouse.


title: In vivo Perturb-Seq in the mouse brain

summary: Functional genomics that knocks out individual genes is ideal for investigating gene functions. Examining these perturbations in vivo, within native tissue architecture, is crucial for accurately assessing the impact of genetic modifications both within the cell and on its microenvironment.

overall_design:
We stereotaxically injected an AAV library targeting 18 genes directly into the mouse hippocampus to induce sparse perturbations, then performed 10X 3' scRNA-seq. All 5 mice listed here are biological replicates, done across 3 batches (B1_1, B1_2, B2_1, B2_2, B3_1).
The 18 genes are:  mSafe1, Trem2, Rraga, Flcn, Fasn, Olig2, Gfap, Clu, Dpp6, Tbk1, C9orf72, Cfap410, Stk39, Lrrk2, Ndufaf2, Sh3gl2, Srf, Rbfox3.


title: Muscarinic agonism restores degenerated salivary glands through a calcium-ATP metabolic axis [snRNA-Seq]

first: Sarah

last: Knox

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

summary: Chronic damage to tissues and organs is deemed irreversible. This has led to a focus on the development of regenerative therapies that replace tissues. Here, we break with this dogma by demonstrating that the chronically injured degenerating salivary gland can be functionally and structurally restored through a nerve-associated mechanism. Extensive disruption of the chronically injured secretory acinar-nerve niche can be reversed by muscarinic agonism, with the tissue maintaining a homeostatic-like state months after treatment ends. In addition, the proportion of de-differentiated acinar cell types that appear with chronic damage are greatly reduced by muscarinic stimulation, suggesting recovery of cells critical for function. This reversal is due, in part, to re-balancing a calcium-dependent metabolic pathway that enables cell replacement. Finally, we show that radiation damaged hair follicles also benefit from muscarinic stimulation through a similar mechanism. Thus, these data challenge the concept that chronic damage is irreversible and provide a new avenue for the development of restorative treatments, a paradigm shift that can be explored more broadly.

overall_design: To investigated changes in cell identities and signaling pathways on the molecular level in the different treatment groups, single nucleus RNA sequencing was performed

first: Jianlong

last: Li


title: CITEseq of migratory nLCncDC1 of skin-draining lymph nodes from MC903-treated mice

first: Mei

summary: Characterization of OX40L-expressing migratory DC and their Siglech-lineage tracing in skin-draining lymph nodes

overall_design: We performed scRNA-seq to characterize migratory non-LC-non-cDC1 from MC903-treated BFP and RFP dual reporter SiglechiCreTg/0ROSA26LoxP-STOP-LoxP-RFPTnfsf4KI/+ mice. We used Hashtag oligos (HTO) to label 4 populations according to the expression of reporters: BFP+RFP+ (B+R+), BFP-RFP+ (B-R+), BFP+RFP- (B+R-) or BFP-RFP- (B-R-) for multiplexing. We also used Antibody Derived Tags (ADT) labeling in ordre to retrieve protein expression level for surface markers.

first: Marine

last: Guivarch

first: Matthieu

last: Jung

first: Tao

last: Ye


title: Sirt5 regulates chondrocyte metabolism and osteoarthritis development through protein lysine malonylation

