title: Regulatory T cells converted from T helper 1 cells in tumors suppress cancer immunity via CD39 [scRNA-seq]

city: Zhejiang

first: Sang Nee

last: Tan

address: Hangzhou

department: School of Medicine

institute: Westlake University

summary: Although regulatory T (Treg) cells are widely believed to impede anti-tumor immunity, their regulation and functional mechanisms are not well understood. Here, through characterization of multiple cancer models, we identified substantial periphery-induced Treg cells in the tumor microenvironment (TME), depletion of which provoked anti-tumor responses and conferred potent therapeutic effects by increasing functional CD8+ T cells. Through fate-mapping and transfer experiments, we found IFN-γ-expressing T helper (Th) 1 cells developed into Treg cells in tumors, in response to TGF-β signaling. Pseudotime trajectory further revealed the terminal differentiation of Th1-like Treg cells from Th1 cells in the TME. Hence, tumor-resident Treg cells highly expressed T-bet, which was essential for their function in the TME. CD39, highly expressed by T-bet+ Treg cells in both mouse and human tumors, is required for Treg suppression of CD8+ T cell response. In summary, our study has elucidated a developmental pathway of intra-tumoral Treg cells and implicated new ways of targeting them in cancer patients.

overall_design: We performed single-cell transcriptomics on Treg cells sorted from Hepa1-6 tumors of Foxp3YFP-cre and Foxp3YFP-cre Tbx21fl/fl mice. We sorted Treg cells (CD4+YFP+) from Hepa1-6 tumors of Foxp3YFP-cre and Foxp3YFP-cre Tbx21fl/fl mice. Conventional CD4+ T cells (CD4+YFP-) and Treg cells (CD4+YFP+) sorted from Hepa1-6 tumors and tumor-free LN of Foxp3YFP-cre mice respectively were included for comparison.

first: Sang-Nee

first: Jing

last: Hao

last: Ge

first: Meng

last: Lin

first: Genyu

first: Ni

last: Ling

first: Chen

last: Dong


title: Single-Cell RNA Sequencing unveils dynamic transcriptional profiles during the process of donkey spermatogenesis and maturation

status: Public on Dec 30 2024

city: Qingda

first: yadan

last: Jin

state: 山东Shandong

address: Qingdao

country: China

institute: Qingdao Agricultural University

type: Expression profiling by high throughput sequencing

summary: With the increasing demand for donkey production, there has been a growing focus on the breeding of donkeys. However, our current understanding of the mechanisms underlying spermatogenesis and maturation in donkeys during reproduction remains limited.In this study, we constructed a single-cell RNA dataset to study the single-cell landscape of donkey spermatogenesis and maturation. This method allows us to analyze the cell composition in testicular and epididymal tissue, providing insights into the changes that occur during donkey spermatogenesis and maturation. In addition, different gene expression signatures associated with various spermatogenic cell types were found

overall_design: Testis and epididymis tissues of 3 sexually mature male donkeys were collected for single cell sequencing to explore the mechanism of spermatogenesis and maturation


title: Spatial transcriptomics reveal spatial characteristics of nonalcoholic fatty liver (NAFLD)

city: Beijing

first: Lijuan

last: Zhou

state: State

address: No.5 North Line Pavilion, Xicheng District, Beijing

institute: Guang’anmen Hospital, China Academy of Chinese Medical Sciences

summary: To fully parse the spatial characteristics of NAFLD liver, we combined spatial transcriptomics (ST), which allowed us to characterize spatial position information within the tissue

overall_design: Following hepatic perfusion, mouse liver tissues were collected for ST.

first: Jingyi

last: Zhao

first: Kaile

last: Ma

first: Min

last: Li

first: Xiaolin

last: Tong


title: Gene expression profile of non-alcoholic fatty liver (NAFLD) liver at the single-cell level

summary: To fully parse the cellular and molecular characteristics of NAFLD liver, we combined single-cell RNA sequencing (scRNA-Seq), which allowed us to characterize the transcriptome of individual cells and reveal cell subpopulations within the tissue

overall_design: Following hepatic perfusion, mouse liver tissues were collected for scRNA-seq analysis.


title: Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [CUT&RUN]

city: Bethesda

first: Sakshi

last: Chauhan

state: Maryland

address: Building 6A, Room 2A11,6 Center Drive

country: USA

institute: NICHD

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Variant histone H3.3 is thought to be critical for survival of many cells, since it is deposited in expressed genes, a feature different from core histones. For example, H3.3 deletion leads to embryonic lethality in mice.  However, requirement of H3.3 in later stage of development has remained unclear.  The aim of this work was to elucidate the role of H3.3 for development of myeloid lineage, important for innate immunity.  We conditionally knocked out (cKO) the H3.3 genes in myeloid progenitor cells differentiating into bone marrow derived macrophages (BMDMs). Progenitor cells lacking H3.3 were defective in replication, suffered from extensive DNA damage, and underwent apoptosis.  Surviving H3.3cKO cells expressed many interferon stimulated genes (ISGs) throughout differentiation.  Further, H3.3cKO BMDMs possessed chromatin accessible sites, and histone posttranslational modifications consistent with the gene expression profiles, Accordingly, H3.3cKO BMDMs retained general  nucleosomal structure genome wide.  In summary, H3.3 is required for proliferation of myeloid progenitor cells, but is in large part dispensable for differentiation of BMDMs.

overall_design:
CUT & RUN seq for histone variant H3.3 in H3f3b-HA tagged BMDM using HA antibody.
CUT & RUN seq for histone post translational modification H3K27ac in WT and H3.3 cKO BMDMs.
CUT & RUN seq for histone post translational modification H3K36me3 in WT and H3.3 cKO BMDMs.


title: Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [RNA-seq]

overall_design:
RNA seq of WT and H3.3 cKO cells on day3, 5 and day7 of M-CSF induced differentiation.
RNA seq of WT and H3.3 cKO BMDM on day8 of M-CSF induced differentiation under untreated and IFNγ treated (12 hrs) conditions
RNA seq of WT and H3.3 cKO  peritoneal macrophages.
RNA seq of WT and cKO BMDMs under no antibody, control antibody and IFNAR1 antibody conditions.
RNA seq of WT, H3.3cKO and H3.3cKO:Sting KO BMDMs.
RNA seq of WT, H3.3cKO and H3.3cKO:Mavs KO BMDMs.
RNA seq of WT, H3.3cKO and H3.3cKO:Irf7 KO BMDMs.


title: Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [ATAC-seq]

overall_design: ATAC seq with WT and H3.3 cKO BMDMs.


title: Metabolic reprogramming driven by TFE3 fusions unveils novel vulnerabilities in translocation renal cell carcinoma [ChIP-Seq]

city: Boston

first: Dipanjan

last: Chowdhury

state: MA

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

summary: Translocation renal cell carcinoma (tRCC) is an aggressive subtype of kidney cancer driven by TFE3 gene fusions, which act via poorly characterized downstream mechanisms. Here we report that TFE3 fusions transcriptionally rewire tRCCs toward oxidative phosphorylation (OXPHOS), contrasting with the highly glycolytic metabolism of most other RCCs. The transcriptional program driven by TFE3 fusions sustains high NRF2 signaling and glutathione production, which offsets reactive oxygen species generated by OXPHOS but renders tRCC cells sensitive to reductive stress. Genome-scale CRISPR screening identifies tRCC-selective vulnerabilities linked to maintaining this metabolic balance, including EGLN1, which hydroxylates HIF-1α and targets it for proteolysis. Inhibition of EGLN1compromises tRCC cell growth by stabilizing HIF-1a and promoting glycolytic reprogramming. Our study defines a distinctive tRCC-essential metabolic program driven by TFE3 fusions and nominates EGLN1inhibition as a therapeutic strategy to counteract fusion-induced metabolic rewiring.

overall_design: To investigate the epigenomics in tRCC, we performed H3K27ac ChIP-Seq in tRCC. And to investigate the role of TFE3 fusion in tRCC, we performed TFE3 ChIP-Seq in three tRCC cell lines.

first: Jiao

first: Srinivas

middle: R

last: Viswanathan


title: Temperature dependent sex determination in the turtle Trachemys scripta

city: Berlin

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary: Sex determination is the process by which and original bipotential gonad differentiate into either a testis or ovaries. While mammals and birds determine their sex solely by genetic clues (genetic sex determination, GSD), other vertebrates like the turtle Trachemys scripta are influenced by environmental factors, like temperature (environmental sex determination, ESD). In both cases an initially bipotential gonad develops into either testes or ovaries in response to GSD or ESD cues. In order to shed light into the differences and similarities between sex determination systems we performed single-cell RNA-seq on Trachemys scripta developing gonads during the sex determination window.

overall_design: We performed 10x single-cell RNA seq experiments on dissected Trachemys scripta gonads of three different developmental stages: 15 , 18 and 23. They come from embryos incubated either at male or female producing temperatures (FPT - 32ºC, MPT - 26ºC).

middle: D

first: Boris

last: Tezak

first: Wai

middle: Y

last: Chung

first: Ceri

last: Webber

first: Irene

last: Mota

first: Alicia

last: Hurtado

first: Blanche

last: Capel

first: Darío

middle: G

last: Lupiáñez


title: Identification of puberty related miRNAs in the hypothalamus of female mice

city: Nicosia

first: Leonidas

middle: A

last: Phylactou

state: Not US or Canada

address: 6 Iroon Avenue, Ayios Dometios

department: Molecular Genetics, Function & Therapy Department

country: Cyprus

institute: The Cyprus Institute of Neurology and Genetics

summary: Puberty is the crucial developmental stage of transition from childhood to adulthood, organized by complex hormonal signaling within the neuroendocrine system with the hypothalamus regulating functions through the hypothalamic-pituitary-gonadal axis. Genetic predisposition and environmental factors influence the pubertal timing, while miRNAs appear as potential regulators by either repressing genes or activating them by inhibiting their repressors. We investigated miRNA’s involvement in puberty control, by comparing the total population of miRNAs in the hypothalamus of female mice before, during and after puberty, through RNA sequencing. Our results present up- or down-regulation of expression on several miRNAs from pre-pubertal to pubertal stage. Monitoring these levels post-pubertally revealed four expression patterns, in which pathway analysis displayed associations with developmental processes, cell cycle regulation, metabolic biosynthesis and epigenetic regulation. These findings improve our understanding of the molecular pathways underlying puberty and stress the significance of miRNAs in fine-tuning gene expression within the hypothalamus.

overall_design: RNA-seq of the whole miRNAs population in the hypothalamus of female C57BL/6 mice at three age groups, before puberty (postnatal day 14), during puberty (postnatal day 35) and after puberty (postnatal day 56).

first: Pavlos

last: Fanis

first: Maria

last: Morrou

first: Marios

last: Tomazou

first: Hend

last: Alghol

first: George

middle: M

last: Spyrou

first: Vassos

last: Neocleous


title: Drug Repurposing: Therapeutic Role of Aripiprazole  in the Cartilage Defect

