title: CIRCULATING SERUM MICRO-RNA AS NON-INVASIVE DIAGNOSTIC BIOMARKERS OF ENDOMETRIOSIS

city: Brescia

first: Stefano

last: Calza

state: Brescia

address: Viale Europa 11

department: DMMT

country: Italy

institute: University of Brescia

summary: Total RNA was extracted from 400 ul of serum with the miRNeasy Serum/Plasma advanced Kit (Qiagen)  and quantified using the Qubit microRNA assay kit (Thermo Fisher Scientific). cDNA templates were prepared using the TaqMan Advanced miRNA cDNA Synthesis Kit (Thermo Fisher Scientific), starting from 10 ng of RNA.  RT-qPCR carried out on a QuantStudio 12K Flex (Applied Biosystems) using the TaqMan OpenArray miRNA panel.

overall_design: This study was conducted on serum samples collected prior to surgery from 67 patients with endometriosis and 60 control women with benign gynecological conditions not linked to endometriosis, as confirmed by histological examination.

first: Antonella

last: Ravaggi


title: RNA-seq for L1 stage wildtype, csb-1 and xpc-1 C.elegans

status: Public on Oct 30 2024

city: Chapel Hill

first: Cansu

last: Kose

state: NC

address: 120 Mason Farm Rd.

department: Biochemistry and Biophysics

country: USA

institute: UNC-Chapel Hill

type: Expression profiling by high throughput sequencing

summary: RNA-seq analysis was conducted to quantify the gene expression levels in each strain.

overall_design: RNA-seq was performed for L1 stage wildtype, csb-1 and xpc-1 strains to analyse the effect of transcription on nucleotide excision repair.


title: Decreased mitochondrial-related gene expression in adipose tissue after acute sprint exercise in humans

city: Stockholm

first: Hakan

middle: Claes

last: Rundqvist

state: Huddinge

address: Alfred Nobels ale 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska institutet

summary: The aim was to examine the acute effects of sprint exercise (SIT) on global gene expression in subcutaneous adipose tissue (AT) in healthy subjects to improve the understanding of how SIT may contribute to the maintenance of a healthy body weight. An SIT-induced upregulation of genes related to mitochondrial and fat metabolism was hypothesized. A total of 15 subjects performed three 30-s all-out sprints (SIT). Samples from AT, skeletal muscle (SM) and blood (brachial artery and a superficial subcutaneous abdominal vein) were obtained, up to 15 min after the last sprint. Purines such as hypoxanthine, xanthine or uric acid, sources of oxidative stress, increased markedly by SIT in both the artery and the abdominal vein. Purines also increased in AT and SM tissue. In response to SIT, a decreased signaling was predicted from the differential gene expression (z-score < -2 and -log(p-value) > 4) for mitochondrial related pathways such as oxidative phosphorylation, electron transport, ATP synthesis and heat production by uncoupling, mitochondrial fatty acid beta oxidation. Contrary to the hypothesis, a downregulation of various gene sets related to oxidative metabolism was shown after SIT. This could counteract possible negative effects of SIT-induced oxidative stress by an early stage “shutdown” of the mitochondria.

overall_design: Human subcutaneous abdominal adipose tissue gene expression at rest and after acute sprint interval exercise (3x30-s all-out cycle sprints). Biopsies were taken before sprint 1 (preexercise), 15 min after sprint 2 and 15 min after sprint 3 (postexercise). The first and last biopsies were performed on separate sides of the umbilicus. The biopsies taken after sprint 2 were not used for gene expression analysis.

first: Håkan

middle: C


title: SNORD113-114 cluster regulates self-renewal of hematopoietic stem cells via orchestrating the translation machinery

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

country: China

institute: Peking Union Medical College

summary: Hematopoietic stem cells (HSCs) play a crucial role in maintaining the steady supply of blood cells throughout an organism’s lifetime. Understanding the regulatory mechanisms governing HSC homeostasis is of particular importance for regenerative medicine and stem cell-based therapies. Translatome refers to the ensemble mRNA transcripts being actively translated on ribosomes within a cell type, under specific physio/pathological conditions. Translatome profiling provides insights into the regulation of gene expression at the translational level, going beyond traditional transcriptome analysis. In this study, we systematically profiled the translatome landscapes of hematopoietic cells, and unraveled novel insights on HSC functionality and regulation mechanisms. Moreover, for further exploring underlying regulation mechanisms of translatome, we systematically screened the snoRNAs in hematopoietic cells and uncovered an indispensable role for the maternally expressed snoRNA cluster SNORD113-114 at the Dlk1-Gtl2 imprinting region in regulation of HSC self-renewal. Maternal knockout of this cluster (Mat-KO) significantly impaired HSC self-renewal, while loss of the paternal allele caused no obvious abnormal hematological phenotype. Mechanistically, Mat-KO resulted in dysregulation of translation machinery, in terms of 2’-O-Me modifications on rRNAs, rRNA processing, ribosome function and translatome. Finally, Loss of SNORD113-114 cluster induced impaired ribosome biogenesis checkpoint/nucleolar stress in HSCs, which exempted p53 from proteasomal degradation and eventually led to apoptosis in HSCs. Collectively, our findings shed light on the intricate molecular mechanisms governing HSC behavior and provide potential therapeutic targets for enhancing HSC function and advancing regenerative medicine. Understanding the translation regulation of gene expression in HSCs has significant implications for stem cell biology and offers promising avenues for clinical applications.

overall_design: To investigate the translation regulation in hematopoietic cells, we performed ultra-low input Ribo-seq on 10 types of hematopoietic cells, which were sorted by FACS. WT HSCs, along with Mat-KO HSCs losing SNORD113-114 cluster, were also sorted and subjected to ultra-low input Ribo-seq. The RPF fragment isolated from these sorted hematopoietic cells were then converted to sequencing library for RNA-seq. Each cell type contains 2 biological replicates, which contains 2 technical replicates each, so there are 4 replicates in all for each cell type. Translatome profile, that is results of RNA-seq of RPF fragments, were then analyzed and compared between 10 hematopoietic cells.  Analysis and comparison were also carried out between WT and Mat-KO HSCs.


title: Drug repurposing for the treatment of HIV-Associated Neurocognitive Disorder by AI-based literature mining

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: HIV-1 Associated Neurocognitive Disorder (HAND) is a common and clinically detrimental complication of HIV infection. Viral proteins including Tat, released from infected cells, cause neuronal toxicity. Substance abuse in HIV-infected patients greatly exacerbates the severity of neuronal damage. To repurpose small molecule inhibitors for anti-HAND therapy, we employed MOLIERE, an AI-based literature mining system that we developed. All human genes were analyzed and prioritized by MOLIERE to find previously unknown targets connected to HAND. The list was narrowed to those with known small molecule inhibitors developed for other applications and lacking systemic toxicity in animal models. We tested the activity of small molecules targeted against the proteins of five prioritized genes to protect against the combined neurotoxicity of HIV-Tat and cocaine in primary neuronal cultures. Four prevented Tat and cocaine toxicity. The compounds are: the FDA approved drugs Amlexanox and Tazemetostat (EPZ-6438), Itaconate and Senicapoc. Despite the disparate molecular targets of these drugs, analysis revealed a common mechanism of neuroprotection; namely that modulation of astrocyte and microglia status prevents the toxicity of Tat and cocaine.

overall_design: To investigate the effects of the compounds (i) Rat Primary Neuronal cultures were  treated with or without HIV-Tat for 48 hours  in the presence or absence of small molecules or vehicle control (ii)  The culture had been treated with cocaine for the next 24 hours. Upon treatment cells were lyzed followed by RNA purification Experiments had been performed in triplicates. Small molecule compounds used in experiment are  senicapoc, 4-octyl-itaconate, amlexanox and tazemetostat. Concentrations of the compounds, HIV-Tat protein and cocaine is described in samples description table.

first: Marina

last: Aksenova

first: Michael

last: Shtutman

first: Hao

last: Ji

first: B

last: Cui


title: Differentially expressed genes between WT and AtC3H3 OX, and WT and AtC3H26 OX

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

summary: Salinity is a pressing issue causing widespread crop loss, prompting plants to adapt through changes in gene expression. This study investigated the role of the non-tandem CCCH zinc finger protein gene AtC3H3 in Arabidopsis in response to salt stress. AtC3H3, a gene from the non-TZF gene family and known for its RNA-binding and ribonuclease activity, was found to be upregulated under osmotic stresses such as high salt and drought. When overexpressed in Arabidopsis, AtC3H3 led to increased tolerance to salt stress, not drought stress. qRT-PCR analysis showed that the expression of both well-known ABA-dependent salt stress-responsive genes, such as RAB18, RD29B, and RD22, and representative ABA-independent salt stress-responsive genes, such as DREB2A and DREB2B, was significantly higher in AtC3H3 OXs than WT under NaCl treatment, indicating its involvement in both ABA-dependent and ABA-independent signaling pathways. mRNA-Seq analysis using NaCl-treated WT and AtC3H3 OXs revealed no potential target mRNAs of the RNase function of AtC3H3, suggesting that the potential targets of AtC3H3 might be non-coding RNAs, not mRNAs.  The study conclusively demonstrates that AtC3H3 plays a crucial role in salt stress tolerance by influencing the expression of salt stress-responsive genes. These findings have opened a new avenue for understanding plant stress mechanisms and suggest potential strategies for enhancing crop resilience to salinity.

overall_design: Differential gene expression between WT and AtC3H3 OX, as well as between WT and AtC3H26 OX, was examined under both no treatment and NaCl treatment conditions at 10 days after germination under SD conditions (8-hour-light and 16-hour-dark cycle) on a whole-genome level.

first: Hye-Yeon

last: Seok

first: Sun-Young

last: Lee


title: Inactivity of Stat3 in sensory and non-sensory cells of the mature cochlea

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

summary: Signal transducer and activator of transcription 3 (Stat3) plays a role in various cellular processes such as differentiation, inflammation, cell survival and microtubule dynamics, depending on the cell type and the activated signaling pathway. Stat3 is highly expressed in the hair cells and supporting cells of the cochlea and is essential for the differentiation of mouse hair cells in the early embryonic stage. However, it is unclear how Stat3 contributes to the correct function of cells in the organ of Corti postnatally. To investigate this, an inducible Cre/loxp system was used to knock out Stat3 in either the outer hair cells or the supporting cells. The results showed that the absence of Stat3 in either the outer hair cells or the supporting cells resulted in hearing loss without altering the morphology of the organ of Corti. Molecular analysis of the outer hair cells revealed an inflammatory process with increased cytokine production and upregulation of the NF-kB pathway. However, the absence of Stat3 in the supporting cells resulted in reduced microtubule stability. In conclusion, Stat3 is a critical protein for the sensory epithelium of the cochlea and hearing and functions in a cell and function-specific manner

overall_design: To investigate this, an inducible Cre/loxp system was used to knock out Stat3 either in the outer hair cells or the supporting cells of the organ of Corti. Audiological examination were performed with a small animal audiological setup. The tissue undergo immunohistological and immunocytological investigation to evaluate the morphology. Additionally, mRNA bulk sequencing were performed to analyze down or upregulated genes in the outer hair cells.

