title: Visium spatial transcriptomics and proteomics identifies novel hepatic cell populations and transcriptomic signatures of alcohol-associated hepatitis

last: Rouchka

summary: Background: Alcohol-associated hepatitis (AH) is the clinical manifestation of alcohol-associated liver disease (ALD). AH is a complex disease encompassing the dysregulation of many cells and cell subpopulations. This study used a hepatic spatial transcriptomic and proteomic approach (10X Genomics Visium) to identify hepatic cell populations and their associated transcriptomic and proteomic alterations in human AH. Methods: Formalin fixed parraffin embedded liver tissue from AH patients (n=2) and non-ALD controls (donors) (n=2) were used for Visium spatial transcriptomic and proteomic analysis. Results: AH cell clusters and cell markers were drastically different in regard to tissue pattern and number of cell type as compared to non-ALD controls. Cholangiocytes, endothelial cells, macrophages, and stellate cells were more profuse in AH relative to non-ALD controls. Transcriptionally, proliferating cell nuclear antigen positive (PCNA+) hepatocytes in AH more closely resembled cholangiocytes suggesting they were non-functional hepatocytes derived from cholangiocytes. Further, mitochondria protein coding genes were reduced in AH vs non-ALD control hepatocytes, suggesting reduced functionality and loss of regenerative mechanisms. Macrophages in AH exhibited elevated gene expression involved in exosomes as compared to non-ALD controls. The most upregulated macrophage genes observed in AH were those involved in exosome trafficking and cellular migration. Gene and protein signatures of disease associated hepatocytes (ANXA2+/CXCL1+/CEACAM8+) were elevated in AH and could visually identify a pre-malignant lesion. Conclusions: This study identified global cell type alterations in AH and distinct transcriptomic changes between AH and non-ALD controls. These findings characterizes cellular plasticity and profuse transcriptomic and proteomic changes that are apparent in AH and contributes to the identification of novel therapeutics.

overall_design: FFPE liver sections from non-ALD controls (n=2) and alcohol-associated hepatitis patients (n=3) were used for Visium spatial transcriptomic and proteomic analysis.

first: Tyler

last: Gripshover

first: Rui

last: Treves

first: Julia

middle: H

last: Chariker

first: Shirong

last: Zheng

first: Elizabeth

last: Hudson

first: Melissa

middle: L

last: Smith

first: Ashwani

last: Singal

first: Craig

middle: J

last: McClain

first: Josiah

last: Hardesty


title: RNA helicase DDX5 maintains cardiac function by regulating CamkIIδ alternative splicing [RIP-seq]

status: Public on Dec 02 2024

city: Shanghai

first: Kangni

last: Jia

state: Shanghai

address: 227 Chongqing South Road, Huangpu District, Shanghai, China

country: China

institute: Shanghai Jiaotong University

summary: The cardiomyocyte-specific deletion of Ddx5 in mice resulted in heart failure characterized by diminished cardiac function, enlarged heart chambers, and heightened fibrosis. Proteomic analysis unveiled the involvement of DDX5 in RNA splicing within cardiomyocytes. Our study identified DDX5 as a regulator of the abnormal splicing of CamkIIδ, preventing the generation of CaMKIIδA. This isoform activates LTCC through serine phosphorylation of Cacna1c, disrupting Ca2+ homeostasis. Consistently, DDX5-depleted cardiomyocytes exhibited elevated intracellular Ca2+ transients and increased sarcoplasmic reticulum Ca2+ content.

overall_design: To investigate the role of DDX5 in the heart, we obtained cardiac tissues from 8-week-old DDX5fl/flMYH6Cre+ mice (mCKO), with age-matched DDX5fl/fl mouse cardiac tissues serving as controls (CTR1). Additionally, we collected cardiac tissues from Ddx5flox/flox Myh6MerCreMer mice (iCKO) after 7 days of intraperitoneal tamoxifen injection, with age-matched DDX5fl/fl mouse cardiac tissues injected with the same dose of tamoxifen serving as controls (CTR2). RNA sequencing was performed for each condition, followed by differential gene expression analysis and alternative splicing analysis against their respective controls. In addition, we conducted RNA immunoprecipitation followed by sequencing (RIP-seq) using a DDX5-specific antibody in neonatal rat cardiomyocytes.

first: Haomai

last: Cheng

first: Wenqi

last: Ma

first: Xiaoxiang

last: Yan


title: Chemerin attenuates acute kidney injury by inhibiting ferroptosis via the AMPK/NRF2/SLC7A11 axis

status: Public on Dec 01 2024

city: Nantong

first: Jinyu

address: 19 Qixiu Road, Nantong 226001, China.

institute: Nantong University

type: Expression profiling by high throughput sequencing

summary: Acute kidney injury (AKI) is a common and life-threatening condition associated with cell death, where ferroptosis plays a critical role. Chemerin, primarily produced in white adipose tissue, has multiple biological functions in renal pathophysiology. However, to date, whether and how chemerin regulates the progression of AKI remain unclear. Here, we found that chemerin expression was reduced in both AKI model mice and cells. Similarly, serum chemerin levels were also decreased in AKI patients. The administration of recombinant chemerin improves renal function in ischemia-reperfusion (I/R) model mice. Chemerin significantly attenuates ferroptosis in kidneys. In TCMK-1 cells, chemerin knockdown further aggravates ferroptosis. Mechanistically, chemerin activates AMP-activated protein kinase (AMPK), which induces the phosphorylation of nuclear factor erythroid 2-related factor 2 (NRF2) in renal tubular cells. Subsequently, NRF2 translocates into the nucleus, where it stimulates the expression of cystine/glutamate antiporter solute carrier (SLC7A11). As a result, cystine uptake and glutathione (GSH) biosynthesis in renal tubular cells were increased, which confers cells with higher capacity against ferroptosis. Overall, our findings indicate that chemerin plays a protective role in AKI by repressing ferroptosis in renal tubular cells, which is likely due to the activation in the AMPK/NRF2/SLC7A11 axis.

overall_design: Kidney tissues from I/R and Chemerin-9 treated I/R mice were prepared for RNA-seq analysis.

first: Yidan

first: Shengnan

last: Fei

first: Xu

last: Chen

first: Yuanyuan

last: Gui

first: Bing

last: Zhou

first: Tianya

last: Xiang

first: Jianhang

last: Liu

first: Kun

last: Yue

first: Qingxin

last: Li

first: Wei

last: Jiang

first: Cheng

last: Sun

first: Xinzhong

last: Huang


title: USP1 identified as an important factor in the progression of gastric cancer

city: Zhenjiang

first: Yong

last: Peng

state: 未选择

address: No. 8, Power Road

institute: Zhenjiang First People's Hospital

summary: Gastric cancer is one of the leading causes of cancer-related deaths, and through in vivo and in vitro genetic screens, we identified USP1 as an important factor in promoting tumor progression. Here, we analyzed the transcriptome of sh-USP after knockdown with the aim of identifying downstream effectors of USP1

overall_design: RNA-seq analysis of human gastric cancer cell line AGS using shCtrl or shUSP1

first: Z

middle: Y

last: Qiu


title: Effect of the Mbov_0496 mutation on gene expression of Mycoplasma bovis under normal and high potassium conditions

city: Wuhan

first: Jiongxi

address: No.1, Shizishan Street, Hongshan District

department: College of Animal Science & Technology

institute: Huazhong Agriclutural University

summary: Cyclic di-AMP is an essential and ubiquitous second messenger that regulates bacterial potassium (K+) concentrations to maintain osmotic equilibrium. And its specific K+ regulation mechanism in Mycoplasma has rarely been investigated. We used the ruminant pathogen Mycoplasma bovis (M. bovis) to investigate this mechanism. We verified that MbovP496 is a c-di-AMP synthetase and its mutant T5.415 showed growth inhibition under high K+ condition. To deliver why the mutant strain T5.415 can regulate M. bovis growth, we held a RNA-seq analysis to reveal that the differentially expressed genes between WT and T5.415 under normal condition and high K+ condition. The K+ transport pathways and metabolism related pathways were enriched. In conclusion, we found that the mutation of c-di-AMP synthetase, MbovP496 can broadly influence not only the metal ions transport pathway, but also has an effect on metabolism pathways,which could significantly contribute to understanding the regulation of growth by c-di-AMP synthetase in mycoplasmas.

overall_design: RNA-seq profiling of wild-type Mycoplasma bovis and the MbovP496 mutant T5.415 under normal PPLO culture conditions and PPLO medium supplemented with 50 mM K+


title: Prolonged Crowding Drives Cancer Cell Invasiveness

city: Beijing

first: Min

last: Tan

address: XueYuan Road No.37,HaiDian District

institute: Beihang University

summary: Our study found that prolonged crowding drives cancer cell invasiveness with memory retention. To further characterize gene expression regulated by prolonged crowding, RNA sequencing was performed in crowding-primed cells (20 days) followed by sparse culture for different times (0, 1, 3, or 10 days).

overall_design: We examined the duration of the crowding-induced mechanomemory by priming cells for 20 days in crowded or uncrowded culture, followed by sparse culture for 1, 2, 3, or 10 days.


title: RNA sequencing data of piglet intestinal tissue following different dietary treatments

