title: Tumor-intrinsic kinome landscape of pancreatic cancer reveals new therapeutic approaches

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

summary: Effective therapies for pancreatic ductal adenocarcinoma (PDAC) have been largely elusive. Prior proteogenomic studies of PDAC have been limited to bulk samples limiting the ability to define tumor-intrinsic targets and understanding tumor heterogeneity. Here, we perform Multiplexed kinase Inhibitor Beads and Mass Spectrometry (MIB-MS) on 102 patient derived xenografts (PDX) derived from 14 unique primary PDAC to define the tumor-intrinsic kinome landscape. Our findings uncover three kinome subgroups making up two dominant tumor-intrinsic kinome subtypes that we call kinotypes. The kinotypes show enrichment of different kinase classes and explain the biological differences in previously described molecular subtypes, basal-like and classical. The kinotype characterizing basal-like tumors shows enrichment of receptor tyrosine kinases, whereas the kinotype characterizing classical tumors is enriched in understudied kinases involved in Wnt signaling and immune pathways. We validate our findings in two clinical trials and show that only patients with basal-like kinotype tumors, who are thought to be refractory to chemotherapy, derive significant benefit from EGFR inhibitors. Our results provide a comprehensive tumor-intrinsic kinome landscape of PDAC that strongly supports actionable kinotype specific kinase targets, potential for sensitive quantitation of patient samples, and provides a roadmap for the use of kinase inhibitors for the treatment of PDAC.

overall_design:
RNAseq of 13 Pancreatic ductal adenocarcinoma (PDAC) tumor lines from PDX models with replicates for each sample

Raw FASTQ files are not uploaded because the samples are from human patients and there is a concern of patient-privacy.

first: Xianlu

last: Peng

first: Yi


title: IL-18 engineered to avoid decoy-receptor binding enhances tumor rejection by anti-CTLA-4 in kidney cancer models through immune microenvironment remodeling.

status: Public on Nov 01 2024

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

country: USA

institute: Yale Cancer Center

type: Expression profiling by high throughput sequencing

summary: The cytokine interleukin-18 (IL-18) has immunostimulatory effects but is negatively regulated by a secreted binding protein, IL-18BP, that limits IL-18’s anti-cancer efficacy. A “decoy-resistant” form of IL-18 (DR-18), that avoids sequestration by IL-18BP while maintaining its immunostimulatory potential has recently been developed. Here, we investigate the therapeutic potential of DR-18 in renal cell carcinoma (RCC). We used immunocompetent RCC murine models to assess the efficacy of DR-18 in combination with single- and dual-agent anti-PD-1 and anti-CTLA-4. In contrast to preclinical models of other tumor types, in RCC models DR-18 enhanced the activity of anti-CTLA-4 but not anti-PD-1 treatment. This activity correlated with intra-tumoral enrichment and clonal expansion of effector CD8+ T cells, decreased regulatory T cell levels, and enrichment of pro-inflammatory, anti-tumor myeloid cell populations, as assessed by scRNA- and scTCR-seq.

overall_design: We performed scRNA-seq and scTCR-seq on Renca tumors impanted subcutaneously into Balb/c mice and treated with one of the following regimens: PBS; DR-18; anti-CTLA-4; or the combination ("Combo") of DR-18 and anti-CTLA-4. Tumor tissue from 3 mice per treatment condition were pooled for sequencing.

middle: A


title: Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response via AP1 dichotomy in pancreatic cancer [ChIP-seq]

city: Göttingen

first: Shiv

middle: K.

last: Singh

address: Robert-Koch-Straße 40

department: Gastroenterology, GI-Oncology and Endocrinology

country: Germany

institute: University Medical Center Göttingen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pancreatic ductal adenocarcinoma (PDAC) displays a high degree of spatial subtype heterogeneity. This intratumoral co-existence of classical and basal-like programs is evident in multi-scale transcriptomic and spatial analyses of resected, advanced-stage and chemotherapy-treated specimens and reciprocally linked to a diverse stromal immune microenvironment as well as worse clinical outcome. However, the underlying mechanisms of intratumoral subtype heterogeneity remain largely unclear. Here, by combining preclinical models, multi-center clinical, bulk and compartment-specific transcriptomic, proteomic, and bioimaging data from human specimens, we identified an interplay between neoplastic intrinsic AP1 transcription factor dichotomy and extrinsic CD68+ macrophages as a driver of intratumoral subtype co-existence along with an immunosuppressive tumor microenvironment with T cell exclusion. Our ATAC , ChIP-, and RNA-seq analyses revealed that JUNB/AP1- and HDAC-mediated epigenetic programs repress pro-inflammatory immune signatures in tumor cells, antagonizing cJUN/AP1 signaling to favor a therapy-responsive classical neoplastic identity. Through the tumor microenvironment, this dichotomous regulation was further amplified via regional macrophage populations. Moreover, CD68+/TNF-α+ cells associated with a reactive phenotype and reduced CD8+ T cell infiltration in human PDAC tumors. Consequently, combined anti-TNF-α immunotherapy and chemotherapy resulted in reduced macrophage counts and promoted CD3+/CD8+ T cell infiltration in basal-like PDAC, leading to improved survival in preclinical murine models. We conclude that tumor cell intrinsic epigenetic programs, together with extrinsic microenvironmental cues, facilitate intratumoral subtype heterogeneity and disease progression.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for histone deacetylase 1 (HDAC1) and histone 3 lysine 27 acetylation (H3K27ac) in CAPAN1 cells in presence or absence of JUNB-targeting siRNA (siJUNB) or control siRNA (siCtrl).


title: Integrated Multi-Omics Profiling Reveals Neutrophil Extracellular Traps Promote Aortic Dissection

city: Shanghai

first: Qinghai

last: Ye

state: Shanghai

address: 180 Fenglin Road, Shanghai 200032, China

country: China

institute: Zhongshan Hospital, Fudan University

summary: Adverse aortic remodeling increases the risk of aorta-related adverse events (AAEs) after thoracic endovascular aortic repair (TEVAR) and affects the overall prognosis of aortic dissection (AD). It is imperative to delve into the exploration of prognostic indicators to We performed single-cell transcriptomic and proteomic profiling of aortic lesions and peripheral blood samples, respectively, from patients with AD and healthy subjects. We then integrated single-cell RNA to identify phenotype-relevant subpopulations.

overall_design: Healthy normal aortas and dissected aortas were collected from participants.

first: Yufei

last: Zhao

first: Ziang

last: Zuo

first: Lixin

last: Wang


title: Nucleo-cytoplasmic distribution of SAP18 reveals its dual function in splicing regulation and heat stress responses in Arabidopsis

status: Public on Oct 31 2024

city: Bellaterra

first: Alvaro

middle: Santiago

last: Larran

state: Barcelona

address: C/ de la Vall Moronta s/n, Campus UAB

country: Spain

institute: CRAG

summary: RNA-seq experiment of Col0, sr45, and sap18 mutants

overall_design: Col0, sr45, and sap18 plants were grown on MS medium under 16:8 photoperiod at 22 °C for 11 days. RNA was extracted from 100 mg of seedlings using RNeasy plant mini kit (Qiagen) following manufacturer’s instructions. RNA was quantified in a Qubit 2.0 fluorometer using Qubit RNA Assay Kit and following by an integrity check on Bioanalyzer. 2 μg of RNA per sample was sent to Macrogen for library preparation and sequencing performing (Truseq stranded mRNA Library + NovaSeq6000, 150 x 2bp, 30M reads/sample, 4.5Gb/sample).

middle: S

first: Julia

middle: I

last: Qüesta

first: Guiomar

last: Martín


title: Gene expression profile at the single cell level of effector memory CD4+ T cells from PBMC of healthy donors and patients with arrythmogenic cardiomyopathy

city: Toulouse

first: Victorine

last: Douin-Echinard

address: 4bis Avenue Hubert Curien

country: France

institute: RESTORE UMR-1301 INSERM

summary: Study of effector/memory CCR4+ CD45RO+ regulatory CD4+ T cells in ACM patients compared to age-matched controls

overall_design: Flow cytometry cell sorted singlet CD4+ CD3+ CCR4+ CD25+ CD45RO+ CCR7+/- CD14- CD19- CD56- LiveDead - from PBMC

first: Elena

last: Sommariva

first: Jason

last: Iacovoni

first: Ignacio

last: Gonzalez

first: Salwa

last: Soussi


title: Cellular Feimin enhances exercise performance by suppressing muscle thermogenesis

city: Beijing

first: Yiguo

address: Tsinghua University, Haidian District

department: School of Life Sciences

institute: Tsinghua University

summary: Exercise can rapidly increase core body temperature, and research has indicated that elevated internal body temperature can independently contribute to fatigue during physical activity. However, the precise mechanisms responsible for regulating thermogenesis in muscles during exercise have remained unclear. Here, we demonstrate that cellular Feimin (cFeimin) enhances exercise performance by inhibiting muscle thermogenesis during physical activity. Mechanistically, we found that AMPK phosphorylates cFeimin and facilitates its translocation into the cell nucleus during exercise. Within the nucleus, cFeimin binds to the forkhead transcription factor FOXC2, leading to the suppressed expression of Sarcolipin (Sln), which is a key regulator of muscle thermogenesis. In addition, our results further reveal that short-term AMPK agonist treatments can enhance exercise performance through the activation of the AMPK-cFeimin signaling pathway. In summary, these results underscore the crucial role of cFeimin in enhancing exercise performance by modulating SLN-mediated thermogenesis.

overall_design: To further assess the impact of cFeimin on exercise performance and energy utilization, we employed a low-intensity exercise protocol where mice ran at a constant speed equivalent to 60% of their maximal running speed. This protocol was employed for subsequent experiments in our study. In comparison to control littermates, cFeimin MKO mice exhibited reduced running time and distance compared to their WT little mates. The gastrocnemius muscles of sedentary (Sed) and 90-min exercised (Exe) fl/fl (WT) and cFeimin MKO (MKO) male mice were harvested for total RNA extraction, and RNA-seq analysis was performed.

first: Jia

last: Liangjie

first: Peng

last: Ying


title: Bone marrow niches orchestrate stem cell hierarchy and immune tolerance

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

summary: Stem cells reside in specialized microenvironments, termed niches, at several different locations within tissues1-3. The differential functions of heterogeneous stem cells and niches are important given increasing clinical applications of stem cell transplantation and immunotherapy. It remains unknown whether hierarchical structures amongst stem cells at distinct niches exist, and further control aspects of immune tolerance. Here, we propose novel hierarchical arrangements within hematopoietic stem cells (HSCs) and bone marrow (BM) niches, that dictate both regenerative potential and immune privilege. High level nitric oxide-generating (NOHi) HSCs are refractory to immune attack and exhibit "delayed" albeit robust long-term reconstitution. Such highly immune privileged, primitive NOHi HSCs colocalize with distinctive capillaries, characterized by primary ciliated endothelium and high levels of the immune checkpoint molecule CD200. These capillaries regulate the regenerative functions of NOHi HSCs through ciliary protein IFT20/CD200/eNOS/autophagy signals, further mediating immune protection. Notably, previously described niche constituents, sinusoidal cells and Type H vessels2-10, co-localize with less immune privileged and less potent NOLow HSCs. Therefore, we have identified highly immune privileged, "late-rising" primitive HSCs and characterized their immunoprotective niches constituted of specialized vascular domains. Our studies suggest the niche may orchestrate hierarchy in stem cells and immune tolerance, delineating future immunotherapeutic targets.