first: Linda

last: Bieniussa

first: Clara

last: Stolte

first: Panagiota

last: Arampatzi

first: Jonas

last: Engert

first: Johannes

last: Völker

first: Rudolf

last: Hagen

first: Stephan

last: Hackenberg

first: Kristen

last: Rak


title: Global transcriptomic alterations in MDA-MB-231 cells following high salt treatment

city: Tezpur

first: Aditya

last: Kumar

state: Assam

address: R107, Dept Of Molecular Biology & Biotechnology

department: Molecular Biology and Biotechnology

country: India

institute: Tezpur University

summary: Difference in salt concentration may cause dramatic alterations in tumor microenvironment, progression of cancer and overall outcome of cancer therapy. Immune cells in tumor microenvironment are mostly immunosuppressed under the influence of tumor cells. Recent studies has shown that high salt induces immune cells to pro-inflammatory state in the tumor microenvironment. On contrary, it hinders the immunosuppressive functions of regulatory T cells, which plays an important role in inhibiting anti-cancer immune responses in tumor microenvironment. Salt- mediated induction of the immune cells to pro-inflammatory state could potentially enhance their transition from the immunosuppressed state to their innate pro- inflammatory state, thereby facilitating their effectiveness in combating the tumor and suppressing tumor progression. The role of high salt in cancer is controversial with only a few studies suggesting the potential pro-tumorigenic effect of high salt. Dietary salt increased the risk of gastric cancer, contributing to both the incidence and mortality of the disease by damaging the gastric mucosal lining. Another research indicated that a high salt diet could stimulate the growth of breast cancer and promote lung metastasis by elevating Th17 cell levels. In contrast, high salt containing diets significantly inhibited tumor growth, primarily through the depletion and functional modulation of myeloid-derived suppressor cells (MDSCs), highlighting its anti-cancer efficacy. High salt reduced cytokine production necessary for the expansion of myeloid-derived suppressor cells (MDSCs) and decreases MDSC accumulation in blood, spleen, and tumors. High salt diet in mice also showed increased Bifidobacterium abundance and heightened gut permeability, leading to intratumor localization of Bifidobacterium and enhancing NK cell functions. This facilitated tumor regression, suggesting potential role of high salt in cancer immunotherapy. The overall impact of high-salt diets is not fully understood, which necessitates further research to elucidate their influence in altering tumor microenvironment and fate of cancer cells. This study aimed to investigate the effects of high salt on a triple-negative breast cancer cell line (in vitro), exploring its impact on cancer progression and associated global transcriptomic changes.

overall_design: To study the effect of high salt in triple negative breast cancer cell line (MDA MB-231), control (1 Sample) and high salt (2 Replicates) treated cell line were subjected to RNA Seq analysis. Total RNA was extracted and subjected to RNA Seq analysis.The impact of high salt on breast cancer cells has not been previously explored. Therefore, in this study, we investigated the influence of high salt on the triple-negative MDA MB-231 in-vitro.

first: Manoj

last: Sharma

first: Upalabdha

last: Dey

first: Kaushika

last: Olymon

first: Rupak

last: Mukhopadhyay


title: Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa [snATAC-seq]

city: Guangzhou

first: Yingying

last: Liu

address: Tianhe

institute: Sun Yat-sen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Focal cortical dysplasia (FCD) is a heterogeneous group of cortical developmental malformations that constitute a common cause of medically intractable epilepsy. Multiomic integration was conducted via single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assays for transposase-accessible chromatin sequencing (snATAC-seq) to analyse cell type-specific alterations in chromatin accessibility and correlate them with gene expression changes in the epileptogenic cortex of FCD type IIIa (FCD IIIa).

overall_design: Highly epileptogenic temporal neocortical tissue from the FCD IIIa patients (n=4) and controls (n=3) was analysed via snRNA-seq and snATAC-seq. Transcriptomic and epigenetic datasets were specifically generated from equally divided samples from the same brain tissue.

first: Liemin

last: Zhou


title: Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa [snRNA-seq]


title: Transcriptomics of C. chinensis and E. ulmoides treated aged C. elegans

city: Berlin

first: Nadine

last: Saul

address: Philippstr. 13, House 22

department: Department of Biology

institute: Humboldt-Universitaet zu Berlin

summary: The nematode Caenorhabditis elegans was treated with extracts of the Traditional Chinese Medicine plants Cuscuta chinensis and Eucommia ulmoides from the L4 stage. In aged worms (on the 7th and 12th day of adulthood) different health parameters were determined. Besides the prolongation of lifespan, we found that C. chinensis improved the swimming behavior, pharyngeal pumping rate, stress resistance, mechanosensation and memory of aged C. elegans. Furthermore, the extract treatment reduced the autofluorescence, which is a known biomarker of ageing. Thus, we concluded that C. chinensis is an overall healthspan enhancer. In contrast, the E. ulmoides extract specifically enhanced the lifespan and stress resistance of aged C. elegans, but did not improve any other health aspect. To reveal the mechanism behind the healthspan enhancing effects of C. chinensis, the transcriptome of treated and untreated C. elegans on the 12th day of adulthood was analysed. For comparison purposes, E. ulmoides treated nematodes were included in the analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C. elegans treated with C. chinensis or E. ulmoides. DMSO treated nematodes were used as control. The treatment of nematodes took place from L4 until the 12th day of adulthood. Five biological repeats were prepared per treatment group.

first: Shimaa

middle: M

last: Sayed

first: Anna

last: Pitas

first: Christian

last: Schmitz-Linneweber


title: Altered TE-derived genes leads to pathogenesis of FXD [ShortReadRNASeq]

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

summary: We identified known and unknown transposon elements in the cells from healthy donors, FXD patients, and ALL patients by long-read RNA-sequencing. Using these identified TEs, we analyzed the expression of TE-derived genes by shot-read (illumina) RNA-sequencing. We found that expression of some specific TE-derived genes were changed in FXD compared to those in healthy donors. These findings suggested the involvement of modified expressions of TE-derived genes in the pathogenesis of FXD.

overall_design: We analyzed mRNA in 8 kinds of healthy donors' cells, 9 kinds of FXD patients' cells, and 4 kinds of ALL patients' cells.

first: Tamaki

last: Suganuma

first: Madelaine

last: Gogol


title: Altered TE-derived genes leads to pathogenesis of FXD [PacBioRNASeq]

overall_design: We analyzed total RNA and mRNA in 8 kinds of healthy donors' cells, 9 kinds of FXD patients' cells, and 4 kinds of ALL patients' cells.

first: Hassan

last: Huzaifa


title: Transmembrane serine protease 2 and proteolytic activation of the epithelial sodium channel in mouse kidney: Early effects of aldosterone

city: Erlangen

first: Alexandr

middle: V

last: Ilyaskin

address: Waldstr. 6

department: Institute of Cellular and Molecular Physiology

summary: The appropriate regulation of the epithelial sodium channel (ENaC) in the aldosterone-sensitive distal nephron is required for sodium homeostasis and thereby for the long-term regulation of arterial blood pressure. A unique feature of ENaC is its activation by proteolytic cleavage. However, the relevant proteases involved in proteolytic ENaC activation in the kidney remain elusive. Here, we examined a potential role of transmembrane serine protease 2 (TMPRSS2). A mouse cortical collecting duct cell line (mCCDcl1) was used as a model system. We performed RNA-Seq transcriptome analysis of mCCDcl1 cells, which confirmed coexpression of Tmprss2 and all three ENaC subunits (Scnn1a, Scnn1b, Scnn1g) in this cell line. Importantly, high baseline expression of TMPRSS2 was detected in these cells without a stimulatory effect of aldosterone on its function or transcription. TMPRSS2 knockout in mCCDcl1 cells compromised γ-ENaC cleavage and reduced baseline and aldosterone-stimulated transepithelial short-circuit currents, which could be rescued by chymotrypsin. A compensatory transcriptional upregulation of other proteases was not observed. From these findings we conclude that TMPRSS2 is likely to contribute to proteolytic ENaC activation in the kidney.

overall_design: Early effects of aldosterone exposure (2 h) on expression of TMPRSS2 and other serine proteases in wild-type mCCDcl1 cells were investigated. RNA-seq analysis was performed with aldosterone-treated cells (6 samples) versus vehicle-treated cells (6 samples).

first: Florian

last: Sure

first: Sara

last: Afonso

first: Marko

last: Bertog

first: Christoph

last: Korbmacher


title: Transmembrane serine protease 2 and proteolytic activation of the epithelial sodium channel in mouse kidney: Effects of TMPRSS2 knockout

overall_design: Effects of TMPRSS2 knockout on expression of other serine proteases in mCCDcl1 cells were investigated. RNA-seq analysis was performed with TMPRSS2-deficient cells (6 samples) versus nontargeting control cells (6 samples).


title: Histologic transformation induced by EGFR tyrosine kinase inhibitors

city: Nagoya

first: Hiromichi

last: Ebi

state: Aichi

address: 1-1, Kanokoden, Chikusa-ku

department: Division of Molecular Therapeutics

country: Japan

institute: Aichi Cancer Center Research Institute

summary: Although tyrosine kinase inhibitors (TKIs) targeting Epidermal Growth Factor Receptor (EGFR) activating mutations have significantly improved outcomes in EGFR-mutant non-small cell lung cancer, resistance inevitably develops. Despite the heterogeneity of resistance mechanisms, many induce activation of MAPK signaling in the presence of EGFR-TKIs. ARAF gene amplification is identified as one such mechanism that activates MAPK signaling by directly interacting with RAS, yet its clinicopathologic characteristics remain poorly understood. We characterized five cases with ARAF amplification resistant to first- or second-generation EGFR-TKIs and screened an additional 48 re-biopsied specimens following resistance to Osimertinib. Among Osimertinib-resistant tumors, we identified four cases with ARAF amplification. Overall, these nine ARAF-amplified resistant tumors retained their original founder EGFR mutation and lacked secondary alterations. Furthermore, we identified two cases showing histologic transformation from lung adenocarcinoma to small cell lung cancer (SCLC). SCLC can be classified into four subtypes defined by transcriptional signatures driven by specific transcription factors. To estimate the subtypes of these resistant tumors, RNA sequencing analysis was performed in paired samples before and after treatment with EGFR-TKIs.

overall_design:
Paired samples from two cases demonstrated histologic transformation from lung adenocarcinoma to small cell lung cancer following treatment with EGFR tyrosine kinase inhibitors. Post-treatment samples also exhibited ARAF amplification.
Biopsied samples were extracted RNA and sequenced. ARAF amplification was determined by copy number analysis.

first: Ryo

last: Kimura

first: Rui

last: Yamaguchi


title: Transcriptome of Pseudomonas sp OST1909 when grown in the presence of naphthenic acids.

city: Calgary

first: Shawn

last: Lewenza

state: AB

address: 3330 Hospital Drive NW

department: Microbiology, Immunology & Infectious Diseases

country: Canada

institute: University of Calgary

summary: RNA-seq analysis of Pseudomonas sp OST1909 exposed to various preparations of naphthenic acids samples led to the identiifcation of many NA-induced genes.

overall_design: Duplicate cultures were grown to early log phase in the presence of a custom 9x, acyclic commercial (Sigma), or OSPW-extracted NA mixtures of naphthenic acids (150 mg/L). Total RNA was extracted, and then prepared as SOLiD sequencing libraries. Analysis of RNA-Seq data was used to identify genes differentially regulated in response to exposure to naphthenic acids.

first: Tyson

last: Bookout

first: Steve

last: Shideler

first: Evan

last: Cooper

first: Kira

middle: L

last: Goff

first: John

last: Headley

first: Lisa

last: Gieg


title: Development of activation-induced marker assay to identify HCV-specific T cells for single-cell RNA-seq analysis.

