title: Somatic mutations and DNA methylation identify a subgroup of poor prognosis within lower risk myelodysplastic syndromes [RNAseq]

city: Paris

first: David

last: Rombaut

address: 22 rue Méchain

institute: Institut Cochin

summary: Lower-risk (LR) myelodysplastic syndromes (MDS) are heterogeneous hematopoietic stem and progenitor disorders caused by early accumulation of somatic mutations in epigenetic factors and non-epigenetic factors that may produce convergent DNA methylation patterns driving specific gene expression profiles. The integration of genomic, epigenomic and transcriptomic profiling has the potential to spotlight distinct LR-MDS categories on the basis of pathophysiological mechanisms.

overall_design: Transcriptome profiling of 185 BM MNC RNA low-risk MDS patients, including 30 with rapid progression to leukemia, and 7 age-matched healthy controls.

first: Sarah

last: Sandmann

first: Tobias

last: Tekath

first: Simon

last: Crouch

first: Aniek

last: de Graaf

first: Olivier

last: Kosmider

first: Magnus

last: Tobiasson

first: Andreas

last: Lennartsson

first: Bert

last: van der Reijden

first: Sophie

last: Park

first: Maud

last: D'Aveni

first: Borhane

last: Slama

first: Emmanuelle

last: Clappier

first: Pierre

last: Fenaux

first: Lionel

last: Adès

first: Arjan

last: Van de Loosdrecht

first: Saskia

last: M.C. Langemeijer

first: Argiris

last: Symeonidis

first: Jaroslav

last: Čermák

first: Claude

last: Preudhomme

first: Aleksandar

last: Savic

first: Ulrich

last: Germing

first: Reinhard

last: Stauder

last: Bowen

first: Corine

last: van Marrewijk

first: Elsa

last: Bernard

first: Alexandra

last: Smith

last: Painter

first: Theo

last: de Witte

first: Julian

last: Varghese

first: Eva

last: Hellström-Lindberg

first: Martin

last: Dugas

first: Joost

last: Martens

first: Luca

last: Malcovati

first: Joop

last: Jansen

first: Michaela

last: Fontenay


title: parthenogenetic blastoids derived from human parthenogenetic embryonic stem cells

status: Public on Jan 29 2025

city: beijing

first: yuxin

last: luo

address: NO.49 Huanyuanbei Road Haidian District

country: China

institute: Peking University Third Hospital

type: Expression profiling by high throughput sequencing

summary: Parthenogenetic embryos derive their genomes entirely from maternal genome, and lack paternal imprint patterns. Many achievements have been made in the study of genomic imprinting using parthenogenetic embryonic stem cells (hPES cells). However, due to the developmental defects and ethical limits, the comprehensive understanding of parthenogenetic embryo development is still lacking. Here, we induced naive hPES cells into parthenogenic blastoids using a published two-step 3D induction protocol. Morphological and molecular analysis showed that parthenogenetic blastoids contain crucial cell lineages similar to natural human blastocysts.

overall_design: To exaimine the similarity and difference between human parthenogenetic-blastoids and bi-parental blastoids (control)


title: Annexin A8 deficiency delayed atherosclerosis progression

city: Madrid

first: Pablo

last: Minguez

state: Madrid

address: Av. Reyes Catolicos 2

department: Genetics and Genomics

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz (IIS-FJD), UAM

summary: Background Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipids and leukocytes within the arterial wall. By investigating the aortic transcriptome of atherosclerosis prone apolipoprotein E (ApoE-/-) mice, we aimed to identify new players in the development and progression of atherosclerosis. Methods RNA-Seq from aorta ApoE-/- mice was compared to healthy aorta. AnxA8 expression was assessed in human and mice atherosclerotic tissue and healthy aorta. ApoE-/- mice lacking systemic AnxA8 (ApoE-/-AnxA8-/-) were generated to assess the functional role of AnxA8. Bone marrow transplantation (BMT) was also done to generate ApoE-/- lacking AnxA8 specifically in bone marrow-derived cells. Intravital microscopy was used to analyze platelets and leukocyte adhesion in atheroprone mice. The role of AnxA8 was analyzed in cultured endothelial cells. Results RNA-Seq unveiled AnxA8 as one of the most significantly up-regulated genes in atherosclerotic aorta of ApoE-/- mice compared with wild type. Moreover, AnxA8 was also upregulated in human atherosclerotic plaques. Germline deletion of AnxA8 decreased atherosclerotic burden and atherosclerotic plaques size and volume in the aortic root. Plaques of ApoE-/-AnxA8-/- were characterized by a less lipid and inflammatory content compared with those in ApoE-/-AnxA8+/+. BMT showed that hematopoietic AnxA8 deficiency had no effect on atherosclerotic development. Oxidized-LDL (ox-LDL) increased AnxA8 mRNA and protein expression in murine aortic endothelial cells (MAECs). Subsequent in vitro experiments revealed that AnxA8 deficiency in MAECs suppressed P/E-selectin and CD31 expression and secretion induced by ox-LDL with a concomitant reduction in platelets and leukocyte adhesion. Intravital microscopy confirmed the decrease in leukocyte rolling and adhesion, and platelets adhesion, in ApoE-/-AnxA8-/- mice.  Conclusion Our findings demonstrate that AnxA8 deficiency decreases atherosclerosis progression through regulating leukocyte infiltration and vascular inflammation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from aortas of wild type or ApoE knockout mice

first: Luis

middle: M

last: Blanco-Colio


title: Gene-specific reactivation of X-linked genes upon Xist loss is linked to the chromatin states in extraembryonic endoderm and epiblast stem cells

status: Public on Jan 28 2025

city: Bangalore

first: SRIMONTA

last: GAYEN

state: Karnataka

address: GE14, new biological science building, Indian institute of Science

department: Department of Developmental biology and Genetics

country: India

institute: Indian Institute of Science, Bangalore, India

summary: In this study, we have explored the role of Xist and DNA methylation in the maintenance of X-linked gene silencing in extraembryonic endoderm and epiblast stem cells. We show that only a subset of genes are dependent on Xist and DNA methylation to maintain their inactive state. Moreover, we show that the reactivation potential of X-linked genes upon loss of Xist is connected to the epigenomic states.

overall_design: We performed RNA-seq in WT vs Xist knock out  XEN and EpiSC  to investigated the effect of loss of Xist upstream deletion in XEN cells.  We also performed RNA-seq in Azacytidine treated XEN cells.

first: Maniteja

last: Arava

first: Sudeshna

last: Majumdar

first: Lakshmi

last: Sowjanya Bammidi

first: Hemant

last: Chandru Naik

first: Runumi

last: Baro

first: Srimonta

last: Gayen


title: Effects of MRSA and FTY720 S-phosphonate on H3K9 acetylation in human lung endothelial cells

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Methicillin-resistant Staph. Aureus (MRSA) is a common cause of severe pneumonia and sepsis that can lead to Acute Respiratory Distress Syndrome (ARDS). MRSA causes lung endothelial cell (EC) dysfunction, a critical step in the pathogenesis and progression of lung injury. Our previous studies have demonstrated that FTY720 S-phosphonate (Tysiponate, Tys), an analog of sphingosine-1-phosphate, ameliorates MRSA-induced lung EC activation and barrier disruption (PMID: 35015568). To advance our mechanistic understanding of MRSA and Tys effects on lung EC, we investigated associated epigenetic changes. Specifically, we studied histone lysine acetylation, which is a central epigenetic alteration that has been linked to gene transcription and functional regulation of endothelial responses to inflammatory stimuli. We therefore  determined the effects of MRSA exposure in the presence or absence of Tys on lung EC acetylation at the 9th lysine residue of the histone H3 protein (H3K9ac), which is an important chromatin modification associated with active promoters and gene activation. ChIP-seq analysis was employed to perform an unbiased genome-wide profiling of H3K9ac epigenetic patterns in human lung EC. This analysis identified multiple genes that are differentially targeted by acetylation when EC are exposed to MRSA±Tys.

overall_design: Chromatin immunoprecipitation sequencing (Chip-Seq) for histone modification H3K9 acetylation in human pulmonary artery endothelial cells treated with heat-killed methicillin resistant Staph Aureus (HK-MRSA), Tysiponate (FTY720 S-phosphonate; S1P analogue),or  HK-MRSA +Tys for 30 min. Cells treated only with vehicle were used as control.

first: Alison

middle: W

last: Ha

first: Lucille

middle: N

last: Meliton

first: Lichun

last: Wang

first: Eleftheria

last: Letsiou

first: Steven

last: Dudek


title: Molecular mechanism of MLF1 in AC16 cell line

city: Shenzhen

first: Zhihua

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

summary: Previous studies found that MLF1 mRNA levels tended to decline in aging hearts. Functional studies found that knockdown of MLF1 ameliorated the drug-induced cellular senescence phenotype. Here, we apply transcriptomics to explore the underlying molecular mechanisms.

overall_design: Cardiomyocyte AC16 cells were cultured in DMEM/F12 and DMEM (high glucose), respectively. DMEM supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 100 U/mL penicillin, and 100 μg/ml streptomycin. Medium without FBS was replaced before transfection. Negative control siRNA and Mlf1 siRNA were transfected into AC16 cells at ~70% confluence using jetPRIME® (Polyplus-transfection, NY, USA). After 12 h of transfection, fresh complete medium was replaced.  RNA  extracted according to the manufacturer's instructions using Trizol reagent. RNA libraries were prepared for sequencing according to manufacturer's instructions of Beijing Genomics Institution (BGI)

first: Jian

last: Lv

first: Ningning

last: Guo

first: Yu

last: Fang

first: Zhenyi

last: Zhao

first: Sai

last: Zeng

first: Qiuxiao

first: Lili

last: Li

first: Zhaoyang

last: Chen


title: Transcriptome Profiling of Heart Ageing Reveals Distinct Pathological Gene Network

summary: Age-related changes in cardiac homeostasis lead to myocardial dysfunction and cardiovascular diseases, which predict the healthspan of ageing. Age is a prominent risk factor for cardiac-related diseases. During ageing, the heart undergoes structural remodeling (increased cardiac weight and myocardial fibrosis) and functional decline (reduced diastolic and systolic functions), causing vulnerability of the heart to extra stress. Consequently, these pathological changes lead to increased cardiovascular mortality and morbidity in elderly adults. The underlying mechanism of cardiac ageing remains largely unexplored; and no pharmacological agent is currently available to improve or delay cardiac senescence.

overall_design:
Male mice of ages 2-months and 22-months old were raised in a stable environment (room temperature, 24 ± 3 °C; room humidity, 55 ± 5%) with a 12-h light/12-h dark cycle, and were fed normal chow. The mice were anaesthetized with inhalational anaesthetic and euthanized by cervical dislocation. Hearts were immediately dissected and stored at -80°C. Three independent biological replicate samples from Young or Old group were used for RNA extraction. RNA-seq was completed by Novogene.
Please note that raw data has been lost and thus is not provided.


title: Targeting non-junctional Claudin-1 with monoclonal antibodies to treat hepatocellular carcinoma

