title: RNA-Binding Protein RBM20 Upregulation Enhances Dilated Cardiomyopathy by Alternative Splicing of Atp6v0a1

city: Shanghai

first: Zhihong

last: Sun

email: sunzh0819@gmail.com, sszh0819@163.com

address: Second Ruijin Road

institute: Ruijin hospital

summary: Dilated cardiomyopathy (DCM) is a common cause of heart failure and mutations in RNA-binding motif protein 20 (RBM20) are linked to hereditary DCM. However, the role of unmutated RBM20 in idiopathic DCM is still ambiguous. In this study, we found that RBM20 expression was upregulated by the transcription factor c-JUN in idiopathic DCM. Mice with cardiomyocyte-specific RBM20 overexpression (RBM20cKI) resulted in heart failure with ventricle dilation and lysosome accumulation. Using LysoTracker and a tandem fluorescence RFP-GFP-LC3 reporter system, we elucidated RBM20 blocks autophagic flux in DCM by alkalinizing lysosomal pH. RNA sequencing revealed RBM20 overexpression leads to vacuolar H+-ATPase proton translocation domain subunit a1 (Atp6v0a1) exon6 and exon7 exclusion, which was validated by sanger sequencing and serial amplification product electrophoresis. Transgenic expression of full-length Atp6v0a1 isotype attenuated cardiac dysfunction and restored lysosomal acidification in RBM20cKI mice. Our data suggest that RBM20 activity precisely regulates various cellular process in cardiomyocytes and any therapy targeting RBM20 requires extra cautious.

overall_design: The objective of this study was to determine the role of unmutated RBM20 in idiopathic DCMusing Dox-induced DCM models and a tamoxifen-inducible cardiomyocyte-specific RBM20 knock-in mouse model. The regulatory factor of RBM20 was determined through luciferase assay and chromatin immunoprecipitation in vitro. Autophagic flux was evaluated by transmission electron microscope, Lysotracker and a tandem fluorescence RFP-GFP-LC3 reporter system in vivo and in vitro. RBM20-dependent splicing events were identified by rMATS 3.2.5 on the RNA-sequencing data. AAV9 transfections were used to test the therapeutic potential of full exon length Atp6v0a1 in RBM20cKI mice.


title: Intercellular Adhesion Molecule 1-Positive Dental Pulp Stem Cells

status: Public on Jan 01 2026

city: Hangzhou

first: Yi

last: Zhang

state: Zhejiang

address: 166 North Qiutao Rd

department: Department of Endodontics

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary: Objectives: Dental pulp stem cells are crucial in immune response regulation. However, sub-clusters of these cells involved in deep caries progression remain unidentified. This study explores the role of Intercellular adhesion molecule 1-positive dental pulp stem cells (ICAM1+DPSCs) within the immune microenvironment of dental pulp tissue affected by deep caries, aiming to establish a theoretical foundation and novel strategies for its prevention and treatment.Methods: Use flow cytometry to sort ICAM1+ DPSCs and ICAM1- DPSCs for RNA-seq.

overall_design: Use flow cytometry to sort human dental pulp stem cells into ICAM1+ DPSCs and ICAM1- DPSCs for RNA-seq.

first: Yulian

last: Chen

first: Wenzhi

last: Wu

first: Jianwei

first: Xiatong

first: Jingchen

first: Zhuo


title: Advancing diagnosis and early risk assessment of preeclampsia through non-invasive cell-free DNA methylation profiling

city: Ghent

first: Bram

last: Van Gaever

address: C. Heymanlsaan 10

country: Belgium

institute: Ghent University

type: Methylation profiling by high throughput sequencing

summary: Aberrant embryo implantation and suboptimal placentation can lead to (severe) complications such as preeclampsia and fetal growth restriction later in pregnancy. Current identification of high-risk pregnancies relies on a combination of risk factors, biomarkers, and ultrasound examinations, a relatively inaccurate approach. Previously, aberrant DNA methylation due to placental hypoxia has been identified as a potential marker of placental insufficiency and, hence, potential (future) pregnancy complications. The goal of the Early Prediction of prEgnancy Complications Testing, or the ExPECT study, is to validate a genome-wide, cell-free DNA (cfDNA) methylation strategy to diagnose preeclampsia accurately. More importantly, the predictive potential of this strategy is also explored to reliably identify high-risk pregnancies early in gestation. Furthermore, a longitudinal study was conducted, including sequential blood samples from pregnant individuals experiencing both uneventful and complicated gestations, to assess the methylation dynamics of cfDNA throughout these pregnancies. This study offers valuable insights into methylation changes at specific genomic regions throughout pregnancy, revealing critical differences between normal and complicated pregnancies. The power of non-invasive cfDNA methylation profiling was successfully proven, suggesting the potential to integrate this non-invasive approach into routine prenatal care. A significant strength of this study is its enzymatic digest, which enriches CpG-rich regions across the genome without the need for proprietary reagents or prior selection of regions of interest. This makes it useful for the cost-effective discovery of novel markers. Investigation of methylation patterns throughout pregnancy showed different methylation trends between unaffected and affected pregnancies. We detected differentially methylated regions (DMRs) in pregnancies complicated with preeclampsia as early as 12 weeks of gestation, with distinct differences in the methylation profile between early and late pregnancy. Two classification models were developed to diagnose and predict preeclampsia, demonstrating promising results on a small set of validation samples.

overall_design: Reduced representation bisulphite sequencing of cell-free DNA collected from pregnant individuals at various moments throughout pregnancy duration. Both from healthy induviduals as well as individuals diagnosed with preeclampsia later in pregnancy. Samples are split into two groups (early and late pregnancy). Longitudinal samples from several case and control samples are also included.

first: Van Gaever

last: Bram

first: Baetens

last: Machteld


title: Effect of EFNA3 protein on gene expression in luminal cells

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

summary: EFNA3 protein is a cell membrane protein. In our study, we found that during the process of collective migration, basal cells promote the migration of luminal cells through EFNA3. Through this sequencing, we discovered that stimulation of luminal cells by EFNA3 protein activates the oxidative phosphorylation pathway and upregulates the expression of genes related to oxidative phosphorylation.

overall_design: To investigate the effects of EFNA3 on luminal cells, we cultured primary luminal cells. After a 12-hour starvation period, we stimulated the cells with a medium containing EFNA3 protein for 24 hours before collecting samples.

first: Jing

first: Rongze

last: Ma

first: Deyi

last: Feng


title: Gene expression of basal alonal, luminal alonal, basal and luminal aggregates during collective migration

summary: Breast epithelium has two types of epithelial cells: basal and luminal. We found that basal cells promote the leadership of luminal cells during duct development and collective migration, but it is not clear how. Here, through this sequencing, we found that basal cells promote oxidative phosphorylation of luminal cells through EFNA3, allowing it to play a role in migration.

overall_design: To investigate the role of basal and luminal cells in collective migration at the mRNA level, we separately aggregated basal cells, luminal cells, and a 50% mixture of both basal and luminal cells. The samples were collected after migrating for 56 hours under the induction of FGF10 beads.


title: Type-I Interferon drives T-cell responses to Amyloid-beta in the central nervous system

city: Heidelberg

first: Julius

last: Michel

address: Im Neueunheimer Feld 280

department: Neuroimmunology and brain tumor immunology

country: Germany

summary: Amyloid beta (Aβ) plaque deposition in the central nervous system (CNS) is a hallmark of Alzheimer’s disease (AD) and cerebral amyloid angiopathy (CAA), triggering an innate immune response. However, the role of the adaptive immune system is less clear. We investigated immune microenvironment dynamics in APP23 transgenic (APP23-tg) mice modelling CNS amyloid pathology, using single-cell transcriptomics. A significant increase in T-cell populations, particularly CD8+ T-cells, was observed in late stages, clustering around Aβ plaques, indicating a targeted response. A novel Aβ plaque-associated subset of CD8+ T-cells expressing interferon-stimulated genes (ISGs), was found to drive Type-I interferon responses. This subset also produced CXCL10, which mediated non-ISG T-cell trafficking via the CXCL10-CXCR3 axis. Importantly, we corroborated our observations by identifying similar Type-I interferon responses near plaques in human CNS amyloid pathology. These findings highlight a shift from microglia-driven to T-cell-mediated neuroinflammation as amyloid pathology progresses, with implications for time-resolved therapy development.

overall_design: to investigate the immune landscape in response to amyloid beta deposition we analysed RNAseq data of mouse brain immune cells (CD45+); comparison between APP23 transgenic mice vs wildtype littermates; two difffernt time points used: 14-month old mice and 24-month old mice;

first: Khwab

last: Sanghvi

first: Lukas

last: Bunse


title: Foxa1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity

city: New York

first: Erik

last: Ladewig

state: New York

address: 435 East 65th Street

country: USA

institute: MSKCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Foxa1 mutants induce distinct transcriptomic and DNA accessibilities, prominent aberrant epithelial lineage gene expression, and enhance prostate tumorigenicity in vivo

overall_design: Murine organoids established from adult mouse prostate were transduced with lentivirus for pCW-EV and pCW-Foxa1 (WT and mutant cDNA). Following sorting and 3D culturing organoids, single nuclei were extracted from mouse prostate organoids. Joint scRNA- and scATAC libraries were prepared using the 10x Genomics platform.


title: LKB1 Loss Sensitizes Lung Cancer Cells to PRMT5 inhibition by upregulating NNMT

city: 上海市

first: 欣怡

last: 夏

state: 上海

address: 杨浦区淞沪路2005号

institute: 复旦大学代谢与整合生物写研究院

summary: Cancer is a major obstacle to health of modern people, in which lung cancer has a fairly high incidence and mortality rate, according to the results of the WHO IARC agency in 2021. Lung cancer is known for its hard treatment because of its genetic complexity and heterogeneity, especially the KRAS-mutant and LKB1-lost NSCLC. Here we show that LKB1 inactivation upregulates NNMT through SIK1/2-CRTC2 axis, which decreases the ratio of SAM/SAH. Low ratio of SAM/SAH predicts high sensitivity to PRMT5 inhibition in NSCLC independent of MTA abundance, which was previously broadcast negative to PRMT5 activity in MTAP-absent cancer cells. What’s more, PRMT5 inhibition induces senescence in LKB1-mutant NSCLC cells by upregulating P21. Although there has been quite researches on the mechanism of metabolic remodeling of K/L lung cancer, the treatment methods for this type of lung cancer are still relatively limited. So this project attempts to find the unique metabolic remodeling mode of K/L mutant NSCLC and give specific treatment options.

overall_design: To investigate why NSCLC cells grow slower under treatment of PRMT5 inhibition, we established A549 and H460 cells treated with or without 0.1 μM GSK3326595 for 48h. We then performed transcriptomic profiling using RNA-seq data of 4 groups of 2 cells including A549 with or without treatment and H460 with or without treatment.

first: Xinyi

last: Xia

first: Fuming

last: Li


title: A transient tumoral challenge is sufficient to negatively im-print the generated memory CD8 T cells

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

country: France

institute: AltraBio

summary: The objective of this study is to compare the transcriptome of memory CD8 T cells generated following an acute viral infection (VV-CD8) or a transient tumoral challenge with a tumor that is eleminated by the immune system (EL4-CD8), in quiescent condition or following a brief in vitro stimulation with their cognate peptide. Naive CD8 T cells were used as control.

