title: Sirtuin 6 mitigates thoracic aortic aneurysm progression via maintenance of mitochondria homeostasis in vascular smooth muscle cells

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Aortic aneurysm and dissection (AAD) is a life-threatening disease without effective pharmacological treatments. The progressive loss of vascular smooth muscle cells (VSMCs) is the fundamental pathophysiological basis for AAD, but the underlying mechanisms are largely unknown. Sirtuin 6 (SIRT6), a class III histone deacetylase, is critical for maintenance of VSMC homeostasis and consequent prevention of vascular remodeling-related diseases. However, its role in AAD development requires further investigation. Here, we show that SIRT6 expression was significantly reduced in VSMCs of the thoracic aorta in AAD patients. Sirt6 deficiency in VSMCs dramatically accelerated angiotensin Ⅱ (Ang Ⅱ) infusion-induced AAD formation and rupture even without an Apoe-deficient background. In vitro studies demonstrated that Sirt6 deficiency led to mitochondrial dysfunction and accelerated VSMC senescence. Mechanistically, SIRT6 could bind and deacetylate NRF2, a key transcription factor for mitochondrial biogenesis, however, Sirt6 deficiency inhibited NRF2 and reduced mRNAs encoding mitochondrial complex. Notably, MDL-811, a newly developed small-molecule SIRT6 agonist, effectively reversed Ang Ⅱ-induced mitochondrial dysfunctions in human aortic smooth muscle cells. More importantly, MDL-811 also mitigated AAD progression in mice. These findings suggest that SIRT6 plays a protective role in AAD development and targeting SIRT6 with small-molecule activators such as MDL-811 could represent a promising therapeutic strategy for AAD.

overall_design: RNA-seq profiling of Sirt6fl/fl mice and VSMC-specific Sirt6 knockout mice treated with saline or angiotensin II for 14 days.

first: Xiaoting

last: Yu

last: Zhao

first: Yutao

last: Ma

first: Jinmeng

last: Jia

first: Yanting

first: Xiaoyan

last: Liu

first: Yao

last: Xiao

first: Guangming

first: Jinhan

last: He

first: Sheng

first: Junming

last: Zhu

first: Frank

middle: J

last: Gonzalez

first: Aijuan

last: Qu


title: The m6A profile of mouse hypothalamic neural progenitor cells

status: Public on Mar 07 2025

city: Philadelphia

first: Yachen

last: Shen

address: 3400 Civic Center Blvd, Philadelphia, PA 19104

country: USA

institute: University of Pennsylvania

summary: m6A, the most prevalent internal modification on mRNAs, plays important roles in the nervous system. Whether neurogenesis in the hypothalamus, a region critical for controlling appetite, is regulated by m6A signaling, especially in humans, remains unclear. Here we showed that deletion of m6A writer Mettl14 in the mouse embryonic hypothalamus led to adult obesity, with impaired glucose-insulin homoeostasis and increased energy intake. Mechanistically, deletion of Mettl14 leads to hypothalamic arcuate nucleus neurogenesis deficits with reduced generation of feeding-related neurons and dysregulation of neurogenesis-related m6A-tagged transcripts. Deletion of m6A writer Mettl3, or m6A reader Ythdc1, shared similar phenotypes. METTL14 or YTHDC1 knockdown also led to reduced generation of feeding-related neurons in human brain subregion-specific arcuate nucleus organoids. Our studies reveal a conserved role of m6A signaling in arcuate nucleus neurogenesis in mice and human organoids and shed light on the developmental basis of epitranscriptomic regulation of food intake and energy homeostasis.

overall_design: m6A sequencing of control and Mettl14 knockout primary neural progenitor cells (NPCs) derived from the mouse hypothalamus

first: Hongjun

last: Song


title: Selective identification of epigenetic regulators at methylated genomic sites by SelectID [RNA-seq]

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary: DNA methylation is a significant component in proximal chromatin regulation and plays crucial roles in regulating gene expression and maintaining the repressive state of retrotransposon elements. However, accurate profiling of the proteomics which simultaneously identifies specific DNA sequences and their associated epigenetic modifications remains a challenge. Here, we report SelectID, which introduced methylated DNA binding domain into dCas9-mediated proximity labeling system to enable in situ protein capture at repetitive elements with 5-methylcytosine (5mC) modifications. SelectID were demonstrated as feasible as dCas9-TurboID system at specific DNA methylation regions, such as the chromosome 9 satellite. Using SelectID, we successfully identified CHD4 as potential repressors of methylated LINE-1 retrotransposon through direct binding at the 5’UTR of young LINE-1 elements. Overall, our SelectID approach has opened up new avenues for uncovering potential regulators of specific DNA regions with DNA methylation, which will greatly facilitate future studies on epigenetic regulation.

overall_design: The RNA-seq assay was carried out in the stable Hela cell lines with the expression of shNC (control) and shCHD4.


title: Increasing MG1-Mediated Death in HIV-Infected Cells with SMAC Mimetics

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: It was previously shown that interferon defects in latently HIV infected cells make them permissive to MG1 mediated killing. To increase effectiveness of MG1 therapy, we have combined MG1 with the SMAC mimetic birinapant to increase MG1 mediated killing in latently infected J1.1 cells. Increased cell death was observed compared to either treatment alone and was accompanied by increased caspase-3/7 and caspase-1 expression. However, cell death could not be blocked by the pan-caspase inhibitor ZVAD-fmk or the necroptosis inhibitor necrostatin1-s, alone or in combination, indicating that cell death does not occur via a single pathway. Furthermore, it was shown that SMAC mimetic treatment results in decreased transcription of genes that take part in the immune signalling pathway, which is likely one the ways how SMAC mimetic treament senstizes HIV infected cells to MG1 mediated death.

overall_design: 12 samples of J1.1 cells were analyzed using RNA-seq under 4 conditions containing 3 replicates each; untreated, infected with MG1_eGFP, infected with MG1_eGFP and treated with Birinapant, and treated with Birinipant only.

first: Bengisu

middle: M

last: Yildirir

first: Jonathan

last: Angel


title: An endothelial SOX18-mevalonate pathway axis enables repurposing of statins for infantile hemangioma [Day 6]

city: Boston

first: Joyce

last: Bischoff

state: MA

address: 300 Longwood Ave, Karp Research Building 12.212

department: Vascular Biology Program

institute: Boston Children's Hospital

summary: Infantile hemangioma (IH) is the most common tumor in children and a paradigm for pathological vasculogenesis, angiogenesis and regression. Propranolol is the mainstay of treatment for IH. It inhibits hemangioma vessel formation via a β-adrenergic receptor independent effect of its R(+) enantiomer on the endothelial specific transcription factor sex-determining region Y (SRY)  box transcription factor 18 (SOX18). Transcriptomic profiling of patient-derived hemangioma stem cells uncovered the mevalonate pathway (MVP) as a target of R(+) propranolol. Loss of SOX18 function confirmed R(+) propranolol mode of action on the MVP.  Functional validation in preclinical IH models revealed that statins - targeting the MVP - are potent inhibitors of hemangioma vessel formation. We propose a novel SOX18-MVP-axis as a central regulator of IH pathogenesis and suggest statin repurposing to treat IH.

overall_design: Hemangioma stem cells (HemSC) isolated from 6 different proliferating phase infantile hemangioma (2 to 6 months of age) were induced to undergo endothelial differentiation for 6 days.  On Day 6 of differentiation, HemSC were treated with or without 20uM R (+) propranolol for 2 hours. Cells were lysed for total RNA isolation and library preparation using TruSeq stranded mRNA LT Sample Prep Kit and sequenced by Illumina paired end sequencing.  Bulk-RNA-seq analysis was conducted with trimmomatic v0.39 to trim the low-quality next generation sequencing reads Subsequently, only the high-quality trimmed reads were aligned to the human reference genome (hg38) using STAR v2.7.2b . The reads counts were calculated by featureCounts software. Differentially expressed genes were identified by using the DESeq2 R package (adjusted p-value < 0.05).


title: An endothelial SOX18-mevalonate pathway axis enables repurposing of statins for infantile hemangioma [Day 4]

overall_design: Hemangioma stem cells (HemSC) isolated from 3 different proliferating phase infantile hemangioma (3 to 6 months of age) were induced to undergo endothelial differentiation for 4 days.  On Day 4 of differentiation, HemSC were treated with or without 20uM R(+) propranolol for 2 hours. Cells were lysed for RNA isolation. Bulk-RNA-seq was conducted with trimmomatic v0.39 to trim the low-quality next generation sequencing (NGS) reads (-threads 20 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Subsequently, only the high-quality trimmed reads were aligned to the human reference genome (hg38) using STAR v2.7.2b. The read counts were calculated by featureCounts software. Differentially expressed genes (DEGs) were identified by using the DESeq2 R package (adjusted p-value < 0.05).


title: Ginsenoside compound K plays an anti-inflammatory effect without inducing glucose metabolism disorder in adjuvant-induced arthritis rats

city: Shanghai

first: Li

last: Cheng

state: Shanghai

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: We studied hepatic mRNA expression levels in normal Wistar rats, adjuvant arthritic (AA) rats, and AA rats administered by gavage (ginsenoside CK or dexamethasone). The aim of the study was to determine the differences in the effects of ginsenoside CK and dexamethasone on hepatic mRNA levels in AA rats. The dexamethasone group may have a greater effect on mRNA in the liver.

first: Jingyu

last: Chen


title: Relevance of the regulation of the brain-placental axis to the nocturnal bottleneck of mammals

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

summary: This study comapred gene expression patterns in aged-matached placenta and fetal brain of pig.

overall_design: Single-nuclei RNA sequencing was performed to identify genes expressed in day-45 placenta and fetal brain of pig.

first: Shankar

middle: P

last: Poudel

first: Susanta

middle: K

last: Behura


title: Trained Immunity Causes Myeloid Cell Hypercoagulability

city: Dublin

first: Roger

last: Preston

state: Dublin

address: 123 St Stephen's Green

country: Ireland

institute: Royal College of Surgeons in Ireland (RCSI)

summary: Venous thromboembolism is common in individuals with chronic inflammatory diseases, but the pathogenic basis for this increased thrombotic risk remains poorly understood. Myeloid cell ‘trained immunity’ describes persistent innate immune cell memory arising from prior exposure to an inflammatory stimulus, leading to an enhanced immune response to subsequent unrelated stimuli. We identify enhanced myeloid cell prothrombotic activity as a novel maladaptive consequence of trained immunity. LPS stimulation of murine bone marrow-derived macrophages trained previously with either β-glucan or free haem exhibited significantly enhanced procoagulant and antifibrinolytic gene expression and activity compared to macrophages stimulated with LPS alone. The β-glucan training-mediated increase in activated myeloid cell procoagulant activity was mediated by enhanced acid sphingomyelinase-mediated tissue factor (TF) functional decryption. Furthermore, pre-treatment with methyltransferase and acetyltransferase inhibitors to erase epigenetic marks associated with innate immune memory diminished trained macrophage TF gene expression in β-glucan-trained macrophages. Functional analysis of splenic monocytes isolated from β-glucan-trained mice revealed enhanced procoagulant activity up to 4 weeks after β-glucan administration compared to monocytes from control mice over the same time period. Remarkably, monocyte procoagulant activity increased proportionately with time since β-glucan administration, before plateauing at 4 weeks. Furthermore, haematopoietic progenitor cells and bone marrow interstitial fluid isolated from β-glucan-trained mice possessed enhanced procoagulant activity compared to control mice. Trained immunity and associated metabolic perturbations may therefore represent novel therapeutic vulnerabilities in immunothrombotic disease development, opening new avenues for targeted intervention.