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

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

overall_design: Refer to individual Series


title: Targeting non-junctional Claudin-1 with monoclonal antibodies to treat hepatocellular carcinoma [scRNA-seq]

summary: Abstract: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. Despite new treatment approvals, treatment response and prognosis of patients with advanced HCC remains poor. Claudin-1 (CLDN1) is a membrane protein expressed in tight junctions but also non-junctionally at the basolateral membrane of hepatocytes. While the function of CLDN1 within tight junctions is well characterized, the role of non-junctional (NJ) CLDN1 in HCC remains unexplored. Here we show that targeting NJ-CLDN1 with a humanized monoclonal antibody (mAb) suppresses tumor growth in different pre-clinical models. Mechanistic studies including single cell RNA sequencing of multicellular patient tumorspheres suggest that non-junctional CLDN1 regulates tumor stemness, metabolism and oncogenic signaling with impact on the tumor immune microenvironment. Our results provide the rationale for targeting NJ-CLDN1 in HCC and pave the way to novel therapeutic interventions with NJ-CLDN1 mAbs aimed at improving the limited efficacy of current therapies.

overall_design: To investigate the molecular effects of CLDN1 mAb on HCC tumor cells and its tumor microenvironment, multicellular spheroids were generated from tumorous HCC tissue and treated with CLDN1 mAb or Control mAb for 24 hours. Spheroids were then dissociated into single cells and sorted for scRNAseq in an unbiased way.

first: Natascha

last: Roehlen

first: Clara

last: Ponsolles

first: Thomas

last: Baumert


title: Targeting non-junctional Claudin-1 with monoclonal antibodies to treat hepatocellular carcinoma [RNA-seq]

overall_design: Fresh tumor tissues from mice bearing established primary human liver cancer (PDX models LI6280, LI6716, LI6688, LI6723, LI1055 and LI1068) were harvested and cut into small pieces (approximately 2-3 mm in diameter) and inoculated subcutaneously at the upper right dorsal flank into female BALB/c nude mice for tumor development. The randomization started when the mean tumor size reached 100 mm3. A total of 5 mice were enrolled in each model. Randomization into groups receiving CLDN1 mAb (10 mg/kg, 10 mL/kg, once weekly (QW), n=3 mice) or vehicle control (10 mL/kg, QW, n=2 mice) was performed based on "Matched distribution" method. The date of grouping was denoted as day 1 (5/12/2020). Dosing was started on day 1 and continued through day 25. Mice were sacrificed at day 28 and tumor tissue was harvested and stored snap frozen. Liver tissue was lysed in TRI-reagent (Molecular Research Center), and RNA was purified using Direct-zol RNA MiniPrep (Zymo Research) according to the manufacturer’s instructions. RNAseq was performed at Biomedical Sequencing Facility (BSF) at Ce-M-M, Vienna.

first: Markus

last: Meyer


title: Expression of sense and cis-natural antisense transcripts in the human B lymphoblastic cell line IM-9 after X-ray irradiation

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

summary: Ionizing radiation (IR) causes DNA injury and induces multiple signal mechanisms, including the regulation of DNA repair, the cell cycle and gene expression through the activation of p53-related pathways. Cis-natural antisense transcripts (cis-NATs), which are transcribed from the DNA strand opposite to that for mRNA of the gene, are recognized as important regulators of gene expression in eukaryotic cells, but the effects on cis-NAT expression by IR are unknown to date. Therefore, we investigated the effects of X-ray irradiation on sense and cis-NAT expression together with mRNA expression using a human B lymphoblast cell line (IM-9) and a custom-microarray.

overall_design: In the present study, the cis-NATs, up- and down-regulated by X-ray irradiation (0 Gy, 1 Gy, 2 Gy and 4 Gy), were investigated using IM-9 cells having a high sensitivity to ionizing radiation and using a custom-microarray containing human sense/antisense probes for approximately 21,000 genes.


title: Next Generation Sequencing of OVA-treated MutuDC Transcriptome

city: Beijing

first: Zhongfei

last: Ma

address: DongDanSanTiao, DongCheng district

institute: Chinese Academy of Medical Sciences

summary: The goal of this study is to get the profile of the OVA-treated MutuDC transcriptome. Based on the dada of transcriptome, we processed our sgRNA sequencing data of genome-wide CRISPR/Cas9 screening. Briefly, after we have obtained the enriched gene list from our sgRNA sequencing, we excluded the  genes undetected in OVA-treated MutuDC transcriptome to further refine our screening gene list.

overall_design: To get the profile of the OVA-treated MutuDC transcriptome, we did the next generation sequencing of MutuDC at 9 h after treated with 3 mg/ml OVA.

first: Yaxin

last: Liu

first: Xuetao

last: Cao


title: Global gene expression profiling of circulating endothelial cells in SARS-CoV-2-infected cynomolgus macaques

city: seoul

first: hyewon

last: chung

address: Seoul National University College of Medicine

country: South Korea

institute: seoul national university

summary: Vascular disruption caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leads to elevated levels of circulating endothelial cells (CECs); however, the role of CECs in SARS-CoV-2 remains uncharacterized. Here, we analyzed transcriptional changes in CECs from SARS-CoV-2-infected cynomolgus macaques that could reflect the pathophysiology of patients with coronavirus disease 2019 (COVID-19). We found that genes involved in metabolic processes and dysregulated immune responses were upregulated in CECs upon infection with SARS-CoV-2 compared with uninfected controls. Notably, immunization with a recombinant SARS-CoV-2 spike glycoprotein (GBP 510) stimulates CEC-induced protective immunity, marked by enhanced T cell proliferation and reduced neutrophil migration, both of which have been shown to contribute to the pathogenesis of severe COVID-19. These data provide insight into the clinical significance of CECs and suggest a potential novel therapeutic strategy for COVID-19.

overall_design: RNA-seq profiling of CECs (CD31+CD45- cells)  isolated in PBMCs from cynomolgus macaques before (0 dpi) and 7 d (7 dpi) after SARS-CoV-2 infection with (G)/without immunization ©

first: Hyewon

last: Chung

first: Seung Hyeok

last: Seok


title: Functional redundancy of the three insulin receptors of cockroaches

city: Barcelona

first: Jose Luis

last: Maestro

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37-49

department: Complexity of Life

institute: Institute of Evolutionary Biology

summary: Gene duplication is a fundamental evolutionary process which allows to provide opportunities to acquire new gene functions. In the case of the insulin receptor (InR) gene in cockroaches and close-related insects, two successive duplications determined the occurrence of three InR genes: InR2, InR1 and InR3, the last two forming a sister cluster of InR2. The analysis of the sequences in different species and groups did not led to detect positive selection in the divergence of InR1 and InR3. Using the cockroach Blattella germanica as a model, we have determined that InR2 is the gene with the highest expression levels in all the tissues analyzed, both in adult females and males, as well as in nymphs and embryos. InR3 is second in expression levels while InR1 is expressed at lower levels and only in some tissues. The selective depletion by RNAi of each of the three InRs, analyzed in terms of phenotype and fat body transcriptomes, produced essentially redundant effects, with a magnitude approximately proportional to the level of expression of the respective InR. Therefore, the results indicate that the InR duplicates experienced a subfunctionalization process, by which the three InRs maintained similar functions but contributing to those functions proportionally to their expression levels.

overall_design: Two micrograms of dsRNA (dsInR1, dsInR2, dsInR3 or dsMock) were injected into the abdomen of Blattella germanica females on the first day of ootheca transport. The treatment was repeated 7 days later. On the 12th day, oothecae were removed. Dissections were performed at the fifth day of the second reproductive cycle.

first: Pujal

last: David

first: Escudero

last: Jorge

first: Cabrera

last: Pol

first: Bos

last: Laura

first: Vargas-Chávez

last: Carlos

first: Fernández

last: Rosa

first: Bellés

last: Xavier

first: Maestro

last: José L.


title: Serum and Tear Autoantibodies from NOD and NOR Mice as Potential Diagnostic Indicators of Local and Systemic Inflammation in Sjögren's Disease [MCF_SSK_546]

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: Sjögren's Disease (SjD) is an autoimmune disease characterized by lymphocytic infiltration of salivary and lacrimal glands (LG). The LG produces the protein-rich aqueous component of tears, and SjD-associated autoimmune dacryoadenitis (AD) may thus alter tear autoantibody composition.  The presence of tertiary lymphoid structures (TLS) in LG from two murine models of SjD-associated AD, male non-obese diabetic (NOD) and male non-obese insulitis resistant (NOR) mice, were evaluated using immunofluorescence. IgG and IgA reactivity in serum and tears from these models were probed in three studies against a panel of 80-120 autoantigens using autoantibody microarrays relative to serum and tears from healthy male BALB/c mice. Sources of Ig in tears were investigated using scRNA-Seq of the LG (GSE132420). Data were analyzed by R package Limma and Seurat.  Analysis of immunofluorescence in LG sections from both SjD models showed TLS. Only one autoantibody was significantly elevated in tears and serum in both SjD models across all studies. Three autoantibodies were significantly elevated in serum but not in tears in both SjD models across all studies. Conversely, six IgG and thirteen IgA autoantibodies (6 sharing the same autoantigen) were significantly elevated in tears but not serum in both SjD models. Igha and Ighg2b expressing cells were identified in the plasma cell cluster of NOD.H2b LG.  NOD and NOR mice with SjD-associated AD have distinct autoantibody profiles in tears and serum. Tear IgA isotype autoantibodies showed a greater diversity than tear IgG autoantibodies. TLS observed in LG are a likely source of the tear autoantibodies.

sample_organism:
Mus musculus
blank sample

overall_design: Tear: male NOD (14 weeks, N=5), male NOR (16 weeks, N=4), male BALB/c (16 weeks, N=6). Serum: male NOD (14 weeks, N=5), male NOR (16 weeks, N=4), male BALB/c (16 weeks, N=6)

first: Shruti

middle: S

last: Kakan

first: Yaping

last: Ju

first: Maria

last: Edman

first: Indu

last: Raman

first: J

middle: A

last: Mackay

first: Prithvi

last: Raj

first: Sarah

last: Hamm-Alvarez


title: Effect of HTLV-1 bZIP factor(HBZ) on microRNA expression profile.

city: Nanjing

first: Benquan

last: Liu

address: 639 Longmian Avenue, Jiangning District

institute: China Pharmaceutical University

summary: This data is mainly used to determine the effect of HBZ on microRNA expression in cells and to identify the microRNAs regulated by HBZ, including upregulation and downregulation.

overall_design: We constructed Jurkat cells stably expressing HBZ(Jurkat-HBZ) or control vectors(Jurkat-Ctrl) by lentiviral transduction for RNA extraction and hybridization on Affymetrix microarrays.Both stable cell lines were cultured in vitro under appropriate culture conditions and harvested in their logarithmic growth phase for RNA extraction.