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

institute: CRCHUM

summary: Identification and isolation of antigen-specific T cells is  important for many immunological research areas, including cancer, infectious diseases, and vaccines. We optimized an activation-induced markers (AIM) assay that facilitated detection and scRNA analysis of HCV-specific T cells.

overall_design: Using AIM assay HCV-specific CD4 and CD8 T-cells were sorted from total PBMC's and processed for scRNA-seq.

first: Eisa

last: Mohamed

first: Nicol

last: Flores

first: Omar

last: Khedr

first: Elsa

last: Gomez-Escobar

first: Nathalie

last: Bédard

first: Nourtan

middle: F

last: Abdeltawab

first: Julie

last: Bruneau

first: Arash

last: Grakoui

middle: H


title: Multiple cell trypes, incluiding melanocytes, contribute to elastogenesis in the developing murine aortic valve

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: Elastic fibers are required for expansion and recoil during contraction and relaxation of vessels and heart valves. The aortic valve (AoV) extracellular matrix is generated and maintained by valvular interstitial cells (VICs), a heterogeneous population of cells derived from a mixture of developmental precursors such as endocardium, neural crest and second heart field. Although most studies have focused on VICs that exhibit a fibroblastic phenotype, significant subpopulations present with neuronal, glial, smooth muscle and melanocytic phenotypes. Relatively little is known about which sub population of VICs regulate and produce elastic fibers, though elastin (Eln) abnormalities result in congenital AoV defects and Eln degradation initiates AoV diseases. The present study establishes the timing ofElnexpression in the murine AoV. We performed RT-qPCR and found thatElnpeaks at late embryogenesis (embryonic day 17.5) and early postnatal (P) stages and decreases to low levels in adulthood. Using spatial transcriptomics in postnatal day 3 AoV, we segregated AoV cells from other cardiac cells and demonstrated thatElnexpression correlates with that of genes known to regulate elastogenesis, including the common smooth muscle cell marker - Acta2. By combining RNAscopein situhybridization with immunofluorescence, we confirmed that VICs that expressElnco-express alpha smooth muscle actin. Additionally, some of theEln/alpha smooth muscle actin expressing cells also express melanocytic markers. As previously reported in adult mice, we show a relationship between AoV pigment and elastic fiber patterning during early postnatal stages and further show that melanocytes may play a critical role in elastogenesis. Our results indicate that in the murine AoVElnis produced during early postnatal stages by cells that co-express phenotypic markers of various cell types, including smooth muscle actin and melanocytic specific genes.

overall_design: To investigate the cell types and relevant mechanisms of elastinogenesis in the developing aortic valve. Mouse aortic valve tissues from postnatal day 3 and day 30 aged mice were snap frozen, OCT embedded, and sectioned using a cryostat. We used the 10xGenomics Visium Spatial Gene Expression kit to determine spatially encoded gene expression profiles on the tissues.

first: Sana

last: Nasim

first: Beatriz

middle: A

last: Abujamra

first: Daniel

last: Chaparro

first: Perony

last: Nogueira

first: Joshua

middle: D

last: Hutcheson

first: Lidia

last: Kos


title: DNA damage-activated mitochondrial fatty acid oxidation drives senescence

city: Tokyo

first: Takao

last: Fujisawa

address: 7-3-1, Hongo, Bunkyo-ku

institute: The University of Tokyo

summary: Cellular senescence is a stress-induced irreversible cell cycle arrest involved in tumor suppression and aging. Many stresses, such as telomere shortening and oncogene activation, induce senescence by damaging nuclear DNA. However, the mechanisms linking DNA damage to senescence remain unclear. Here, we show that DNA damage response (DDR) signaling to mitochondria triggers senescence. A genome-wide siRNA screen implicated the outer mitochondrial transmembrane protein BNIP3 in senescence induction. We found that BNIP3 is a substrate of the DDR kinase ATM and contributes to an increase in the number of mitochondrial cristae upon DNA damage. Stable isotope labeling metabolomics indicated that this increase in cristae enhances the oxidation of fatty acids to acetyl-CoA. Notably, pharmacological activation of fatty acid oxidation alone induced senescence both in vitro and in vivo. Our findings suggest that mitochondrial energy metabolism plays a critical role in senescence induction and is a potential intervention target to control senescence.

overall_design: IMR-90 cells treated with each siRNA (non-targeting or BNIP3) were stimulated with doxorubicin. Then RNA was isolated using ISOGEN and subjected to RNA-seq.

first: Shota

last: Yamauchi

first: Satoshi

last: Takenaka


title: Transcriptome analysis in the Treatment of Diabetic Foot Ulcer Healing by Tibial Cortex Transverse Distraction

city: Nanchang

first: Zhi-Qiang

last: Fan

address: 152 Ai Guo Road, Nanchang

institute: Jiangxi Provincial People's Hospital

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: To investigate mRNA Expression profile and associated signaling pathways in the treatment of diabetic foot ulcer healing by tibial cortex transverse distraction.   Methods: Tissue samples were collected from the wound edge before and after the surgery. After reference genome transcriptome sequencing and subsequent bioinformatics analysis, the differentially expressed genes and related pathways were explored, and functional analysis of important genes and pathways was conducted.

overall_design: In this study, we collected marginal tissue samples from patients with diabetic foot ulcers. By comparing the gene expression in the marginal tissues before and after TCTD, the differentially expressed genes in the tissues after TCTD were detected, and the associated signaling pathways were analyzed through bioinformatics analysis. This study helps us to better understand the molecular regulatory mechanism of TCTD in the healing process of diabetic foot ulcer.

first: Bao-Fu

last: Yu


title: Trimethylamine N-oxide Aggravates Neuro-inflammation via lncRNA Fendrr/miR-145-5p/PXN axis in Vascular Dementia Rats

city: nanjing

first: Rui

last: Duan

address: Yanshan road 139

institute: Nanjing First hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Vascular dementia (2VO) is the second-most cause of dementia, and our previous investigation showed that Trimethylamine-N-oxide (TMAO) exacerbates cognitive dysfunction and neuropathological changes in 2VO rats. Therefore, this study is aimed to evaluate the mechanism of TMAO in 2VO. Bilateral common carotid artery (2VO) model was established in rats and TMAO (120 mg/kg) was administered for 8 consecutive weeks, 4 weeks preoperatively and 4 weeks postoperatively. High-throughput sequencing was performed to find out the effects of TMAO treatment on lncRNA expression in rat hippocampus and bioinformatics analysis was conducted to identify potential downstream targets. Learning and spatial memory capacities were measured, as well as inflammatory factors. Nissl staining was used to observe neuronal injury in the CA1 area of the hippocampus. TMAO administration upregulated lncRNA Fendrr expression in the rat hippocampus, while the damaging effects of TMAO were counteracted after knockdown of Fendrr. Fendrr was highly expressed in 2VO rats and sponged miR-145-5p, which targets PXN. Silencing of Fendrr or PXN, or promotion of miR-145-5p improved neurological function injury, reduced neuronal damage, as well as repressed inflammation response. Inhibition of miR-145-5p abrogated up Fendrr knockdown mediated influence on 2VO rats. Taken together, our results showed that TMAO inhibits the miR-145-5p/PXN axis by increasing the Fendrr expression, thus exacerbating the development of 2VO.

overall_design: The hippocampal tissues of lncRNA profiles in 2VO rats  and 2VO rats were continuously administered TMAO

first: Yang

last: Deng

first: Junqing

last: Zou

first: Xiangliang

last: Chen


title: Immunogenic cell death inducer cEmsy boosted cancer immunotherapy in lung adenocarcinoma

city: Nanjing

first: yijian

last: zhang

state: None Selected

address: Baiziting 42, Nanjing, P.R. China, 210009

institute: NanJing Medical University

summary: Immunogenic cell death (ICD) represents a spectacular approach to boosting tumor immunotherapy by inducing an adaptive immune response, and it is urgent to identify effective and safe ICD inducers. Here, we identified a conserved, ICD-related circular RNA-cEmsy/cEMSY by performing a systematic screening utilizing immunogenic cell death models induced by multiple cell stressors in lung adenocarcinoma (LUAD). cEmsy/cEMSY triggers ICD in LUAD both in vitro and in vivo, leading to the release of damage-associated molecular patterns (DAMPs) and promoting T-cell cross-priming by dendritic cells (DCs). Notably, in the immunosuppressive tumor model, intratumoral delivery of in vitro-transcribed cEmsy encapsulated in lipid nanoparticles (LNP) induces a potent anti-tumor immune response, which synergizes with PD-1 blockade to facilitate long-term cancer immunity with no apparent toxicities. Mechanistically, cEmsy/cEMSY facilitates TDP-43 aggregation in mitochondria and leverages mitochondrial DNA leakage, activating the cGAS-STING pathway and initiating an antiviral immune response. Clinically, elevated expression level of cEMSY correlates with enhanced DCs and CD8+ T cell infiltration, and favorable immunotherapy response in LUAD. Hence, cEmsy/cEMSY emerges as a safe and potent ICD inducer, offering a dual advantage as a mechanism-based target and a biomarker for enhancing ICI responses in LUAD treatment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To identify the potential ICD inducer derived from circRNAs, whole transcriptome sequencing of stressor-treated(anthracyclines (Doxorubicin), DNA-damaging agents (Oxaliplatin), tyrosine kinase inhibitors ((R)-crizotinib), and platinum-based doublet chemotherapy (Pemetrexed and Cisplatin chemotherapy), alongside proteasomal (Bortezomib) and DNA intercalator (Dactinomycin)) LLC1 cells was analyzed.
To investigate the mechanisms by which cEmsy augments ICB therapy efficacy and triggers ICD, we conducted a comprehensive transcriptome analysis on EV and circRNA-overexpressed LLC1 and H358 cell lines.