overall_design: B6 mice were transferred with naive CD8 T cells from F5 transgenic mice. The next day, mice were challenge with vaccinia virus (VV) or EL4 tumor cells, both expressing NP68 peptide. CD45.1+ F5 memory cells were sorted from the spleens of VV- or EL4-immunised mice 9 weeks after the primary challenge. Naive F5 cells were sorted from the spleen of F5 x CD45.1 mice. Enriched CD8 T cells were stimulated (VV-CD8_R, EL4-CD8_R, naive_R)  or not (VV-CD8, EL4-CD8, Naive) with NP68 peptide (10 nM) for 2h at 37 °C.

first: Daphné

last: Laubreton

first: Margaux

last: Prieux

first: Sophia

last: Djebali

first: Maxence

last: Dubois

first: Olivier

last: Gandrillon

first: Christophe

last: Arpin

first: Jacqueline

last: Marvel


title: Epigenetic regulation of cilia stability and kidney development by the chromatin remodeling SWI/SNF complexes [72hpf]

city: shanghai

first: xiaoyu

last: cheng

address: siping road

institute: tongji university

summary: Cilia are important subcellular organelles and are regulated by transcription factors including Foxj1 and Rfx proteins. Whether and how are cilia regulated at epigenetic level remains unknown. We addressed this question by knocking down or knocking out of chromatin remodeling genes. Interestingly, depletion of multiple components of the switch/sucrose non-fermentable (SWI/SNF) complexes lead to ciliopathy-like phenotypes in zebrafish embryos. Specifically, depletion of Actl6a, one of the components of the SWI/SNF complexes lead cilia disassembly and cystic kidney, but do not affect cilia motility. Omics studies show that in Actl6a-depleted embryos, a set of cilia genes including Foxj1a and Rfx2, the master regulators of cilia assembly, were downregulated at transcriptional level, chromatin accessibility and the SWI/SNF complexes binding. Thus, our study reveals that the SWI/SNF complexes regulate cilia stability and kidney development by direct modulating the expression Foxj1a and Rfx2.

overall_design:
To investigate the role of actl6a in protonephros development and ciliary stability in zebrafish, we used CRISPR/Cas9 to knockout actl6a and constructed a mutant strain. The sibling and mutant embryos were cleaved and the tissue of pronephric duct was isolated.
We then perfomed gene expression profiling analysis using data obtain from RNA-seq of 10 different pronephric duct per group between sibling and actl6a-/-.
Comparative gene expression profiling analysis of RNA-seq data for pronephric duct of 72hpf sibling and actl6a-/-.

first: Xiaoyu

last: Cheng

first: Qianshu

last: Zhu

first: Shilin

last: Ma

last: Peng

first: Guanliang

last: Huang

first: Guifen

last: Liu

first: Wentao

last: Zhang

first: Yong

first: Cizhong

last: Jiang

first: Ying

last: Cao


title: The RNA-binding protein HuR impairs adipose tissue anabolism in pancreatic cancer cachexia

city: Tualatin

first: Peter

last: Pham

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Radiation Medicine

institute: OHSU

summary: Cachexia, a wasting condition defined by chronic loss of fat and muscle, is a frequent complication of pancreatic ductal adenocarcinoma (PDAC) that negatively impacts quality of life and confers poor patient survival. Nutritional supplementation cannot fully reverse adipose and muscle tissue wasting, and the mechanisms underlying this phenotype are unclear.  This work aims to define the relative contributions of catabolism and anabolism to adipose wasting in PDAC-bearing mice. Human antigen R (HuR) is an RNA-binding protein recently shown to suppress adipogenesis. We hypothesize that fat wasting results from a loss of adipose anabolism driven by increased HuR activity in adipocytes of PDAC mice.

overall_design:
Adult C57BL/6J mice received orthotopic PDAC cell (KrasG12D; p53R172H/+; Pdx1-cre) or PBS (sham) injections.

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Due to a data transfer issue occurring between two cloud storage vendors, the raw data files (FASTQ and BAM) were lost.
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first: Paige

middle: C

last: Arneson-Wissink

first: Katherine

last: Pelz

first: Beth

last: Worley

first: Heike

last: Mendez

first: Grace

last: McCarthy

first: Alex

last: Chitsazan

first: Jonathan

last: Brody

first: Aaron

middle: J

last: Grossberg


title: Depletion of MFF from oocytes impairs mitochondrial dynamics, leading to inhibited oocyte maturation and early embryonic development in mice

city: Shenzhen

first: Renwu

last: Hua

address: Haiyuan 1st Road

institute: HKU-SZH

summary: To investigate the effect of mitochondrial fission factor (MFF) on oocyte competence and female fertility using an oocyte-specific Mff knockout mouse model. Oocyte-specific Mff deficiency hindered oocyte maturation and early embryonic development via regulation of mitochondrial dynamics, resulting in female subfertility. What is known already: Emerging studies have demonstrated that mitochondrial dynamics play a vital role in oocyte maturation and early embryo development. MFF is one of the crucial proteins regulating mitochondrial dynamics. Our previous studies have indicated that Mff is necessary for oocyte competence and fertility using a global Mff knockout mouse model. However, further investigation is needed to determine whether the deletion of Mff in oocytes could affect oocyte competence and early embryonic development by regulating mitochondrial dynamics.The Mfffl/fl; Gdf9-Cre mice consistently exhibited reduced fertility with a significant decrease in litter size, number of litters per female, and number of pups per female compared to the Mfffl/fl mice. The numbers of GV oocytes, ovulated oocytes and 2-cell embryos  were significantly lower in the Mfffl/fl; Gdf9-Cre mice. The blastocyst (32.32% vs. 68.44%, p<0.05) embryo development rate per 2-cell embryos was also significantly lower. In vitro maturation revealed that of Mfffl/fl; Gdf9-Cre GV oocytes had significantly lower rates of GV break-down and polar body extrusion . The ratios of aberrant spindle and misaligned chromosomesin ovulated oocytes from Mfffl/fl; Gdf9-Cre mice were significantly increased. In terms of mitochondrial dynamics, the mitochondrial size and the ratio of abnormal mitochondrial distribution (unevenly aggregated) in Mfffl/fl; Gdf9-Cre oocytes significantly elevated. This study found that the Mff played a crucial role in oocyte maturation and early embryonic development. These results shed light on the important role played by MFF in ensuring proper mitochondrial dynamics in oocytes and underscore the significance of this protein in female fertility. This study provides insights into potential therapeutic targets for infertility and related diseases in humans.

overall_design: RNA-seq profiling of oocyte-specific knockout MFF of GV (germinal vesicle) and ovulated oocytes in mice

first: Tianren

last: Wang


title: Single-nucleotide resolution m6A peak and their unqiue characteristics in developing mouse forebrain

city: Daejeon

first: Ki-Jun

last: Yoon

address: 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: We investigated the accurate location and methylation stochiometry for Mettl14-dependent m6A peaks in the samples from P0 mouse forebrains using m6A-SAC-seq. We found that m6A-modified transcripts showed strong enrichment for genes associated with synapse organization, axonogenesis, positive regulation of cell projection organization, and regulation of synapse, implying that m6A-modified RNAs play a key role in neuronal differentiation during early postnatal cortical development .

overall_design: To investigate the single-nucleotide resolution of m6A peak and their quantitative stoichiometry in P0 forebrain, we conducted m6A-SAC-seq from WT and Nestin-Cre Mettl14 conditional knockout mouse. By comparing WT and Mettl14 cKO, we extracted Mettl14 dependent m6A peak in P0 forebrain.

first: Huiseon

last: Hwang

first: Bonsang

last: Koo

first: Ajeet

last: Kumar

first: Sung-Min

last: Lee


title: Development of a microarray to study the role of the genes veA and patL genes and the effect of DMSO in regulating the transcriptome in Penicillium expansum.

city: TOULOUSE

first: Olivier

last: PUEL

address: 180 chemin de Tournefeuille

department: TOXALIM UMR 1331

institute: INRAE

summary: The transcriptome of Penicillium expansum between the wild-type strain and strains deleted for transcription factors was studied in order to better understand the regulation of biosynthetic pathways for specialized metabolites and then modulate their production.

overall_design: The transcriptome of control and  control + DMSO (280 mM) strains and strains deleted for veA or patL was analyzed at t=5 days. Six replicates were done for each condition.

first: Ophélie

last: Rocher

first: Sophie

last: Lorber

last: Puel

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Investigate the effect of depletion of Mettl14 or Ythdf2 on RNA stability in primary cultured cortical neurons

summary: Across the transcriptome, m6A-modified transcripts showed increased relative stability in the Mettl14 cKO condition , and the number of m6A sites affected the stability. The stability of transcripts with m6A only in the CDS changed slightly less, while the stability of transcripts with m6A only in the 3' UTR or with m6A in both regions increased more significantly, suggesting that m6A in the 3' UTR has a more pronounced effect on mRNA stability. Unexpectedly, m6A-modified transcripts showed only a slight stability change in the DF2 cKO condition.

overall_design: To indentify the stability of each gene from neurone, cultured primary cortical neurons from WT and Mettl14 cKO mice, or WT and Ythdf2 cKO mice were treated with Actinomycin D, and RNA-seq was performed at 0 and 5 hours to calculate the RNA stability of each transcript.


title: Mast Cell Derived Histamine Negatively Regulates Hematopoiesis

city: Cleveland

first: Bailey

last: Klein

state: OH

address: 10900 Euclid Ave

institute: Case Western University

summary: Hematopoietic stem cells (HSCs) are essential for generating all blood cell types and maintaining immune function and oxygen transport. This requires tight regulation of self-renewal,  differentiation, and quiescence, driven by intrinsic and extrinsic signals. While the influence of  many HSC progeny on HSC decisions are recognized, the role of mast cells (MCs) remain  understudied. MCs are known for their immunomodulatory functions through the secretion of  factors such as histamine and could offer new insights into HSC regulation. In this study, we  describe a novel role for MC-derived histamine in modulating HSC behavior. We observed that  genetically MC-deficient “SASH” mice exhibit increased hematopoietic output and bone marrow (BM) HSCs, characterized by an enhanced quiescent signature that increases resistance to  myeloablative chemotherapy. The SASH microenvironment also contained increased frequencies of HSC-supportive cell types and expression of genes conducive to HSC maintenance, which  together accelerated HSC engraftment when wild-type BM was transplanted into SASH  recipients. Moreover, we found lower serum histamine levels in SASH mice, and that the  enhanced hematopoietic phenotype observed in these mice could be reversed by administering  exogenous histamine. Subsequent experiments with FDA-approved antihistamines in wild-type  mice revealed that cetirizine, an H1R inverse agonist, notably increased HSC frequency in the  BM. Overall, our findings implicate MCs are negative regulators of HSC function. This lays the  groundwork for future studies to elucidate the underlying mechanisms and explore the  therapeutic potential of modulating histamine signaling to promote hematopoiesis.