overall_design: To investigate the role of trained immunity in modulating macrophage procoagulant function, we treated murine bone marrow derived macrophages (BMDMs) with whole glucan particle (WGP). After this cells were left for a rest period of 7 days before being rechallenged with lipopolysacharide (LPS). We then isolated RNA from untreated BMDMs, LPS-treated BMDMs and WGP+LPS BMDMs and performed RNA sequencing to compared gene expression between these treatment groups

first: Aisling

last: Rehill

first: Seán

last: McCluskey

first: Anna

middle: E

last: Ledwith

first: Tristram

middle: A

last: Ryan

first: Gemma

last: Leon

first: Hugo

last: Charles-Messance

first: Edmund

middle: H

last: Gilbert

first: Emily

last: Daly

first: Corrina

last: McMahon

first: James

middle: S

last: O'Donnell

first: Annie

last: Curtis

first: Luke

last: O'Neill

first: Frederick

last: Sheedy


title: Gene expression and variation in Bladder Carcinoma

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Identification of visual cortex transcriptome of Mmp9 UTRmut mice (B6.CBA Mmp9em1Iimcb/Tar)

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: As microRNAs have emerged as important regulators of molecular events occurring at the synapses, new questions about their regulatory effect on the behavior have arisen. In the present study, we elucidated the physiological consequences of miR132-Mmp9 mRNA interaction in vivo. To address this question, we created a new mouse model with a disrupted miR132 binding site in Mmp9 mRNA 3’UTR. In the current manuscript, we show for the first time that the dysregulated specific targeting of miR132 to Mmp9 mRNA in the mouse brain results in the increased level of Mmp9, which affects synaptic plasticity and has an effect on mice behavior. Our data points at the importance of complex and precise regulation of Mmp9 level by miR132 in the brain.

overall_design: Examination of mouse visual cortex transcriptome in Mmp9UTR mut, heterozygous and WT mice, performed in two replicates.

first: B

last: Kuźniewska

first: K

first: A

last: Dziembowski

first: M

last: Dziembowska


title: Bladder Carcinoma gene expression data

summary:
We used Affymetrix U133 plus 2.0 arrays to study the gene expression patterns of primaryBladder tumors (43 MIBC and 20 NMIBC)
Total of 63 patients suffering from bladder cancer were included in our study, none of which received any prior therapy before surgery. Selected tumors belong to the CIT (“Carte d’Identité des Tumeurs”) discovery series.

overall_design: Gene expression of 63 samples bladder tumor assesed using the Hg-U133 Plus 2.0 Affymetrix array

first: François

last: Radvanyi

first: Isabelle

last: Bernard-Pierrot

last: Chapeaublanc


title: Impact of ATEVs and EV-DNA on transcriptional profile of dendritic cells in lymph nodes

status: Public on Mar 06 2025

city: New Ypok

first: Mengying

last: Hu

state: New York

address: 413 E 69th St, New York, NY 10021

institute: Weill Cornell Medical College

summary: Antigen processing and presentation (APP) is essential for adaptive immunosurveillance in all nucleated cells. Here we describe a novel mechanism through which secreted factors other than cytokines, specifically extracellular vesicles (EVs) released from activated T cells (ATEVs) drive a positive feedback loop that enhances antigen presentation and immune responses in normal physiology and cancer. ATEV-induced immunogenicity relies on extravesicular double-stranded DNA (EVDNA) and granzyme B (Gzmb). ATEV-DNA is notably abundant, primarily consisting of genomic DNA enriched in copies of specific genes, including numerous APP machinery genes. Mechanistically, ATEV transfer of APP machinery genes to recipient dendritic or tumor cells is facilitated by Gzmb disruption of recipient cell nuclear integrity. DNAse treatment of ATEVs removed the majority of EVDNA, preventing APP machinery upregulation in recipient cells, which in turn failed to recruit T lymphocytes into tumors. Notably, ATEVs hold promise as an immune-boosting therapeutic, particularly in restoring MHC-I antigen processing and presentation, and synergize with checkpoint blockade therapy in several immunotherapy-refractory tumors. Collectively, our findings uncover a novel mechanism through which ATEVs boost APP and anti-tumor immunity. Gzmb-mediated nuclear transfer opens new avenues for non-viral gene delivery, offering potential for enhanced intranuclear gene transport and expression efficiency.

overall_design: Naïve C57BL/6 mice received i.v. injections retro-orbitally of PBS, 50 µg of NTEVs or 25 µg of ATEVs (containing 10 µg of EV-DNA), or 25 µg of Baseline-ZERO DNase-pretreated ATEVs every other day for in total 3 doses. Subsequently, cervical lymph nodes were subjected to FACS sorting of CD45+CD11b-CD11c+ dendritic cells (DCs) for RNAseq profiling


title: HIV-2 evolved ZAP resistance despite increased CpG levels

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: Simian immunodeficiency viruses infecting sooty mangabeys (SIVsmm) have been transmitted to humans on multiple occasions, giving rise to human immunodeficiency virus type 2 (HIV-2) groups A to I. However, only groups A and B spread significantly in humans causing an epidemic in West Africa. The reasons for this are poorly understood. Here, we show that genetically diverse SIVsmm strains efficiently infect primary human T cells. However, they are highly sensitive to type I IFN, indicating that interferon-stimulated genes (ISGs) pose a barrier to the successful spread of SIVsmm in humans. One well-known ISG is the zinc finger antiviral protein (ZAP), which specifically targets CpG dinucleotides in viral RNAs. To evade ZAP restriction, many viruses, including HIV-1, suppress their CpG content. Unexpectedly, we found that HIV-2 is less sensitive to restriction by ZAP than HIV-1 and SIVsmm despite significantly higher CpG content. Analyses of chimeric HIV-2/SIVsmm constructs, together with binding site mapping using eCLIP, revealed that the determinants of ZAP resistance map to the U3 region of the 3’ LTR that overlaps with the nef gene. Our results indicate that ZAP poses a barrier to the efficient spread of SIVsmm in humans and that epidemic HIV-2 evolved a unique mechanism to evade it.

sample_organism:
Homo sapiens
Human immunodeficiency virus 2
Simian immunodeficiency virus

overall_design: Characterization of protein-RNA interaction sites of the host protein ZAP in HIV-2 and SIVsmm infected HEK293T ZAP KO cells by using enhanced crosslinking and immunoprecipitation (eCLIP) in combination with RNA-sequencing.

first: Dorota

last: Kmiec

first: Rayhane

last: Nchioua

first: Asimenia

last: Vlachou

first: Sabina

last: Ganskih

first: Sümeyye

last: Erdemci-Evin

first: Stacey

last: Lapp

first: Diane

last: Carnathan

first: Steven

last: Bosinger

first: Ben

last: Berkhout

first: Atze

middle: T

last: Das

first: Mathias

last: Munschauer

first: Frank

last: Kirchhoff


title: Bladder tumor genome variation profiling by genome tiling array

first: Elodie

last: chapeaublanc

summary: We used 5K BAC-CGH arrays to study the genome alteration patterns of bladder tumors.

overall_design: 63 Samples on a 5K BAC-CGH array

last: Radvanyi


title: FGF21 deficiency aggravates adipose tissue loss in thermoneutrality-associated cancer cachexia

city: Vienna

first: Tamina

last: Österreicher

state: Vienna

address: Währingerstraße 10

department: Institute of Medical Chemistry and Pathobiochemistry

country: Austria

institute: Medical University of Vienna

summary: Cancer-associated cachexia (CAC) is a multifactorial, metabolic wasting syndrome that coincides with cancer malignancies of multiple entities. CAC is characterized by progressive loss of muscle mass and adipose tissue and diminishes therapy responsiveness. Here, we show that the expression of FGF21 is induced in livers of tumor-bearing mice with CAC. FGF21 deficiency promotes weight loss, exacerbates adipose tissue wasting and increases systemic inflammation, pointing towards a protective role of FGF21 in CAC. In line, IL6-mediated STAT3 activation induces FGF21 expression in hepatocytes as well as adipocytes. FGF21 promotes anabolic signaling cascades, increases cellular glucose uptake in response to IL6 exposure and counteracts cytokine-mediated glycerol release, thereby opposing adipose tissue loss in CAC. Eventually, we find that FGF21 is increased in cancer patients with clinical CAC. Together, we reveal a protective role for FGF21 in experimental CAC and identify the protein as a potential biomarker in clinical cachexia.

overall_design: Illumina RNA Sequencing of livers from E0771 breast tumor bearing mice housed at different temperature conditions (6°C, 22°C, 29°C).

first: Raimund

last: Oberle


title: Functional Analysis of Histone ZmH2B in Regulating Maize Resistance to Bipolaris maydis

city: Beijing

first: Ying

last: Ding

address: No.2 Yuanmingyuan West Road, Haidian

institute: Chinese Academy of Agricultural Sciences

summary: Maize histone ZmH2B belongs to the histone H2B family. In the current field of molecular biology, the majority of histone-related studies focus on their post-translational modification functions. However, studies specifically addressing histone H2B itself are relatively scarce, particularly concerning its response mechanism against Bipolaris maydis.In this study, a nucleus-localized ZmH2B was identified. To characterize the disease resistance phenotype of ZmH2B, we employed virus-induced gene silencing (VIGS) and transient overexpression (VOX) techniques to obtain ZmH2B-silenced material FoMV:ZmH2B and overexpressed material FoMV:ZmH2B-VOX. It was discovered that FoMV:ZmH2B promoted the infestation of B. maydis and inhibit the reactive oxygen species (ROS) burst induced by chitin. Conversely, FoMV:ZmH2B-VOX exhibited the opposite effects. Furthermore, ZmH2B was verified to positively regulate the infestation of B. maydis through pathogenesis-related (PR) genes. Subsequently, transcriptome analysis was carried out on the ZmH2B-silenced material and the differentially expressed genes were predominantly enriched in photosynthesis-related pathways.Collectively, these results suggested that ZmH2B plays a positive role in regulating maize resistance to B. maydis.

overall_design: The fourth leaves of maize plants with virus-induced silencing of ZmH2B or EV and T2 transgenic maize plants overexpressing ZmEIP1 and WT plants were collected for total RNA extraction and RNA-seq library construction. The RNA-seq libraries were sequenced on an Illumina HiSeq platform in paired-end mode with a read length of 150 bp (Novogene, Beijing, China). The raw reads were filtered using ht2-filter in the HTQC package (1.92.1) with default parameters to remove low-quality reads. The filtered reads were compared to the reference maize genome (Zea mays RefGen_V4) using TopHat (2.0.11) to remove host genome sequences. The mapped reads were assembled, and fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks. The Cufflinks output GTF file and the TopHat output BAM file were loaded into rMATS.3.2.2 to identify differential AS events. AS events with a P value < 0.05 were considered to be differential AS events.