first: Guangyong

last: Ma


title: Multi-omic analysis of chronic myelomonocytic leukemia monocytes reveals metabolic and immune dysregulation leading to altered macrophage polarization [RNAseq]

city: Manchester

first: Kiran

last: Batta

address: Paterson Building

department: Division of cancer Sciences

country: United Kingdom

institute: The University of Manchester

summary: Chronic myelomonocytic leukemia (CMML) is a myelodysplastic/myeloproliferative overlap neoplasm with few treatment options and generally poor prognosis. A defining feature is expansion of classical monocytes, which are responsible for various clinical sequelae and thus represent viable therapeutic targets. Given the near-ubiquity of mutations involving epigenetic regulators, we profiled the epigenome (open chromatin configuration; H3K4-monomethylation; H3K27-acetylation; H3K27/H3K4-trimethylation) and transcriptome of primary CD14+ monocytes from CMML patients and age-matched healthy controls. Compared with healthy monocytes, CMML monocytes displayed heterogeneous but distinct epigenetic and transcriptome signatures. Most epigenetic changes mapped to distal elements, suggesting generalized enhancer dysregulation.  We observed strong epigenetic (but not transcriptional) suppression of the NF-κB pathway, suggesting poised potential to repress downstream targets and modulate inflammatory responses. RNA-seq revealed up-regulation of genes involved in the oxidative phosphorylation (OxPhos) machinery, with significantly heightened OxPhos activity of primary CMML monocytes validated in mitochondrial stress tests, highlighting a potentially tractable therapeutic vulnerability. In line with the observed metabolic phenotype of CMML monocytes, unpolarized CMML monocyte-derived macrophages exhibited transcriptional bias towards an M2 (“anti-inflammatory”) phenotype, reflected by an increased Th2/Th1 ratio in comparison with control monocytes. These observations may be germane to the observed clinical heterogeneity and prominent immune dysfunction characteristic of CMML.

overall_design: CD14-Positive monocyte were sorted from PBMNCs obtained from healthy controls (HV-X) and CMML patients(BC-XXX). Sorted monocytes were subject to RNA-Seq.

first: Hasse

last: Addinsell


title: Inhibiting CXCR4 Attenuates TOX-Programmed Exhausted Phenotype of CD8+ T cells via Regulating JAK2/STAT3 Pathway [scATAC-seq; scRNA-seq]

city: Wuhan

first: Canhui

last: Cao

state: China

address: Jiefang Road 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Tec

summary: T-cell exhaustion (Tex) phenotype has limited the efficacy of single-agent immune checkpoint blockade (ICB) in cancer immunotherapy, underscoring the need to target upstream pathways. Clinical trials have indicated that CXCR4 antagonists enhance anti-cancer activity. However, the specific mechanisms through which CXCR4 contributes to immune cell phenotypes are not fully understood. By targeting CXCR4 using antagonists or transgenic mice (Cxcr4flox/flox LckCre), we effectively attenuated the Tex phenotype and enhanced the functional T-cell phenotype in vivo. Additionally, single-cell RNA/TCR-seq analyses demonstrated that CXCR4 inhibition promotes anti-PD-1 immunotherapy by reducing CD8+ Tex phenotype and enriching the abundance of TCR clonotypes in vivo. Mechanically, we found that CXCR4-blocking T cells mitigate Tex phenotype by regulating the JAK2-STAT3 pathway, reducing the interaction between p-STAT3 and TOX. Single-cell ATAC/RNA-seq validated that CXCR4 deficiency epigenetically orchestrates the transition from functional to exhausted phenotypes in CD8+ T cells. Altogether, we demonstrate a mechanism of targeting CXCR4 to orchestrate CD8+ Tex cells in cancers and provide a rationale for the combined CXCR4 antagonists and ICBs in clinical trials.

overall_design: In this study, we explored single-cell transcriptome data from normal and tumors to identify CXCR4 expression patterns in T cells and found that CXCR4 is highly expressed in CD8+ PD-1high Tex cells. CXCR4 antagonists and transgenic mice (Cxcr4flox/flox LckCre) in multi-tumor models were used to identify the molecular mechanisms of CXCR4 in maintaining CD8+ Tex phenotypes in tumors. Furthermore, single-cell RNA/TCR-seq and RNA/ATAC-seq were employed to validate the TOX-mediated Tex phenotype triggered by CXCR4 in vitro and in vivo. Our findings provide a novel insight into molecular mechanisms underlying CXCR4 in maintaining the Tex phenotype in tumors, thereby providing a rationale for combination strategies between CXCR4 inhibitors and ICB in cancers.

first: Miaochun

last: Xu

first: Ye

last: Wei

first: Ting

last: Peng

first: Shitong

last: Lin

first: Xiaojie

first: Yashi

first: Tian

last: Chu

first: Shiyi

first: Bai

last: Hu

first: Wencheng

last: Ding

first: Li

last: Li

first: Ding

first: Peng

last: Wu


title: Serum Autoantibodies from NOD Mice as Potential Diagnostic Indicators of Local and Systemic Inflammation in Sjögren's Disease [IgG_MCF_SH_179]

first: Chengsong

last: Zhu

summary: Male Non-Obese Diabetic (NOD) mice develops autoimmune dacryoadenitis beginning 6-8 weeks of age including lymphocytic infiltration of the lacrimal glands, reduced tear production, increased cysteine tear proteases and restructuring of extracellular membrane structural proteins. Autoantigens with high antibody reactivity in serum of disease model mice may have diagnostic potential for Sjögren's Disease. Serum was collected from mice at early (8 weeks,), intermediate (24 weeks) and advanced (33 weeks) stage of autoimmune dacryoadenitis. Serum was also collected from healthy control BALB/c mice at 8 and 28 weeks of age. Approximately 0.8 mL of blood was collected by cardiac puncture into serum separator tubes. Following cold centrifugation, serum was collected. 10 uL of serum per sample was used to determine reactivity against 94 autoantigens using proteinarray. Additionally, effect of age on the level of reactivity was also studied to determine if aging was a confounding the observed up or downregulation of serum autoantibodies.

overall_design: Diseased male NOD mice (8 weeks, N=3), (24 weeks, N=3), (33 weeks, N=3); Healthy male BALB/c control mice. (8 weeks, N=3), (28 weeks, N=3)

first: Yaping

last: Ju

first: Maria

last: Edman

first: Indu

last: Raman

first: J

last: Mackay

first: Prithvi

first: Sarah


title: Single cell analysis of immune cells from synovial tissues during the progression of osteoarthritis and obesity

city: Salt Lake City

first: Natalia

middle: Sara

last: Harasymowicz

state: UT

address: 26 Medical Dr N

department: Orthopaedics

institute: University of Utah

summary: Utilizing transcriptomic analysis we characterized the presence and fate of multiple populations of immune cells found in the knee joint capsule.

overall_design: Single, live synovial CD45+ cells were isolated by flow cytometry sorting and subsequently analyzed by scRNA-seq. Single-cell capture was performed on a 10x Chromium Controller (10xGenomics, Pleasanton, CA). Approximately 1000 cells/µL were loaded into an eight-channel microfluidic chip, which encapsulated them with gel beads (GEMs) and barcoded with a unique molecular identifier (UMI) using 10xGenomics Single Cell 3′ reagent kit following manufacturer instructions (10xGenomics, Pleasanton, CA). A single-cell RNA-seq library from each biological replicate was run independently on Illumina NovaSeq flow cell with 26x98 bp reads and generated approximately 38,000-1,000,000 mean reads per library capturing 700-16000 cells per mice (see details in sTable 3). The obtained reads were aligned to the mouse UCSC mm10 reference genome. The alignment results were used to quantify the gene expression level and to generate a gene-barcode matrix. Based on mitochondrial genes, the number of genes and UMIs expressed in each cell, low-quality cells, and potentially dead cells were removed. The Seurat R package (version 4.1) (44) was used to perform single-cell transcriptomic analysis and clustering. Briefly, for each dataset, we filtered out potential low-quality cells using the QC parameters of nUMI >= 500, nGene >= 550 per cell, and <10% of mitochondrial genes. All remaining variable genes were used for downstream analyses, and counts were normalized using the function NormalizeData. All 12 analyzed biological replicates were integrated using the SCT function with rpca reduction and CellCycle Scoring. For data alignment, we selected 3,000 highly variable genes in each data matrix and performed the ‘FindIntegrationAnchors’ and ‘IntegrateData’ functions in Seurat 4.1. Next, for clustering analysis, the FindNeighbors() and FindClusters() functions of the Seurat package were used. FindClusters() function was set to ‘0.3’ granularity. For the identification of differentially expressed genes (DEGs), we used the FindMarkers, FindConservedMarkers, or FindAllMarkers function (test. use = ’t,’ logfc. threshold = log[0.25]) based on normalized data. Differentially expressed genes (DEGs) for each of the clusters are presented in Table 5.

first: Farshid

last: Guilak


title: Inhibiting CXCR4 Attenuates TOX-Programmed Exhausted Phenotype of CD8+ T cells via Regulating JAK2/STAT3 Pathway

first: Canhui

last: Cao

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A niche driven mechanism determines response and a mutation-independent therapeutic approach for myeloid malignancies [mouse]

city: New York

first: Anqi

last: Wang

state: NY

address: 530 West 166th Street

department: Systems Biology

institute: Columbia University

summary: Myeloid cancers such as myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) remain resistant to standard of care (SOC) and targeted therapies. Here, we identify an oncogenic signal from the niche as a mechanism determining response to all trans-retinoic acid (ATRA), a regimen with disparate results in AML. In samples from clinical trials, responsiveness to ATRA correlates with activation of b-catenin/JAG1 in osteoblastic lineage cells and Notch1 signaling in MDS/AML cells of patients. ATRA inhibits b-catenin activation in patients and leukemic mice. As a result, it specifically suppresses growth and survival and promotes differentiation of MDS/AML cells solely from patients with active b-catenin/JAG1 signaling. This event is independent of cytogenetics and mutational profile. ATRA also improves disease outcome in mice with no evidence of relapse and a superior safety profile to SOC. A circulating skeletal stem cell population expressing activated b-catenin allows patient stratification and monitoring treatment response. A human blocking antibody against JAG1 further improves efficacy, curing mice from leukemia and maintaining the beneficial effects on patient-derived MDS/AML cells. These results demonstrate a niche-directed therapeutic approach, tailored to at least 1/3 of MDS/AML patients that can evade relapse and overcome SOC toxicity, highlighting the therapeutic potential of targeting the niche. b-catenin activation provides an explanation for the differential response to ATRA and a mechanistic biomarker for immediate ATRA repurposing in myeloid malignancies, potentially extending in a broad range of cancers.

overall_design: We performed RNA-seq on three mice with constitutive acitve beta catenin signaling in their osteoblasts (bcat(ex3)osb mice)  and three wild type littermates.

first: Stavroula

last: Kousteni

first: Ioanna

last: Mosialou

first: Raul

last: Rabadan


title: Inhibiting CXCR4 Attenuates TOX-Programmed Exhausted Phenotype of CD8+ T cells via Regulating JAK2/STAT3 Pathway [ChIP-Seq]

first: Miaochun

last: Xu

first: Ye

last: Wei

first: Ting

last: Peng

first: Shitong

last: Lin

first: Xiaojie

last: Liu

first: Yashi

first: Tian

last: Chu

first: Shiyi

first: Bai

first: Wencheng

first: Li

last: Ma


title: N-cadherin antagonism is bronchoprotective in severe asthma models

city: Boston

first: Zheming

last: An

state: Massachusetts

address: 3 Blackfan Street

department: Division of Genetics and Genomics

institute: Boston Children's Hospital

summary: Severe asthma induces substantial mortality and chronic disability due to intractable airway obstruction, which may become resistant to currently available therapies including corticosteroids and b-adrenergic agonist bronchodilators. A key effector of these changes is exaggerated airway smooth muscle (ASM) cell contraction to spasmogens. Unfortunately, no drugs in clinical use effectively prevent ASM hyperresponsiveness in asthma across all severities. Here we show that N-cadherin, a plasma membrane associated cell-cell adhesion protein upregulated in ASM cells derived from patients with severe asthma, is required for the development of airway obstruction induced by allergic airway inflammation in mice. Pharmacological inhibition of N-cadherin by ADH-1 reduced airway hyperresponsiveness independent of allergic inflammation. ADH-1 prevented bronchoconstriction and actively promoted bronchodilation of airways ex vivo. In human ASM cells, ADH-1 inhibited agonist-induced contraction by disrupting N-cadherin-d-catenin interactions, which decreased intracellular actin remodeling. These data provide evidence for an intercellular communication pathway mediating ASM contraction and identify N-cadherin as a potential therapeutic target for inhibiting bronchoconstriction in asthma.