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

country: South Korea

institute: CHA university

summary: Owing to the limited regenerative capacity of articular cartilage, damaged cartilage does not spontaneously heal over time. Various scientific efforts have been made to improve damaged articular cartilage. Nevertheless, no single approach has achieved a promising outcome for the damaged cartilage. Meanwhile, owing to the increasing cost of drug development, drug repositioning has been actively attempted. We aimed to identify the drug that can improve the cartilage defect, using chondrogenesis related microarray data recruited from the Gene Expression Omnibus (GEO) public database. Furthermore, we attempted to experiment using cellular and animal models to verify the cartilage regeneration potential for the identified drug. To screen for drugs that promote cartilage restoring,  chondrogenesis related microarray data were collected from the GEO public database. The GSE69110, GSE107649, GSE111822, and GSE116173 datasets from the GEO were used to identify cartilage differentiation-related genes. Differentially expressed genes were identified using StringTie, and drug data were extracted from the Drug-Gene Interaction database. The effect of aripiprazole on cartilage was evaluated in aripiprazole-treated adipose-derived mesenchymal stem cells (ADMSCs) and chondrocyte using qRT-PCR and 3D pellet culture. The cartilage restoring efficacy was verified in vivo by mixing it with a scaffold and introducing it into the artificially damaged cartilage of Sprague-Dawley rats. Next, mRNA was sequenced for mechanistic analysis. As a result, aripiprazole significantly increased the mRNA expression of COL2A1 and SOX9, two cartilage differentiation-related genes, and chondrogenic condensation in vitro. Moreover, it effectively promoted cartilage regeneration in the cartilage defect rat model. Analysis of mRNA sequencing data from chondrocyte treated with aripiprazole, using KEGG and GOBP, indicated that aripiprazole significantly upregulates genes associated with ribosomes and cytoplasmic translation, thus promoting chondrogenesis. In conclusion, we discovered that aripiprazole can effectively improve damaged cartilage, providing a promising approach for cartilage regeneration.

overall_design: Quantification of changes in mRNA expression by treating ADMSC with Aripiprazole


title: The ChAHP chromatin remodelling complex regulates neurodevelopmental disorder risk genes to scale the production of neocortical layers

city: Ottawa

first: José Alex

last: Lourenço Fernandes

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

summary: Although chromatin remodellers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), the roles of these complexes during brain development are in many cases unclear. Here, we focused on the recently discovered ChAHP chromatin remodelling complex. The zinc finger and homeodomain transcription factor ADNP is a core subunit of this complex, andde novo ADNPmutations lead to intellectual disability and autism spectrum disorder. However, germlineAdnpknockout mice were previously shown to exhibit early embryonic lethality, obscuring subsequent roles for the ChAHP complex in neurogenesis. Here, we employed single cell transcriptomics, cut&run-seq, and histological approaches to characterize mice conditionally ablated for the ChAHP subunitsAdnpandChd4. We show that during neocortical development, Adnp and Chd4 orchestrate the production of late-born, upper-layer neurons through a two-step process. First, Adnp is required to sustain progenitor proliferation specifically during the developmental window for upper-layer cortical neurogenesis. Accordingly, we found that Adnp recruits Chd4 to genes associated with progenitor proliferation. Second, in postmitotic differentiated neurons, we define a network of risk genes linked to NDDs that are regulated by Adnp and Chd4. Taken together, these data demonstrate that ChAHP is critical for driving the expansion upper-layer cortical neurons, and for regulating neuronal gene expression programs, suggesting that these processes may potentially contribute to NDD etiology.

overall_design: Embryos were harvested and the dorsal telencephalon was microdissected.

first: Pierre

last: Mattar


title: Vascular damage and axcessive proliferation compromise liver function after extended hepatectomy in mice

city: Brussels

first: Isabelle

last: Leclercq

address: Avenue E. Mounier

country: Belgium

institute: UCLouvain

summary: Surgical resection remains the gold standard for liver tumor treatment, yet the emergence of post-operative liver failure, known as the small for size syndrome (SFSS), poses a significant challenge. The activation of hypoxia sensors in a SFSS liver remnant initiated early angiogenesis, improving vascular architecture, safeguarding against liver failure and reducing mortality. The study aimed to elucidate vascular remodeling mechanisms in SFSS, its impact on hepatocyte function and subsequent liver failure. Mice underwent extended partial hepatectomy to induce SFSS, with a subset  exposed to hypoxia immediately after surgery. Hypoxia bolstered post-hepatectomy survival rates. Early proliferation of liver sinusoidal cells coupled with recruitment of putative endothelial progenitor cells (EPC) via the VEGF/SDF-1α pathway, increased vascular density, improved lobular perfusion, and limited hemorrhagic events in the regenerating liver under hypoxia. Administration of G-CSF in hepatectomized mice mimicked the effects of hypoxia on vascular remodeling and EPC recruitment, but failed to rescue survival. Compared to normoxia, hypoxia favored hepatocyte function over proliferation, , promoting functional preservation in the regenerating remnant. Injection of AAV8-TBG-HNF4α virus for hepatocyte-specific overexpression of HNF4α, the master regulator of hepatocyte function, enforced functionality in proliferating hepatocytes but did not rescue survival. Only the combination of HNF4α overexpression and G-CSF treatment rescued survival afterSFSS-setting hepatectomy. In summary, SFSS arises from an imbalance and desynchronized interplay between functional regeneration and vascular restructuring. To enhance survival following SFSS-hepatectomy, a two-pronged strategy is essential, addressing the preservation of function in the proliferating parenchymal cells alongside the simultaneous mitigation of vascular harm.

overall_design: RNA-seq experiment was performed to compare the gene expression level in 4 different conditions: PHx70% (n=3), PHx80% (n=3), PHx80%-HC (n=3), G-CSF+HNF4a-PHx80% (n=3).

first: Maxime

last: De Rudder

first: Rita

last: Manco

first: Laurent

last: Coubeau

first: Alix

last: Fontaine

first: Claude

last: Bertrand

first: Alexandra

last: Dili


title: Asymmetric crosstalk between the BMP and TGFb pathways resolves signaling ambiguity

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: The BMP and TGFβ signaling pathways control cellular fate decisions in diverse biological contexts, often playing opposing roles. Despite extensive knowledge of these pathways, understanding how cells respond to environments containing these opposing cues remains a challenge. Here, we systematically analyze the activation of BMP and TGFβ pathways under combinatorial signaling environments. We find that TGFβ ligands inhibit BMP signaling, while BMP ligands enhance TGFβ transcriptional response, across concentrations, ligand variants, and cell types. This asymmetric crosstalk results in the activation of a single specific transcriptional response, even under mixed signaling conditions, effectively reducing signal ambiguity. Furthermore, we show that this crosstalk originates downstream of the SMAD proteins phosphorylation. Using mathematical models we predict, and experimentally verify, that promiscuous interactions between SMAD proteins provide the mechanism for the observed crosstalk. Our findings challenge the canonical models of signaling pathways, suggesting an active role for mediator proteins in determining biological responses.

overall_design:
To examine the activation of the BMP and TGFb pathways under complex signaling environment we established an NMuMG dual reporter cell line. Cells contained transcriptional reporters for BMP (Smad1/5/8 response element) controlling the expression of mCherry and TGFb (Smad2/3 response element) controlling the expression of mCitrine.
We then examined the gene expression profile of the dual reporter cells using bulk RNA-sequencing in cells cultured under four ligand conditions.

first: Johannes

last: Auth

first: Inbal

last: Eizenberg-Magar

first: Omer

last: Erez

first: Meytar

last: A Berrebi

first: Ariel

last: Tennenhouse

first: Yaron

middle: E

last: Antebi


title: Effect of graded normobaric hypoxia on Genome-wide expression in healthy individuals

city: Delhi

first: Bhavana

last: Prasher

state: Delhi

address: Sukhdev Vihar

department: Genomics and Molecular Medicine

country: India

institute: CSIR-IGIB

summary: The regulation of oxygen homeostasis is critical in physiology and disease pathogenesis. Studying transcriptomic profiles after hypoxia exposure could potentially uncover valuable biomarkers for predicting responses. To this end, 6 healthy individuals were recruited and exposed to graded normobaric hypoxia (FiO2 ~ 0.19 up till 0.13 in steps of 2% decrement in 10 minutes). A blood sample was collected before (at room air) and after the graded normobaric hypoxia exposure (at FiO2 ~ 0.13)  for the gene-expression profiles. Results provide important information about early molecular differences induced by our experimental protocol in young, healthy individuals.

overall_design: Peripheral Blood samples were obtained from healthy individuals. RNA was extracted. Labeled cRNA was hybridized to Illumina Human HT-12 V4 Beadchips.

first: Ritu

last: Rani

first: Rintu

last: Kutum

first: Vishal

last: Bansal


title: Improvement of liver cirrhosis using hepatocyte-derived liver progenitor-like cells (HepLPCs): a prospective, open label, single arm, safety trial

city: Shanghai

first: hexin

last: Yan

address: Pujian Road

institute: Shanghai Reji Hospital

summary: The escalating demand for liver transplantation, coupled with the scarcity of donor organs and inherent transplantation risks, underscores the urgent need for innovative cirrhosis treatments. To address this, we have developed a protocol for transforming human primary hepatocytes into expandable Hepatocyte-Derived Liver Progenitor-Like Cells (HepLPCs). In animal models, these cells exhibited anti-fibrotic properties and facilitated liver regeneration. This study comprises a pre-clinical phase and an inaugural clinical trial involving nine cirrhosis patients to assess the feasibility and safety of HepLPC treatment. The HepLPCs infusion was well-tolerated, devoid of transfusion reactions or dose-limiting toxicities. Primary outcome measures, encompassing safety and feasibility, were successfully met. Notably, the results revealed enhanced liver function following HepLPCs infusion, indicating significant improvements in cirrhosis indicators over a 6-month observation period. These promising findings advocate for the therapeutic potential of HepLPCs as an innovative strategy for liver cirrhosis, warranting further exploration through clinical trials, particularly in decompensated cirrhosis and acute-on-chronic liver failure patients.

overall_design: global expression analysis of RNA sequencing data of expression levels of human hepatocytes and expandable hepatocytes derived liver progenitor-like cells state (designated as HepLPCs)

first: Wei-jian

last: Huang

first: He-xin


title: Microglial APOE3 Christchurch protects neurons from Tau pathology in a human iPSC-based model of Alzheimer's disease

city: Monrovia

first: Xiwei

last: Wu

state: CA

address: 655 HUNTINGTON DR.

institute: City of Hope

summary: We generated microglia-like cells (MG) from iPSCs and fibroblast-direct reprogrammed neurons (DRNs), which preserves the aging signatures. We performed RNA seq analysis on microglia which cocultured with either old DRNs or young DRNs. By studying the microglia cocultured with DRNs, we identified CX3CL1 as the critical communication factor that is defective in the DRNs derived from old and Alzheimer’s disease (AD) fibroblasts in comparison to from the young fibroblasts. Microglia displayed weakened phagocytosis activity when cocultured with old DRNs, comparing to young DRNs. The myosin-binding protein Lymphocyte-specific factor 1 (LSP1) could be a potential target of CX3CL1. The reduction of phagocytosis in old DRN MG coculture could be due to lack of LSP1 in microglia. Furthermore, supplementing the old or AD DRN-microglia coculture system with CX3CL1 ameliorated the phagocytosis defect.