overall_design: CD200Hi capillaries (CD200HiSca1+CD31+EMCN-CD45-), Type H vessels (EMCN+Sca1+CD31+CD45-), other arterial cells (CD200-Sca1+CD31+CD45-), and sinusoidal cells (CD31+Sca1+CD45-) were sorted from BM cells obtained from crushed bone (tibia, femur, and iliac tissues). RNA was isolated from sorted cells lysed in TRIzol. Biological triplicates were prepared using six B6 mice. RNA quality was assessed using Agilent Bioanalyzer RNA-Pico kit (Agilent Technologies, USA). Libraries were prepared using the Clontech Ultra Low v4 kit (Takara Bio) for cDNA synthesis, followed by NexteraXT (Illumina, USA), and sequenced on an Illumina NovaSeq6000 (Illumina, USA), resulting in libraries with read lengths of 150bp.

first: K

last: Furuhashi

first: M

last: Kakiuchi

first: R

last: Ueda

first: H

last: Oda

first: S

last: Ummarino

first: A

middle: L

last: Ebralidze

first: C

last: Meng

last: Sato

first: J

last: Lyu

first: M-G

last: Han

last: Maruyama

first: Y

last: Watanabe

last: Sawa

first: D

last: Kato

last: Wake

first: B

last: Reizis

last: Frangos

middle: M

last: Owens

middle: G

last: Tenen

first: I

middle: C

last: Ghiran

last: Robson

last: Fujisaki


title: Effect of Botrytis cinerea infection in Col-0 and erfVII pentuple mutant

city: San Giuliano Terme

first: Simone

last: Castellana

state: PIsa

address: Via Giovanni Guidiccioni, 8/10

department: Istitute of Plant Science

country: Italy

institute: Scuola Superiore Sant'Anna

summary: Pathogens infection exerts major effects on gene expression, which is reconfigured to raise the defences of the attacked plant. In the recent years the establishment of an hypoxic environment during Botrytis   infection was described. We used the pentuple erfVII mutant to evaluate the contribution of ERFVII members to plant reaction to Botrytis and their effect on gene expression.

overall_design: Each group is represented by one biological replicates. Each one was obtained by pooling 5 plants. Genotypes of Arabidopsis thaliana used included Col-0 ecotype (wild-type) and the pentuple erfVII mutant. Plants were grown in pots for 3-4 weeks at 23°C with a 12/12 h photoperiod at 120 μmol photons m–2 s–1 before being utilized for experiments. Plants were infected with Botrytis for 48h at high umidity before sampling.

first: Pierdomenico

last: Perata

first: Elena

last: Loreti


title: The Novel miR_146-Tfdp2 Axis Antagonizes METH-Induced Apoptosis and Cell Cycle Abnormalities in Tree Shrew Primary Neurons

city: Kunming City

first: shu wei

last: zhang

state: Yunnan Province

address: Chenggong District

department: School of Forensic Medicine

institute: Kunming Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: This project focuses on the neurotoxic effects of methamphetamine (METH) abuse and its impact on the central nervous system. Methamphetamine is a highly addictive synthetic drug that can cause severe cognitive and behavioral changes, as well as neurodegenerative diseases. We conducted transcriptome sequencing on METH-treated primary neurons from tree shrews to investigate the underlying mechanisms of METH-induced neuronal damage.

overall_design: This project involves isolating cells with dopaminergic neuronal activity from neonatal tree shrews. We conducted transcriptome sequencing on primary neurons from tree shrews treated with methamphetamine (METH) to investigate the underlying mechanisms of METH-induced neuronal damage.

first: Shuwei

last: Zhang

first: Xiaofeng

last: Zeng

first: Juan

last: Li

first: Chan

last: Wang


title: Transcriptome analysis of the effect of HERV-K env gene knockout in ovarian cancer cell lines

city: Busan

first: EUNJI

last: KO

address: Busan

country: South Korea

institute: Kosin University College of Medicine

summary: Transcriptome analysis revealed that 23 differentially expressed genes (DEGs) were upregulated and 17 DEGs were downregulated in SKOV3 cells. In OVCAR3 cells, 198 DEGs were upregulated, and 17 DEGs were downregulated. Notably, 53 DEGs exhibited statistically significant differences among the 1,612 DEGs identified. Our findings indicate that HERV-K env gene KO exerts a profound influence on gene expression patterns in OVCAR3 cells, while genetic alterations in expression were relatively modest in SKOV3 cells. Nevertheless, genes ND1, ND2, and CYTB displayed a common increase in expression, while ERRFI1 and NDRG1 exhibited a decrease in expression in both cell lines.

overall_design: HERV-K env gene KO was achieved in SKOV3 and OVCAR3 ovarian cancer cell lines using the CRISPR-Cas9 system. Next-generation mRNA sequencing was employed to assess the gene expression profiles of both mock and HERV-K env KO ovarian cancer cells. Furthermore, comprehensive analyses involving gene ontology and pathway assessments were conducted.

first: Eun-Ji

last: Ko

first: Dong

last: S Suh

first: Hongbae

last: Kim

first: Ji

middle: Y

last: Lee

first: Wan

middle: K

last: Eo

first: Heungyeol

first: Ki

middle: H

first: Hee-Jae

last: Cha


title: Ginkgolide B increase healthspan and lifespan of female mice

city: Taichung

first: Chien-Wei

address: 2 Yuh-Der Road

country: Taiwan

institute: CMUH

summary: Various anti-aging interventions exhibit potential in extending lifespan, yet most of these interventions are inefficacy or even have deleterious effects on healthspan. Ginkgolide B (GB) is a Ginkgo biloba-derived small molecule that reduces aging-related morbidities; however, the effects of GB on healthspan and longevity remain elusive. Here, we report that continuous oral GB administration in mice starting at 20 months extended their lifespan by 20% and reduced tumour incidence. Besides, GB administration significantly improved healthspan evidenced by enhancement in muscle quality, physical performance, grip strength, metabolism, frailty index, systemic inflammation, and senescence. Moreover, GB administration ameliorated aging-related pathologies without any apparent adverse effects. Single-nucleus RNA sequencing (snRNA-seq) revealed that GB improved aging-associated abnormal cell-type composition, intracellular signalling pathways, and cell-cell communication in skeletal muscles. GB also reduced the levels of aging-induced novel Runx1+ type 2B myonuclei, which are associated with apoptotic burden and aging-related signatures. Runx1 derived senescence, as shown by gain- and loss-of-function assays. Together, a new function of GB in extending the healthspan in aging is identified, which contributes to lifespan extension. The senomorphic effects of GB on the multifactorial aging process may provide new prospects for achieving healthy aging and longevity extension.

overall_design: RNA sequencing on GA tissue of Aged+Vehicle vs Young+Vehicle and Aged+GB vs Aged+Vehicle


title: Elevated microRNA-187 causes cardiac endothelial dysplasia to promote congenital heart disease through inhibition of NIPBL [Heart  RNA-Seq]

status: Public on Nov 03 2024

city: shanghai

first: tan

last: zizheng

address: songhu road

institute: Fudan university

summary: Dysplasia of cardiac endothelial cells significantly contributes to congenital heart disease (CHD), the most common congenital disability. The regulatory role of miRNAs in this process remains elusive. This study identified elevated miR-187 expression in embryonic heart endothelial cells from CHD fetuses. Using a conditional knock-in model, we showed that increased miR-187 levels in embryonic endothelial cells induce CHD in homozygous fetal mice, closely mirroring human CHD. Mechanistically, miR-187 targets NIPBL, which is responsible for recruiting the cohesin complex and facilitating chromatin accessibility between enhancers and promoters. Consequently, the endothelial cell-specific upregulation of miR-187 inhibited NIPBL, leading to reduced chromatin accessibility and impaired gene expression, which hindered endothelial cell development and ultimately caused heart septal defects and reduced heart size both in vitro and in vivo. Importantly, exogenous miR-187 expression in human cardiac organoids mimicked developmental defects in the cardiac endothelial cells, reversible by NIPBL replenishment. Our findings establish the miR-187/NIPBL axis as a potent regulator that inhibits cardiac endothelial cell development by attenuating the transcription of numerous endothelial genes, with our mouse and human cardiac organoid models effectively replicating severe defects from minor perturbations.

overall_design: To investigate the effect of increased miR-187 expression on the transcriptome of mouse hearts, we performed RNA seq sequencing on the heart tissues of WT mice and miR-187 overexpressing mice during the P0 period.

first: Chao

first: Zizheng

last: Tan

first: Hongdou

first: Xiaoying

last: Yao

first: Chuyue

last: Peng

first: Yue

last: Qi

first: Bo

last: Wu

first: Tongjin

last: Zhao

first: Chentao

first: Jianfeng

last: Shen

first: Hongyan


title: Trigger inducible tertiary lymphoid structure formation using covalent organic frameworks for cancer immunotherapy

city: Wuhan

first: Boxin

last: Zhang

address: 237 Luoyu Road

institute: Wuhan University

summary: The discovery of tertiary lymphoid structures (TLS) within the tumor tissues provides a promising avenue to promote the response rate of cancer immunotherapy. Yet, the lack of effective strategies to promote TLS formation poses a substantial obstacle. Thus, the exploration of potential inducers for TLS formation is of great interest but remains challenging. Here, inspired by the mechanism of artificially cultivated pearls, a covalent organic frameworks (COFs) was employed to promote the formation of TLS. Single-cell sequencing analysis revealed that this was achieved by promoting the cytokine hypersecretion to facilitate the maturation, proliferation, and migration of T and B cells, critical for trigger TLS formation. Furthermore, the high efficacy of COF-mediated phototherapy in inducing TLS formation was validated in both the MC38 and 4MOSC1 tumor models. Moreover, an efficient synergism between COF-mediated phototherapy and αCTLA-4 was observed, which was able to effectively eradicate both primary and distant tumors, and inhibit tumor recurrence. This study underscores a new approach of boosting cancer immunotherapy through COF triggered TLS formation.

overall_design: Tumor tissues from 4T1 tumor-bearing mice that had undergone AIE COF-mediated phototherapy and those that had not received AIE COF-mediated phototherapy

first: Liang

first: Jacky

last: Lam

first: Ben

middle: Z

last: Tang

first: Zhi-Jun

last: Sun


title: Argonaute3-SF3B3 complex controls pre-mRNA splicing to restrain Type-2 immunity

city: South San Francisco

first: Jason

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

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

overall_design: Refer to individual Series


title: miRNA profiling of lung epithelial cells (BEAS-2B cells) exposed to manganese (Mn)

status: Public on Nov 02 2024

city: Bhopal

first: Deepa

last: Gandhi

address: Saket Nagar

country: India

institute: AIIMS Bhopal

summary: Investigating the molecular mechanism and role of microRNAs in Mn-induced pulmonary toxicity

overall_design: miRNA seq analysis was performed for Mn treated BEAS-2B cells with control.