title: The role of cholesterol/ALKBH1/ITGA2B in thrombosis in placental vessels of preeclampsia

city: Wuxi

first: Zhang

last: Eryun

state: jiangsu

address: 48 Huaishu Lane

institute: Wuxi Maternity and Child Health Care Hospital

type: Methylation profiling by high throughput sequencing

summary: The risk of multiple placental thrombosis is increased in preeclampsia (PE) and vascular endothelium plays vital roles in coagulation such as secreting ITGA2B, vWF and TF. However, the pathological mechanism is unclear. Placental blood vessels were collected from PE and normal pregnancies. The protein level of ITGA2B was up-regulated in PE compared to the control, indicating enhanced coagulation function in the placenta of PE. Higher cholesterol levels and lower ALKBH1 expression were found in placental blood vessels of PE while the whole DNA N6-methyldeoxyadenosine levels (6mA) were up-regulated. However, DNA 6mA level of ITGA2B promoter was decreased. The Cholesterol overload experiment in human umbilical vein endothelial cells (HUVECs) showed that cholesterol regulated the protein expressions of ALKBH1 and ITGA2B, which was related to cholesterol concentration. ITGA2B protein expression was increased after ALKBH1 knockout. These data provide important information on cholesterol levels, ALKBH1 and ITGA2B expressions in coagulation function in placental blood vessels, which may be helpful for further investigations of potential targets and early prevention of placental thrombosis in PE.

overall_design: human MeDIP-Seq:placental vascular


title: Deep-Red and Ultrafast Photocatalytic Proximity Labeling Empowered in situ Dissection of Tumor-Immune Interactions in Primary Tissues

first: Xinyuan

last: Fan

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: College of Chemistry and Molecular Engineering

institute: Peking university

summary: Immunotherapy efficacy in solid tumors varies greatly, influenced by the tumor microenvironment (TME) and the dynamic tumor-immune interactions within it. Decoding these interactions in situ with minimal interference to native tissue architecture and delicate immune responses is critical for understanding tumor progression and optimizing therapeutic strategies. Here, we introduce CAT-Tissue, a novel deep-red photocatalytic proximity labeling method that enables ultrafast, high-resolution profiling of tumor-immune interactions in primary tissues. By leveraging nanobody-Chlorin e6 as the photocatalyst and biotin-aniline as the probe, CAT-Tissue enabled the rapid and comprehensive detection of various tumor-immune interactions in both coculture systems and primary tumor sections. Coupled with bulk RNA-sequencing, CAT-Tissue revealed distinct gene expression patterns between tumor-neighboring and tumor-distal lymphocytes, highlighting the recognition and immune responses of tumor-neighboring CD8+ T cells, which exhibited activated, effector, and exhausted phenotypes. By leveraging a deep-red photocatalytic proximity cell labeling strategy with excellent tissue penetration and biocompatibility, CAT-Tissue offers a non-genetically encoded platform with high sensitivity and spatiotemporal controllability for rapid profiling tumor-immune interactions within complex tissue environments in situ, which may advance our understanding of tumor immunology and guide the development of more effective immunotherapies.

overall_design: RNA-seq of tumor-neighboring (Biotin+) CD8+ T and tumor-distal (Biotin-) CD8+ T cells of TILs isolated from MC38-hPD-L1 tumor (12 days) on C57BL/6N mice, in triplicate.

first: Zhizheng

last: Lou

first: Yan

last: Zhang

first: Peng

middle: R

last: Chen


title: sc-RNA-seq for study: A human-specific enhancer fine-tunes radial glia potency and corticogenesis

city: Durham

first: Jing

last: Liu

state: NC

address: 218 CARL buildling

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Humans evolved an extraordinarily expanded and complex cerebral cortex, associated with developmental and gene regulatory modifications1-3. Human accelerated regions (HARs) are highly conserved DNA sequences with human-specific nucleotide substitutions. Although there are thousands of annotated HARs, their functional contribution to species-specific cortical development is largely unknown4,5. HARE5 is a HAR transcriptional enhancer of the WNT signaling receptor Frizzled8 (FZD8) active during brain development6. Here, using genome-edited mouse and primate models, we demonstrate that human (Hs) HARE5 fine-tunes cortical development and connectivity by controlling the proliferative and neurogenic capacity of neural progenitor cells (NPCs). Hs-HARE5 knock-in mice have significantly enlarged neocortices, which contain more excitatory neurons. By measuring neural dynamics in vivo we show these anatomical features result in increased functional independence between cortical regions. To understand the underlying developmental mechanisms, we assess progenitor fate using fixed and live imaging, lineage analysis, and single-cell RNA sequencing. We discover Hs-HARE5 modifies radial glial progenitor behavior, with increased self-renewal at early developmental stages followed by expanded neurogenic potential later.  We use genome-edited human and chimpanzee (Pt) NPCs and cortical organoids to assess the relative enhancer activity and function of Hs-HARE5 and Pt-HARE5. Using these orthogonal strategies we show four human-specific variants in HARE5 drive increased enhancer activity which promotes progenitor proliferation. Finally, we show that Hs-HARE5 promotes progenitor proliferation by increasing canonical WNT signaling. These findings illustrate how small changes in regulatory DNA can directly impact critical signaling pathways to modulate brain development. Our study uncovers new functions for HARs as key regulatory elements crucial for the expansion and complexity of the human cerebral cortex.

overall_design: sc-RNA seq of E14.5 cortices from wildtype littermates and HARE5 knock-in mice. Two replicates each genotype.Conditions:  E14.5 WT, E14.5 HARE5Hs/Hs.

first: Debra

last: Silver


title: A human-specific enhancer fine-tunes radial glia potency and corticogenesis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype and HARE5Hs/Hs knock-in mice cortices at two timepoint, E12.5 and E14.5.  Three biological replicates have been collected for each condition. Conditions:  E12.5 WT, E12.5 HARE5Hs/Hs,  E14.5 WT, E14.5 HARE5Hs/Hs.


title: Transcriptomic disruption and functional hypoactivity in DYT-SGCE MGE-patterned inhibitory neurons

city: Cardiff

first: Zongze

last: Li

country: United Kingdom

summary: Myoclonus Dystonia is a Mendelian inherited, childhood-onset dystonic disorder, caused by mutations in the autosomal dominantly inherited SGCE gene, and in which both motor and psychiatric phenotypes are observed. Results from murine and in vivo human studies suggest dystonia is caused by disruption to neuronal networks, and in particular the basal gangliacerebello- thalamo-cortical circuit. Work focused on the cortical component implicates disruption to neuronal excitatory/inhibitory balance as being a key contributor in the observed phenotypes. Our previous work, focused on cortical excitatory glutamatergic neurons, demonstrated a hyperexcitable phenotype and more complex dendritic arborisation in an in vitro model of Myoclonus Dystonia. By contrast, human electrophysiological studies have suggested that it is the loss of inhibitory tone in this region that contributes to the overall hyperkinesis. To explore this further we have evaluated the impact of SGCE mutations on medial ganglionic eminence-derived inhibitory GABAergic neurons using the same patientderived induced pluripotent and gene edited embryonic stem cell lines, comparing each to their isogenic wild-type control. Differentiation towards inhibitory interneurons demonstrated no significant differences in neither early (NKX2.1, FOXG1), nor late stage (GAD67, GABA), developmental markers. Single-cell RNA sequencing additionally confirmed evidence of markers consistent with Medial Ganglionic Eminence-derived GABAergic neurons, and when compared to two publicly available human foetal ganglionic eminence transcriptomic datasets, confirmed that the cells generated resembled those found in vivo. Further analysis of this data demonstrated transcriptomic dysregulation in genes related to axonal organization, synaptic signalling and action potential generation in the SGCEmutation positive neurons. Subsequent characterisation of dendritic morphology found SGCE-mutation positive neurons to have shorter branches, fewer higher order branches and reduced branching complexity, compared to their wild-type controls. Functional analyses using Ca2+ imaging and MEA approaches to examine network activity identified significantly lower calcium responses to GABA and reduced spike and burst frequencies in the SGCEmutation carrying lines, compared to their isogenic controls. Reduced activity was also observed in single-cell patch clamp studies with fewer neurons firing action potential trains, coupled with fewer spontaneous post-synaptic currents, compared to controls. Collectively, this work indicates lower neuronal inhibitory activity and complexity of the dendritic arbor in the context of SGCE mutations, further contributing to the disruption of neuronal excitatory/inhibitory balance in motor circuits and potentially underlying the observed clinical hyperkinetic phenotype. These changes may also represent common characteristics across the wider dystonia spectrum, with potential for future target identification with amenability to therapeutic intervention

overall_design: Medial ganglionic eminence-derived inhibitory GABAergic neurons were differentiated from patient-derived induced pluripotent stem cells carrying SGCE mutation for 80 days and processed with Takara iCell8 for full-length single-cell RNA sequencing.

first: Laura

last: Abram

first: Maria

last: Cruz-Santos

first: Olena

last: Petter

first: Kathryn

last: Peall


title: An Intraepithelial ILC1-like Natural Killer Cell Subset Produces IL-13

city: Palo Alto

first: John

middle: B

last: Sunwoo

state: CA

address: 801 Welch Rd

department: Otolaryngology – Head & Neck Surgery

institute: Stanford School of Medicine

summary: Natural killer (NK) cells are innate immune effectors with considerable heterogeneity and potent antitumor capabilities. Intraepithelial ILC1 (ieILC1)-like NK cells, a population of cytotoxic tissue-resident innate lymphoid cells, have recently been documented in the microenvironment of head and neck squamous cell carcinomas (HNSCC) and other solid tumors. These cells have antitumor cytolytic potential and are potent producers of type 1 cytokines, including IFNy. Here, we identify a subpopulation of ex vivo differentiated ieILC1-like NK cells that produce IL-13 upon stimulation. Functional characterization revealed that these cells co-expressed IFNy and IL-13 while maintaining an ILC1 transcriptional signature. IL-13 was induced either upon co-culture with tumor cell lines, or in response to TGF-B and IL-15. IL-13-expressing ieILC1-like NK cells were identified among tumor infiltrating lymphocytes expanded from patient HNSCC tumors, in support of their existence in primary tumors. These data demonstrate additional heterogeneity within the ieILC1-like NK cell population than previously appreciated and highlight a unique form of ILC plasticity in which cells with clear ILC1 transcriptional profiles express a type 2 cytokine. With the known roles of IL-13 in cancer cell growth dynamics and immunoregulation, the identification of this subset within tumor microenvironments presents a potential target for therapeutic manipulation.

overall_design: RNAseq profiling of IL-13+ and IL-13- ieILC1-like NK cells sorted via FACS after PMA and Ionomycin stimulation of ieILC1-like NK cells differentiated from peripheral blood NK cells in vitro.