overall_design: Examination of RNA seq profiling of microglia which have been cocultured with the neurons directly reprogrammed from old fibroblasts and from young fibroblasts.

first: Yahong

last: Shi

first: Guoqiang

last: Sun


title: Transcriptome RNA sequencing data of sarcomatoid renal cell carcinoma cell line SRCC and its subclones with different phenotypes.

city: shanghai

first: ren

last: xiangyu

address: 盘山路8号

institute: naval medical university

summary: Two subsets of early genetic mutations closely related to the malignant behavior of renal sarcomatoid carcinoma were identified by exon sequencing, transcriptome sequencing, protein profiling and clonal evolution of self-established renal sarcomatoid carcinoma cell lines and subclones of different secretion states

first: Xiaojie

last: Tan

first: Yan

last: Liu

first: Jianguo

last: Hou

first: Yongwei

last: Yu

first: Guangwen

last: Cao


title: Genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA as noninvasive diagnostic markers for gastric cancer

city: Changchun

first: Jing

last: Jiang

state: Jilin

address: No.1 Xinmin Street

department: Division of Clinical Epidemiology

institute: First Hospital of Jilin University

summary: Background: Gastric cancer (GC) remains the third leading cause of cancer death worldwide due to the absence of sensitive and specific biomarkers for its early detection. 5-hydroxymethylcytosine (5hmC)-enriched gene profiles and regions show tissue-specific and tumor specific, and cell-free DNA (cfDNA) 5hmC modification feature sequencing provides a robust tool for gastric cancer detection.Methods: A matched case‒control study design with 50 gastric cancer patients and 50 controls was performed to sequence the 5hmC modification of cfDNA. Significantly differential 5hmC modification genes were identified to construct a gastric cancer diagnostic model. The data set from Gene Expression Omnibus consisted of 61 gastric cancer patients, 90 healthy individuals and 22 benign gastric disease controls was used as an external testing set to test the robustness of the diagnostic model. Results: The vast majority of 5hmC peaks were distributed in the gene body, accounting for more than 90% of the total 5hmC peaks in both the GC and control groups. The diagnostic model was developed based on five different 5hmC modification genes, FBXL7, PDE3A, TPO, SNTG2 and SXBP5. The model could clearly distinguish gastric cancer patients from controls in the training (AUC=0.95, sensitivity=88.6%, specificity=94.3%), validation (AUC=0.87, sensitivity=73.3%, specificity=93.3%) and testing (AUC=0.90, sensitivity=81.9%, specificity=90.2%) sets. The predicted risk scores of the controls were significantly lower than those of GC patients in our own data (P<0.001) or GEO external testing data (P<0.001), but no significant difference was observed between different TNM stage groups (P=0.09 and 0.66). Furthermore, the risk scores of healthy and benign gastric disease controls in the testing set were also not different (P=0.10). Conclusions: The characteristics of 5hmC in cfDNA are specific to GC patients, and the diagnostic model constructed by the 5hmC features of five genes could effectively identify GC patients.

first: Yingli

last: Fu

first: Donghui

first: Yanhua

first: Zhifang

last: Jia

first: Yangyu

last: Zhang

first: Dongming

last: Li

first: Yingnan

last: Cui

first: Yuzheng

first: Xueyuan


title: Beneficial rhizobacteria and virus infection modulate the feeding preferences of the virus vector Epilachna varivestis by modifying key metabolic pathways

city: Zurich

first: Hannier

last: Pulido

state: Switzerland

address: Schmelzbergstrasse, 9 / LFO

department: D-USYS

country: Switzerland

institute: ETHZ

summary: There is growing evidence that microbial plant symbionts shape interactions between plants and other organisms by modulating gene expression and metabolism. However, the detailed mechanisms mediating such effects are not well understood, particularly in systems where plants interact simultaneously with multiple symbionts and antagonists. In this study, we employed a multi-factorial design to explore the individual and combined effects of two plant-beneficial rhizobacteria (Delftia acidovorans and Bradyrhizobium japonicum) and a pathogen (Bean pod mottle virus: BPMV) on gene expression and metabolite production by soybean plants, as well as downstream effects on plant interactions with a beetle vector of BPMV Epilachna varivestis. Our results document microbial effects on basic metabolism and defense pathways, resulting in increased levels of primary metabolites and depletion of secondary metabolites. These changes are consistent with the observed feeding preferences of beetles for rhizobia- inoculated and virus-infected plants, potentially increasing the likelihood to disperse the virus to uninfected plants. Together, our results indicate that BPMV infection and rhizobacteria colonization cause dramatic changes in plant metabolites related to nutrition and defense, with significant consequences for an agriculturally important pathosystem.

overall_design: We used a multi-factorial design including single, dual, and triple colonization by the PGPR Delftia acidovorans, the nitrogen-fixing root symbiont Bradyrhizobium japonicum, and the virus pathogen BPMV.

first: Kerry

last: Mauck

first: Consuelo

last: De Moraes

first: Mark

last: Mescher


title: DNA methylation signature for detection of early-stage hepatocellular carcinoma

city: Seoul

first: Dawon

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

institute: Yonsei University

type: Methylation profiling by genome tiling array

summary:
A total of 180 Hepatocellular carcinoma (HCC) and 125 adjacent normal samples were examined. Genome-wide DNA methylation profiling was done with Illumina HumanMethylation850 Beadchip of approximately 850,000 CpG sites.
Aims: To identify HCC-specific methylation based biomarkers which are suitable for liquid biopsy.

overall_design: Total of 305 samples from HCC resected patients were analyzed for DNA methylation microarray with Illumina HumanMethylation850 Beadchip.

first: Da

middle: W


title: lncRNA profiling in lungs of Th17-mediated neutrophil-predominant asthma mice vs Th2-mediated eosinophil-predominant asthma mice and control mice

city: Changsha

first: Xudong

last: Xiang

address: NO.139 Middle Renmin Road

institute: Central South University

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

summary: Recently, epigenetic regulation was shown to play an important role in asthma development. In particular, lncRNA, as one of the important epigenetic modifications, has been proved to be related to the pathogenesis of asthma. However, little is known about the lncRNA expression in Th17-mediated neutrophil-predominant asthma. To investigate the potential functions of lncRNA that affect the pathogenesis of Th17-mediated neutrophil-predominant asthma, a Agilent Mouse lncRNA （4*180K，Design ID：049801）Array was used to detect the lncRNA and mRNA profiles of lungs from Th17-mediated neutrophil-predominant asthma mice.

overall_design: Three samples are analyzed, lungs of Th17-mediated neutrophil-predominant asthma mice vs Th2-mediated eosinophil-predominant asthma mice and control mice

first: Wenjin

last: Sun


title: Discovery and application of postnatal nucleus pulposus progenitors essential for intervertebral disc homeostasis and degeneration.

city: 市辖区

first: zaiqi

last: xie

state: 徐汇区

address: 上海市徐汇区岳阳路320号

institute: chinese academy of science

summary: Intervertebral disc degeneration (IDD) results from dysfunction of nucleus pulposus cells (NPs) and exhaustion of NP progenitors (ProNPs). Cellular applications of NPs during IDD are currently limited by lack of in vivo studies showing whether NPs are heterogenous and contain ProNPs throughout postnatal stages. Here, using single-cell RNA sequencing of purified NPs, we mapped four molecularly defined populations and identified Urotensin II receptor (UTS2R)-expressing postnatal ProNPs, which markedly exhausted during IDD, in mouse and human specimens. Lineage tracing showed that UTS2R+ ProNPs preferentially reside in the NP periphery with its niche factor-Tenascin-C and give rise to functional NPs. We also demonstrate that transplanting UTS2R+ ProNPs with Tenascin-C to injured intervertebral discs attenuates the progression of IDD. Our findings provide a novel NP cell atlas, identify resident ProNPs with regenerative potential and reveal promising diagnostic and therapeutic targets for IDD.

overall_design: To produce a cell atlas of purified NPs along with their representative cellular functions, Shh-Cre;Ai9+ single NP cells were harvested from 1-month-old Shh-Cre;Ai9 mice and analyzed with a BD Rhapsody Single-Cell RNA Sequencing platform.

first: Bo

last: Gao

first: wenhui

last: Xing


title: MUTE overexpression in mature Kalanchoë laxiflora leaves

status: Public on Dec 29 2024

city: BERN

first: Michael

middle: T

last: Raissig

address: Altenbergrain 21

department: Institute of Plant Sciences

institute: University of Bern

summary: Overexpression of KlaxMUTE1 induced asymmetric, subsidiary-cell-like divisions. To determine the downstream target genes induced, an RNA-sequencing experiment of mature wild-type and mature leaves that overexpress KlaxMUTE1 and show many ectopic asymmetric cell divisions was performed.

overall_design: mature leaf tissue of wild-type and KlaxMUTE1 overexpression lines; 4 and 3 biological replicates, respectively

first: Heike

last: Lindner

first: Xin

last: Cheng


title: Single cell RNA-Seq result of  spinal cord of AR-97Q mice and AR-24Q mice at 6 weeks

city: Nagoya city

first: Madoka

last: Iida

address: Tsurumai 65

country: Japan

institute: Nagoya University

summary: To understand the early pathogenesis of SBMA and to systematically assess the role of different cells in the spinal cord of SBMA, we conducted snRNA-seq on the spinal cord of AR-97Q and AR-24Q mice at 6 weeks. The genes related to ion channel and synapse function were up-regulated in oligodendrocytes of AR-97Q mice.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) was conducted on spinal cord samples from AR-97Q and AR-24Q mice at pre-onset stage (6 weeks of age). Spinal cords from 4 mice per a sample were pooled for homogenization and nuclear isolation.

first: Tomohiro

last: Akashi

first: Kunihiko

last: Hinohara

first: Masahisa

last: Katsuno


title: Reseveratrol and Rosiglitazone regulation of epididymal tissue gene expression in ZDF rats

status: Public on Dec 31 2024

city: Guelph

first: David

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

summary: The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and peripheral blood mononuclear cells.

overall_design: A total of 5 microarrays were run for each group, for a total of n=20 samples. For each sample, 100 ng of total RNA was prepared for hybridization to Affymetrix Rat Gene 2.1 ST array strips, according to the manufacturer’s instructions (Affymetrix Inc., Fremont, CA, USA).