first: Yijian

last: Zhang

first: Xuming

last: Song

first: Yipeng

last: Feng

first: Yuxian

last: Qian


title: SND1 is a novel regulator of endothelial function

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

summary: Staphylococcal nuclease and tudor domain containing protein 1 (SND1), which is also known as p100 or Tudor-SN, is a recently identified protein that is highly expressed in multiple cancers including breast cancer, liver cancer, and colon cancer. Endothelial function and vascular integrity are critical modulators in cancer metastasis and progression. Although much progress has been made in studying SND1’s oncogenic role, the involvement of SND1 in endothelial function has never been explored.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three lines of hiPSC-EC  transfected with either scramble shRNA or SND1 shRNA for 48 hours.

first: Zhenbo

last: Han

first: Sang-Ging

last: Ong


title: See GSE205592

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

summary: PMID 38781074 quotes GSE205594 instead of GSE205592.


title: Transcriptome sequencing (RNA-Seq) of kidney and liver tissues from Lxrα-/- mices or wild type mices.

first: Lan

last: Tang

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

summary: As a cholesterol sensor, nuclear receptor liver X receptor (Lxr) activated by oxysterols is an important factor regulating cholesterol homeostasis and plays central roles in the transcriptional control of cholesterol metabolism. Lxrα is one of the liver X receptor(Lxrs) subtypes. Lxrα is abundantly expressed in liver, small intestine, adipose, kidney, adrenal tissues, and macrophages. Lxrα's regulation of lipid metabolism is well known but its regulation of other downstream genes remains unclear.In order to investigate the regulating effect of Lxrα on other genes, we used the second-generation transcriptome sequencing(RNA-seq) to determine the expression changes of each gene in Lxrα-/- mices comparing with wild type mices.

overall_design: Kidney and liver mRNA profiles of 5 Lxrα-/- mices or 5 wild type mices were generated by deep sequencing, using Illumina HiSeqTM 4000.


title: Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa

first: Yingying

last: Liu

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

overall_design: Refer to individual Series


title: Altered TE-derived genes leads to pathogenesis of FXD

first: Huzaifa

last: Hassan


title: A Switch from Glial to Neuronal Gene Expression Alterations in the Spinal Cord of SIV-infected Macaques on Antiretroviral Therapy

city: Baltimore

first: Joseph

last: Mankowski

address: 733 N Broadway

institute: Johns Hopkins University

summary: Despite antiretroviral therapy (ART), HIV-associated peripheral neuropathy remains one of the most prevalent neurologic manifestations of HIV infection. The spinal cord is an essential component of sensory pathways, but spinal cord sampling and evaluation in people with HIV has been very limited, especially in those on ART. The SIV/macaque model allows for assessment of the spinal cord at key time points throughout infection with and without ART. In this study, RNA was isolated from the spinal cord of uninfected, SIV+, and SIV+ART animals to track alterations in gene expression using global RNA-seq. Next, the SeqSeek platform was used to map changes in gene expression to specific cell types. Pathway analysis of differentially expressed genes demonstrated that highly upregulated genes in SIV-infected spinal cord aligned with interferon and viral response pathways. Additionally, this upregulated gene set significantly overlapped with those expressed in myeloid-derived cells including microglia. Downregulated genes were involved in cholesterol and collagen biosynthesis, and TGF-b regulation of extracellular matrix. In contrast, enriched pathways identified in SIV+ART animals included neurotransmitter receptors and post synaptic signaling regulators, and transmission across chemical synapses. SeqSeek analysis suggested that upregulated genes were primarily expressed by neurons rather than glia. These findings propose that pathways activated in the spinal cord of SIV + ART macaques are involved in neuronal signaling rather than proinflammatory pathways. These findings provide the basis for further evaluation of mechanisms of SIV infection + ART within the spinal cord with a focus on therapeutic interventions to maintain synaptodendritic homeostasis.

overall_design:
SIV+ animals were inoculated intravenously with molecular clone SIV/17E-Fr and the immunosuppressive swarm SIV/DeltaB670. SIV+ART animals were inoculated with the same SIV combination and received ART beginning 12 days post-inoculation until study end.
RNA was isolated from 100 mg frozen lumbar spinal cord samples. For transcriptome sequence sample preparation, isolated RNA samples were purified and cDNA libraies were prepared.
SIV viral RNA loads in plasma were measured at serial time points by quanitative RT-PCR targeting the SIV gag gene.
DNA was isolated from frozen lumbar spinal cord samples of animals receiving ART.
Viral DNA was measured in tissues by ddPCR using primers in the SIV gag region and macaque beta interferon for sample normalization and cellular quantitation.
Transcriptomic data was collected by RNA sequencing from spinal cord samples of pigtailed macaques and read alignment was performed, followed by quality checking with Fastqc. Gene and transcript expression levels were computed and pathway analysis of differentially expressed genes was performed.
Generated cDNA was amplified and diluted. qPCR was performed.


title: Single cell transcriptomics reveals obesity-induced endothelial and neurovascular dysfunction in brain: implications for cognitive decline

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary: Obesity is a global pandemic and a key risk factor for several neurodegenerative diseases including Alzheimer’s disease (AD), Parkinson’s disease, or dementia. The neurovascular unit (NVU), essential for blood-brain barrier (BBB) integrity and comprised of endothelial cells, glial cells (microglia and astrocytes), and neurons, plays an important role in the pathogenesis of neurodegenerative diseases. However, molecular mechanisms underlying the effects of obesity on endothelial and other cells of and its contribution to neurodegeneration remains largely unknown. In this study we aimed to decipher in-dept molecular modifications induced by obesity in cells of neurovascular unit by integrative multiomics analysis of endothelial cells, neurons, microglial cells, and astrocytes from the hippocampus of ob/ob mice. Hippocampus were isolated from ob/ob and C57BL/6J male mice at 17-18 weeks of age. Gene expression profiles of cells of hippocampus were obtained using single nuclei RNA sequencing (snRNAseq) and data analyzed using in-dept bioinformatic analyses. snRNAseq and UMAP analysis revealed 19 cell types in hippocampus. Comparisons of global gene expression profiles identified different global profiles between ob/ob and WT for each of the cell types of the NVU. Statistical analyses revealed 4463 DEGs in neuronal cells, 1386 DEGs in astrocytes, 125DEGs in endothelial cells, and 155 DEGs in microglia cells, suggesting that obesity significantly impacts the expression profiles of NUV cells. Enrichment analyses revealed that these genes are involved in cellular processing like focal adhesion, cell interactions, inflammation, and metabolism. Changes in the expression in endothelial cells were positively correlated with genomic changes in other cell types, changes that we correlated with tendency in increase in BBB observed using functional MRI. Taken together, obesity exert significant cell-specific changes in global gene expression, genes that are associated with development of Alzheimer’s disease or dementia.

overall_design:
Wild type (C57BL/6J) and ob/ob male mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and single nuclei RNA sequencing was performed. Brain hippocampal endothelial cells, microglial cells, astrocytes, and neuronal cells gene expression was analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, gene networks, functional pathways, and transcription factors. Blood brain barrier permeability was assessed.
The Wild type data described in this study are avalilable in GSM7717249 [Samples 5,11,17, and 21].

first: Dragan

last: Milenkovic

first: Jennifer

last: Norman

first: Amparo

last: Villablanca


title: Collective oscillatory signaling acts as a developmental timer initiated by weak coupling of a noisy pulsatile signal

status: Public on Oct 29 2024

city: London

first: Christopher

last: Thompson

address: Gower Street

country: United Kingdom

institute: University College London

summary: Oscillatory phenomena are ubiquitous across different biological scales, from individual cells to tissues and whole organisms. In physical systems, oscillatory behaviour can emerge from weak coupling of independent stochastic elements. Once established, oscillations can drive coordinated group behaviour and encode robust information through oscillation frequency or amplitude. Here we use experimentation and modelling to understand the emergence and information coding properties of oscillatory cyclic adenosine monophosphate (cAMP) signaling in D. discoideum. Oscillatory cAMP signaling drives aggregation of individual amoebae and coordinated temporal shifts in gene expression. However, it is unknown how the collective behaviour emerges and attenuates in an auto-regulatory manner where temporal transcriptional regulation must decode variation in cAMP pulse count, frequency, or amplitude. To address these questions, we identified a transcription factor, Hbx5, that is essential for the initiation of collective behaviour and its activity provides a single-cell readout of the earliest sign of cAMP signaling. This reveals stochastic pulses in cAMP signaling precede collective oscillations, with Hbx5 dependent transcriptional feedback enhancing signal sensitivity necessary for the emergence of collective oscillations. We demonstrate that once collective oscillations have been established, another cAMP-regulated transcription factor, GtaC, required for subsequent developmental progression becomes activated. Modelling and experimentation suggest that temporal differences in transcription factor activation arise from differences in the threshold at which the protein kinase, ErkB, influences their activity. This leads us to propose that changes in the amplitude of cAMP oscillations during development encode temporal information, driving the orderly progression of development. These studies thus provide crucial insights into the principles driving collective behaviour and the evolution of multicellular systems.

overall_design: RNA-seq of wild type and Hbx5 mutant cells at 0, 1, 2 , 5, 8 hours development. Three thechnical replicates


title: Transcriptional landscape of human adipose tissue in infancy and childhood

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

summary: Incidence of obesity is increasingly prevalent among children: global pediatric obesity incidence raised by 30% globally in the last two decades and increased tenfold in the last four decades. Being obese as a child increases the likelihood of being obese as an adult, and suffer from obesity-related health complications. Adipose tissue development in the first year of life may determine adiposity in early childhood. Our aim is to understand mechanisms that control healthy adipose tissue development from infancy to childhood. We collected adipose tissue specimens during elective surgery from the inguinal region of human infants and children, with normal BMI and without known metabolic or endocrine diseases. Samples were proceesed for extraction of total RNA, using phenol:chlorophorm extraction. Next generation RNA sequencing were performed.

overall_design: Samples are labeled as patient groups ("infants", "children"). Our aim was to identigy differentially expressed genes (DEGs) in the adipose tissue of the the human infant and child, to understand molecular mechanisms and cellular processes that affect adipose tissue development.

first: Röszer

last: Tamás


title: P53 terminates the regenerative state after colitis-associated injury

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

institute: Charité Universitätsmedizin

summary: Cell clones that lack P53 signaling occur frequently in ulcerative colitis (UC) and are considered drivers in UC-associated colorectal cancer. Trp53 mutant cells often display decreased P53 signaling and have previously been shown to outcompete wild type (WT) cells in a mouse model of colitis (DSS colitis), but not in healthy mice. However, the mechanism responsible for the observed context-dependent effects of P53 are not understood.   Therefore, we aimed to explore this by studying the behavior of Trp53-deficient cells specifically in injured mucosa. We have developed murine and organoid-based models to study the context dependent role of Trp53 knock-out (KO). We use inducible KO systems in mouse models of DSS colitis to study the loss of Trp53 in the injury and regenerative state. Colon organoids are employed to recapitulate the in vivo findings in order to elucidate the pathways involved.