first: Gandhi

last: Deepa

first: Subbiah

last: Rajasekaran


title: Gene expression analysis conducted 3 or 4 days after 6 Gy IR exposure in H460 cells.

status: Public on Oct 30 2024

city: Incheon

first: Jae-Seon

last: Lee

address: Inha-ro

institute: Inha University

summary: To identify key regulators of PD-L1 glycosylation in senescent cancer cells, we examined the expression profiles in a microarray dataset derived from IR-induced senescent H460 cancer cells.

overall_design: Total RNA obtained from H460 cells 3 or 4 days after exposure to 6 Gy IR was compared with that from untreated control H460 cells.

first: H

middle: J

last: Hwang

first: D

last: Kang

first: J


title: Single cell RNAseq of murine tissues after, sham operation, myocaradial infarction (MI) or MI and sleep fragmentation (SF)

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

summary: It remains unclear how sleep influences inflammatory pathways after myocardial infarction (SF). In this study, we relied on established murine models and assessed how sleep fragmentation (SF) alters transcriptional programing in the blood, heart, and brain after MI.

overall_design: Female C57BL/6 mice 10-12 weeks of age were subjected to sham operation or permanent ligation of the left anterior descending coronary artery (MI). Half the mice subjected to MI were exposed to SF daily during the light period beginning immediately after surgical recovery (∼1 hour after MI). The other half of the MI mice and all the sham mice were left undisturbed and allowed to sleep habitually. There were five mice in each of the three experimental groups: sham, MI, MI+SF. Three days after sham or MI operation, all mice were perfused with cold PBS. The hearts were collected from the MI and MI+SF mice; brains were collected from the sham and MI mice; blood was collected from mice in all experimental groups. From the hearts, the infarcted left ventricle area from MI mice or the corresponding uninfarcted tissue from sham mice was isolated, enzymatically digested, and subjected to MACS bead sorting to enrich for CD45+ leukocytes. Brains were enzymatically digested, subjected to a percoll gradient, and CD45+ leukocytes were also enriched for using MACS bead sorting. For the blood samples, whole blood was subjected red blood cell lysis, and the remaining leukocytes were collected. All single cell suspensions from the same tissues and experimental groups were pooled, washed, and subjected to scRNAseq.

first: Cameron

last: McAlpine

first: Pacific

last: Huynh

first: Jan

last: Hoffmann


title: Cardiac conduction system regeneration prevents arrhythmias after myocardial infarction

city: Oxford

first: Judy

middle: R

last: Sayers

address: Institute of Developmental and Regenerative Medicine, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Headington

country: United Kingdom

institute: University of Oxford

summary: Arrhythmias are a hallmark of myocardial infarction (MI) and increase patient mortality. The cardiac conduction system is implicated in arrhythmias, but how it is altered following MI is poorly understood. We demonstrate complete conduction system restoration during neonatal mouse heart regeneration, versus pathological remodelling at non-regenerative stages. Tissue-cleared whole-organ imaging identified disorganised bundling of conduction fibres after MI, global His/Purkinje disruption and regional loss of connexin-40. Single-cell RNA-sequencing revealed that Purkinje cells undergo specific molecular changes to regenerate the network, versus sustained aberrant electrical alterations during fibrotic repair. This manifested functionally as transition from normal rhythm to pathological conduction delay beyond the regenerative window. Modelling the non-regenerative phenotype in the infarcted human heart implicated these changes as causative for bundle branch block and ventricular dyssynchrony, as observed in patients. These findings elucidate the mechanisms underpinning conduction system regeneration versus repair and reveal the consequences of MI-induced damage for clinical arrhythmogenesis.

overall_design: Characterisation of the regenerating and non-regenerating murine cardiac conduction system after myocardial infarction, by single-cell RNA-sequencing.

first: Hector

last: Mrtinez-Navarro

first: Xin

first: Carla

last: de Villiers

first: Sarah

last: Sigal

first: Leto

last: Riebel

first: Lucas

last: Berg

first: Julia

last: Camps

first: Neil

last: Herring

first: Blanca

last: Rodriguez

first: Tatjana

last: Sauka-Spengler

first: Paul

last: Riley


title: Single cell RNAseq analysis of PBMCs isolated from healthy adults subjeccted to sleep restriction

summary: How sleep influences the transcriptional programing of blood leukocytes in humans remains incompletely undertstood. Volunteers with adequate sleep participated in a 6 week cross-over design trial. During the habitual sleep (HS) phase, participants did not alter their sleep and slept adequately. During the sleep restriction phase (SR), participants restricted their sleep by ∼1.5 hours per night. PBMCs from 8 individuals (4 HS and 4 SR) were collected  subjected to scRNAseq.

overall_design: Peripheral blood mononuclear cells (PBMCs) were collected in the evening (target time: 15:00–17:00) from men and women, aged 20–75 y with BMI <35 kg/m2, participating in a 6-week randomized crossover study in which chronic mild insufficient sleep was imposed on volunteers with adequate habitual sleep duration. To examine if sleep shapes the transcriptional landscape of monocytes, we performed scRNAseq of PBMCs on eight distinct participants whose sleep duration, measured objectively with nightly actigraphy, was 7.5±0.1 hours/night during the habitual sleep (HS) phase and 6.2±0.1 hours/night during the sleep restriction (SR) phase.

first: Faris

last: Zuraikat

first: Marie-Pierre

last: St-Onge


title: The detection of Prunus virus F and its distribution in Hungarian sour cherry orchards

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: Viromes of sour and sweet cherry trees in Hungarian germ line collections were surveyed using small RNA HTS as an unbiased method. RNA from leaf samples of different cultivars were purified and used to produce seven pools from which small RNA HTS libraries were prepared. The sequenced reads were analyzed using bioinformatic methods to revel the presence of viruses in the samples. Presence of the viruses were validated using RT-PCR.

sample_organism:
Prunus avium
Prunus cerasus

platform_organism:
Prunus avium
Prunus cerasus

overall_design: sRNA HTS based diagnostics from leaf samples of the presenting viruses in different sour and sweet cherry cultivars

first: Francesco

last: Desiderio

first: Zsuzsanna

last: Nagyné Galbács

first: Éva

last: Várallyay


title: Ribosome profiling analysis of Denr and Eif2d depleted cells reveals the absence of re-initiation function of EIF2D

city: Lausanne

first: Romane

last: Meurs

state: Vaud

address: Genopode

department: Center for Integrative Genomics

country: Switzerland

institute: Universite de Lausanne

summary: Among the transcript features that regulate translation rate, upstream open reading frames (uORFs) have emerged as a major class of inhibitory elements which limit how many scanning ribosomes reach the start codon of the main protein coding sequence (CDS). Two processes are implicated in ensuring that CDS translation of uORF-containing transcripts can take place nevertheless: first, leaky-scanning, which involves the bypassing of uORF start codons by the scanning 40S ribosome, and second, re-initiation (REI), which allows the 40S subunit of the ribosome that terminated on the uORF stop codon to resume scanning to reach a downstream start codon. REI has remained particularly enigmatic, as it is at odds with generally accepted principles of conventional translation initiation, termination and post-termination subunit recycling. MCTS1-DENR is the first re-initiation-specific factor that has been identified. Its homolog, EIF2D, is assumed to act in uORF REI as well, yet formal proof of EIF2D-mediated REI has remained scarce. In our study, we present our in vivo analyses of DENR and EIF2D in translation re-initiation in mammalian cells. At the transcriptome-wide scale, ribosome profiling clearly identifies DENR-dependent REI, yet disproves the assumption that EIF2D also functions as a REI-factor.

overall_design: NIH3t3 cells were knocked-down by transduction with control shRNAs (scramble and a non-functional Eif2d shRNA) or shRNA targeting Denr or Eif2d. Biological replicates of each condition were harvested and flash frozen. Ribosome profiling and parallel RNA-seq were prepared and sequenced to compare the effect of Eif2d and Denr knock-down on translation efficiency.

first: David

last: Gatfield


title: Ginkgolide B administration improves health span and lifespan in aged mice

city: Taichung City

first: Chien-Wei

last: Lee

address: No. 2, Yude Road, North District

department: Department of Medical Research

institute: Translational Cell Therapy Center, China Medical University Hospital, China Medical University, Taiwan

summary: Ginkgolide B (GB) is a small molecule from Ginkgo biloba and implicates the reduction of certain aging-related morbidities; however, whether GB improves overall healthspan and longevity remains unknown. By single-nucleus RNA sequencing (snRNA-seq), we revealed that GB partially restored the aging-related dysregulation in cell-type composition, intracellular signaling pathways, and cell-cell communication in skeletal muscle. Notably, GB reduced the quantity of aging-induced novel Runx1+ type 2B myonuclei, which are particularly associated with an apoptotic burden and aging-related signatures.

overall_design: 3- (young), and 20-month-old (aged) female C57BL/6 mice were administered 12 mg/kg body weight GB or vehicle daily by oral gavage for two months. Gastrocnemius (GA) muscle of mice were minced, resuspended and labelled with DAPI. Labelled nuclei were sorted by FACS Aria II Cell Sorter and collected. Nuclei from 2 mice were pooled together for each sample and processed using Chromium Single Cell 3’ kit for downstream single-nuclei RNA sequencing.

first: Belle

last: Wang

first: Shing

last: Wong

first: Yi-Fan

last: Chen

first: Qin

last: Cao

first: Allen

middle: W

last: Hsiao

first: Sin-Hang

last: Fung

first: Stephen

last: Tsui

first: Oscar


title: Coupling of response biomarkers between tumour and peripheral blood in patients undergoing chemoimmunotherapy

city: Nedlands

first: Nicola

last: Principe

state: WA

address: 6 Verdun St

country: Australia

institute: University of Western Australia

summary: Platinum-based chemotherapy in combination with anti-PD-L1 antibodies has shown promising results in mesothelioma. However, the immunological mechanisms underlying its efficacy are not well understood and there are no predictive biomarkers of clinical outcomes to guide treatment decisions. Here, we combine time-course RNA sequencing of peripheral blood mononuclear cells with pre-treatment tumour transcriptome data from the 54-patient cohort in the single arm phase II DREAM study. In peripheral blood, CD8 + T effector memory cells with stem-like properties are more abundant in responders at baseline, 3 weeks, and 6 weeks into therapy. These peripheral blood changes are linked to the transcriptional state of the tumour microenvironment. The identified immunological correlates are predictive of response and provide further evidence for the additive nature of the interaction between platinum-based chemotherapy and PD-L1 antibodies. Our study highlights the complex, but predictive interactions between the tumour and immune cells in peripheral blood during the response to chemoimmunotherapy.