overall_design: To determine the importance of N-cadherin for ASM contraction and discovered that N-cadherin is essential for the development of AHR in allergen-challenged mice and contractile force development in human ASM cells through its effects on collective force transmission and actin remodeling.

first: Nicolas

middle: L

last: Pereira

first: Niccole

last: Schaible

first: Abhishek

last: Desai

first: Eunice

middle: C

last: Chan

first: Ararat

middle: J

last: Ablooglu

first: Jacqueline

last: Capuano

first: Erika

first: Eric

last: Gebski

first: William

last: Jester

first: Sundar

last: Ganesan

first: Nariman

last: Balenga

first: Cynthia

last: Koziol-White

first: Reynold

last: Panettieri Jr

first: Sangita

last: Choudhury

first: Ramaswamy

last: Krishnan

first: Kirk

last: Druey


title: miRNome from 20 High-Grade Serous Ovarian Cancer Patients tissue and paired control ovarian tissue

city: Valencia

first: Joaquin

last: Panadero

state: Valencia

address: Avenida Fernando Abril Martorell, 106 Torre A

department: Genomics

institute: Instituto Investigación Sanitaria La Fe

type: Non-coding RNA profiling by high throughput sequencing

summary: High-grade serous ovarian cancer (HGSOC) poses a formidable challenge as the most lethal gynecologic cancer lacking a curative treatment. Emerging evidence underscores the pivotal role of epigenetic mechanisms, such as miRNAs and DNA methylation, in governing gene expression throughout cancer development stages (i.e. initiation, promotion, and progression, including metastasis). However, the precise involvement of these mechanisms in HGSOC remains elusive. By using high-throughput techniques, we identified dysregulated miRNAs in HGSOC cells, opening new avenues in the therapeutic arsenal targeting miRNAs in this disease.

overall_design: The study consists of a retrospective multicentre study. Patients (n=20) were surgically treated and recruited either at the General University Hospital of Valencia or the General University Hospital of Castellon (Spain) between October 2017 and July 2021. From each patient, both tumoural and paired control non-tumoural ovarian tissue (PCOT) samples were obtained. Inclusion criteria comprehended patients undergoing surgical resection for suspected OC with histological confirmation of HGSOC in the affected ovary and absence of malignancy in the paired control ovary and patients who signed the informed consent. Exclusion criteria comprehended patients undergoing surgical resection for suspected OC with a diagnosis different from HGSOC and, patients with absence of paired control non-tumoural ovarian tissue. Demographic variables (age, BMI, ethnicity) were obtained in the pre-surgical interview. Surgical variables were obtained during surgery (stage, PCI). Patients were staged in accordance with the 2014 International Federation of Obstetrics and Gynaecology (FIGO) staging system.

first: Juan

last: Gilabert-Estellés

first: Josep

last: Marí-Alexandre

first: Mariana

last: Braga-Monteiro

first: Eva

last: González-Cantó

first: Vicente

last: Pérez-García


title: A deep intronic splice-altering AIRE variant causes APECED syndrome through antisense oligonucleotide-targetable pseudoexon inclusion

city: Bethesda

first: Behdad (Ben)

last: Afzali

state: MD

address: 10 Center Drive, Building 10

department: NIDDK

institute: National Institutes of Health

summary: Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a life-threatening monogenic autoimmune disorder primarily caused by biallelic deleterious variants in the autoimmune regulator (AIRE) gene. We prospectively evaluated 104 patients with clinically diagnosed APECED syndrome and identified 17 patients (16%) from 14 kindreds lacking biallelic AIRE variants in exons or flanking intronic regions; 15 had Puerto Rican ancestry. Through whole-genome sequencing, we identified a deep intronic AIRE variant (c.1504-818 G>A) cosegregating with the disease in all 17 patients. We developed a culture system of AIRE-expressing primary patient monocyte-derived dendritic cells and demonstrated that c.1504-818 G>A creates a cryptic splice site and activates inclusion of a 109-base pair frame-shifting pseudoexon. We also found low-level AIRE expression in patient-derived lymphoblastoid cell lines (LCLs) and confirmed pseudoexon inclusion in independent extrathymic AIRE-expressing cell lines. Through protein modeling and transcriptomic analyses of AIRE-transfected human embryonic kidney 293 and thymic epithelial cell 4D6 cells, we showed that this variant alters the carboxyl terminus of the AIRE protein, abrogating its function. Last, we developed an antisense oligonucleotide (ASO) that reversed pseudoexon inclusion and restored the normal AIRE transcript sequence in LCLs. Thus, our findings revealed c.1504-818 G>A as a founder APECED-causing AIRE variant in the Puerto Rican population and uncovered pseudoexon inclusion as an ASO-reversible genetic mechanism underlying APECED.

overall_design: We performed RNA sequencing (RNA-seq) on total RNA extracted from thymic epithelial cells derived from TEC4D6 lines. These cells were transfected with plasmids carrying either wild-type AIRE (WT_AIRE) or mutant AIRE (Mu_AIRE). Additionally, TEC4D6 cells transfected with GFP were utilized as negative controls

first: Sebastian

last: Ochoa

first: Amy

middle: P

last: Hsu

first: Andrew

last: Oler

first: Dhaneshwar

last: Kumar

first: Daniel

last: Chauss

first: Jan

last: Piet van Hamburg

first: Gustaaf

middle: G

last: van Laar

first: Vasileios

last: Oikonomou

first: Elise

last: Ferré

first: Monica

last: Schmitt

first: Tom

last: DiMaggio

first: Princess

last: Barber

first: Gregory

last: Constantine

first: Lindsey

middle: B

last: Rosen

first: Paul

last: Auwaerter

first: Bhumika

last: Gandhi

first: Jennifer

last: Miller

first: Rachel

last: Eisenberg

first: Arye

last: Rubinstein

first: Edith

last: Schussler

first: Erjola

last: Balliu

first: Shashi

last: Vandana

first: Olaf

last: Neth

first: Peter

last: Olbrich

first: Kim

last: Le

first: Nanni

last: Mamia

first: Saila

last: Laakso

first: Pasi

middle: I

last: Nevalainen

first: Juha

last: Grönholm

first: Mikko

middle: R

last: Seppänen

first: Louis

last: Boon

first: Gulbu

last: Uzel

first: Luis

last: Franco

first: Theo

last: Heller

first: Karen

middle: K

last: Winer

first: Rajarshi

last: Ghosh

first: Bryce

last: Seifert


title: A niche driven mechanism determines response and a mutation-independent therapeutic approach for myeloid malignancies

first: Anqi

last: Wang

overall_design: We performed RNA-seq on three patients with high beta catenin and three patients with low beta catenin.

first: Stavroula

last: Kousteni

first: Ioanna

last: Mosialou

first: Raul

last: Rabadan


title: Inactivation of DET1 causes neurological defects and lethality in mice and humans II

city: Toronto

first: Neha

last: Rohatgi

address: Roche 7070

country: Canada

institute: Roche

summary: COP1 and DET1 are components of an E3 ubiquitin ligase that is conserved from plants to humans. Mammalian COP1 binds to DET1 and is a substrate adaptor for the CUL4A-DDB1-RBX1 RING E3 ligase. Its transcription factor substrates, including c-Jun, ETV4, and ETV5, are targeted for proteasomal degradation to effect rapid transcriptional changes in response to cues such as growth factor deprivation. Here we show that a homozygous DET1R26W mutation that is linked to lethal developmental abnormalities in humans disrupts DET1 binding to DDB1 and compromises E3 ligase function. Human-induced pluripotent stem cells bearing the homozygous DET1R26W mutation expressed ETV4 and ETV5 highly, had alterations in mitochondrial protein expression, and exhibited impaired neuronal differentiation. Mice lacking Det1 died during embryogenesis, while Det1 deletion just in neural stem cells elicited hydrocephalus, cerebellar dysplasia, and neonatal lethality. Our findings highlight an important role for DET1 in the neurological development of mice and humans.

overall_design: WT human iPSCs and a DET1 p.R26W knock-in clone were cultured in mTeSR Plus media on Matrigel-coated dishes, with media refreshed every other day. At ~75% confluency, cells were rinsed with DPBS, treated with Accutase, neutralized with mTeSR Plus, filtered through 40 µm strainers, and centrifuged at 300g for 5 minutes. iPSCs were resuspended in induction media, counted, and seeded at 30,000 cells/cm² on iMatrix-511-coated dishes. Induction media was replaced daily from days 1 to 4. On day 5, neurons were detached, dissociated, strained, counted, and replated onto PDL- (50 µg/mL) and iMatrix-coated dishes at 20,000 cells/cm² in maturation media. Neurons were grown for two more days before collection on day 7. The experiment was performed in triplicate.

first: R

last: Reja

first: N


title: Inactivation of DET1 causes neurological defects and lethality in mice and humans I

overall_design: A375 human melanoma cells expressing Flag-tagged WT DET1 or DET1 p.R26W were treated with DMSO or 1 µM Cobimetinib (a MEK1/2 inhibitor) for an hour, in triplicate.


title: VprBP regulates osteoclast differentiation via histone H2A phosphorylation

city: Los Angeles

first: Yonghwan

last: Shin

state: CA

address: 1450 Biggy St

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: Bone remodeling is a continuous and balanced process which relies on the dynamic equilibrium between osteoclastic bone resorption and osteoblastic bone formation. During osteoclast differentiation, pro-osteoclastogenic and anti-osteoclastogenic genes are selectively targeted by positive and negative transcription regulators, respectively. VprBP, also known as DCAF1, is a recently identified kinase and plays an important role in driving epigenetic gene silencing and oncogenic transformation. However, nothing is currently known about a possible involvement of VprBP in signaling pathways that regulates other cellular processes. Here, we demonstrate that VprBP stimulates RANKL-induced osteoclast differentiation by attenuating the expression of anti-osteoclastogenic genes through phosphorylating histone H2A at threonine 120 (H2AT120p). H2AT120p is critical for VprBP function, because abrogating VprBP kinase activity toward H2AT120 significantly attenuates the differentiation of osteoclast precursor cells (OCPs) into mature osteoclasts. Consistent with this notion, our in vivo studies established the importance of VprBP-mediated H2AT120p in low bone mass phenotypes and osteoporosis caused by overactive osteoclasts. Together, our data reveal a previously unrecognized function of VprBP in supporting osteoclast differentiation and the molecular mechanism underlying its action as a negative regulator of anti-osteoclastogenic genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDM  (Control shRNA, and VprBP1 shRNA).

