title: ZMAT2 condensates regulate the alternative splicing of TRIM28 to promote the proliferation of hepatocellular carcinoma cells

city: Changsha

first: Yaning

last: Zhu

address: No.138, Tongzipo Road

department: Department of Radiology

institute: The Third Xiangya Hospital, Central South University

summary: Dysregulation of splicing factor expression plays a crucial role in the progression of hepatocellular carcinoma (HCC). Our research found that the expression level of splicing factor ZMAT2 is increased in HCC, promoting the proliferation of hepatocellular carcinoma cells. RNA-seq data indicated that ZMAT2 regulated exon skipping of mRNA, while RIP-seq data further revealed the binding motifs of ZMAT2. A comprehensive analysis of RNA-seq and RIP-seq data indicateed that ZMAT2 plays a crucial role in the maturation process of TRIM28 mRNA. Deletion of ZMAT2 led to the deletion of 25 bases in exon 11 of TRIM28, ultimately resulting in nonsense-mediated decay (NMD). Previous studies have demonstrated a close association between TRIM28 and the proliferation of hepatocellular carcinoma. Our experiments have revealed that TRIM28 serves as a critical factor for ZMAT2 in facilitating the proliferative process of hepatocellular carcinoma. Studies have demonstrated a close correlation between the mRNA splicing process and the occurrence of phase separation. Our research discovered that ZMAT2 is capable of undergoing phase separation, resulting in the formation of liquid droplet condensates within hepatocellular carcinoma cells. Additionally, it was found that ZMAT2 is able to form protein-nucleic acid condensates with TRIM28 mRNA. In summary, we hypothesize that ZMAT2 and TRIM28 mRNA form protein-nucleic acid condensates, thereby regulating the splicing of TRIM28 mRNA. The augmented expression of ZMAT2 in hepatocellular carcinoma cells results in the upregulation of TRIM28 expression, ultimately driving the proliferation of hepatocellular carcinoma cells.

overall_design: To investigate whether ZMAT2 influences the progression of HCC via its mRNA splicing function


title: Impact of Palbociclib (PD-0332991; CDK4/6 inhibitor) on gene expression of MCF7 cells

status: Public on Jul 17 2024

city: Mainz

first: Christian

last: Schwarzenbach

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

country: Germany

institute: University medical center Mainz

type: Expression profiling by high throughput sequencing

summary: Studying DNA damage-induced senescence, we observed a similar phenotype upon CDK4/6 inhibition in breast cancer cells. We used RNA sequencing to investigate the gene expression profile of MCF7 cells upon CDK4/6 inhibition five days after exposure.

overall_design: MCF7 cells were exposed or unexposed for 120 h to 1 µM Palbociclib (PD-0332991, inhibiting CDK4/6). We then performed comparative gene expression profiling analysis using RNA-seq data obtained from 3 independent experiments of exposed and unexposed cells.

first: Sebastian

last: Allmann

first: Ariane

last: Schmidt

first: Markus

last: Christmann

first: Sergi

last: Sayols Puig


title: CARM1 interacts and hypermethylates the NuRD chromatin remodeling complex to promote gene transcriptional activation and cell cycle progression

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

country: China

institute: Xiamen University

summary: Protein arginine methyltransferase CARM1 has been shown to methylate a large number of non-histone proteins, and play important roles in gene transcriptional activation, cell cycle progress, and tumorigenesis. However, the critical substrates through which CARM1 exerts its functions remain to be fully characterized. Here, we reported that CARM1 directly interacts with the GATAD2A/2B subunit in the nucleosome remodeling and deacetylase (NuRD) complex, expanding the activities of NuRD to include protein arginine methylation. CARM1 and NuRD bind and activate a large cohort of genes with implications in cell cycle control to facilitate the G1 to S phase transition. This gene activation process requires CARM1 to hypermethylate GATAD2A/2B at a cluster of arginines, which is critical for the recruitment of the NuRD complex. The clinical significance of this gene activation mechanism is underscored by the high expression of CARM1 and NuRD in breast cancers, and the fact that knockdown CARM1 and NuRD inhibits breast cancer cell growth in vitro and tumorigenesis in vivo. These findings reveal a gene activation program that requires the dual specificity established by CARM1 on chromatin and a key chromatin remodeler.

overall_design: RNA-seq performed in this study was designed to understand the molecular mechanisms underlying CARM1/NuRD in gene transcriptional activation.

first: Wen

last: Liu

first: Xue

last: Chen

first: Yaohui

last: He

first: Wenjuan

last: Zhang

first: Mingfeng

last: Huang


title: Dynamic analysis of mononuclear transcription profiles of fat in different parts of mice during aging

city: chengdu

first: lu

last: lu

state: sichuan

address: 211 Huimin Road, Wenjiang District

department: animal science and technology

institute: Sichuan Agricultural University

summary: Adipose tissue shows significant changes during aging. Here, we used single-nucleus RNA-seq to map the single-nucleus transcription profiles of mouse subcutaneous adipose tissue ( SAT ) and visceral adipose tissue ( VAT ) at a single-nucleus resolution, showing the differences in visceral and subcutaneous adipose tissue changes with aging. The mononuclear sequencing method enabled us to restore all major cell types in mouse white adipose tissue, and we characterized adipocytes, immune cells, and preadipocytes. We demonstrated the existence of different adipocyte subsets and showed that aging leads to a decrease in adipogenic subsets. In addition, with aging, both subcutaneous adipose tissue and visceral adipose tissue showed a decrease in immune mechanisms.

overall_design: Subcutaneous mouse adipose tissue depots were dissected from 2 months and 26 months female C57BL/6J mice into ice-cold PBS. diluted in diethyl pyrocarbonate (DEPC) water.White adipose tissue (SAT and VAT) was surgically removed and placed in 1x PBS on ice. Cells were then stained with desired antibodies, and subjected to FACS or snRNA-seq.

first: Yujie

last: Wu

first: Long

first: Xingyan

last: Tong

first: Can

first: Mingzhou

last: Li

last: Jin

first: Ying

last: Sun


title: Adenoviral Transduction of ARL11 in NHU-hTERT cells

city: Houston

first: Bogdan

last: Czerniak

state: TX

address: 1515 Holcombe

department: Pathology

country: USA

institute: UT MD Anderson Cancer Center

summary: Analyses of the whole genome mRNA gene expression profiling performed on ARL11-transducted normal urothelium cells. The results revealed that TP53, RB1 and CDKN2A pathways were activated and the E2F1 and MYC pathways were inhibited in cells expressing ARL11. ARL11-transducted cells also inhibited RAS pathway activation.

overall_design: Total RNA was extracted from NHU-hTERT cells transducted with ARL11 and cells with empty vector

first: Sangkyou

last: Lee

first: Tadeusz

last: Majewski


title: Gene expression profile with the p38 inhibitor treatment

status: Public on Jul 16 2024

first: Yong

last: Lu

address: 6565 Fannin St

institute: Houston Methodist

summary: Mice bone marrow cells induced dendritic cells were treated with a p38 inhibitor, we used Microgenearry to analyze the dendritic cell-related gene expression, which was induced by a p38 inhibitor. Mice were treated with CAR-T cells with or without p38 inhibitor treatment, we used Microgenearry to analyze the dendritic cell-related gene expression in the tumor environment. Tumor tissues (~100 mg/mouse, 12 days after ACT) were harvested and total RNA was extracted with the RNeasy Mini kit (Qiagen).

overall_design: Murine BM cells were cultured and supplemented with mGM-CSF with or without p38 inhibitors. On day 6, semi-adherent cells were collected and total RNA was extracted with the RNeasy Mini kit (Qiagen).

first: Ningbo

last: Zheng


title: Inhibiting phosphatidylcholine remodeling in adipose tissue increases insulin sensitivity [scRNA-Seq]

city: Brooklyn

first: Xian-Cheng

last: Jiang

state: New York

address: 450 Clarkson Ave

department: Cell Biology

institute: SUNY Downstate Medical Center

summary: Cell membrane phosphatidylcholine composition is regulated by lysophosphatidylcholine acyltransferase (LPCAT); changes in membrane phosphatidylcholine saturation are implicated in metabolic disorders. Here, we identified LPCAT3 as the major isoform of LPCAT in adipose tissues and created adipocyte-specific Lpcat3-knockout mice to study adipose tissue lipid metabolism. Transcriptome sequencing and plasma adipokine profiling were used to investigate how LPCAT3 regulates adipose tissue insulin signaling. LPCAT3 deficiency reduced polyunsaturated phosphatidylcholines in adipocyte plasma membranes, increasing insulin sensitivity. LPCAT3 deficiency influenced membrane lipid rafts, which activated insulin receptors and AKT in adipose tissue, and attenuated diet-induced insulin resistance. Conversely, higher LPCAT3 activity in adipose tissues from ob/ob, db/db, and high-fat diet-fed mice reduced insulin signaling. Adding polyunsaturated phosphatidylcholines to mature human or mouse adipocytes in vitro worsened insulin signaling. We suggest that targeting LPCAT3 in adipose tissues to manipulate membrane phospholipid saturation is a new strategy to treat insulin resistance.

overall_design: We collected sWAT isolated from 2-month-old CD-fed wild-type and LPCAT3-AKO mice for RNA sequencing, and SVF for scRNA sequencing.

first: Mulin

first: Victoria

last: Tung

first: Oleg

last: Evgrafov


title: scRNA-seq analysis of ATII's responses to IL-4 cytokines during aging

city: South San Francisco

first: David

last: Garfield

state: CA

address: 1 DNA Way

department: OMNI Bx

institute: Genentech

summary: Wound healing in response to acute injury is mediated by the coordinated and transient activation of parenchymal, stromal, and immune cells that resolves to homeostasis. Environmental, genetic, and epigenetic factors associated with inflammation and aging can lead to persistent activation of the microenvironment and fibrosis. Here, we identify opposing roles of IL-4 cytokine signaling in interstitial macrophages and type II alveolar epithelial cells (ATIIs). We show that IL4Ra signaling in macrophages promotes regeneration of the alveolar epithelium after bleomycin-induced lung injury. Using organoids and mouse models, we show that IL-4 directly acts on a subset of ATIIs to induce the expression of the transcription factor SOX9 and reprograms them toward a progenitor-like state with both airway and alveolar lineage potential. In the contexts of aging and bleomycin-induced lung injury, this leads to aberrant epithelial cell differentiation and bronchiolization, consistent with cellular and histological changes observed in interstitial lung disease.

overall_design: When culturing mouse alveolarspheres, we will seed mouse ATIIs from young and old mice, and grow them using serum-free and feeder-free system. On day 3, 10ng/ml IL14 will be added to corresponding wells while PBS will be added as the control group. Cells were collected for scRNA-seq analysis on day 13.