overall_design: This study investigated the transcriptional differencees between bulk bone marrow and lineage depleted bone marrow between WT (c57 mice) and mast cell deficiient SASH mice

middle: R

first: Julianne NP

last: Smith

first: Ramachandra

last: Kathabula

first: Rahul

last: Chaudhary

first: Zhenxiang

last: Gao

first: Brittany

last: Cordova

first: Frederick

last: Petroze

first: Riya

last: Tiwari

first: Stanton

middle: L

last: Gerson

first: Rong

last: Xu

first: Koen

last: van Besien

first: Sanford

middle: D

last: Markowitz

first: Amar

middle: B

last: Desai


title: Single Cell Transcriptomics for Tbc1d23ΔE15/ΔE15 and wild-type mice bone marrow

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

summary: Compare bone marrow cell population and gene regulation changes in Tbc1d23ΔE15/ΔE15 and wild-type mice

overall_design: Bone marrow cells were isolated from 8-week-old female of C57BL/6J wild-type and Tbc1d23ΔE15/ΔE15 mice. The cells were sorted with  EasySep™ Mouse Hematopoietic Cell Isolation Kit for analysis with scRNA-seq.

first: Li

last: Chen

first: Xiao

last: Hu

first: JinRui

last: Wang

first: Qing

last: Yang


title: Shiga Toxin kidney

city: Fuzhou

first: Zhimin

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

summary: We performed single-cell transcriptome sequencing on control and shiga toxin induced kidneys to reveal kidney injury characteristics

first: Yanfang

first: Jianfu

last: Zhou


title: Effect of m6A on neuronal mRNA translocation from soma to neurites in the developing brain

first: Ki-Jun

last: Yoon

summary: Neurons are highly polarized cells with extensive neuronal processes, including dendrites and axons. All the RNA required by neurons is synthesized in the soma, while distinct neurites still require various RNAs. The soma and neurites contain different transcriptomes tailored to their specialized functions. m6A modification, the most abundant RNA modification in eukaryotes, can affect RNA stability and translation efficiency. Here, we suggest that m6A also affects RNA translocation in neurons and can alter the transcriptome in distal neurites. To investigate this, we micro-dissected soma and axons from the corpus callosum of P0 mouse brains and conducted RNA-seq on both WT and Nestin-Cre Mettl14 conditional knockout mice. We found that m6A modification positively promotes the neurite localization of a subset of mRNAs related to axonogenesis and growth cone regulation, which is essential for normal axonogenesis.

overall_design: To examine the functional contribution of m6A modification in developing axons, we conducted RNA-seq using microdissected tissue from the axon-enriched Corpus Callosum of cortical projection neurons (layer 2/3) at P4, a time-point at which the maximum number of axons are distally projected in the callosal region and remain in the white matter before entering the cortical plates.

first: Bonsang

last: Koo

first: Huiseon

last: Hwang

first: Ajeet

last: Kumar


title: Epigenetic regulation of cilia stability and kidney development by the chromatin remodeling SWI/SNF complexes [FitCUT&RUN]

first: xiaoyu

last: cheng

overall_design: To detect changes in the binding of SWI/SNF complexes in the genome after actl6a knockdown, we used Fit-Cleavage Under Targets & Release Using Nuclease (FitCUT&RUN) for smarca4a in actl6a morphant.

first: Xiaoyu

last: Cheng

first: Qianshu

last: Zhu

first: Shilin

last: Ma

last: Peng

first: Guanliang

last: Huang

first: Guifen

last: Liu

first: Wentao

last: Zhang

first: Yong

first: Cizhong

last: Jiang

first: Ying

last: Cao


title: Epigenetic regulation of cilia stability and kidney development by the chromatin remodeling SWI/SNF complexes [ATAC-seq]

overall_design:
In order to investigate which chromatin regions were affected by actl6a deficiency in protonephros of zebrafish, and ultimately determine which genes may have been affected in transcriptional regulation, we used morpholino microinjection to knock down actl6a in one-cell stage embryos (Tg (atp1a1a.4:EGFP), the transgenic line has GFP fluorescence in the pronephros). The 30hpf treated embryos were cleaved and the tissue of pronephric duct was isolated for ATAC-seq.
Then, we collected 10000 to 20000 pronephric duct cells from ctrl and morphant, respectively, and constructed a library. Perform chromatin accessibility analysis on the data obtained from ATAC seq.
Comparative chromatin accessibility analysis of ATAC-seq data for pronephric duct of 30 hpf ctrl and morphant.


title: Aryl-hydrocarbon receptor in smooth muscle cells protect against dioxin induced adverse remodeling of atherosclerosis [RNA-seq]

city: Stanford

first: Juyong

middle: Brian

last: Kim

state: CA

address: 300 Pasteur Dr.

institute: Stanford University

summary: Introduction: Environmental exposure to dioxin has been linked to increased myocardial infarction. Smooth muscle cells (SMC) in the coronary vasculature play a critical role in atherosclerotic plaque remodeling due to their phenotypic plasticity, however, the detailed mechanism linking dioxin exposure to adverse SMC modulation is not well understood. Methods: Single-cell RNA and ATAC sequencing and histological analyses were performed on the aorta from mouse models of atherosclerosis exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or control. Primary human coronary artery SMC (HCASMC) treated in culture with TCDD were used to perform RNA-Seq, ATAC-Seq, and functional phenotypic assays. ChIP-Seq was performed with antibodies against Aryl-hydrocarbon receptor (AHR) and TCF21.  Results: Modulated SMC were the most transcriptionally responsive cell type to dioxin in the atherosclerotic aorta. Dioxin accelerated disease phenotype by promoting a modulated SMC phenotype early, resulting in increased lesion size, migration of SMC, and macrophage recruitment to the lesion. We found C3 expressing modulated SMCs to be likely contributing to the increased macrophage recruitment and inflammation. Analysis of the RNA-Seq data from HCASMC treated with TCDD showed differential enrichment of biological pathways related to cell migration, localization, and inflammation. Further, ATAC-Seq data showed a significant activation for pathways regulating vascular development, cell migration, inflammation, and apoptosis. Also, there was enrichment of AHR ChIP-Seq peaks as expected, however, the TCF21 enrichment decreased significantly with TCDD treatment. The SMC-specific Ahr knockout resulted in increased oxidative stress in SMC, increased lesion size and macrophage content, and loss of SMC lineage cells in the lesion cap when exposed to TCDD. Conclusion: Dioxin adversely remodels atherosclerotic plaque by accelerating the SMC-phenotypic modulation, and increasing inflammation and oxidative stress resulting in increased macrophage recruitment and lesion size. Dioxin may adversely affect the SMC phenotype and disease state by affecting the TCF21 occupancy in the open chromatin regions. Ahr in SMC confers protection against dioxin by promoting a stable plaque phenotype and reducing dioxin induced oxidative stress.

overall_design: The RNA expression profiling of human coronary artery smooth muscle cells (HCASMC) grown in serum were evaluated with DMSO, CSE (cigarette smoke extract) or TCDD treatment.

first: Guyu

last: Qin

first: Quanyi

last: Zhao

first: Brian


title: Aryl-hydrocarbon receptor in smooth muscle cells protect against dioxin induced adverse remodeling of atherosclerosis

overall_design: Human coronary artery smooth muscle cells (HCASMC) grown with DMSO or Dioxin were evaluated with an antibody to AHR, TCF21, or input control.


title: Wnt/β-catenin/ATF3 signaling promotes AKI to CKD progression by regulating mitophagy in mice [HKC-8]

city: Xiamen

first: Liangxiang

last: Xiao

address: No. 201-209, Hubin South Road

institute: Zhongshan Hospital of Xiamen University

summary: Sustained activation of Wnt/β-catenin signaling has been shown to promote AKI to CKD progression. However, its underlying mechanisms remain largely unclear. In this study, we investigated this issue via unilateral ischemia/reperfusion injury in mice and hypoxia/reoxygenation (H/R) in HKC-8 cells. Both in vitro and in vivo, overexpression of Wnt1 promoted mitochondrial dynamics and mitophagy damage. Furthermore, we revealed that ATF3 not only is a transcriptional target of canonical Wnt/β-catenin signaling but is also an important pathogenic mediator of kidney disease. ATF3 was expressed in various CKD animal models, including UUO, UIRI, ADR and 5/6NX. In vitro, exogenous ATF3 induced mitochondrial dynamics and mitophagy, and silenced ATF3 expression protected mitochondrial function. Finally, compared with normal individuals, patients with various kidney diseases presented markedly elevated levels of ATF3. In addition, ATF3 levels are closely correlated with renal injury markers and renal fibrosis area in patients. Thus, these results suggest that Wnt/β-catenin/ATF3 signaling activation promotes AKI to CKD progression by regulating mitochondrial dynamics and mitophagy. ATF3 can serve as a promising potential biomarker for AKI to CKD progression.

overall_design: In the HKC-8 cells, the cells transfected with either p-Wnt-1 or pcDNA3 were sequenced. The cells transfected with p-Wnt-1 and treated with KP6 were also sequenced.

first: Gewenhan

last: Chen

first: Yanni

last: Zhou

first: Mengjiao

last: Lin

first: Anting

last: Li

first: Shijie

last: Lu

first: Xue

last: Hong


title: Cytosolic Bacteria in Tumor Cells Promote Immune Evasion during Breast Cancer Metastatic Recurrence

city: HangZhou

first: Xiaoqin

state: ZheJiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

institute: Westlake University

summary: Intratumor microbiota represents an understudied yet influential component of the cancer ecosystem, impacting the physical, chemical and immunological tumor microenvironment. However, the interplay between intratumor microbiota and the tumor-immune network as well as its physiological significance remain poorly understood. In this study, we investigated the long-term developmental process of metastatic seeds from PyMT breast tumor, and identified the key role of intratumor bacteria for efficient metastasis outgrowth after tumor cell colonization in distant organ in an immune-mediated process. Cytosolic bacteria, the dominant form of intratumor bacteria in PyMT tumors, promote metastatic tumor cell immune evasion through activating tumor cell intrinsic cGAS-STING-Il17b response pathway, ultimately inducing neutrophil into a protumor state to suppress cytotoxic T cells. Intriguingly, the upregulation of Il17b is dependent on the intracellular invasion of bacteria and accumulation of cytosolic dsDNA. The extracellular bacteria can not activate the STING pathway but induce neutrophils into an anti-tumor state instead. Under the physiological condition, the eradication of intracellular bacteria effectively abrogates metastatic immune suppression and prevents post-surgical metastatic recurrence, akin to the effect of introducing extracellular bacteria. Our findings underscore the critical role of intratumor bacteria in modulating the immune landscape of recurrent metastatic niches, and emphasize the bacteria-host interaction mode as a novel key factor for immune regulation.

overall_design: For FVB mouse experiment, lungs were harvested from PBS(injected PBS), Bacteria(injected bacteria), woBac(injected tumor cell co-cultured with bacteria which showed negative bacteria signal) , withBac(injected tumor cell co-cultured with bacteria which showed positive bacteria signal). For germ free mouse experiment, lungs were harvested from WT(wild type), Control(injected tumor cells co-cultured with bacteria) and ATBx(injected tumor cell co-cultured with bac but use Antibiotics treated) mice at the end of point of experiment. Then lungs were dissected into single cells. Live cells were sorted by FACS to do 10X scRNA-seq. For RNA seq experiment, tumor cells co-cultured with live or dead bacteria. Then tumor cell containing live or dead bacteria were sorted by FACS to do bulk RNA-seq.