first: Monica

middle: H

last: Wong

first: Brittany

last: MacIntyre


title: DNA methylation profiling in lungs of Th17-mediated neutrophil-predominant asthma mice vs control mice

summary: Recently, epigenetic regulation was shown to play an important role in asthma development. In particular, DNA methylation, as one of the important epigenetic modifications, has been proved to be related to the pathogenesis of asthma. However, little is known about the DNA methylation status in Th17-mediated neutrophil-predominant asthma. To investigate the potential functions of DNA methylation that affect the pathogenesis of Th17-mediated neutrophil-predominant asthma, a methylated DNA immunoprecipitation (MeDIP) chip was used to detect the whole genome single-base DNA methylation profiles of lungs from Th17-mediated neutrophil-predominant asthma mice.

overall_design: Two samples are analyzed, lungs of Th17-mediated neutrophil-predominant asthma mice vs control mice


title: Diabetic hyperglycemia-induced glycation regulates tumor vasculature integrity via NF-κB-mediated GM-CSF secretion by tumor cells

status: Public on Dec 28 2024

city: Houston

first: Cynthia

last: Reinhart-King

state: TX

address: 6100 Main Street

department: Biomedical Engineering

institute: Rice University

summary: To identify the mechanism by which tumor cell secretions in response to glycation result in impaired endothelial barrier function, we conducted bulk RNA sequencing on control, diabetic, and diabetic tumors treated with ALT711.

overall_design: FVB/N-Tg(MMTV-PyVT)634Mul/J (MMTV- PyMT) female mice were utilized in this study. All mice were maintained following a protocol approved by the Vanderbilt University Institutional Animal Care and Use Committee (Protocol # M1700029-01). Female MMTV-PyMT mice of the FVB strain background (Jackson Laboratory, Bar Harbor, ME, USA) were fed with D12492 high-fat diet (NC0004611, research diet Inc, New Brunswck, NJ, USA) starting at 4 weeks of age. To induce diabetes, mice were given 5 consecutive daily doses of streptozotocin (STZ, MilliporeSigma) through intraperitoneal injection at 70 mg/kg body weight as described previously15. The control group of mice were injected with citrate buffer (0.1 mmol/L, pH 4.5; MilliporeSigma) as vehicle control. For STZ-injected mice receiving aminoguanidine, mice were treated with 3 mg/kg body weight aminoguanidine (MilliporeSigma) in drinking water until the study endpoint. For STZ-injected mice receiving alagebrium (ALT711) treatment, mice were treated with 1 mg/kg body weight alagebrium (MedChemExpress, Monmouth Junction, NJ, USA) injected daily intraperitoneally until study endpoint. Seven weeks after STZ injection, the mice were humanely sacrificed by CO2 asphyxiation and necropsied.

first: Wenjun

last: Wang

first: Paul

last: Taufalele


title: Integrated Profiling of Extracellular Vesicles microRNA Impact on Trabecular Meshwork mRNA Expression: Insights from Microarray Analysis

city: Beer-Sheva

first: Isana

last: Veksler-Lublinsky

address: P.O.B. 653 Beer-Sheva

institute: Ben-Gurion university of the Negev

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

summary:
Oxidative stress in non-pigmented ciliary epithelial cells leads to secretion of extracellular vesicles containing microRNAs that alter gene expression in trabecular meshwork cells. This study identified differentially expressed miRNAs and genes, revealing potential mechanisms in primary open-angle glaucoma progression and suggesting new therapeutic targets.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

platform_organism:
Homo sapiens
synthetic construct

overall_design: We exposed NPCE cells to oxidative stress and isolated extracellular vesicles (EVs) from both control and stressed cells. HTM cells were then treated with these EVs, and microarray analysis was conducted to identify differentially expressed microRNAs in the EVs and mRNAs in the HTM cells. Subsequent bioinformatics analysis explored miRNA-mRNA interactions and identified enriched Gene Ontology (GO) terms. This approach revealed 54 differentially expressed miRNAs in stressed NPCE-EVs, with 88 genes upregulated and 58 downregulated in treated HTM cells, highlighting pathways implicated in POAG progression, including extracellular matrix organization and cell adhesion

first: Elie

last: Beit-Yannai


title: Drosophila non-gonadal PIWI protein Aubergine regulates regenerative stem cell proliferation and tumourigenesis in the adult intestine [RNA-seq]

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

summary: Somatic stem cells are executors of physiological and pathological proliferation of adult self-renewing tissues, such as the intestine. The actions of intestinal stem cells (ISCs) rely on the integration of cell intrinsic and niche-derived signals, which are necessary to achieve a balanced response to the multiple stimuli that constantly challenge tissue homeostasis and organismal health. Disruption of such balance is causative of age-associated tissue dysfunction and hyperproliferative conditions, including inflammation and cancer.  The highly conserved PIWI-interacting RNAs (piRNAs) biosynthesis pathway, also known as the PIWI pathway, has been classically studied in the Drosophila germline for its role in the repression of transposable elements (TEs) and the regulation of germline stem cell homeostasis. Recent reports have emerged on a role of Piwi, the founding member of the pathway, in the maintenance of ISC homeostasis in the adult Drosophila midgut. The implications of these findings regarding a general role of the PIWI pathway and piRNAs in the intestine remain to be addressed. Here, we characterise a cell autonomous role of the PIWI family protein Aubergine (Aub) in ISCs. We show that, while dispensable for homeostatic self-renewal of the midgut, inducible Aub is essential to regulate ISC proliferation following acute damage of the intestinal epithelium and in oncogenic settings. Our work suggests that the role of Aub in ISCs is independent of its piRNAs regulatory function. Instead, Aub drives ISC proliferation through the induction of regenerative stem cell factors Myc and Sox21a, and through the initiation of protein translation by the eukaryotic initiation factor 3 complex (eIF3). In summary, our results discover a role of Aub in damage induced proliferation of the adult Drosophila intestine involving the regulation of major regenerative signalling pathways and the protein translation machinery. Furthermore, we present genetically distinct hyperplastic settings fostering a role of Aub as an intestinal tumour promoter or suppressor.

overall_design: The study aims at understanding the role of the PIWI family protein Aubergine in the proliferation of intestinal stem cells (ISCs) upon damage in Drosophila melanogaster. We generated oxidised small RNA sequencing libraries from freshly dissected midguts, sorted ISCs/Enteroblasts (marked by escargot-Gal4) and ovaries. We also generated RNA sequencing libraries from poly-A plus RNA to determine the abundance of transposon mRNAs expressed in the ISCs/Enteroblasts.

first: Karen

last: Bellec


title: RNA-seq of resting and stimulated CD4+ and CD8+ T cells from wt and Raptor-deleted mice

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: To explore RNA expression in resting and activated T cells total RNA without rRNA depletion was analyzed.

overall_design: Magnetically sorted CD4+ and CD8+ T cells from wt and Raptor-deleted mice were incubated with IL-7 (unstimulated) or plate-bound CD3 and CD28 mAbs. Live cells were sorted as FVD780- and MFG-E8-negative for flow cytometry.

first: R

last: Obst

first: S

last: Pennavaria

first: T


title: Drosophila non-gonadal PIWI protein Aubergine regulates regenerative stem cell proliferation and tumourigenesis in the adult intestine [ncRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing


title: High-throughput sequencing analysis of placental tissue from pregnant women with gestational diabetes and gestational hypertension

city: Jining

first: Chunyu

last: bai

address: NO133，Hehua Road

institute: Jining Medical University

summary: In this study, transcriptome sequencing was conducted on placentas obtained from both normal pregnancies and pregnancies with GDM to investigate the molecular mechanisms underlying this condition. Placental tissue samples were immersed in ice-cold phosphate-buffered saline (PBS) to remove blood contamination. Sections with a thickness of 4 µm were cut from the block and stained with Hematoxylin and eosin (HE) staining. The resulting slides were examined and photographed under a light microscope (Olympus).The original sequencing data were subjected to sequencing analysis, resulting in the identification of 935 upregulated genes and 256 downregulated genes. The Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analysis techniques on differential genes uncovered evidence suggesting that the phosphoinositide 3-kinase (PI3K) /Akt signaling pathway may contribute to the pathogenesis of GDM. Subsequent analysis indicated that the expression levels of MMP11, MMP12, MMP14, and MMP15, which are regulated by the PI3K/Akt pathway, were upregulated in the placentas of patients with GDM when compared to those of individuals with normal placental function. Additionally, our investigation into alternative splicing patterns revealed an increase in exon skipping alternative splicing of CSF3R in the placenta of patients with GDM compared to that in the control group.

overall_design: Placental tissue samples were obtained from women with singleton term pregnancies who underwent caesarean delivery prior to the initiation of labor at the Affiliated Hospital of Jining Medical University (Jining, China) between March 2020 and December 2022. None of the participants had preexisting acute or chronic complications, such as chronic hypertension or disorders affecting glucose metabolism, and none were subjected to any dietary restrictions. In both the groups, placental delivery was followed by immediate sample collection.For the experimental sequencing method, three placentas from the normal control group and three placentas from the GDM group were selected for transcriptome analysis. Total RNA was extracted from these samples to compare the expression levels of differentially expressed genes (DEGs). Total RNA was extracted, and RNA quality was assessed. After the RNA samples were qualified, common transcriptome libraries were constructed, and Illumina NovaSeq 6000 was used for sequencing.

first: Zhang

last: Yanan

first: Bai

last: Chunyu

first: Hu

last: Chuanbing


title: The transcriptional landscape of microspore embryogenesis induction in barley

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

summary: The effectiveness of microspore embryogenesis and plant formation from in vitro cultivated microspores is determined by a complex network of internal and environmental factors. Plant breeding and genetic engineering widely use haploids/doubled haploids (DHs) derived from in vitro-cultured microspores, but the mechanism of ME induction remains poorly defined. Here, RNA-sequencing was used to characterize the transcriptional landscapes of four early stages of ME in two barley cultivars (Golden Promise and Igri) that are contrastingly responsive in the microspore-derived plant formation. Our experimental setup revealed fundamental regulatory networks, key marker genes of ME (628 stage-specific markers), and 160 candidate genes crucial for genotype-dependent responsiveness/resistance to ME. We found that transcription factors probably give rise to embryo-like structure and callus formation at stage III and determine their further development. Our high-resolution temporal transcriptome atlas provides an important resource for future functional studies aiming at unravelling the genetic control of microspore transition.

overall_design: Microspores isolated at four developmental stages of microspore embryogenesis; species barley (Hordeum vulgare) ; Microspores isolated from two cultivars: Golden Promise and Igri; each stage - four biological replicates

first: Anna

last: Nowicka

first: Martin

last: Kovacik

last: Maksylewicz

first: Przemysław

last: Kopeć

first: Ewa

last: Dubas

first: Monika

last: Krzewska

first: Agnieszka

last: Janas

first: Robert

last: Hoffie

first: DiaaEldin

middle: S

last: Daghma

first: Jochen

last: Kumlehn

first: Iwona

last: Żur


title: Effects of Trem2 depletion on gene expressions in a mouse photothrombotic stroke model

city: Shenzhen

first: Kunyu

last: Li

state: Guangdong

address: No. 1068 Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

summary: Ischemic stroke is a major threat to public health. Microglia-mediated neuroinflammation is a double-edged sword for neuronal survival after stroke. Triggering receptor expressed on myeloid cells 2 (Trem2) is specifically expressed on the surface of myeloid cell, including microglia. Here, we applied a photothrombotic mouse model of stroke to better understand the role of Trem2 in post-stroke neuroinflammation. In this model, Trem2 was sufficiently induced with sustainably elevated inflammatory responses. Our results demonstrated that Trem2-depletion can ameliorate ischemic injury with enhanced neuronal survival, reduced pro-inflammatory cytokine levels, and improved neurological functions. Our results suggested that Trem2 depletion is neuroprotective during ischemic stroke.