first: Xiaoyu

middle: T

last: Cai

first: Minxue

last: Jia

first: Jason

last: Rock


title: Identification of mutant KRAS-related genes associated with malignant phenotypes in NSCLC

city: Maebashi

first: Noriaki

last: Sunaga

state: Gunma

address: 3-39-15 Showa-machi

department: Department of Respiratory Medicine

country: Japan

institute: Gunma University Graduate School of Medicine

summary: Oncogenic KRAS is found in more than 25% of lung adenocarcinomas, the major histologic subtype of non–small cell lung cancer (NSCLC), and is an important target for drug development. To this end, we generated four NSCLC lines with stable knockdown selective for oncogenic KRAS. As expected, stable knockdown of oncogenic KRAS led to inhibition of in vitro and in vivo tumor growth in the KRAS-mutant NSCLC cells, but not in NSCLC cells that have wild-type KRAS (but mutant NRAS). Surprisingly, we did not see large-scale induction of cell death and the growth inhibitory effect was not complete. To further understand the ability of NSCLCs to grow despite selective removal of mutant KRAS expression, we conducted microarray expression profiling of NSCLC cell lines with or without mutant KRAS knockdown and isogenic human bronchial epithelial cell lines with and without oncogenic KRAS. We found that although the mitogen-activated protein kinase pathway is significantly downregulated after mutant KRAS knockdown, these NSCLCs showed increased levels of phospho-STAT3 and phospho–epidermal growth factor receptor, and variable changes in phospho-Akt. In addition, mutant KRAS knockdown sensitized the NSCLCs to p38 and EGFR inhibitors. Our findings suggest that targeting oncogenic KRAS by itself will not be sufficient treatment, but may offer possibilities of combining anti-KRAS strategies with other targeted drugs. Detailed information on the microarray results are available in a previous study (Sunaga N, et al. Mol Cancer Ther. 2011;10:336-46).

overall_design: Gene expression was examined in shRNA-mediated mutant KRAS-silenced and KRAS-retained NSCLC cell lines harboring KRAS-G12C (H23, H358, and H1792) or KRAS-G12V (H441) mutations. Mutant KRAS expressions in these NSCLC cells were silenced with mutant KRAS-specific shRNA vectors. The H1299 NSCLC cell line was used as a KRAS non-mutated control. For HBEC samples, mutant KRAS-G12V transduction was mediated by the mutant KRAS-V12V expression vector, whereas p53 expression was silenced by the shRNA vector targeting the TP53 gene in the HBEC3 immortalized human bronchial epithelial cell line, which was established by hTERT and Cdk4 gene transduction. Gene expression was examined in mutant KRAS-G12V-expressing or mutant KRAS-nonexpressing HBEC3 cells with or without shRNA-mediated p53 knockdown. H23-Ctrl: H23 with control shRNA; H23-KRAS-C12: H23 with shRNA targeting mutant KRAS-G12C; H358-Ctrl: H358 with control shRNA; H358-KRAS-C12: H358 with shRNA targeting mutant KRAS-G12C; H1792-Ctrl: H1792 with control shRNA; H1792-KRAS-C12: H1792 with shRNA targeting mutant KRAS-G12C; H441-Ctrl: H441 with control shRNA; H441-KRAS-V12: H441 with shRNA targeting mutant KRAS-G12V; H1299-Ctrl: H1299 with control shRNA; H1299-KRAS-C12: H1299 with shRNA targeting mutant KRAS-G12C; H1299-KRAS-V12: H1299 with shRNA targeting mutant KRAS-G12V; HBEC3: the immortalized human bronchial epithelial cell line, which harbors wild-type KRAS and retains p53 expression; HBEC3-K: HBEC3 expressing mutant KRAS-G12V; HBEC3-p53: HBEC with p53 knockdown; HBEC3-p53K: HBEC3 with p53 knockdown but expressing mutant KRAS-G12V.

first: Luc

last: Girard

first: Mitsuo

last: Sato


title: West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles

city: New Haven

first: Nicholas

last: Huston

state: Connecticut

address: 260 Whitney Avenue, YSB 308

institute: Yale University

summary: SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero or C6/36 cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minuse reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. After sequencing and alignment, the reactivity profiles of 'modified' and 'unmodified' samples are used to calculate SHAPE reactivity of each base

sample_organism:
Aedes albopictus
Chlorocebus aethiops

platform_organism:
Aedes albopictus
Chlorocebus aethiops

overall_design: SHAPE-MaP on West Nile virus genomic RNA growing in Vero or C6/36 cells

middle: C

first: Douglas

last: Brackney

first: Anna

last: Pyle


title: BRD4770 functions as a novel ferroptosis inhibitor to protect against aortic dissection

city: Wuhan

first: yue

last: chen

state: Hubei Province

address: no.1095 Jiefang Avenue

department: Tongji Hospital

institute: Huazhong University of Science and Technology

summary: Smooth muscle cell (SMC) loss is the characteristic feature in the pathogenesis of aortic dissection (AD), and ferroptosis is a novel iron-dependent regulated cell death driven by the excessive lipid peroxidation accumula_x0002_tion. However, whether targeting ferroptosis is an effective approach for SMC loss and AD treatment remains unclear. Here, we found that the iron level, ferroptosis-related molecules TFR, HOMX1, ferritin and the lipid peroxidation product 4-hydroxynonenal were increased in the aorta of AD. Then, we screened several inhibitors of histone methyltransferases and found that BRD4770 had a protective effect on cystine deprivation-, imidazole ketone erastin- or RSL3-induced ferroptosis of SMCs. The classic ferroptosis pathways, System Xc--GPX4, FSP1- CoQ10 and GCH1-BH4 pathways which were inhibited by ferroptosis inducers, were re-activated by BRD4770 via inhibiting mono-, di- and tri- methylated histone H3 at lysine 9 (H3K9me1/2/3). RNA-sequencing analysis revealed that there was a positive feedback regulation between ferroptosis and inflammatory response, and BRD4770 can reverse the effects of inflammation activation on ferroptosis. More importantly, treatment with BRD4770 attenuated aortic dilation and decreased morbidity and mortality in a β-Aminopropionitrile monofumarate-induced mouse AD model via inhibiting the inflammatory response, lipid peroxidation and fer_x0002_roptosis. Taken together, our findings demonstrate that ferroptosis is a novel and critical pathological mechanism that is involved in SMC loss and AD development. BRD4770 is a novel ferroptosis inhibitor and has equivalent protective effect to Ferrostatin-1 at the optimal concentration. Translating insights into the anti-ferroptosis ef_x0002_fects of BRD4770 may reveal a potential therapeutic approach for targeting SMC ferroptosis in AD.

overall_design: Human aortic smooth muscle cells (SMCs) were subjected to various interventions to induce ferroptosis and examine the protective effects of BRD4770, an inhibitor of histone methyltransferases. The experimental groups included: DMSO control group, Imidazole ketone erastin group, Imidazole ketone erastin + BRD4770 group, Cystine deprivation group,Cystine deprivation + BRD4770 group. RNA sequencing (RNA-seq) was performed on these groups to analyze gene expression changes.

first: Yue

last: Chen

first: Dingsheng

first: Xiang

last: Wei

first: Xin

last: Yi


title: 4C-Seq Drosophila Imaginal Disc HP6/Umbrea

city: NEW YORK

first: UnJin

last: Lee

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: Chromosomal conformation capture in Drosophila melanogaster with a viewpoint of the HP6/Umbrea locus

overall_design: imaginal disc tissue is dissected in 1x PBS in 10m intervals, flash frozen. Single nucleus suspension, then double digestion using DpnII and XbaI.


title: Bulk RNAseq analysis of Cx3cr1+ macrophages with and without IL4Ra deletion during bleomycin-induced lung fibrosis.

overall_design: When culturing mouse alveolarspheres, we will seed mouse ATIIs from young and old mice, and grow them using serum-free and feeder-free system. On day 9, cells were infected with either AAV9_Cre or AAV9_Sox9Cre (to overexpress Sox9 together with Cre recombinase. Then we switched the culture medium to ATII differentiation medium to induce ATI differentiation for 4 days. We collected tdTomato+ cells by FACS and extracted nuclei for sc-multiome analysis.


title: The m6A writer KIAA1429 regulates photoaging progression via MFAP4-dependent collagen synthesis

city: Chongqing

first: Mingwang

last: Zhang

state: Chongqing

address: Department of Dermatology, Southwest Hospital, Army Medical University, 400038 C

institute: Army Medical University

summary: Background: N6-Methyladenosine (m6A) methylation, a common form of RNA modification, play an important role in the pathogenesis of various diseases and in the ontogeny of organisms. Nevertheless, the precise function of m6A methylation in photoaging remains unknown. Objectives: This study aims to investigate the biological role and underlying mechanism of m6A methylation in photoaging. Methods: m6A dot blot, Real-time quantitative PCR (RT-qPCR), western blot and immunohistochemical (IHC) assays were employed to detect the m6A level and specific m6A methylase in ultraviolet ray (UVR)-induced photoaging tissue. The profile of m6A-tagged mRNA was identified by methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-seq analysis. Finally, we investigated the regulatory mechanism of KIAA1429 by MeRIP-qPCR, RNA knockdown and immunofluorescence assay. Results: m6A levels were increased in photoaging and were closely associated with the upregulation of KIAA1429 expression. 1331 differentially m6A methylated genes were identified in the UVR group compared with the control group, of which 1192 (90%) were hypermethylated. Gene ontology analysis showed that genes with m6A hypermethylation and mRNA downregulation were mainly involved in extracellular matrix metabolism and collagen metabolism-related processes. Furthermore, KIAA1429 knockdown abolished the downregulation of TGF-R and upregulation of MMP1 in UVR-irradiated HDFs. Mechanically, we identified MFAP4 as a target of KIAA1429-mediated m6A modification and KIAA1429 might suppress collagen synthesis through an m6A-MFAP4-mediated process. Conclusions: The increased expression of KIAA1429 hinders collagen synthesis during UVR-induced photoaging, suggesting that KIAA1429 represents a potential candidate for targeted therapy to mitigate UVR-driven photoaging.

first: Yuanyuan

last: Liu


title: in vitro and in vivo transcriptomics profile of Lactobacillus johnsonii MR1

status: Public on Jul 15 2024

city: Ann Arbor

first: Keerthikka

last: Ravi

state: Michigan

address: 1105 N University st

department: Molecular, Cellular and Developmental Biology

institute: University of Michigan

summary: Lactobacillus johnsonii, a Gram-positive, gut bacterium is well studied for its several health-beneficial properties. This

overall_design: Lactobacillus johnsonii was grown anaerobically at 37 °Cs. The in vitro transcriptomics profile was acquired by collecting cells at the exponential phase and stationary phase. The in vivo transcriptomics profile was acquired by harvesting cells from the cecal content of germ-free Balb/c mice inoculated with L. johnsonii.