first: Woojin

last: An


title: Modeling extrahepatic hepatitis E virus infection in induced human primary neurons

city: Bochum

first: André

last: Gömer

address: University Street 150

department: MMV

country: Germany

institute: Ruhr University Bochum

summary: Hepatitis E virus (HEV) infections are one of the most common causes of acute viral hepatitis, annually causing over 3 million symptomatic cases and 70,000 deaths worldwide. Historically, HEV was described as a hepatotropic virus, but has recently been associated with various extrahepatic manifestations including neurological disorders such as Guillain-Barré syndrome and neuralgic amyotrophy. However, the underlying pathogenesis of these neurological diseases remains largely unknown. The aim of this study was to investigate extrahepatic HEV manifestations in a neuronal model system using human induced primary neurons (iPNs). Renal epithelial cells from human urine were reprogrammed to induced pluripotent stem cells (iPSCs) to generate neuronal progenitor cells, which were subsequently differentiated into iPNs over 21 days. These iPNs supported HEV infection preferentially in neurite-bearing cells. Transcriptional profiling of the neuronal development process as well as viral infection dynamics in iPNs uncovered a lack of antiviral innate immune responses to HEV infection with only an intrinsic expression of distinct interferon-regulated genes (ISGs) and signaling molecules. Viral open reading frame 2 (ORF2) encoded capsid protein could be visualized by volumetric three-dimensional reconstitution within the neurites, which were reduced in length in an HEV inoculation-dependent manner. In conclusion, this neuron-derived human model system provides a powerful tool for studying extrahepatic manifestations of HEV infection. It further indicates a potential mechanism of pathogenesis driven by the interaction between host and viral factors.

overall_design:
Different differentiation stages of induced primary neurons (days 2, 7, 14, and 21) were subjected to HEV infection for five days. As a control, medium without viral particles was used for each differentiation stage and incubated for five days or for 48 hours for cells that were two days old.
Analysis was performed to characterize the global gene expression changes during the differentiation process, followed by a comparison of Mock versus infected samples. Particular emphasis was placed on innate immune genes and interferon-regulated genes.
For each sample an individual run was performed.

first: Michelle

last: Jagst

first: Sanja

last: Augustyniak

first: Mara

last: Klöhn

first: Rainer

last: Ulrich

first: Verian

last: Bader

first: Konstanze

last: Winklhofer

first: Yannick

last: Brüggemann

first: Ralf

last: Gold

first: Barbara

last: Gisevius

first: Daniel

last: Todt

first: Eike

last: Steinmann


title: irCLIP-RNP reveals patterns of dynamic protein associations on RNA [RNA-seq]

city: Stanford

first: Luca

last: Ducoli

address: 269 Campus Drive CCSR 2150

institute: Stanford University

summary: RNA binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport, and translation. Dysfunctional RNA-RBP interactions contribute to the pathogenesis of human disease, however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. To address this, non-isotopic ligation-based ultraviolet crosslinking immunoprecipitation was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest. irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, uncovering previously unknown patterns of RBP-RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodeling in response to epidermal growth factor (EGF), uncovering EGF-induced recruitment of UPF1 adjacent to HNRNPC to effect splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships seen in irCLIP-RNP and identified HNRNPC and UPF1 RBP co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.

overall_design: RNA sequencing experiments  for the analysis of splicing , mRNA stability after the knockdown of HNRNPC and UPF1 as well as the effect EGF stimulation in A431 cells.

first: Leandra

middle: V

last: Jackrazi

first: Douglas

middle: F

last: Porter


title: A core pattern-induced transcribed enhancer regulates the immune response to fungi in Arabidopsis by regulating the synthesis of camalexin

first: Ying

last: Zhang

address: Shizishan

institute: Huazhong Agricultural University

summary: Effective plant defense against pathogens relies on highly coordinated regulation of immune gene expression. Enhancers, as cis-regulatory elements, are indispensable determinants of the dynamic gene regulation, but the molecular functions in plant immunity are not well understood. In this study, we identified a novel enhancer, CORE PATTERN-INDUCED ENHANCER 35 (CPIE35), is rapidly activated upon pathogenic elicitation and negatively regulates camalexin synthesis and anti-fungal resistance through modulating WRKY15 expression. During immune activation, CPIE35 activates the transcription of WRKY15 by forming chromatin loops with the promoter of WRKY15 in a WRKY18/40/60-, WRKY33-, and MYC2-dependent manner. WRKY15 directly binds to the promoters of GSTU4 and PAD3 and suppresses their expression, leading to the reduced camalexin synthesis and resistance. Interestingly, the CPIE35 region is evolutionally conserved among distantly related dicots, and the CPIE35-WRKY15 module exerts similar functions in Brassica napus to negatively regulates antifungal resistance. Our work reveals the “TFs-enhancer-promoter” regulatory mechanism in maintenance of immune hemostasis and highlights the importance and conservation of enhancers in fine-tuning immune gene expression in plants.

overall_design: Three replicates of Arabidopsis thaliana seedlings treated by  chitin.


title: irCLIP-RNP reveals patterns of dynamic protein associations on RNA [CLIP-seq]

overall_design: infrared crosslinking immunoprecipiation followed by RNA sequencing (irCLIPv2) and sequential immunoprecipitation irCLIP (re-CLIP) followed by RNA sequencing for several RBPs in HEK293T and EGF-stimulated A431 cells.

first: Brian

last: Zarnegar

first: Robin

middle: M

last: Meyers


title: Endometriotic stromal cell-derived exosomal miR-25-3p induces endometrial collagen Ⅰ deposition impairing embryo implantation via targeting PTEN in endometriosis

city: China

first: Yuan

last: Zhu

address: Hankou Road 22, Nanjing 210008

institute: Nanjing University medical school

summary: Background  Reduced endometrial receptivity is a major factor for impaired fertility in endometriosis (EMS). Endometrial deposition of collagen I proteins may account for poor endometrial receptivity in endometriosis.   Methods  We investigated the expression of collagen I expression in endometrium of endometriosis patients and in constructed EMS mice model. Effect of collagen I on ESCs was evaluated. Co-culture of exosomes with ESCs was conducted to evaluate the uptake of  exosomes by different endometrial cell lines  and the effect on decidualization of eutopic ESCs and embryo implantation. MiRNA expression profiles were compared between ectopic ESC derived exosomes and eutopic ESC derived exosomes. Luciferase reporter and its mutant plasmids were applied to confirm the direct target of miR-25-3p.  Findings  Here we found endometrial collagen I deposition with impaired decidualization in endometriosis patients and EMS mice model. Treatment of collagen I with ESCs contributed to impaired decidualization and inhibited BLS expansion in vitro. Endometriotic stromal cell-derived exosomes were detected in eutopic endometrium and the ectopic endometrial stromal cell derived exosomes were more taken-up by the same cell line in eutopic endometrium. Treatment of endometriotic stromal cell-derived exosomes increased the expression of endometrial collagen I in vitro and in vivo, while inhibited BLS expansion.  Exosomal miR-25-3p was significantly increased in endometriotic stromal cell-derived exosomes compared with control group, and PTEN is a certain target of miR-25-3p. The promotion of endometrial miR-25-3p significantly increased collagen I expression in vitro through the PTEN/Akt pathway.   Interpretation  These results suggested that endometriotic stromal cell-derived exosomal miR-25-3p played key role in inducing endometrial collagen I deposition to impair embryo expansion in endometriosis via PTEN/Akt pathway.  Funding  National Nature Science Foundation of China (82271702), National Natural Science Foundation of China (81771537).   Keywords: endometriosis; exosome; collagen I; miRNA; collagen deposition

overall_design: EMS ectopic endometrial stromal cell derived exosomes and ctrl endometrial stromal cell derived exosomes were collected and miRNA sequencing was employed

first: Bo

last: Zheng

first: Yuting

first: Jianjun

last: Zhou


title: High throughput sequencing of small cell lung cancer chemosensitive H69 and corresponding chemoresistant H69AR

city: Guangzhou

first: Qiong

last: Lyu

state: Guang Dong

address: 253 GongYe Road

department: Oncology

institute: Zhujiang Hospital, Southern Medical University

summary: Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer. Although most patients are initially sensitive to first-line chemotherapy with combined cisplatin and etoposide, chemotherapy drugs resistance easily develops and quickly leads to tumor progression. Therefore, understanding mechanisms of chemotherapy drugs resistance and how to reverse it is key to improving the prognosis of patients with SCLC. The parental SCLC cell lines H69 and corresponding doxorubicin-induced multidrug resistant variant (H69AR)  were used to explore the mechanism of chemoresistance in SCLC.

overall_design: RNA was extracted from SCLC cells (H69 and H69AR). The RNA quality was assessed with a Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies), and samples with an RNA integrity number (RIN) of over 7 were further analyzed by RNA-seq. All sequencing reactions were performed on an Illumina HiSeq 2000 instrument (Illumina, San Diego, CA, USA). We used HISAT2 (version 2.1.0) with the default setting to map the RNA-seq data to the human reference genome (NCBI38/hg38).We aggregated the read counts at the gene level using HTSeq.

first: Yueqin

last: Sun

first: Weitao

last: Shen

first: Shulu

last: Hu


title: NLRX1 Limits Inflammatory Neurodegeneration in the Anterior Visual Pathway

city: Baltimore

first: Matthew

middle: D

last: Smith

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

summary: Chronic innate immune activation in the central nervous system (CNS) significantly contributes to neurodegeneration in progressive multiple sclerosis (MS). Using multiple EAE models, we explored the potential of the innate immune sensor NLRX1 to protect neurons in the anterior visual pathway from inflammatory neurodegeneration. To do this, we assessed retinal ganglion cell (RGC) density and optic nerve axonal degeneration, gliosis, and T-cell infiltration in Nlrx1-/- and wild-type (WT) EAE mice. Our results indicate that Nlrx1-/- mice exhibit significantly increased RGC loss and axonal injury compared to WT mice in both active immunization EAE and spontaneous opticospinal encephalomyelitis models. Adoptive transfer experiments, in which wild type T cells were transferred into lymphocyte-deficient Rag-/- mice to minimize the effects of Nlrx1 knockout on peripheral lymphocyte priming, revealed more severe microgliosis and astrogliosis in the optic nerve of Nlrx1-/-Rag-/- mice compared to Rag-/- mice, suggesting a regulatory role of NLRX1 in innate immune compartments. Transcriptome analysis in primary astrocytes demonstrated that NLRX1 negatively regulates TLR-mediated NF-κB activation. The novel pharmacologic NLRX1 activator LABP-66 decreased LPS-mediated gene expression of inflammatory cytokines and chemokines in mixed glial cultures. Moreover, treating EAE mice with oral LABP-66 after the onset of paralysis resulted in less anterior visual pathway neurodegeneration compared to vehicle. These data suggest that a pharmacologic NLRX1 activators attenuates glial immune activation and has the potential to limit inflammatory neurodegeneration in diseases, such as MS, where chronic CNS-compartmentalized inflammation may drive neurodegenerative pathology. This study highlights that NLRX1 could serve as a promising target for neuroprotection in progressive MS and other neurodegenerative diseases where chronic compartmentalized innate immune activation and neuroinflammation play a role.