city: Saltlake city

first: Michael

last: Jurynec

state: UT

institute: University of Utah

summary: Chondrocyte metabolic dysfunction plays an important role in osteoarthritis (OA) development during aging and obesity. However, it is unknown how metabolic dysfunction occurs during these two conditions. Proteins post-translational modifications (PTMs) have recently emerged as an important regulator of cellular metabolism. We previously reported that one type of PTM, lysine malonylation (MaK) was increased in cartilage during obesity. Sirt5, the only known mammalian demalonylase, declines in cartilage during aging. To elucidate the interplay between Sirt5 deficiency and obesity in joint degeneration, we deploy systemic and cartilage-specific conditional knockout mouse models. Our findings reveal that the combination of Sirt5 deficiency and obesity exacerbates joint degeneration in mice. Through comprehensive proteomics analysis, we delineate the malonylome in chondrocytes, pinpointing MaK's predominant impact on various metabolic pathways such as carbon metabolism and glycolysis. Further biochemical investigation focuses on glyceraldehyde 3-phosphate dehydrogenase (GAPDH), a target of MaK, confirming a reduction in its enzymatic activity and functionality by MaK. Lastly, we identified a rare coding mutation in SIRT5 that dominantly segregates in a family with hand OA. The mutation results in substitution of an evolutionally invariant phenylalanine (Phe–F) to leucine (Leu–L) (F101L), which is located in the catalytic domain. F101L mutant results in higher MaK level and decreased expression of cartilage ECM genes (e.g., Acan and Col2a1) and upregulation of inflammation associated genes (e.g., Il6 and Nos2). In conclusion, we found that Sirt5 mediated MaK is an important regulator of chondrocyte cellular metabolism and dysregulation of Sirt5-MaK could be an important mechanism underlying aging and obesity associated OA development.

overall_design: Primary mouse chondrocytes were transfected with either  Wildtype or SIRT5F101L mutant plasmids.

first: Huanhuan

last: Liu

first: Anupama

last: Binoy

first: Siqi

last: Ren

first: Thomas

middle: C

last: Martino

first: Anna

middle: E

last: Miller

first: Craig

last: Willis

first: Shivakumar

last: Veerabhadraiah

first: Abhijit

last: Sukul

first: Martin

middle: K

last: Lotz

first: Rachel

first: Anne-Marie

last: Malfait

middle: J

first: Shouan

last: Zhu


title: Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing

city: Aurora

first: Laura

last: White

state: CO

address: 12801 E 17th Avenue RC1S

department: Biochemistry & Molecular Genetics

institute: University of Colorado

summary: Transfer RNAs are the fundamental adapter molecules of protein synthesis and the most abundant and heterogeneous class of noncoding RNA molecules in cells. The study of tRNA repertoires remains challenging, complicated by the presence of dozens of post transcriptional modifications. Nanopore sequencing is an emerging technology with promise for both tRNA sequencing and the detection of RNA modifications; however, such studies have been limited by the throughput and accuracy of direct RNA sequencing methods. Moreover, detection of the complete set of tRNA modifications by nanopore sequencing remains challenging. Here we show that recent updates to nanopore direct RNA sequencing chemistry (RNA004) combined with our own optimizations to tRNA sequencing protocols and analysis workflows enable high throughput coverage of tRNA molecules and characterization of nanopore signals produced by 43 distinct RNA modifications. We share best practices and protocols for nanopore sequencing of tRNA and further report successful detection of low abundance mitochondrial and viral tRNAs, providing proof of concept for use of nanopore sequencing to study tRNA populations in the context of infection and organelle biology. This work provides a roadmap to guide future efforts towards de novo detection of RNA modifications across multiple organisms using nanopore sequencing.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae
Tetrahymena thermophila
Drosophila melanogaster
Danio rerio
Homo sapiens

overall_design: Matched tRNA samples from six different organisms were sequenced by Oxford Nanopore direct RNA sequencing on the RNA002 or RNA004 chemistry.

first: Kezia

last: Dobson

first: Samantha

last: del Pozo

first: Jill

last: Bilodeaux

first: Shelby

last: Andersen

first: Amber

last: Baldwin

first: Chloe

last: Barrington

first: Nadine

last: Körtel

first: Federico

last: Martinez-Seidel

first: Saylor

last: Strugar

first: Kristin

last: Watt

first: Neelanjan

last: Mukherjee

first: Jay

last: Hesselberth


title: Pluripotency factor OCT4 enhances the firing efficiency of late DNA replication origins in mouse em-bryonic stem cells [Repli-seq]

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

summary: DNA replication initiates at specific genomic regions known as initiation zones (IZs), which follow a defined spatiotemporal program partially dependent on cell type. Here, we examined the replication initiation patterns of pluripotent mouse embryonic stem cells (mESCs), which are characterized by a very short G1 phase and rapid entry into S phase. Using EdU-seq combined with cell cycle synchroni-zation and Repli-seq, we identified IZs, that are activated during S phase in mESCs and classified them as early, mid, or late, according to the replication timing (RT) domain to which they mapped. Remarka-bly, we found that some IZs mapping to mid or late RT domains were activated within 1–2 hours of entry into S phase. Chromatin and nascent transcriptome profiling revealed that these IZs were associated with regions of open chromatin structure that were bound by the pluripotency factor OCT4. Transient OCT4 depletion was associated with reduced chromatin accessibility and replication initiation efficiency at these sites. These results provide an example of a pioneer factor, OCT4, facilitating DNA replication initiation by promoting local chromatin accessibility.