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Pigs were reared artificially on either milk replacer, milk replacer with liquid creep feed, milk replacer with creep feed + whey, or milk replacer with creep feed + benzoic acid.

overall_design: Piglets were given the dietary treatments for 28 days before euthanasia, and RNA extarcted from the middle of the small intestine

middle: R


title: Stem-cell-derived limb developmental cell type characterization.

city: Chavannes-près-Renens

first: Can

last: Aztekin

address: Swiss Federal Institute of Technology Lausanne (EPFL)

country: Switzerland

institute: EPFL

summary: Mouse embryonic stem cells were used to generate cell types of limb development and characterized using single-cell mRNA-sequencing.

overall_design: Time course in vitro differentiation samples.


title: C57BL/6 mice: gut-specific GDE5 (Gpcpd1)-deficient mice (Gde5 gutKO mice)

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

summary: Transcriptional profiling of mouse intestine. The objective of this study is to explore gene expression profiles of intestine in response to Gpcpd1 (GDE5) deficiency by DNA microarray analysis.

overall_design: Two-condition experiment, intestine of five WT and Gde5 gutKO mice at 20 weeks of age

first: Noriyuki

last: Yanaka


title: Transcriptional Regulation of Protein Synthesis by Mediator Kinase Represents a Therapeutic Vulnerability in MYC-driven Medulloblastoma

city: Aurora

first: Dong

last: Wang

state: CO

country: USA

institute: University of Colorado, Anschutz Campus

summary: MYC-driven medulloblastoma (MB) is a highly aggressive cancer type with poor prognosis and limited treatment options. Through CRISPR-Cas9 screening of MB cell lines, we identified the Mediator-associated kinase CDK8 as a critical regulator of MYC-driven MB. Loss of CDK8 substantially reduces MYC expression, induces pronounced transcriptional changes, suppresses monosome assembly, and decreases ribosome biogenesis and protein synthesis, consequently inhibiting MB growth. Mechanistically, CDK8 regulates the occupancy of RNA polymerase II at specific chromatin loci, facilitating an epigenetic alteration that promotes the transcriptional regulation of ribosomal genes. Targeting CDK8 effectively diminishes the stem-like neoplastic cells characterized by hyperactive ribosome biogenesis. Furthermore, we demonstrated that the combined inhibition of CDK8 and mTOR synergizes to optimize therapeutic outcomes in vivo and in vivo. Overall, our findings establish a connection between CDK8-mediated transcriptional regulation and mRNA translation, suggesting a promising new therapeutic approach that targets the protein synthesis for MYC-driven MB.

overall_design: To study the role of CDK8 in MYC-driven medullolbastoma, we performed RNA-Seq and cut&run of MB cells after genetic knockdown or pharmacological inhibition of CDK8

first: Rajeev

last: Vibhakar


title: Sodium phenylbutyrate rescues thyroid hormone transport in brain endothelial cells

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

country: Germany

institute: Universitätsklinikum Bonn

summary: Monocarboxylate transporter 8 (MCT8) deficiency is a rare genetic disease leading to a severe developmental delay. Some MCT8 deficient patients are not as severely affected than others due to residual thyroid hormone (TH) transport. Previously, we hypothesized that these patients’ mutations destabilize the MCT8 protein, which consequently will be sent for degradation. We have already demonstrated that the chemical chaperone sodium phenylbutyrate (NaPB) rescues the function of these mutants by stabilizing their protein expression in an overexpressing cell system. Here we expand our previous work and used human iPSC-derived brain microvascular endothelial-like cells (iBMECs) as a model. We could show that NaPB rescues decreased mutant MCT8 expression and restores transport function. Furthermore, we identified MCT10 as another TH transporter that contributes to T3 uptake. The decrease in mutant protein expression could be explained by the activation of components of the unfolded protein response (UPR) machinery. Increased expression after NaPB treatment is a consequence of UPR attenuation and the stabilization of MCT8 mRNA. In conclusion, we demonstrate that NaPB is suitable to stabilize pathogenic missense mutations and activate transport function in a human-derived cell model opening the possibility of repurposing the FDA-approved drug NaPB for MCT8 deficiency.

overall_design: 3' Poly(A) RNA-sequencing of N = 10 human BMEC with N = 2 of 5 different mutations in MCT8 (SLC16A2). Ribosome profiling  with N = 2 of 2 different  mutations and one mutation with Phenylbutyrate (2PB) treatment.

first: Doreen

last: Braun

first: Simon

last: Bohleber


city: Jinzhong

first: jiagang

last: wang

address: Shanxi Agricultural University, Taigu District, Jinzhong City, Shanxi Province, China

summary: RNA-seq of tobacco explants cultured by different NAA concentrations during in vitro tissue culture provides high-resolution transcriptome data,which provides a novel direction and theoretical basis for improving gene editing efficiency in plants by modulating chromatin accessibility through auxin signaling and tissue culture conditions.

overall_design: Approximately 80 tobacco explants were harvested from the media containing 0.1 mg/L or 0.5 mg/L NAA after 2 weeks culture for the following RNA-seq analysis，respectively.


title: Structure-guided development of high-performance antibodies targeting site-specific post-translational modifications

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Post-translational modifications (PTMs) of proteins play critical roles in regulating many cellular events. Antibodies targeting site-specific PTMs are essential tools for detecting and enriching PTMs at sites of interest. However, fundamental difficulties in molecular recognition of both PTM and surrounding peptide sequence have hindered the efficient generation of highly specific anti-PTM antibodies. Furthermore, the widespread use of potentially inconsistent, non-renewable and molecularly undefined antibodies presents experimental challenges thought to contribute to the reproducibility crisis in biomedical research. In this study, we describe the structure-guided development of a platform that efficiently generates potent and selective recombinant antibodies to PTMs that are molecularly-defined and infinitely renewable. Our platform is built on our previous discovery of an unconventional binding mode of anti-PTM antibodies, antigen clasping, where two antigen binding sites cooperatively clasp  a single antigen, creating extensive interactions with the antigen and leading to high selectivity and potency. We designed the platform that generates clasping antibodies with two distinct binding units, resulting in efficient generation of antibodies to a set of trimethylated histone H3  with high levels of specificity and affinity. Performance comparison in chromatin immunoprecipitation (ChIP), a common application in epigenomics, revealed that an anti-H3K27me3 clasping antibody exhibited superior specificity to a widely-used conventional antibody and captured symmetric and asymmetric nucleosomes in a less biased manner. We further generated clasping antibodies to phosphotyrosine antigens by using the same principle. These results suggest the broad applicability of our platform to generating high-performance clasping antibodies to diverse PTMs.

overall_design: Internally calibrated chromatin immunoprecipitation (ICeChIP) against H3K27me3 using commercially available antibody (Cell Signaling Technologies C36B11) or 3C2-H2 clasping Fab.

first: Mariapia

last: Riso

middle: N

first: Akiko

last: Koide

first: Alexander

last: Ruthenburg

first: Shohei

first: Takamitsu

last: Hattori


title: LK immunophenotype cells after sleep deprivation.

city: 重庆Chongqing

first: Zeyu

last: Fu

state: 重庆Chongqing

address: 高滩岩正街

department: College of Preventive Medicine

institute: AMU

summary: To investigate the effects of sleep deprivation on hematopoietic stem cells in the bone marrow and the changes in the bone marrow microenvironment, we constructed a single-cell atlas.

overall_design: After sorting the total bone marrow cells using LK (lin- c-kit+) magnetic beads and mixing the total bone marrow cells in a 1:1 ratio, single-cell library preparation and sequencing were performed.

first: Shilei

last: Chen

first: Kangfu

last: Sun

first: Junping


title: Microstructures regulate distant cellular interactions during heart formation

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: Communication between endocardium and myocardium, separated by cardiac jelly, is essential for cardiac morphogenesis. How membrane-localized receptors and ligands achieve interaction across the cardiac jelly is not understood. Utilizing a number of approaches, including genetic labeling of cell-cell contacts, we found that myocardium and endocardium interact directly via microstructures, termed Tunneling Nanotube-Like microstructures (TNTLs). TNTLs extend from cardiomyocytes to directly contact endocardial cells (ECs). TNTLs transport cytoplasmic proteins, transduce signals between cardiomyocytes and ECs, and initiate myocardial growth toward the lumen to form ventricular trabeculae-like structures. Loss of TNTLs disturbs signaling interactions and, subsequently, ventricular patterning.

overall_design: Whole hearts from E9.5 control and myocardial Cdc42 knockout (MCKO) are analyzed, each set contains three hearts.

first: Mingfu

last: Wu

first: Lianjie

last: Miao


title: Transcriptome of P. aeruginosa ∆pilY1

city: Johnson City

first: Chris

last: Pritchett

state: TN

address: 325 Treasure Lane

department: Health Sciences

institute: East Tennessee State University

summary: PilY1 is a component of the type IV pili, an important virulence factor for P. aeruginosa. PilY1 has demonstrated signaling function and we wanteed to define the signal transduction pathways tht PilY1 controls. We found that PilY1 controls both cAMP and c-di-GMP. We determined the mechanism for how Pily1 influences cAMP production in P. aeruginosa.

overall_design: Three biological replicates were doen for each strain.