overall_design: 55 pleural mesothelioma patients were recruited from 8 Australian sites as a part of the phase II DREAM study. Patients were treated with up to 6 cycles of chemo-immunotherapy that included 3-weekly cisplatin or carboplatin in combination with pemetrexed and durvalumab. Maintenance included 12 months of durvalumab on a 4-weekly basis. Peripheral blood samples were drawn at three timepoints. The first was taken at pretreatment baseline prior to dexamethasone pre-medication (timepoint 0, BL). The subsequent two samples were taken before the second (timepoint 1, C2D1) and third cycles (timepoint 2, C3D1) of chemoimmunotherapy treatment. Single cell TCRseq was performed on the peripheral blood samples.

first: Jonathan

last: Chee

first: Joel

last: Kidman


title: SNORD113-114 cluster maintains hematopoietic stem cell self-renewal via orchestrating the translation machinery

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Hematopoietic stem cells (HSCs) self-renew and differentiate to replenish the pool of blood cells, which require a low but finely-tuned protein synthesis rate. Nonetheless, the translatome landscape in HSCs and how the translation machinery influences HSC self-renewal remain largely elusive. Here, we perform the ultra-low-input Ribo-seq in HSCs, progenitor and lineage cells, and reveal HSCs specifically translated genes involved in rRNA processing. We then systematically profiled the snoRNAs and uncover an indispensable role of SNORD113-114 cluster at the Dlk1-Gtl2 imprinting locus in regulating HSC self-renewal. Maternal knockout of this cluster (Mat-KO) significantly impairs HSC self-renewal, while loss of the paternal allele shows no obvious phenotype. Mechanistically, Mat-KO results in dysregulation of translation machinery (rRNA 2’-O-Me modifications, pre-rRNA processing, 60S ribosome assembly, and translation) and induces nucleolar stress in HSCs, which exempts p53 from MDM2 mediated proteasomal degradation and eventually leads to apoptosis. Finally, overexpression of snoRNAs or L-leucine mediated translation recovery rescues deficiency in Mat-KO HSCs. Collectively, our study provides a new facet to our understanding of snoRNA-mediated regulation in HSC homeostasis.

overall_design: 3 wildtype and 3 mutant knockout mice to get DE genes on bulk RNA-seq analysis

first: Hui

first: Zhaoru

last: Zhang

first: Chenxi

last: Han

first: Penglei

last: Jiang

first: Jiayue

last: Xu

first: Yingli

first: Deyu

last: Huang

first: Jian

last: Li

first: Jie

last: Zhou

first: Yaxin

last: Liu

first: Jinghao

last: Sheng

first: Jianzhao

first: Michael

last: Durnin

first: Bing

first: Jia

last: Yu

first: Fang

first: Pengxu

last: Qian


title: Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [methylation]

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

type: Methylation profiling by genome tiling array

summary: Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by systemic inflammation that involves various immune cell types. Monocytes are central players in promoting and regulating inflammation. Different monocyte subsets exist and change their proportions during physiological immune responses and under pathological conditions, including SLE, supporting different roles in inflammatory responses. In this study, we obtained the epigenetic and transcriptomic profiles of the three monocyte subsets, classical, intermediate and non-classical monocytes in an SLE cohort. We found different common and subset-specific alterations. While SLE classical monocytes had a stronger proinflammatory profile with an important interferon influence priming them towards macrophage differentiation, non-classical monocytes had a phenotype related to T cell differentiation regulation, with several indications pointing towards a Th17 promoting behavior. Integration of these bulk datasets with single-cell RNA-seq data of an SLE cohort shed light on the heterogeneity of our monocytes, confirming the interferon signature profile of classical monocytes and pointing towards intermediate and non-classical populations associated with exacerbated complement activation pathways, among others. With this analysis, we confirm the differential role of monocyte subsets in the pathogenesis of SLE and give insight into their regulatory mechanisms.

overall_design: DNA methylation analysis of sorted classical monocyte, intermediate monocyte and non-classical monocyte subsets from 20 SLE patients at flare and follow-up visit, and 10 healthy donors

first: Anna

last: Ferrete-Bonastre

first: Monica

last: Martinez-Gallo

first: Octavio

last: Morante-Palacios

first: Celia

last: Calvillo

first: Josep

last: Calafell-Segura

first: Javier

last: Rodriguez-Ubreva

first: Manel

last: Esteller

first: Josefina

last: Cortes-Hernandez


title: Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus


title: RNA-seq of danshen injection, astaxanthin and diosmetin for the treatment of anthracycline-induced cardiotoxicity in H9c2 cardiomyocytes

city: Shiyan City, Hubei Province

first: yijun

last: pan

address: 30 Renmin South Road, Shiyan City, Hubei Province

institute: Hubei university of medicine

summary: Doxorubicin (DOX) and other anthracyclines are effective chemotherapeutic agents, however, their use is influenced by the risk of cardiotoxicity. We still have an incomplete understanding of the cardiomyocyte protective pathways activated after anthracycline-induced cardiotoxicity (AIC).Danshen injection (DSI), astaxanthin (AXT) and diosmetin (DMT) are effective in the treatment of cardiovascular diseases, but the mechanism of protection against adriamycin-induced cardiotoxicity is unclear. Here, we performed RNA-seq screening in H9c2 cardiomyocytes to determine the potential protective mechanisms of Danshen injection, astaxanthin and diosmetin against AIC.

overall_design: To investigate the therapeutic effects of danshen injection, astaxanthin and diosmetin, respectively, in  anthracycline-induced cardiotoxicity, we divided cultured H9c2 cells into five groups:a control group treated with PBS, a model group exposed to 2μM DOX, a treatment group subjected to 2μM DOX in combination with 50μL DSI diluted 1/20 in culture volume, a treatment group subjected to 2μM DOX in combination with 5μM AXT and a treatment group subjected to 2μM DOX in combination with 10μM DMT. Each group consisted of three samples, with DOX added after 4 hours of DSI, AXT an DMT  treatment. The cells were harvested 24 hours after DOX treatment, then we performed gene expression profiling analysis using data obtained from RNA-seq. Comparative gene expression profiling analysis of RNA-seq data.

first: Guoxing

last: Wan

first: Xiwen

last: Zhu

first: Yijun

last: Pan

first: Mengyao

last: Chen


title: Longitudinal omics data followed by preclinical treatment studies identify proteasome inhibition as potential salvage strategy for ibrutinib-resistant CLL

status: Public on Oct 29 2024

city: Heidelberg

first: Marc

last: Zapatka

state: Select State

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Chronic lymphocytic leukemia (CLL) is a malignant lymphoproliferative disorder characterized by the accumulation of small mature B cells in blood and secondary lymphoid tissues. Novel drugs, such as the Bruton tyrosine kinase (BTK) inhibitor ibrutinib, have greatly improved survival expectations of CLL patients, nevertheless acquired drug resistance represents a major challenge and the complete molecular mechanisms of which have not been elucidated yet. In order to fill this knowledge gap, we generated a mouse model of ibrutinib resistance by treating mice upon adoptive transfer of Eµ-TCL1 leukemia (TCL1-CLL) continuously with ibrutinib. After an initial response to the treatment, relapse under therapy occurs with an aggressive outgrowth of the malignant cells, resembling observations in patients. To unravel relapse mechanism, we performed transcriptome and proteome analyses of sorted TCL1-CLL cells both during treatment and after relapse. Comparative analysis of these omics layers suggested alterations in the proteasome activity as a driver of ibrutinib resistance. Accordingly, we showed that preclinical treatment with the irreversible proteasome inhibitor (PI) carfilzomib administered upon ibrutinib resistance prolonged survival of mice, thus acting as salvage therapy. Longitudinal proteomic analysis of CLL patients with ibrutinib resistance identified deregulation in protein post-translational modifications. In addition, CLL cells from ibrutinib-resistant patients effectively responded to several PIs in co-culture assays. Altogether, our results from orthogonal omics approaches identified proteasome inhibition as potentially attractive innovative salvage treatment option for CLL patients resistant or refractory to ibrutinib.

overall_design: Comparative analysis of vehicle or ibrutinib treated TCL1 mice after adoptive transfer of tumor cells

first: Martina

last: Seiffert

first: Lavinia

last: Arseni

first: Haniyeh

last: Yazdanparast

first: Norman

last: Mack

first: Sibylle

last: Ohl

first: Verena

last: Kalter

first: Murat

last: Iskar

first: Yashna

last: Paul

first: Philipp

last: Roessner

first: Peter

last: Lichter


title: Transcriptional changes and RNA expression profiles during ischemia-induced DRP1-mediated macrophage reprogramming

status: Public on Oct 28 2024

city: Detroit

first: Yang

last: Shi

state: MI

address: 4100 John R St MM03BI

department: Karmanos Cancer Institute

institute: Wayne State University Schhol of Medicine

summary: To reveal the molecular mechanisms underlying DRP1-mediated macrophage reprogramming during hypoxia serum starvation (HSS) an in vitro ischemia model, we performed bulk RNA-seq analysis on mouse bone marrow derived macrophages (BMDM) upon HSS-induced DRP1 mediated macrophage reprogramming.

overall_design: Transcriptomic (total RNA) expression profiles of wildtype (WT) and DRP1 Knock-out (DRP1-KO) BMDM after 8 h of HSS ( in vitro ischemia) stimulation were compared by RNA-seq.

first: Masuko

last: Ushio-Fukai

first: Tohru

last: Fukai

first: Shikha

last: Yadav


title: Inhibition of adipose triglyceride lipase alleviates non-alcoholic steatohepatitis in diabetic mice via impaired PPARa signalling favouring hydrophilic bile acid composition

city: Vienna

first: Emmanuel

middle: Dauda

last: Dixon

state: Vienna

address: Waehringer Guertel 18-20,

department: Dept. of Internal Medicine III

country: Austria

institute: Medical University of Vienna

summary: Inhibition of adipocyte triglyceride lipase (ATGL/PNPLA2) activity in insulin resistance and non-alcoholic fatty liver disease is an attractive therapeutic target. This study evaluated the impact of Atglistatin-mediated ATGL inhibition on non-alcoholic steatohepatitis (NASH) development in diabetic and hyperlipidaemic mice. Streptozotocin-injected male mice were fed an HFD to induce NASH. We analysed liver histology, hepatic lipid content, immunohistochemistry, RNA sequencing, and serum biochemistry. Mechanistically, we treated Caco2 cells, human primary ileum-derived organoids, and HepG2 ATGL KD cells with the novel human ATGL inhibitor NG-497 and WY14643.  Atglistatin reduced body and liver weights, total liver lipid content, and improved blood sugar levels consistent with improved liver enzymes, histological liver injury, and NAFLD activity scores. Mechanistically, Atglistatin reduced Cpt1a and Abca1, suggesting impaired Ppara signalling that favours hydrophilic bile acids (BA) synthesis since Cyp7a1, Cyp27a1, and Cyp2c70 were increased while Cyp8b1 was reduced. Accordingly, Intestinal lipid transporters, Abca1 and Cd36, were reduced, consistent with the reduction of liver TAG species, mostly linoleic acids. We used human-specific ATGL inhibitor NG-497 to validate the mouse findings. The NG-497-treated human primary ileum organoids and Caco2 cells showed reduced ATGL, ABCA1, FATP5, CD36, and MTTP. PPARa signalling was impaired in the ileum organoids and HepG2 treated with NG-497 and in HepG2 ATGL KD since PPARa, CPT1a, AOX, ABCA1, and CYP8B1 were reduced, and CYP7A1 increased. Inhibition of ATGL activity reduces the availability of ligands for Ppara activation leading to impaired Ppara signalling, which translate into hydrophilic BA that interferes with dietary lipid absorption, improving metabolic disturbances. The validation with the NG-497 should open a new clinical avenue for NAFLD clinical trial and treatment.