overall_design: Astrocytes isolated from WT (C57BL6J) and NLRX1-/- murine pups were cultured in vitro then stimulated with LPS+IFNγ or Vehicle for 24 hours. RNA was collected and poly-A capture RNAseq performed. There are 4 biological replicates per genotype, and each replicate has 2 conditions - unstimulated and stimulated. Each replicate has paired samples where the Vehicle and LPS+IFNG were two wells from the same set of mice grown at the same

first: Alexander

last: Gill

first: Peter

last: Calabresi

first: Marjan

last: Gharagozloo


title: Dietary restriction promotes anti-tumor immunity via T cell mediated ketone body metabolism

city: Grand Rapids

first: Brandon

last: Oswald

state: MI

address: 333 Bostwick Ave NE

department: Metabolism

institute: Van Andel Institute

summary: Diet can shape immune function in vivo, but the molecular mechanism remains poorly defined. In this study, we investigated how a reduction in food intake (hereafter referred to as dietary restriction or DR) affects CD8+ T cell function in multiple models. We found that DR reduced tumor burden in mice in a CD8+ T cell-dependent manner, indicating that the anti-tumor effects of DR are mediated by the immune system. Consistent with this observation, DR increased CD8+ T cell effector function, including production of interferon-γ and granzyme B. Moreover, analysis of tumor infiltrating CD8+ T cells showed DR led to a decrease in markers of T cell exhaustion (PD1, TIM3, TOX) and an increase in markers of cell stemness (LY108, TCF1). In a model of Listeria infection, we further showed that DR enhances CD8+ T cell mitochondrial fitness and bioenergetic capacity, indicating that DR impacts both CD8+ T cell metabolism and effector function. Using stable isotope tracing, we identified that CD8+ T cells from mice on DR preferentially consumed the ketone body β-hydroxybutyrate (βOHB), which is elevated 3-fold in serum of in mice on DR relative to ad libitum-fed mice. Notably, the effects of DR on anti-tumor immunity were attenuated in conditional knockout mice in which T cells are unable to catabolize βOHB, supporting that DR enhances anti-tumor immunity, in part, through increasing βOHB availability and metabolism by T cells. Current and future studies are exploring the effects of DR on different immune cell populations within tumors to further delineate the mechanism(s) by which DR enhances the immune response in cancer.

overall_design: B16-OVA cells were injected into B6 mice for tumor establisment. Mice were on either dietary restriction (DR) or ad-libitium (AL) diets n =4. 12 days post tumor injection, tumors were harvested and live CD45+ cells were isolated and stained with antibodies (HTO/ADT). Cells were then preped for CITE-Seq.

first: Michael

last: Dahabieh

first: Lisa

last: DeCamp

first: Nicholas

last: Bunda

first: Joesph

last: Longo

first: Russell

last: Jones


title: Rugulation of TNF-mediated macrophage differentiation and function by RBP-J

first: Baohong

last: Zhao

address: 535 E70th ST

institute: Hospital for Special Surgery

summary: RBP-J was initially identified as a key regulator in the canonical Notch signaling pathway. More recent studies have unveiled its important role as a significant player in macrophage polarization, TLR and TNF signaling pathways. Since TNF activates RBP-J, we investigated the transcriptomic changes in murine bone marrow macrophages treated without or with TNF.

overall_design: Mouse bone marrow derived macrophages from wild type control (WT) and Rbpj conditional knock out (KO) mice, in which Rbpj is specifically deleted in myeloid lineage macrophages by crossing Rbpj flox/flox mice with LysMcre mice (Rbpj f/f;LysMCre; hereafter referred to as RbpjKO),  were treated without or with TNF (40ng/ml) for 2 days. The total RNA samples were obtained from WT and RbpjKO BMMs at 0 and d2 after TNF treatment. Two independent experiments were performed.

first: Yuhan

last: Xia

first: Kazuki

last: Inoue


title: Cardiac organoids for Hypertophic cardiomyopathy

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Outcome Spatial molecular imaging to evaluate the difference between organoids generated from WT and D389V mutant carrier.

overall_design: contains data for both Mutant and NC organoids

first: Darshini

last: Desai

first: Akhil

last: baby

first: Rohit

last: singh

first: Song

middle: T

last: Jeong

first: James

last: Mcnamara

last: green

first: Pooneh

last: Nabavizadeh

first: Sholeh

last: Bazrafshan

first: Mark

last: Erickson

first: Sankar

last: Natesan

first: Sakthivel

last: Sadayappan


title: Cardiac Organoids for Modeling Hypertrophic Cardiomyopathy

summary: BACKGROUND: MYBPC3 is one of the most mutated gene known to cause hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms of how mutations in MYBPC3 lead to the onset and progression of HCM are poorly understood. Thus, advancing in-vitro studies to define these mechanisms of mutations leading to HCM are still warranted. Thus, the primary objective of this study was to investigate the molecular mechanisms underlying the pathogenesis of HCM associated with MYBPC3 mutation utilizing isogenic human-induced pluripotent stem cell (hiPSC)-derived cardiac organoids (hCOs).

overall_design: To investigate the  impact of  D389V mutation in MYBPC3 gene using hiPSC derived cardiac organoids.

last: Baby

last: Singh

first: Taejeong

last: Song

last: McNamara

first: Lisa

last: Green


title: Cardiac Organoids for Cardiomyopathy

last: Choi

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

overall_design: Refer to individual Series


title: Global gene expression profile of cortices from FUS and TDP mutant and control mouse

city: Dublin

first: Jochen

middle: H. M.

last: Prehn

address: 123 St. Stephen's Green

department: Physiology and Medical Physics

country: Ireland

institute: Royal College of Surgeons in Ireland (RCSI)

summary: In this study, global transcriptome profiling was performed for FUS and TDP mutant (as model of ALS) and control samples from mouse cortices, More than 20 million high-quality reads were obtained from each sample using Illumina platform. A consensus reference-guided assembly was generated for the transcriptome data from all samples and gene expression was analysed.

overall_design: Total RNA was extracted from mutant and control samples and cDNA libraries were prepared. Sequencing was performed on Illumina HiSeq 4000 platform to generate 51 bp single-end reads. Pre-processing was performed to remove adapters and low-quality reads. Filtered high-quality reads were mapped on the mouse genome (mm10) using STAR aligner. To analyze gene expression, Htseq-count were used to quantify genes expression and EdgeR were used for differential expression.

first: Niamh

last: Connolly

first: Niraj

last: Khemka

first: Ingrid

last: Arijs

first: Orla

last: Watters


title: Integrated analysis of early transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders


title: Cpt1a WT vs Pdx1-cre Islet RNA

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

summary: Discovery of pathways altered when mitochondrial fatty acid oxidation is impaired in the islet

overall_design: Islet RNA from 6 month old male WT and KO mice

first: Susan

last: Burke

first: Sujoy

last: Ghosh


title: Global gene expression profile of cortices from Aifm1 KI and Hq mutant and control mouse

summary: In this study, global transcriptome profiling was performed for Aifm1-KI and Hq mutant (as model of mitochondial defect) and control samples from mouse cortices, More than 20 million high-quality reads were obtained from each sample using Illumina platform. A consensus reference-guided assembly was generated for the transcriptome data from all samples and gene expression was analysed.

first: Daniele

last: Bano

first: Lena

last: Wischhof


title: TGFBR2-High mesenchymal glioma stem cells phenocopy regulatory T cells to suppress CD4+ and CD8+ T cell function

status: Public on Jan 27 2025

first: Amanda

middle: Leigh

last: Johnson

address: 707 N Broadway St, Rm 408

institute: Johns Hopkins School Of Medicine

summary: Attempts to activate an anti-tumor immune response in glioblastoma (GBM) have been met with many challenges due to its inherently immunosuppressive tumor microenvironment. The degree and mechanisms by which molecularly and phenotypically diverse tumor-propagating glioma stem cells (GSCs) contribute to this state are poorly defined. In this study, our multifaceted approach combining bioinformatics analyses of clinical and experimental datasets, single-cell sequencing, and molecular and pharmacologic manipulation of patient-derived cells identified GSCs expressing immunosuppressive effectors mimicking regulatory T cells (Tregs). We show that this Immunosuppressive Treg-Like (ITL) GSC state is specific to the mesenchymal GSC subset and is associated with and driven specifically by TGF-beta type II receptor (TGFBR2) in contrast to TGFBR1. Transgenic TGFBR2 expression in patient-derived GBM neurospheres promoted a mesenchymal transition and induced a 6-gene ITL signature consisting of CD274 (PD-L1), NT5E (CD73), ENTPD1 (CD39), LGALS1 (galectin-1), PDCD1LG2 (PD-L2), and TGFB1. This TGFBR2-driven ITL signature was identified in clinical GBM specimens, patient-derived GSCs and systemic mesenchymal malignancies. TGFBR2High GSCs inhibited CD4+ and CD8+ T cell viability and their capacity to kill GBM cells, effects reversed by pharmacologic and shRNA-based TGFBR2 inhibition. Collectively, our data identify an immunosuppressive GSC state that is TGFBR2-dependent and susceptible to TGFBR2-targeted therapeutics.

overall_design: GBM1A neurospheres derived from patient GBMs were transduced to transgenically express both POU5F1 (Oct4) and SOX2. Parental cells (GBM1A) and cells co-expressing transgenic Oct4 and Sox2 (GBM1A-OS) were analyzed using scRNA-seq.

first: Harmon

middle: S

last: Khela

first: Jack

last: Korleski

first: Sophie

last: Sall

first: Yunqing

last: Li

first: Weiqiang

last: Zhou

first: Karen

last: Smith-Connor

first: Hernando

last: Lopez-Bertoni

first: John

last: Laterra


title: Comprehensive mutational characterization of the calcium-sensing STIM1 EF-hand reveals residues essential for structure and function

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

summary: Calcium signaling is a fundamental molecular means of cellular regulation. Store operated calcium entry (SOCE) is a major intracellular signaling module, wherein calcium release from the endoplasmic reticulum triggers transmembrane STIM1 proteins to conformationally shift and oligomerize to prompt calcium influx from the extracellular environment. STIM1 senses ER calcium concentrations with its canonical EF-hand domain, and missense variants can dysregulate SOCE and cause Tubular Aggregate Myopathy, Stormorken Syndrome or immunodeficiency. Few STIM1 EF-hand variants are characterized, obscuring how STIM1 sequence controls its function, and hampering clinical interpretation of STIM1 variants observed in patients. We leveraged fitness costs caused by overexpression of STIM1 variants in cultured human cells to functionally characterize 706 of the 720 possible single amino acid variants of the STIM1 canonical EF-hand. The calcium-coordinating EF-hand residues exhibited varying mutational patterns. The trailing helix possessed a core of immutable residues, even depleting during library propagation in bacteria, implicating residues normally restraining STIM1 aggregation. The leading helix only exhibited toxicity in cells with endogenous STIM1, implicating a multimerization-dependent STIM1 regulatory module. No cytotoxic STIM1 variants were observed in healthy human populations. Some disease-associated variants had low scores, but most pathogenic variants were not overtly cytotoxic in our assay. We demonstrate that orthogonal measurements for STIM1 oligomerization, cytoplasmic calcium influx, and cellular stress complement the cytotoxicity phenotypes to enhance variant understanding. Collectively, these data reveal the complex molecular roles embedded in the STIM1 canonical EF-hand sequence for its function in promoting calcium signaling through SOCE.