first: Nicole

middle: R

last: Falkowski

first: Gary

middle: B

last: Huffnagle


title: A long-lasting prolactin to combat lactation insufficiency

city: Boston

first: Kasia

last: Kready

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard University

summary: Human infants are born to breastfeed. While 50% of lactating persons report struggling to make enough milk, there are no governmentally-approved drugs to enhance lactation1. Here, we engineer a variant of the naturally-occurring driver of lactation, the hormone Prolactin, to increase its serum half-life and produce a viable drug candidate. Our engineered variant,Prolactin-eXtra Long-acting(Prolactin-XL), is comprised of endogenously active human prolactin fused to an engineered human IgG1 Fc domain designed to overcome the unique drug development challenges specific to the lactating person-infant dyad. Our Prolactin-XL has a serum half-life of 70.9h in mice, 2,625-fold longer than endogenously active prolactin alone (70.9h v. 0.027h). We demonstrate that Prolactin-XL increases milk production and restores growth of pups fed by dams with pharmacologically-ablated lactation. We show that Prolactin-XL-enhanced lactation is accompanied by reversible, alveolar cell-driven changes in mammary gland morphology. Prolactin-XL treatment was associated with no identifiable pathology or adverse side effect in the lactating mice or nursing pups. This work establishes long-acting prolactins as a potentially powerful pharmacologic means to combat insufficient lactation. Implications for future research in lactating mammary gland biology and a potential preclinical path for developing Prolactin-XL for use in lactating persons are discussed.

overall_design: All animal work was approved by the Harvard Medical School IACUC under protocol IS00003310. C57bl/6j mice (Jackson; 000664) were mated at 8 weeks of age. On day 7 postpartum, litters were normalized to 5 pups per dam. Pups were weighed daily until they were weaned at day 21 postpartum or they reached endpoint (20% weight loss compared to positive controls). Beginning on day 7 postpartum, and every other day thereafter, dams were administered 5mg/kg dose of Fc-PRL-13 or a PBS control by subcutaneous. Dams were dosed until their pups were weaned at day 21 postpartum. Abdominal mammary glands were harvested and stored in RNAlater (Thermo Fisher Scientific, AM7020) overnight at 4C. Samples were then stored at -80C until submitted to Azenta/Genewiz for standard RNA sequencing.

first: Kailyn

last: Doiron

first: Katherine

last: Chan

first: Jeffrey

last: Way

first: Quincey

last: Justman

first: Camille

middle: E

last: Powe

first: Pamela

last: Silver


title: Epigallocatechin Gallate modulates microglia phenotype

city: Bath

first: Robert

middle: J

last: Williams

address: University Of Bath, The Avenue, Claverton Down

country: United Kingdom

institute: University of Bath

summary: We have identified Epigallocatechin Gallate (EGCG) as a potent modulator of microglia function. Our aim was to determine whether EGCG affects the transcriptome of microglia and identify genes and gene sets that may underly the effects of EGCG on microglia function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary murine (CD1) microglia treated with 1uM EGCG or equivalent DMSO control for 24 hours in serum free media. 2 indendent biological replicates were included for both treatment conditions.

first: Philip

last: Regan

first: Julia

last: Sero


title: CUT & RUN for P63, Gata3, Jun in murine keratinocytes and Tcf1 and Jun in murine CD8 Naive T-cells across two age stages, young (2 months) and aged (20-24 months).

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

summary: We performed CUT&RUN and assessed cumulative TF binding signal shifts between age-opening and closing regions in young (2 months) and aged (20-24 months) murine samples.

overall_design: TF Binding signal shifts between age-closing and age-opening regions were assessed. Differentially Accessible Regions (DARs) were derived from the same cell types, namely keratinocytes and CD8 Naive T-cells from young (2 months) vs aged (20-24 months) murine sample groups.

middle: M

first: Jingyu

first: Yifei

last: Huang

first: Xiaoli

last: Chen

first: Ralph

last: Patrick

first: Marina

last: Naval-Sanchez


title: Competition between two HUSH complexes orchestrates the immune response to retroelement invasion

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series

first: Joshua Miguel

last: Danac

middle: A


title: Comprehensive Human Embryogenesis Reference Tool using Single-Cell RNA-Sequencing Data

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

summary: Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of embryo models hinges on their molecular, cellular and structural fidelities to their in vivo counterparts. To authenticate human embryo models, single-cell RNA-sequencing has been utilised for unbiased transcriptional profiling of human embryo models. However, a well-organised and integrated human single-cell RNA-sequencing dataset, serving as a universal reference tool for benchmarking human embryo models, remains unavailable. Herein, we developed such a reference, through integration of six published human datasets covering developmental stages from the zygote to the gastrula. Lineage annotations are contrasted and validated with available human and non-human primate datasets. Using stabilised UMAP we constructed a web tool, where query datasets can be projected on the reference and annotated with predicted cell identities. Using this reference tool, we examined several recent human embryo models, highlighting the risk of misannotation when relevant references are lacking.

overall_design: Primed hPSC growing on hrLN-521 (10 μg/mL, Biolamina, LN521-02)  and NutriStem hPSC XF (Biological Industries, 05-100-1A) were enzymatically dissociated and seeded onto new plates also coated with hrLN-521 at a cell density of 1,84x104 cells/cm2. 24h after seeding, hPSC were moved to a 5% CO2/5% O2 incubator and were differentiated into trophoblastic cells using NutriStem hPSC XF without bFGF and TGFb that was supplemented with 10ng/mL BMP4 (Biotechne), 1µM A83-01 (Biotechne) and 0,1µM PD173074 (Biotechne) (BAP treated).

first: Alvaro

last: Plaza Reyes

first: John

middle: P

last: Schell

first: Jere

last: Weltner

first: Nicolás

last: Ortega

first: Yi

last: Zheng

first: Åsa

middle: K

last: Björklund

first: Laura

last: Baqué-Vidal

first: Joonas

last: Sokka

first: Ras

last: Torokovic

first: Brian

last: Cox

first: Janet

last: Rossant

first: Jianping

last: Fu

first: Sophie

last: Petropoulos

first: Fredrik

last: Lanner


title: Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [scRNA-seq HF]

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisallee 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

summary:
BACKGROUND:
Activation of the immune system contributes to cardiovascular diseases. The role of human-specific long noncoding RNAs in cardioimmunology is poorly understood.
METHODS:
Single-cell sequencing in peripheral blood mononuclear cells revealed a novel human-specific long noncoding RNA called HEAT4 (heart failure–associated transcript 4). HEAT4 expression was assessed in several in vitro and ex vivo models of immune cell activation, as well as in the blood of patients with heart failure (HF), acute myocardial infarction, or cardiogenic shock. The transcriptional regulation of HEAT4 was verified through cytokine treatment and single-cell sequencing. Loss-of-function and gain-of-function studies and multiple RNA–protein interaction assays uncovered a mechanistic role of HEAT4 in the monocyte anti-inflammatory gene program. HEAT4 expression and function was characterized in a vascular injury model in NOD.CB17-Prkdc scid/Rj mice.
RESULTS:
HEAT4 expression was increased in the blood of patients with HF, acute myocardial infarction, or cardiogenic shock. HEAT4 levels distinguished patients with HF from people without HF and predicted all-cause mortality in a cohort of patients with HF over 7 years of follow-up. Monocytes, particularly anti-inflammatory CD16+ monocytes, which are increased in patients with HF, are the primary source of HEAT4 expression in the blood. HEAT4 is transcriptionally activated by treatment with anti-inflammatory interleukin-10. HEAT4 activates anti-inflammatory and inhibits proinflammatory gene expression. Increased HEAT4 levels result in a shift toward more CD16+ monocytes. HEAT4 binds to S100A9, causing a monocyte subtype switch, thereby reducing inflammation. As a result, HEAT4 improves endothelial barrier integrity during inflammation and promotes vascular healing after injury in mice.
CONCLUSIONS:
These results characterize a novel endogenous anti-inflammatory pathway that involves the conversion of monocyte subtypes into anti-inflammatory CD16+ monocytes. The data identify a novel function for the class of long noncoding RNAs by preventing protein secretion and suggest long noncoding RNAs as potential targets for interventions in the field of cardioimmunology.

overall_design: Single-cell RNA sequencing (scRNA-seq.) was performed on PBMCs from controls (n=3) and HF patients (n=8).

first: Jasmin

last: Kneuer

first: Ignacy

last: Grajek


title: Glial Guidance Drives Postnatal Intestinal Reinnervation by Enteric Neurons

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary: This study investigates the phenomenon of postnatal plasticity within the enteric nervous system (ENS), specifically investigating the reinnervation potential of post-mitotic enteric neurons. Employing BAF53b-Cre for selective tracing, the reinnervation capabilities of postnatal enteric neurons in multiple model systems are shown. Denervated enteric neurons exhibit the ability to regenerate neurites in vitro, with neurite complexity and direction notably influenced by contact with enteric glial cells (EGCs). In vivo nerve fibers from transplanted enteric neurons exclusively interface with EGCs. Resident EGCs are sustained after Cre dependent ablation of enteric neurons and govern the architecture of the ENS by reinnervating enteric neurons. Transplantation experiments underscore the swift reintegration and reinnervation potential of post-mitotic neurons, leading to restored muscle function within two weeks. Optogenetic investigations further delineate time-dependent functional recovery via transplantation of isolated enteric ganglia. These revelations demonstrate the structural and functional reinnervation capacity of post-mitotic enteric neurons, underscored by EGC guidance.

overall_design: To ablate enteric neurons expressing inducible diphtheria toxin receptor (iDTR), BAF53b::iDTR mice were generated. Diphtheria toxin (Sigma Aldrich, St. Louise, MO, USA, #D0564) was prepared by dilution in PBS and India ink to a final dose of 0.33ng/μL of DT and 10% India ink at final volume.  Mice were anesthetized by isoflurane to perform laparotomy and delivery of 4μL of the DT solution by microinjection to the muscularis propria with the India ink used to confirm the injection site. Injection of the solution DT was performed in littermate mice lacking iDTR expression as experimental controls.

first: Ahmed

last: Rahman

first: Christopher

middle: Y

last: Han

first: Abigail

last: Leavitt

first: Leah

last: Ott

first: Ryo

last: Hotta

first: Allan

last: Goldstein


title: Small RNA next genration sequencing of microRNAs in withaferin A treated breast normal epithelial cell line MCF10A

city: Bathinda

first: Shashank

last: Kumar

state: Punjab

address: VPO Guddha

department: Biochemistry

country: India

institute: CENTRAL UNIVERSITY OF PUNJAB

summary: This study was amied to identify the diffenetiall expressed miRNAs in Withaferin A (WA) treated breast normal cells (MCF10A) in comparision to non-treated cells


title: Inhibiting phosphatidylcholine remodeling in adipose tissue increases insulin sensitivity

first: Xian-Cheng

last: Jiang


title: Gene expression profiling of FaDu cells overexpressing TINCR-HA-FLAG

city: New York

first: Jessie

last: Brown

address: 1130 St. Nicholas Ave, 401B

institute: Columbia University Medical Center

summary: Differential gene expression analysis of FaDu cells overexpressing TINCR-HA-FLAG or an empty vector.