overall_design: Tissue of P53 KO mice were compared to mice with P53 WT in two independent biological replicates. In both arms, mice were treated for 5-7 days with DSS and sacrificed at 2 months after DSS.   Organoids from with P53 KO, P53 WT and P53 KO organoids grown in Wnt-deficient medium were compared to each other in two independent biological replicates.

first: Kimberly

last: Hartl

first: Hans

last: Mollenkopf

first: Hilmar

last: Berger


title: Transcriptomic exploration of decidualizing human endometrial stromal cell dynamics

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

summary: Spontaneous decidualization of the endometrium in response to progesterone signaling is confined to menstruating species, including humans and other higher primates. During this process, endometrial stromal cells (EnSCs) differentiate into specialized decidual cells that control embryo implantation. We subjected undifferentiated and decidualizing human EnSCs to RNA-sequencing (RNA-seq) to measure global changes in transcription.

overall_design: We subjected decidualising primary human endometrial stromal cells to RNA sequencing (RNA-seq) to map the underlying gene expression changes.

first: Pavle

last: Vrljicak

first: Emma

last: Lucas

first: Sascha

last: Ott


title: Epigenomic exploration of decidualizing human endometrial stromal cell dynamics

summary: Spontaneous decidualization of the endometrium in response to progesterone signaling is confined to menstruating species, including humans and other higher primates. During this process, endometrial stromal cells (EnSCs) differentiate into specialized decidual cells that control embryo implantation. We subjected undifferentiated and decidualizing human EnSCs to Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to map the underlying chromatin changes.

overall_design: We subjected decidualising primary human endometrial stromal cells to Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to map the underlying chromatin changes.


title: Methylomic signatures of tau and beta amyloid in transgenic mouse models of Alzheimer’s disease neuropathology

city: Exeter

last: Walker

address: RILD Barrack Rd

institute: University of Exeter

type: Methylation profiling by high throughput sequencing

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Methylomic signatures of tau and beta amyloid in transgenic mouse models of Alzheimer’s disease neuropathology [RRBS]

summary: We identified widespread DNA methylation changes associated with the development of both tau and amyloid neuropathology, including differentially methylated positions (DMPs) and regions (DMRs) at loci previously implicated in AD and overlapping changes identified in our ongoing analyses of human post-mortem AD brains.

overall_design: DNA was collected from mouse entorhinal cortex samples and methylation levels quantified using both array and RRBS technology. Array data was measured using the HorvathMammalMethylChip40 Methylation Beadchip on the Illumina platform.

first: Isabel

last: Castanho

first: Szi

middle: K

last: Leung

first: Stefania

last: Policicchio

first: Dorothea

last: Seiler Vellame

first: Joshua

last: Harvey

first: Hedley

last: Baulf

last: Dempster

first: Gemma

last: Shireby

first: Karen

last: Moore

first: David

last: Collier

first: Zeshan

last: Ahmed

first: Eilis

last: Hannon

first: Jonathan

last: Mill


title: Sevoflurane increases FKBP5 expression in microglia in the brains of aged marmosets and mice

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Background: Inhalation anesthetics may trigger the hypothalamic–pituitary–adrenal (HPA) axis. FK-506 binding protein (FKBP5) is a critical factor that regulates the HPA axis and is associated with perioperative neurocognitive impairment. However, it is unclear how inhalation anesthetics affects the expression of FKBP5 in different neural cells in the brain. Methods: We used single-nucleus RNA sequencing to characterize hippocampal transcriptome profiles in the brains of aged marmosets and mice after sevoflurane anesthesia. Results: Higher levels of FKBP5 were found in the hippocampi of aged mice after sevoflurane anesthesia. Single nuclear RNA sequencing results from aged mice and marmosets showed that the increased expression of FKBP5 mainly occurred in microglia. The expression of FKBP5 in the hippocampi of aged marmosets and mice increased following long-term exposure to sevoflurane anesthesia. Additionally, the brains of these animals displayed a marked increase in the expression of FKBP5 in microglia after sevoflurane anesthesia. Conclusion: Long-term exposure to sevoflurane augments FKBP5 expression in the hippocampi of aged marmosets and mice, specifically in the microglia.

overall_design: Control and sevoflurane anesthetized hippocampi of aged mice and aged marmosets

first: Zhengjie

last: Miao

first: Jiao

last: Zhu

first: Haoli

last: Mao

first: Hong

last: Jiang

first: Lei

last: Zhang


title: Methylomic signatures of tau and beta amyloid in transgenic mouse models of Alzheimer’s disease neuropathology [HorvathMammalMethylChip40 Methylation Beadchip]

first: Emma

last: Walker

overall_design: DNA was collected from mouse entorhinal cortex and hippocampus samples and methylation levels quantified using both array and RRBS technology. Array data was measured using the HorvathMammalMethylChip40 Methylation Beadchip on the Illumina platform.

first: Isabel

last: Castanho

first: Szi

last: Leung

last: Policicchio


title: CEACAM6 orchestrates gallbladder cancer aggressiveness through molecular interplay with Integrin and PRKCD.

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg


title: NFkB Signaling is Required for Xist RNA Localization at the Inactive X and for X-Chromosome Inactivation Maintenance Following T cell Activation

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: Rosenthal Building- 3800 Spruce St, Room 304

department: Department of Biomedical Sciences

institute: University of Pennyslvania School of Veterinary Medicine


title: NFkB Signaling is Required for Xist RNA Localization at the Inactive X and for X-Chromosome Inactivation Maintenance Following T cell Activation [RNAseq_ESCAPE_stimulation]

summary: X Chromosome Inactivation (XCI) is a female-specific process which balances X-linked gene dosage between sexes. Unstimulated T cells lack cytological enrichment of Xist RNA and heterochromatic modifications on the inactive X chromosome (Xi), and these modifications become enriched at the Xi after cell stimulation. Here, we examined allele-specific gene expression and epigenomic profiling of the Xi following T cell stimulation. We found that the Xi in unstimulated T cells is dosage compensated, and is enriched with the repressive H3K27me3 modification, but not H2AK119-ubiquitin (Ub) mark, including at promoters of XCI escape genes. Upon CD3/CD28 mediated T cell stimulation, the Xi accumulates H2AK119-Ub and H3K27me3 across the Xi. Next, we examined the T cell stimulation pathways responsible for Xist RNA localization to the Xi and found that T cell receptor (TCR) engagement, specifically NFkB signaling downstream of TCR, is required. Disruption of NFkB signaling, using inhibitors or genetic deletions, in mice and patients with immunodeficiencies prevents Xist/XIST RNA accumulation at the Xi and alters expression of some X-linked genes. Our findings reveal a novel connection between NFkB signaling pathways which impact XCI maintenance in female T cells.

overall_design: RNAseq from F1 mus x cast CD3+ T cells that were unstimulated or stimulated with anti-CD3/anti-CD28 for 48 hours (n=3 per condition). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.

first: Katherine

middle: S

last: Forsyth

first: Natalie

middle: E

last: Toothacre


title: Steroid receptor coactivation of NRF2 signaling in cardiac fibroblasts promotes resistance to oxidative stress

city: Houaton

first: Rainer

middle: B

last: Lanz

state: TX

address: One Baylor Plaza

department: Molecular and Cellular biology

institute: Baylor College of Medicine

summary: We recently discovered that steroid receptor coactivators (SRCs) SRCs-1, 2 and 3, are abundantly expressed in cardiac fibroblasts (CFs) and their activation with the SRC small molecule stimulator MCB-613 improves cardiac function and dramatically lowers pro-fibrotic signaling in CFs post-myocardial infarction (MI). These findings suggest that CF-derived SRC activation could be beneficial in the mitigation of chronic heart failure after ischemic insult. However, the cardioprotective mechanisms by which CFs contribute to cardiac pathological remodeling are unclear.  These studies were designed to identify the molecular and cellular circuitry that governs the anti-fibrotic effects of an MCB-613 derivative, MCB-613-10-1, in CFs. To achieve this, we performed cytokine profiling and whole transcriptome analyses of CF-derived signals in response to MCB-613-10-1. We identified the NRF2 pathway as an MCB-613-10-1 therapeutic target for promoting resistance to oxidative stress in CFs.   We show that MCB-613-10-1 promotes cell survival of anti-fibrotic CFs exposed to oxidative stress by suppressing apoptosis.   We demonstrate that an increase in HMOX1 expression contributes to CF resistance to oxidative stress-mediated apoptosis via a mechanism involving SRC co-activation of NRF2, hence reducing inflammation and fibrosis. We provide evidence that MCB-613-10-1 acts as a protectant against oxidative stress-induced mitochondrial damage. Our data reveal that SRC stimulation of the NRF2 transcriptional network promotes resistance to oxidative stress and highlights a mechanistic approach towards addressing pathologic cardiac remodeling.

overall_design: These studies were designed to identify the molecular and cellular circuitry that governs the anti-fibrotic effects of an MCB-613 derivative, MCB-613-10-1, in CFs. To achieve this, we performed  whole transcriptome analyses of CF-derived signals in response to MCB-613-10-1.

first: Lisa

last: McClendon


title: ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner

city: Giessen

first: Sandra

middle: Brigitte

last: Hake

state: Hessen

address: Heinrich-Buff-Ring 58-62

department: Faculty 08 Biology and Chemistry

institute: Institute for Genetics

summary: The evolutionary conserved histone variant H2A.Z plays a crucial role in various DNA-based processes but the underlying mechanisms are not completely understood. Recently, we identified the zinc finger (ZNF) protein ZNF512B as an H2A.Z-, HMG20A- and PWWP2A-associated protein. Here, we report ZNF512B as a novel nucleosome remodeling and deacetylase (NuRD) complex binding protein. We discovered a conserved amino acid sequence within ZNF512B that resembles a NuRD-interaction domain (NIM) previously identified in FOG-1. By solving the crystal structure of this domain directly bound to the NuRD component RBBP4 and by applying several biochemical assays we demonstrate that this novel internal NIM sequence is both necessary and sufficient for high-affinity NuRD binding. Transcriptome analyses and reporter assays identify ZNF512B as regulator (repressor) of gene expression, in both NuRD-dependent and -independent modes. Surprisingly, high levels of ZNF512B expression lead to concomitant nuclear protein and chromatin aggregation foci that form independent of the interaction with the NuRD complex but depend on ZNF512B’s zinc fingers. Our study has implications for diseases in which ZNF512B’s expression is deregulated, such as cancer and neurodegenerative diseases and reveal the existence of more proteins as potential NuRD interactors.