overall_design: Photothromobotic stroke was induced in adult Trem2 wildtype (WT) or knockout (KO) mice by intraperitoneally injecting 50 mg/kg Rose Bengal followed by illumination with a 125 mW laser (525 nm wavelength) in specific cortical area. All the mice were male, 8-10 weeks old, with a C57Bl6 background. The cortical lesion region was restricted to a 3 mm-diameter circle centered approximately 2 mm lateral and -1 mm rostral to the bregma.The animals were perfused at 7 days post-injury (DPI), and their brains were stained with TTC for the precise isolation of infarction core (I), peri-infarction zone (P) and contralateral site (C).

first: Siyu

last: Liu

first: Xianyuan

last: Xiang

first: Xinzhou

last: Zhu


title: Drosophila non-gonadal PIWI protein Aubergine regulates regenerative stem cell proliferation and tumourigenesis in the adult intestine

first: Rippei

last: Hayashi

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

overall_design: Refer to individual Series


title: The VNAR high-throughput sequencing data of the Whitespotted Bamboo Shark (Chiloscyllium plagiosum)

city: hangzhou

first: bo

last: zhong

state: zhejiang

address: No. 928, 2nd Street, Xiasha Higher Education Park, Qiantang District, Hangzhou City, Zhejiang Province

institute: Zhejiang Sci-Tech University

summary: IgNAR exhibits significant promise in the fields of cancer and anti-virus biotherapies. Notably, the variable regions of IgNAR (VNAR) possess comparable antigen binding affinity with much smaller molecular weight (~12 kDa) compared to IgNAR.Next-generation sequencing (NGS) will be another method for VNAR screening with a number of advantages.Sequencing the obtained VNAR libraries through NGS can quickly and efficiently obtain immune-specific sequence information, which provides a basis for further screening of specific high-affinity antibodies.

overall_design: Following eight doses of immunization with Cre, Cre_NT, and BSA antigens, total RNA was isolated from the spleens and PBMCs of the sharks, and reverse transcribed into cDNA. The VNAR library was then amplified using white-spotted bamboo shark-specific VNAR primers.

first: Bo

last: Zhong

first: Junjie

last: Yang

first: Zhengbing

last: Lyu

first: Guodong

last: Chen


title: Single-cell transcriptome landscape in hepatocellular carcinoma of BALB/C mice after azvudine treatment

city: Shanghai

first: Haiyu

last: Wang

address: Pudongxinqu

institute: Mobio

summary: Hepatocellular carcinoma is the sixth most common malignant tumor in the world, but there is a lack of effective drugs for the treatment of HCC, so it is urgent to find new treatment strategies. Azvudine is the world's first dual-target innovative anti-AIDS drug, which can selectively enter CD4+T lymphocytes to exert immunomodulatory effects. In the early stage, we found through a retrospective cohort study that azivudine can significantly reduce all-cause mortality and the incidence of composite disease progression in COVID-19 patients with tumors compared with COVID-19 patients without tumors. Therefore, we performed single-cell RNA sequencing on tumor tissues of BALB/C mice treated with azivudine or treated with vehicle to reveal the changes in the tumor microenvironment of azivudine against liver cancer.

overall_design: Four- to six-week-old male BALB/c mice weighing 20.0 ± 2 g were purchased from BEJING HFK BIOSCIENCE Co., Ltd. (Beijing, China). Mice were housed in a specific pathogen-free environment. Each mouse was subcutaneously injected with 5×10^5 H22 cells into the right flank. When the tumors reached approximately 100 mm^3, the mice were randomly divided into three groups to receive oral treatment: the azvudine group (1 mg/kg, QD), and the control group (solvent). The solvent was prepared by sequentially adding the following reagents: 5% DMSO, 40% PEG300, 5% Tween-80, and 50% saline. Tumor volumes were measured daily using a caliper and calculated with the following formula: volume = (length × width2)/2. The mice were euthanized when the tumor volume exceeded 1500 mm^3 or if the maximum tumor diameter exceeded 15 mm. Tumor tissues were subsequently used to performe single-cell RNA sequencing.

first: Benchen

last: Rao

first: Zhigang

last: Ren


title: CUT&RUN of  3 months old wild type and hepatocyte-specific ATF6 overexpression mice

city: München

first: Robert

middle: Stefan

last: Piecyk

state: Bayern

address: Marchioninistr. 15

department: Klinik und Poliklinik für Strahlentherapie und Radioonkologie

institute: LMU Klinikum

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We generated hepatocyte specific n-ATF6 overexpression transgenic mice via Cre-mediated recombination.

overall_design: At 3 months age, livers from the transgenic mice and their wild type controls were harvested for CUT&Run.

first: Borja

last: Gomez Ramos

first: Xin

first: Kristian

last: Unger

first: Moritz

last: Mall

first: Mathias

last: Heikenwälder


title: Single-cell transcriptomic characterization of immune cells from hepatic tumors of wild type and ATF6 transgenic mice

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We isolated CD45+ cells from livers tumors (induced by HDTVi) of hepatocyte-specific nATF6 overexprerssion mice receiving anti-IgG/PD1 treatment for scRNAseq to decrible the the immune cell population.

overall_design: In total 6 ATF6 transgenic mice were induced, 3 were treated with anti-IgG and 3 were treated with anti-PD1.

last: Li

first: Menjie

last: Qiu


title: Single-cell RNA sequencing combined with multiplex immunofluorescence probes the role of MFAP5+ fibroblasts in the microenvironment of pancreatic ductal adenocarcinoma

city: Anhui

first: 午洋

last: 张

state: State

address: No.17 Lujiang Road, Hefei City, Anhui Province, China

institute: The First Affiliated Hospital of USTC

summary: we employed single-cell RNA sequencing to examine the biological characteristics of MFAP5+ fibroblasts in PDAC and their interaction with vascular endothelial cells within tumors. We then utilized a proposed temporal sequencing analysis technique to infer the evolution of cellular subtypes of cancer-associated fibroblasts. To verify our hypothesis, we employed a multiplex immunofluorescence technique to observe the spatial distribution of MFAP5+ fibroblasts and endothelial cells.

overall_design: This study investigated the tumor heterogeneity of PDAC, elucidating intricate cellular interactions within the tumor microenvironment through a comprehensive analysis of 23,905 cells. The biology of MFAP5+ fibroblasts in pancreatic ductal adenocarcinoma was investigated, and it was found that MFAP5+ fibroblasts engage in active biosignaling exchanges with FABP4+ endothelial cells and other endothelial cells through the activation of key tumor-promoting signaling pathways, such as TGF-β, VEGF, and FGF. These pathways provide support for the tumor's invasive and malignant behavior. Our hypothesis was validated by multiplex immunofluorescence and subsequent semi-quantitative analysis, which demonstrated a notable increase in the prevalence of FABP4+ and VWF+ endothelial cells in the area with elevated MFAP5+ fibroblast expression. Furthermore, our study revealed that vascular endothelial growth factor and FGF2 signaling were highly expressed in the region with high MFAP5+ fibroblast expression.

first: Wuyang

last: Zhang

first: Ming

first: Yuyi

last: Liu

first: Shuai

last: Ming

first: Mengru

first: Wei

last: Wei


title: Single-cell RNA-seq analysis of the lungs of Nkx2.1 Cre;Lkb1f/f and Lkb1f/f mice

city: Tianjin

first: Yu

address: 890 Jingu Road, Jinnan District

institute: Tianjin haihe hospital

summary: To investigate the molecular mechanism of LKB1 in the regulation of lung development, we performed single-cell RNA-seq analysis of the lungs of Nkx2.1 Cre;Lkb1f/f and Lkb1f/f mice. In total, 30,408 lung cells were collected for the scRNA-seq analysis of the whole lung cells isolated from 5-week-old Nkx2.1 Cre;Lkb1f/f or Lkb1f/f mice, when the Nkx2.1 Cre;Lkb1f/f mice began to die.

overall_design: The total lung cells isolated from three Lkb1f/f or Nkx2.1Cre;Lkb1f/f mice were pooled and processed to prepare scRNA-seq libraries using Chromium Single Cell 3’ Reagent v3 Kits (10x Genomics, Pleasanton, CA, USA).

first: Huaiyong


title: MicroRNA expression profiling in the adult offspring of rats with periodontal disease

city: Bilac

first: MARIA

middle: SARA DE LIMA COUTINHO

last: MATTERA

state: SP

address: Rua Atlanta, 575

country: Brazil

institute: São Paulo State University (UNESP), School of Dentistry, Araçatuba

summary:
The present study investigated whether maternal periodontal disease modifies the microRNA expression profile in adult offspring.

***************************************************************

This study was supported by the São Paulo Research Foundation (FAPESP)
[grant #2019/04183-9; #2022/08872-6; #2023/03786-7; #2023/12488-0;
#2023/01400-4] and CNPq [grant 151151/2023-7], São Paulo, SP, Brazil.

The grants #2019/04183-9; #2023/12488-0; #2023/01400-4 and 151151/2023-7 were awarded to the author Maria Sara de Lima Coutinho Mattera.

The grant #2022/08872-6 was awarded to Heloisa Macedo Sampaio.

The grant #2023/03786-7 was awarded to Gabriele Fernandes Baliero.