first: Bingqing

last: Yao

first: Xiunan

last: Fang

first: Yajing

last: Guo

first: Shang

last: Cai


title: Chromosomal rearrangement-enhanced mRNA stability drives the carcinogenicity of oncofusion in pediatric leukemia

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

summary: Acute lymphoblastic leukemia (ALL), the most common type of pediatric leukemia, is directly driven by chromosomal rearrangement-induced fusion genes. Compared to wild-type genes, various oncofusions exhibit heightened expression levels and continuous enhanced function to drive tumorigenesis. However, the underlying mechanism by which chromosomal rearrangements lead to functional enhancement remains largely elusive. Meanwhile, although large-scale sequencing has illuminated numerous fusion events, most of their functional implications is unknown. Here, we uncover for the first time that mRNA stability enhancement is a common and important tumorigenic mechanism for oncogenic fusions, such as classical PAX5 fusions. Based on this universal mechanism, we have identified a novel oncogenic fusion, STK38-PXT1, which exhibits upregulated STK38 mRNA levels and directly drives the development of ALL. Mechanically, the increased mRNA stability arises from enhanced m6A modification of oncofusions, which is primarily due to “gene truncation”, such as PAX5 fusion, and “partner collaboration”, such as STK38-PXT1. Furthermore, IGF2BP3, an m6A reader specifically up-regulated in these fusions-driven leukemia, is crucial for maintaining the high mRNA stability of oncofusions. We further propose venetoclax as an innovative and clinically available drug for ALL driven by these high-stability oncofusions. Our study not only sheds light on mRNA stabilization as a general mechanism for fusions to drive tumorigenesis, but also presents a promising therapeutic drug target and strategy for ALL patients.

overall_design: Ba/F3 cells infected with corresponding lentivirus

first: Meidan

last: Ying

first: Zhimei

last: Xia


title: Aryl-hydrocarbon receptor in smooth muscle cells protect against dioxin induced adverse remodeling of atherosclerosis [ATAC-seq]

first: Juyong

last: Kim

overall_design: The chromatin acessibility of human coronary artery smooth muscle cells (HCASMC) grown in serum were evaluated with DMSO or TCDD treatment.

first: Guyu

first: Quanyi


title: The role of suv4-20h1 in Xenopus multiciliogenesis

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

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

overall_design: Refer to individual Series


title: The role of suv4-20h1 in Xenopus multiciliogenesis [RNA]

summary: Histone post-translational modifications (PTM) greatly influence gene expression and are widely considered to regulate progression through development. However, the function of some PTMs remain elusive. H4K20 is sequentially methylated in concert with the cell cycle. In proliferating cells, SET8/KTM5A writes the monomethyl mark in G2/M phase, which then is converted to the di- and trimethylated states by SUV4-20H1/H2 (KMT5B/KMT5C) methyltransferases in the next G1 and S phase. In quiescent, differentiated cells, H4K20me2 represents the most abundant histone modification present in vertebrate chromatin. To address the function of H4K20 methyl states in development, we blocked the deposition of H4K20me2 and H4K20me3 by depleting the SUV4-20H1 in Xenopus embryos. This results in a severe ciliogenic defect in multiciliated cells (MCCs), as well as the repression of hundreds of cytoskeleton and cilium related genes. Further, we demonstrate that this defect can be rescued by wildtype, but not catalytically inactive SUV4-20h1, as well as by overexpressing PHF8, an H4K20me1-specific histone demethylase. Ciliogenic defects cannot be rescued by master regulators of ciliogenesis on the phenotypic or transcriptional levels. Taken together, this indicates that SUV4-20H1 plays a critical role in multiciliogenesis.

overall_design: To investigate the effect of suv4-20h1/2 knockdown on Xenopus animal caps, we injected embryos with translation blocking morpholinos again suv4-20h1 and suv4-20h2 and then cut epidermal explants (animal caps). Separately, we were interested in the effect of multicilin overexpression in conjunction with suv4-20h1 depletion, so we co-injected hormone inducible multicilin mRNA (mci-hGR) and induced with dexamethasone. At NF 16, we harvested animal caps and performed RNA-seq.

first: Janet

last: Tait

first: Ralph

last: Rupp


title: Molecular mechanism of Forsythia suspensa glycoside promoting innate immunity by activating ER stress.

city: Zunyi

first: yan

last: Zhang

state: Guizhou

address: Honghuagang

department: College of Basic Medicine

institute: Zunyi Medical University

summary: Forsythia suspensa glycoside is a phenylethanoid glycoside extracted from the bark, leaves, flowers, fruits, and seeds of the Oleaceae plant Forsythia suspensa. As a major active ingredient in the Chinese herbal medicine Forsythia suspensa, it has a wide range of pharmacological activities. It not only inhibits various Gram positive and negative bacteria that cause infections, but also has strong antiviral effects. However, the role of Forsythia suspensa glycosides in innate immunity is not yet clear.

overall_design: Expose C. elegans to 10 μM Forsythia and place the nematodes in Pseudomonas aeruginosa to test their innate immune ability.

first: Mengqi

last: Wang

first: Yi

last: Xiao


title: The role of suv4-20h1 in Xenopus multiciliogenesis [ATAC]

overall_design: To investigate the effect of suv4-20h1 knockdown on Xenopus animal caps, we injected embryos with translation blocking morpholinos again suv4-20h1 and cut epidermal explants (animal caps).  At NF 16, we harvested animal caps and performed ATAC-seq to profile changes in chromatin accessibility upon suv4-20h1 depletion.


title: RNA changes upon glucose starvation treat with or without NAC

city: xiamen

first: feng

last: deyi

address: Xiamen University

institute: xiamen university

summary: The adaptation of tumor cells to metabolic stress is crucial for tumordevelopment, We demonstrate that the translation of NRF2, a master regulatorof antioxidant response, is controlled by the OGDH-METTL3 axis in melanomafor glucose starvation adaptation, To elucidate the regulatory mechanism ofthe OGDH-METTL3 axis during glucose starvation,we conducted coimmunoprecipitation and mass spectrometry analysis to identify the bindingpartner of OGDH that governs both the OGDH-METTL3 axis and tumor celladaptation to qlucose deprivation.

overall_design: Control and OGDH knockdown A375 cells treated with or without NAC were starved with glucose for 5 hours respectively, and then collected by trizol. Three parallel groups of sampleswere collected for each experiment.

first: I

last: Zhou

first: X

last: chen

first: K

last: Xu


title: Transcriptome analysis of 92.1-parental and 92.1-resistant uveal melanoma cells

city: Shanghai

first: Tianyu

last: Zhu

address: Zhizaoju Road

institute: Shanghai Ninth People's hospital

summary: To study the mechanism of cisplatin resistance in uveal melanoma, we performed RNA-seq of 92.1-parental and 92.1-resistant uveal melanoma cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 92.1-parental cells (Ctrl, n=2) and resistant cells (Res,n=2).


title: NEDDylation modifies mitochondrial transcription to maintain oocyte quality (Ovary)

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Aging decreases oocyte quality, leading to infertility, miscarriage, and birth defects. Major contributors to this decline include mitochondrial dysfunction and chromosome dynamics dysregulation. Here, we show that oocyte-specific deletion of Uba3, which encodes the catalytic subunit of the E1 NEDDylation activating complex (NAE), in mice causes sterility and premature depletion of the ovarian reserve. Fully grown Uba3 conditional knockout oocytes show hallmarks of mitochondrial abnormalities, including increased reactive oxygen species, decreased oxidative phosphorylation, and increased unhealthy mitochondria. These discoveries provide insight into mechanisms governing oocyte quality and a regulatory role of NEDDylation for mitochondrial transcription in gametes.

overall_design: We performed RNA-sequencing analysis on 5 control and 5 Uba3 cKO ovaries collected from 3-week-old non-stimulated mice.

first: Stephanie

middle: A

last: Pangas

first: Avery

last: Ahmed


title: NEDDylation modifies mitochondrial transcription to maintain oocyte quality


title: Epigenetic regulation of cilia stability and kidney development by the chromatin remodeling SWI/SNF complexes [30hpf]

city: shanghai

first: xiaoyu

last: cheng

address: siping road

institute: tongji university

summary: Cilia are important subcellular organelles and are regulated by transcription factors including Foxj1 and Rfx proteins. Whether and how are cilia regulated at epigenetic level remains unknown. We addressed this question by knocking down or knocking out of chromatin remodeling genes. Interestingly, depletion of multiple components of the switch/sucrose non-fermentable (SWI/SNF) complexes lead to ciliopathy-like phenotypes in zebrafish embryos. Specifically, depletion of Actl6a, one of the components of the SWI/SNF complexes lead cilia disassembly and cystic kidney, but do not affect cilia motility. Omics studies show that in Actl6a-depleted embryos, a set of cilia genes including Foxj1a and Rfx2, the master regulators of cilia assembly, were downregulated at transcriptional level, chromatin accessibility and the SWI/SNF complexes binding. Thus, our study reveals that the SWI/SNF complexes regulate cilia stability and kidney development by direct modulating the expression Foxj1a and Rfx2.

overall_design:
To investigate the role of actl6a in protonephros development and ciliary stability in zebrafish, we used morpholino microinjection to knock down actl6a in one-cell stage embryos (Na, K-ATPase alpha1A4:GFP, the transgenic line has GFP fluorescence in the pronephros). The treated embryos were cleaved and the tissue of pronephric duct was isolated.
We then perfomed gene expression profiling analysis using data obtain from RNA-seq of 10 different pronephric duct per group between control and knockdown.
Comparative gene expression profiling analysis of RNA-seq data for pronephric duct of 30hpf ctrl morpholino injected embryos and actl6a knockdown embryos (ctrl and actl6a morphants)

first: Xiaoyu

last: Cheng

first: Qianshu

first: Shilin

last: Ma

last: Peng

first: Guanliang

last: Huang

first: Guifen

last: Liu

first: Wentao

first: Yong

first: Cizhong

first: Ying

last: Cao


title: H3K9ac and H3K27ac analysis of 92.1-parental and 92.1-resistant uveal melanoma cells

summary: To study the mechanism of cisplatin resistance in uveal melanoma, we performed H3K9ac and H3K27ac Cut&Tag in 92.1-parental and 92.1-resistant uveal melanoma cells.

overall_design: Cut&Tag for H3K9 and H3K27 acetylation in 92.1 parental and resistant uveal melanoma cells.


title: mRNA splicing in midbody is essential for proper cell abscission in mitosis

city: 北京

first: YU

last: ZHANG

state: non-US Resident

address: XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building

institute: Peking Univ.

summary: Midbody is a transient structure assembled in the last step of mitosis and is currently conceptualized as a structural remnant subject to degradation following cytokinesis. However, our findings indicate that midbody regulation is more complicated than original thought. Knockdown spliceosome proteins in cells showed a multinuclear phenotype and abnormal midbody. Spliceosome and ribosome components are enriched in midbody. We further found that mRNA splicing and protein translation occurs in the midbody during last step of mitosis, which are necessary events for proper abscission of nascent daughter cells. Midbody spliced and translated PRC1 and NINL are essential for proper midbody function. Either PRC1 or NINL knockdown also showed a multinuclear phenotype and abnormal midbody. Treating cancer cells with both chemotherapy and spliceosome inhibitors dramatically lowers the concentration of both drugs, avoiding more severe side effects. Our study discovers a novel regulating mechanism for mitosis and provides a new strategy for cancer therapy.