overall_design: To investigate the role of ZNF512B in the regulation of gene expression, we overexpressed GFP-ZNF512B (OE), together with GFP-ZNF512B_K423A (OE) mutant, and depleted ZNF512B (KD) by siRNA treatment in HeLaK cells, respectively. We then performed high-throughput RNA sequencing. Each experiment has at least two biological replicates. Differential gene expression analysis was performed in pair-wise conditions, that is GFP-ZNF512B OE vs GFP control, GFP-ZNF512B_K423A OE vs GFP control as well as ZNF512B KD vs siRNA scrambled control.

first: Tim

last: Wunderlich

first: Chandrika

last: Deshpande

first: Lena

middle: W

last: Paasche

first: Tobias

last: Friedrich

first: Felix

last: Diegmüller

first: Elias

last: Haddad

first: Carlotta

last: Kreienbaum

first: Haniya

last: Naseer

first: Sophie

last: Stebel

first: Nadine

last: Daus

first: Jörg

last: Leers

first: Jie

last: Lan

first: Van Tuan

last: Trinh

first: Olalla

last: Vázquez

first: Falk

last: Butter

first: Marek

last: Bartkuhn

first: Joel

middle: P

last: Mackay


title: KSRP deficiency attenuates the course of pulmonary aspergil-losis, associated with elevated pathogen-killing activity of in-nate myeloid immune cells

city: Mainz

first: Matthias

last: Bros

address: Langenbeckstrasse 1

department: Dermatology

institute: University Medical Center Mainz

summary: The mRNA-binding protein KSRP (KH-type splicing regulatory protein) is known to modulate immune cell functions post-transcriptionally e.g. by reducing the mRNA stability of cytokines. It is known that KSRP binds AU-rich motifs (ARE) within the 3´-untranslated region of mRNA spe-cies, which in many cases encode dynamically regulated proteins like cytokines. Innate myeloid immune cells, such as polymorphonuclear neutrophils (PMN) or macrophages (MAC) eliminate pathogens by multiple mechanisms, including phagocytosis, as well as secretion of chemo- and cytokines. Here, we investigated the role of KSRP on the phenotype and functions of both innate immune cell types in mouse model of invasive pulmonary aspergillosis (IPA). Here, KSRP-/- mice showed lower levels of Aspergillus fumigatus conidia (AFC) and an increase in the frequencies of PMN and MAC in the lungs. Our results showed that PMN and MAC from KSRP-/- mice exhibited enhanced phagocytic uptake of AFC, accompanied by increased ROS production in PMN upon stimulation. As a comparison of RNA sequencing data revealed that 64 genes related to inflam-matory and immune responses were shared between PMN and MAC. The majority of genes up-regulated in PMN were involved in metabolic processes, cell cycle and DNA repair. In agreement, KSRP-deficient PMN displayed reduced levels of apoptosis. In conclusion, our results indicate that KSRP serves as a critical negative regulator of PMN and MAC anti-pathogen activity.

overall_design: Polymorphonuclear neutrophils (PMN) were purified from bone marrow of WT and KSRP-/- mice and were either treated with 1 µg/µl LPS for 6 h or left untreated. 1x10^6 cells of each samples were lysed and total RNA was purified for sequencing.

first: Bros

last: Matthias

first: Bolduan

last: Vanessa


title: Effects of oxygen consumption rate and ammonia excretion rate and transcriptome analysis of Mactra veneriformis with different shell colors under ocean acidification stress

city: Tianjin

first: chen

last: limei

address: Jin jing road 22

institute: Tianjin Agriculture University

summary: In recent years, increasing levels of dissolved carbon dioxide in seawater have led to an increase of ocean acidification (OA), which constitutes a major threat to marine ecosystems. As an important economically marine bivalve, Mactra veneriformis is highly susceptible to ocean acidification. In this study, we recorded and observed the mortality rate,   oxygen consumption rate and ammonia excretion rate of different shell colour groups of M. veneriformis under the stress of ocean acidification (pH=7.6), and conducted transcriptome analysis of the mantle tissues of M. veneriformis with white and purple shell colours in the acidified group (pH=7.6) and the control group (pH=8.1) under the two conditions, which showed that there was a significant difference in mortality rate between the acidified group and the control group at day 30, but there was a significant difference in mortality rate between the white colors group and the purple colors group at day 30, which was not significant. The results showed that there was a significant difference in mortality between the acidified and control groups at day 30, but the difference in mortality between the white and purple shell colour groups at day 30 was not significant. In the transcriptome analysis, fatty acid synthase gene was up-regulated in two shell colours of M. veneriformis under acidification stress, which may be a molecular compensatory mechanism to reduce the susceptibility of organisms to oxidative damage of lipids; tyrosinase gene was up-regulated, which may be a compensatory mechanism of Tyr's regulatory mechanism to the formation of shell damages under acidification; carbonic anhydrase gene was up-regulated in the purple group of M. veneriformis under acidification stress, which may be a compensatory mechanism for the acidity of M. veneriformis to cope with environmental stress; the white group of M. veneriformis under acidification stress was up-regulated. The carbonic anhydrase gene was up-regulated in the purple group under acidification stress, which may be an acidity compensation mechanism of M. veneriformis in response to the environmental stress.

overall_design: Mactra veneriformis from different shell colors were randmly divided into acidizing stress treament groupsand a control group. The two acidizing stress groups with different shell colors (  Acd-p ) were exposed to high pH

first: Limei

last: Chen

first: Gengyin

last: Huang


title: A cell-matrix interaction regulates the undifferentiated state and self-renewal capacity of avian primordial germ cells

city: Midlothian

first: Kennosuke

last: Ichikawa

address: Easter Bush Campus

department: The Roslin Institute

institute: The University of Edinburgh

summary: Primordial germ cells (PGCs) are lineage restricted precursor cells of sperm and eggs. While avian PGCs from chicken can be cultured and modified to produce genome-edited chickens, the long-term culture of PGCs from other bird species has not been achieved. Here, we explored the effects of a cell-matrix interaction on the in vitro propagation of chicken PGCs. Blocking integrin signaling severely reduced the self-renewal of the PGC, indicating that a PGC-matrix interaction is an essential process for self-renewal. We investigated the properties of somatic cell differentiated PGCs and expression analyses suggested that the PGCs undergo a partial epithelial-to-mesenchymal transition caused by excess PGC-matrix interactions. Finally, we conducted a long-term culture of chicken PGCs with matrix components, resulting in significant induction of their somatic conversion. These results suggested that a high level of PGC-matrix interaction can cause somatic conversion, while a moderate level is essential for their proliferation. Overall, we identified a molecular aspect of self-renewal and maintaining undifferentiated states of avian PGCs.

overall_design: To identify the genetic pathways activated in PGCs undergoing somatic cell conversion, we conducted gene expression profiling using RNA-seq analysis on undifferentiated and the somatic differentiated PGCs. replicates = 3.

first: Yuzuha

last: Motoe

first: Tenkai

last: Watanabe

first: Ryo

last: Ezaki

first: Mei

last: Matsuzaki

first: Hiroyuki

last: Horiuchi

first: Michael

last: McGrew


title: Effect of depletion of Spi1, Cebpb, and Jun on gene expression during therapy-induced-senescence of primary, murine Eµ-myc;bcl2 B-cell lymphomas

first: Paulina

last: Richter-Pechanska

address: Augustenburgerplatz 1

institute: Charite

summary:
Therapy-induced senescence associates with expression of lineage-aberrant transcript profiles. Spi1, Cebpb and Jun encode important hematopoietic transcription factors. To investigate their impact on lineage-adherence in therapy-induced senescence of B-cell lymphomas, we engineered several senescence-susceptible and senescence-deficient individual primary, murine Eµ-myc lymphomas overexpressing Bcl2, in which each target gene has been knocked down by shRNA.
We then treated lymphomas with adriamycin (doxorubicin) to induce senescence and performed gene expression analysis using data obtained from RNA-seq of the individual lymphoma samples.

overall_design: Examine differentially expressed gene transcripts in senescent and non-senescent conditions between control (sh_Ctrl) and specifically targeted (sh_Spi1, sh_Cebpb, sh_Jun) lymphoma derivatives.

first: Dimitri

last: Belenki

first: Clemens

last: Schmitt


title: RNA-seq of Myla cell line after FOXM1 knockdown

city: Beijing

first: Kecen

last: Liu

address: Xishiku Street 8th

institute: Peking University First Hospital

summary: FOXM1 is a vital transcription factor associated with proliferation, expressed extensively and dynamically throughout the cell cycle. Its overexpression in mycosis fungoides correlates with a poor prognosis. However, the specific role of FOXM1 in the pathogenesis of mycosis fungoides remains unclear. In this study, we silenced FOXM1 in the MyLa cell line, which is representative of mycosis fungoides, by transducing it with a lentivirus vector containing shRNA targeting the FOXM1 gene. By comparing MyLa cells transduced with scrambled shRNA as the control, we observed distinct gene expression profiles, notably a decrease in the expression of cell cycle-related genes and an increase in apoptosis-related genes. These changes align with the phenotypic alterations of MyLa cells following FOXM1 silencing.

overall_design: We transduced cell lines with lentiviral vectors. Two-condition experiment, FOXM1-VC Myla vs. shFOXM1 Myla cells. Biological replicates: 2 control replicates, 2 shFOXM1 replicates.

first: Jingru

last: Sun


title: Obesity-instructed TREM2-high macrophages identified by comparative analysis of diabetic mouse and human kidney at single-cell resolution [scRNA-seq: DKD_mouse]

city: Cambridge

first: Ayshwarya

last: Subramanian

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

summary:
The cross-species molecular heterogeneity from mice to patients poses grand challenges for translational research endeavors. A high-fat diet (HFD) model and a genetic model (BTBR ob/ob) at different stand points were used to generate cell atlases of diabetic and obese mise.
We identified a previously unrecognized, expanding Trem2-High macrophage population in kidneys of HFD mice that modeled human TREM2-high macrophages in obese patients. Taken together, our cross-species comparison highlights shared immune and metabolic cell-state changes.

overall_design: For the BTBR ob/ob genetic mouse model, we included n=5 and n=3 biological replicates for the 5- and 10-week time-point respectively for both ob/ob and wildtype strains. For the High-Fat diet (HFD) model, we combined n=4 biological replicates into a pooled “aged” group, in each of the chow and HFD conditions. The “aged” group ranged from 66 to 100 weeks old (schematic Figure 4A). For 3 biological replicates in each condition (Chow: ages 94,100; HFD: ages 83,100), there were 2 technical replicates or 10x channels run from the same cortical sample leading to a total of 7 libraries per condition.