title: GBM-derived Exosomes Containing GLUT3 Increase the Migratory Potential of Monocytes

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Glioblastoma (GBM) remains a challenging malignancy with dismal prognoses despite aggressive treatment regimens. Intratumoral heterogeneity contributes to therapeutic resistance, with roles for stem cell-like brain tumor initiating cells (GBMs), glioma associated macrophages (GAMs), and communication between them. GAMs are derived from infiltrating lymphocytes, and monocyte migration is increased by GBM cell release of extracellular vesicles, including exosomes. GBM survival is promoted by the glucose transporter GLUT3, which was recently shown to alter macrophage activation states. We found that GBM-derived exosomes contain GLUT3 and that exosomes from GLUT3 expressing GBMs significantly increased monocyte migration in comparison to controls. Monocytes transfected with GLUT3 (but not GLUT1) also had significantly increased migration, demonstrating a direct role for GLUT3 in monocytes migration. Analysis of the transcriptome of exosome treated monocytes demonstrated that exosomes derived from GLUT3 expressing GBMs increasedGDF-15in monocytes. GDF-15 is a known regulator of monocyte migration, and we determined that knockdown of GDF-15 blocked the migration induced by GBM-derived exosomes. As GDF-15 induced monocyte migration is thought to involve MMP12, we next evaluated MMP12 as a potential mediator of the pro-migratory phenotype.MMP12was significantly increased in monocytes upon treatment with exosomes derived from GLUT3 expressing GBMs as was MMP12 activity. Together, our findings suggest a novel mechanism by which GBMs facilitate immune evasion and tumor progression: GBM-derived exosomes transfer GLUT3 to monocytes to increase a GDF-15/MMP12 pathway that promotes monocyte migration. The data also highlight the importance of understanding and targeting cell-cell interactions to improve glioblastoma treatment.

overall_design: We performed QuantSeq 3' RNAseq FWD on THP1 cells overexpressed or not with GLUT3 that were treated with exosomes or PBS.

first: Sarah

middle: E

last: Williford

first: Zainab

last: Ibrahim

first: Abhishek

last: Guha

first: Emily

last: Gordon

last: Mitchell

first: Peter

last: King

first: Anita

middle: B

last: Hjelmeland


title: effect of PPA2 knockdown on gene expression under normoxia or hypoxia of DLD1 colerectal cancer cells

city: Guangzhou

first: xiang

last: zhang

state: Guangzhou

address: 58 Zhongshan Second Road, Yuexiu District

department: Department of General Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Metastatic colorectal cancer (mCRC) is the major cause of death in patients with CRC. Hypoxia is a hallmark of solid tumors that promotes cell metabolic adaptation and metastasis. However, the mechanism linking mCRC to hypoxia-regulated metabolic adaptation remains unclear. Here, we found that inorganic pyrophosphatase 2 (PPA2) suppresses mCRC progression via its phosphatase function. PPA2 is expressed at low levels in mCRC specimens and lowly expressed PPA2 mediates better responses to hypoxia to enhance CRC glycolysis and metastasis by promoting hypoxia-inducible factor-1α (HIF-1α) signaling. Mechanistically, PPA2 decreases HIF-1α stability through noncanonical ubiquitin-mediated proteasomal degradation via recruitment of E3 ligase neural precursor cell-expressed developmentally downregulated gene 4 (NEDD4), which inhibits glycolysis and metastasis-related gene expression. Furthermore, PPA2 directly interacts with NEDD4 and dephosphorylates NEDD4 at the T758 residue, leading to the increased interaction between NEDD4 and HIF-1α. Under hypoxic stress, NAD-dependent protein deacetylase sirtuin-5 (SIRT5) promotes the dissociation of PPA2 and NEDD4 by inducing PPA2 desuccinylation at the K176 residue, which ultimately contributes to the improved stability of HIF-1α under hypoxic conditions. Our findings reveal the suppressive role of PPA2 in HIF-1α-dependent mCRC, suggesting that the SIRT5-PPA2-NEDD4-HIF-1α axis can be assessed for integrated prognosis evaluation and represents a potential therapeutic target.

overall_design: PPA2-depleted DLD1 cells were establised by shRNA, and were incobated under normoxia (HO) or hypoxia (LO) for 12h before sample collection.

first: Xiang

last: Zhang

first: Ziyang

last: Wang


title: Latent Epigenetic Programs in Müller Glia Contribute to Stress, Injury, and Disease Response in the Retina [scRNA-seq]

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

summary: Previous studies have demonstrated the dynamic changes in chromatin structure during retinal development that correlate with changes in gene expression. However, a major limitation of those prior studies was the lack of cellular resolution. Here, we integrate single-cell (sc) RNA-seq and scATAC-seq with bulk retinal data sets to identify cell type–specific changes in the chromatin structure during development. Although most genes’ promoter activity is strongly correlated with chromatin accessibility, we discovered several hundred genes that were transcriptionally silent but had accessible chromatin at their promoters. Most of those silent/accessible gene promoters were in the Müller glial cells. The Müller cells are radial glia of the retina and perform a variety of essential functions to maintain retinal homeostasis and respond to stress, injury, or disease. The silent/accessible genes in Müller glia are enriched in pathways related to inflammation, angiogenesis, and other types of cell-cell signaling and were rapidly activated when we tested 15 different physiologically relevant conditions to mimic retinal stress, injury, or disease in human and murine retinae. We refer to these as “pliancy genes” because they allow the Müller glia to rapidly change their gene expression and cellular state in response to different types of retinal insults. The Müller glial cell pliancy program is established during development, and we demonstrate that pliancy genes are necessary and sufficient for regulating inflammation in the murine retina in vivo. In zebrafish, Müller glia can de-differentiate and form retinal progenitor cells that replace lost neurons. The pro-inflammatory pliancy gene cascade is not activated in zebrafish Müller glia following injury, and we propose a model in which species-specific pliancy programs underly the differential response to retinal damage in species that can regenerate retinal neurons (zebrafish) versus those that cannot (humans and mice).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Retina were dissected from the eye cup in Retinal Explant Media (REM). 1.5mm punches were taken from each eye using a biopsy punch and placed on a Nuclepore 1.0uM membrane floating on 2mL of REM (+/- stress) in a 12-well dish. 50uL of REM was removed from the dish and placed on the retinal punches. The retinal punches were incubated for 24 hours (37C, 5% CO2) for culture control retina. After culture, retinal punches dissociated in papain, spun down in a 4% BSA cushion and single cell RNA-sequencing was preformed using the 10x Genomics platform.

first: Jackie

last: Norrie


title: Extracellular Vesicles Derived from Wharton’s Jelly Mesenchymal Stem Cells Inhibit Inflammatory Responses to SARS-CoV-2 and Influenza Viral Proteins via the miR-146a/ NF-κB pathway

city: Tsukuba shi

first: Neni

last: Anggraeni

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: small RNAseq analyses were conducted to identify the key miRNAs which involves in the suppression of inflammatory respons via NF-kB pathway in the Wharton's Jelly Mesehchymal Stem Cell-derived EV (WJ-EV).
Methode: WJ-MSC were cultured using EV-Depleted medium for 24 hr. for hWJ-EV, after reach 80% confluences the cells were cultured under a hypoxic condition (1%O2) for 48 hr. The conditioned medium from WJ-MSC and hWJ-MSC then were collected and centrifuged to get the EVs.
Result: miR-21, miR-143, and miR-146a were involved in the regulation of the NF-κB signaling pathway and inflammatory cytokines.

overall_design: miRNA profiles of WJ-EV and hWJ-EV

first: Cat-Khanh

last: Vuong

first: Precella

last: Silvia

first: Mizuho

last: Fukushige

first: Toshiharu

last: Yamashita

first: Mana

last: Obata-Yasuoka

first: Hiromi

last: Hamada

first: Osamu

last: Ohneda


title: Resolving single-cell gene expression by pseudo-temporal integration of transcriptomic and proteomic datasets.

city: Brisbane

first: Robin

middle: William

last: Palfreyman

state: QLD

address: Old Cooper Road

department: AIBN

country: Australia

institute: The University of Queensland

summary: One of the greatest prospects of multimodal single-cell analysis is the ability to integrate single-cell transcriptomic and proteomic datasets to compare transcription and translation profiles to investigate regulation between phenotypes. However, the integration of these complex datasets remains challenging. In this study, we demonstrate the use of  pseudo-temporal cell orders as a mutual axis for integrating of scRNA-Seq and scp-MS data. We collected temporal samples of HEK293F cells undergoing hypoxia to isolate the variance of hypoxia from the tightly coupled variance of cell cycle. Markers for hypoxia were then used to construct pseudo-temporal orders in each dataset which were used to reveal transcription and translation dynamics of attenuated respiration in single cells. This approach allowed us to integrate  single-cell transcriptomics and proteomics methods to understand the regulatory mechanisms governing biological phenotypes.

overall_design: HEK293F cells undergoing hypoxia

first: Craig

last: Barry

first: Timothy

last: Mercer

first: Lars

last: Nielsen

first: Esteban

last: Marcellin


title: Improved split prime editors enable efficient in vivo genome editing [Amplicon_Seq_in_vitro]