overall_design: The STAM mouse was established by subcutaneously injecting 200 µg streptozotocin in 2-days-old male mice and feeding a HFD supplemented with Atglistatin (STAM + ATGLi) or without Atglistatin (STAM) after 4 weeks of age for further 4 weeks. Control mice (noSTZ + NC) were fed chow diet and neither receive STZ nor Atglistatin.

middle: D

first: Thierry

last: Claudel

first: Alexander

last: Nardo

first: Michael

last: Trauner


title: YmoA functions as a molecular stress sensor in Yersinia

city: Uppsala

first: Helen

last: Wang

address: Husargatan 3

country: Sweden

institute: Uppsala University

summary: Pathogenic bacteria sense and respond to environmental fluctuations, a capability essential for establishing successful infections. The YmoA/Hha protein family are conserved transcription regulators in Enterobacteriaceae, playing a critical role in these responses. Specifically, YmoA in Yersinia adjusts the expression of virulence-associated traits upon temperature shift. Still, the molecular mechanisms transducing environmental signals through YmoA remain elusive. Our study employed nuclear magnetic resonance spectroscopy, biological assays and RNA-seq analysis to elucidate these mechanisms. We demonstrated that YmoA underwent structural fluctuations and conformational dynamics in response to temperature and osmolarity changes, correlating with changes in plasmid copy number, bacterial fitness and virulence function. Notably, chemical shift analysis identified key roles of a few specific residues and of the C-terminus region in sensing both temperature and salt-driven switch. These findings demonstrate that YmoA acts as a central stress sensor in Yersinia, fine-tuning virulence gene expression and balancing metabolic trade-offs.

overall_design: A wildtype and a ∆ymoA mutant of Yersinia pseudotuberculosis were used for this experiment. Strains were grown overnight  at 26°C and subsequently diluted 1:25 into fresh media and cultured for 5h at 26°C at which point samples were taken. Each conditions was repeated 3 times independently.


title: Maternal ELL3 loss-of-function leads to oocyte aneuploidy and early miscarriage

city: Nanjing

first: Jingjing

last: He

state: 2 Sipailou

address: 2 Sipailou

department: School of Life Science and Technology

institute: Southeast University

summary: Up to one-tenth of women experience miscarriage in their lifetime. Embryonic aneuploidy is a leading cause of infertility, miscarrage and congenital defects. Here, we identify loss-of-function variants of ELL3, a gene encoding a transcription elongation factor, from couples experienced consecutive early spontaneous miscarriages due to embryonic aneuploidy. Maternal ELL3 knockout leads to oocyte aneuploidy. Furthermore, we found that ELL3 localizes to the spindle during meiosis, and that ELL3 depletion in both mouse and human oocytes increases the incidence of meiotic spindle abnormality. Biochemically, ELL3 competes with TPX2 to interact with the microtubule motor KIF11, promoting its ATP utilization. Live imaging  analysis shows that ELL3 is essential for promoting spindle elongation rate and driving chromosome movement. Our findings demonstrate that ELL3 loss-of-function variations could lead to oocyte aneuploidy and early miscarriage.

overall_design: To rule out the effect of transcription on meiosis, we performed transcriptomic analyses on Ctrl and Ell3 KD GV oocytes.Female mice were intraperitoneally injected with 7.5 IU PMSG and humanely euthanized after 48 h to collect oocytes at the GV stage. 2 sets of samples were collected for each group (5 oocytes per sample) in lysis buffer. GV oocytes was carried out using a protocol for SMART-seq2.

first: Shiqi

last: Zhu


title: Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [RNA-seq]

first: Esteban

last: Ballestar

summary: Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by systemic inflammation that involves various immune cell types. Monocytes play a central role in promoting and regulating inflammation. Peripheral blood classical monocytes subsequently differentiate into intermediate monocytes and then non-classical monocytes, assuming diverse roles and undergoing changes in their proportions during physiological immune responses and pathological conditions, including SLE. In this study, we obtained the epigenetic and transcriptomic profiles of these three monocyte subsets in an SLE cohort. We found different common and subset-specific alterations. While SLE classical monocytes had a stronger proinflammatory profile with an important interferon influence priming them towards macrophage differentiation, non-classical monocytes had a phenotype related to T cell differentiation regulation, with several indications pointing towards a Th17 promoting behavior. Integration of these bulk datasets with single-cell RNA-seq data of an SLE cohort shed light on the heterogeneity of our monocytes, confirming the interferon signature profile of classical monocytes and pointing towards intermediate and non-classical populations associated with exacerbated complement activation pathways, among others. Our results indicate a subversion of the epigenome and transcriptome in monocyte differentiation toward non-classical subsets in SLE, involving the STAT1 pathway and impacting function in relation to disease activity.

overall_design: Transcriptomic analysis of sorted classical monocyte, intermediate monocyte and non-classical monocyte subsets from 12 SLE patients and 7 healthy donors

first: Anna

last: Ferrete-Bonastre

first: Monica

last: Martinez-Gallo

first: Octavio

last: Morante-Palacios

first: Celia

last: Calvillo

first: Josep

last: Calafell-Segura

first: Javier

last: Rodriguez-Ubreva

first: Manel

last: Esteller

first: Josefina

last: Cortes-Hernandez


title: Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma [CUT&Run]

status: Public on Oct 25 2024

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: Rhabdomyosarcoma (RMS), a malignancy of impaired myogenic differentiation, is the most common soft tissue pediatric cancer. PAX3-FOXO1 oncofusions drive the majority of the clinically more aggressive fusion-positive rhabdomyosarcoma (FP-RMS). Recent studies have established an epigenetic basis for PAX3-FOXO1-driven oncogenic processes. However, details of PAX3-FOXO1 epigenetic mechanisms, including interactions with, and dependence on, other chromatin and transcription factors, are incompletely understood. We previously identified a novel disease-promoting epigenetic axis in RMS, involving the histone demethylase KDM3A and the ETS1 transcription factor, and demonstrated that this epigenetic axis interfaces with PAX3-FOXO1 both phenotypically and transcriptomically, including co-regulation of biological processes and genes important to FP-RMS progression. In this study, we demonstrate that KDM3A and ETS1 colocalize with PAX3-FOXO1 to enhancers of important disease-promoting genes in FP-RMS, including FGF8, IL4R, and MEST, as well as PODXL, which we define herein as a new FP-RMS-promoting gene. We show that ETS1, which is induced by both PAX3-FOXO1 and KDM3A, exists in complex with PAX3-FOXO1, and augments PAX3-FOXO1 chromatin occupancy. We further show that the PAX3-FOXO1/ETS1 complex can be disrupted by the clinically relevant small molecule inhibitor YK-4-279. YK-4-279 displaces PAX3-FOXO1 from chromatin and interferes with PAX3-FOXO1-dependent gene regulation, resulting in potent inhibition of growth and invasive properties in FP-RMS, along with downregulation of FGF8, IL4R, MEST and PODXL expression. We additionally show that, in some FP-RMS, KDM3A also increases PAX3-FOXO1 levels. Together, our studies illuminate mechanisms of action of the KDM3A/ETS1 regulatory module, and reveal novel targetable mechanisms of PAX3-FOXO1 chromatin complex regulation, in FP-RMS.

overall_design: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) was used to profile the FP-RMS cistrome at baseline, and in response to different perturbations (factor depletion and drug treatment).

first: Paul

last: Jedlicka

first: Joseph

last: Hsieh

first: Charles

last: Owens

first: Janet

last: Parrish

first: Nathan

last: Nowling

first: Arthur

last: Wolin

first: Stephen

last: Purdy

first: Sheera

last: Rosenbaum

first: Atma

last: Ivancevic

first: Edward

middle: B

last: Chuong

first: Heide

last: Ford


title: miRNA profiles of plasma and tumor-derived exosomes of cardiac myxoma-related ischemic stroke

city: Beijing

first: Lin

last: Ma

address: No. 2 Anzhen Rd District, Beijing, China

institute: Beijing Anzhen Hospital

summary: Cardiac myxoma (CM) is an important aetiology of stroke in young adults, and its diagnosis is difficult in patients having stroke because of the lack of diagnostic biomarkers. Tumour-derived exosomes play a crucial role in tumour growth, metastasis, and immune regulation, and monitor disease development. We established an RNA-sequencing dataset for long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) in the plasma and tumour-derived exosomes from four patients with cardiac myxoma-related ischaemic stroke (CM-IS) and six patients with cardiac myxoma without ischaemic stroke (non-IS CM). Clean data (15.48 Gb) were obtained for lncRNAs and mRNAs. Moreover, 5,533 lncRNAs, 1,331 known miRNAs, and 412 new miRNAs were identified. Finally, gene expression profiles and differentially expressed genes were analysed in 20 samples. In the plasma samples, 74 miRNAs, 12 lncRNAs, and 693 mRNAs were identified. Tumour-derived tissue samples contained 61 miRNAs, 67 lncRNAs, and 433 mRNAs. This dataset provides a significant resource for relevant researchers to explore the potential dysregulated lncRNAs, miRNAs, and mRNAs of plasma and tumour-derived exosomes in CM-IS versus CM without stroke.

first: Guangzhi

last: Liu


title: Nucleosome wrapping states encode principles of 3D genome organizatio

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University

summary: In this research, we investigated the wrapping length of DNA on nucleosomes across the whole genome using wrapping-seq. We discovered that the mouse genome chromatin forms nucleosome wrapping domains (NRDs). NRDs are conserved from flies to human cells. Additionally, our study found that the degree of nucleosome wrapping decreases and matures after DNA replication. Moreover, the degree of nucleosome wrapping is associated with the transcriptional status of genes. Furthermore, we observed that nucleosome unwrapping states delineate 3-D genome organization. In conclusion, our wrapping-seq analysis has revealed a novel higher-order chromatin organization.

overall_design: We performed wrapping-seq for histone H3, H4 and MNase input samples with two biological replicates. We sequenced the H3 library more deeply. We also performed wrapping-seq with MNase input under conditions such as time-course digestion, cell cycle sorting and during DNA replication.


title: Transcriptomic analysis of sex differences in hematopoietic stem cell aging

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

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

overall_design: Refer to individual Series


title: Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma


title: Heart Repair with Engineered Heart Muscle

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

summary: Releated to the single nucleus RNA sequencing data displayed in Extended Data Figure 1