first: Anna

last: Greka


title: The interactions among Tumor-infiltrating T lymphocytes (TILS) induced by Stellera chamaejasme and anti-PD-1 therapy with Sing-cell Expression Profiling

city: Shanghai

first: s

middle: y

last: h

state: Shanghai

summary: Tumor-infiltrating T lymphocytes (TILS) plays a pivotal role in immunotherapy, but the dynamic relationships of the T cells reacted on the therapy remains elusive. T cell receptor (TCR) repertoire, serving as lineage tags, could track these tumor-infiltrating T lymphocytes. Here, in order to deconvolve TILS heterogeneity after therapy in a comprehensive catalog, we presented single T-cell analysis by RNA-seq and TCR tracking of a 22,590 T cells from colorectal carcinoma under control conditions and during Stellera chamaejasme and anti-PD-1 activation. We reveal a highly complex microenvironment which profoundly molds T lymphocytes, as well as the combinatorial impact of TCR utilization on phenotypic diversity. scRNA-seq identified distinct CD8 T cells subtypes CD8 naïve and CD8 cytoxic cells(CD8 CTL), also, CD4 T cell subpopulations Regulatory T(Tregs) cells and T helper cell 17(Th-17). Stellera chamaejasme activation triggered CTSW, ICOS, etc. in CD8 T cells, whose the dramatic differentiation into from a single time point. At the same time, Stellera chamaejasme plus anti-PD-1 therapy have a strikingly effect on the balance between Tregs and Th-17. Our integrated analyses provide a powerful avenue to disclose the TILS in CRC based on TCR and demonstrate novel functional interactions among TILS subpopulations during Stellera chamaejasme plus anti-PD-1 therapy.

overall_design: samples from colorectal carcinoma under control conditions and during Stellera chamaejasme and anti-PD-1 activation.

first: Yibai

last: Xiong


title: Effects of Allulose and Erythritol Consumption on a High-Fat Diet

status: Public on Oct 28 2024

city: Daegu

first: Seong-su

last: Choi

address: Daehak-ro 9-gil, Buk-gu

institute: Kyungpook National Univ.

summary: Long-term consumption of erythritol, a widely used sugar substitute, has been associated with increased risks of thrombosis and cardiometabolic diseases. In this study, we investigated the effects and mechanisms of allulose in mitigating these risks compared to erythritol using the clusterProfiler tool. Since a high-fat diet (HFD) is known to enhance platelet aggregation, we compared the pathways related to these processes between groups of mice treated with allulose and those treated with erythritol. While erythritol exacerbated HFD-induced increased platelet aggregation, allulose treatment significantly reduced it. The groups consisted of a normal diet group (ND, with 10% of calories derived from fat), a high-fat diet group (HFD, with 40% of calories from fat), a high-fat diet with 5% allulose supplementation (ALLU), and a high-fat diet with 5% erythritol supplementation (ERY).

overall_design: Total RNA was extracted from C57BL/6J mice that have been induced to obesity via a high-fat diet to investigate the effects of  D-allulose and erythritol ingested with a high-fat diet on the liver.

first: Seong-Su

first: Eun-ji

last: Kim


title: Effect of depletion of TRIM47 on gene expression in human brain microvascular endothelial cells (HBMEC)

city: Pessac

first: Claire

last: Peghaire

address: 1 avenue de Magellan

country: France

institute: University of Bordeaux-INSERM 1034

summary: To investigate the transcriptional programme regulated by TRIM47 in HBMEC, we treated these cells with a siRNA targeted TRIM47 or a control siRNA for 72h.We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different conditions (siRNA control or siRNA TRIM47).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HBMEC treated with siControl or siTRIM47 for 72h

first: Juliette

last: Vaurs

first: Carole

last: Proust

first: Béatrice

last: Jaspard Vinassa

first: Thierry

last: Couffinhal

first: Cécile

last: Duplàa


title: Oncogenic Transformation from Actinic Cheilosis to Squamous Cell Carcinoma of the Lip

city: Seoul

first: Myoung Eun

address: Song-pa gu

institute: Asan medical center

summary: Lip is an anatomical junction between skin and mucosa and the squamous cell carcinoma (SCC) is the most frequent lip cancers. Lip SCC is frequently developed from actinic cheilitis, presented as ulcerative lesions. However, changes in transcriptomes and tumor microenvironment driving oncogenic transformation from actinic cheilitis to lip SCC and determinants of differentiation of lip SCC are largely unknown. This study aimed to investigate differences between lip SCC and its premalignant actinic cheilitis and factors related to tumor differentiation.

overall_design: We selected patients who received biopsies for actinic cheilitis which progressed to lip SCC several years later. In addition, biopsy samples of well-differentiated lip SCC and moderately- to poorly-differentiated lip SCC were used for spatial transcriptomic analysis. PanCK and CD45 were used as morphology markers and a total of 60 regions of interest (ROIs) were selected.

first: Chong Hyun

last: Won


title: Gene expression analysis of mouse adipose tissue macrophages

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

institute: University of Ulm

summary: We collected adipose tissue macrophages from C57Black/6 mice on postnatal day 6 (P6) and postnatal day 56 (P56) by enzyntic digestion of the inguinal fat depots and megnetic cell sorting of F4/80 antigen positive macrophages. Total RNA was isolated and used for next generation RNA sequencing.

overall_design: Samples are labeled as P6 (infant) and P56 (adult) ATMs (adipose tissue macrophages).

first: Röszer

last: Tamás


title: Single-cell transcriptome analysis revealed cellular reprogramming following Tetramethylpyrazine treatment in LPS-induced acute lung injury

first: janghong

last: bin

address: 507 Zhengmin Road, Yangpu District, Shanghai

institute: Department of Emergency Medicine

summary: Tetramethylpyrazine (TMP) has shown potential in the treatment of acute respiratory infections. We used single-cell RNA sequencing to investigate the mechanism and potential therapeutic effect of TMP in the treatment of acute lung injury

overall_design: The mice (n = 12) were randomly divided into four groups: control group (n=3), model group (n=3) administered with intraperitoneal injection of 30mg/ml lipopolysaccharide (LPS) in saline to induce ALI, LPS+dexamethasone (Dex) group (n=3), and LPS+TMP group treated with 5mg/ml dexamethasone (Dex) or 50mg/ml ligustrazine (TMP) one hour before LPS administration. After a 72-hour treatment period, lung tissues were collected and andanalyzed using scRNAseg.

first: Mingyan

last: Wu

first: Shanmei

last: Wang

first: Xiaolan

last: Chen

first: Shen

last: li

first: Jurong

last: Ding

first: Hongbin

last: Jiang


title: GCN2-SLC7A11 axis coordinates autophagy, cell cycle and apoptosis and regulates cell growth in retinoblastoma upon arginine deprivation

city: Hong Kong

first: Dan

last: WANG

address: Lo Kwee-Seong Integrated Biomedical Sciences Building

institute: the Chinese University of Hong Kong

summary: Background: Arginine deprivation was shown previously to inhibit retinoblastoma cell proliferation and induce cell death in vitro. However, the mechanisms by which retinoblastoma cells respond to arginine deprivation remain to be elucidated. Methods: Human derived retinoblastoma cell lines Y79 and WERI-Rb-1 were exposed to arginine depletion, and the effects on inhibiting cell growth and survival were evaluated. The study investigated potential mechanisms, including autophagy, cell cycle arrest, and apoptosis. Moreover, the roles of GCN2 and mTOR signaling pathways in these processes were examined. Results: We demonstrated that arginine deprivation effectively inhibited the growth of retinoblastoma cells in vitro. This treatment caused an increase in autophagic response. Additionally, we found that prolonged arginine shortage induced G2 cell cycle arrest and was accompanied by an increase in early apoptotic cells. Importantly, arginine depletion also caused an activation of GCN2 and an inhibition of mTOR signaling. We also discovered that the activation of SLC7A11 was regulated by GCN2 upon arginine deprivation. Knockdown of SLC7A11 rendered retinoblastoma cells partially resistant to arginine deprivation. Furthermore, we found that knockdown of GCN2 led to a decrease in autophagic response in WERI-Rb-1 cells and arrested more cells in S phase, which was accompanied by fewer apoptotic cells. Moreover, knockdown of GCN2 caused constant expression of ATF4, phosphorylation of 70S6K, and 4E-BP1 regardless of arginine deprivation. Conclusions: Collectively, our findings suggest that the GCN2-SLC7A11 axis regulates cell growth and survival upon arginine deprivation through coordinating autophagy, cell cycle arrest, and apoptosis in retinoblastoma cells. This work paves the way for the development of a novel treatment for retinoblastoma.

overall_design: mRNA profiles of Y79 cell lines cultured in the presence or absence of arginine for 72 hours

first: Wai Kit

last: Chu

first: Jason Cheuk Sing

last: Yam

first: Chi Pui

last: Pang

first: Yun Chung

last: Leung

first: Alisa Sau Wun

last: Shum

first: Sun-On

last: Chan


title: Cellular senescence contributes to spontaneous repair of rat meniscus

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

institute: Institute of Science Tokyo

summary: We performed RNA sequence analysis for intact knees and knees 1 week after sham and pMx surgery to identify genes specifically expressed in regenerative meniscus tissue.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for synovium/regenerative tissue from intact knees and knees 1 weeks after the pMx and sham surgery.

first: Yusuke

last: Aimono


title: Platelet factor 4 ameliorates motor and mood deficits in Parkinson’s disease

city: Chengdu

first: Haoran

last: Tai

state: Sichuan

address: #783 Xindu Avenue

department: Department of Histology and Embryology

institute: Chengdu Medical College

summary: Parkinson's disease (PD) is a neurodegenerative disorder characterized by motor and non-motor symptoms(1). Platelet factor 4 (PF4) is a platelets-secreted chemokine that can be activated by physical exercise. Recent studies showed that PF4 could improve cognition in aged mice(2), though whether it influences other neurological functions is vague. Here we investigated the role of PF4 in PD and normal aging mice. Intravenous administration of exogenous PF4 ameliorated both motor and non-motor symptoms of MPTP-induced PD mice, accompanying with reduced loss of nigrostriatal dopaminergic neurons and attenuated neuroinflammation in these regions. RNA sequencing showed that pathways related to inflammation were suppressed by PF4, which were confirmed by qPCR and immunohistochemical analysis. More interestingly, PF4 can also ameliorate the motor and non-motor symptoms after the loss of nigrostriatal dopaminergic neurons, and the efficacy can last for 3 weeks after PF4 administration. In addition, an improvement of motor performance and mood by PF4 was also observed in aged but not young mice. Collectively, our results show the potential of PF4 that not only be a therapeutic candidate for PD patients, but also be an option for aged people to improve their neurological performance.

overall_design:
We investigated the role of PF4 in MPTP-induced PD mice. MPTP was injected intraperitoneally for 7 days. PF4 was injected intravenously every 3 days encompassing the whole experiment.
The midbrains of 3 C57BL/6 mice from each group were used for RNA sequencing.