overall_design: two plates of cells were incubated with full culture medium containing 500μM biotin-phenol, while one plate of cells was supplied with 100nM PlaB until cells entered cytokinesis, which usually took approximately 40 minutes. Following this, 1mM H2O2 was added to all three plates of cells for 3 minutes. The reaction was stopped by replacing the medium with quenching buffer (10 mM sodium ascorbate, 10 mM sodium azide, and 5 mM Trolox in Dulbecco’s Phosphate Buffered Saline [DPBS]). Cells were washed three times with quenching buffer and collected. Total RNAs were extracted using Trizol. For the enrichment of biotinylated RNAs, total RNAs were mixed with 20μL of Dynabeads MyOne Streptavidin Beads C1, rotating overnight at 4°C, and eluted as previously described. Eluted RNAs were purified using GeneJet RNA Concentration Kits (ThermoFisher) and the RNA concentration was determined using the Agilent 2100 Bioanalyzer.

first: Yu

last: Zhang

first: Jianyuan

last: Luo


title: Therapeutic efficacy of CDK7 inhibition in pancreatic cancer through proliferation arrest and inducing replication stress [8898T]

city: Boston

first: Ziyue

last: Li

state: Massachusetts

address: 450 Brookline Ave, D718

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Pancreatic ductal adenocarcinoma (PDAC) is a devastating cancer with few effective therapies. Here, we demonstrate that cyclin dependent kinase 7 (CDK7) is essential for the proliferation and viability of PDAC cells by showing potent anti-tumor efficacy for the CDK7-specific inhibitor YKL-5-124 in preclinical PDAC models. Selective CDK7 inhibition leads to G2/M cell cycle arrest and apoptosis in PDAC, while mediating a more modest transcriptional response compared with multi-targeted CDK7/12/13 inhibitors. YKL-5-124 treatment impairs DNA damage repair (DDR) pathways in PDAC cells and evokes genomic instability by inducing R-loop formation and DNA replication stress in telomeric regions leading to chromosomal bridging and micronuclei formation. Furthermore, we demonstrate that selective CDK7 inhibition has in vitro and in vivo combinatorial efficacy with gemcitabine chemotherapy through pronounced induction of replication stress and apoptosis. Collectively, these findings support selective CDK7 inhibition as a promising therapeutic strategy for PDAC.

overall_design: Examination of the Pancreatic cell line PATU-8988T treated with DMSO vs CDK7 inhibitors (THZ1 or YKL-5-124) for 4-hour or 24-hour.

first: Annan

last: Yang

first: Kevin

last: Kapner

first: Andrew

last: Aguirre


title: MARSseq of the artificial IFN-I receptor VS HeLa treated with IFN-beta

city: Rehovot

first: Gideon

last: Schreiber

address: Herzel st

country: Israel

institute: Weizmann Institute of Science

summary: MARSseq experiment demonstrated that engaging the artificial AIR receptor system induced very similar transcriptional changes and upregulation of interferon response genes compared to treatment with native IFN-β, validating the ability of AIR to mimic the natural IFN-I receptor functionally.

overall_design: MARSseq experiment was conducted to compare the gene expression profiles induced by IFN-β treatment versus treatment with the artificial IFN-I receptor in HeLa cells.

first: Eyal

last: Zoler


title: Machine learning identifies spatial signatures of kidney resident immune cells

city: Bonn

first: Junping

last: Yin

state: State

address: Venusberg-Campus, 1

institute: uniklinikum bonn

summary: Immune cells are spatially distributed in many organs and may be affected by the local microenvironment. The identification of spatial fingerprints that allow predicting the positioning of immune cells analysed by single cell sequencing (scRNAseq) would facilitate better understanding of their roles in health and disease. Here we aimed to identify such fingerprints by employing machine learning methods. We used the kidney as model organ because it can be divided into regions with distinct functions and microenvironmental cues, the cortex and the outer and inner medulla. We generated 3 scRNAseq datasets of immune cells by manually dissecting these three areas from healthy mouse kidney. Several machine learning algorithms including Neuronet, RandomForest, DecisionForest, multilayer perceptron (MLP) and others were utilized to identify genes harboring spatial information. Two external spatial datasets were used to validate the broad utility of the identified spatial marker genes. We found that the MLP algorithm identified a set of high variable genes that predicted the position of kidney-resident macrophages with accuracy of >75%. External validation substantiated the predictive power of this fingerprint. Gene-set enrichment analysis informed about the biological context of spatial marker genes. These marker genes were enriched in pathways relating to microenvironmental responses and cellular adaptation and showed a gender bias. Prediction was poor for motile immune cells like monocytes derived macrophages, T cells and B cells. Our algorithm even predicted the position of immune cells in an external spatial human dataset with comparable efficiency. Applying our strategy to an external spatial scRNAseq dataset of brain microglia allowed predicting the position of brain microglia. In conclusion, we identified a set of spatial marker genes that can predict the location of resident immune cells in the human and murine kidney and demonstrate that our strategy can be transposed to other organs.

overall_design: Murine kidneys were dissected to Cortex, OM and IM. CD45+ immune cells from each compartment were sorted and loaded for 10x single cell RNA sequencing.

first: Christian

last: Kurts


title: NEDDylation modifies mitochondrial transcription to maintain oocyte quality (Oocyte)

first: Peixin

last: Jiang

overall_design: We performed RNA-sequencing analysis on 3 control and 3 Uba3 cKO pools of ~150 GV oocytes per pool

first: Stephanie

last: Pangas

first: Avery

last: Ahmed


title: The lncRNA LENT interacts with DHX36 to regulate translation and suppress autophagy in melanoma.

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

summary: The melanocyte lineage determining Microphthalmia-associated transcription factor (MITF) drives proliferation and survival of melanocytic melanoma cells through regulation of both coding genes and long non-coding RNAs (LncRNAs). Here we characterize LINC00520 (hereafter called LncRNA ENhancer of Translation, LENT) regulated by MITF and strongly expressed in melanocytic melanoma cells. LENT is essential for proliferation and survival of cultured melanocytic melanoma cells and xenograft tumours. LENT interacts with the G4 quadruplex resolvase DHX36 and both associate with the ribosome in the 80S and light polysome fractions. LENT modulates DHX36 association with a collection of mRNAs regulating their engagement in polysomes and their subsequent translation. These mRNAs encode proteins involved in endoplasmic reticulum (ER) and mitochondrial homeostasis as well as auto/mitophagy. Consequently, LENT silencing leads to extensive auto/mitophagy, compromised oxidative phosphorylation capacity and proteotoxic stress characterized by increased translation and mis-localization of mitochondrial proteins leading to apoptosis. The LENT-DHX36 axis therefore fine-tunes translation of proteins involved in ER and mitochondrial homeostasis to suppress auto/mitophagy and promote survival and proliferation of melanoma cells.

overall_design: Melanoma cell-line 501M was sequenced in triplicates by RNA-seq (using either whole extract or 80S/Light/Heavy fractions) and RIP-seq (using either control IgG or DHX36 antibody)  following si/shRNA silencing.

first: Alexandre

last: Haller

first: Giovanni

last: Gambi

first: Mattia

last: D’Agostino

first: Antonin

last: Lallement

first: Gabrielle

last: Mengus

last: Bec

first: Angelita

last: Simonetti

first: Eric

last: Ennifar

first: Irwin


title: Therapeutic efficacy of CDK7 inhibition in pancreatic cancer through proliferation arrest and inducing replication stress [PDX]

first: Ziyue

last: Li

first: Annan

last: Yang

first: Kevin

last: Kapner

first: Andrew

last: Aguirre


title: Single-cell transcriptome reveals drug-resistance signature and immunosuppressive microenvironment in lung adenocarcinoma harboring EGFR mutation

city: Ningbo

first: Shibo

last: Wu

address: Ningbo Medical Center

institute: Department of Respiratory Medicine, Lihuili Hospital

summary: A majority of EGFR-mutated lung adenocarcinoma (LUAD) inevitably develops acquired resistance to tyrosine kinase inhibitor (TKI) therapy within 2 years. Due to the heterogeneous tumor microenvironment (TME) and discrepant immunotherapy responses in patients with different EGFR mutation statuses, it is necessary to characterize the immune signatures during tumor resistance, facilitating the explorations of resistance mechanisms and drug discoveries.

overall_design: Six advanced LUAD patients harboring EGFR mutations were enrolled in this study, and tumor tissues were collected from 3 initially diagnosed (ID group) and 3 EGFR-TKIs resistant (Resistance group) individuals. Single-cell transcriptome landscapes of tumor samples were profiled. Subsequently, the differences in TME composition, functional phenotype of clusters, and cell-cell communications between the two groups were systematically analyzed.

first: Zhuowei

last: Shao

first: Weizhuang

last: Chen

first: Wenrui

last: Jiao

first: Lishen

last: Zhang

first: Li

last: Wang

first: Liuqing

last: Zheng


title: Transcriptional condensates enrich phosphorylated PRMT2 to stimulate H3R8me2a deposition and hypoxic response in cancers-RNA-seq

city: Tianjin

first: feng

last: dong

address: Qixiangtai Road 22

institute: Tianjin Medical University

summary: Histone arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), is crucial for transcription regulation and increasingly associated with cancer progression. However, some PRMTs present challenges as drug targets due to their unique, context-dependent activities. Here we report that hypoxia induces rapid condensation of PRMT2, which is required for its activity on histone H3R8 asymmetric dimethylation (H3R8me2a). Consistent with its roles in transcription activation, PRMT2 is enriched in transcriptional condensates and relies on its phosphorylation at Ser 12 (PRMT2S12ph). This phosphorylation, situated within the N-terminal intrinsic disordered regions of PRMT2, facilitates its integration into transcriptional condensates and H3R8me2a deposition. Consequently, PRMT2S12 phosphorylation is indispensable for transcription activation of the hypoxia-inducible genes and tumor progression in vivo. Notably, transcription-associated Cyclin-Dependent Kinases (CDK7-CDK9) is imperative for PRMT2S12 phosphorylation. As a result, CDK9 inhibitors suppress hypoxia-induced H3R8me2a activity and transcription, and they synergize with Temozolomide (TMZ) in halting tumor progression, partly reliant on blocking PRMT2S12ph. Therefore, our study uncovers novel roles of transcriptional condensation in augmenting methyltransferase activity and provide a fresh anti-cancer mechanism for CDK9 inhibitors by restricting context-dependent transcriptional programs.