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

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

department: School of Life Sciences

institute: Westlake university

summary: Prime editor (PE) is a precise genome-editing tool capable of all possible base conversions, as well as insertions and deletions without DSBs or donor DNA. The efficient delivery of PE in vivo is critical for realizing its full potential in disease modeling and therapeutic correction. Although PE has been divided into two halves and delivered using dual adeno-associated viruses (AAVs), editing efficiency at different gene loci varies among split sites, and efficient split sites within Cas9 nickase are limited. In this study, by screening multiple split sites, we demonstrated a series of efficient split site when delivering PE by dual-AAV. Additionally, we utilized a feature reported by others recently that RNase could be detached from the Cas9n and designed split sites in the first half of Cas9n. To test the editing efficiency in vivo, a novel dual-AAV split-ePE3 was packaged in AAV9 and delivered via tail vein injection in mice, achieving 24.4% precise genome editing 3 weeks post-injection. Our findings establish an alternative split-PE architecture that could achieve robust gene editing efficiency, facilitating the potential utility both in model organisms and as a therapeutic modality.

overall_design: Split PE from different split sites was cloned into the AAV genome plasmid, and a series of split-PE systems were established by employing different promoters, truncated reverse transcriptase and untethered reverse transcriptase under the size restriction condition of the AAV packaging. Cells transfected with plasmids and mice infected with dual-AAV virus, the desired editing was integrated into the genome of host cells. Cells were harvested 72 hours after plasmid transfection, and mouse livers were collected 3 weeks after the virus injection into the tail vein. To detect the outcome of prime editing, we amplified the gDNA harvested from the edited cells and subjected the amplicons to high-throughput sequencing.

first: Rongwei

last: Wei

first: Zhenxing

last: Yu

first: Zhike

last: Lu


title: KAT7-acetylated YBX1 promotes HCC proliferation and sorafenib resistance by reprogramming nucleotide metabolism

city: Lanzhou

first: He

last: Huang

address: Donggang Street

institute: Lanzhou university

summary: To investigate the function of KAT7 in the regulation of hepatocellular carcinoma, Huh7 cells were transfected with specific shRNAs targeting KAT7 or control shRNA. Total RNA was extracted at 48h after transfection to performed gene expression profiling analysis by high throughput RNA-seq.

overall_design: We established Huh7 cell lines with/without KAT7 knockdown. Then, we performed gene expression profiling analysis using data obtained from RNA-seq of Huh7 cells.

first: Yongqiang

last: Zhou


title: Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B

city: Paris

first: Pontoglio

last: Marco

address: 160 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades

summary: HNF1B (Hepatocyte Nuclear Factor 1-Beta) is a POU-homeobox transcription factor expressed in kidney and frequently mutated in patients suffering from Congenital Anomalies of the Kidney and the Urinary Tract (CAKUT). HNF1B is a bookmarking factor, able to bind mitotic chromatin and necessary for the post-mitotic reactivation of gene expression. In order to characterize the molecular functions of HNF1B as a bookmarking factor, we performed ChIPseq on asynchronous and mitotic renal cells. We developed a novel ChIP method with a non-aqueous crosslinking (NAQC) to circumvent the well-known artefactual effects of formaldehyde crosslinking of mitotic chromosomes. NAQC-ChIP allowed the retention of the mitotic signal that was lost with a regular ChIP. With this novel methodology, we show that the vast majority HNF1B binding sites detected in asynchronous cells are also bound in mitosis.

overall_design: ATACseq was performed in asynchronous and mitotic KEC cells.

first: Alessia

last: Bagattin

first: Salvina

last: Tammaccaro

first: Magali

last: Chiral

first: Munevver

middle: P

last: Makinistoglu

first: Jonathan

last: Lerner

first: Serge

last: Garbay

first: Nicolas

last: Kuperwasser

first: Marco

last: Pontoglio


title: RELMα establishes a permissive environment for influenza infection through direct effects on lung epithelial cells

city: Riverside

first: Brandon

last: Le

state: CA

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

summary: Beyond a physical barrier, the lung epithelium provides an essential line of defense against infectious pathogens, such as Influenza A viruses (IAV), through antimicrobial factors and triggering innate and adaptive immunity. On the other hand, IAV infects lung epithelial cells and manipulates their function to establish a non-protective, permissive environment. Identification of epithelial factors and pathways that can be targeted to restore optimal immunity would provide new therapeutic options against IAV. Here, we demonstrate an unexpected non-immune function for the cytokine RELMɑ in mediating a permissive environment for IAV infection through lung epithelial cell-intrinsic effects. Murine infection with IAV A/California/04/2009 (H1N1) led to the significant RELMɑ secretion by IAV-infected EpCam+ epithelial cells. Both constitutive and club cell-specific RELMɑ-deficient mice (Retnla-/- and RetnlaΔCC10) had significantly reduced IAV virus, specifically in epithelial cells, whereas the lung immune response was unaffected. RELMɑ treatment increased IAV infection of murine lung epithelial cell lines (MLE), and transcriptomic analysis indicated that RELMɑ-induced permissiveness to IAV was associated with cell-intrinsic changes in metabolic activity. Collectively, these studies indicate a direct non-immune role for RELMɑ in mediating a virus-permissive environment in epithelial cells potentially through modulation of cellular metabolism.

overall_design:
To investigate transcriptional changes in mouse lung epithelial cells (Mle2) in response to Influenza A virus (IAV) in the presence or absence of RELMα (Ra) treament
Cells were either treated with PBS or RELMα prior to IAV infection and recovered for gene expression profiling with RNA-seq
The dataset is comprised of four groups (ctrl, Ra, ctrl+IAV, Ra+IAV) each with four independent biological replicates. Comparative expression analysis was carried out for each group

first: Meera

last: Nair

first: Sang

last: Kim

first: Stefanie

last: Sveiven


title: Longitudinal Multiomic Profiling and Corticosteroid Modulation of the Immediate Innate Immune Response to an Adenovirus-vector Vaccine

city: Bundang-gu, Seongnam-si

first: Seong Jin

last: Choi

state: Gyeonggi-do

address: Dolma-ro, 172

department: Internal Medicine

country: South Korea

institute: Seoul National University Bundang Hospital

summary: Among new vaccine technologies contributed to the control of the COVID-19 pandemic, ChAdOx1 nCoV-19, a chimpanzee adenovirus (ChAd)-vector vaccine expressing the SARS-CoV-2 spike protein, could be administered globally owing to its low production cost and lack of a requirement for frozen storage. Despite its benefits, most recipients have reported immediate inflammatory reactions after the initial dose vaccination. We comprehensively examined the immune landscape following ChAdOx1 nCoV-19 vaccination based on the single-cell transcriptomes of immune cells and epigenomic profiles of monocytes. Monocyte and innate-like activated T cell populations expressing interferon-stimulated genes (ISGs) increased 1 day post-vaccination with appearance of distinct subtype of ISG-activated cells, returning to baseline by day 14. Pre-treatment with oral corticosteroids effectively curtailed these ISG-associated inflammatory responses by decreasing chromatin accessibility of major ISGs, without hampering vaccine immunogenicity. Our findings provide insights into the human immune response following ChAd-based vaccination and propose a method to reduce inflammatory side effects.

overall_design: Single cell RNA sequencing & TCR sequencing + ATAC sequencing of before and after ChAdOx1 vaccination (D0, D1, D3, D14)

first: SeongJin

first: Wonhyo

last: Lee

first: SangCheol

first: Hye-Yeong

last: Jo

first: Hyun-Young

last: Park

first: HongBin

first: Woong-Yang

first: SungHo

first: Jae-Hoon

last: Ko

first: JeongSeok


title: Effect of D-serine on gene expression in Neuro2a cells

city: Tokyo

first: Jumpei

last: Sasabe

address: 35 Shinanomachi, Shinjuku

department: Pharmacology

institute: Keio University School of Medicine

summary: Serine metabolism provides essential metabolites for cellular growth and proliferation, and also produces neurotransmitters. However, how serine metabolism coordinates with functional development of neurons remains unclear. We report neurotransmitter D-serine inhibit growth of immature cells. Metabolomic analysis of neural progenitors revealed that D-serine decreases glycine synthesis thereby diminishes one-carbon metabolism, in which L-serine is a crucial carbon donor. D-serine inhibits one-carbon metabolism by competing transport of cytosolic L-serine to mitochondria, which restrains proliferation and triggers apoptosis of neural progenitors as well as neural tumor cells, but not mature neurons, in vitro and ex vivo. This RNA-seq data supports the idea that D-serine inhibits polarization and growth/proliferation of immature neurons and further indicate that immature neurons counteracts D-serine-induced cellular stress through enhancing mitochondrial function, including energy synthesis.

overall_design: Neuro2a cells were cultured in D-MEM with 10% FBS. The medium was changed to D-MEM(-SG) including 10% FBS with or without 5 mM D-serine. Cells were harvested in Trizol after 18 hours of incubation at 37 °C in a CO2 incubator. RNA was extracted from cells according to the manufacture’s protocol. mRNA libraries of each samples were prepared using a TruSeq Stranded mRNA library Kit (Illumina, San Diego, CA) according to the manufactures’ protocol and paired end sequences were read by NovaSeq (Illumina).