overall_design: Technical replicates of FaDu cells overexpressing TINCR-HA-FLAG or an empty vector were extracted for RNA for RNAseq analysis.

first: Ferrando

last: Adolfo


title: A brain organoid/ALL co-culture model reveals the AP-1 pathway as critically associated with CNS involvement of BCP-ALL

city: Düsseldorf

first: Julian

last: Schliehe-Diecks

address: Moorenstr. 5

institute: Uniklinik Düsseldorf

summary: Central nervous system (CNS) involvement remains a clinical hurdle in treating childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL). The disease mechanisms of CNS leukemia are primarily investigated using 2D cell culture and mouse models. Given the variations in cellular identity and architecture between the human and murine CNS, it becomes imperative to seek complementary models to study CNS leukemia. Here, we present a first-of-its-kind 3D co-culture model combining human brain organoids and BCP-ALL-cells. We noticed significantly higher engraftment of BCP-ALL cell lines and patient-derived xenograft (PDX) cells in cerebral organoids as compared to non-ALL-cells. To validate translatability between organoid co-culture and in vivo murine models, we confirmed that targeting CNS leukemia relevant pathways like CD79a/Igα or CXCR4- SDF1 reduced the invasion of BCP-ALL-cells into organoids. RNA sequencing and functional validations of organoid-invading leukemia cells compared to the non-invaded fraction revealed significant upregulation of AP-1 transcription factor-complex members in organoid-invading cells. Moreover, we detected a significant enrichment of AP-1 pathway genes in ALL-PDX-cells recovered from the CNS compared to spleen blasts of mice transplanted with TCF3::PBX1+ PDX-cells, substantiating the role of AP-1 signaling in CNS disease. Accordingly, we found significantly higher levels of the AP-1-gene JUN in patients initially diagnosed as CNS-positive compared to CNS negative cases as well as CNS-relapse vs non-CNS-relapse cases in a cohort of 100 BCP-ALL-patients. Our results suggest CNS-organoids as a novel model to investigate CNS-involvement and identify the AP-1 pathway as a critical driver of CNS-disease in BCP-ALL.

overall_design: 1*10^5 cells of the two B cell precursor leukemia cell lines 697 and Kasumi 2 were cococultured with iPSC derived human cerebral organoids over the time course of 14 days. The cells that remainied in suspension and did not invade were used as controlls against the invading cells. The orgainoids were disolved via strainers and the leukemia cells were isolated via CD19+ Selection. The library preparation was performed according to the manufacturer's protocol using the 'Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus' (Illumina Inc.) kit, after purity and viability controlls. Bead-purified libraries were normalized and sequenced on the NextSeq2000 system.

first: Philipp

last: Gebing

first: Sanil

last: Bhatia


title: Contrasting defence mechanisms against spider mite infestation in Cyanogenic and Non-Cyanogenic legumes

city: Pozuelo de Alarcón

first: Isabel

last: Díaz

state: Madrid

address: Campus Montegarcedo

department: Interacción de las Plantas con el Medio

country: Spain

institute: CBGP-INIA-UPM

summary: Understanding the complex interactions between plants and herbivores is essential for improving crop resistance. To deep into the role of cyanogenesis in plant defence, we investigated the response of the cyanogenic Phaseolus lunatus (lima bean) and the non-cyanogenic Phaseolus vulgaris (common bean) to Tetranychus urticae infestation. Despite spider mite infesting both legumes, severity of leaf damage was reduced in lima bean. Comparative transcriptome analysis revealed that both species exhibited substantial metabolic and transcriptional changes upon infestation, yet the response in P. lunatus was significantly more pronounced. Specific differences in amino acid homeostasis and in the expression of key genes of the cyanogenic pathway were observed in P. lunatus. Moreover, the mandelonitrile lyase gene (PlMNL1) was upregulated following T. urticae feeding concomitantly to an enzyme activity increase. Lima bean plants also displayed an induction of β-cyanoalanine synthase (PlCYSC1), a key enzyme for cyanide detoxification, suggesting an internal regulatory mechanism to manage the toxicity of their defence responses. These findings contribute to have a major comprehension of the plant-insect interactions and underscore the potential role of cyanogenesis in the elaboration of unique specific defensive responses, even within the same genus, which may reflect distinctive evolutionary adaptations or varying metabolic capabilities between species.

sample_organism:
Phaseolus lunatus
Phaseolus vulgaris

platform_organism:
Phaseolus lunatus
Phaseolus vulgaris

overall_design: To understand the genetic regulation of the differential responses between P. vulgaris and P. lunatus to mite infestation, RNA sequencing (RNA-seq) was performed on leaves from both species 24 hours post T. urticae infestation.

first: Marta

last: Boter


title: RPTOR, a novel target of miR-155, regulates the fibrotic phenotype of cystic fibrosis lung epithelium by upregulating CTGF

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

type:
Expression profiling by array
Other

summary: Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, the most frequent of which is F508del-CFTR.  CF is characterized by excessive secretion of pro-inflammatory chemokines into the airway lumen, inducing a highly inflammatory cellular phenotype.  This process triggers fibrosis, causing airway destruction and leading to high morbidity and mortality.  We previously reported that miR-155 is up-regulated in CF lung epithelial cells, but the molecular mechanisms by which miR-155 affects the disease phenotype is not understood.  Here we report that the protein RPTOR (regulatory associated protein of mTOR, complex 1) is a novel target of miR-155 in CF lung epithelial cells.  The suppression of RPTOR expression and subsequent activation of TGF-β signaling resulted in the induction of fibrosis by up-regulation of connective tissue growth factor (CTGF) in CF lung epithelial cells.  Thus, we propose that miR-155 can regulate fibrosis of CF lungs through the RPTOR-TGF-β-CTGF axis, highlighting its potential value in CF therapy.

overall_design: Elevated expression of miR-155 in CF bronchial epithelial cells induces expression of the pro-inflammatory cytokine IL8 via increased PI3K/Akt signaling 10, and we sought to identify miR-155 targets that regulate the CF disease phenotype.  Two experimental strategies were employed in a concurrent gene expression study: in the first, a 3'-end-biotinylated miR-155 (N=3) or biotinylated cel-miR-67 control (N=2) was transfected into IB3-1/S9 lung epithelial cells. Streptavidin bead-based affinity purification was used to enrich cell lysates for mRNA:miR-155 complexes, which were extracted and compared using microarray analysis to the cel-miR-67 control. In the second, IB3-1/S9 cells were incubated with either a miR-155 (N=2) or a control mimic (N=2). From the microarray analysis, potential mRNA targets of miR-155 are expected to be enriched in the affinity-based isolation employing biotinylated-miR-155, and should be down-regulated in cells where miR-155 is overexpressed.  Thus, we identified genes with positive Z-ratio from the former group (upregulated mRNAs that bind miR-155) and with negative Z-ratio from the latter group (transcripts that are downregulated if miR-155 is overexpressed).

first: Motohiro

last: Tsuchiya

first: Swathi

last: Kalurupalle

first: Parameet

first: Sarani

last: Ghoshal

first: Yongqing

last: Zhang

first: Elin

last: Lehrmann

first: Kevin

middle: G

last: Becker

first: Myriam

last: Gorospe

first: Roopa

last: Biswas


title: Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [ChIP-seq]

first: Jes-Niels

last: Boeckel

overall_design: Human primary monocytes were isolated from PBMCs, transfected with control or HEAT4-encoding plasmids and treated with IL-10 for 24 h. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for S100A9 was performed.

first: Jasmin

last: Kneuer

first: Ignacy

last: Grajek

first: Stephan

last: Erbe


title: Trancriptome profiling of glioma cell line U87 and U251 with LAMP2A knockdown

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

institute: China Medical University

summary: The objective of the study was to examine the gene expression changes in glioma cell line U87 and U251 with LAMP2A knockdown.  There were 15 samples in total- U87-1, U87-2, U87-3, U87-1812-1, U87-1812-2, U87-1812-3, U251-1, U251-2, U251-3, U251-1812-1, U251-1812-2, U251-1812-3, U251-1813-1, U251-1813-2, and U251-1813-3. U87-1 to U87-3 and U251--1 to U251-3 were used as the control groups (CON). U87-1812-1 to U871812-3,  U251-1812-1 to U251-1812-3, and U251-1813-1 to U251-1813-3  were used as the experimental groups (shLAMP2A-1 and shLAMP2A-2). The total RNA of each sample was extracted from the stable transfected glioma cells by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. There were two types of libraries: the circRNA, mRNA, and lncRNA were all constructed by removing rRNA (one library, three types of RNA were analyzed together), and the insert fragment was about 300bp; the small RNA was constructed and analyzed separately, mainly microRNA of about 22bp. Results: among 60612 cleaned mRNAs, 781 were differentially expressed in U87-1812 group compared with U87 group, 146 were differentially expressed in U251-1812 group compared with U251 group, 43 were differentially expressed in U251-1813 group compared with U251 group  (padj ≤ 0.05 and expression change ≥2 fold). The differential expressed genes distributed in all chromosomes. Functional annotation with  GO and KEGG enrichment revealed the top functional groups including inflammation, DNA replication, cell adhesion, TNF, IL17, and axon guidance signaling pathways.

overall_design: Transcriptome profiling of 6 control (3 U87 and 3 U251, glioma cell lines) and 9 experimental (3 U87-1812, 3 U251-1812, and 3 U251-1813, glioma cell lines stably transfected with shRNA (1 or 2) of LAMP2A ) samples.

first: Jie

last: Lu

first: Fangyuan

last: Zhou


title: Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [RIP-seq]

overall_design: Human primary monocytes were isolated from PBMCs. RNA immunoprecipitation sequencing (RIP-seq) for S100A9 was performed.


title: DNA methylation enables recurrent endogenisation of giant viruses in an animal relative

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. However, in many eukaryotes 5mC has gained complex roles in gene regulation beyond parasite control. Animals are a paradigmatic case for 5mC evolution, as they show widespread variability across lineages, ranging from gene regulation and transposable element control to loss of this base modification. Here we show that the protist animal relative Amoebidium appalachense displays both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, large hypermethylated regions of the Amoebidium genome derive from viral insertions, including hundreds of endogenised giant viruses contributing 14% of the encoded genes. Using a combination of inhibitors and functional genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenisation and purging. Therefore we propose that 5mC is critical for the controlled co-existence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic genomes.