***************************************************************

overall_design: Sixteen Wistar rats, weighing approximately 200 g and 3 months old, were submitted to the Ethics Committee at São Paulo State University (Unesp) for a study on experimental periodontal disease, approved under protocol no. 00407-2019. The rats were divided into two groups: CN, control (n = 8), and PED, with periodontal disease induced by ligature on the mandibular molars. After one week, they were mated with healthy males and housed individually after confirming pregnancy. Only male pups were kept for further analyses (n=4). At 75 days of age, the pups were anesthetized for blood and tissue collection. RNA was extracted using the miRVana™ miRNA Isolation Kit, and quality was assessed before microtranscriptome analysis using the Affymetrix® microarray. Validation of selected miRNAs was performed by real-time PCR using specific primers.

first: Maria Sara

middle: L

last: Mattera

first: Natália

middle: F

last: Scaramele

first: Flávia

last: Lopes

first: Bianca

last: Belardi

first: Thaís

middle: V

last: Tsosura

first: Heloisa

last: Sampaio

first: Fernando

last: Chiba

first: Renato

last: Pereira

first: Rodrigo

last: Santos

first: Edilson

last: Ervolino

first: Gabriele

last: Baliero

first: Ana Carla

last: Nobumoto

first: Anna Clara

last: Cachoni

first: Antonio

last: Chaves-Neto

first: Doris

last: Matsushita


title: ATAC-seq of 3 months old wild type and hepatocyte-specific ATF6 overexpression mice

first: Robert

last: Piecyk

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We generated hepatocyte specific n-ATF6 overexpression transgenic mice via Cre-mediated recombination. At 3 months age, livers from the transgenic mice and their wild type controls were harvested for ATAC-sequencing.

overall_design: In total 9 mice were included, 4 from wild type mice and 5 from ATF6 transgenic mice.

first: Borja

last: Gomez Ramos

first: Xin

last: Li

first: Kristian

last: Unger

first: Moritz

last: Mall

first: Mathias

last: Heikenwälder


title: The role of MiRNAs in the golden pompano’s (Trachinotus blochii) response to different reoxygenation rates after hypoxic stress

city: Haikou

first: tian

last: jiang

address: 58 of Ren min Road

institute: Hainan University

summary: to investigated the effect of two reoxygenation treatments on T. blochii after 12 h of hypoxic stress (1.9 ± 0.2 mg/L): gradual reoxygenation (GRG: DO recovery within 3 h) and rapid reoxygenation (RRG: DO recovery within 10 mins).

overall_design: We used high-throughput sequencing to determine the expression of miRNAs in T. blochii under hypoxic stress and different reoxygenation treatments (rapid reoxygenation (RRG) and gradual reoxygenation (GRG)). We analyzed the expression profiles of miRNAs and the miRNA functions during hypoxia and in the two reoxygenation treatments.

first: Tian

last: Jiang

first: Jun

last: Sun

first: Jian

last: Luo


title: Liver transcriptomic profile of  wild type and hepatocyte-specific ATF6 knockout mice feeding CD-HFD

summary: RNA were isolated and treated with RNAse-free DNAse, and sequenced with Novaseq 6K PE 100 S4 split.

overall_design: In total 11 samples were included, 6 from wild type mice and 5 from ATF6 knockout mice.


title: Gene expression profile at single cell level of CD56+ natural killer cells and CD8+ T cells from blood, spleen and HCC-PDX in humanized mice

city: Singapore

first: Wai Nam

last: Liu

address: 61 Biopolis Drive

country: Singapore

institute: Agency for Science, Technology and Research

summary: In solid tumors, the exhaustion of natural killer (NK) cells and cytotoxic T cells in the immunosuppressive tumor microenvironment poses challenges for effective tumor control. Conventional humanized mouse models of hepatocellular carcinoma-patient-derived xenografts (HCC-PDX) encounter limitations in NK-cell infiltration, hindering studies on NK-cell immunobiology. Here, we introduce an improved humanized mouse model with restored NK-cell reconstitution and infiltration in HCC-PDX, coupled with single-cell RNA-sequencing (scRNA-seq) to identify potential anti-HCC treatments. A single administration of adeno-associated virus carrying human interleukin-15 (AAV-hIL15) reinstated persistent NK-cell reconstitution and infiltration in HCC-PDX in humanized mice. ScRNA-seq revealed exhausted NK-cell and T-cell subpopulations with heightened PDCD1 and TIGIT levels. Notably, combination therapy with anti-PD-1 and anti-TIGIT antibodies alleviated HCC burden in humanized mice, demonstrating NK cell-dependent efficacy. Bulk-RNA sequencing analysis also revealed significant alterations in the tumor transcriptome that may contribute to further resistance after combination therapy, warranting further investigations. As an emerging strategy, ongoing clinical trials with anti-PD-1 and anti-TIGIT antibodies provide limited data. The improved humanized mouse HCC-PDX model not only sheds light on the pivotal role of NK cells but also serves as a robust platform for evaluating safety and anti-tumor efficacy of combination therapies and other potential regimens, complementing clinical insights.

overall_design: Humanized mice were intravenously injected with AAV-hIL15, followed by the transplant of HCC-PDX. Eight weeks after transplant, blood samples, spleens and tumors were harvested from the mice. These samples were first digested to generate single-cell suspensions. After that, the cells were subjected to dead cell removal and mouse cell depletion, using the Dead Cell Removal Kit (Miltenyi Biotec) and Mouse Cell Depletion Kit (Miltenyi Biotec), respectively. Viable human CD56+ NK cells and CD8+ T cells from these samples were then selected using CD56 MicroBeads, Human (Miltenyi Biotec) and CD8 MicroBeads, Human (Miltenyi Biotec). Subsequently, the cells were resuspended in Dulbecco's Phosphate Buffered Saline without calcium and magnesium ions (STEMCELL Technologies) to reach a density of 1,200 cells/µl.

first: Wai-Nam

first: Sarah

last: Harden

first: Qingfeng

last: Chen


title: Long non-coding RNA sequencing (RiboZero) analysis of monocytes-derived dendritic cells

city: Chicago

first: Afsar

middle: Raza

last: Naqvi

state: Illinois

address: 801 S Pauline

department: Periodontics

institute: University of Illinois

summary: Analysis of lncRNA differential expression in Monocytes-derived Dendritic cells at 18h, Day 3, Day 5, and Day 7. StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown.

overall_design: Freshly prepared buffy coats were collected from healthy donors (Oklahoma Blood Institute, Oklahoma City, OK, USA) and CD14+ monocytes were obtained by density gradient centrifugation and magnetic bead isolation. Monocytes were plated at a density of 2X10^6/ml in DMEM, supplemented with penicillin (100 U/ml), streptomycin (100 mg/ml), and gentamicin (50 mg/ml). After 2 h, the media were substituted with media containing 10% heat-inactivated FBS, rhGM-CSF, and IL-4 (both 50 ng/ml; PeproTech, Rocky Hill, NJ, USA). Media were replaced every 72 hours. Cells were harvested at 18h, day 3, 5, and 7 for total RNA isolation.

first: Araceli

last: Valverde

first: Raza


title: Physiological and transcriptomic analyses reveal the immune and metabolic responses in gills of rainbow trout (Oncorhynchus mykiss) under moderate and severe hypoxia stress

city: Gansu Province/Lanzhou City/Anning District

first: Xujuan

last: Fu

address: No.1 Yingmen Village, Anning District, Lanzhou City, Gansu Province, China

department: College of Animal Science and Technology

institute: Gansu Agricultural University

summary: Rainbow trout (Oncorhynchus mykiss), an important economically fish with high food value in China, is very sensitive to hypoxia. The gills are the first tissue to be attacked after hypoxia stress. However, the regulatory mechanisms in gills of rainbow trout to moderate and severe hypoxia stress are unclear. In this study, we determined the changes of biochemical parameters and gene expression in gills of rainbow trout during different periods of hypoxia (4, 8, 12, 24 h, and 1 month) and reoxygenation for 24 h, and analyzed the tissue and transcriptomic changes under moderate hypoxia for 12 h (Tm12G) and severe hypoxia for 12 h (Ts12G) compared with control (CG). The results showed that gill lamellae were bent and ILCM was reduced in the Tm12G group, while this phenomenon was more pronounced in the Ts12G group. At one month of hypoxia, we found that the gill lamellae epithelium was detached. Based on biochemical parameters and transcriptomic analysis, we found that the antioxidant and immune responses were activated, and glucose metabolism, lipid metabolism, and amino acid metabolism were enhanced, however, vitamin metabolism was suppressed under moderate hypoxia stress. Antioxidant and immune responses were activated, and glucose metabolism, lipid metabolism, and amino acid metabolism were enhanced, and nucleotide metabolism also was activated under severe hypoxia stress. From the analysis of gene expression pattern, we found that the expression of hsp90a, tnf, caspase3, mgst1, fih1, hif1a, ddit4, and egln3 showed a tendency to increase and then decrease and recovered after reoxygenation under moderate and severe hypoxia stress. Except for mgst1, the expression of other genes was significantly higher than the control at 12 h of stress. Under hypoxia stress, antioxidant and metabolic responses were first elevated and then decreased with time, and metabolic and immune pathways were activated, which coordinated with each other in response to hypoxia stress. These results provide basic information for an in-depth investigation of the physiological and molecular mechanisms in gills of rainbow trout under hypoxia stress.

overall_design: Fish weighing (130 ± 5.0) g were selected and temporarily reared for two weeks in a flow-through aquaculture system with DO of 8.5 ± 0.1 mg/L, water temperature of 12 ± 0.1℃. Fish were fed a commercial pellet feed twice a day. All procedures were conducted in accordance with the approval of the Animal Ethics Committee of Gansu Agricultural University and followed the protocols approved by the institutional guidelines.Healthy rainbow trout were randomly divided into three groups, including normoxia, moderate hypoxia, and severe hypoxia groups, the oxygen levels were maintained at 8.5 ± 0.1, 4.5 ± 0.1, and 3.0 ± 0.1 mg/L, respectively, and the low oxygen environment was created by mixing oxygen and nitrogen. The reoxygenation experiment was conducted immediately after 24 h of hypoxia stress and the DO level was maintained at 8.5 ± 0.1 mg/L during the experiment. Controls were divided into C (0 h control) and CM (1 month control), and the gills of the normoxia group were collected immediately before the start of the hypoxia experiment and 1 month after the start of the experiment. After hypoxia stress, gill tissues were collected at 4 h, 8 h, 12 h, 24 h, TMM (moderate hypoxia for 1 month), and TMS (severe hypoxia for 1 month), as well as R12 (hypoxia for 24 h + reoxygenation for 12 h) and R24 h (hypoxia for 24 h + reoxygenation for 24 h) in each group (moderate hypoxia group and severe hypoxia group), respectively. Gill samples were collected after fish MS-222 treatment. After collection, some samples were used for histological observation, other samples were frozen immediately in liquid nitrogen, and then transferred to -80℃ refrigerator for storage for biochemical parameters, gene expression and RNA-seq assays.

first: Jinqiang

last: Huang

first: Yongjuan

first: Shenji

last: Wu

first: Lu

last: Zhao


title: Effect of anti-PD-1 and/or anti-TIGIT antibodies on hepatocellular carcinoma-patient derived xenografts in humanized mice

overall_design: Humanized mice were intravenously injected with AAV-hIL15, followed by the transplant of HCC-PDX. The mice were then treated with saline, anti-PD-1 and/or anti-TIGIT antibodies. At experimental endpoint, HCC-PDX from each group (n = 3 for all groups) was subjected to bulk RNA-seq.