first: Sainiteesh

last: Maddineni

first: Krishna

last: Sharma

first: Imran

last: Mohammad

first: Alistaire

middle: D

last: Ruggiero-Sherman

first: Ivan

last: Stepanek

first: June Ho

last: Shin

first: Jennifer

last: Bando


title: Immune Landscape of Intrathoracic Lymph Nodes with Metastasis in Primary Lung Malignancy using EBUS-TBNA samples

city: Chicago

first: Gye Young

last: Park

state: IL

address: 840 S. Wood St

department: Medicine, Pulmonary

institute: University of Illinois at Chicago

summary: Malignant cells modulate immune cell phenotype and function to generate a favorable microenvironment for tumor survival and progression. The draining lymph node (LN) is the most frequent and often first site of cancer metastasis. Notwithstanding, our understanding of how cancer, metastatic to LNs, alters the immune cells therein remains limited. Although LN biopsy is frequently performed as a standard practice in cancer diagnosis and staging, immunologic studies employing these samples are rare. The present study investigates the immune cell alterations in metastatic intrathoracic LNs. With the advent of single-cell technologies, we comprehensively analyzed immune cells in a series of bronchoscopic LN biopsies from human subjects undergoing diagnostic workup of cancer. Using single-cell RNA sequencing and mass cytometry analyses, we compared intrathoracic LN samples from 18 subjects with pathologically confirmed metastasis and four controls without evidence of metastasis. We found that immune cell composition and gene expression patterns differed markedly between metastatic and control LNs. In particular, metastatic LNs contained relatively more neutrophils and APOE-high myeloid cells, with the latter exhibiting significant transcriptional derangement and a powerful intercellular interaction signature. Additionally, CD8 T cells in metastatic LNs demonstrated a unique exhausted phenotype. Notably, our findings are corroborated in a publicly available lung adenocarcinoma cohort derived from surgical LN biopsies. Immune cell phenotypes and gene expression patterns from bronchoscopic LN biopsies can be leveraged to advance understanding of cancer immunology and may have independent diagnostic value when malignant cells fail to be identified on histopathology.

overall_design: This study was conducted in accordance with the Declaration of Helsinki. Study approval was granted by the institutional review boards of the Jesse Brown VA Medical Center and the University of Illinois at Chicago (UIC) Hospital and Health Sciences System. Briefly, subjects aged 18 years or older who were planned to undergo standard-of-care diagnostic bronchoscopy with EBUS to evaluate radiological abnormalities were screened for study enrollment. Subjects were included in the study upon providing informed consent if they did not meet exclusion criteria, which included the use of systemic corticosteroids or other immunosuppressants and/or a history of respiratory tract infections within 8 or 4 weeks prior to the diagnostic procedure, respectively. Study subjects were retrospectively divided into metastatic, or non-metastatic (control) groups based on histopathologic presence or absence of cancerous cells within sampled intrathoracic LNs. Since all subjects underwent clinically indicated EBUS sampling, additional criteria were established for inclusion into the control group. These included either no evidence of LN disease and no primary lung malignancy with at least six months of follow-up or confirmed negative tumor involvement from surgical LN dissection with no evidence of recurrence for at least one year of follow-up.

first: Seung-jae

last: Kim

first: Minhyung

first: Sungyong

last: You

first: Pinal

last: Kanabar


title: Dipeptidyl peptidase DPF-3 is a gatekeeper of microRNA Argonaute compensation in animals

city: Québec

first: Louis-Mathieu

last: Harvey

address: 9, rue McMahon

institute: CRCHUQ-UL

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are essential regulators involved in multiple biological processes. To achieve their gene repression function, they are loaded in miRNA-specific Argonautes to form the miRNA-induced silencing complex (miRISC). Mammalians and C. elegans intriguingly possess more than one paralog of miRNA-specific Argonautes and the dynamic between them remains unclear. Here, using C. elegans as a model system, we report dipeptidyl peptidase DPF-3 as a new interactor of miRNA-specific Argonautes ALG-1 and ALG-2. Knockout of dpf-3 rescues miRNA-related defects observed in alg-1 null animals and allows ALG-2 to better compensate for the lack of its paralog through higher expression and activity. While DPF-3 can cleave a N-terminal dipeptide of ALG-2 in vitro, we show that it is likely not the molecular mechanism used by DPF-3 to regulate ALG-2. This study uncovers the importance of a dipeptidyl peptidase in the miRNA pathway and provide insights in miRNA-specific Argonautes regulation dynamics in animals.

overall_design: We compared the microRNA expression profile of young C. elegans adult animals of WT, dpf-3(xe68), alg-1(gk214) and alg-1(gk214);dpf-3(xe68) genetic background.

first: Pierre-Marc

last: Frédérick

first: Pascale

last: Michaud

first: François

last: Houle

first: Daniel

last: Young

first: Catherine

last: Desbiens

first: Shanna

last: Ladouceur

first: Rajani

last: Kanth Gudipati

first: Antoine

last: Dufour

first: Helge

last: Großhans

first: Martin

last: J. Simard


title: Matrix stiffness modulates androgen response genes and chromatin state in prostate cancer (RNA-seq)

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: The interplay between the extracellular matrix (ECM) and prostate cancer (PCa) tumor has been shown to increase ECM stiffness, correlating with more aggressive disease forms. However, the impact of ECM stiffness on the androgen receptor (AR), a primary PCa treatment target, remains elusive. Here, we aimed to explore whether matrix stiffness influences PCa progression, transcriptional regulation, chromatin state, and AR function in AR-positive PCa cells under varying ECM stiffness conditions. We utilized ATAC-seq and RNAseq in different ECM conditions and the SUC2 metastatic prostate adenocarcinoma patient dataset to understand the role of ECM stiffness on chromatin state, androgen response genes and to evaluate the effect of matrix stiffness on prostate cancer progression. Results showed that increased ECM stiffness elevated the expression of genes related to proliferation and differentiation. In contrast, androgen response genes were most induced in soft ECM conditions. Combining chromatin accessibility with transcriptomic results revealed that androgen response genes were more transcriptionally available in soft ECM conditions. Additionally, increased ECM stiffness upregulated genes associated with low overall survival in the SUC2 dataset. Taken together, our results indicate that high expression of hard matrix stiffness genes potentially promotes prostate cancer progression leading to more aggressive forms of the disease with poor survival rate.

overall_design: Gene expression profiling by RNA-seq from C4-2B prostate cancer cells grown in plastic plates or hydrogel plates with 50 kPa or 0.5 kPa stiffness. Sequencing was done with Illumina NextSeq 500.

first: Roosa

last: Kaarijärvi

first: Kirsi

last: Ketola


title: Treatment of neurologic disorders by brain-wide microglia replacement using a non-conditioning strategy

city: 厦门

first: 大典

last: 陈

address: 福建省厦门市翔安区翔安南路4221号

institute: 厦门大学

summary: Genetic evidence indicates that microglial dysfunctions contribute to the development and progression of various neurologic diseases, emphasizing microglia replacement as a promising therapeutic strategy. However, traditional bone marrow transplantation (BMT) aimed at replenishing brain microglia faces challenges due to low efficiency and potential brain injury from preconditioning with irradiation or chemotherapy. Moreover, the BM-derived cells that migrate to the brain fail to replicate the characteristics of resident microglia. Here, we present a simple yet highly effective microglia transplantation strategy devoid of any conditioning, termed "Tri-Cyclic Microglial Depletion for Transplantation" (TCMDT). This approach leverages three cycles of microglial depletion using the CSF1R inhibitor PLX3397, creating a critical window for the efficient engraftment of exogenous microglia. Notably, transplanting primary cultured microglia via the TCMDT strategy achieves their full restoration to the identity and functions of native microglia. To evaluate the therapeutic potential, we applied our strategy to a Sandhoff disease mouse model, a form of neurodegenerative lysosomal storage disorder (LSD) caused by Hexb deficiency. The results revealed that our strategy facilitated the efficient replacement of deficient microglia, leading to a notable decrease in neurodegeneration and an enhancement in motor performance. Similarly, in an Alzheimer's disease (AD) mouse model carrying the Trem2 R47H mutation, our transplantation strategy corrected microglial dysfunction and alleviated AD-related pathology. Overall, our study presents a practical approach for microglia replacement that is simple, efficient, and safe, offering significant therapeutic potential for treating microglia-associated disorders.

overall_design: We employed our high-efficiency TCMDT method and used fluorescence-activated cell sorting (FACS) to purify transplanted microglia (TP) three months post-transplantation (Fig. 2A and fig. S2). Simultaneously, primary microglia (PMG) and resident microglia (Res) were collected as control samples for RNA-seq analysis to assess the ability of TP to adopt the naive microglial transcriptional program.

first: Li

last: Zhong

first: Dadian

last: Chen


title: Targeting CD38 immunometabolic checkpoint improves metabolic fitness and cognition in a mouse model of Alzheimer’s disease.

city: Rehovot

first: Rafael

last: Valdés Mas

address: Herzl St 234

country: Israel

institute: Weizmann Institute

summary: Protective immunity, essential for brain maintenance and repair, may be compromised in Alzheimer’s disease (AD). Here, using high-dimensional single-cell mass cytometry, we find a unique immunometabolic signature in circulating CD4+ T cells preceding symptom onset in individuals with familial AD, featured by the elevation of CD38 expression. Using female 5xFAD mice, a mouse model of AD, we show that treatment with an antibody directed to CD38 leads to restored metabolic fitness, improved cognitive performance, and attenuated local neuroinflammation. Comprehensive profiling across distinct immunological niches in 5xFAD mice, reveals a high level of disease-associated CD4+ T cells that produce IL-17A in the dural meninges, previously linked to cognitive decline. Targeting CD38 leads to abrogation of meningeal TH17 immunity and cortical IL-1beta, breaking the negative feedback loop between these two compartments. Taken together, the present findings suggest CD38 as an immunometabolic checkpoint that could be adopted as a pre-clinical biomarker for early diagnosis of AD and might also be therapeutically targeted alone or in combination with other immunotherapies for disease modification.

overall_design: bulk RN-seq

first: Peralta Ramos

last: Javier

first: Castellani

last: Giulia

first: Kviatcovsky

last: Denise

first: Croese

last: Tommaso


title: Matrix stiffness modulates androgen response genes and chromatin state in prostate cancer (ATAC-seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of chromatin accessibility by ATAC-seq from C4-2B prostate cancer cells grown in plastic plates or hydrogel plates with 50 kPa or 0.5 kPa stiffness. Sequencing was done with Illumina NextSeq 500.


title: Comprehensive molecular profiling of FH-deficient renal cell carcinoma identifies molecular subtypes and novel therapeutic targets

city: Sichuan

first: Hao

last: Zeng

address: Department of Urology, Third Inpatient Building, West China Hospital, Sichuan University, Chengdu,

institute: West China Hospital, Sichuan University

summary: Conducting an in-depth exploration of the multi-omics landscape of Fumarate Hydratase (FH)-deficient renal cell carcinoma (RCC), the study aimed to unravel the intricate molecular mechanisms underlying this rare and aggressive form of renal cancer. Analyzing 126 patients with FH-deficient RCC, we identified distinct variant spectrum of FH gene, with truncating mutation correlated with adverse prognostic factors and a worse response to immune checkpoint blockade. The identification of three molecular subtypes with diverse clinical/genomic characteristics and varying response to systemic treatment further enriched the understanding of the heterogeneous tumor microenvironment (particularly immune-related) in FH-deficient RCC, and suggested potential therapeutic targets. These findings offer a basis for molecular stratification, shedding light on the tailored therapeutic strategies in improving treatment response of FH-deficient RCC.