overall_design: The hypoxia induced genes expression in U87 PRMT2-WT-Hypoxia,  U87 PRMT2-S12A-Hypoxia ,  U87 DMSO-hypoxia and U87 TG02-Hypoxia

first: Xudong

first: Feng

last: Dong

first: Xuan

last: Cheng


title: CDK1/S6K1-PYGO2 axis regulates eIF3D-dependent translational initiation during mitosis

city: Suwon-si

first: Daeho

last: Joe

state: Gyeonggi-do

address: 2066, Seobu-ro

institute: Sungkyunkwan University

summary: mRNA translation represents the conclusive step of the gene expression program, which is crucial in most cellular processes including cell cycle progression, cell growth and proliferation, and is tightly controlled throughout the cell cycle. Although global translation rates are decreased during mitosis, the significance of translation in mitosis resides in the fact that the proteins produced during this phase are vital for the proper progression of mitosis and subsequent cell division. Protein synthesis is driven by translation factors that interact with the ribosome, but translation factors which regulate mitotic translation and their regulatory mechanism remain poorly elucidated. Here we describe a regulatory mechanism of mitotic translation, governed by eIF3D-dependent translation initiation that relies on a novel translation factor PYGO2 downstream of CDK1 and S6K1 signaling pathway. PYGO2 is phosphorylated on serine (S) 40 and S97 by CDK1/Cyclin B1, and on S48 by S6K1 during mitosis. PYGO2 localizes at mitotic spindle and cytosol, interacts with eukaryotic translation initiation factor 3 (eIF3) complex proteins including direct cap-binding protein eIF3D, and promotes cap-binding affinity of eIF3D during mitosis in a manner of CDK1- and S6K1-dependent phosphorylation. Indeed, PYGO2 is required for mRNA translation during mitosis. In the absence of PYGO2 or its phosphorylation on S40, S48 and S97, cells display increased level of mitotic defect due to reduced level of protein synthesis. Moreover, PYGO2 differentially regulates translation of mRNA subsets which are each involved in transcription, translation, RNA processing or ribosome biogenesis. Collectively, our data provide a mechanism how the cells regulate translation of each subset of mRNAs through dynamic signaling pathways that promote eIF3D-dependent translation initiation during mitosis.

overall_design: To identify the specific mRNAs that are affected by PYGO2 depletion during mitosis, we performed active ribosome profiling (Active-Ribo-seq) with mitotic HeLa TO cell lines transfected with control and PYGO2 siRNA. RNA-seq of the same samples was also conducted to control for differences in transcript abundance. We then performed gene expression profiling analysis using our paired transcriptome and translatome datasets.

first: Min

middle: G

last: Lee

first: Hwamok

last: Oh

first: Seunghee

last: Jeong

first: Jaecheol

first: Jeung-Whan

last: Han


title: Effect of  leaves from 3-week-old NPB and OsWHY1-overexpressed rice plants at 24 hours post-inoculation with Magnaporthe oryzae

city: Changsha

first: Xuanning

last: Zeng

address: Hunan Agricultural University

institute: College of Plant Protection

summary: To gain a deeper understanding of the role of OsWHY1 in mediating rice transcriptional regulation during plant immune responses, we conducted a comprehensive transcriptome analysis comparing the gene expression profiles of NPB and OsWHY1-overexpressed plants at 24 hpi with M. oryzae.

overall_design: Leaves from 3-week-old NPB and OsWHY1-overexpressed rice plants, infected with Magnaporthe oryzae at 24 hours post-inoculation

first: Bing

first: Weiye

last: Peng

first: Chenting

last: Huang


title: Safe focused ultrasound-mediated blood-brain barrier opening is driven primarily by transient reorganization of tight junctions

city: New York

first: Elisa

middle: E

last: Konofagou

state: NY

department: Biomedical Engineering

institute: Columbia University

summary: Single-cell sequencing performed on endothelial cells after exposure to focused ultrasound in vivo to determine the transcriptomic signature of the response to intervention.

overall_design: Focused Ultrasound Blood-Brain Barrier Opening was performed in eGFP-Cldn5 mice targeting the striatum and putamen.  The animals were sacrificed after 1 or 72 hours and the targeted brain tissue was dissected out and prepared for FACS. The cells were sorted based on eGFP expression to isolate endothelial cells using FACS, and the cells were submitted for single cell RNA sequencing.

first: Rebecca

last: Noel

first: Sanjid

last: Shahriar

first: Dritan

last: Agai


title: A Novel Acute Erythroleukemia Cell Line Derived from Ascitic Fluid in a Patient with Congenital Acute Myeloid Leukemia

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

summary: An erythroleukemia cell line has been established from ascitic fluid cells obtained after the first cycle of chemotherapy in a patient with congenital acute erythroleukemia

overall_design: Ascitic fluid leukemia cells were grown in various culture conditions and characterized by morphology, flow cytometry, cell cycle, cytogenetic, and molecular genetic analysis, proliferation and drug sensitivity experiments in comparison with a known erythroleukemia cell line; cells were also shown to cause leukemia in a PDX model

first: Prasiksha

last: Sitaula

first: Manisha

last: Gadgeel

first: Holly

last: Edwards

first: Lisa

last: Polin

first: Juiwanna

last: Kushner

first: Sijana

middle: H

last: Dzinic

first: Kathryn

last: White

first: Yubin

last: Ge

first: Jeffrey

middle: W

last: Taub

first: Roselle

last: Arlene

first: David

last: Carr

first: Süreyya

last: Savaşan


title: Analysis of EZH2 target genes in senescent nucleus pulposus mesenchymal stem cells by integrating CUT&Tag and RNA-seq data [CUT&Tag]

city: Shenzhen

first: Jianrui

last: Zheng

address: No.1120 Lianhua Road, Futian District

institute: Peking University Shenzhen Hospital

summary: Intervertebral disc degeneration (IVDD) is one of the leading factors for low back pain, which has an enormous socioeconomic burden. Nucleus pulposus (NP) tissue is the core unit of the intervertebral disc (IVD) and contains nucleus pulposus mesenchymal stem cells (NPMSCs). NPMSCs are important for the health of NP tissue and IVDs. In the process of IVDD, NPMSCs undergo cellular senescence under the influence of various unfavourable factors, but the specific molecular mechanism remains unclear. Enhancer of Zeste Homologue 2 (EZH2) is a transcriptional regulator associated with cell senescence and can bind to the promoter region of downstream genes or transcription factors. In this study, decreased EZH2 expression in senescent NPMSCs from both human and rat IVDD specimens was observed, human nucleus pulposus mesenchymal stem cells (hNPMSCs) were isolated from human NP tissues, and tert-butyl hydroperoxide (TBHP) was used to induce hNPMSC senescence. The expression levels of P16 and P21 were significantly increased in senescent hNPMSCs, and the expression of EZH2 was significantly reduced. To elucidate the function of EZH2 in IVDD, RNA sequencing (RNA-seq) and Cleavage Under Targets and Tagmentation (CUT&Tag) were used to analyse the gene expression changes and the target genes of EZH2 in senescent hNPMSCs. The cross analysis of RNA-seq and CUT&Tag results showed that 58 target genes were directly regulated by EZH2, including 16 upregulated genes and 42 downregulated genes. Finally, protein-protein interaction (PPI) network analysis identified the hub genes associated with the mitotic cell cycle and cell proliferation, including threonine tyrosine kinase (TTK), minichromosome maintenance complex component 6 (MCM6), Aurora Kinase B (AURKB), Non-SMC condensin I complex subunit G (NCAPG), and cell division cycle associated 8 (CDCA8). In summary, this study analysed the genomic targets and hub gene network of EZH2 in senescent NPMSCs. The hub gene network revealed the important role of EZH2 in mitosis and cell cycle process. The decreased expression of EZH2 and hub genes might be one of the causes of hNPMSC senescence. Targeting EZH2 may be a potential treatment for IVDD, but the transcriptional regulatory function of EZH2 in IVDD still needs to be investigated further.

overall_design: To study the changes in gene expression levels in senescent hNPMSCs, RNA-seq was performed on the cells of the senescent hNPMSC group (75 µM treatment) and control group.

first: Lixiang

last: Xue

first: Zhen

last: Tan

first: Deli

last: Wang


title: Gene expression profile at single cell level of all CD45+ cells infiltrating B16-SIY-dsRed syngeneic tumors implanted subcutaneously after 26 days of tumor growth in Wildtype and PRKCD KO bone marrow engrafted animals

city: Chicago

first: Thomas

middle: F

last: Gajewski

state: IL

address: 5841 S Maryland Ave

department: Ben May

institute: University of Chicago

summary: Based on the notion that hypomorphic germline genetic variants are linked to autoimmune diseases, we reasoned that novel targets for cancer immunotherapy might be identified through germline variants associated with greater T-cell infiltration into tumors. Investigating germline polymorphisms associated with a tumor immune gene signature, we identified PKCd as a candidate. Genetic deletion of PKCd in mice resulted in improved endogenous anti-tumor immunity and increased efficacy of anti-PD-L1. Single cell RNAseq revealed myeloid cell expression of Prkcd, and PKCd deletion caused a shift in macrophage gene expression from an M2-like to an M1-like phenotype. Conditional deletion of PKCd in myeloid cells recapitulated improved tumor control that was augmented further with anti-PD-L1. Analysis of clinical samples confirmed an association between PRKCD variants and M1/M2 phenotype, as well as between a PKCd KO-like gene signature and clinical benefit from anti-PD-1. Our results identify PKCd as a candidate therapeutic target that modulates myeloid cell states.

overall_design: Loss of hematopoietic PKC-delta results in an immune dependent delay in tumor growth. To investigate the mechanisms underlying this delay, we performed a scRNAseq analysis of immune cells isolated from tumors grown in C57BL/6 mice with either Prkcd+/+ or Prkcd-/- hematopoietic cells. B16-SIY tumors were implanted and live CD45.2+ cells were isolated from the tumor microenvironments via fluorescence activated cell sorting (FACS) after 26 days of tumor growth. Each sample is the combination from 2 independently grown tumors, each group is an N of 4 samples, collected across 2 independent collection days.

first: Kyle

last: Cron


title: Assessment of innate immune regulators in pancreatic cancer

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: Pancreatic ductal adenocarcinoma (PDAC) accounts for 90% of all pancreatic cancer cases, and is among the most aggressive and lethal malignancies worldwide. PDAC is driven by genetic alterations in the pancreatic epithelium (e.g. KRAS, TRP53) coupled with a dysregulated innate immune response, the latter leading to an inflammatory tumor microenvironment enriched in innate immune cells (e.g. macrophages). However, immune-based treatment regimens for PDAC patients have primarily focused on immunotherapy with adaptive immune checkpoint inhibitors (e.g. PD-1) which disappointingly have yielded minimal clinical benefit. Thus, there is an unmet clinical need to identity disease-associated innate immune regulators as therapeutic targets in PDAC.  Innate immune responses depend on a series of cell surface, endosomal and cytosolic pattern recognition receptors (PRRs) that are expressed in immune and non-immune cells. PRRs are classified into several structurally and functionally conserved subfamilies, including Toll-like receptors (TLRs), Absent in melanoma 2 (AIM2)-like receptors (ALRs), and Nod-like receptors (NLRs). A subset of NLRs and AIM2 are also well documented for their formation of multiprotein complexes called ‘inflammasomes’ - comprising the adaptor ASC and Caspase-1 - which direct the maturation and release of bioactive pro-inflammatory cytokines, IL-18 and IL-1beta. However, the role of these critical innate immune regulators in PDAC has been underexplored, and is virtually unknown. Here, using the genetically engineered KPC PDAC mouse model, we performed whole transcriptome profiling to identify unique ASC-inflammasome driven downstream molecular networks associated with a range of oncogenic cellular processes in pancreatic tumorigenesis.