overall_design: Monitor DNA replication by Repli-seq

first: Eddie

last: Rodriguez-Carballo

first: Sotirios

middle: G

last: Ntallis

first: Lilia

last: Bernasconi

first: Ezgi

last: Keskin

first: Thanos

last: Halazonetis


title: Pluripotency factor OCT4 enhances the firing efficiency of late DNA replication origins in mouse em-bryonic stem cells [EUseq]

overall_design: Monitor nascent transcription by EUseq


title: Generation of an EHE Extended Primary Cell Culture

first: Michael

last: Chimenti

overall_design: We collected RNA 3 EHE Tumors, 4 EHE extended primary cell cultures (in triplicate) and human primary aortic endothial cells to compare expression profiles of the cultured cells relative to a primary endothelial cell control and the donor tumors

first: Nicholas

last: Scalora

first: Gillian

last: DeWane

first: Lullia

last: Drebot

first: Ali

last: Khan

first: Souradip

last: Sinha

first: Denise

last: Robinson

first: Patricia

last: Cogswell

first: Munir

last: Tanas


title: Pluripotency factor OCT4 enhances the firing efficiency of late DNA replication origins in mouse em-bryonic stem cells [EdUseq]

overall_design: Monitor DNA replication by EdUseq


title: Cell cycle arrest enhances CD8+ T cell effector function by potentiating glucose metabolism and IL-2 signaling

city: Leiden

first: Ramon

last: Arens

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

summary: Cell cycle-inhibiting chemotherapeutics are widely used in cancer treatment. Although their primary aim is to block tumor cell proliferation, their clinical efficacy also involves specific effector CD8+ T cells that undergo synchronized proliferation and differentiation. How CD8+ T cells are programmed when these processes are uncoupled as occurs during cell cycle inhibition is unclear. Here, we demonstrate that activated CD8+ T cells arrested in their cell cycle can still undergo effector differentiation. Cell-cycle arrested CD8+ T cells become metabolically reprogrammed into a highly energized state, enabling rapid and enhanced proliferation upon release from arrest. This metabolic imprinting is driven by increased nutrient uptake, storage, and processing, leading to enhanced glycolysis in cell cycle-arrested cells. The nutrient sensible mTORC1 pathway, however, was not crucial. Instead, elevated IL-2 production during arrest activates STAT5 signaling, which supports expansion of the energized CD8+ T cells following arrest. Transient arrest in vivo enables superior CD8+ T cell-mediated tumor control across models of immune checkpoint blockade, adoptive cell transfer, and therapeutic vaccination. Thus, transient uncoupling of CD8+ T cell differentiation from cell cycle progression programs a favorable metabolic state that supports the efficacy of effector T cell-mediated immunotherapies.

overall_design: To investigate the mechanisms underlying enhanced cell cycle progression after temporal cell cycle arrest, we characterized the transcriptional activity in unstimulated, arrested, released and non-arrested CD8+ T cells. To this end, we made single cell suspensions from pooled spleen samples from mice. CD8 T cells were enriched and we had 4 different conditions: unstimulated (60 hours), blocked (60 hours stimulated with aCD3 and aCD28 in the presence of hydroxyurea), non-arrested (60 hours stimulated with aCD3 and aCD28) or released (stimulated with aCD3 and aCD28 in the presence of hydroxyurea which was washed away. These cells could proliferate for 60 hours. Next, live CD8 T cells were sorted (BD FACS aria). For the "non-arrested" and "released" conditions only the cells that had at least 1 cell division were selected on the basis of CFSE dilution. Next, gene expression profiling analysis was performed using data obtained from RNA-seq of the four different conditions.