first: Kenichiro

last: Adachi

first: Masataka

last: Suzuki


title: Mycobacterial Pstp Impairs Host RNA Alternative Splicing by Dephosphorylation of Spliceosome RBMX at S189

city: shanghai

first: Tianxian

last: Liu

address: meilong road 130

institute: east china university of science and technology

summary: Mycobacterium tuberculosis (Mtb) infection can widely affect host signal transduction and protein function. Recent studies have revealed that Mtb virulence factors could regulate host immune activation and promote intracellular survival of the pathogen. However, no systematic research has been conducted on Mtb infection. Here, we analyzed mycobacteria-infected cells using multi-omics (proteomics, phosphoproteomics, transcriptomics, and interactomics) and observed that mycobacteria could regulate host alternative splicing by decreasing spliceosomes phosphorylation level. Using phosphoproteomics and interactomics, we connected decreased host phosphorylation with mycobacterial serine/threonine protein phosphatase PstP and observed that Pstp can regulate host Pla2g7 gene alternative splicing by dephosphorylating the spliceosome RBMX S189 site. Further studies showed that PLA2G7 exon9 including rather than excluding form, promotes the inflammatory response. In conclusion, our findings revealed the global landscape and Pstp functions during Mtb infection, which could lead to a deeper understanding of Mtb-host interactions.

overall_design: To investigate the RNA splicing in the host after infected by Mtb, RNA-seq was desigened.


title: NF1 modulates microtubular repair and dictates sensitivity to maytansinoid antibody-drug conjugates in HER2-positive breast cancer

city: Milan

first: Luca

last: Mazzarella

state: M

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO European Institute of Oncology IRCCS

summary: NF1 is a tumor suppressor widely mutated across several cancers. Its best characterized function is the inhibition of RAS signaling through its GTPase-Activating Protein (GAP) domain. Additional functions have been proposed but not deeply investigated, due to its large size and complex domain structure. Here, combining patient data, in vitro/in vivo models and protein biochemistry, we show that NF1 is a novel Microtubule-Associated Protein (MAP) that modulates microtubular dynamics and intra-tubular repair. NF1 loss results in mitotic defects such as prolonged mitosis, supranumerary centrosomes and chromosome missegregation, leading to low-grade aneuploidy in cell lines and patients. Loss of NF1-mediated intratubular repair creates a liability specifically targetable by maytansinoids, a class of microtubule-depolymerizing agents widely used as payloads in Antibody-Drug Conjugates such as Trastuzumab-Emtansine (T-DM1). Our results directly imply loss of intratubular repair as a driver of tumorigenesis, and NF1 as the first ADC payload-associated biomarker.

overall_design: To investigate the biological consequences of NF1 loss in Breast Cancer (BC), we generated NF1 knockout (KO) clones of the widely used HER2+ BC cell lines BT-474. To further characterize the global changes induced by NF1 loss and T-DM1 treatment, we analysed the transcriptome of BT-474 KO and BT-474 WT cells subjected to T-DM1 treatment. Then we compared transcriptional changes induced by T-DM1 with the WT.

first: Emanuele

last: Bonetti

first: Eleonora

last: Messuti

first: Bruno

last: Duso


title: Latent Epigenetic Programs in Müller Glia Contribute to Stress, Injury, and Disease Response in the Retina

first: Michael

last: Dyer

overall_design: Retina were dissected from the eye cup in Retinal Explant Media (REM). 1.5mm punches were taken from each eye using a biopsy punch and placed on a Nuclepore 1.0uM membrane floating on 2mL of REM (+/- stress) in a 12-well dish. 50uL of REM was removed from the dish and placed on the retinal punches. The retinal punches were incubated for 24 hours (37C, 5% CO2) for culture control retina. After culture, retinal punches were dissociated in Trizol and RNA was extracted and submitted for RNAseq.

first: Jackie

last: Norrie


title: T cells expressing modified Fc receptor infiltrate solid tumors and provide long-term anti-tumor protection

city: Tel Aviv

first: Alon

last: Richter

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: The clinical success of T cells armed with chimeric antigen receptor (CAR-T) to cure patients with hematological malignancies, has demonstrated the immense therapeutic potential of equipping T cells with synthetic receptors. Nonetheless, the scarcity of tumor-specific antigens and the limited capacity of T cells to infiltrate the tumor microenvironment significantly limit its clinical use in solid tumors.  Here, we provide evidence of FcγRI expressing CD8+ T cells presence in both mouse and human tumors as well as inflammation sites. Inspired by this discovery, we engineered a novel FcγRI-based receptor for T cells. This design allows T cells to target tumor cells indirectly through antibody intermediates, separating the processes of antigen recognition and T cell activation. This approach allows T cells to initiate killing exclusively against cells with antigen overexpression, thus minimizing on-target off-tumor cytotoxicity.  Interestingly, the modified FcγRI expression in T cells unexpectedly induces constitutive expression of the CD11b integrin. This additional effect enables the engineered T cells to efficiently infiltrate the tumor basement membrane and develop an effector memory phenotype, potentially promoting long-term anti-tumor activity. The presence of these effector memory subsets characterized complete responders and mediated tumor regression upon rechallenge. Overall, T cell-mediated ADCC suggests an alternative, novel strategy for conventional CAR-T cell design, enables T cells to differentiate between target cells expressing the same antigen, and overcomes the physical barriers of the tumor microenvironment.

overall_design: Gene profile comparison between AG2G, CAR Her2 and Sham transduced T cells

first: Yaron

last: Carmi


title: Matrix topography induces a cytoskeletal and transcriptional memory supporting metastasis

city: London

first: Oscar

last: Maiques

address: Charterhouse Square

department: Tumour Microenvironment

country: United Kingdom

institute: Queen Mary's University of London- Cancer Research UK Barts Centre

summary: The extracellular matrix (ECM) is a crucial component of solid tumours. Using digital pathology in human and mouse tissues, we define 3 matrix regions: the tumour body (TB), the proximal invasive front (PIF)- and a further distal invasive front (DIF) Increased matrix density coupled to larger fibre thickness, length and alignment are all features of both invasive areas. Importantly, radial fibre orientation is a characteristic of the distal invasive front. Using several in vivo and in vitro 3-dimensional (3D) models, we show that matrix density and alignment induces RhoA/C-ROCK-Myosin activity in cancer cells, while maximal amoeboid directed migration correlates with areas of radial fibre orientation. Importantly, matrix topographical features are enough to prime cancer cells for successful local invasion and metastatic colonisation. Using several spatial OMICs, we describe a mechano-inflammatory transcriptional program linked to matrix topographical features in the invasive fronts of primary tumours that is preserved in metastatic lesions and strongly linked to worse prognosis in patients.

overall_design: 4599 murine melanoma cells isolated from different tumour parts (TB, PIF, DIF and MET) were seeded on Fibrillar bovine dermal collagen 1.7 mg/ml (PureCol, Cat. 5005 Advanced BioMatrix) for 24h DMEM+10% FBS.  Media was changed to DMEM+1% FBS during 24h before the RNA extraction. RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) followed by QIAGEN RNeasy Midi Kit. RNA integrity and quality was evaluated using RNA QubitTM assay. Sequencing was performed using 150bp paired end sequencing strategy using Illumina sequencing platform and PE150 Technology

first: Victoria

last: Sanz-Moreno


title: Maternal Asthma During Pregnancy Imprints Fetal Lung Group 2 Innate Lymphoid Cells and Enhances Their Function in Adulthood [scATAC-Seq]

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: We investigated the effects on the lungs during fetal in the offspring of asthmatic mothers. ILC2 in the fetal and adult lungs of offspring of asthmatic mothers showed overlapping chromatin accessible altered regions

overall_design: Fetal lungs were harvested on gestation day 18 from OVA- or PBS- treated mothers and adult lungs were 8 weeks old offspring of OVA- or PBS- treated mothers. (E18-OVA, n = 8; E18-PBS, n = 9; Adult-OVA-PBS, n = 6; Adult-OVA-PBS, n = 7).

first: Tomoaki

last: Takao


title: Maternal Stress During Pregnancy Imprints Fetal Lung Group 2 Innate Lymphoid Cells

summary: We investigated the gene expression on the feral lungs (E18) in the offspring of dexamethasone (DEX)- or PBS- treated mothers by single cell RNA sequence.

overall_design: Fetal lungs were harvested on gestation day 18 from each of two mice that had received water containing DEX or PBS since gestation day 12. Fetal lungs (DEX-1, n = 8; DEX-2, n = 9; PBS-1, n = 5; PBS-2, n = 8) were pooled per sample. Fetal lungs cells were prepared by single-cell suspension protocol of fetal lungs.


title: Maternal Asthma During Pregnancy Imprints Fetal Lung Group 2 Innate Lymphoid Cells [snRNA-Seq]

summary: We investigated the effects on the lungs during fetal in the offspring of asthmatic mothers. Lung ILC2 of offspring of asthmatic mothers altered phenotypically during fetal life.

overall_design: Fetal lungs were harvested on gestation day 18 from OVA-induced athsmatic mother or PBS-treated control mother. Fetal lungs (E18-OVA, n = 8; E18-PBS, n = 9) were pooled per sample. Fetal lungs cells were prepared by single-cell suspension protocol of fetal lungs.