overall_design: Mice on a mixed 129Sv x C57BL/6 background were aged 20 weeks, and pancreas was collected and snap-frozen.

first: Bassam

last: Kashgari

first: Brendan

last: Jenkins

first: Linden


title: Integrated Multiomic Analysis Reveals disulfidptosis Subtypes in Glioblastoma

city: Beijing

first: Xue

last: Yang

address: No. 119, South Fourth Ring Road West

institute: Beijing Tiantan Hospital Affiliated to the Capital Medical University

summary: Glioblastoma (GBM) stands out as the most aggressive and deadly brain tumor, presenting an alarming scarcity of viable treatment alternatives. Recognizing the pronounced heterogeneity in the prognosis of GBM patients and subtyping them is crucial for precision treatment. disulfidptosis, recently identified as a form of cell death, is closely associated with tumor glucose metabolism abnormalities and disulfide stress, primarily occurring in tumors with elevated expression of SLC7A11. Previous studies have shown that gliomas exhibit high expression of SLC7A11, high metabolism, and glucose deficiency. Therefore, we conducted an in-depth investigation into the role of disulfidptosis in glioblastoma. Samples from glioblastoma patients who underwent surgical treatment at Tiantan Hospital from January 2022 to December 2023 were collected for transcriptome sequencing. Simultaneously, patient data from the CGGA and TCGA databases were gathered. Based on the disulfidptosis features, GBM patients were classified into two subtypes using consensus clustering, with patients in disulfidptosis related group cluster(DRGcluster) A exhibiting significantly improved overall survival (OS), whereas those in DRGcluster B demonstrated the opposite trend. Additionally, the two DRGcluster subtypes exhibited distinct patterns in the tumor immune microenvironment, including differences in immune cell infiltration or cytokine expression. Additional scrutiny of immune dysfunction, exclusion, and subclass mapping in tumor analysis revealed a heightened likelihood of positive responses to immunotherapy, notably anti-PD1 treatment, among patients categorized in DRGcluster A. The pRRophetic algorithm further uncovered noteworthy distinctions in IC50 values for prevalent chemotherapeutic and targeted treatments across diverse DRGclusters. Lastly, utilizing gene sets closely associated with glioblastoma occurrence from the  Weighted correlation network analysis (WGCNA) model and significantly differential gene sets between DRGcluster A and B patients, we developed an 8-gene disulfidptosis high-low risk subtype predictor using the Least absolute shrinkage and selection operator (LASSO) machine learning algorithm. The predictor was validated for survival in an external independent GBM cohort from CGGA. This novel disulfidptosis-based classification holds promise as a prognostic predictor for GBM. Furthermore, the pRRophetic algorithm indicated significant differences in half maximal inhibitory concentration 50 (IC50) values for common chemotherapy and targeted therapy among patients in different risk groups, suggesting potential guidance for physicians in selecting patients with advantages in chemotherapy and targeted therapy.

overall_design:
we conducted an in-depth investigation into the role of disulfidptosis in glioblastoma. Samples from glioblastoma patients who underwent surgical treatment at Tiantan Hospital from January 2022 to December 2023 were collected for transcriptome sequencing. Simultaneously, patient data from the CGGA and TCGA databases were gathered. Based on the disulfidptosis features, GBM patients were classified into two subtypes using consensus clustering, with patients in disulfidptosis related group cluster(DRGcluster) A exhibiting significantly improved overall survival (OS), whereas those in DRGcluster B demonstrated the opposite trend. Additionally, the two DRGcluster subtypes exhibited distinct patterns in the tumor immune microenvironment, including differences in immune cell infiltration or cytokine expression. Additional scrutiny of immune dysfunction, exclusion, and subclass mapping in tumor analysis revealed a heightened likelihood of positive responses to immunotherapy, notably anti-PD1 treatment, among patients categorized in DRGcluster A. The pRRophetic algorithm further uncovered noteworthy distinctions in IC50 values for prevalent chemotherapeutic and targeted treatments across diverse DRGclusters.

>>>Submitter states that raw data are not available due to potential patient privacy concerns.<<<

first: Wenbin

last: Li

first: Chenggang

last: Jiang


title: APC loss promotes intestinal transformation though B-CATENIN-independent dysregulation of a GSK3-AJUBA-YAP signaling axis

city: Philadelphia

first: Ning

state: Pennsylvania

address: 3800 Spruce St.

department: Biomedical Sciences

institute: UPENN

summary: The majority of colorectal cancer (CRC) cases are believed to be initiated by the genetic inactivation of the APC tumor suppressor, which negatively regulates the Wnt effector beta-catenin. This has led to the prevailing view that loss of APC drives tumorigenesis through constitutive activation of the Wnt/beta-catenin pathway. Although activation of beta-catenin is necessary for tumor initiation, activating mutations in beta-catenin are rare in CRC. Instead, CRC typically exhibits poorly understood mechanisms that favor the genetic inactivation of APC over activating mutations in beta-catenin or other Wnt pathway components, which are more commonly seen in other types of carcinoma. In this study, we profiled single cells isolated from organoids with floxed alleles of Apc (Apc f/f), beta-catenin (beta-Catenin Exon3 f/f), or organoids expressing a dominant-negative form of Tcf4 with floxed alleles of Apc (Apc f/f).

overall_design: Organoids were cultured for 24 hours before processing. Single cells were isolated from organoids with floxed alleles of Apc (Apc f/f), beta-catenin (beta-Catenin Exon3 f/f), or organoids expressing a dominant-negative form of Tcf4 with floxed alleles of Apc (Apc f/f).

first: Christopher

last: Lengner


title: Nuclear-localized HDAC4 promotes neuroprotection of retinal ganglion cells after optic nerve injury

city: Palo Alto

first: Wenjun

last: Yan

state: California

address: 1651 Page Mill Rd

department: Department of Ophthalmology, Byers Eye Institute, Mary M. and Sash A. Spencer Center for Vision Research, Stanford University School of Medicine

institute: Stanford University

summary: Background: As the sole output neurons for the retina, retinal ganglion cells (RGCs) transmit all visual information from the retina via the optic nerve to the brain. RGCs do not regenerate when injured, and effective therapies for promoting RGC survival and axon regeneration in optic neuropathies comprise an unmet clinical need, including in the common disease glaucoma. Histone deacetylases (HDACs) are epigenetic modifiers that repress gene transcription and play a key role in retinal development and disease.  In this study, we identify the role of HDAC4 in RGC neurodegeneration and axon regeneration. Methods: The role of HDAC4 in the regulation of RGC neuroprotection and axon regeneration was studied in the mouse optic nerve crush (ONC) model for optic neuropathy by transduction of RGCs in vivo with adeno-associated virus (AAV) vectors. HDAC4- and ONC-dependent gene expression in vivo were studied by single cell RNA sequencing (scRNA-seq) of isolated RGCs.  Results: A loss-of-function screen for the role of HDACs in RGC survival after optic nerve crush (ONC) injury identified HDAC4 as essential element for RGC survival. Accordingly, expression of a constitutively nuclear HDAC4 S246/467/632A missense mutant (3SA) increased RGC survival and axon regeneration after ONC injury. Similar beneficial effects were conferred by expression of an N-terminal fragment of HDAC4 (HDAC4 NT) that constitutively represses gene expression. scRNA-seq showed that one day after ONC injury, transcriptomic profiles of RGCs were altered such that HDAC4 NT and to a lesser degree the HDAC4 3SA mutant attenuated the gene expression changes associated with injury.  Conclusions:  This study demonstrates that enhancement of nuclear HDAC4 activity will promote RGC survival and axon regeneration in the ONC model of RGC injury, identifying HDAC4 as a novel target in the development of therapeutics for RGC protection and restoration of visual function.

first: Ying

last: Zhu

first: Minjuan

last: Bian

first: Xin

last: Xia

first: Michael

last: Nahmou

first: Ramesh

middle: V

last: Nair

first: Jinliang

first: Xueyi

first: Hrishikesh

last: Singh Thakur

first: Kristina

last: Russano

first: Ziming

last: Luo

first: Jeffrey

last: Goldberg

middle: S

last: Kapiloff


title: Octopus-inspired triple-engineered bacteria for precision cancer immunotherapy

city: Nanjing

first: Zichun

last: Hua

state: Jiangsu

address: Xianlin Road No.163

department: School of Life Sciences

institute: Nanjing University

summary: Bacterial cancer therapies face precision and safety challenges, which limit their clinical application. This study presents a triple-engineered Salmonella typhimurium strain (OITE-bacteria), designed for targeted cancer therapy, inspired by octopus biology and leveraging synthetic biology and biomimetic principles. The strain incorporates SpyTag proteins on the outer membrane, allowing covalent attachment of SpyCatcher-fused quadruple RGD peptides to enhance tumor adhesion via integrin αvβ3 interactions. This promotes bacterial enrichment in various solid tumors and lung metastases. Subsequently, Quorum sensing induces expression of strain HtrA protein within tumors, enhancing extracellular polysaccharide-mediated immunogenicity for activating immune cells. Additionally, the bacteria locally release anti-PD1 nanobodies to anti-immunosuppressive. In murine models, OITE-bacteria achieved a ninefold increase in tumor colonization within 12 hours and sustained melanoma growth suppression for over 40 days, with a 100% response rate. This modular approach, integrating safety and efficacy, provides a new strategy in microbial therapeutics for solid tumors.

overall_design: A total of 2×10^5 B16F10 cells were inoculated into C57BL/6 mice (7 weeks old, female) in the right axillary region. Once the tumor volume reached 80-120 mm^3, the mice were randomly divided into groups. Subsequently, the mice were intraperitoneally injected with physiological saline, the respective VNP bacterial strain, or modified strains (1.0×10^6 CFU per mouse). Three days later, tumor tissues were collected. To avoid spatial heterogeneity, the entire tumor was homogenized and thoroughly mixed before RNA extraction from the tissue.The extracted RNA was then subjected to RNA sequencing.

first: Leyang

last: Wu

first: Lin


title: Transcriptional condensates enrich phosphorylated PRMT2 to stimulate H3R8me2a deposition and hypoxic response in cancers- Cut&tag

first: feng

last: dong

overall_design: The H3R8me2a profiles of U87 control-Normoxia, U87 control-Hypoxia ,  U87 TG02-Hypoxia , U87 PRMT2-WT-Hypoxia and U87 PRMT2-S12A-Hypoxia

first: Xudong

first: Feng

last: Dong

first: Xuan

last: Cheng


title: The effect of fluid shear stress on the mRNA expression profile of immature dendritic cells.