first: Floortje

last: van Haften

first: Tetje

last: van der Sluis

first: Hanna

last: Hepp

first: Nils

last: Mülling

first: Reza

last: Nadafi

first: Bharath

last: Sampadi

first: Suzanne

last: van Duikeren

first: Shirin

last: Mostert

first: Rosemarijn

last: van der Sterre

first: Peter

last: van Veelen

first: Graham

last: Heieis

first: Dominique

last: Veerkamp

first: Thomas

middle: H

last: Wesselink

first: Ward

last: Vleeshouwers

first: Macha

last: Beijnes

first: Iris

middle: N

last: Pardieck

first: Eralin

middle: L

last: van Horssen

first: Anne

middle: F

last: de Groot

first: Manon

last: van der Ploeg

first: Judith

last: Kroep

first: Noel

last: de Miranda

first: Sabina

last: van der Zanden

first: Jacques

last: Neefjes

first: Hailiang

last: Mei

first: Alfred

last: Vertegaal

first: Bart

last: Everts

first: Sjoerd

last: van der Burg


title: The chromatin remodeler Brg1 is essential for cochlear sensory epithelium differentiation and patterning

city: Qingdao

first: Yuning

last: Song

address: 72 Binhai Road

department: School of Life Sciences

institute: Shandong  University

summary: The development of the organ of Corti requires the coordination of cell differentiation and patterning, which results in the formation of unique functional units critical for sound detection. Here, we investigated the role of the epigenetic factor Brg1 during the differentiation and development of the auditory sensory epithelium, a crucial period for the formation of the organ of Corti. Our findings indicate that deletion of Brg1 leads to premature hair cell (HC) differentiation by inactivating Sonic hedgehog (Shh) signaling. Despite the formation of HCs, subsequent differentiation of inner hair cells (IHCs) and outer hair cells (OHCs) was impaired. Additionally, we observed that the mosaic-like arrangement of HCs and supporting cells (SCs) was disrupted resulting in abnormal sensory epithelium patterning. Furthermore, we found the planar cell polarity of the Brg1-deficient cochlea was abnormal. Our study demonstrates the pivotal role of Brg1 in the differentiation and patterning of the auditory sensory epithelium.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  different samples from konck out Brg1  or Control groups.

first: Jiangang

last: Gao

first: Yecheng

last: Jin


title: TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). Using a reporter model, we observed a gradual upregulation of TREM2 with increasing plaque proximity. Isolated microglia were sorted based on reporter expression, to determine fluorodeoxyglucose (FDG) uptake and the metabolomic, lipidomic, and transcriptomic signatures. Uptake of FDG correlated with the gradual increase of TREM2 expression.  TREM2 expression improved cellular redox, energetics, and cholesterol homeostasis in the presence or absence of amyloid pathology. Bulk RNA sequencing analysis identified major changes in immunometabolic pathways. Genes associated with oxidative phosphorylation or cholesterol homeostasis were enriched in the TREM2 high expressing clusters. Finally, chronic treatment with a brain penetrant TREM2 agonist identified a window of TREM2 expression where microglia are most accessible for protective responses providing important information for the current efforts to bring TREM2 agonists into the clinic.

overall_design: Inspection of cell type composition, examination of differential expression and assessment of gene co-expression networks in RNA-seq data of healthy and disease mouse microglia with different Trem2 levels.