overall_design: Genomically engineered HEK293T cells with amplicons derived from exogenous DNA that has recombined using the Bxb1 bacteriophage integrase and various complementary Bxb1 attP and attB sites.

first: Nisha

last: Kamath

middle: A


title: Mechanical confinement governs phenotypic plasticity in melanoma [RNA-Seq]

first: Miranda

last: Hunter

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: Phenotype switching is a form of cellular plasticity in which cancer cells reversibly move between two opposite extremes - proliferative versus invasive states. While it has long been hypothesised that such switching is triggered by external cues, the identity of these cues has remained elusive. Here, we demonstrate that mechanical confinement mediates phenotype switching through chromatin remodelling. Using a zebrafish model of melanoma coupled with human samples, we profiled tumour cells at the interface between the tumour and surrounding microenvironment. Morphological analysis of these rare cells showed flattened, elliptical nuclei suggestive of mechanical confinement by nearby adjacent tissue. Spatial and single-cell transcriptomics demonstrated that the interface cells adopted a gene program of neuronal invasion, including acquisition of an acetylated tubulin cage that protects the nucleus during migration. We identified the DNA-bending protein HMGB2 as a confinement-induced mediator of the neuronal state. HMGB2 is upregulated in confined cells, and quantitative modelling revealed that confinement prolongs contact time between HMGB2 and chromatin, leading to changes in chromatin configuration that favour the neuronal phenotype. Genetic disruption of HMGB2 showed that it regulates the trade-off between proliferative and invasive states, in which confined HMGB2high tumour cells are less proliferative but more drug resistant. Our results implicate the mechanical microenvironment as a mechanism for phenotype switching in melanoma.

overall_design: Bulk RNA-sequencing of SKMEL5 human melanoma cells expressing nontargeting (NT) gRNA or gRNA targeting HMGB2.

first: Miranda V


title: Inhibiting CXCR4 Attenuates TOX-Programmed Exhausted Phenotype of CD8+ T cells via Regulating JAK2/STAT3 Pathway [RNA-Seq]

city: Wuhan

first: Canhui

last: Cao

address: Jiefang Road 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Tec

summary: T-cell exhaustion (Tex) phenotype has limited the efficacy of single-agent immune checkpoint blockade (ICB) in cancer immunotherapy, underscoring the need to target upstream pathways. Clinical trials have indicated that CXCR4 antagonists enhance anti-cancer activity. However, the specific mechanisms through which CXCR4 contributes to immune cell phenotypes are not fully understood. By targeting CXCR4 using antagonists or transgenic mice (Cxcr4flox/flox LckCre), we effectively attenuated the Tex phenotype and enhanced the functional T-cell phenotype in vivo. Additionally, single-cell RNA/TCR-seq analyses demonstrated that CXCR4 inhibition promotes anti-PD-1 immunotherapy by reducing CD8+ Tex phenotype and enriching the abundance of TCR clonotypes in vivo. Mechanically, we found that CXCR4-blocking T cells mitigate Tex phenotype by regulating the JAK2-STAT3 pathway, reducing the interaction between p-STAT3 and TOX. Single-cell ATAC/RNA-seq validated that CXCR4 deficiency epigenetically orchestrates the transition from functional to exhausted phenotypes in CD8+ T cells. Altogether, we demonstrate a mechanism of targeting CXCR4 to orchestrate CD8+ Tex cells in cancers and provide a rationale for the combined CXCR4 antagonists and ICBs in clinical trials.

overall_design: In this study, we explored single-cell transcriptome data from normal and tumors to identify CXCR4 expression patterns in T cells and found that CXCR4 is highly expressed in CD8+ PD-1high Tex cells. CXCR4 antagonists and transgenic mice (Cxcr4flox/flox LckCre) in multi-tumor models were used to identify the molecular mechanisms of CXCR4 in maintaining CD8+ Tex phenotypes in tumors. Furthermore, single-cell RNA/TCR-seq and RNA/ATAC-seq were employed to validate the TOX-mediated Tex phenotype triggered by CXCR4 in vitro and in vivo. Our findings provide a novel insight into molecular mechanisms underlying CXCR4 in maintaining the Tex phenotype in tumors, thereby providing a rationale for combination strategies between CXCR4 inhibitors and ICB in cancers.

first: Miaochun

last: Xu

first: Ye

last: Wei

first: Ting

last: Peng

first: Shitong

last: Lin

first: Xiaojie

last: Liu

first: Yashi

first: Tian

last: Chu

first: Shiyi

first: Bai

last: Hu

first: Wencheng

last: Ding

first: Li

first: Ding

last: Ma

first: Peng

last: Wu


title: Molecular and cellular rhythms in excitatory and inhibitory neurons in the mouse prefrontal cortex

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

institute: University of Pittsburgh

summary: While studies have shown that there are rhythms in gene expression in the prefrontal cortex (PFC), the contribution of different cell types and potential variation by sex has not been determined. Of particular interest are excitatory pyramidal cells and inhibitory parvalbumin (PV) interneurons, as interactions between these cell types are essential for maintaining the excitation/inhibition balance. Here, we identify cell-type specific rhythms in the translatome of PV and pyramidal cells in the mouse PFC and assess rhythms in PV cell electrophysiology. We find that while core molecular clock genes are conserved and synchronized between cell types, pyramidal cells have nearly twice as many rhythmic transcripts as PV cells (35% vs. 18%). Rhythmic transcripts in pyramidal cells also show a high degree of overlap between sexes, whereas in PV cells, rhythmic transcripts are largely distinct between sexes. Additionally, we find sex-specific effects of phase on action potential properties in PV cells. This study demonstrates that rhythms in gene expression and electrophysiological properties in the PFC vary by both cell type and sex. Moreover, the biological processes associated with rhythmic transcripts may provide insight into the unique functions of rhythms in these cells, as well as their selective vulnerabilities to circadian disruption.

overall_design: Ribosome associated RNA from PV and pyramidal cells in the mouse prefrontal cortex, isolated across 6 times of day.

first: Jennifer

middle: N

last: Burns

first: Aaron

last: Jenkins

first: RuoFei

last: Yin

first: Wei

last: Zong

first: Lauren

last: DePoy

first: Kaitlyn

last: Petersen

first: Mariya

last: Kaminsky

first: Chelsea

last: Vadnie

first: Madeline

last: Scott

first: George

middle: C

last: Tseng

first: Yanhua

last: Huang


title: Inhibiting CXCR4 Attenuates TOX-Programmed Exhausted Phenotype of CD8+ T cells via Regulating JAK2/STAT3 Pathway [scRNA_VDJ-seq]

first: Canhui

last: Cao

first: Miaochun

last: Xu

first: Ye

last: Wei

first: Ting

last: Peng

first: Shitong

last: Lin

first: Xiaojie

last: Liu

first: Yashi

first: Tian

last: Chu

first: Shiyi

first: Bai

last: Li


title: SOX9 is a key factor for the postnatal maturation of the intrahepatic bile duct network.

city: Kumaoto

first: Hiroki

last: Hirao

state: Kumamoto

address: 1-1-1, Honjo, Chuo-ku,

institute: Kumamoto university

summary: It is widely recognized that sex-determining region Y-box 9 (SOX9) plays a critical role in the development of intrahepatic bile ducts (IHBDs) during the embryonic stage. IHBDs are composed of two distinct networks: a hierarchical network and a homogeneous network. The hierarchical network consists of large bile ducts that run along the portal veins (PVs) and branch into smaller bile ducts, forming a reticular structure around the PVs. By contrast, the homogeneous network is an early tubular structure composed of bile ductules surrounding the PVs and serves as a precursor to the mature hierarchical network. This study examined the role of SOX9 in the postnatal development of these networks using three-dimensional imaging analysis and a mouse model in which SOX9 deficiency predominates after birth. Our findings indicate that SOX9 is essential for the maturation and structural organization of the IHBD, particularly in terms of facilitating the proper connection between bile ductules and bile canaliculi. Furthermore, transcriptional changes in Sox9 conditional knockout mice activated compensatory pathways involved in bile acid transport and metabolism, while downregulating intercellular adhesion pathways, thereby impairing cholangiocyte adhesion and structural integrity. These results indicate that SOX9 plays a more pivotal role in the development of the bile duct network than previously thought.

overall_design: C57BL/6J mice (Japan SLC, Shizuoka, Japan), Sox9flox/flox mice (strain #013106, The Jackson Laboratory, Bar Harbor, ME) and Albumin (Alb)-Cre mice (strain #003574, The Jackson Laboratory) were used in this study. To delete Sox9 in liver epithelial cells, Sox9flox/flox mice were crossed with Alb-Cre mice to give Alb-Cre+/+;Sox9 flox/flox (Sox9 cKO) mice. For RNA-seq analysis of mouse liver samples (CT n=3, SOX9 cKO n=3), total RNA was prepared using Trizol extraction (Thermo Fisher, Waltham, MA, USA), and the quality of the total RNA was confirmed using a BioAnalyzer 2100 (RNA integrity number > 9). DNA libraries were prepared according to the Illumina TruSeq protocol using a TruSeq Stranded mRNA LT sample prep kit (Illumina, San Diego, CA, USA) and sequenced using an Illumina NextSeq 500 (Illumina) with a NextSeq 500/550 High Output v2 kit (Illumina) to obtain single-end, 75-nt reads. RNA-seq data were aligned to the human genome (UCSC mm10) using STAR ver. 2.6.0a after trimming to remove adapter sequences and removal of low-quality ends using Trim Galore! v0.5.0 (cutadapt v1.16). Gene expression levels are reported as transcripts per million, as determined using RSEM v1.3.1.

first: Daiki

last: Yoshii

first: Shigeyuki

last: Esumi

first: Ahmad

last: Adawy

first: Yukio

last: Fujiwara

first: Masaki

last: Honda

first: Yuji

last: Yokouchi

first: Taizo

last: Hibi

first: Yoshihiro

last: Komohara


title: Single-cell characteristics of longitudinal immune profiling in subjects with breakthrough infections caused by Omicron BA.5 sublineages

city: Beijing

first: Yanhua

address: No.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Background Omicron subvariants have led to millions of coronavirus disease 2019 (COVID-19) cases worldwide. Although Omicron breakthrough infections (BTIs) exhibit lower hospitalization rates than previous variants, post-COVID conditions persist. However, the immune response dynamics, lymphocyte subsets, and immune repertoire features following BA.5 sublineage BTI remain poorly understood. Methods In a longitudinal cohort, we monitored the recovery dynamics in patients with BTI at various time points. We employed single-cell transcriptomics, T cell receptor (TCR)/BCR sequencing, and antibody mass spectrometry to sequentially assess the immune response following BA.5.2 or BF.7 BTI. Findings Serological analysis revealed active cellular and humoral immunity 2 weeks post-BTI, with significant increases in cytokines (CKs) like IFN-γ, TNFβ, IL-2, and neutralizing antibodies. CK levels reverted to pre-infection levels, while broadly neutralizing antibodies remained high 1 month post-infection. Single-cell sequencing demonstrated robust immune activation and antiviral responses in NK, T, and B lymphocytes within 1 month post-BTI. Interestingly, the immune system maintained its strength to combat viral infection at 2 weeks post-BTI, transitioning toward repair and tissue damage elimination at 1 month. TCR/BCR library analysis revealed a higher clonal type in the BTI_2w group, mainly in NKT, memory T or B, and plasma cells, crucial for immune memory and antigen clearance. The BTI_1m group exhibited more IgG and IgA BCR subtypes, with somatic hypermutation indicating mature antibodies. Biological function verification of IgG and IgA-type monoclonal antibodies corresponding to expanded BCRs revealed antigen-specific and broad-spectrum antibodies. Interpretation Our study elucidated the dynamic immune profiling of individuals 2 weeks and 1 month after Omicron BA.5 sublineage BTI. This provided essential insights into pathogenicity, sequential immune status, recovery mechanisms of Omicron subvariant BTI, and novel concepts for broad-spectrum antibody development.

overall_design:
We did single-cell RNA sequencing on 16 human samples that experienced BA.5.2 or BF.7 breakthrough infection at 2 weeks and 1 month post infection.