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: 10X genomics single-cell seq data; 7 samples each with 4 replicates

first: Wolfram-Hubertus

last: Zimmermann

first: Malte

last: Tiburcy

first: Dennis

last: Krüger


title: Genome-wide identification of transcriptional targets for H3K23ac, H3K27ac, and H4K5ac in vascular smooth muscle cells of aneurysmal aortas [CUT&Tag]

first: Hao

last: Wu

address: Xueyuan Road 38

institute: Peking University

summary: In this study, we found that H3K23ac, H3K27ac, and H4K5ac level are elevated in VSMCs of aneurysmal aortas. To further explore the potential functional significance of H3K23ac, H3K27ac, and H4K5ac in aortic aneurysm, we performed genome-wide cleavage under targets and tagmentation (CUT&Tag) analysis to identify candidate genes regulated by H3K23ac, H3K27ac, or H4K5ac in rat VSMC. Following CUT&Tag, H3K23ac, H3K27ac, or H4K5ac-associated DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 150PE.

overall_design: Genome binding/occupancy profiling by high throughput sequencing

first: Zhiqing

last: Li


title: lncRNA and mRNA profiles of plasma and tumor-derived exosomes of cardiac myxoma-related ischemic stroke

overall_design: We established an RNA-sequencing dataset for long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) in the plasma and tumour-derived exosomes from four patients with cardiac myxoma-related ischaemic stroke (CM-IS) and six patients with cardiac myxoma without ischaemic stroke (non-IS CM).


title: RNAseq analysis of sex differences of young and old hematopoietic stem cells

summary: Bulk RNA sequencing (RNAseq) analysis of hematopoietic stem/progenitor cells purifiied from young and longevity mice, both male and female.

overall_design: Lineage negative side population was sorted by flow cytometry from 3- and 28-month-old male and female BALB/c mice, with 2 to 4 mice pooled per group. RNA was extracted and subjected to 10x Genomics analysis of RNAseq.

first: Chunxiao

last: Zhang

first: Taisen

last: Hao

first: WenYong

last: Chen


title: Single cell atlas of human islet and acinar zonated endothelial cells in health and disease

city: New

first: Sean

last: Houghton

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: scRNAseq data set of fresh human pancreas autopsies, CD31+CD45- cells and negative fraction

overall_design: We employed protocols for procuring human deceased donor pancreas with subsequent rapid islet isolation and endothelial cell purification with minimal delay or culturing in order to acquire high-yield and high-quality ISECs and ASECs. Islet and acinar portions were isolated from three donors who spanned a range of ages and body mass index. Flow cytometric sorting of CD31+CD45- endothelial cells from the islet and acinar fractions resulted in putative ISECs and ASECs alongside non-endothelial proportions (4 per donor) that were prepared for 10X genomics scRNA-seq v3 library preparation

first: David

last: Redmond

first: Rebecca

last: Craig-Schapiro

first: Ge

first: Shahin

last: Rafii


title: CPSF6-RARγ Interacts with HDAC3 to Promote Myeloid Transformation [human CD34+ cells_CUT-Tag seq_HDAC3]

status: Public on Oct 24 2024

city: Suzhou

first: meng

last: shan

address: shizi street

institute: Soochow university

summary: Acute myeloid leukemia (AML) with RARG fusions, which clinic features resemble acute promyelocytic leukemia (APL), have been identified as a new subtype with poor clinical outcomes. The underlying mechanism of RARG fusion is poorly understood, which needs to be explored urgently to develop effective therapeutic strategies. Using hematopoietic specific knock-in mouse model and xenograft mouse model transplanted with oncogene transduced human CD34+ cells, we revealed that CPSF6-RARG (CR) fusion, one of the most prevalent recurrent RARG translocations, enhances expansion of immature cells and impairs myeloid maturation, synergizing with RAS mutation to drive more aggressive myeloid malignancies. Mechanistically, CR recruits the histone deacetylase 3 (HDAC3) to suppress the transcription of PU.1, a key transcription factor for myeloid lineage specification. CR driven leukemia is more sensitive to HDAC inhibitors in vitro and in vivo. Hence, our data reveals the molecular bases of the oncogenic CR fusion and provides a potential targeted therapeutic approach against AML with CR fusions.

overall_design: Cleavage Under Targets and Tagmentation sequencing (CUT&Tag-seq) for flag tagged CRL, CRS or RARG in Kasumi-1 stably expressing CRL, CRS or RARG


title: CPSF6-RARγ Interacts with HDAC3 to Promote Myeloid Transformation [human CD34+ cells_CUT-Tag seq_ H3K27me3]


title: RNA-seq analysis identifies gene expression profile in rat ANK-deficiency VSMCs

summary: To obtain deeper insight into the underlying mechanisms linking ANK to the pathogenesis of AA, high-throughput RNA-sequencing of ANK-deficient rat VSMCs via small interfering RNA was performed. A total of 972 upregulated differentially expressed genes (DEGs) were identified in ANK-deficient rat VSMCs, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis presented several pathways highly related to inflammation and energy metabolism

overall_design: Genome-wide transcriptional profiling by high throughput sequencing


title: CPSF6-RARγ Interacts with HDAC3 to Promote Myeloid Transformation [CUT&Tag in CD34+ cells]

overall_design:
Cleavage Under Targets and Tagmentation sequencing (CUT&Tag-seq) for flag tagged CRL, CRS or RARG in human CD34+ cells cultured in myeloid medium for 15 days
Cleavage Under Targets and Tagmentation sequencing (CUT&Tag-seq)  in human CD34+ cells expressing flag-CRL, or flag-CRS treated with RGFP966 or tucidinostat using flag antibody


title: CPSF6-RARγ Interacts with HDAC3 to Promote Myeloid Transformation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma [RNA-Seq]

first: Etienne

last: Danis

overall_design: RNAseq was used to compare the effects of YK-4-279, relative to vehicle control, on gene expression in FP-RMS cells.

first: Paul

last: Jedlicka

first: Joseph

last: Hsieh

first: Charles

last: Owens

first: Janet

last: Parrish

first: Nathan

last: Nowling

first: Arthur

last: Wolin

first: Stephen

last: Purdy

first: Sheera

last: Rosenbaum

first: Atma

last: Ivancevic

first: Edward

last: Chuong

first: Heide

last: Ford


title: CPSF6-RARγ Interacts with HDAC3 to Promote Myeloid Transformation [CR-N_mice_scRNA-seq]

overall_design: BM Mac1+ and c-kit+ cells from WT/V, WT/N, CRL/V, CRL/N, CRS/V and CRS/N mice were sorted and mixed with 1:1 ratio to perform single-cell RNA sequencing.


title: Comparative Analysis of the Physiological and Transport Functions of Various Sources of Renal Proximal Tubule Cells Under Static and Fluidic Conditions in PhysioMimix TC12 Platform

status: Public on Oct 23 2024

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

summary: Drugs and other xenobiotics are not only secreted/reabsorbed by the renal proximal tubule epithelial cells (RPTEC) but may also adversely impact kidney function. In vitro models that can afford prediction of toxic effects and model directional transport are in high demand in both drug and chemical safety; accordingly, active development of new models is underway. The objective of this study was to investigate physiological and transport function of various sources of human RPTECs under static and fluidic conditions. We tested TERT1-immortalized RPTECs, including OAT1-, OCT2- and OAT3-overexpressing variants) and two primary RPETC sources. Cells were cultured on transwell membranes in two conditions – static (24-well transwells) and fluidic (transwells placed into PhysioMimix TC12 organ-on-chip platform with 2 L/s flow). We evaluated barrier formation, transport, and gene expression. We show that primary RPTECs may not be suitable for studies of directional transport on transwell membranes because they form an inferior barrier even though they show generally more relevant expression of key transporters, especially when shear stress is present. Both TERT1 and -OAT1 and -OAT3 overexpressing cells formed robust barrier, but it was unaffected by shear stress. TERT1-OAT1 cells exhibited inhibitable pAH transport; shear stress increased pAH transport function of these cells. However, efficient tenofovir secretion and perfluorooctanoic acid (PFOA) reabsorption by TERT1-OAT1 cells were not modulated by shear stress. With respect to gene expression profiles, we found that both TERT1 and TERT1-OAT1 cells exhibited human kidney-like transcriptomes, but that shear stress did not result in an apparent enhancement of the kidney phenotype. Overall, our data show that addition of flow to in vitro studies of the renal proximal tubule may afford benefits in some aspects of kidney function, but that careful consideration of the impact such studies would have on the cost and throughput of the experiments is needed.

overall_design: Comparative gene expression profiling analysis of TempO-Seq data for RPTEC cells using different platforms, cells that over-expressed certain transporter proteins, and chemical treatment conditions.

first: Courtney

last: Sakolish

first: Haley

last: Moyer

first: Han-Hsuan

last: Tsai

first: Lucie

first: Allison

middle: N

last: Dickey


title: Single cell transcriptomics of sex differences of young and old hematopoietic stem cells

first: Hsun

last: Ku

summary: Single cell RNA sequencing (scRNAseq) analysis of hematopoietic stem/progenitor cells purifiied from young and longevity mice, both male and female.

overall_design: Lineage negative side population was sorted by flow cytometry from 3- and 28-month-old male and female BALB/c mice, with 2 to 4 mice pooled per group. Around 1,000 cells each were analyzed by 10x Genomics single cell RNAseq platforms.

first: Chunxiao

last: Zhang

first: Taisen

last: Hao

first: WenYong

last: Chen


title: Investigating the role of  FOS/AP-1 in OnF reprogramming  during tumor intiation

status: Public on Oct 17 2024

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: To investigate the role of  FOS/AP-1 in early OnF reprogramming,  we blocked its activity during tumor intiation by overexpressing a dominant negative form of FOS.

overall_design: We overexpressed a dominant negative form of FOS in APCflox/flox organoids, which were then terated with OHT to iduce APC Loss-of-function.

first: Slim

last: Mzoughi

first: Kevin

last: Mohamed

first: Gulay

last: Ulukaya

first: Deniz

last: Demircioglu


title: Investigating the role of YAP and FOS in driving OnF reporgramming  during tumor intiation

summary: To investigate the role of YAP and FOS in early OnF reporgramming, we knocked down either gene during tumor intiation  induced by APC depletion.

overall_design: YAP or FOS was knocked down in LGR5-2A-Ert2-Cre_APCflx/flx organoids before treating them with OHT.


title: CPSF6-RARγ Interacts with HDAC3 to Promote Myeloid Transformation [RNA-seq]

first: meng

last: shan

overall_design: To investigate myeloid abnormalities resulting from CR fusions expression on HSPCs, we expressed CRL or CRS fusion in human CD34+ cells, and culured in myeloid medium for 15 days.


title: Ugonin inhibits chondrosarcoma metastasis through suppressing cathepsin V via promoting miR-4799-5p expression

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

institute: China Medical University

summary: Chondrosarcoma is a rare type of bone cancer that develops in cartilage cells. Ugonin V is a flavonoid compound that has been extracted from the plant Helminthostachys zeylanica (L.) Hook. This study examined the molecular therapeutic effects of ugonin V on chondrosarcoma metastasis.

overall_design: To identify differentially expressed miRNAs regulated by Ugonin V, JJ012 cells were treated with Ugonin V (10 μM) for 24 h in the culture medium, and miRNA sequencing was performed.