overall_design: To comprehensively explore the molecular landscape and biological subtypes of FH-deficient RCC, offering insights for novel therapies, we performed RNA-seq on primary tumors of FH-deficient RCC from 56 patients and 37 paired adjacent normal kidney tissues to conduct gene expression profiling analysis.


title: Single-cell transcriptomic analysis of cell lines derived from a metaplastic breast cancer with squamous metaplasia (MBC-SM) tissue

city: Taipei

first: Wen-Hsuan

last: Yu

address: No.7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: Although epithelial–mesenchymal transition (EMT) is the favored hypothesis for why cancer metastasis occurs, the cause–effect relationship remains unclear due to inconsistent clinical evidence. In this study, we establised epithelial– and mesenhcymal–predominant cell clones from a patient derived-metaplastic breast carcinoma with squamous metaplasia tissue (MBC-SM), followed by in-depth characterization of the derived cell clones.

overall_design: Before cells reaching confluence, total RNA of each cell clone was extracted with TRIzol reagent (Thermo Fischer Scientific, Waltham, MA, USA), including epithelial-predominant (n=3), E/M hybrid (n=2) and mesenchymal-predominant (n=3). Briefly, transcriptome libraries from the mRNA fractions were generated by Chromium Next GEM Single Cell 3' Reagent Kits v3.1 and sequenced on an Illumina NovaSeq X Plus.

first: Huang-Chun

last: Lien


title: Characterization of the genes that were regulated by infection with Malassezia furfur

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

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

country: Japan

institute: Koyto Univ.

summary: In the present study, we investigated the pathogenicity of infection with Malassezia furfur using Caenorhabditis elegans as a model animal. The lifespan of the adult C. elegans infeted with Malassezia furfur was significantly longer than that of uninfected animals (control). Transcriptional profiling comparing infected- and uninfected animals suggested that genes related to the innate immunity were upregulated by infection with Malassezia furfur.

overall_design: Transcriptional profiling of three-day-old worms that were infected or uninfected with Malassezia furfur for six hours, by deep sequencing, using Illumina HiSeq.


title: Urine Cell-Free RNA versus Plasma Cell-Free RNA for Monitoring of Immune and Urinary Tract Complications

city: Ithaca

first: Iwijn

last: De Vlaminck

address: 237 Tower Road, Weill Hall 301

department: Biomedical Engineering

institute: Cornell University

summary: While it is well known that cell-free RNA (cfRNA) can be isolated from urine, the diagnostic potential of this urine cfRNA, especially in comparison to plasma cfRNA, remains underexplored. Here, we directly compared the utility of urine cfRNA and plasma cfRNA for the monitoring of systemic and urinary tract related complications. We analyzed 272 matched plasma and urine cfRNA isolates obtained from three cohorts of patients: Hematopoietic Stem Cell Transplant (HSCT) recipients, patients with acute kidney injury (AKI), and healthy volunteers. The data highlight the unique cellular origins and properties of urinary and plasma RNA. Most importantly, we find that although plasma cfRNA is a superior analyte for monitoring immune and systemic complications, urinary cfRNA is more sensitive to complications of the urinary tract, including cell-type specific injury in the kidney. These findings highlight the potential of urine cfRNA as a novel analyte in diagnostic medicine.

overall_design:
We isolated and sequenced cell-free RNA from 272 matched plasma and urine samples from healthy volunteers (n=5), HSCT recipients (n=97), and patients who developed acute kidney injury (AKI) in the setting of receiving immune checkpoint inhibitor (ICI) therapy (n=34,

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Omary

last: Mzava

first: Conor

last: Loy

first: Isabel

last: Gonzalez-Bocco

first: Liz-Audrey

last: Djomnang Kounatse

first: Andrew

last: Bliss

first: Sophia

middle: L

last: Wells

first: Joan

last: Lenz

first: Emma

last: Belcher

first: Kaiwen

last: Koo

first: Lindsey

last: Baden

first: Tinyi

last: Chu

first: Matthew

last: Cheng

first: Jerome

last: Ritz


title: Analysis of striped bass (Morone saxatilis) and white bass (M. chrysops) spleen transcriptome following Streptococcus iniae infection

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Streptococcal disease results in major mortality events of both marine and freshwater fishes worldwide. Streptococcus iniae is among the prominent causative bacterial strains as it has been found to cause a higher incidence of mortality and act as a zoonotic pathogen. Here we examine the susceptibility of two important aquaculture species in the United States, striped bass (Morone saxatilis) and white bass (Morone chrysops), to S. iniae. A high incidence of mortality was observed in both species, although striped bass succumbed more rapidly than white bass. Spleen gene expression at three time points following infection was analyzed to further elucidate the mechanisms underlying these observations. The down-regulation of gene transcripts associated with pathogen detection (tlr1, tlr8, tlr9), antigen processing (cd74a), immune cell recruitment and migration (ccl44, ccr6b, ccr7), macrophage function (csf1ra), T-cell signaling and NF-kB activation (card11, fyna, tirap) was detected in both species. These findings potentially indicate impairment in these critical early immune system processes such that both species were ultimately highly susceptible to S. iniae infection despite the detected up-regulation of transcripts typically associated with effective immune response, such as cytokines (il1β, il8, il12b2, il17rc, tnfb) and hepcidins (hamp, hamp2). The presented results collectively identify several candidate genes and associated pathways for further investigation to characterize the vulnerability of striped bass and white bass to S. iniae and that may be considered for selective breeding efforts, biotechnological intervention, and/or exploitation in the development of vaccines and alternative treatments.

sample_organism:
Morone saxatilis
Morone chrysops

platform_organism:
Morone saxatilis
Morone chrysops

overall_design: Spleen tissue was sampled from 48 indiviudals at four timepoints prior to (t= 0 hr control) or following exposure to Streptococcus iniae  (t= 1 hr, 4 hr, and 24 hr post treatment) (n=24 striped bass, SB, and n=24 white bass, WB, total: 6 of each sampled at each of the four timepoints)

first: Linnea

last: Andersen

middle: W


title: Fate determination of msc by inflammatory niche in HO [scRNA-Seq]

city: Hefei

first: Chen

last: Kan

state: Anhui

address: 81 Meishan road

department: Pathophysiology

institute: Anhui Medical University

summary: Heterotopic ossification (HO), usually following traumatic challenges, is initiated by the aberrant osteochondral differentiation of mesenchymal stem cell (MSC). However, the role of trauma-induced inflammatory exposure in MSC fate determination remains unclear. Here, we found that quiescent MSC transited into cycling MSC and later gave rise to chondrogenic (cMSC) and/or osteogenic (oMSC) commitment following either muscle or tendon injury via single-cell RNA sequencing and lineage tracing analysis. Further spatial transcriptome analysis revealed that cycling MSC, cMSC and oMSC resided in the inflammatory niche comprised of monocytes/macrophages, neutrophils, dendritic cells (DCs), NK cells, T and B lymphocytes. We uncovered the diversity of each type of immune cells during MSC development and demonstrated that macrophages, including M1 and M2 subtypes, dynamically promotes proliferation and osteochondral differentiation of MSCs. Additionally, neutrophils and NK cells are essential for cycling MSC transition from quiescent MSC. CD4+ and CD8+ T lymphocytes promotes chondrogenesis. CellchatDB analysis and regulon analysis identify several gene networks, which could be essential for aberrant MSC proliferation and osteochondral differentiation respectively. Collectively, our findings indicate that inflammation is necessary to regulate MSC fate and uncovered the molecular landscape of osteoimmunological interactions that occur during aberrant osteochondral differentiation that could be useful for HO treatment.

overall_design: Single cell RNA-sequencing and spatial transcriptome assays were used to examine the strucutre of inflammatory niche in the HO and depletion of each type immune cells via chemical or genetic approaches was applied to assess the function of inflammatory niche in MSC fate determination.

first: Haitao

last: Fan

first: Jiazhao

last: Yang

first: Hong

last: Zheng


title: Uncovering Stage-Specific Biomarkers in Colorectal Cancer: RNA-Seq Analysis of Adenoma and Carcinoma Progression

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: Colorectal cancer (CRC) progresses through distinct molecular mechanisms, tumor stage playing a pivotal role in prognosis and treatment outcomes. Despite advances in CRC treatment, the lack of stage-specific biomarkers limits the potential for reliable diagnostic and treatment strategies. This study aims to identify stage-specific gene expression profiles and the molecular mechanisms through comparative transcriptomic analysis of adenoma (n = 10), carcinoma in situ (n = 8) and adenocarcinoma (n = 11) samples. Utilizing RNA-seq from FFPE samples processed with absGSEA, we identified significant cellular pathways influenced from each CRC stage. In adenocarcinoma, pathways related to transcriptional co-regulatory mechanisms and protein kinase functional activity, critical for tumor growth and metastasis, were significantly enriched compared to adenoma. While apoptotic processes and Wnt signaling pathways were prominent in carcinoma in situ compared to adenoma samples. Extracellular matrix organization pathway was significantly enriched between adenocarcinoma and carcinoma in situ. Transcriptomics data and bioinformatics analysis revealed that in adenocarcinoma cohorts, genes such as COL1A2, CEBPZ, MED10, and PAWR were overexpressed, highlighting their potential roles in advanced disease progression. Conversely, in adenoma samples, the overexpression of genes such as ARRB1, CTBP1, and CTBP2 underscores their involvement in early tumorigenesis. COL1A2 and CEBPZ were implicated in extracellular matrix remodeling and transcriptional regulation respectively, while and ARRB1 were associated with early tumorigenesis. These findings highlight the complexity of gene regulation in CRC and provide a foundation for developing stage-specific diagnostic and prognostic biomarkers, and to ultimately improve therapeutic strategies.

overall_design:
10 adenoma samples
11 adenocarcinoma samples
8 Carcinoma In Situ samples
Abbreviations: (AD: Adenoma patients, CA: Carcinoma patients, CIS: Carcinoma In Situ)

first: Faisal

last: Alhosani

first: Reem

last: Alhamidi

first: Burcu

middle: Y

last: Ilce

first: Alaa

last: Altaie

first: Nival

last: Ali

first: Axel

last: Kunstner

first: Cyrus

last: Khandanpour

first: Hauke

last: Busch

first: Basel

last: Al-Ramadi

first: Rania

last: Harati

first: Kadria

last: Sayed

first: Ali

last: Al Fazari

first: Riyad

last: Bendardaf


title: Fate determination of msc by inflammatory niche in HO

first: Chen

last: Kan

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

overall_design: Refer to individual Series


title: Gene expression of KP4 and A549 cells regulated by matrix stiffness and ATF5

city: Sapporo

first: Hisashi

last: Haga

address: Kita-10 Nishi-8, Kita-ku

institute: Hokkaido University

summary:
Cancer tissues are stiffer than normal tissues. Carcinogenesis stiffens the extracellular matrix (ECM) of cancerous tissues, to which cancer cells respond by activating transcription factors.
We show that activating transcription factor 5 (ATF5), highly expressed in tumors, is activated by ECM stiffness and promotes the proliferation of cancer cells, including that of pancreatic cancer cells (KP4) and lung cancer cells (A549). In addition, ATF5 suppressed the expression of early growth response 1 (EGR1), thereby accelerating cancer cell proliferation. Stiff ECMs trigger the JAK-MYC pathway which activates ATF5.