title: Profiling and Bioinformatics Analyses of Differential Circular RNA Expression in Glioblastoma Multiforme Cells under Hypoxia

first: Ming

address: 1665 Kong Jiang Road

department: Neurosurgery

institute: Xinhua Hospital of Shanghai Jiaotong University School of Medicine

summary:
Background: The hypoxia microenvironment is highly associated with GBM’s malignant phenotypes. CircRNAs were reported involved in GBM’s biological characteristics and regulated by HIF-1α. However, the differential expression profile and role of circRNAs in GBM cells under hypoxia are still unclear.
Methods: The expression profiles of circRNAs in LN229 and T98G under hypoxia were explored via circRNA sequencing analysis. Those circRNAs significantly dysregulated both in LN229 and T98G, and could be found in circBase were selected and validated by qRT-PCR, RNase R digestion reaction and Sanger sequencing. Normal cell line and fresh GBM tissues were also used for qRT-PCR validation. The roles of differentially expressed circRNAs were evaluated by bioinformatics analyses.
Results: There were 672 dysregulated circRNAs in LN229 and 698 dysregulated circRNAs in T98G. GO analysis indicated that the alteration of circRNAs expression related to GBM cell’s biogenesis and metabolism. KEGG analysis demonstrated that TGF-β signaling pathway, HIF-1 signaling pathway and metabolism related signaling pathway were closely associated with differentially expressed circRNAs under hypoxia. The 6 selected and dysregulated circRNAs both in LN229 and T98G including hsa_circ_0000745, hsa_circ_0020093, hsa_circ_0020094, hsa_circ_0000943, hsa_circ_0004874 and hsa_circ_0002359 were validated by qRT-PCR. HIF-1α centered circRNA-miRNA-mRNA networks analysis showed that the 6 validated circRNAs could cross-talk with 11 related miRNAs.
Conclusion: The circRNA expressions are dysregulated in GBM cell under hypoxia. The 6 validated circRNAs could participate in GBM’s development and progression when hypoxia occurs. They might be the candidates for prognostic markers and adjuvant therapeutics of GBM in the future.

overall_design: Examination of circRNA expression in 2 GBM cell lines (LN229 and T98G) under hypoxia and normoxia.

first: Zheng


title: RNA-seq of human adipose-derived stromal/stem cells with significant differences in osteogenic differentiation

city: Goyang

first: JAE YEON

last: MOON

address: Dongguk-ro 32

institute: Dongguk university

summary:
RNA sequencing (RNA-seq) was performed to obtain a global profile of gene expression related to osteogenic differentiation and find its predictive markers in hASCs.
Based on Alizarin Red staining, ASCs from each donor were classified into two groups: a high osteogenic group and a low osteogenic group.

overall_design:
12 ASC clones from 12 individual donors (6 with high osteogenic differentiation and 6 with low osteogenic differentiation) were used.
The hASCs were established from lipoaspirates from 12 patients (mean age: 42 years, range: 21-58 years). A statement of consent was informed to all donors. All experiments were performed according to the relevant guidelines and regulations.


title: Stimulation with THBS4 activates pathways that regulate proliferation, migration and inflammation in primary human keratinocytes

city: Tartu

first: Mariliis

last: Klaas

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

summary: Atopic dermatitis, which is a common inflammatory skin disease characterized by persistent epidermal barrier dysfunction, is a systemic health burden reducing overall quality of life of the person. Recently, we showed that the nonstructural extracellular matrix molecule Thrombospondin-4 (THBS4) was upregulated in psoriatic skin lesions by more than 2-fold. In addition, THBS4 contributed to both skin regeneration and wound healing in vitro and in vivo. In the present work we found that THBS4 is also abundantly expressed in AD patient skin biopsies. By using a proteotransciptomic approach we show that stimulation of primary keratinocytes with THBS4 activates multiple factors, including inflammation, migration, proliferation, keratinocyte differentiation, by which THBS4 could participate in AD progression and contribute to the wound healing process.

overall_design: Changes in human primary skin keratinocyte RNA profile in response to stimulation with recombinant THBS4 protein

first: Kristina

last: Mäemets-Allas

first: Viljar

last: Jaks


title: PIEZO-dependent mechano-sensing of the niche is essential for intestinal stem cell fate decision and maintenance

status: Public on Dec 27 2024

city: Paris

first: Meryem

last: Baghdadi

address: 12 rue Lhomond

country: France

institute: Institut curie

summary: Stem cells perceive and respond to biochemical and physical signals to maintain homeostasis. Yet, it remains unclear how stem cells sense mechanical signals from their niche in vivo. Here, we investigated the roles of PIEZO mechanosensitive channels in intestinal stem cell (ISC) niche. By employing mouse genetics and single-cell RNAseq analysis, we revealed the requirement for PIEZO channels in ISC maintenance. In vivo measurement of basement membrane stiffness showed that ISCs reside in a more rigid microenvironment at the bottom of the crypt. Using 3D and 2D organoid systems combined with bioengineered substrates and stretching device, we found that PIEZO sense extracellular mechanical stimuli to modulate ISC function. This study delineates the mechanistic cascade of PIEZO activation that coordinates ISC fate decision and maintenance.

overall_design: Crypt were isolated and pooled from 3 control and Piezo-deleted mice.


title: Cancer therapy induced effects on lung organoids as suitable in vitro model

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

summary: Generation of lung organoids as model for genotoxic stress

overall_design: iPSC-derived lung organoids were either treated with radiation or not prior RNAseq analysis

first: Chiara

last: Kroepel

first: Lisa-Marie

last: Stasch

first: Diana

last: Klein


title: microRNA switch reveals the role of LIN28A-let-7a-5p-NR6A1 axis in megakaryocytes for platelet biogenesis

city: Kyoto

first: Koji

last: Eto

address: 54, Kawaharacho, Shogoin

department: CiRA

institute: Kyoto University

summary: To identify the gene which is regulated by Let-7a-5p, we performed global gene expression analysis of immortalized megakaryocyte cell lines.

overall_design: Examination of 2 different Let-7a-5p activity status

first: Kazuya

last: Hashimto

first: Takuya

last: Yamamoto


title: Efficient suppression of premature termination codons with alanine by engineered chimeric pyrrolysine tRNAs [Ribo-Seq]

city: Indianapolis

first: Jeffery

last: Tharp

state: Indiana

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Mutations that introduce premature termination codons (PTCs) within protein-coding genes are associated with incurable and severe genetic diseases. Many PTC-associated disorders are life-threatening and have no approved medical treatment options. Suppressor transfer RNAs (sup-tRNAs) with the capacity to promote translational readthrough of PTCs represent a promising therapeutic strategy to treat these conditions; however, developing novel sup-tRNAs with high efficiency and specificity often requires extensive engineering and screening. Moreover, these efforts are not always successful at producing more efficient sup-tRNAs. Here we show that a pyrrolysine tRNA (tRNAPyl), which naturally translates the UAG stop codon, offers an attractive scaffold for developing effective sup-tRNAs that restore protein synthesis from PTC-containing genes. We created a series of rationally designed Pyrrolysine tRNA Scaffold Suppressor-tRNAs (PASS-tRNAs) that are substrates of bacterial and human alanyl-tRNA synthetase. Using a PTC-containing fluorescent reporter gene, PASS-tRNAs restore protein synthesis to wild-type levels in bacterial cells. In human cells, PASS-tRNAs display robust and consistent PTC suppression in multiple reporter genes, including pathogenic mutations in the tumor suppressor gene BRCA1 associated with breast and ovarian cancer. Moreover, PTC suppression occurred with high codon specificity and no observed cytotoxic effects. Collectively, these results unveil a class of sup-tRNAs with great potential for tRNA-based therapeutics.

overall_design: Ribosome protected footprint libraries were prepared from HEK 293 cells transfected with a sup-tRNA-expressing plasmid or an empty vector control to determine the impact of sup-tRNA expression on native stop codon readthrough.

first: Oscar

last: Vargas-Rodriguez


title: PIF4 promotes stomatal movement during fluctuating light coincidant with drought stress via the SAL1-PAP signaling pathway (ChIP-Seq)

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

country: China

institute: Yangzhou Univerisity

summary: Fluctuating light (FL) usually occur concomitantly with drought stress (DS); this combined (FL-DS) condition influences intrinsic water use efficiency (iWUE) pattern during FL and DS response. However, the molecular mechanisms governing iWUE during FL-DS combined events in rice remain unexplored. In this study, we quantified iWUE kinetics in 200 rice accessions exposed to a 20-day FL-DS. Using genome-wide association studies (GWAS), we identified a significant gene variation in the phytochrome-interacting factor (OsPIF4) gene which significantly associated with a novel trait, iWUEFL. This gene variation was highly expressed in the high iWUEFL subgroup. Two haplotypes containing nine SNPs of OsPIF4 were classified, where the mutation of v3 SNP at its promoter shows substantially reduced activities of promoter and greatest sensitivity to FL among mutation of other SNPs via protoplast transient transformation approach. Mutation at v3 SNP (PIF4v3m) and overexpression of OsPIF4 resulted in at least 20% reduction and 25% increase in iWUEFL under FL-DS, compared it to WT, respectively. Two genes (OsSAL1 and OsNHX1) were identified with the most significant differences in expression between PIF4v3m and WT based on transcriptome analysis. PIF4v3m displayed an 85% reduction in adenosine 3', 5'-diphosphate (PAP) levels and a 73% increase in OsSAL1 gene expression compared to WT. Moreover, our results revealed that OsPIF4 has a dual role in repressing OsSAL1 transcriptionally and activating OsNHX1 by binding to their G-box motifs. This regulatory mechanism increased by 16% (sal1) and 10% (OsNHX1-OE) in iWUEFL compared to WT under FL-DS. OsPIF4 haplotypic distribution is strongly associated with the local light regime where accessions originated. This study highlights the key role of OsPIF4 in enhancing iWUEFL during FL-DS by regulating chloroplast retrograde signaling pathways and vacuolar ion exchanges.

overall_design: The submission includes samples from chromatin immunoprecipitation sequencing (ChIP-seq) experiments conducted on rice leaves of PIF4 overexpression line exposed to FL-DS. The primary objective of these experiments is to investigate the binding sites and genomic regions associated with SAL1, a key regulator in stomatal movement.

first: Suyang

last: Fang

first: Jemaa

last: Essemine

first: Zhan

last: Xu


title: In vitro model of retinoblastoma derived tumor and stromal cells for tumor microenvironment (TME) studies

summary: Retinoblastoma (RB) is an intraocular tumor arising from retinal progenitor cells affecting young children. In the last couple of years, RB treatment evolved towards eye preserving therapies. Therefore, investigating intratumoral differences and RB`s tumor microenvironment (TME), regulating tumorigenesis and metastasis, is crucial. How RB cells and their TME are involved in tumor development needs to be elucidated using in vitro models including RB derived stromal cells. In the study presented, we established primary RB derived tumor and stromal cell cultures and compared them by RNAseq analysis to identify their gene expression signatures. RB tumor cells cultivated in serum containing medium were more differentiated compared to RB tumor cells grown in serum-free medium displaying a stem cell like phenotype. In addition, we identified differentially expressed genes for RB tumor and RB stromal derived cells. Furthermore, we immortalized cells of a RB1 mutated, MYCN amplified and Trefoil Factor Family peptid 1 (TFF1) positive RB tumor and RB derived non-tumor stromal tissue. We characterized both immortalized cell lines using a human oncology proteome array, immunofluorescence staining of different markers and in vitro cell growth analyses. Tumor formation of the immortalized RB tumor cell line was investigated in a chicken chorioallantoic membrane (CAM) model. Our studies revealed that the RB stromal derived cell line comprises tumor associated macrophages (TAMs), glia and cancer associated fibroblasts (CAFs), we were able to successfully separate via magnetic cell separation (MACS). For co-cultivation studies, we established a 3D spheroid model with RB tumor and RB derived stromal cells. In summary, we established an in vitro model system to investigate the interaction of RB tumor cells with their TME. Our findings contribute to a better understanding of the relationship between RB tumor malignancy and its TME and will facilitate the development of effective treatment options for eye preserving therapies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RB tumor cells under different culture conditions and between RB tumor and tumor derived stromal cells.