first: Bao-Tran

last: Nguyen


title: Comparing the chromatin accessibility landscapes of WT organoids, RXRi organoids and APCko tumoroids

summary:
To compare the effects of RXR inhibition to APC depletion on chromatin landscapes, WT organoids were treated with either HX531 (RXRi) or vehicle (WT). APCko tumorids treated with vehicle only were used as a benchmark.
We then performed differential accessibility analysis using data obtained from ATAC-seq of the indicated organoid lines.

overall_design: Wild type intestinal organoids (WT), RXRi and  ApcKO (A) were cultured in media with either HX531 or vehicle before collecting the nuclei for DNA transposition.

first: Xuedi

last: Wang


title: Characterizing the transcriptome of WT organoids, RXRi organoids and APCko tumoroids

summary:
To compare the effects of RXR inhibition to those of APC depletion on the intestinal epithelium, WT organoids were treated with either HX531 (RXRi) or vehicle (WT) and APCko tumorids were treated with vehicle only.
We then performed gene expression profiling analysis using data obtained from mRNA-seq of the indicated organoid lines.

overall_design: Wild type intestinal organoids (WT), RXRi and  ApcKO (A) were cultured in media with either HX531 or vehicle before collecting for RNA extraction.


title: ATAC-sequencing of genetically engineered intestinal organoid lines modeling colorectal cancer (CRC) progression

summary:
To characterize changes in chromatin accessibility acorss the CRC malignancy continum, wild type organoids (WT), ApcKO (A) and ApcKO::KrasG12D::Smad4KO::Trp53KO (AKSP) tumoroids were subjected to bulk ATAC-seq.
We then performed differential accessibility analysis using data obtained from ATAC-seq of the indicated organoid lines.

overall_design: Wild type intestinal organoids (WT), ApcKO (A) and ApcKO::KrasG12D::Smad4KO::Trp53KO (AKSP) tumoroids were collected for nuclei isolation and DNA transpostion when they reached confluence.


title: Transcriptional profiling of intestinal organoids following ectopic expression of YAP (S6) +/- FOS.

summary:
To elucidate the roles of YAP and FOS/AP-1 in driving OnF reporgramming, we tested the effects of their ecotpic expression in healthy intestinal organoids.
The sequential overperession recapitulates the chornnology of deregulation of both axes during CRC evolution.

overall_design: We overexpressed either constituvely active YAP alone, in WT  intestinal organoids,  or we subsequently added FOS.


title: Transcriptional profiling of single cells from epithelial organoids modelling Intestinal tumorigenesis

summary: To chart cell state dynamics across the malignancy continuum of colorectal cancer, wild type organoids (WT), ApcKO (A) and ApcKO::KrasG12D::Smad4KO::Trp53KO (AKSP) tumoroids were subjected to single cell RNA-seq.

overall_design: Isogenic lines with the indicated genotypes were collected for s.cRNA-seq before reaching confluency to minimize cell death.


title: CPSF6-RARγ Interacts with HDAC3 to Promote Myeloid Transformation [BM Mac1+ and c-kit+ cells RNA-seq]

overall_design: BM Mac1+ and c-kit+ cells from WT, LysM-CRL or LysM-CRS mice were sorted and mixed with 1:1 ratio to perform single-cell RNA sequencing


title: Regulation of eNOS by METTL3 in endothelial cells controls blood pressure via RUNX1b

city: Tianjin

first: xiaoxiao

last: Yang

state: Tianjin

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: As a core subunit of the m6A methyltransferase complex, the downregulation of METTL3 expression in response to Ang II suggests the potential regulation of m6A modification. Our data suggests METTL3 may mediate the dynamic change in m6A landscapes between Ang II with and without overexpression of METTL3.

overall_design: Examination of gene expressive levels, m6A enrichment levels in Ang II with and without overexpression of METTL3.


title: Revealing the key role of the folate synthesis regulatory gene DHNA in tobacco leaf yellowing based on BSA-seq, RNA-seq, and proteomic sequencing

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

institute: Guizhou University

summary: The degree of yellowing in tobacco leaves is an important indicator for determining the maturity and harvesting time of tobacco leaves. Reduction in chlorophyll is of utility for promoting the concentrated maturation of tobacco leaves and achieving mechanised harvesting and mining, and utilising tobacco yellow leaf regulatory genes is of great significance for the selection and breeding of tobacco varieties suitable for mechanised harvesting and the resolution of the molecular mechanisms controlling leaf colouration. In this study, the phenotypes of the yellow-leaf K326 and K326 varieties were analysed, and it was observed that the yellow-leaf K326 variety exhibited a distinct yellow leaf phenotype with a significant reduction in chlorophyll content. Subsequently, using a combination of BSA-seq, transcriptomic sequencing (RNA-seq), and proteomic sequencing approaches, we identified the candidate gene Nitab4.5_0008674g0010 that encodes dihydroneopterin aldolase as a factor associated with tobacco leaf yellowing. Finally, by measuring the folate content in K326 and Huangye K326, the folate content in Huangye K326 was observed to be significantly lower than that in K326, thus indicating that folate synthesis plays a crucial role in phenotypic changes in tobacco yellow leaves. This study is the first to use BSA-seq combined with RNA-seq and proteomic sequencing to identify candidate genes in tobacco yellow leaves. The results provide a theoretical basis for the analysis of the mechanism of tobacco yellow leaf mutations.

overall_design: 9 samples were analyzed, including 3 plant materials, each with three replicates.

first: Renxiang

last: Liu

first: Qiuhe

last: Pan


title: Secretome from human placenta–derived mesenchymal stem cells rescues ovarian function and circadian rhythm in mice with cyclophosphamide-induced primary ovarian insufficiency

city: Taipei

first: Le

middle: Duy

last: Cuong

state: Xinyi

address: 6th Floor, No 3-6 Wuxing street, Xinyi, Taipei

department: IPCTRM

institute: Taipei Medical University

summary: Primary ovarian insufficiency (POI) is an early decline in ovarian function that leads to infertility. Conventional treatments for chemotherapy-induced POI are unsatisfactory. Mesenchymal stem cells (MSCs) have emerged as a therapeutic option, but the impact of estrogen niche-respond MSC secretome on ovarian regeneration and circadian rhythm remains unknown. This study revealed that the secretome of ER+pcMSCs (conditioned medium [CM] and E2-CM, respectively) significantly reduced the CTX-induced defects in ovarian folliculogenesis and circadian rhythm. The CM/E2-CM also reduced granulosa cell apoptosis and rescued angiogenesis in POI ovarian tissues. E2-CM presented a better effect than the CM. Cytokine array analysis showed a significant increase in cytokine/growth factors associated with immunomodulation and angiogenesis (including angiogenin). Neutralizing angiogenin in the CM/E2-CM significantly decreased its ability to promote HUVEC tube formation in vitro. Importantly, the ER+pcMSC secretome restored the CTX-induced circadian rhythm defects, including the expression of both the genes and proteins associated with ovarian circadian clock (such as Rora, E4bp4, Rev-erbα, and Dbp) and the locomotor activity. Further exosomal miRNA analysis showed the involved miRNAs in targeting the genes associated with POI rescue (Pten and Pdcd4), Caspase-3, estrogen synthesis (Cyp19a1), and importantly the ovarian clock regulation (E4bp4, Rev-erbα and Rev-erbβ).

overall_design: Conditioned medium (CM) and estradiol-conditioned medium (E2-CM) were generated by priming estrogen receptor-expressing MSCs (ER+pcMSCs) from human placenta with or without estradiol (100 nM). POI models were established using C57BL/6 mice (in vivo) and KGN cells (in vitro) treated with cyclophosphamide (CTX) or 4-hydroperoxycyclophosphamide (4-OOH-CP) to evaluate CM/E2-CM’s therapeutic efficacy. The expressions of clock-controlled genes/proteins were detected by RT-qPCR, western blotting, and immunohistochemistry assays. Locomotor activity experiments assessed behavioral circadian rhythmicity. The cytokine array and miRNA sequencing were performed to explore the potential underlying mechanism of CM/E2-CM in POI treatment.

first: Duy-Cuong

last: Le

first: Yen-Hua

last: Huang

first: Jihwan

last: Myung

first: Heng-Kien

last: Au

first: Chung-Yen

last: Lin

first: Mai-Huong

last: Ngo


title: Validation of the Oncofetal (OnF) phenotypic reporter

first: BiNGS

last: Core

summary:
To test its specificity, VAKSP tumoroids expressing the OnF reporter were sorted based on their GFP expression status.
We then performed gene expression profiling analysis using data obtained from mRNA-seq of GFP high and GFP negative VAKPS cells.

overall_design: We first generated a VAKPS line stably expressing the OnF reporter. After selection, these tumoroids were expanded. Then GFP high and GFP negative cells were collected for RNA extraction using Fluorescence-Activated Cell Sorting.

first: Slim

last: Mzoughi

first: Kevin

last: Mohamed

first: Gulay

last: Ulukaya


title: Single-Cell RNA Sequencing of Human Embryonic Stem Cells and Feeder-free Extended Pluripotent Stem Cells

status: Public on Oct 16 2024

city: Wuhan

first: Wei

last: Jiang

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

summary: This dataset features transcriptomic profiles of feeder-free extended pluripotent stem cells (ffEPSCs) and their parentalderived from human embryonic stem cells (ESCs). ffEPSCs were generated using a Matrigel-based feeder-free system combined with a chemical cocktail to convert conventional ESCs into ffEPSCs. Generated using Smart-seq2 and sequenced on Illumina HiSeq 2000, the dataset explores transcriptional profiles and heterogeneity of ESCs and ffEPSCs, providing insights into early human development and stem cell biology.

overall_design: The samples in this submission include human embryonic stem cells (ESCs) and extended pluripotent stem cells (ffEPSCs) derived from ESCs. Specifically, the human ESC line H9 was used for conversion into ffEPSCs. Both ESCs and ffEPSCs were analyzed at the single-cell level using Smart-seq2 sequencing. Replicates were included, as the experiments were performed on multiple cells from each condition. There are reference samples (ESCs) as well as experimental samples (ffEPSCs) to investigate the transition from ESC to ffEPSC. The primary variables under investigation are the differences in gene expression between these two states under controlled experimental conditions.

first: Jiang

last: Wei

first: Zhu

last: Lihang

first: Zheng

last: Ran

first: Wen

last: Shanshan


title: Role of copper in progression of clear cell renal cell carcinoma [RNA-seq]

status: Public on Oct 18 2024

city: CINCINNATI

first: Behrouz

last: Shamsaei

state: OH

institute: university of Cincinnati

summary: Copper (Cu) is an essential trace element required for mitochondrial respiration. We show that Cu drives coordinated metabolic remodeling of bioenergy, biosynthesis and redox homeostasis and progression of clear cell renal cell carcinoma (ccRCC). Cu stimulates tumor growth. Late-stage ccRCCs accumulate Cu and allocate it to cytochrome c oxidase stimulating bioenergy production. Cu induces TCA cycle-dependent oxidation of glucose and its utilization for biosynthesis of a glutathione pool that protects against H2O2 generated during mitochondrial respiration, therefore coordinating bioenergy production with redox protection.

overall_design: 786-O RCC cells were adapted to 30 uM Cu in the culture media as a model to study the role of Cu in driving metabolic reprogramming  in ccRCC. Control cells were treated identically except for the additon of Cu. RNA was extracted and processed for RNA-seq.