first: Astrid

last: Feiten

first: Kilian

last: Dahm

first: Kathryn

last: Monroe

first: Christian

last: Haass


title: Integrative Functional Genomics Analysis of Kaposis Sarcoma Cohorts

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: Kaposi’s sarcoma (KS) is an AIDS-defining cancer and a significant global health challenge caused by Kaposi's sarcoma-associated herpesvirus (KSHV). KS lesions have been profiled by NGS-based approaches in a very limited number of studies compared with other neoplastic diseases. Here we present a compiled and harmonized dataset of 131 KS and non-tumor cutaneous samples in the context of their predicted pathway activities, immune infiltrate, KSHV and HIV gene expression profiles and their associated clinical data representing patient populations from Argentina, USA and Sub-Saharan Africa cohorts. First, RNA-seq data from 9 Argentinian KS lesions were generated and integrated with previously published datasets derived form USA and sub-Saharan African cohorts from Tanzania, Zambia and Uganda. Second, the compiled RNA-seq profile is shared with the research community through the UCSC Xena browser for further visualization, download and analysis (http://xena.ucsc.edu/). Third, unsupervised analysis of 131 KS related samples allowed us to identify four KS clusters based on their host and KSHV gene expression profiles, immune infiltrate and in the activity of specific signaling pathways. These resources will allow biologists without bioinformatics knowledge to explore and correlate the host and viral (KSHV and HIV) transcriptome in a curated dataset of different KS RNA-seq-based cohorts, which can lead to novel biological insights and biomarker discovery.

overall_design: Nine KS skin lesions were collected from an Argentinian cohort of Men who have Sex with Men (MSM) and Transgender Women (TGW) with HIV.

first: Abba

last: Martín Carlos

first: Lacunza

last: Ezequiel


title: Impact of Enteric Neuronal Loss on Intestinal Cell Composition

city: Rotterdam

first: Naomi

last: Kakiailatu

address: Naomi

department: Clinical Genetics

institute: Erasmus MC

summary: This study describes the intestinal composition in wildtype and ret mutant zebrafish intestines using single cell RNA sequencing (scRNA-seq).

overall_design: In this study, we investigated the impact of ENS loss on intestinal composition using a rethu2846/hu2846 mutant tg(phox2bb:GFP) zebrafish. At 4 dpf,  rethu2846/hu2846 mutant tg(phox2bb:GFP) zebrafish showing a total colonic HSCR phenotype were selected. Zebrafish intestines were manually isolated at 5dpf and dissociated into a single cell suspension. Live, single cells were sorted by Fluorescence-activated cell sorting (FACS) according to the presence or absence of DAPI signal. Sorted cells were processed and analyzed using 10X scRNAseq. To provide a comprehensive analysis, the ret mutant data was integrated with previously published wildtype zebrafish intestines (GSE225510)

first: N

first: L

last: Kuil

first: J

middle: D

last: Windster

first: E

last: Bindels

last: Zink

first: M.

last: Vermeulen

first: B

last: de Graaf

first: D

last: Sahadew

first: T

last: van den Bosch

last: Huijgen

first: C

last: Sloots

first: R

last: Wijnen

last: Hofstra

first: V

last: Melotte

first: M

last: Alves


title: Macrophage Involvement in the Pathology of Chronic Thromboembolic Pulmonary Hypertension: Lessons from Single-Cell and Single-Nucleus RNA Sequencing

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

summary: We revealed the detailed landscape of myeloid cells in CTEPH and identified cell-cell interactions between myeloid and non-immune cells using both scRNA-seq and snRNA-seq. The interaction between SPP1/FN1+ macrophages and FAP+ FBs or MyoFBs may be a therapeutic target in CTEPH.

overall_design: scRNA-seq

first: Yu

last: Taniguchi


title: Heterobifunctional proteomimetic polymers for targeted degradation of MYC and KRAS

city: Chicago

first: Mihai

middle: Ioan

last: Truica

state: Illinois

address: 303 E Superior

department: Urology

institute: Northwestern University

summary: Targeted protein degradation has unlocked new strategies for modulating previously undruggable proteins; however, existing small molecule approaches are challenging to optimize and largely limited to targets with ligandable pockets. To overcome these challenges, we introduce the HYbrid DegRAding Copolymer (HYDRAC), a polymer-based platform that integrates target-binding peptides with peptide or small-molecule degrons for the selective degradation of disease-relevant proteins. HYDRACs are synthesized easily, exhibit structural tunability, and facilitate the attachment of multivalent payloads. The modular payload capability accommodates diverse target-binding motifs and E3 ligase recruiters—such as VHL, KEAP1, and CRBN—broadening the design space. We apply HYDRACs against two historically intractable targets, MYC and KRAS, achieving robust degradation in vitro and sustained tumor inhibition in murine models. Notably, HYDRACs containing consensus RAS-binding motifs effectively degrade KRAS in cells harboring different alleles, suggesting pan-KRAS potential. We envision the HYDRAC platform as a generalizable approach, greatly expanding the armamentarium for TPD.