title: A novel, butyrate-producing Gram-positive bacterium from the human gut, Hoskinsella mucinolytica, selectively targets N-acetylhexosamine sugars in host mucins

city: Ann Arbor

first: Nicholas

last: Pudlo

address: 1150 W. Medical Center Dr.

institute: University of Michigan

summary: We used culturing of fecal sample enrichments on solid medium containing gastric mucin as the main carbon source to isolate a novel bacterium that is largely restricted to using the N-acetylglucosamine and N-acetylgalactosamine sugars from mucin. This butyrate-producing bacterium accesses these sugars from both polymeric gastric mucin and chemically released oligosaccharides and has a genome with correspondingly restricted carbohydrate-active enzyme content. Sequencing data was curated to determine gene expression profiles when comparing N-acetylgalactosamine, N-acetylglucosamine, gastric mucin oligosaccharides and cellobiose.

sample_organism: Erysipelotrichaceae bacterium DSM 116809

overall_design: Hoskinsella mucinolytica DSM116809 was grown in biological replicate cultures to mid-log phase under anaerobic conditions at 37ºC on Depleted Medium (DM) containing either N-acetylgalactosamine, N-acetylglucosamine, gastric mucin oligosaccharides (gMO) or cellobiose. Total RNA was extracted using phenol:chloroform and rRNA was removed. Sequencing of mRNA (RNA-sequencing) analysis was performed to determine differential gene expression among these substrates.

first: Gabriel

middle: V

last: Pereira

first: Eric

middle: C

last: Martens


title: Maternal Asthma During Pregnancy Imprints Histone Modification of Lung Group 2 Innate Lymphoid Cells

summary: We investigated the effects on the lungs during fetal in the offspring of asthmatic mothers. We examined H3K4me3 modification of ILC2 in the adult lungs of offspring of asthmatic mothers.

overall_design: Lung ILC2 were harvested from 8 weeks old offspring of OVA- or PBS- treated mothers and performed ChIPseq alalysis.

first: Tomoak

first: Azusa

last: Inoue


title: Effect of myeloid-specific knockout of Glul on gene expression after either DSS or H2O challenge

city: Shanghai

first: Jianghong

last: Yu

state: State...

address: Dong'an Road

institute: Fudan University

summary: To identifythe the functional roles of genes in mouse colitis, We performed transcriptome analysis in colon tissues of Glul flox/flox and Glul∆Lyz2 mice treated with DSS.

overall_design: Both Glul∆Lyz2 mice and Glul flox/flox littermates were treated with H2O or DSS. Total RNA from mouse colon tissues was extracted using the TRIzol reagent, according to the manufacturer’s instructions.

first: Jie

last: Liu

first: Huilu

last: Zhang

first: Menglin

last: Shi


title: A microbial-inspired antibody-drug conjugate for cancer immunotherapy

city: Houston

first: Benjamin

last: Schrank

state: TX

address: 1400 Pressler St

institute: MD Anderson Cancer Center

summary: Generating antitumor immune responses requires the phagocytosis of tumor cells and subsequent cross-presentation of tumor-derived antigens by antigen-presenting cells. However, these processes are impeded by phagocytosis checkpoints and inefficient cytosolic transport of antigenic peptides from phagolysosomes. Here, using a microbial-inspired strategy, we engineered an antibody-drug conjugate (ADC) that targets the “don’t eat me” signal CD47 linked to the bacterial toxin listeriolysin O from the intracellular bacterium Listeria monocytogenes via a cleavable linker (CD47-LLO). CD47-LLO promotes the phagocytosis of cancer cells followed by the release and activation of LLO to form pores on phagolysosomal membranes that allow cytosolic entry of tumor-derived contents, leading to enhanced antigen cross-presentation of tumor-derived peptides and activation of cytosolic immune sensors. CD47-LLO treatment in vivo significantly inhibited the growth of both localized and metastatic tumors and improved animal survival as monotherapy or in combination with checkpoint blockade. Together, these results demonstrate that designing ADCs to promote immune recognition of tumor cells represents a promising therapeutic strategy for treating multiple cancers.

overall_design: To define the identities of innate and adaptive immune cells that accumulate in tumors upon CD47-LLO treatment, we performed single cell RNA (scRNA-seq) on CD45+ cells isolated from EO771 tumors. CD45+ cells were rare in IgG or anti-CD47 treated animals (Fig. 4a,b). In contrast, we observed a 30-fold increase in CD45+ cells upon CD47-LLO treatment. After rigorous quality control, we used our previously published methodsto annotate cells and interpret changes in their abundance and gene expression (n= 13,891 cells total).

first: Wen

last: Jiang

first: Kyuson

last: Yum

first: Nhat

last: Tran


title: Differences in miRNA expression profiles of follicular fluid exosomes between Premature ovarian insufficiency and normal ovarian reserve

city: Guangzhou

first: Xiaofei

address: 1838 North Guangzhou Avenue

department: Department of Gynecology and Obstetrics

institute: Nanfang Hospital, Southern Medical University

summary: Premature ovarian insufficiency (POI) refers to the severe decline and failure of ovarian function in women before the age of 40, and current treatment methods have significant limitations. In order to screen miRNAs with good anti-apoptotic effect, we used high-throughput sequencing technology to study the differences in  exosomal miRNA expression profiles from human follicular fluid between patients with POI and patients with normal ovarian reserve.

overall_design: In order to screen miRNAs with good anti-apoptotic effect from human follicular fluid exosomes, we selected three cases of follicular fluid from POI patients and three cases of follicular fluid from control group patients, extracted follicular fluid exosomes, extracted total RNA of exosomes, and screened 18-30nt sRNA for high-throughput sequencing.


title: RNAseq sequencing signatures of Diffuse Large B-cell Lymphoma cells after beta-sitosterol treatment

city: Tianjin

first: Minghan

last: Qiu

state: Tianjin

address: Department of Oncology, Tianjin Union Medical Center of Nankai Univercity, 190 Jieyuan Street, Hongqiao District, Tianjin, China.

department: Department of Oncology

summary: Resistance to Rituximab is a significant challenge in treating Diffuse Large B-cell Lymphoma (DLBCL).  β-Sitosterol (β-ST) is a plant sterol that has been found in a broad variety of fruits, spices, and medicinal plants. While the anti-neoplastic properties of β-Sitosterol (β-ST) are established in various solid malignancies, its impact on DLBCL is uncharted. To further investigation the mechanism of β-ST on DLBCL, we employed RNAseq transcriptome analysis to detect differential expression genes (DEGs) between β-ST treated and untreated DLBCL cells. Our findings indicate that β-ST impedes DLBCL cell proliferation in a concentration and time-dependent manner. It appears to alter sphingolipid metabolism, facilitate (ASM translocation to the plasma membrane, augment ceramide platforms through increased ceramide synthesis, and consequently precipitate apoptosis in DLBCL cells.

overall_design: SU-DHL-8 cells were treated with 15μM β-ST for 24 hours, with an equal concentration of DMSO as the control, in three replicate experiments.

first: Guoping

last: He

first: Miao

first: Huaqing

last: Wang


title: Bioinspired cell silicification of the model diatom Phaeodactylum tricornutum and its effects on cell metabolism

city: Zhoushan

first: Jiwei

last: Chen

address: Ocean College Zhejiang University

institute: Ocean College Zhejiang University

summary: Biosilicification enhances the mechanical strength and chemical stability of organisms. Diatoms are the natural model for studying cell silicification, with the model diatom Phaeodactylum tricornutum being known as the only species that could transition from non-silicified cells to silicified cells under environmental stress. In this study, single-cell sequencing was employed to investigate the wild-type P. tricornutum strain (WT-Pt) without cell silicification and the engineered strain (SG-Pt) with silicified cells. Our results indicate that SG-Pt exhibits clearly cellular clustering and enhanced iron metabolic function compared to WT-Pt.

overall_design: Genetically modified diatoms exhibit a distribution of silica shells and altered morphology, while wild-type diatoms lack silica shell distribution and have spindle-shaped morphology. Single-cell sequencing of different morphological cells from the same species is conducted to explore their distinct physiological states.

first: Weiqi

last: Fu

first: Kourosh

last: Salehi-Ashtiani

first: Hangjin


title: Contradictory Effect of ANGPTL4 on Hedgehog pathway by Galectin-7 and its Influence on Cancer metastasis and Angiogenesis

city: Changsha

first: wenjie

last: Feng

state: hunan

address: Xiangya Street

department: burn and reconstruction department

institute: central south university

summary: Background: Gastric cancer (GC) is a serious malignant disease of digestive system over the world. Angiopoietin-like protein 4 (ANGPTL4) was a secreted glycoprotein, which involved in multiple pathophysiological process, such as metabolic reprogramming, angiogenesis, proliferation and metastasis. Nevertheless, the expression, function, and prognostic significance of ANGPTL4 in GC are still contradictory. Methods: Bioinformatic analysis to confirm the expression and prognosis of ANGPTLs in GC. IF staining was used to detect ANGPTL4 protein in GC samples. The molecular biological effect of ANGPTL4 was confirmed by EdU, MTT, FCS, wound healing, transwell, tube formation chorioallantoic membrane model, and nude mice model assay in GC cell lines. RNA-seq was used to confirm the potential downstream mechanism of ANGPTL4, which verified by PCR, WB, IF, co-IP and molecular docking.  Results: ANGPTL4, as an important ANGPTLs, was significantly correlated with poor diagnosis in GC patients. The proliferation, migration, invasion, apoptosis escaping, angiogenesis ability was enhanced by ANGPTL4 in SNU5 and MKN7, but repressed in AGS. LGALS7 could be upregulated in AGS transfected with ANGPTL4 OE, which was one of the key factors that cause ANGPTL4 to produce an anticancer phenotype. Conclusion: LGALS7 was a key factor for the contradictory effect of ANGPTL4 on activating hedgehog pathway to driving GC progression, including proliferation, migration, apoptosis escaping, angiogenesis and lymphangiogenesis.