first: Emily

last: Alefeld

first: André

last: Haase

first: Dario

last: Van Meenen

first: Oliver

last: Dräger

first: Natalia

last: Miroschnikov

first: Saskia

last: Ting

first: Deniz

last: Kanber

first: Eva

last: Biewald

first: Nikolaos

last: Bechrakis

first: Nicole

last: Dünker

first: Maike

last: Anna Busch


title: Leydig Cells in Spermatogenesis-Deficient Testes Experience Stress, but Proliferate to Enhance Testosterone Synthesis II

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: We investigated somatic cell dynamics in testicular tissue lacking spermatogenesis using model mice with testis-specific deletion of the histone H3 variant gene H3t.  Leydig cells in testes lacking spermatogenesis led to increased testosterone synthesis that occurred alongside a high inflammatory response and oxidative stress.

overall_design: We generated H3t deletion mice that were used for testis section transcriptomics and spatial transcriptomics analyses of Leydig cells in testes with disruption of spermatogenesis.

first: Akihito

last: Harada

first: Kazumitsu

last: Maehara


title: Lactylated histone promotes rheumatoid arthritis progression by increasing NFATc2 expression and the production of anti-lactylated histone autoantibodies

city: Wenzhou

first: Wu

last: Gan

address: Chashan Street, Ouhai District

institute: Wenzhou Medical University

summary: The elevated lactate in the joint microenvironment of patients with rheumatoid arthritis (RA) is crucial for disease progression, although the underlying mechanism remains to be elucidated. In this study, we observed significantly increased global lactylation levels within fibroblast-like synoviocytes (FLS) of RA patients compared to HC (healthy controls), and lactylated proteins were enriched in histones. Furthermore, we found that anti-lactated histone antibodies were detected in almost RA patients and positively correlated with Disease Activity Score 28 (DAS28). Then we identified NFATc2 as a key target gene regulated by histone H3 lysine 9 lactylation (H3K9la) using CUT&Tag combined with RNA-seq. Functional studies revealed that NFATc2 promotes migration of RA-FLSs. Additionally, using server combined immune-deficiency (SCID) and collagen-induced arthritis (CIA) mouse models, we demonstrated that NFATc2 exacerbates RA disease progression through enhanced FLS cartilage invasion function. Collectively, our findings suggest that upregulated target gene NFATc2 by lactate-dependent histone lactylation, can be used as a potential therapeutic target for intervention, anti-lactated histone autoantibodies is promising as a diagnostic marker for RA.

overall_design: RNA-seq profiling of fibroblast-like synoviocytes (FLS) from RA patients and healthy controls

first: Gan

last: Wu


title: CHRNA9 and MICU1 Govern the Potency of the Mitochondrial Permeability Transition Pore in Necroptotic Oral Cancer Progression

city: New Delhi

first: Tanveer

last: Ahmad

address: 110025, Jamia Millia Islamia, Jamia Nagar, Okhla

department: Multidisciplinary Centre for Advanced Research and Studies (MCARS)

institute: Jamia Millia Islamia

summary: Our study included 30 tissue samples in total, which included 15 samples from OSCC patients, 10 from OSMF patients, and 5 normal control samples. To explore the involvement of genes associated with the changes observed in OSMF tissue biopsy samples, we performed RNA sequencing (RNA seq) analysis of moderately advanced (OSMF-III) and advanced (OSMF-IV) conditions. Additionally, we obtained tissue biopsies from patients diagnosed with OSCC occurring concomitantly with OSMF. For sequencing, QIAGEN Pure mRNA beads enriched the mRNA. The bound mRNA was isolated and enriched after bead binding. Subsequently, FastSelect reagent was added for enrichment before heat fragmentation. RNA processing used RNase H-Reverse Transcriptase with random primers for first-strand synthesis. Second-strand synthesis used 5′ phosphorylated primers for strand-specific ligation. Adapters were added to inserts in a strand-specific manner. Libraries were purified with QIAseq CleanStart PCR reagents to remove previous NGS libraries. Prepared libraries were compatible with Illumina NGS systems (NovaSeqTM 6000) with specified read lengths and index reads based on index types. For bulk transcriptome analysis, sequencing data were in FastQ format. Data pre-processing involved quality checks, adapter removal, trimming, and data filtering. QC-passed samples were processed and analysed using the nf-core pipeline to generate a gene expression matrix. Differential expression gene (DEG) analysis was carried out with the iGeak RNA-seq software to normalize the raw gene expression data and analyse expression variances between the groups.

first: Md

middle: I

last: Faizan


title: Leydig Cells in Spermatogenesis-Deficient Testes Experience Stress, but Proliferate to Enhance Testosterone Synthesis I


title: Metformin Regulates Ferroptosis in Skin Cutaneous Melanoma

city: Jinan

first: Weiting

last: Kang

state: Shandong

address: No. 324, Jingwu Road and Weiqi Road

department: Department of Urology

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: To explore the effects of metformin on the proliferation and ferroptosis of skin cutaneous melanoma (SKCM) and its potential molecular mechanisms, providing a new theoretical basis and strategy for the treatment of cutaneous melanoma. RNA-seq sequencing and related analyses were used to screen differentially expressed genes and explore their involved biological functions and signaling pathways. RNA-seq analysis found 2068 differentially expressed genes, of which 897 were up-regulated and 1171 were down-regulated. The related pathways such as iron metabolism disorders and ferroptosis were activated.

overall_design: Exploring the molecular mechanism of metformin in regulating A375 melanoma cells in the skin

first: Da

last: Gu


title: Epigenomic landscape of human cumulus cells in premature ovarian insufficiency using single-base resolution methylome and hydroxymethylome. [scWGBS_seq]

city: Xi'an

first: Wenhao

last: Shi

state: Shaanxi

address: Houzai Gate 73#

department: The assisted Reproduction Center

institute: Northwest Women’s and Children’s Hospital

type: Methylation profiling by high throughput sequencing

summary: Premature ovarian insufficiency (POI) has recently been reported to be linked with epigenetic changes. Previous studies have focused on the regulation of individual genes associated with ovarian function through single-gene epigenetic variations, however, there is a deficiency in the comprehensive comprehension of the epigenetic profile for POI. Therefore, we conducted a multi-omics study integrating methylation, hydroxymethylation, and transcriptome sequencing analyses in cumulus cells from women with POI and their matched controls. Our results showed significantly higher global methylation and hydroxymethylation levels in POI women compared to controls. The number of hyper-methylated/hyper-hydroxymethylated regions exceeded hypo-methylated/hypo-hydroxymethylated regions in differentially methylated and hydroxymethylated regions across chromosomes and genetic elements. Methylation within genebodies remained high and exhibited a slight negative correlation with gene expression. Variation in methylation levels was notable among promoter regions, with gene expression decreasing as methylation levels increased (displaying a pronounced negative correlation). Hydroxymethylation levels in both the genebody and promoter regions remained consistently low and showed no overall association with gene expression. Furthermore, we found that changes in methylation were linked to the epigenetic age clock rather than being specifically associated with POI causative genes or ovarian function genes. Our study sheds light on critical features of POI, characterized by widespread DNA hyper-methylation and hyper-hydroxymethylation across the genome. The observed relationship between hyper/hypo-methylation and gene expression regulation may provide valuable insights for identifying potential epigenetic biomarkers and treatment targets for POI.

overall_design: We conducted WGBS-seq, ACE-seq, and RNA-seq analyses on six samples obtained from cumulus cells of three women with POI and three age- and BMI-matched control women.

first: Dongyang

last: Wang

first: Juanzi

first: Chen

last: Huang


title: The neurodevelopmental regulatory role and clinical value of the multi-molecular axis in early-onset schizophrenia [circRNA]

city: Taiyuan

first: Sha

last: Liu

state: Shanxi

address: No. 56 Xinjian South Road, Yingze District, Taiyuan, Shanxi province

department: Department of Psychiatry

institute: First Hospital of Shanxi Medical University

summary: Background: Biomarkers identified by previous epigenetic studies of schizophrenia have focused solely on diagnostics or pathology, potentially leading to a disconnection between them. This study focused on early-onset schizophrenia (EOS), aiming to identify the multi-molecular axis centered on circular RNAs (circRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) with both neurobiological function and diagnostic value. Methods: Based on the discovery cohort and validation cohort-1, screening of candidate genes on the axis were completed via high-throughput sequencing, expressive and structural validation. Combining dual-luciferase reporter assays with overexpression/knockdown experiments, the axis with binding and regulatory relationships has been established. Subsequently, the functions of genes on the axis were explored through zebrafish embryo manipulation and neural differentiation. The clinical value of the entire axis was assessed in the validation cohort-2. Results: The regulatory effects of hsa-circ-CORO1C on hsa-miR-708-3p, hsa-miR-708-3p on target JARID2 and LNPEP were elucidated. Among them, hsa-miR-708-3p caused aberrant phenotypes including significant craniocerebral malformation and impaired neuron axon growth. JARID2 and LNPEP could facilitate neuronal differentiation and augment synaptic formation. The combined diagnostic efficacy of the whole axis, where hsa-circ-CORO1C could serve as a sponge for hsa-miR-708-3p to alleviate its suppressive effects on JARID2 and LNPEP, surpassed any individual gene we found in EOS. Conclusions: Our study demonstrated a multi-molecular axis, hsa-circ-CORO1C–hsa-miR-708-3p–JARID2+LNPEP, in EOS for the first time. By integrating evidence from genetic, neurophenotypic, and clinical perspectives, we have expanded the comprehension of the pathological mechanism and provided the reference for identifying reliable objective diagnostic biomarkers for EOS.

overall_design: In the cohort of 10 drug-naïve, first-episode patients with early-onset schizophrenia and 10 matched healthy controls, differentially expressed circRNAs and miRNAs were identified via Illumina high-throughput sequencing.

first: Zexuan

last: Li

first: Xinzhe

last: Du

first: Yong

last: Xu


title: Expression profiling of response to BET inhibition in agressive  B-Cell lymphoma cell lines

city: Grenoble

first: Anouk

last: Emadali

address: Allée des Alpes, Site Santé La Tronche, BP170, Cedex 9

department: Institute for Advanced Biosciences

institute: Grenoble University Hospital

summary: We studied  response to JQ1, a BET inhibitor, on gene expression profiles for 10 B-cell lymphoma cell line

overall_design: Cells cere treated for 24h with 500 nM JQ1 and compared to DMS0-treated counterparts.

first: Emilie

last: Montaut