sample_organism:
Amoebidium parasiticum
Sphaeroforma arctica
Creolimax fragrantissima
Amoebidium appalachense
Ichthyosporea sp. XGB-2017a

overall_design: Profiling of cytosine methylation for Amoebidium appalachense and other ichthyosporeans using Enzymatic Methyl-seq, as well as 5-Azacytidine treatment vs control RNA-seq and Enzymatic Methyl-seq.

first: Luke

last: Sarre


title: Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [scRNA-seq]

overall_design: Human primary monocytes were isolated from PBMCs. Monocytes were seeded in cell culture plates in RPMI-1640 medium (Merck, #R8758) supplemented with 10% fetal bovine serum (FBS; Gibco, #10500064) and Opti-MEM-PEI-plasmid mixture (3.5 ml Opti-MEM (ThermoFisher, #31985070), 7.5 µl PEI (Polysciences, #23966-1) and plasmid) was added. Monocytes were transfected with control (pcDNA) or Heat4-encoding plasmids for 24 h. Single cell RNA-sequencing (scRNA-seq.) was performed.


title: The Role and Mechanism of TEAD4 in Preimplantation Embryonic Development in Mice and Cattle

city: Hangzhou

first: Bingjie

last: Hu

address: Yuhangtang Rd, Hangzhou, Zhejiang , China

institute: Zhejiang University

summary: Tead4 is a critical transcription factor expressed during preimplantation development and is essential for the expression of trophectoderm-specific genes in mice. However, the mechanism of Tead4’s function in mouse preimplantation development and its conservation across mammals remains unclear. Here, we report that Tead4 is a crucial transcription factor necessary for blastocyst formation in mice. Disruption of TEAD4 through base editing results in developmental arrest at the morula stage. Additionally, RNA-seq analysis reveals dysregulation of 670 genes in Tead4 knockout embryos. As anticipated, Tead4 knockout leads to a decrease in trophectoderm genes CDX2 and GATA3. Intriguingly, we observed a reduction in KRT8, suggesting that Tead4 influences the integrity of the trophectoderm epithelium in mice. More importantly, we noted a decrease in nuclear YAP for Tead4-deficient embryos, indicating that Tead4 directly regulates Hippo signaling. In contrast, bovine embryos with TEAD4 depletion can still develop to blastocysts with normal expression of CDX2, GATA3, and SOX2, albeit with a decrease in total cell number and ICM cell number. In conclusion, we propose that Tead4 regulates mouse blastocyst formation via Krt8 and Yap, both of which are critical regulators of mouse preimplantation development.

sample_organism:
Bos taurus
Mus musculus

platform_organism:
Bos taurus
Mus musculus

overall_design: PolyA RNA profiles of  bovine and mouse embryos


title: Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [RNA-seq_KD]

overall_design: Human primary monocytes were isolated from PBMCs and siRNA-mediated knockdown of HEAT4 was performed via electroporation. Monocytes were cultured for 48 h. 6 h prior harvest, monocytes were treated with LPS. Bulk RNA-sequencing (RNA-seq) was performed.


title: Ultrasound-mediated blood–spinal cord barrier opening prolongs survival in an ALS mouse model

city: Paris

first: Severine

last: Boillee

address: 47 Blvd de l'Hopital

country: France

institute: ICM - Paris Brain Institute, INSERM, CNRS, Sorbonne University

summary: Background: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by a progressive loss of motor neurons. The limited efficacy of recent therapies in clinical development may be linked to lack of drug penetration to the affected motor neurons due to the blood-brain barrier (BBB) and blood-spinal cord barrier (BSCB). Methods: In this work, the safety and efficacy of repeated short transient opening of the BSCB by low intensity pulsed ultrasound (US, sonication) was studied in females of an ALS mouse model (B6.Cg-Tg(SOD1*G93A)1Gur/J). The BSCB was disrupted using a 1 MHz ultrasound transducer coupled to the spinal cord, with and without injection of insulin-like growth factor 1 (IGF1), a neurotrophic factor that has previously shown efficacy in ALS models.  Findings: Results in healthy mouse models demonstrated that the BSCB can be safely disrupted and IGF1 concentrations significantly enhanced after a single session of transient BSCB disruption (176 ±32 µg/g vs. 0.16 ±0.008 µg/g, p<0.0001). Five repeated weekly US performed in female ALS mice demonstrated a survival advantage in mice treated with IGF1 and ultrasound (US+IGF1) compared to treatment with IGF1 alone (176 vs. 166 days, p=0.0038). Surprisingly, this survival advantage was also present in mice treated with ultrasound (US) alone vs untreated mice (178.5 vs. 166.5 days, p=0.0061). Analysis of glial cell immunoreactivity and microglial transcriptome showing reduced cell proliferation pathways, in addition to lymphocyte infiltration, suggested that the beneficial effect of US or US+IGF1 could act through immune cell modulation. Interpretation: These results show the first step towards a possible beneficial impact of transient BSCB opening for ALS therapy and suggest implication of immune cells.

overall_design: Comparative gene expression profiling analysis of mRNA sequenquencing  data from CD11b+ microglial cells isolated from lumbar spinal cord of hSOD1G93A ALS mouse model exposed or not to low intensity pulsed ultrasound (US) at the level of the lumbar spinal cord.

first: Anne-Sophie

last: Montero

first: Ilyes

last: Aliouat

first: Matthieu

last: Ribon

first: Michael

last: Canney

first: Lauriane

last: Goldwirt

first: Samia

last: Mourah

first: Félix

last: Berriat

first: Christian

middle: S

last: Lobsiger

first: Pierre-François

last: Pradat

first: François

last: Salachas

first: Gaelle

last: Bruneteau

first: Alexandre

last: Carpentier

first: Séverine

last: Boillée


title: Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing

first: Jes-Niels

last: Boeckel

first: Jasmin

last: Kneuer

first: Ignacy

last: Grajek

first: Melanie

last: Winkler

first: Stephan

last: Erbe

first: Tim

last: Meinecke


title: Micro-RNAs from Plasma-Derived Small Extracellular Vesicles as Potential Biomarkers for Tic Disorders Diagnosis

first: Yilong

last: Wang

state: Zhejiang

address: NO.3333 binsheng Road

department: Department of Neurology

institute: Children’s Hospital, Zhejiang University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: tic disorders (TDs) are a series of childhood neuropsychiatric disorders characterized by invol-untary motor and/or vocal tics and commonly comorbid with several other psychopathological and/or behavioral disorders. In the present study, we aimed to identify serum small extracellular vesicles (sEVs) derived microRNAs (miRNAs) from the serum samples of children for Tic Disorders Diagnosis

overall_design:
Expression of circulating miRNAs  from serum sEVs between Tic Disorders and healthy  children was assessed in this multiphase case-control study.
Definitions:
TTD: transient tic disorder
CTD:chronic motor or vocal tic disorder
TS:Tourette Syndrome
HC: healty control

first: Xuebin

last: Xu

first: Haihua

last: Chen

first: Mengying

last: Zhu

first: Xiaotong

last: Guo

first: Feng

last: Gao


title: The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1–linked chromatin opening

first: Christian

last: Nefzger

overall_design: Refer to individual Series


title: Exploring the Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aged Brain

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

institute: Peter MacCallum Cancer Centre

first: Simão

last: Rocha

first: Samantha

last: Mancino

last: Eckersley-Maslin


title: MLL-AF9 lates transcriptional initiation in mixed lineage leukemic cells

city: Shang Hai

first: Zimei

last: Yang

address: Dongchuan road 800

institute: Shang Hai Jiaotong University

summary: MLL-fusion proteins (MLL-FPs) are believed to maintain gene activation and induce mixed lineage leukemia (MLL) through aberrantly stimulating transcriptional elongation, but the underlying mechanisms are incompletely understood. Here we show that both MLL1 and AF9, one of the major fusion partners of MLL1, mainly occupy promoters and distal intergenic regions, exhibiting chromatin occupancy patterns resembling that of RNA polymerase II (Pol II) in HEL, a human cell line without MLL1 arrangement (MLLr). MLL1 and AF9 only co-regulate over a dozen genes despite of their co-occupancy on thousands of genes. They do not interact with each other, and their chromatin occupancy is also independent of each other. Moreover, AF9 deficiency in HEL cells decreases global TBP occupancy while decreases CDK9 occupancy on a small number of genes, suggesting an accessory role of AF9 in CDK9 recruitment and a possible major role in transcriptional initiation via initiation factor recruitment. Importantly, MLL1 and MLL-AF9 occupy promoters and distal intergenic regions, exhibiting identical chromatin occupancy patterns in MLL cells, and MLL-AF9 deficiency decreased occupancy of TBP and TFIIE on major target genes of MLL-AF9 in iMA9, a murine acute myeloid leukemia (AML) cell line inducibly expressing MLL-AF9, suggesting that it can also regulate initiation. These results suggest that there is no difference between MLL1 and MLL-AF9 with respect to location and size of occupancy sites, contrary to what people have believed, and that MLL-AF9 may also regulate transcriptional initiation in addition to widely-believed elongation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CUT&Tag, PRO-Seq, and RNA-Seq

first: Ming

last: Yu

first: Ruoyu

last: Zhao


title: Bulk RNA-seq in young (2 months) and aged (22-24 months) mice across 23 cell-types

address: 306 Carmody Road

institute: The University of Queensland

summary: To understand how age rewires the chromatin accessibility landscape, we molecularly profiled 23 purified cell types from 11 tissues and organs by assessing the cumulative signature of 15-25 young and aged mice for robust difference detection.

overall_design:
We performed RNA-seq for young (2 months) and aged (22-24 months) mice for FACS sorted cell-types.

A 3-prime biased approach was used to generate sequencing libraries as described previously
(Sun et al.  Nat Comms 2021;  https://doi.org/10.1038/s41467-021-22863-0).
Barcoded 19bp R1 and 111bp R2 paired-end reads per sequencing lane were assigned to individual samples using the sabre software (version 80faf94) with options “-u –m 2 –l 10" (https://github.com/najoshi/sabre) (Tsyganov et al. JOSS 2018; https://doi.org/10.21105/joss.00583).