overall_design: comparative  gene expression of profiling analysis of RNA-seq data for AGS cells(ANGPTL4 victor) and its derivatives( oe-ANGPTL4，oe-ANGPTL4 1,and oe-ANGPTL4 2 )

first: Juan

last: Xie

first: Tian

last: Zeng

first: Ting-yu

last: Fan

first: Han-Guo

last: Shan


title: GTP Cyclohydrolase I Confers Metabolic Protection Against Lipid Peroxidation in Glioblastoma

city: Huntsville

first: Sara

last: Cooper

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Guanosine triphosphate cyclohydrolase I (GCH1) was previously identified as a regulator of reactive oxygen species (ROS) in brain tumor initiating cells (BTICs). Elucidating the GCH1/Tetrahydrobiopterin (BH4) pathway in BTICs has unveiled the necessity for GCH1 to protect BTICs from lipid peroxidation. Within this study, we observed differences in lipid pathways and lipid metabolites during GCH1 modulation. Alteration to polyunsaturated fatty acids (PUFAs), a species of oxidatively vulnerable lipids, were altered during GCH1 knockdown. Pharmacological inhibition of BH4 with drugs known to cross the blood brain barrier (sulfasalazine and pyrimethamine) successfully reduced growth in GCH1 overexpressed BTICs, induced lipid peroxidation.

overall_design: GBM 456 were genetically modified to overexpress (OE) GCH1 or knocked down (KD) with GCH1 short hairpin (Sh) RNA. Empty vector (EV) and nontargeting controls (NT) were utilized throughout the study.  Cells were transiently co-transfected with psPAX2, pCMV-VSVG and shRNA constructs using FuGENE® HD Transfection Reagent (Promega) as previously reported(67). Virus titer was determined using Lenti-X qRT-PCR Titration Kit (Takara). Lentivirus pLenti6.3/V5 GCH1 (HsCD00941202) was purchased from DNASU while pLenti6.3 EV was purchased from Addgene. For lentivirus expressing GCH1 shRNAs (TRCN0000050744 and TRCN0000050745) and non-targeting control shRNA were purchased from Sigma. Both shRNA constructs were designed against the GCH1 coding sequence. The shRNA sequences were as follows: GCH1 Sh4:5’CCATATTGGTTATCTTCCT’3’ and GCH1 Sh5: 5’GATGTCCTAAACGATGCTA3’

first: Emily

last: Gordon

first: Kaysaw

last: Tuy

first: Anita

last: Hjelmeland


title: Combination of SD70 and MI-503 exerts a synergistic effect against MLL:: AF9-driven AML

first: Wenqi

last: zhu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

summary: Acute myeloid leukemia (AML), a heterogeneous hematologic malignancy, is the most common form of acute leukemia in adults. MLL rearrangements (MLL-r) are observed in approximately 10% of AML and are associated with a relatively poor prognosis, highlighting the need for new treatment regimens. MLL fusions recruit KDM4C to mediate epigenetic reprogramming, which is required for maintenance of MLL-r leukemia. In this study, we used a combinatorial drug screen to selectively identify synergistic treatment partners for the KDM4C inhibitor SD70. The results showed that the drug combination of SD70 and MI-503, a potent Menin-MLL inhibitor, induced synergistically enhanced apoptosis in MLL-r leukemia cells without affecting normal CD34+ cells. In vivo treatment with SD70 and MI-503 significantly prolongs survival in AML xenograft models. Differential Gene expression analysis by RNA-seq following combined pharmacological inhibition of SD70 and MI-503 revealed changes in numerous genes, with MYC target genes being the most significantly downregulated. Taken together, these data provide preclinical evidence that the combination of SD70 and MI-503 is a potential dual-target therapy for MLL-r AML.

overall_design: To investigate the molecular mechanism underlying the synergistic effect of SD70 and MI-503, we performed RNA-seq analysis on MOLM13 cells treated with DMSO, single agent alone, or the combination.

first: Xiaotong

last: Ma

last: Zhu


title: miRNA profiling of fibro/adipogenic progenitors isolated from normal muscles, CTX-injured muscles or denervated muscles

city: Chengdu

first: Xia

last: Kang

address: Rongdu Avenue, #270

institute: General Hospital of Western Theater Command

summary: The aim of this study is to explore the differentially expressed miRNAs in FAPs from different injured muscle models.

overall_design: miRNA-Seq of fibro/adipogenic progenitors isolated from normal muscles, CTX injured muscles at 5 days post injury or sciatic denervated muscles at 3 weeks post surgery

first: Zhen

last: Dong

first: Jin

last: Qian

first: Kang-lai

last: Tang


title: The effect of age on crystalline silica-induced pulmonary toxicity-aged rats

city: Morgantown

first: Pius

last: Joseph

address: 1000 Frederick Lane

institute: NIOSH

summary: The effect, if any, of age on the pulmonary toxicity induced by Min-U-Sil 5 crystalline silica exposure was investigated in rats. As part of the study, the changes in global gene expression profiles in the blood and lungs of the animals were determined.  To conduct these studies, to determine if age influences the pulmonary response to crystalline silica exposure, two different age groups of healthy, male F344 rats were used.  In this study the old age group of rats (12 months old at the time of exposure) was exposed to either air or crystalline silica (Min-U-Sil 5) (15 mg/m3, 6 hours/day, 5 days) by whole body inhalation. The old age group of rats simulates a group of workers who would be 45 to 50 years old.  At two crystalline silica post-exposure time periods (1-day and 6-months) animals were euthanized and pulmonary inflammatory, cytotoxic, and oxidant responses were determined.  Analysis of bronchoalveolar lavage parameters of toxicity such as oxidant generation and inflammation revealed significant changes in pulmonary toxicity in the crystalline silica exposed rats compared with the time-matched, air exposed control rats. The blood gene expression profiles showed only minimal changes, at both the time points, in the crystalline silica exposed rats compared with the controls. Specifically, no genes were significantly differentially expressed (fold change >1.5 and FDR p<0.05) in the one-day post-exposure group and only 6 genes were significantly differentially expressed in the 6-month post-exposure group. However, the lung gene expression profiles showed substantial changes in the crystalline silica exposed animals at both one-day and 6-month post-exposure.  Specifically, there were a total of 325 genes significantly differentially expressed (fold change >1.5 and FDR p<0.05) at the one-day post-exposure group and 3348 genes significantly differentially expressed at the 6-month post-exposure. The data obtained from the present study demonstrated that crystalline silica inhalation exposure, under the conditions employed in the present study, resulted in significant changes in lung toxicity parameters and lung gene expression profile in the rats at both 1-day and 6-month post-exposure.

overall_design: Rats were exposed by whole-body inhalation to filtered air or crystalline silica (Min-U-Sil 5) (15 mg/m3, 6 hours/day, 5 days).  At post exposure time intervals of 1- day and 6-months, rats were euthanized, and lung and blood samples collected.

first: Tina

middle: M

last: Sager


title: Effect of Lcn2 on gene expression during osteoclast differentiation of RAW 264.7 cells in the presence of Cpn60 treatment

city: Seoul

first: Heeeun

last: Woo

address: 1, Anam-dong 5(o)-ga, Seongbuk-gu

institute: Korea University

summary: To investigate the clear relation between chaperonin 60 kDa and Lcn2 in the inhibition of osteoclast differentiation, we performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RAW 264.7 cells in the presence of Cpn60 treatment.

first: Younghee

last: Lim

first: Jooyoung

last: Cho


title: Gene expression profile at single cell level of lung and tracheobronchial lymph nodes leukocytes of healthy and influenza-infected pigs

city: Columbia

first: John

last: Driver

state: MO

address: 1201 Rollins Street

institute: University of Missouri

summary: We characterized the single cell landscape of lung leukocytes of healthy pigs and then compared them to pigs infected with H1N1 A/California/04/2009 with or without oseltamivir antiviral therapy.

overall_design: Live lung leukocytes of 6-week-old mixed breed pigs were isolated by fluorescence-activated cell sorting (FACS) according to the absence of propidium iodide signal and analyzed using scRNAseq.