first: Maria

middle: F

last: Czyzyk-Krzeska

first: Jarek

last: Meller

first: Jacek

last: Biesiada

first: Megan

last: Bischoff

first: Juechen

last: Yang


title: Role of copper in progression of clear cell renal cell carcinoma [Spatial transcriptomics]

summary: Copper (Cu) is an essential trace element required for mitochondrial respiration. We show that Cu drives coordinated metabolic remodeling of bioenergy, biosynthesis and redox homeostasis and promotes tumor growth and progression of clear cell renal cell carcinoma (ccRCC). Late-stage ccRCCs accumulate Cu and allocate it to cytochrome c oxidase stimulating bioenergy production. Cu induces TCA cycle-dependent oxidation of glucose and its utilization for biosynthesis of a glutathione pool that protects against H2O2 generated during mitochondrial respiration, therefore coordinating bioenergy production with redox protection. Single cell transcriptomics determined induction of mitochondrial electron transport chain, expression of NRF2 targets and glutathione biosynthesis, and decrease in HIF activity, the hallmark of ccRCC, during disease progression. Spatial transcriptomics identified that cancer cells with proliferative phenotype are embedded in clusters of cells with oxidative metabolism supporting effects of metabolic states on ccRCC progression. Our work establishes novel vulnerabilities with potential for therapeutic interventions in ccRCC.

overall_design:
We have analyzed 5 spatial transcriptomic tissue sections from simple stage-3 clear cell Renal Cell Carcinoma tumors. FFPE tumor sections were placed on Visium gene expression slide and stained for morphological context using H&E. Spatial transcriptomics was performed by 10x Genomics Visium Certified Service Providers. ccRCC tissues were obtained from UC Tumor Bank. The results were processed by spaceRanger software to acquire expression matrix of each sample.
Spatial transcriptomics images and expression files.


title: Elucidating the role of RXR in driving the OnF porgram  along the CRC malignancy contiuum.

summary:
To investigate the role of RXR during eraly OnF reporgramming, we perturbed the APC/RXR regulatory axis during tumor intiation.
To investigate the role of RXR in sustaining the OnF state in advanced CRC, we perturbed its expression in AKSP tumoroids.

overall_design: We forced RXR expression in APC flox/flox oprganoids, to block its downregulation following APC depletion (tumor intiation), or  in advanced CRC tumoroids (AKSP)

first: Deniz

last: Demircioglu


title: A novel anti-epileptogenesis strategy of temporal lobe epilepsy based on nitric oxide donor

status: Public on Oct 21 2024

first: fan

last: meng

address: Longmian Avenue 101

institute: Nanjing Medical University

summary: The molecular mechanism underlying the role of hippocampal hilar interneuron degeneration in temporal lobe epilepsy (TLE) remains unclear. Especially, very few studies have focused on the role of neuronal nitric oxide synthase (nNOS, encoded by Nos1) containing hilar interneurons in TLE. In the present study, Nos1 conditional knockout mice were constructed, and we found that selective deletion of Nos1 in hilar interneurons rather than dentate granular cells (DGCs) triggered epileptogenesis. The level of nNOS was downregulated in patients and mice with TLE. Nos1 deletion led to excessive epilepsy-like excitatory input circuit formation and hyperexcitation of DGCs. Replenishment of hilar nNOS protein blocked epileptogenic development and memory impairment in pilocarpine-induced TLE mice. Moreover, chronic treatment with DETA/NONOate, a slowly released exogenous nitric oxide (NO) donor, prevented aberrant neural circuits of DGCs and the consequent epileptogenesis without acute antiseizure effects. Therefore, we concluded that NO donor therapy may be a novel anti-epileptogenesis strategy, different from existing antiseizure medications (ASMs), for curing TLE.

overall_design: Young adult male mice (6-8 weeks old) were subcutaneously injected with pilocarpine to induce status epilepticus and PBS for control. Multiple dentate gyri were taken out (pilocarpine = 14 , PBS = 9 ) and pooled to create a composite sample for single-nuclei RNA sequencing after 10 weeks post-status when animals were in the chronic epileptic phase.


title: Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer

first: BiNGS

last: Core

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

overall_design: Refer to individual Series


title: RNA-sequencing of genetically engineered intestinal organoid lines modeling colorectal cancer (CRC) progression

summary:
To characterize the transcriptional changes acorss the CRC malignancy continum, wild type organoids (WT), ApcKO (A) and ApcKO::KrasG12D::Smad4KO::Trp53KO (AKSP) tumoroids were subjected to bulk RNA_seq.
We then performed gene expression profiling analysis using data obtained from mRNA-seq of the indicated organoid lines.

overall_design: Wild type intestinal organoids (WT), ApcKO (A) and ApcKO::KrasG12D::Smad4KO::Trp53KO (AKSP) tumoroids were collected for RNA extraction when they reached confluence.

first: Slim

last: Mzoughi

first: Xuedi

last: Wang


title: Transcriptional profiling of advanced CRC tumoroids (AKSP) follwoing RXR inhbition

summary: To investigate the role of RXR in regulating the OnF state in advanced CRC, we inhbited its acitvity in AKSP tumoroids.

overall_design: AKSP tumorids were treated with either HX531 (2.5uM)  or equal volume of DMSO for 72hrs.

first: Kevin

last: Mohamed

first: Gulay

last: Ulukaya


title: Transcriptional profiling of AKSP tumoroids  following knockdown of either YAP or FOS.

summary: To elucidate the role of YAP and FOS in sustaining the OnF state in davnaced CRC, we knocked down either gene in AKSP tumoroids.

overall_design: Yap or FOS were knocked down, using specific shRNAs, in AKSP tumorids before profiling their transcriptome. A scarmbled shRNA was used as control.


title: p53 binds to the regulatory regions of dsRNA-containing genes in 2153L tumor cells

city: houston

first: Longyong

last: Xu

address: SCRB4, 1901 East Road

department: ET

institute: University of Texas MD Anderson Cancer Center

summary: We analyzed the genome-wide p53 binding profile in 2153L tumor cells. We found p53 binds to the regulatory regions of dsRNAs-containing genes. our result suggests that p53 may directly repress the expression of these genes.

overall_design: 2153L tumor cells were transduced with empty vector or p53ERTAM. Cells were treated by 4-OH Tamoxifen (100 nM) for 48 hours before harvest for ChIP.

first: Fei

last: Yuan

first: Xingyu

last: Li


title: The single-cell assessment of transcriptiomic profile and chromain accessibility for the brain myeloid cells in rhesus macaques with SIV-induced encephalitis

status: Public on Oct 15 2024

city: Omaha

first: Howard

middle: S

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

summary: Human immunodeficiency virus (HIV) is widely recognized for its striking impact on the immune system, and it also significantly impacts the central nervous system (CNS). The primary immune constituents in the brain, microglia and macrophages, are the target for HIV in people and the simian immunodeficiency virus (SIV) in nonhuman primates. This infection can lead to neurological dysfunction, known as HIV-associated neurocognitive disorder (HAND) and pathological entities such as HIV-induced encephalitis (HIVE). Given the gaps in our knowledge on how these cells respond in vivo to CNS infection, we performed single-cell multiomic sequencing, including gene expression and ATAC-seq on myeloid cells from the brains of two rhesus macaques with SIV-induced encephalitis (SIVE) as well as two uninfected controls. We used both RNA expression and chromatin accessibility to identify cell clusters. We found that the myeloid cell populations were significantly changed by SIVE, which differed greatly from those found in the uninfected brains. We categorized myeloid cells in the SIVE brains into two primary phenotypes: microglia-like and CAM-like, which were different from each other regarding trancriptomic profile and chromatin accessibility. We found that these microglia-like cells express high levels of chemoattractants for capable of recruiting highly the activated CAM-like cells to the site of infection/inflammation. Additionally, we observed a dramatic shift of upstream gene regulators and their targets in brain myeloid cells during SIVE. The transcription factors (TFs) highly enriched in SIVE-specific cell clusters were related to IRF/STAT and NF-κB mediated interferon and other proinflammatory cytokines production. Interestingly, some of these TF binding sites were also enriched in the open chromatin identified in the SIV DNA provirus in infected myeloid cells, indicating the immune activation in the host cells might also promote HIV/SIV gene expression and regulation  . In summary, this study further uncover the trancriptome, gene regulaory events and potenital roles of differenet brain myeloid phenotypes in SIVE.

overall_design: The 104T and 106T were uninfected control samples; the other two (21T and 34T) were in the SIV encephalitis (SIVE) group. One of the SIVE animals (21T) in the SIVE group was infected with the SIV for 92 days and another animal (34T) was infected for 49 days before necropsy. The 34T was also injected with methamphetamine for 60 days before SIV infection in a dose of 2.5mg/kg.

first: Brenda

last: Morsey

first: Benjamin

last: Lamberty

first: Katy

last: Emanuel

first: Meng

last: Niu

first: Xiaoke


title: Transcriptional profiling of FOLFIRI treated VAKPS Tumoroids

summary:
To determine the effects of chemotherapy on cell state dyanmics, VAKPS tumroids were treated with FOLFIRI or DMSO for 72hrs before analyzing their transcriptome.
We then performed gene expression profiling analysis using data obtained from mRNA-seq of the indicated tumoroid lines.

overall_design: VAKSP tumoroids were terated with DMSO or FOLFIRI for 72hrs before collecting for RNA extraction.


title: Distinct pathways for removal of defective RNA polymerase II transcription complexes at a promoter-proximal pause checkpoint [RN21114 Ttchemn-Seq]

status: Public on Nov 05 2024

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: The purpose and function of Integrator and RNA polymerase II (RNAPII) promoter-proximal pausing remain uncertain. Here, we show that when Integrator function is compromised by loss of INTS6, RNAPII interacts increasingly with proteins from alternative pathways for its DNA dissociation, including CUL3-ARMC5 (CRL3ARMC5), which ubiquitylates Ser5-phosphorylated Rpb1 and targets it for degradation. ARMC5-dependent RNAPII ubiquitylation is activated by defects in factors required for correctly regulated promoter-proximal pausing, including Integrator, DSIF and mRNA capping enzyme. This ARMC5 checkpoint curtails an appreciable fraction of RNAPII transcription, with ARMC5 knockout cells producing uncapped, nascent RNA transcripts that fail to mature into stable mRNA. Concomitant loss of INTS6 and ARMC5 greatly stabilizes RNAPII at the pause and has severe consequences for cell growth and viability. Our data support a model in which CRL3ARMC5 functions alongside Integrator in a checkpoint mechanism that removes faulty RNAPII complexes at promoter-proximal pause sites to safeguard transcription integrity.

overall_design: TTchem-seq (Gregersen et al., 2020) looking at the effects of siRNA-mediated knockdown of INTS6 in HEK293 FlpIn TREx cells.

first: Daniel

last: Blears

first: Jiangman

last: Lou

first: Nova

last: Fong

first: Ryan

last: Sheridan

first: David

last: Bentley

first: Jesper

last: Svejstrup