Here we present the single-end demultiplexed reads per sample which were mapped to the mouse GRCm38.p6/mm10 genome primary assembly using Spliced Transcripts Alignment to a Reference (STAR) software version 2.5.2b (Dobin et al. Bioinformatics 2013; https://doi.org/10.1093/bioinformatics/bts635). STAR was run with mode alignReads with parameters “--outFileterMatchMinOverLred 0.3 --outFilerScoreMinOverLread 0.3 --twopassMode Basic –sjdbGTFfile –quanMode GeneCounts”. Reads with duplicated UMIs were removed using the software Je version 2.0.RC option markdupes (Girardot et al. BMC Bioinformatics, 2016; https://doi.org/10.1186/s12859-016-1284-2). Transcript quantification was performed using featureCounts version 2.0.1 with parameters “–Q10 -M"" (exonic regions of GENCODE’s vM24 annotation version) (Liao et al. NAR 2019; https://doi.org/10.1093/nar/gkz114).

first: Marina

last: Naval-Sanchez

first: Ralph

last: Patrick

first: Nikita

last: Depanhe


title: Exploring the Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aged Brain (IMPLICON-Seq)

summary: DNA methylation is a common mechanism regulating monoallelic expression of different genes, including imprinted genes. How age-induced alterations of methylation levels vary across alleles and impact on monoallelic expression is unknown. In the brain, this phenomenon may contribute mechanistically to neuronal dysfunction and disease. In order to investigate the allele-specific transcriptional and epigenetic signatures of aging, we used key brain areas, hippocampus and cerebellum, of juvenile and old hybrid mice obtained from BL6×CAST reciprocal crosses. We set out to explore whether epigenetic drift affects global DNA methylation machinery by investigating 5- methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels. Mass spectrometry analysis showed a significant increase of 5hmC levels in hippocampus of old mice, but this was not accompanied by measurable differences in methylating or demethylating enzymes. The expression of several repetitive elements (LINEs, SINEs, IAP) was also analysed with a reduction of the intracisternal A-particle (IAP) retrotransposons seen in HCP of old mice. We uncovered the allelic-specific DNA methylation profile of aging using genomic imprinting as a read-out by IMPLICON and allelic-expression by RNA sequencing. Here, imprinting is not substantially changed during aging, not affecting their normal monoallelic expression. This work provides the first epigenetic and transcriptional landscape of aging with allelic resolution and confirms that genomic imprinting is a stable epigenetic phenomenon across the whole lifespan.

overall_design: We used key brain areas, mostly focused in hippocampus (HCP) and cerebellum (CB), of juvenile and old hybrid mice obtained from BL6×CAST reciprocal crosses. We set out to explore whether epigenetic drift affects global DNA methylation machinery by investigating 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels by Liquid Chromatography with tandem mass spectrometry and the genes enconding for enzymes implicated in this process by RT-PCR and RNAseq, the later in HCP only . The expression of several repetitive elements (LINEs, SINEs, IAP) was also analysed by RTq-PCR and also by RNAseq in HCP . We uncovered the allelic-specific DNA methylation profile of aging using genomic imprinting as a read-out by IMPLICON in several brain areas such as hippocampus (HCP), cerebellum (CB), prefrontal cortex (PFC), hypothalamus (HY), nucleus accumbens (NA) and a control region such as lung. Allelic expression analysis by RNA sequencing was performed in HCP.

first: Annalisa

last: Mupo

first: Felix

last: Krueger

first: Oxley

last: Oxley

first: Melanie


title: Exploring the Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aged Brain (RNA-Seq)

summary: DNA methylation is a common mechanism regulating monoallelic expression of different genes, including imprinted genes. How age-induced alterations of methylation levels vary across alleles and impact on monoallelic expression is unknown. In the brain, this phenomenon may contribute mechanistically to neuronal dysfunction and disease. In order to investigate the allele specific transcriptional and epigenetic signatures of aging, we used key brain areas, hippocampus and cerebellum, of juvenile and old hybrid mice obtained from BL6×CAST/EiJ (CAST) reciprocal crosses. We set out to explore whether epigenetic drift affects global DNA methylation machinery by investigating 5- methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels. Mass spectrometry analysis showed a significant increase of 5hmC levels in hippocampus of old mice, but this was not accompanied by measurable differences in methylating and demethylating enzymes. The expression of several repetitive elements (LINEs, SINEs, IAP) was also analysed, strictly dependent on 5mC and 5hmC levels, and reporting a reduction of the intracisternal A-particle (IAP) retrotransposons in HCP of old mice. We uncovered the allelic-specific DNA methylation profile of aging using genomic imprinting as a read-out by IMPLICON and allelic expression by RNA sequencing. Here, imprinting is not substantially changed during aging, not affecting their normal monoallelic expression. This work provides the first epigenetic and transcriptional landscape of aging with allelic resolution and confirms that genomic imprinting is a stable epigenetic phenomenon across the whole lifespan.


title: Hop stunt viroid infection alters heterochromatin in Cucumis sativus

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

institute: Swedish University of Agricultural Sciences

summary: Viroids are pathogenic non-coding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including an interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes and transposable elements. Indeed, several genes connected to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.

overall_design: ChIP-seq.  Here we have analyzed the changes taking place in Cucumis sativus facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3.

first: Joan

last: Marquez-Molins

first: Maria

middle: L

last: Annacondia

first: Jinping

last: Cheng

first: Vasti

last: Juarez-Gonzalez


title: Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [RNA-seq_OE]

first: Jes-Niels

last: Boeckel

summary:
BACKGROUND:
Activation of the immune system contributes to cardiovascular diseases. The role of human-specific long noncoding RNAs in cardioimmunology is poorly understood.
METHODS:
Single-cell sequencing in peripheral blood mononuclear cells revealed a novel human-specific long noncoding RNA called HEAT4 (heart failure–associated transcript 4). HEAT4 expression was assessed in several in vitro and ex vivo models of immune cell activation, as well as in the blood of patients with heart failure (HF), acute myocardial infarction, or cardiogenic shock. The transcriptional regulation of HEAT4 was verified through cytokine treatment and single-cell sequencing. Loss-of-function and gain-of-function studies and multiple RNA–protein interaction assays uncovered a mechanistic role of HEAT4 in the monocyte anti-inflammatory gene program. HEAT4 expression and function was characterized in a vascular injury model in NOD.CB17-Prkdc scid/Rj mice.
RESULTS:
HEAT4 expression was increased in the blood of patients with HF, acute myocardial infarction, or cardiogenic shock. HEAT4 levels distinguished patients with HF from people without HF and predicted all-cause mortality in a cohort of patients with HF over 7 years of follow-up. Monocytes, particularly anti-inflammatory CD16+ monocytes, which are increased in patients with HF, are the primary source of HEAT4 expression in the blood. HEAT4 is transcriptionally activated by treatment with anti-inflammatory interleukin-10. HEAT4 activates anti-inflammatory and inhibits proinflammatory gene expression. Increased HEAT4 levels result in a shift toward more CD16+ monocytes. HEAT4 binds to S100A9, causing a monocyte subtype switch, thereby reducing inflammation. As a result, HEAT4 improves endothelial barrier integrity during inflammation and promotes vascular healing after injury in mice.
CONCLUSIONS:
These results characterize a novel endogenous anti-inflammatory pathway that involves the conversion of monocyte subtypes into anti-inflammatory CD16+ monocytes. The data identify a novel function for the class of long noncoding RNAs by preventing protein secretion and suggest long noncoding RNAs as potential targets for interventions in the field of cardioimmunology.

overall_design: Human primary monocytes were isolated from PBMCs and transfected with control or HEAT4-encoding plasmids for 24 h. Bulk RNA-sequencing (RNA-seq) was performed.

first: Jasmin

last: Kneuer

first: Ignacy

last: Grajek


title: Fosl2 overexpression and Ezh2 inhibition in mouse embryonic fibroblasts

first: Christian

last: Nefzger

summary:
To assess the impact of AP-1 chromatin remodelling,  we over-expressed one AP-1 family member, namely Fra2 (encoded by Fosl2), in mouse embryonic fibroblasts (MEFs).

To assess the impact of general chromatin depression, we inhibited the activity of PRC2 component histone-lysine N-methyltransferase Ezh2 in MEFS.

overall_design:
Fosl2 overexpression: We transduced mouse embryonic fibroblasts (MEFs) with a CRISPRa-VPR-mCherry construct and assessed more immediate and longer term effects of Fra2 over-expression by performing OMNI-ATACseq on FACS purified mCherry+/THY1+ cells 4 and 11 days following lentiviral infection with Fra2 gRNAs or scrambled control.

For Ezh2 inbition: Following three days of treatment with the Ezh2 inhibitor (Sigma-Aldrich, GSK343) at 4microM and a washout day, MEFs were submitted to the ATAC-seq assay.

first: Jingyu

last: Zhang

first: Xiaoli

last: Chen


title: CBLL1 promotes endometrial stromal cell senescence via inhibiting PTEN in recurrent spontaneous abortion

status: Public on Jul 14 2024

city: Shanghai

first: Xueqing

last: Liu

state: Shanghai

address: 910 Hengshan

institute: International Peace Maternity and Child Health Hospital

summary: Cellular senescence of human endometrial stromal cells (HESCs) is one of the important mechanisms underlying RSA. We have demonstrated that CBLL1 overexpression promoted HESCs senescence and knockout of CBLL1 alleviated cellular senescence induced by oxidative inducers. Transcriptomic sequencing results and further research revealed PTEN as one of the important downstream target genes of CBLL1, and upregulation of CBLL1 led to downregulation of PTEN. Knockdown of PTEN promoted HESCs senescence, elevated oxidative stress, and inhibited proliferation. CBLL1 overexpression induced-cellular senescence was rescued by overexpression of PTEN. In vivo experiments demonstrated that overexpression of CBLL1 in the endometrium significantly increased the embryo absorption rate in mice. In conclusion, our findings discovered that elevated CBLL1 expression is a significant contributor to RSA, and its mechanism may be related to the elevation of CBLL1 leading to a decrease in PTEN, resulting in the senescence of HESCs. This finding could provide new avenues for treatment of RSA.

overall_design: To investigate the role of CBLL1 in regulating endometrial stromal cell function, we established HESC cell lines in which CBLL1 has been overexpressed by lentivirus.


title: Itaconate mediates an immunometabolic crosstalk between osteoclasts and osteoblasts

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: In this report, we show that both glucose and glutamine are essential during OC differentiation, and both contribute to the maintenance of the TCA cycle. Early differentiation is associated with a broken TCA cycle, with IRG1 siphoning TCA intermediates for the production of itaconate, which accumulates extracellularly, stimulating the function of osteoblasts in vitro an in vivo and in vivo and is necessary to retain bone mass in mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow derived cells treated with MCSF or MCSF+RANKL with or without glutamine or glucose

first: Markus

last: Kieler

first: Stephan

last: Blüml


title: Ribosomal protein control of hematopoietic stem cell transformation through direct, non-canonical regulation of metabolism.

city: PHILADELPHIA

first: David

middle: Lynn

last: Wiest

state: PA

address: 333 COTTMAN AVENUE, REIMANN BUILDING, LAB  R364

department: Nuclear Dynamics and Cancer Program

institute: FOX CHASE CANCER CENTER

summary: We report here that expression of the ribosomal protein, RPL22, is frequently reduced in human myelodysplastic syndrome (MDS) and acute myelogenous leukemia (AML); reduced RPL22 expression is associated with worse outcomes. Mice null for Rpl22 display characteristics of an MDS-like syndrome and develop leukemia at an accelerated rate. Rpl22-deficient mice also display enhanced hematopoietic stem cell (HSC) self-renewal and obstructed differentiation potential, which arises not from reduced protein synthesis but from increased expression of the Rpl22 target, Alox12, an upstream regulator of fatty acid oxidation (FAO). The increased FAO mediated by Rpl22-deficiency also persists in leukemia cells and promotes their survival. Altogether, these findings reveal that Rpl22 insufficiency enhances the leukemia potential of HSC via non-canonical de-repression of its target, Alox12, which enhances FAO, a process that may serve as a therapeutic vulnerability of Rpl22 low MDS and AML leukemia cells.