first: Yanan


title: YTHDF1 loss in dendritic cells potentiates radiationinduced antitumor immunity via STING-dependent type I IFN production

city: Chicago

first: chuangyu

last: wen

state: IL

address: 900E 57th Street

department: Department of Radiation and Cellular Oncology

institute: University of Chicago

summary: The RNA N6-methyladenosine (m6A) reader YTHDF1 is implicated in cancer etiology and progression. We discovered that radiotherapy (RT) increased YTHDF1 expression in dendritic cells (DCs) of PBMCs from patients with cancer, but not in other immune cells tested. Elevated YTHDF1 expression in DCs was associated with poor outcomes for patients receiving RT. We found that loss of Ythdf1 in DCs enhanced the antitumor effects of ionizing radiation (IR) by increasing the cross-priming capacity of DCs across multiple murine cancer models. Mechanistically, IR upregulated YTHDF1 expression in DCs through stimulator of IFN genes/type I IFN (STING/IFN-I) signaling. YTHDF1 in turn triggered STING degradation by increasing lysosomal cathepsins, thereby reducing IFN-I production. We created a YTHDF1 deletion/inhibition prototype DC vaccine that significantly improved the therapeutic effect of RT and radioimmunotherapy in a murine melanoma model. Our findings reveal a layer of regulation between YTHDF1/m6A and STING in response to IR, which opens new paths for the development of YTHDF1-targeting therapies.

overall_design: BMDCs from WT and Ythdf1-cKO mice were cocultured with B16-OZ cells for 8 hours. The purified CD11c+ cells were incubated for an additional 2 days. RNA was extracted using an RNeasy Plus Mini Kit (QIAGEN, catalog 74136) and used to generate the complementary DNA library via a SMARTer Stranded Total RNA-Seq kit, version 2 (TaKaRa, catalog 634411). RNA-Seq was performed on an Illumina NovaSeq X platform by the Genomics Facility at The University of Chicago. We aligned reads using STAR and removed alignments with a mapping quality of less than 30. We used DESeq2 for differential gene expression analysis in which a negative binomial general linearized model fitting was used to generate P values, and P values were adjusted using the Benjamini Hochberg method. GSEA version 4.3.2 was used for the rank-based test of enrichment performed using log-fold change values shrunken with the “apeglm” method from DESeq2.

first: Chuangyu

last: Wen

first: Liangliang

first: Katarzyna

last: Zawieracz


title: Resistance to Spindle inhibitors in Glioblastoma Depends on STAT3 and Therapy Induced Senescence

city: New York

first: Athanassios

last: Dovas

state: NY

address: 1130St Nicholas Avenue

institute: Columbia University

summary: While mitotic spindle inhibitors specifically kill proliferating tumor cells without the toxicities of microtubule poisons, resistance has limited their clinical utility.  Treating glioblastomas with the spindle inhibitors ispinesib, alisertib, or volasertib creates a subpopulation of therapy induced senescent cells that resist these drugs by relying upon the anti-apoptotic and metabolic effects of STAT3.  Furthermore, these senescent cells expand the repertoire of resistant cells by secreting an array of factors, including TGFb, which induce proliferating cells to exit mitosis and become quiescent—a state that is also insensitive to spindle inhibitors.  Targeting STAT3 restores sensitivity to each of these drugs by depleting the senescent subpopulation and inducing quiescent cells to enter the mitotic cycle.  We have incorporated our results into a model that explains how STAT3 and therapy induced senescence combine to drive resistance, which can provide insight into how to enhance the efficacy of spindle inhibitors for the treatment of glioblastoma.

overall_design:
We generated mouse glioma cell lines with acquired resistance to Ispinesib, Alisertib or Volasertib in order to explore mechanisms of resistance to this class of spindle inhibitors and identify mechanisms of overcoming it.
We obtained transcriptomic data from three independently-derived cell lines from each drug treatment using RNAseq. We identified key common pathways that are upregulated in the resistant cells using differential gene expression analysis and GSEA.

first: Kenchappa

last: Rajapa

first: Peter

last: Canoll

first: Steven

last: Rosenfeld


title: Single-cell RNA sequencing explores the mechanisms underlying the protective effects of myeloid cell-specific Pkm gene knockout in ALF-modeling mice

city: Changsha

first: Yan

last: Huang

address: Xiangya road

institute: Xiangya hospital

summary: Acute liver failure (ALF) has an extremely high mortality rate and lacks effective treatment. Previous studies have shown that targeting macrophage pyruvate kinase isoenzyme type M2 (PKM2) may be a new approach for ALF treatment, but the exact mechanism remains to be elucidated. In this project, based on Single-cell RNA-sequencing (scRNA-seq), Pkm myeloid selective knockout (PL) mice and wild-type (WT) mice were used to establish ALF model, analyze the single-cell transcriptomic features of liver tissues of WT mice during ALF pathology, and screen for the differentially expressed genes in liver tissues of PL mice. Potential molecular pathways of PKM2 regulation of ALF in macrophages were explored by bioinformatics analysis and validated by molecular biology methods. Result shows that, up-regulated genes in macrophages and neutrophils in mouse liver tissues during ALF were mainly enriched in multiple programmed death, such as pyroptosis, apoptosis and necroptosis, and immune-inflammation pathways. The down-regulated genes in PL mouse liver macrophages and neutrophils were mostly enriched in the above pathways. Among them, Pkm knockdown significantly down-regulated the expression of key genes of NOD-like signaling pathway, such as NLRP3, IL-1β and IL-18, inhibited hepatic macrophage pyroptosis and attenuated ALF. This study will help to elucidate the molecular mechanism of PKM2 regulating macrophage inflammatory response involved in ALF, suggesting that PKM2 may be a potential therapeutic target for ALF, and providing a theoretical basis for further research on new methods of targeting PKM2 in the treatment of ALF.

overall_design: To investigate the function of PKM2 in ALF, we establish ALF model by intraperitoneal injection of D-galactosamine and LPS in Pkm myeloid selective knockout (PL) mice and wild-type (WT) mice. Same volume of PBS was intraperitoneal injected in PL and WT mice to establish negative control (NC) group. Three hours after ALF modeling, mice were sacrificed and hepatic parenchymal and nonparenchymal cells were extracted from liver tissue. After counting, the hepatic parenchymal and non-parenchymal cells were mixed at a ratio of 2:8 and then uploaded for scRNA-seq. We then performed single-cell transcriptomic analysis using data obtained from scRNA-seq of  4 groups.

first: Songman

last: Yu

last: huang


title: NFkB Signaling is Required for Xist RNA Localization at the Inactive X and for X-Chromosome Inactivation Maintenance Following T cell Activation [CUT&Run]

city: Philadelphia

first: Montserrat

middle: C

last: Anguera

address: Rosenthal Building- 3800 Spruce St, Room 304

institute: University of Pennyslvania School of Veterinary Medicine

summary: X Chromosome Inactivation (XCI) is a female-specific process which balances X-linked gene dosage between sexes. Unstimulated T cells lack cytological enrichment of Xist RNA and heterochromatic modifications on the inactive X chromosome (Xi), and these modifications become enriched at the Xi after cell stimulation. Here, we examined allele-specific gene expression and epigenomic profiling of the Xi following T cell stimulation. We found that the Xi in unstimulated T cells is dosage compensated, and is enriched with the repressive H3K27me3 modification, but not H2AK119-ubiquitin (Ub) mark, including at promoters of XCI escape genes. Upon CD3/CD28 mediated T cell stimulation, the Xi accumulates H2AK119-Ub and H3K27me3 across the Xi. Next, we examined the T cell stimulation pathways responsible for Xist RNA localization to the Xi and found that T cell receptor (TCR) engagement, specifically NFkB signaling downstream of TCR, is required. Disruption of NFkB signaling, using inhibitors or genetic deletions, in mice and patients with immunodeficiencies prevents Xist/XIST RNA accumulation at the Xi and alters expression of some X-linked genes. Our findings reveal a novel connection between NFkB signaling pathways which impact XCI maintenance in female T cells.

overall_design: CUT&RUN analysis of Ring1b enrichment from F1 mus x cast CD3+ T cells that were unstimulated or stimulated with anti-CD3/anti-CD28 for 48 hours (n=3 per condition). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.

first: Katherine

last: Forsyth

first: Natalie

last: Toothacre


title: NFkB Signaling is Required for Xist RNA Localization at the Inactive X and for X-Chromosome Inactivation Maintenance Following T cell Activation [RNAseq_geneexpression]

overall_design: RNAseq from F1 mus x cast CD3+ T cells that were unstimulated or stimulated with anti-CD3/anti-CD28 for 48 hours or stimulated with anti-CD3/anti-CD28 for 48 hours in the presence of 2.5uM IMD-0354. (n=3 per condition). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.


title: scRNA-seq of lineage traced mouse aortic smooth muscle cells with cell Hashing

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

overall_design: We performed single-cell RNA-seq analysis with cell hashing of total viable lineage traced aortic smooth muscle cells from reporter mice fed a high fat diet for 3 months

first: Sarah

last: Schäfer

first: Alma

last: Zernecke

first: Antoine-Emmanuel

last: Saliba

first: Clément

last: Cochain


title: NFkB Signaling is Required for Xist RNA Localization at the Inactive X and for X-Chromosome Inactivation Maintenance Following T cell Activation [CUT&RUN]

overall_design: CUT&RUN analysis of H3K27me3 and H2AK119Ub histone modifications from F1 mus x cast CD3+ T cells that were unstimulated or stimulated with anti-CD3/anti-CD28 for 48 hours (n=3 per condition). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.


title: NFkB Signaling is Required for Xist RNA Localization at the Inactive X and for X-Chromosome Inactivation Maintenance Following T cell Activation [RNAseq_ESCAPE_nfkb]

overall_design: RNAseq from F1 mus x cast CD3+ T cells that were stimulated with anti-CD3/anti-CD28 in the presence of 2.5uM IMD-0354 for 48 hours (n=4). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.


title: Gene expression profile at the single cell level of endothelial cells from tumor-draining lymph nodes of the melanoma mouse models

city: Daejeon

first: Jeongwoon

last: Choi

address: 291, Daehak-ro, Yuseong-gu

institute: Institute of basic science

summary: We used single-cell analysis to gain insights into transcriptional changes in endothelial cells in tumor-draining lymph node upon lymph node metastasis.

overall_design: Endothelial cells and other stromal cells in lymph node were sorted by MACS according to absence of CD45, mixed with CD45-positive immune cells, and analyzed using single-cell analysis.

first: Gou

middle: Y

last: Koh


title: Differential transcriptome reprogramming induced by the soybean cyst nematode Type 0 and Type 1.2.5.7 during resistant and susceptible interactions

city: Knoxville

first: Tarek

last: Hewezi

state: TN

address: 2431 Joe Johnson Drive

department: Plant Sciences

institute: University of Tennessee

summary: To investigate the effect of genotype on soybean transcriptomic response to different soybean cyst nematode races

overall_design: Transcriptional profiles of 072 and 137 under Heterodera glycines race 2, 3 and noninfected with three replicates per treatment

first: Hewezi

last: Tarek

first: Hawk

last: Tracy