***************************************************************
Due to relevant policies and regulations of China's Ministry of Science and Technology, the raw data will be deposited to Genome Sequence Archive database.
***************************************************************

first: George

last: Gao

first: Shijie

last: Qin

first: Lei

last: Dong


title: The Role of Interferon-γ in Autoimmune Polyendocrine Syndrome Type 1

city: Bethesda

first: Behdad (Ben)

last: Afzali

address: 10 Center Drive, Building 10

institute: National Institutes of Health

summary:
Background: Autoimmune polyendocrine syndrome type 1 (APS-1) is a life-threatening, autosomal recessive syndrome caused by autoimmune regulator (AIRE) deficiency. In APS-1, self-reactive T cells escape thymic negative selection, infiltrate organs, and drive autoimmune injury. The effector mechanisms governing T-cell-mediated damage in APS-1 remain poorly understood.

Methods: We examined whether APS-1 could be classified as a disease mediated by interferon-γ. We first assessed patients with APS-1 who were participating in a prospective natural history study and evaluated mRNA and protein expression in blood and tissues. We then examined the pathogenic role of interferon-γ using Aire-/-Ifng-/- mice and Aire-/- mice treated with the Janus kinase (JAK) inhibitor ruxolitinib. On the basis of our findings, we used ruxolitinib to treat five patients with APS-1 and assessed clinical, immunologic, histologic, transcriptional, and autoantibody responses.

Results: Patients with APS-1 had enhanced interferon-γ responses in blood and in all examined autoimmunity-affected tissues. Aire-/- mice had selectively increased interferon-γ production by T cells and enhanced interferon-γ, phosphorylated signal transducer and activator of transcription 1 (pSTAT1), and CXCL9 signals in multiple organs. Ifng ablation or ruxolitinib-induced JAK-STAT blockade in Aire-/- mice normalized interferon-γ responses and averted T-cell infiltration and damage in organs. Ruxolitinib treatment of five patients with APS-1 led to decreased levels of T-cell-derived interferon-γ, normalized interferon-γ and CXCL9 levels, and remission of alopecia, oral candidiasis, nail dystrophy, gastritis, enteritis, arthritis, Sjögren's-like syndrome, urticaria, and thyroiditis. No serious adverse effects from ruxolitinib were identified in these patients.

Conclusions: Our findings indicate that APS-1, which is caused by AIRE deficiency, is characterized by excessive, multiorgan interferon-γ-mediated responses. JAK inhibition with ruxolitinib in five patients showed promising results. (Funded by the National Institute of Allergy and Infectious Diseases and others.).

overall_design:
RNA-seq analysis of human oral mucosal tissues in APECED patients and healthy donors.
Genomics andComputational Biology Core (contributor)

first: Vasileios

last: Oikonomou

first: Grace

last: Smith

first: Monica

last: Schmitt

first: Gregory

last: Constantine

first: Elise

last: Ferré

first: Julie

last: Alejo

first: Deanna

last: Riley

first: Dhaneshwar

last: Kumar

first: Yannis

last: Hadjiyannis

first: Daniel

last: Martin

first: Marine

last: Besnard

first: Brendan

last: Snarr

first: Shiva

last: Deljookorani

first: Chyi-chia

last: Lee

first: Lindsey

last: Rosen

first: Aristine

last: Cheng

first: Andre

last: Rastegar

first: Adrianna

last: Almeida de Jesus

first: Hyesun

last: Kuehn

first: Timothy

middle: J

last: Break

first: Theo

last: Heller

first: Karen

last: Winer

first: Heidi

middle: H

last: Kong

first: Leslie

last: Castelo-Soccio

first: Mikko

last: Seppanen

first: Sergio

last: Rosenzweig

first: Anthony

last: Suffredini

first: Mark

last: Anderson

first: Carole

last: Guillonneau

first: Luigi

last: Notarangelo

first: Raphaela

last: Goldbach-Mansky

first: Olaf

last: Neth

first: Maria

last: Monserrat-Garcia

first: Justo

last: Valderde-Fernandez

first: Jose

last: Lucena

first: Ana

middle: L

last: Gomez-Gila

first: Angela

last: Garcia Rojas

first: Hero

last: Matti

first: Saila


title: Identification and characterization of circular RNAs in the A549 cells following Influenza A virus infection

city: Changchun

first: Ming

last: Duan

state: Jilin

address: 5333 Xian Road

institute: Jiin Univiersity

summary: To identify the dysregulated circRNAs expression during IAV infection, A549 cells were inoculated with PR8 (MOI = 2) and harvested at 24 h p.i., while uninfected samples were regarded as controls. Subsequently the high-throughput circRNA microarray was performed (Arraystar Human circRNA Array V2).

overall_design: A549 cells were mock infected or virus infected with PR8 at a multiplicity of infection (MOI) of 2 and harvested at 24 h p.i.. CircRNAs chips by Arraystar Human circRNAs chip (Arraystar) were performed and three replicates were included in both mock- and virus-infected groups.

first: Yidi

last: Guo

first: Xiaohang

last: Yu

first: Ning

last: Su

last: Shi


title: RAD51 family members remodel the NHEJ system to modulate stress-induced biosynthesis of diterpenoid phytoalexins in rice

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

summary: Double-strand break (DSB) damage are primarily repaired via homologous recombination (HR) and non-homologous end joining (NHEJ) in Eukaryotes. We reveals that HR subcomplex RAD51A1-RAD51C in rice (Oryza sativa L.) inhibits classic NHEJ pathway while acts as a transcriptional mediator underlying alternative NHEJ signaling. RAD51C hijacks the KU70 at DSBs, facilitated by the interacting partner RAD51A1 or TOP6B responding environmental cues (pathogens and 4℃). Consequently, the enhanced alternative NHEJ signaling generates the phosphorylated SOG1, which activates the regulatory network in diterpenoid phytoalexin biosynthesis and a group of genes in phenylpropanoid pathway. Intriguingly, SOG1-BRCA1-RAD51 associates with RAD51C-RAD51D-XRCC3 forming a transcription pre-initiation complex in this process. Phenotypically, chemical disease resistance and 4℃-conditioned stomatal closure are compromised in single mutants (atm-3, sog1, and rad51c-1), double mutants (rad51a1 rad51a2 and rad51d xrcc3). In summary, HR pathway integrates classic and alternative NHEJ pathways to orchestrate stress-activated specific metabolism in rice plants. Hierarchical functional collaboration of global DSB-repair machinerys enable plant adaptability to DSB-related environmental stresses.

overall_design: ChlP-seg of the FLAG in the leaves of γ-irradiated SOG1-FLAG-OE1 line. Leaf samples was collected at 20 h after γ-irradiation treatment of 40 Gy.

first: Zhan

last: Xu

first: Jemaa

last: Essemine


title: GemC1 is a critical switch for neural stem cell generation in the postnatal brain

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

summary: The subventricular zone (SVZ) is one of two main niches where neurogenesis persists during adulthood, as it retains neural stem cells (NSCs) with self-renewal capacity and multi-lineage potency. Another critical cellular component of the niche is the population of postmitotic multiciliated ependymal cells. Both cell types are derived from radial glial cells that become specified to each lineage during embryogenesis. We show here that GemC1, encoding Geminin coiled-coil domain-containing protein 1, is associated with congenital hydrocephalus in humans and mice. Our results show that GemC1 deficiency drives cells toward a NSC phenotype, at the expense of multiciliated ependymal cell generation. The increased number of NSCs is accompanied by increased levels of proliferation and neurogenesis in the postnatal SVZ. Finally, GemC1-knockout cells display altered chromatin organization at multiple loci, further supporting a NSC identity. Together, these findings suggest that GemC1 regulates the balance between NSC generation and ependymal cell differentiation, with implications for the pathogenesis of human congenital hydrocephalus.

overall_design: ATAC-seq of mice PGCs (wild type and GemC1 knock out)


title: Transcriptomes of human PBMCs and monocytes in sepsis patients

city: Tel Aviv

first: Rachel

last: Brandes Leibovitz

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: FUSE cohort

overall_design:
PBMCs and Monocytes from 284 healthy subject and 125 sepsis patients
***Raw data not available due to patient privacy concerns***

first: Miha

last: Netea

first: Anca

last: Riza

first: Irit

last: Gat-Viks


title: Maternal cause of early-onset preeclampsia: excessive endometrial gland-derived apolipoprotein D induces placental ferroptosis and developmental abnormalities

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

summary: Early-onset pre-eclampsia (ePE) is a severe pregnancy complication affecting millions of pregnancies worldwide, resulting in significant maternal and fetal morbidity. The etiology of ePE is associated with defective trophoblast functions, leading to abnormal placental development. Regulatory factors released by endometrial glands are crucial for proper placental development. While circumstantial evidence indicates that defective endometrial gland development or function may lead to defective placental development and ePE in humans, direct evidence has been lacking. This study explored the role of endometrial gland-derived factors both in vitro and in vivo and correlated the findings with the clinical phenotypes of ePE. Our findings revealed that the secretome of organoids derived from the endometrial tissues of ePE patients impeded spiral artery remodeling and thus disrupted proper placental perfusion. Transcriptomic and proteomic analyses identified an increased apolipoprotein D (APOD) production in ePE organoids and decidual tissues compared to their normotensive (NT) counterparts. Overexpression of endometrial APOD impaired the vascular remodeling functions of extravillous trophoblasts (EVT) and endothelial cells in vitro. These findings were corroborated using an endometrial-specific APOD knock-in mouse model. APOD-induced ferroptosis through the PI3K/Akt pathway in both human ePE placentas and the mouse model. Moreover, elevated APOD levels were detected in the first-trimester serum of pregnant women who subsequently developed ePE. These results provide the first direct evidence that dysregulated endometrial gland secretome is a maternal cause of defective placental development and ePE. Clinically, APOD could serve as a biomarker for early detection of ePE, enabling early intervention with  the potential to improve outcomes for both mothers and their babies.

overall_design: Study the effect of pre-eclampsia  endometrial organoid secretion on the functions on EVTs in vivo and in vitro.

first: Yang

last: Dong

first: Cheuk-Lun

last: Lee

first: Philip C.N.

last: Chiu