overall_design: Lineage negative CD48-CD150+ hematopoietic stem cells (HSC) were isolated from adult bone marrow from Rpl22+/+ and Rpl22-/- mice by flow cytometry following which differentially expressed genes were identified by RNA-Seq

first: Bryan

last: Harris

first: Shawn

last: Fahl


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild and Myocardial ischemia-reperfusion injury

city: zhengzhou

first: jing

last: xu

address: Jianshe East Road

institute: The First Affiliated College of Zhengzhou University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived myocardial transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Methods: Retinal mRNA profiles of 21-day-old Wild and myocardial ischemia-reperfusion injury mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Jing

last: Xu


title: Analysis of mRNA expression in pleomorphic adenoma

city: Beijing

first: Zhenyuan

last: Han

address: No.22, Zhongguancun South Avenue Haidian District

institute: Peking University School of Stomatology

summary: We identified transcriptional landscape in pleomorphic adenoma (PA).

overall_design: Patients samples of pleomorphic adenoma (PA, n=5) and corresponding normal tissues (control; n=5) were retrieved during surgery and placed in RNA Later stabilization fluid and then kept at minus 80 until required.

first: Z

last: Tian


title: Whole genome expression microarray analysis in hepatocellular carcinoma cell line, Huh7 cells, transfected with hSTYK1

city: Miki-cho

first: Yasunori

last: Sugiyama

state: kagawa

address: ikenobe 2393

department: Department of Life Science

institute: Kagawa University

summary: To identify genes regulated by STYK1 in hepatocellular carcinoma, we performed comprehensive analyses of mRNA expression in Huh7 cells overexpressed STYK1.

overall_design: mRNA expression profile in Huh7 cells overexpressed STYK1.


title: Amino acids fuel FLS activation and arthritis by regulating chemokine expression and leukocyte migration

summary: mTOR plays a significant role in synovial inflammation and suggests that dietary interventions and nutrient availability may influence arthritis severity and disease outcomes. In this study, we tested the effect of AA deprivation on the inflammatory activity of RA FLS and found that AAs specifically influence the expression of a gene set that regulates leukocyte chemotaxis. Using a murine model of inflammatory arthritis, we further demonstrate that low protein diet resulted in amelioration of objective measures of joint inflammation due to a reduced accumulation of inflammatory cells in their joints.

overall_design: Fibroblast-like synoviocytes were stimulated with the prototypic inflammatory stimulus TNF in the presence or absence of AAs in the culture medium and analysed transcriptional responses by RNA-sequencing.

first: Thomas

last: Karonitsch


title: Dynamic Ultrasound Molecular Targeted Imaging of Senescencein Evaluation of Lapatinib Resistance in HER2 Positive Breast Cancer

city: Tianjin

first: Xiao

middle: Yu

state: None Selected

address: Tianjin Medical University Cancer Institute and Hospital

department: Department of Diagnostic and Therapeutic Ultrasonography

summary: Prolonged treatment of HER2+ breast cancer cells with lapatinib (LAP) causes cellular senescence and acquired drug resistance, which often associating with poor prognosis for patients. We aim to explore the correlation between cellular senescence and LAP resistance in HER2+ breast cancer, screening for molecular marker of reversible senescence, and construct targeted nanobubbles for ultrasound molecular imaging and dynamically evaluate LAP resistance. In this study, we established a new cellular model of reversible cellular senescence using LAP and HER2+ breast cancer cells and found that reversible senescence contributed to LAP resistance in HER2+ breast cancer. Then we identified ecto-5'-nucleotidase (NT5E) as a marker of reversible senescence in HER2+ breast cancer. Based on this, we constructed NT5E targeted nanobubbles (NT5E-FITC-NBs) as a new molecular imaging modality which could both target reversible senescent cells and be used for ultrasound imaging. NT5E-FITC-NBs showed excellent physical and imaging characteristics. As an ultrasound contrast agent, NT5E-FITC-NBs could accurately identify reversible senescent cells both in vitro and in vivo. Our data demonstrate that cellular senescence-based ultrasound targeted imaging can identify reversible senescence and evaluate LAP resistance effectively in HER2+ breast cancer, which has the potential to improve cancer outcomes by altering treatment strategies ahead of aggressive recurrences.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of three kinds of cells.These cells were SKBR3 cells(SK), senescent SKBR3 cells(SKBR3 cells were treated with 250 nM lapatinib for two weeks,referred to as SK-S or SK-la) and senescence escaped SKBR3 cells(The senescent SKBR3 cells were then cultured in the absence of lapatinib and the cells began to actively proliferate.The reproliferating cells were identified as senescence escape cells and were referred as SK-T. )

first: Xiaoyu


title: Transcriptome analysis of Auricularia auricula-judae in response to gamma radiation

status: Public on Jul 13 2024

city: Yesan

first: Jeong Heon

last: Kim

address: 54-46 Daehak-ro, Yesan-eup, Yesan-gun, Chungcheongnam-do

country: South Korea

institute: Kongju national university

summary: Differentially expressed genes revealed inhibited expression in amino acid metabolism, carbohydrate metabolism, and cell cycle regulation genes. Furthermore, enhanced cell death promoted resistance by eliminating unstable cells. DNA repair genes were up-regulated, indicating a common defense mechanism of fungi that increases genome integrity by repairing DNA damaged by gamma radiation. Conversely, genes related to antioxidants and laccase were down-regulated, suggesting that resistance response through resolving oxidative stress induced by gamma radiation did not occur.

overall_design: To investigate the response of Auricularua auricula-judae to gamma radiation exposure, A. auricula-judae mycelium was irradiated with 200 Gray gamma radiation and then inoculated into sawdust medium to produce fruit bodies. RNA was extracted from fruit bodies homogenized using liquid nitrogen, cDNA was synthesized, and RNA-seq was performed.

first: Jeong-Heon

first: Youn-Jin

last: Park

first: Myoung-Jun

last: Jang


title: Combination of epigenetic enzyme inhibitors, GSKJ4 and Belinostat, reveals efficacy in IDH1 mutant gliomas

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

summary: Mutations in IDH1 and IDH2 genes are very common in low grade gliomas and secondary GBM. They induce hypermethylation of DNA and histones in tumor cells, and generate a specific epigenetic phenotype. Therefore, we decided to perform a chemical screen consisting of inhibitors of epigenetic regulators on patient-derived IDH mutant cell lines. Dual combinations of hit inhibitors in low doses were also analyzed to increase treatment efficiency. Individual and combinatorial effects of these inhibitors were also analyzed in wild type and IDH mutant pair of A172 GBM cell line that was derived by ectopic overexpression of mutant IDH1. GSK-J4 and Belinostat combination was highly effective on both patient-derived and engineered IDH mutant cells compared to wild type cells. Interestingly, sensitized IDH mutant cells were recovered via mutant IDH inhibitor, GSK864, which is thought as a candidate drug for IDH mutant glioma. On the other hand, viability of non-malignant fibroblasts were not affected from these drugs in these doses. GSK-J4 and Belinostat combination induce apoptosis which was shown by increased Caspase 3/7 activity, PARP cleavage and recovery with general caspase inhibitor (Z-VAD-FMK). Change in histone modifications such as H3K4me3, H3K9me3, H3K27me3 and H3K27ac were observed after mutant IDH overexpression and also drug treatments. RNA-seq and GSEA analysis revealed activation of unfolded protein and viral response pathways in IDH mutant cells which indicate increased cell stress. GSKJ4 and Belinostat induces cell cycle arrest and apoptosis by further increasing cell stress probably because of dramatic changes in chromatin structure.

overall_design: mRNA profile of A172 WT and IDH mutant cells either with GSK864 (mutant IDH inhibitor) treatment or not. Another mRNA profiling from MGG152 patient derived IDH mutant cells either without treatment, or treated with GSK-J4 alone, Belinostat alone or both in combination

first: Alisan

last: Kayabolen

first: Tugba

last: Bagci-Onder


title: Effect of knocking down FOXP4 and YAP1 in gastric cancer cells

city: Hong Kong

first: Bonan

last: Chen

address: The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, The People's Republic of China

country: Hong Kong

institute: the Chinese University of Hong Kong

summary: The Hippo-YAP1 pathway is an evolutionally conserved signaling cascade that controls organ size and tissue regeneration. Its dysregulation has been well-studied to promote tumor initiation and progression, including gastric cancer (GC). Although the Hippo-YAP1 signaling pathway regulates the expression of thousands of target genes, how these target genes contribute to the oncogenic program driven by YAP1 remains unknown. Here we identified the vital role of FOXP4 in YAP1-driven gastric carcinogenesis by maintaining stemness and promoting peritoneal metastasis. Knocking down FOXP4 impairs GC spheroid formation and inhibits stemness marker expression, while its upregulation potentiates the cancer cells with more stemness. RNA-seq analysis revealed SOX12 as functional downstream of FOXP4 in the YAP1-induced carcinogenesis. Targeting FOXP4 by 42-(2-Tetrazolyl) rapamycin in GC cells enhanced the 5-FU efficacies. Our findings have unveiled FOXP4 as a novel stemness marker that promotes tumorigenesis by upregulating SOX12. Additionally, we have identified FOXP4 as a direct target for modulating YAP1 signaling in GC. Therefore, the YAP1-FOXP4-SOX12 axis presents a promising therapeutic target for GC.

overall_design: The potent target genes of FOXP4 were identified by deep sequencing, using Illumina NovaSeq 6000.

first: Xiaoli

last: Liu


title: EDA2R signaling drives cancer-associated skeletal muscle wasting [bulkRNA-Seq]

city: Sarıyer

first: Samet

last: Agca

state: İstanbul

address: Rumelifeneri Yolu

department: Graduate School of Sciences and Engineering

country: Turkey

institute: Koc University

summary: We investigated the impact of EDA-A2-EDA2R signaling in gene expression profiles of mouse primary myotubes. Cells were treated with recombinant EDA-A2 for 24hrs and transcriptional changes were studied by RNA-sequencing.

overall_design: Primary myoblasts were differentiated into myotubes and treated with recombinant EDA-A2 for 24hrs. The RNA was isolated and libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit.