city: Guiyang

first: Peng

last: Yu

address: Guizhou Medical University, 6 Ankang Avenue, GUI 'an New District, Guizhou Province, China

institute: Guizhou Medical University

summary: Dendritic cells (DCs) play crucial roles in T cell activation and guide them polarize to different subsets, which orchestrate the balance between immune response and tolerance maintaining homeostasis of the body’s immune internal environmen. Immature DCs (imDCs) with strong phagocytosis abilities patrol in the peripheral tissues to capture antigens, and they exhibit limited capacity to stimulate T-cell activation and primarily contribute to immune tolerance through the induction of T-cell anergy or differentiation into regulatory T cells (Tregs). Once encountering antigens, imDCs initiate the affairs of antigen-processing and maturation, as well as migrate toward to lymphoid tissues – the destination where mature DCs (mDCs) present antigen-peptide to naïve T cells and efficiently stimulate T cell activation, launching innate and adaptive immune responses. This is a long and arduous “journey” for DCs to fulfill their immunoregulatory mission. Any disturb factors (biochemical or biophysical cues) from the “journey” may alter or impair the immunophenotyes and functions of DCs, suggesting that high plasticity of DCs in vivo – either immunity or tolerance – to adapt to the demand of a special condition.In the process of exerting physiological function, imDCs are always under the Fluid shear stress (FSS) sluicing. How imDCs response to FSS stimuli and furtherly mediate immune response remains unknown.

overall_design: To investigate the effects of FSS on the gene expression of imDCs, we designed a cone-plate shear stress loading system that can supply different magnitude of FSS on cells. According to the numerical range of physiological venous FSS, imDCs were loaded by 10 dyn/cm2 of FSS for 3 hours. Static cultured imDCs were used as the control group.We conducted transcriptome sequencing analysis.

first: Zhu

last: Zeng


title: Analysis of EZH2 target genes in senescent nucleus pulposus mesenchymal stem cells by integrating CUT&Tag and RNA-seq data

first: Jianrui

last: Zheng

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

overall_design: Refer to individual Series


title: Competitive colonization of Akkermansia muciniphila clades by microbial extracellular vesicles through direct inhibition and immune stimulation

city: Goyang-si

first: Moon-Gi

last: Hong

address: 32, Dongguk-ro, Ilsandong-gu

department: R&D Center

institute: Enterobiome Inc.

summary: Akkermansia muciniphila, a candidate for next-generation probiotics, can be classified into several clades with distinct genomic divergence. However, the global distribution and population structure of clade-typed A. muciniphila remain poorly understood. Here, we report on the predominance of single A. muciniphila clades in humans globally. We found that the predominance of the A. muciniphila clade is dynamically regulated by the balance between inter-clade inhibitory and pre-occupancy effects. A. muciniphila clade II (AmII)-derived extracellular vesicles exhibited a unilateral inhibitory effect on the growth of AmI. Clade-specific IgA responses were induced by each clade. AmII clade-specific IgAs, also induced by extracellular vesicles, facilitate the competitive exclusion of AmI. Our findings help toward the development of personalized intervention strategies for A. muciniphila, considering a subject’s A. muciniphila type.

overall_design: The growth inhibitory effect of AmII-derived EVs on AmI is growth dependent. Thus, the DEGs of AmII were identified through RNA-sequencing at two different time points with and without growth inhibitory effects on AmI.

first: Won-Hyong

last: Chung

first: Young-Do

last: Nam


title: TLR5 expression marks brain boarder associated macrophage

first: REN

last: DESHAN

state: --- Select One ---

address: 12 Xuefu-Road, Pukou District  Nanjing 210061, China

institute: Nanjing university

summary: Bacterial meningitis poses a significant threat to prenatal and newborn babies, resulting in a high number of infant deaths worldwide. Infants, with their underdeveloped adaptive immunity, rely on brain macrophages to defend against pathogenic infections. However, the precise characteristics and functions of brain macrophages during the neonatal period remain incompletely understood, necessitating further investigation. Our research initially explores the expression of cell surface Toll-like receptors on brain macrophages in neonatal mice. By utilizing flow cytometry, RNA-seq and immune fluorescence staining, we have uncovered that TLR5 specifically expressed on BAMs but not microglia. Furthermore, our study reveals that priming TLR5 with its ligands enhances the survival rate of neonatal mice when confronted with bacterial meningitis, possibly through recruiting innate immune cells such as monocytes and neutrophils.

overall_design: TLR5+ or TLR5- P0 mouse brain CD45+CD11b+Ly6c- macrophages are sorted. Total RNA was extracted using Trizol (Invitrogen). Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). The library and sequencing were conducted by Novogene (Beijing, China) using illumina NovaSeq 6000.


title: RNA editing enzyme ADAR2 regulates P-glycoprotein expression in murine breast cancer cells via the circRNA-miRNA pathway

city: Fukuoka

first: Satoru

last: Koyanagi

address: 3-1-1 Maidashim Higashi-ku

department: Pharmaceutical Sciences

country: Japan

institute: Kyushu University

summary: Among the various modifications of RNA, adenosine-to-inosine RNA editing, catalyzed by adenosine deaminase acting on RNA (ADAR) family, ADAR1 and ADAR2, is the most common nucleotide conversion in mammalian cells. The pathological relevance of ADARs expression has been highlighted in recent human genetic studies. Low expression of the ADAR2 gene is correlated with poor prognosis in breast cancer patients, but the underlying mechanism remains unclear. In this study, we constructed ADAR2-knockdown (ADAR2-KD) murine breast cancer 4T1 cells and found their reduced susceptibility to chemotherapeutic drug doxorubicin. Downregulation of ADAR2 induced the expression of P-glycoprotein (P-gp), resulting in a reduction of intracellular accumulation of doxorubicin. The upregulation of P-gp occurred at the post-transcriptional level due to the decreased miR-195a-3p function. The search for the underlying cause of the induction of P-gp expression in ADAR2-KD 4T1 cells led to the identification of circular RNA (circRNA) circHif1a as a sponge for miR-195a-3p. Indeed, overexpression of circHif1a inhibited miR-195a-3p function, resulting in the upregulation of P-gp expression. Taken together, the decreased expression of ADAR2 in breast cancer plays a critical role in cellular susceptibility to doxorubicin through the regulation of circRNA/miRNA/P-gp pathway. Our findings may contribute to the elucidation of the mechanism of anticancer drug resistance in breast cancer, leading to the overcoming of chemo-resistance.

overall_design: The change in microRNA expression induced by downregulation of ADAR2 was evaluated in murine breast cancer 4T1 cells. 4T1 cells were infected with lentiviral particles expressing shRNA against the mouse Adar2 gene (sc-37660-V; Santa Cruz Biotechnology) to contrust ADAR2-KD 4T1 cells, or with empty lentiviral particles to construct mock-transduced 4T1 cells for the control.

first: Yuji

last: Omata

first: Mai

last: Haraguchi

first: Sae

last: Yoshinaga

first: Takashi

last: Ogino

first: Maseri

last: Okawa

first: Akito

last: Tsuruta

first: Shigehiro

last: Ohdo


title: RNA sequencig of glioblastoma stem cells after induction of ferroptosis

city: Warsaw

first: Agnieszka

last: Bronisz

address: Pawinskiego 5

country: Poland

institute: Mossakowksi Medical Research Institute

summary: Patient derived glioblastoma stem like cells cultured in vitro were used to investigate the effect of hypoxia and ferroptosis induction on gene expression. Different baseline transcriptomic profiles of studied cells indicated their diverse niche origin within the tumor. Futher analysis revealed that intrinsic gene expression of cells were exceeding the effect of hypoxia or treatment. Response of the cells whose profiles were linked with occupancy of more periferal parts of tumor (leading edge) differed from those that were residing in the tumor core (peri-nectrotic zone). Expression of genes related to respone to hypoxia and ferroptosis indicated more adaptation and possible higher resistance of the cells from tumor core.

overall_design:
Glioblastoma stem like cells derived from patients (GSCs, n=8) treated with DMSO (0.1% final concentration), and ferroptosis inducer at 3 uM (RSL3 in DMSO). Subsequently cells were cultured for 24h in either Normoxia (21% oxygen and 5% CO2) or Hypoxia (1% oxygen, 5% CO2). Cells were centrifuged (500xg, 5 min), medium decanted and pellets snap frozen for RNA after isolation with phenol-chloroform method combined with isopropanol precipitation at -80C overnight.
--------------
Funding:
FBW-05/2022 IMDIK PAN, K. Krawczyński
G-1252-2022/45/B/NZ5/04226 NCN, A. Bronisz

first: Kamil

last: Krawczyński

first: Jakub

last: Godlewski

first: Jeffrey

last: Palatini

first: Krzysztof

last: Goryca


title: Mrc1 facilitates epigenetic inheritance through proper parental histone segregation

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

summary: Chromatin-based epigenetic memory relies on the equal distribution of parental histone tetramers, which serve as templates for duplicating parental chromatin, to newly synthesized daughter DNA strands. Histone chaperones within the replisome, such as the histone binding domains (HBDs) of Mcm2 and Pol alpha, are critical for transferring parental histones to the lagging strand. However, the mechanisms and impact of parental histone transfer on epigenetic inheritance remain debated. Using fission yeast heterochromatin assembly as a model, we discovered that replisome component Mrc1 is crucial for both epigenetic inheritance and transfer of parental histones to the lagging strand, akin to  a Mcm2-HBD mutation. Isolation of separation-of-function mutations revealed that Mrc1’s role in epigenetic inheritance is distinct form its DNA replication checkpoint and replisome speed control functions. Instead, Mrc1 prevents undesirable replisome interactions to facilitate interactions between Mcm2 and Pol alpha for the proper passage of parental histones. These findings unveil a novel function of Mrc1 and underscore the critical role of parental histone segregation in epigenetic inheritance.

overall_design: H3K4me3 eSPAN performed in S.pombe followed by Next Generation Sequencing

first: Yimeng

last: Fang

first: Xu

last: Hua

first: Zhiguo

last: Zhang

first: Songtao

last: Jia


title: Profiling R loop in mouse and human hematopietic cells with low cell input using S9.6 antibody coupled cut&tag [cut&tag K562]

city: NY

first: Bin

last: Lu

address: 417 East 68th Street New York,

institute: mskcc

summary: Present R loop profling oftern requires large amout of material, lacking information about R loop in primary cells. To overcome this setback, we delevopment low input method which integrates in vitro amplication capability of T7 promoter and high binding specificity between nanotag and IgH (mouse)

overall_design: R loop was first recognized and bond by S9.6 antibody, nanobody T5 which recognize mouse IgH kappa was later used to bind S9.6 and ennable the cutting of chromosome site in the vicinity of R loop loci. Fragmaentated DNA was in vitro trancribed by T7 promoter and reverse transcribed to get double strand DNA library for NGS sequencing.

first: Omar

last: Abdel-Wahab


title: Profiling R loop in cd34+ and ckit+ of mouse and human hematopietic cells input using S9.6 antibody coupled cut&tag [single cell]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Dual inhibition of CDK4/6 and XPO1 induced senescence with acquired vulnerability to CRBN-based PROTAC drugs.

city: Shanghai

first: Hui

last: Wang

address: Building 5, No.1630 Dongfang Road

institute: Shanghai Cancer Institute

summary: We first treated senescent  liver cancer cells with vehicle or ARV-825 for 48 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or ARV-825-treated liver cancer cells. ARV-825-induced expression changes were obtained based on the resultant data.

overall_design: Examination of the transcriptome changes of senescence liver cancer cells treated with ARV-825


title: Analysis of EZH2 target genes in senescent nucleus pulposus mesenchymal stem cells by integrating CUT&Tag and RNA-seq data [RNA-seq]

first: Jianrui

last: Zheng

first: Lixiang

last: Xue

first: Zhen

last: Tan

first: Deli