overall_design: KP4 and A549 cells were cultured on stiff (collagen-coated plastic) or soft (collagen gel) matrices. These cells were also transfected with negative control (NC) RNA, siATF5-1, or siATF5-2 and cultured on stiff matrices.

first: Seiichiro

last: Ishihara


title: ATAC-seq of mouse cortex undergoing early degradation after traumatic brain injury (TBI)

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

summary: Advances in molecular diagnostics have enabled accurate disease diagnosis. However, the application of molecular biology technology in the field of forensic medicine, especially in forensic pathology, is still limited. Degraded samples with altered physicochemical properties pose challenges for molecular techniques. Identifying degradation-resistant, sensitive techniques is key for forensic molecular pathology. ATAC-seq maps open chromatin and is increasingly used in disease diagnosis and mechanism studies. Given forensic use of degraded DNA, we explored ATAC-seq's potential for analyzing degraded forensic samples. In a TBI model, ATAC-seq detected injury-induced chromatin changes after 2h degradation. We identified 1,432 TBI-associated loci with robust chromatin changes unaffected by degradation. These loci have potential as a panel of biomarkers for molecular diagnosis from degraded forensic samples.

overall_design: The mice were randomly divided into four groups: Sham_0H, Sham_2H, TBI_0H, and TBI_2H, with three mice in each group.Mice were subjected to a controlled cortical impact (CCI) procedure with craniotomy.Two hours post-operation, the mice were anesthetized and underwent transcardial perfusion with 10ml of isotonic saline. The mice were randomly divided into four groups: Sham_0H, Sham_2H, TBI_0H, and TBI_2H, with three mice in each group.Sham mice did not undergo impact, but all other procedures were the same as those for the TBI mice. Tissue collection was performed 2 hours post-mortem for the Sham_2H and TBI_2H groups, while for the Sham_0H and TBI_0H groups, tissue collection was done immediately after euthanasia.

first: Manrui

last: Li

first: Yuntian

last: Jin

first: Xiameng

last: Chen


title: Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation [CUT&Tag]

status: Public on Mar 05 2025

city: Beijing

first: Ming

last: Wang

address: #15 Datun Road, Chaoyang, Beijing 100101, China

department: Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The Piwi-interacting RNA (piRNA) pathway plays a crucial role in protecting animal germ cells by repressing transposons. However, the mechanism behind this RNA-mediated epigenetic regulation that leads to heterochromatin formation is not yet fully understood. Through RNA interference screens, we discovered Pcf11 and PNUTS, two conserved termination factors of RNA polymerase II (Pol II), as essential for piRNA-guided silencing. When Pcf11 is artificially tethered to a reporter, it leads to co-transcriptional repression and Pol II stalling, both of which are dependent on an alpha-helical region of Pcf11 capable of forming condensates when triggered by the C-terminal repeat domain (CTD) of Pol II. Interestingly, an intrinsically disordered region (IDR) derived from the Plant FCA can substitute for the alpha-helical region of Pcf11 in its silencing capacity and support animal development, demonstrating a causal relationship between phase separation and Pcf11’s function. Further exploration into how Pcf11 causes Pol II stalling revealed a direct interaction between Pcf11’s CTD-interaction domain (CID) and a CTR region of Spt5. The dephosphorylation of Spt5-CTR by PP1/PNUTS is essential for Pcf11’s recruitment during Pol II termination. It appears that the phosphorylated state of CTR inhibits Pcf11 condensate formation, while the phosphorylation of Pol II CTD at Threonine 4 enhances Pcf11’s ability to undergo phase separation. In conclusion, we propose a model in which Pcf11 regulates transcriptional termination by slowing down Pol II elongation, a process that is aided by phase separation with the unphosphorylated Spt5. The ability of Pcf11 to stall Pol II, utilized by the piRNA pathway to initiate heterochromatin formation, might represent a universal strategy for nascent RNA-mediated epigenetic control.

overall_design: To validate Pcf11’s essential role in Panx-mediated silencing, we remove the Pcf11 protein by dTAG treatment for 60 min, 120 min in mESC cell line. We then performed Pol II CUT&Tag and Pcf11-FLAG CUT&Tag.

first: Weiwei

last: Liu

first: Lijun

last: Deng

first: Xuan

last: Ouyang

first: Yang

last: Yu


title: Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation [chrRNA-Seq]

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design:
To validate Pcf11’s essential role in Panx-mediated silencing, we remove the Pcf11 protein by dTAG treatment for 15 min, 30 min, 60 min, 120 min  in mESC cell line. We then performed chrRNA for all samples.
To validate Pcf11’s essential role in Panx-mediated silencing, we remove the Pcf11 protein by IAA treatment in fruitfly . We then performed chrRNA for all samples.


title: Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation [ChIP-Seq]

overall_design:
To validate the effect of Pcf11 on Pol II transcription, we performed Pol II ChIP-seq on a reporter loci in fruitfly while tethering the Pcf11. Compare the Pol II signal for tethered and untethered samples.
To valdate the effect of Pcf11 on Pol II transcription, we performed Pol II ChIP-seq in mESC, while remove the Pcf11 protein by dTAG treatment. Compare the Pol II signal for DMSO and dTAG treatment samples.


title: Matrix stiffness modulates androgen response genes and chromatin state in prostate cancer

first: Ville

last: Paakinaho


title: Effects of fenretinide treatment on gene expression in liver from high-fat diet fed male mice.

city: Aberdeen

first: Elaina

last: Collie-Duguid

address: 23 St Machar Drive

institute: University of Aberdeen

summary: To investigate the effects of long-term high-fat diet (HFD)-feeding and short and long-term fenretinide treatment on mouse liver gene expression.

overall_design: We performed gene expression analysis in liver tissue taken from four groups, mice fed HFD +/- 0.04% Fenretinide for 7 days or 20 weeks.

first: Nimesh

last: Mody

first: Nicola

last: Morrice

first: Shehroz

last: Mahmood

first: George

last: Mcilroy

first: Mirela

last: Delibegovic

first: Dawn

last: Thompson

first: Peter

last: McCaffery


title: Fate determination of msc by inflammatory niche in HO [spatial transcriptomics]

first: Chen

last: Kan

first: Haitao

last: Fan

first: Jiazhao

last: Yang

first: Hong

last: Zheng


title: Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read and single-molecule resolution [Nanopore]

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Faithful epigenetic inheritance across cell divisions is essential to maintaining cell identity and involves numerous epigenetic modifications, whose roles in coordinating chromatin architecture are less understood. Technological approaches to temporally order epigenetic modifications throughout the cell cycle often face limitations in sequence resolution and rely on potentially damaging mitotic labeling or conversion steps. Herein, we present Methylation Pseudotime Analysis Through read-level Heterogeneity (MPATH), a label- and conversion-free method to infer post-replication DNA strand maturity from methylation patterns across single molecules. We use MPATH to temporally order hydroxymethylation throughout mitotic inheritance revealing, for the first time, that CpGs within cis-regulatory elements undergo transitions between methylation states at sub-cell-cycle timescales. When applied to long reads generated by NOMe-seq, MPATH uncovered relationships between nucleosome occupancy and DNA maturity. Finally, extension of MPATH to phased reads reveals allele-specific trends in pseudotime distribution associated with X chromosome inactivation. Our findings suggest that when coupled with multimodal sequencing strategies, MPATH could provide valuable insights into chromatin restoration dynamics.

overall_design:
HUES64 hESCs were subjected to several different experimental conditions prior to DNA extraction for long-read sequencing. In the first experiment, hESCs were treated with 2µg/ml nocodazole for 16h. BrdU pulse-chase experiments were conducted on HUES64 hESCs to investigate DNA methylation patterns during chromatin maturation. For the pulse optimization, cells were subjected to 50 µM BrdU for durations of 10 minutes, 20 minutes, 30 minutes, and 1 hour, followed by genomic DNA collection at 0h (nascent chromatin) and 16h (mature chromatin). Mock controls were included for both 0h and 16h timepoints. Optimized labeling conditions included a 500 µM BrdU pulse (10 minute duration) with 0h and 16h chase points. Unlabeled HUES64 samples were also generated (sequenced to a total of 62x coverage across 2 technical replicates). All long-read data was acquired using ONT sequencing platforms. In a separate sequencing experiment, hESCs were subjected to Repli-ATAC sequencing in order to temporally profile chromatin accessibility across replication-associated timescales.
>>>Raw data in POD5 or FAST5 will be available upon request by the submitter.<<<

first: Navied

last: Akhtar

first: Kwadwo

last: Bonsu

first: Nandor

last: Laszik

first: Asia

last: Mendelevich

first: Tanye

last: Wen

first: Julien

last: P Morival

first: Katelyn

last: Diune

first: Mitchell

last: Frazeur

first: Justin

last: Vega

first: Alexander

last: Gimelbrant

first: Elizabeth

last: Read

first: Timothy

last: Downing


title: Interleukin-4 Antagonizes Inflammation and Aging Caused Hematopoiesis Dysregulation

city: Boston

first: Jingfei

last: Yao

state: Massachusetts

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: IL-4, not only drives Th2 cell differentiation and reprogram macrophages toward an anti-inflammatory state but also plays crucial roles in aging and immunotherapy. However, the role of IL-4-STAT6 signaling in hematopoietic stem and progenitor cells (HSPCs) are less studied. So we sequenced mRNA from IL-4-treated or STAT6-KO HSPCs, LT-HSCs and MPPs, to address the roles of IL-4-STAT6 signaling in hematopoiesis.

overall_design: Gene expression profiling analysis of RNA-seq data from HSCs/MPPs which isolated from different mice. For saline/IL-4c treatment, mice were injected with saline or 2.5µg/kg IL-4c(IL-4 and anti-IL-4 antibody complex) for 24 hours. For aged mice, 18-month-old mice were injected with saline or 2.5µg/kg IL-4c(IL-4 and anti-IL-4 antibody complex) for 24 hours.


title: Microarray Expression Analysis of Circular RNAs in Pancreatic Ductal Adenocarcinoma

city: Guangzhou

first: Fang

last: Zhou

address: No. 106 Zhongshan Second Road

institute: Guangdong Provincial People's Hospital

summary: To investigate the expression profile of circular RNAs (circRNAs) in pancreatic ductal adenocarcinoma(PDAC) and to provide more reliable biomarkers and new potential diagnostic and therapeutic targets for PDAC. The circRNA expression levels were measured in 3 paracancerous tissues and 3 PDAC tissues using Arraystar Human CircRNA Array Analysis. We identified significantly different expression of circRNAs between the two groups and showed distinguishable circRNAs expression patterns in the samples. The levels and patterns of circRNA expression were significantly different between paracancerous tissue and PDAC tissue. This study evaluated circRNAs expression profiles and their ability to serve as reliable biomarkers and new potential diagnostic and therapeutic targets for PDAC.