first: Serkan

last: Kir

first: Sevval

middle: N

last: Bilgic


title: Library-based single-cell analysis of CAR signaling reveals drivers of in vivo persistence

city: Cambridge

first: Caleb

last: Perez

email: crperez@mit.edu, mbirnb@mit.edu

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

summary: The anti-tumor function of engineered T cells expressing chimeric antigen receptors (CARs) is dependent on signals transduced through intracellular signaling domains (ICDs). Different ICDs are known to drive distinct phenotypes, but systematic investigations into how ICD architectures direct T cell function—particularly at the molecular level—are lacking. Here, we use single-cell sequencing to map diverse signaling inputs to transcriptional outputs, focusing on a defined library of clinically relevant ICD architectures. Informed by these observations, we functionally characterize transcriptionally distinct ICD variants across various contexts to build comprehensive maps from ICD composition to phenotypic output. We identify a unique tonic signaling signature associated with a subset of ICD architectures that drives durable in vivo persistence and efficacy in liquid, but not solid, tumors. Our findings work toward decoding CAR signaling design principles, with implications for the rational design of next-generation ICD architectures optimized for in vivo function.

overall_design: CD3+ T cells expressing a library of 35 distinct ICD architectures following various tumor perturbations were single-cell sequenced via Chromium Next GEM Single Cell 5' Kit v2, generating gene expression libraries, CAR BC libraries (see below), and, for samples stained with CITE-seq antibodies, feature barcoding libraries. Each CAR variant is barcoded by a unique 8bp sequence in the 5'UTR, allowing deconvolution of the ICD architecture expressed by each cell. The resulting libraries were pooled to achieve approximately 30000, 5000, and 1000 reads per cell, respectively. Reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38), and a cell–feature matrix was generated using the CellRanger pipeline (10X Genomics; v6.1.2–7.0.1). Downstream analysis was performed using the Seurat package (v4.3.0.1). Several different scRNA-seq datasets are presented, with sample-specific treatments given in the description for each sample.

first: Andrea

last: Garmilla

first: Avlant

last: Nilsson

first: Hratch

last: Baghdassarian

first: Khloe

last: Gordon

first: Louise

last: Lima

first: Blake

last: Smith

first: Marcela

middle: V

last: Maus

first: Douglas

last: Lauffenburger

first: Michael

last: Birnbaum


title: PRTN3 suppresses cytotoxic immune-cell activation and antitumoral immunity through proteolytic cleavage of CXCL9 in KRAS mutant lung adenocarcinoma

first: renle

last: du

address: 94 Weijin Road

institute: Nankai University

summary: The intratumoral activity of chemokine system has important roles in cancer immunotherapy strategies.One of the mechanisms of immune checkpoint blocking (ICB)resistance may be the dysfunction of chemokine signaling. Here, we first report that KRAS mutation in LUAD cells up-regulates the expression of protease 3 (PRTN3), that inhibits cytotoxic immune cell activation in the tumor microenvironment by inhibiting the CXCL9/CXCR3 axis, providing an unconventional mechanism for tumor immune escape. Further mechanism studies demonstrated that PRTN3 was up-regulated by c-Myc transcription and secreted into the tumor microenvironment, where CXCL9 was inactivated by proteolysis, and finally result in inhibiting the activation of natural killer (NK) and CD8+ T cells. Meanwhile, samples from LUAD patients with high PRTN3 expression showed low CXCL9 activity. Furthermore, application of a hydrolysis-resistant CXCL9 protein (H-R CXCL9) effectively improves the immunomodulate effect in LUAD patient organoids. Importantly, PRTN3 knockdown increased the susceptibility of KRAS mutant cells to Anti-pd-1 therapy. Thus, we have identified a previously unknown tumor immune-suppressive mechanism and provided an immunotherapeutic target to improve the effectiveness of ICB therapy in KRAS mutant LUAD.

overall_design: Total RNA from lung tumors of K and KP mice was extracted by using TRIZOL (Invitrogen).The deep RNA sequencing was performed and analyzed on BGI seq500 platform (BGI-Shenzhen, China).

first: Yi

first: Renle

last: Du

first: Yunping

last: Luo


title: B cell-intrinsic IFN-g promotes CD11c+ age-associated B cell differentiation and compromises affinity-based germinal center selection in lupus

first: Fubin

last: Li

address: 280 South Chongqing Road, Shanghai, 200025, China

institute: Shanghai Jiao Tong University School of Medicine

summary: Lupus patients respond less efficiently to vaccinations and are more susceptible to infections. Previously, we have shown, in lupus models, that excessive CD11c+ age-associated B cells (ABCs) not only contribute to autoantibody production but also compromise antigen-specific germinal center (GC) B cell selection and affinity maturation by promoting aberrant T cell activation. Yet, how CD11c+ ABC differentiation is regulated is not fully understood. Here we show that B cell-intrinsic IFN-γ is required for excessive CD11c+ ABC differentiation in lupus mice. B cell-intrinsic IFN-γ is mainly produced by CD11c+ ABCs. IFN-γ-deficiency leads to decreased expression of ABC characteristic genes, including Zeb2, an ABC-specific transcription factor recently described. We further show that ablating IFN-γ can normalize T cell overactivation and rescue antigen-specific GC responses in lupus mice. Our study offers insight into the crucial role of B cell-intrinsic IFN-γ in promoting CD11c+ ABC differentiation and compromising affinity-based germinal center selection and affinity maturation in lupus, providing a potential target for lupus treatment.

overall_design: To understand the impact of B cell-intrinsic IFN-g on CD11c+ ABC differentiation,  we sorted CD11c+ ABCs from spleens of ShipDBIfng-/- and ShipDB mice. Following total RNA extraction, we employed SMART-seq for comprehensive transcriptomic profiling.

first: Shujun

last: Liu

first: Wenqian

last: Zhang

first: Shihao

last: Tian

first: Yan

first: Zhinan

last: Yin

first: Gonghua

last: Huang

first: Huihui


title: Genes regulated by ZNF667 in the HUVECs induced by oxidative stress

city: Changsha

first: Nian

last: Wang

state: Hunan

address: No.110 Xiangya Road

institute: Central south university

summary: To screen the genes and pathways regulated by ZNF667 in the HUVECs induced by oxidative stress, HUVECs were transfected by pcDNA3.1 or pcDNA3.1-ZNF667 respectively and then treated by H2O2.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVECs and its OE derivatives (ZNF667) with or without H2O2 treatment..

first: Kangkai


title: Redox-associated miRNAs regulated by anti-TNBC compounds DET and DETD-35 in MDA-MB-231 cells

city: Taipei

first: Lie-Fen

last: Shyur

address: No. 128, Sec. 2, Academia Road

country: Taiwan

institute: Academia Sinica

summary: Triple-negative breast cancer is a difficult breast cancer subtype to treat that lacks targeted therapies. Specific miRNAs have been reported to be involved in cancer progression and their significance in cancer diagnosis and anti-cancer drug development has been highlighted; however, whether redox-associated miRNAs are potential targets of anti-cancer drugs or bioactive phytocompounds, which deregulate cancer cell activity through modulating ROS dynamics is unclear. This study addressed the anti-TNBC cell effect of phytosesquiterpene lactones deoxyelephantopin (DET) and its derivative DETD-35 by which redox-associated miRNAs were responsive and regulated as demonstrated by comparative miRNA microarray analysis and ROS scavenging approaches.

overall_design: MDA-MB-231 cells were incubated with vehicle (0.5% DMSO), DET (4 µM) or DETD-35 (4 µM) for 1 h, with or without pretreatment of antioxidant N-acetylcysteine (NAC, 5 mM, 1 h) prior to RNA extraction and analysis. Two technical repeats by using two independent arrays were carried out for each sample. miRNA expression levels in vehicle treatment group was used to normalize the data in DET and DETD-35 treatment groups. Similarly, miRNA expressions in NAC-pretreated vehicle group was used to normalize the data in NAC-pretreated DET and DETD-35 groups. A selection criterion of P < 0.05 and log2(ratio over vehicle) < -0.8 or log2(ratio over vehicle) > 0.8 was used to identify specific miRNAs upregulated or downregulated by DET or DETD-35 treatment compared to vehicle group, and to evaluate whether regulation of specific miRNAs by DET or DETD-35 can be affected by NAC pretreatment.

first: Yu-Ting

last: Cheng


title: α-Ketoglutarate Promotes Cardiomyocyte Proliferation and Heart Regeneration after Myocardial Infarction

status: Public on Jul 12 2024

city: chong qing

first: Miao

address: Changjiang zhilu

institute: daping hospital

summary: The neonatal mammalian heart is capable of substantial regeneration following injury through cardiomyocyte proliferation. However, this regenerative capacity is lost by postnatal (P) day 7. How to stimulate the adult cardiomyocyte to re-enter the cell cycle is still unknown. Accumulating evidence suggests that cardiomyocyte proliferation depends on its metabolic state. Due to the tight connection between the tricarboxylic acid cycle (TCA) and cell proliferation, we analyzed the TCA metabolites between P0.5 and P7 mouse hearts and found that α-ketoglutarate (α-KG) ranked first among the decreased metabolites. The intraperitoneal injection of exogenous α-KG extended the window of cardiomyocyte proliferation during heart development and promoted heart regeneration after myocardial infarction (MI) by inducing adult cardiomyocyte proliferation. This was confirmed in Ogdh-siRNA-treated mice with increased α-KG levels. Mechanistically, α-KG activates Jmjd3, a histone lysine demethylase, that decreases H3K27me3 expression and deposition of H3K4me3 at the promoters of cell cycle and structural maturation genes in cardiomyocytes. Our present study shows that α-KG promotes cardiomyocyte proliferation by Jmjd3-dependent demethylation and inactivation of H3K27me3 andH3K4me3, which is a potential therapeutic approach for treating MI and heart failure.

overall_design: To gain insights into the potential pathways by which α-KG induced cardiomyocyte proliferation, we isolated cardiomyocytes from P21 mice that were daily injected with α-KG or PBS (Control) for 2 weeks and performed gene expression profiling analysis using data obtained from RNA-seq.

first: Yu

last: Shi

first: Xiaofang

last: Zhao

first: Luxun

last: Tang


title: Genomic and single-cell landscape of transformed cutaneous T-cell lymphoma

city: Tampa

first: Xiaofei

last: Song

state: FL

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Cutaneous T-cell lymphoma (CTCL) is a malignancy of skin-homing T cells. A subgroup of patients develops large cell transformation with progression to an aggressive lymphoma and with poor survival. We aimed to study the transformed CTCL (tCTCL) ecosystem using integrative approaches spanning whole-exome sequencing (WES), single-cell RNAseq, and immune profiling in a unique cohort of 56 patients with tCTCL

overall_design: We collected 16 fresh skin biopsies from 8 patients with transformed CTCL, each with paired PP and TT, and profiled these cells using complementary 5′ scRNA-seq and scV(D)J-seq strategies

first: Pei-Ling

last: Chen