overall_design:
To investigate effects of MYC-degrading HYDRACs, as well as scrambled sequence (non-targeting) controls, on cellular transcriptional programs in order to ascertain target-engagement and selectivity, we performed gene expression profilling analysis using data obtained from RNA sequencing of PC3 cell line treated for 24 hours with Vehicle (DMSO) or 5 uM of HYDRAC or scrambled negative control.
RNAseq profiling of wild-type PC3, A549 and MycCaP cells treated with HYDRAC and negative control (nontargeting polymer, denoted as sHR) for 24 hours treatment. As well as PC3 cells treated with genetic knockdown of MYC (siMYC and siCNT).

first: Max

last: Wang

first: Brayley

last: Gattis

first: Julia

last: Oktawiecz

first: Vinay

last: Sagar

first: Ananya

last: Basu

first: Paul

last: Bertin

first: Xiaoyu

last: Zhang

first: Nathan

last: Gianneschi

first: Sarki

last: Abdulkadir


title: Epigenetic insights into fertility: involvement of immune cell methylation in dairy cows reproduction

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: Infertility and post-partum reproductive diseases present significant clinical and economic challenges, particularly in cattle farming. Successful gestation is largely contingent upon the ability of the maternal immune system to recognize and tolerate the embryo. The role of immune cells in promoting fetal-maternal immune tolerance is critical, underlining their importance in post-partum fertility. In this context, DNA methylation in hematopoietic cells may play a pivotal role in determining the susceptibility of the animal to post-partum fertility problems. Identifying epigenetic changes linked to infertility is therefore crucial for advancing sustainable animal production. Characterizing the methylome of immune cells in relation to fertility will enable early phenotyping, setting the stage for innovative methods to detect potential subfertility in animals. In our study, whole epigenome sequencing and enzymatic methyl-seq (EM-seq) were employed to analyze the DNA methylation patterns in total blood collected from twelve Holstein cows raised on the same farm before any disease appeared. This approach helped to map the epigenetic modification profiles of genes associated with the varying fertility phenotypes observed the following year, revealing significant differences between fertile and subfertile cows. We identified 216,990 differentially methylated cytosines (DMCs), with three genes, Interferon tau-3 (IFNT3), KIAA0825, and RAS-Related Protein 2A (RAP2A), showing high significance. Additionally, 23 key genes affected by DMCs across five regions (transcription start sites-TSS shores, introns, exons, distal intergenic areas, and downstream of genes) were identified. Notably, Interferon tau-3 emerged as especially crucial due to its role in early embryonic development and the establishment of gestation in cattle, with seven DMCs in its TSS shores in subfertile cows. Similarly, the KLRA1 gene (Ly49), analogous to KIRs in humans and primarily expressed on Natural Killer (NK) cells, was highlighted for its potential impact on fertility. Past research underscored that a balance between activating and inhibiting KIR receptors is essential for embryo implantation and proper placental development. Moreover, interleukin genes, such as IL-6, IL15, IL22, IL-36G, which are vital for conception, contained multiple DMCs, reinforcing the hypothesis of the involvement of the immune system in bovine fertility. These findings illustrate the potential control that immune cell epigenetics exert on cattle post-partum fertility. Additionally, this study suggests that the risk of developing subfertility could potentially be estimated with as few as 220 methylation biomarkers, paving the way for enhanced animal health management and improved fertility treatments.

overall_design: Blood from cows aged between three and eight years and raised under the same conditions at a Vancouver farm, was collected from November 2020 to January 2021. A year later, we selected six cows that were culled during the year due to complications related to reproduction that were not identified at the time of sampling, thus forming the Subfertile Group. We also selected a second group of six cows that were still in the herd and had no fertility issues. This second group represented the Fertile Group.

first: Lotfi

last: Bouzeraa

first: Helene

last: Martin

first: Clement

last: Plessis

first: Pascal

last: Dufour

first: Jessica

last: Marques

first: Sydney

last: Moore

first: Ronaldo

last: Cerri

first: Marc-Andre