overall_design: To investigate the exact mechanism of circRNAs in PDAC, total RNA was extracted from PDAC tissue and paired normal adjacent tissues, and next-generation sequencing was performed to explore the expression profile differences between PDAC tissue and paired normal adjacent groups. The results come from three independent experiments.

first: Rufu

last: Chen


title: Dexamethasone drives macrophage repolarization linked to increased triple-negative breast cancer aggressiveness

city: Solna

first: Ivan

last: Nalvarte

address: Visionsgatan 4, J9:20

department: NVS

country: Sweden

institute: Karolinska Institute

summary: Glucocorticoids (GCs) are known for their anti-inflammatory potential, which includes macrophage polarization into an anti-inflammatory and tissue remodeling state. GCs are routinely co-administered to cancer patients to alleviate the side effects of chemotherapy. However, it is not well known if GCs can modulate tumor-associated macrophages (TAMs) to promote tumor progression. Here, we show that dexamethasone (DEX) induces dose-dependent differentiation of THP-1 monocyte-derived anti-tumorigenic (M1) macrophages into pro-tumorigenic (M2-like) macrophages, even in the presence of M1 cues, and that DEX can repolarize fully differentiated M1 macrophages into an M2-like state. These macrophages have a cytokine profile similar to the pro-tumorigenic (M2) macrophages and can stimulate the proliferation and invasion of triple-negative breast cancer (TNBC) cells in vitro. DEX treatment of an orthotopic mouse model of TNBC attenuated paclitaxel-mediated tumor growth inhibition, increased M2-like TAMs in primary tumors, and enhanced lung metastasis. Transcriptomic analysis of DEX-treated M1 macrophages revealed not only transcriptomic overlap to M2 macrophages, but to human breast cancer TAM transcriptomic data and further to a specific TAM signature associated with aggressive estrogen receptor-negative breast cancer. Our study illustrates a remarkable macrophage repolarization plasticity upon DEX exposure and warrants care in prescribing high doses of GCs to breast cancer patients, especially to those considered for chemotherapy.

first: Mohamed

last: Shamekh

first: Birgitta

last: Lindqvist


title: Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read and single-molecule resolution [ATAC-seq]

first: Annie

last: Trinh

overall_design: HUES64 hESCs were subjected to several different experimental conditions prior to DNA extraction for long-read sequencing. In the first experiment, hESCs were treated with 2µg/ml nocodazole for 16h. BrdU pulse-chase experiments were conducted on HUES64 hESCs to investigate DNA methylation patterns during chromatin maturation. For the pulse optimization, cells were subjected to 50 µM BrdU for durations of 10 minutes, 20 minutes, 30 minutes, and 1 hour, followed by genomic DNA collection at 0h (nascent chromatin) and 16h (mature chromatin). Mock controls were included for both 0h and 16h timepoints. Optimized labeling conditions included a 500 µM BrdU pulse (10 minute duration) with 0h and 16h chase points. Unlabeled HUES64 samples were also generated (sequenced to a total of 62x coverage across 2 technical replicates). All long-read data was acquired using ONT sequencing platforms. In a separate sequencing experiment, hESCs were subjected to Repli-ATAC sequencing in order to temporally profile chromatin accessibility across replication-associated timescales.

first: Navied

last: Akhtar

first: Kwadwo

last: Bonsu


title: IFNλ1 is a STING-dependent mediator of DNA damage and induces Immune activation in lung cancer

city: Aarhus C

first: martin

last: Jakobsen

address: Høegh-Guldbergs Gade 10, Bygn. 1115

department: Biomedicine

country: Denmark

institute: Aarhus University

summary: Introduction: The importance of the cGAS-STING pathway and type I interferon (IFN) in anti-tumor immunity has been widely studied. However, there is limited knowledge about the role of type III IFNs in cancer settings. Type III IFNs, comprising IFNλ1-4, are opposite to type I IFN only expressed by a few cell types, including epithelial cells, and the receptor subunit IFNLR1, is equally only expressed on limited types of cells. Methods: Gene and protein expression of the cGAS-STING signaling pathway was characterized in a series of non-small cell lung cancer (NSCLC) cell lines. Herring-testis DNA stimulation and chemotherapy drugs (doxorubicin and cisplatin) were used to activate the cGAS-STING pathway, and the level of activation was determined by measuring changes in the transcriptomic profile as well as type I and III IFNs by ELISA. Re-expression of IFNLR1 on cancer cell lines was achieved using CRISPR activation (CRISPRa) followed by evaluating chemotherapy-induced apoptosis using flow cytometry assays. Results: STING was not broadly expressed across the NSCLC cell lines. Those cancer cell lines expressing all relevant factors supporting the cGAS-STING pathway secreted IFNλ following STING activation whereas only few of them expressed IFNβ. Treatment with chemotherapy drugs likewise preferentially induced IFNλ, which was abrogated in CRISPR-Cas9 STING knock-out cells. Expression of IFNLR1 was found downregulated in the cancer cell lines compared to the benign epithelial cell line Nuli-1. Rescuing IFNLR1 expression by CRISPRa in multiple cancer cell lines sensitization them to IFNλ-stimulation and resulted in significant reduction in cell viability. Conclusion: Downregulation of IFNLR1 can be an immune evasion mechanism developed by cancer cells to avoid responding to endogenous type III IFNs. Thus, rescuing IFNLR1 expression in NSCLC in conjunction to chemotherapy may potentially be harnessed to elevate the anti-tumoral responses.

overall_design: Cells were seated and allowed to adhere one day pror to a transfection with Herring testis DNA (2μg/mL). An untreated ctr was included for each cell lines. After six hours of stimulation, cells were washed with PBS, lyzed and RNA was purified and sequenced.

first: Stine

last: Godsk

first: Caroline

last: Jensen

first: Trine

middle: V

last: Larsen

first: Johanne

last: Ahrenfeldt

first: Kristine

last: Gammelgaard

first: Martin


title: Transcriptome analysies reveals the role of OsCBM1 in rice defense against Xanthomonas oryzae pv.oryzae

city: 长沙

first: 别帅骏

last: 别

state: 长沙

address: 芙蓉区远大二路892号

department: 实验大楼

institute: 湖南省农业科学院

summary: Carbohydrate-binding malectin/malectin-like domain-containing proteins (CBMs) represent a newly discovered subfamily of lectins that are involved in a range of bio-logical processes across the animal, bacterial, and plant kingdoms. The OsCBM1 gene in rice enhances reactive oxygen species (ROS) burst, in response contributing to drought-stress tolerance. Nonetheless, the functions of OsCBM1 response to biotic stress remain poorly understood. In this study, we found that OsCBM1 was induced by the infection of Xoo and overexpression of OsCBM1 enhances rice resistance to the bacterial blight, while suppression of its expression shows the opposite trend. OsCBM1 may influence resistance to bacterial blight by regulating ROS burst and the SA sig-naling pathway through RNA-seq analysis. Overexpression of OsCBM1 increased SA content and enhanced activities of SOD, POD, and CAT enzymes, whereas knockdown of OsCBM1 exhibited the opposite trend. The expression of genes related to the SA and enzyme activity pathways was validated through qPCR. These results further eluci-date the function of OsCBM1 in biotic stress resistance, providing references for dis-ease-resistant rice breeding.

overall_design: Observing the resistance of WT, OsCBM1-OE, OsCBM1-RNAi  to Xoo,  and analyze the relevant transcriptome data.

first: Shuaijun

last: Bie

first: Youlun

last: Xiao

first: Xiaomin

last: He

first: Renyan

last: Huang


title: Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation [PRO-Seq]

first: Ming

last: Wang

overall_design: To validate Pcf11’s essential role in Panx-mediated silencing, we remove the Pcf11 protein by dTAG treatment for 60 min in mESC cell line. And tethering Pcf11 on reporter loci in fruitfly. We then performed PRO-seq experiment.

first: Weiwei

last: Liu

first: Lijun

last: Deng

first: Xuan

last: Ouyang

first: Yang

last: Yu


title: Construction of a miRNA panel as possible biomarker for separation of glioblastoma and brain metastasis patients with adenocarcinoma origin using next-generation sequencing

city: Debrecen

first: Zsuzsanna

last: Birkó

address: Egyetem tér 1.

department: Humangenetics

country: Hungary

institute: University of Debrecen

summary: Next Generation Sequencing technique was performed to compare the miRNA expression pattern of tumor  brain tissue sample of 6 Glioblastoma patients, and 6 patients with brain metastases (BM) originated from lung adenocarcinoma (LUAD).  In order to analyse the difference on miRNA expresion level between GBM and LUAD-BM cases, we applied cluster analysis on the NGS dataset of 6 samples for each of the two goups  with iDEP 1.1 software. Log2FC values were calculated to determine the exact level of up- and downregulation in case of the deregulated miRNAs, using the iDEP 1.1 web tool applying the DESeq2 algorithm. Evaluate the results of analysis 99 known miRNAs were detected with altered expression using a threshold of false discovery rate (FDR) <0.05 and fold-change> 2. Among them, 62 miRNAs were upregulated (log2FC > 2) and 37 miRNAs were downregulated (log2FC < -2) with biological revelance in tissue LUAD-BM samples compared with the GBM samples. To validate our results obtained by NGS, four upregulated miRNAs: hsa-miR-200c-5p, hsa-miR-141-5p, hsa-miR-200a-5p, hsa-miR-375-3p  and two downregulated miRNAs: hsa-miR-410-3p, hsa-miR-9-5p were chosen for RT-qPCR analysis. As the result of that  hsa-miR-200c-5p, hsa-miR-141-5p, hsa-miR-200a-5p, hsa-miR-375-3p was significantly upregulated, while hsa-miR-410-3p, hsa-miR-9-5p was significantly downregulated in LUAD-BM - GBM comparison.

overall_design: Tissue samples were gathered from brain tumor region of six individuals diagnosed with GBM, and from brain tumor region of six patients with LUAD-BM. All samples in both group were confirmed histopathologically. These intraoperative quick-frozen tissue samples were stored at -80⁰C until further processing. Total RNA was isolated from  the tissue samples of GBM and LUAD-BM as well. Global transcriptomic profile was studied by RNA-sequencing applying the Illumina NextSeq500 platform including microRNA sequencing. In the case of all samples 3 replicates were included. In order to identify up-, or down-regulated microRNAs the LUAD-BM samples were compared to GBM samples..

first: Bernadett

last: Torner

first: Dóra

last: Géczi

first: Álmos

last: Klekner

first: István

last: Balogh

first: András

last: Penyige


title: Rat VTA single nuclei RNA sequencing

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

country: USA

institute: University of Pennsylvania

summary: We performed single nuclei transcriptomics of ventral tegmental area samples from rats sacrificed one hour after a single saline injection and profiled the cell types and their receptor composition.

overall_design: Fresh frozen postmortem rat ventral tegmental area samples were used to generate single nuclei suspensions and the nuclei were processed for the 10x Genomics 3' gene expression assay v3.1.

middle: C

first: Richard

last: Crist


title: IL-15 complex enhances agonistic anti-CD40 + anti-PDL1 by correcting the T-bet to Tox ratio in CD8+ T cells infiltrating pancreatic ductal adenocarcinoma

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

summary: Single cell RNA sequencing paired with single cell V(D)J sequenction of immune cells infiltrating orthotopic KPC2a tumors, spleen cells, and CD8 T cells enriched from spleen cells on day 14 posttumor. Cohorts received no treatment, agonistic anti-CD40, anti-PD-L1 or the combination of agonistic anti-CD40 + anti-PDL1. Treatments were initated on day 7 posttumor.

overall_design: Mice with orthotopic KPC2a tumors were left untreated (control) or treated with anti-PDL1 and/or agonistic anti-CD40 according to detailed methods in manuscript. On day 14 post tumor implantation, immune cells were were isolated and samples were pooled by treatment group. Spleen and tumor single cell suspensions were prepared. Immune cells were enriched from the tumor single cell suspensions using a 44/67% percoll density gradient. Briefly, samples were resuspended in 3 mL of 44% percoll in a 15 mL conical tube and then underlaid with 3 mL of 67% percoll using a glass Pasteur pipette. Samples were centrifuged for 20 minutes at 600 x g at 22°C with an acceleration of 1 and brake of 0. After spinning, cells at the density interface were isolated with a P100 pipette and transferred to 20 mL of complete media for washing. CD8 T cells were isolated from half of the spleen mononuclear cell suspension using a CD8a negative selection magnetic cell separation kit (Miltenyi). For each tissue (intratumoral cells, enriched CD8 T cells from spleen, and bulk unenriched mononuclear cells from spleen), samples from individual treatment groups (control, aPDL1, aCD40, aPDL1+aCD40) were stained with unique hashtags (TotalSeq C, Biolegend) at a concentration of 0.2 mg per 1 x 106 cells. Next, samples were pooled by tissue containing the 4 treatment groups for proceeding with 3 independent captures. Cells were submitted to University of Minnesota Genomics Core for single cell 10X Chromium 5’ GEX and TCR capture targeting 40,000 cells per sample and NovaSeq 2 x 150 S4 sequencing targeting 35,000 reads per cell for GEX and 25,000 reads per cell for V(D)J sequencing.

middle: M


title: Reduction of intestinal RIPK1 ameliorates HFD-induced metabolic disorders in female mice

first: ye

last: yuan

address: YiHeyuan road 5th

country: China

institute: Peking University

summary: Background Metabolic disorders including obesity, impaired glucose tolerance, dyslipidemia, and insulin resistance constitute a global public health problem that increases the risk of cardiovascular and type 2 diabetes. In modern society, a major cause of metabolic disorder is excessive nutrient intake from food. Therefore, as the main site of nutrient absorption, the intestine plays an important role in diet-induced metabolic disorders.  However, it is still largely unknown on how the intestine participates in such a process.  Results Here we show that ‘ileal jejunization’ is responsible for high-fat diet-induced metabolic disorders in female mice. Upon HFD-feeding, the transcriptional profile of the ileum was shifted towards that of jejunum which is characterized by increased expression of jejunal feature genes. Accordantly, the lipids uptake was increased in the ileum. Importantly, the HFD-induced ileal jejunization and metabolic disorders can be profoundly attenuated by intestinal-specific reduction of RIPK1. Interestingly, the HFD-induced increase in the expression of the jejunal feature genes in the ileum, and the effect of RIPK1 reduction were not observed in male mice.

overall_design: We generated receptor-interacting protein kinase 1 (Ripk1) intestine-specific heterozygous knockout mice (Ripk1IEC+/-) and analyzed the phenotypes and the transcriptional profile of Ripk1IEC+/- mice and their wild type (WT) littermates under normal chow diet (ND) and high-fat diet (HFD).

first: Ye

last: Yuan

last: Hu

first: Chunguang

last: Guo

first: Yihua

last: Xu

first: Shihan

last: Li

first: Wei

last: Wen

first: Xinli

first: Fanxin

last: Zeng

first: Weiyi

last: Cui

first: Wenli

last: Chen

first: Xueting

last: Sun

first: Ning

last: Hou

first: Jue

first: Rui-Ping

last: Xiao

first: Xiuqin

last: Zhang


title: Sex Differences in Epigenetic Ageing for Older People Living with HIV

city: New York

first: Michael

last: Corley

state: NY

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

type: Methylation profiling by genome tiling array

summary:
Genome-wide DNA methylation profiling of  blood samples from people living with HIV
HIV-1 infection impacts biological ageing, and epigenetic clocks highlight epigenetic age acceleration in people with HIV. Despite evidence indicating sex differences in clinical, immunological, and virological measures, females have been underrepresented in most HIV epigenetic studies. Hence, we generated a more representative epigenetic dataset to examine sex differences in epigenetic ageing and relationships to clinical phenotypes.

overall_design: Bisulfite converted DNA from whole blood were hybridized to the Illumina MethylationEPIC Beadchip

middle: J


title: Interleukin-37 promotes wound healing in diabetic mice by inhibiting the MAPK/NLRP3 pathway

city: Shanghai

first: xiaoming

last: zhu

state: --- Select One ---

address: 12 wulumuqi road,shanghai

department: Department of Endocrinology and Metabolism,

institute: Huashan Hospital,Fudan University

summary: Diabetic foot ulcer (DFU) is a common complication of diabetes characterized by increased inflammation and a slowed healing process for wounds. Interleukin-37 (IL-37) may act as an alarm to alert the immune system when released by epithelial barrier tissues during trauma or infection, exerting a broad range of protective effects in several diseases. The objective of this study was to examine the regenerative capabilities of IL-37 in improving the healing of diabetic wounds. Using streptozotocin (STZ)-induced diabetic mice, we found that diabetic IL-37Tg mice showed a significantly accelerated healing process. In addition, IL-37 strongly suppressed MAPK signaling pathway by inhibiting phosphorylation of the P38 and ERK. Moreover, IL-37 reduced the expression of Nod-like receptor protein-3 (NLRP3) and mature IL-1β. These results thus indicated that IL-37 inhibition of IL-1β production is mediated by suppressing the initial priming step and by inhibiting the NLRP3 inflammasome activation. Taken together, our findings demonstrated the promising regulatory activity of IL-37 against IL-1β production and indicated that IL-37 has the potential to be effective as a novel therapeutic agent for treatment of wound. Our data indicate a beneficial effect of IL-37 in diabetic wounds, suggesting a therapeutic potential for this cytokine in diabetic ulcer management.

first: Xiaoming

last: Zhu

first: Qiaoli


title: Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read and single-molecule resolution

first: Annie

last: Trinh

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

overall_design: Refer to individual Series


title: Alloferon and IL-22 receptor expression regulation on the pathogenesis of imiquimod-induced psoriasis

city: seoul

first: Tomoyo

last: AGURA

address: 103, Daehak-ro, Jongno-gu, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University College of Medicine

summary:
We investigated the regulatory role of alloferon in the development of psoriasis in an imiquimod (IMQ)-induced psoriasis model through the regulation of IL-22Rα expression.
Psoriasis is an immune-mediated inflammatory skin disease. IL-22, a proinflammatory cytokine, is implicated in psoriasis pathogenesis; however, there is currently no established biological treatment targeting IL-22 or its receptor, IL-22Rα. Alloferon is a short peptide that has an anti inflammatory effect on skin disorders; however, little is known about its anti-inflammatory activity in psoriasis. This study demonstrate that alloferon could be an effective potential drug for the treatment of psoriasis by interrupting IL-22 signaling and factors related to skin inflammation.

overall_design: Male B6 wild-type (WT) mice and IL-22Rα knock-out (KO) mice (n=4 per group) were used to compare the effects of IMQ-induced psoriasis-like inflammation. IMQ cream (83.3 mg, 5%) was applied daily to the dorsal skin and ears of both groups from day 1 to day 7, with treatment mice receiving either vehicle cream or alloferon cream 6 hours after IMQ application. Total RNA was extracted from the dorsal skin of WT and KO mice for comparative transcriptomic analysis.

last: Agura

first: Hyejung

last: Jo

first: Jae Seung

last: Kang

first: Yejin

last: Kim


title: Bulk RNA-seq of HFF cell senescence model induced by oncogene activation

first: Peng

last: Yu

state: Shanghai

address: 2205 Songhu Road, Yangpu District,Shanghai, China

institute: Fudan University

summary: To investiage the mechanism of cellular senescence, we established a model of oncogene RAS-induced cellular senescence in human foreskin fibroblasts (HFF cells). We transduced an  estrogen receptor fused to the H-RASG12V protein (ER:RAS) in HFF, which can be induced by 4-hydroxytamoxifen (4-OHT).

overall_design: Lentiviral packaging of the oncogene-inducible expression vector (pLNC ER:RAS (G12V)) was conducted using HEK293T cells. The collected viral supernatant was then introduced into younger (~P18) HFF cells. Following infection, resistant clones were selected using 200 μg/ml of neomycin at 48-72 hours post-infection. After five days, stable transgenic cell lines were obtained. To activate the expression of H-RAS (G12V), 100 nM of 4-hydroxytamoxifen (4-OHT) was added, and cells exhibiting oncogene-induced senescence (OIS) were harvested one week thereafter.


title: Raver1 links Ripk1 RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance

city: WORCESTER

first: Egil

last: Lien

state: MA

address: 364 plantation st

institute: University of Massachusetts Chan Medical School

summary: Multiple cell death and inflammatory signaling pathways converge on two critical factors: receptor interacting serine/threonine kinase 1 (RIPK1) and caspase-8. Careful regulation of these molecules is critical to control apoptosis, pyroptosis and inflammation. Here we discovered a pivotal role of Raver1 as an essential regulator of Ripk1 pre-mRNA splicing, expression, and functionality, and the subsequent caspase-8-dependent inflammatory cell death. Macrophages from Raver1-deficient mice exhibit altered splicing of Ripk1, accompanied by diminished cell death and reduced activation of caspase-8, Gasdermin D and E, caspase-1, as well as decreased interleukin-18 (IL-18) and IL-1ß production. These effects were triggered by Yersinia bacteria, or by restraining TAK1 or IKKβ in the presence of LPS, TNF family members, or IFNγ. Consequently, animals lacking Raver1 showed heightened susceptibility to Yersinia infection. Raver1 and RIPK1 also controlled the expression and function of the C-type lectin receptor Mincle. Our study underscores the critical regulatory role of Raver1 in modulating innate immune responses and highlights its significance in directing in vivo and in vitro inflammatory processes.

overall_design: To investigate the function of Raver1 in the regulation of cell death and inflammation, we established RNA-seq samples from WT and Raver1-/-  bone marrow-derived macrophages (BMDMs), each from 3 different mice as biological triplicates. Cells were either untreated (NT), TNF or TNF+TAK1-i treated for 1 hour. We then performed differential gene expression profiling and splicing analysis on RNAseq data comparing WT to Raver1-/- cells.

first: Pontus

last: Orning

first: Boyao

first: Athma

last: Pai

first: Jesse

last: Lehman