first: Driver

last: John

first: Madrid

last: Darling Melany C

first: Gu

last: Weihong

first: Warren

last: Wesley


title: A novel pancreatic ductal adenocarcinoma organoid recapitulating tumor microenvironment reveals macrophage-driven enhanced cancer cell survival [RNA-Seq]

city: Minatoku

first: Shunsuke

last: Tabe

address: 4-6-1 shirokanedai

department: Regenetive medicine

institute: Institute of medical and science,the university of Tokyo

summary: Pancreatic ductal adenocarcinoma (PDAC) is a progressive cancer with only about 12 % of a 5-year survival rate. PDAC generally shows strong chemoresistance, which has been correlated with the tumor microenvironment (TME) of PDAC consisting of various types of stromal cells. Recent single-cell RNA sequence (scRNAseq) analyses demonstrate that a high percentage of myeloid cells in TME stroma cells is related to poor prognosis, and, among myeloid cells, tumor associated macrophages (TAM) are the most abundant population. However, their functions in PDAC malignancy remain largely unknown. Previously, we established a PDAC-organoid associated with an artificial TME by co-culturing patient-derived cancer cells, human induced pluripotent stem cell (hiPSC) derived mesenchymal and endothelial cells, which is called fused pancreatic cancer organoid (FPCO). Here, we further incorporated macrophages into FPCO and named it M0-FPCO. After 1 week of organoid culture, the macrophages in M0-FPCO expressed the conventional markers of M2-macrophages, such as CD163 and CD206. However, bulk RNAseq analysis showed that macrophages in M0-FPCO (FPCO-Mac) have distinct characteristics as compared with M2-macrophages induced with IL4 and 13. scRNAseq of M0-FPCO further demonstrated that FPCO-Mac was divided into 6 populations including Granulin+-TAM and SPP1+-TAM, which had been identified in human PDAC tissue. Furthermore, the number of PDAC cells was reduced in FPCO but not in M0-FPCO between 1 and 2 weeks of organoid culture, suggesting that cancer cells could survive longer or are protected from cell death in the presence of TAM. Moreover, the bulk-RNAseq analysis of the surviving M0-FPCO unveiled a GALE potentially associated with a worse prognosis in PDAC patients. Our novel PADC organoid including macrophage (M0-FPCO) replicated the PDAC-TAM features and elucidated their protumorigenic function.

overall_design: The fused pancreatic cancer organoid (FPCO) generated by patient-derived pancreatic cancer organoids (PCOs), hiPSC-derived mesenchymal cells (hiPSC-MC) and vascular endothelial cells (hiPSC-EC) previously described. In addition, THP-1 derived macrophages were introduced into this organoid which was named M0-FPCO. In this research, we analyzed the cancer cell and macrophages mainly. The hiPSC-MC and EC are not analyzed.

first: Kenta

last: Takeuchi

first: Yuya

last: Yamamoto

first: Ryotaro

last: Eto

first: Megumi

last: Matsuo

first: Yasuharu

last: Ueno

first: Takanori

last: Konishi

first: Yoichi

last: Furukawa

first: Kiyoshi

last: yamaguchi

first: Soichiro

last: Morinaga

first: Yohei

last: Miyagi

first: Masayuki

last: Ohtsuka

first: Naoki

last: Tanimizu

first: Hideki

last: Taniguchi


title: A novel pancreatic ductal adenocarcinoma organoid recapitulating tumor microenvironment reveals macrophage-driven enhanced cancer cell survival

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

overall_design: Refer to individual Series


title: Transcriptional Stress as a Cause of DNA Double-Stranded Breaks

first: Priyatansh

last: Gurha

state: Texas

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

summary:
ABSTRACT
Aims: Double-stranded breaks (DSBs) cause genomic instability, a hallmark of aging, and activate the DNA damage response (DDR) and the cytosolic DNA-sensing proteins (CDSP) pathways. The activated pathways induce cell cycle arrest, inflammation, senescence, cell death, fibrosis, and organ dysfunction. The purpose of the study was to identify and characterize genome-wide DSBs at the nucleotide resolution in adult cardiac myocytes.
Methods and Results: We identified the genome-wide DSBs in the genomes of ~ 6 million adult cardiac myocytes (1 million per sample) in the 3 wild-type and 3 myocyte-specific LMNA-deficient mice (Myh6-Cre:LmnaF/F) mice by END-Sequencing. We identified 6,774 differential DSBs between the wild-type and Myh6-Cre:LmnaF/F cardiac myocytes, which, except for 8, were exclusive to the Myh6-Cre:LmnaF/F genotype. The differential DSBs were enriched in the gene regions, transcription initiation sites, cardiac transcription factor motifs, and at the G quadruplex forming structures, suggesting the involvement of the transcriptional stress. Because LMNA regulates transcription, we performed a CUT&RUN assay with an anti-LMNA antibody (N=5) to test the role of transcriptional stress in an increased prevalence of DSBs. We identified an average of 818 genome-wide lamin-associated domains (LADs), which encompassed 30% of the mouse genome. LADs were associated with a 16-fold reduction in the transcript levels of protein-coding genes located at the LAD regions (N=3,975) as opposed to genes located at the non-LAD regions (N=~ 17,778). Consistent with increased transcription at the non-LAD regions DSBs were ~ 6-fold more prevalent in the non-LAD than LAD regions. Likewise, the loss of LAD was associated with a 2.3-fold higher prevalence of differential DSBs in the Myh6-Cre:LmnaF/F cardiac myocyte genomes, which were predominantly localized to the transcription start sites.
Conclusions: To our knowledge, this is the first identification of the DSBs, a hallmark of aging, at the nucleotide resolution in the cardiovascular system. The findings implicate transcriptional stress in the pathogenesis of DSB and the protective role of LMNA against DSBs likely through transcriptional suppression. Given the ubiquitous nature of transcriptional stress, DSBs are expected to be pervasive and pathogenic through activation of the DDR and CDSP pathways not only in cardiovascular diseases but also in other conditions, including aging.

overall_design: End-seq was performed from CM isolated from 3 WT and 3 Myh6-Cre:LmnaF/F mice.

first: Ali

last: Marian

first: Benjamin

last: Cathcart


title: AVP promotes bone marrow myelopoiesis in depression

city: Hangzhou

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

institute: Zhejiang University

summary: Sympathetic nerves have been implicated in the regulation of HSC homeostasis, we investigated whether sympathetic nerves regulated myeloid-biased differentiation of HSCs in CUMS mice. Transcriptome profiling (RNA-seq) and differential gene expression analysis of bone marrow cells were performed. In bone marrow cells of CUMS mice, the expression of arginine vasopressin receptor 2, a receptor of the stress-related neuroendocrine factor AVP, was upregulated through neuroactive ligand-receptor interaction pathway.

overall_design: Total 6 bone marrow samples were analyzed in this study. 3 samples as negtive control, 3 samples as CUMS.

first: Rong

last: Mou

first: Junkai

last: Ma

first: Xuan

last: Ju

first: Yixin

last: Wu

first: Qiuli

last: Chen

first: Tongyao

last: Shang

first: Siying

first: Yue

last: Yang

first: Kaosheng

last: Lv

first: Ying

last: Shen

first: Qi

last: Zhang

first: Tingbo

last: Liang

first: Ye

last: Feng


title: Bone marrow HSPCs differentiate into myeloid cells in depression

summary: It has been known that the numbers of neutrophils and Ly6Chi monocytes are increased in the blood of patients with depression. To better understand how HSPCs sense and adapt disease progression in depression, we used single-cell RNA sequencing (scRNA-seq) to characterize HSPCs in bone marrow from mice models of depression induced by chronic restraint stress (CRS) and chronic unpredictable mild stress (CUMS).We found that bone marrow hematopoiesis was substantially rewired toward myeloid lineages in depression, accompanied by an increase of myeloid score in bone marrow HSPCs, suggesting myeloid biased cell production in bone marrow of depressed mice.

overall_design: We performed single-cell RNA sequencing on flow cytometry-sorted LK cells from the bone marrow of mice exposed to CRS and CUMS.


title: TARGETING NEURONAL FTL1 RESCUES COGNITIVE IMPAIRMENTS IN AGING

city: San Francisco

first: Juliana

last: Sucharov Costa

state: California

address: 2351 Powell Street, Apt 513

institute: UCSF

summary: Understanding cellular and molecular drivers of age-related cognitive decline is necessary to identify targets to restore cognition at old age. Here we report that ferritin light chain 1 (FTL1) is a pro-aging neuronal factor that impairs cognition. Targeting neuronal FTL1 in the hippocampi of aged mice elicits synaptic and metabolic-related molecular changes and rescues cognitive impairments. Our data identify neuronal FTL1 as a key molecular mediator of cognitive rejuvenation.

overall_design: To better determine the effect of selectively targeting the age-related increase in neuronal FTL1, we generated aged temporally controlled neuron specific conditional Ftl1 genetic knockout mice (FTL1 cKO) using a viral-mediated in vivo CRISPR-Cas9 approach by delivering high-titer lentivirus encoding a Synapsin-driven Cre and guide RNA sequences into aged inducible Cas9 transgenic mice. We then performed expression profiling analysis using data obtained from nuclei RNA-seq of controls and Ftl1 cKP aged mice.

first: Laura

last: Remesal

last: Sucharov

first: Saul

last: Villeda


title: Neutrophils stimulation with AVP promote IL36G release

first: Xinjiang

last: Lu

summary: We found that neutrophils were homing back to bone marrow and induced myelopoiesis after AVP treatment.This study investigated how neutrophils promoted HSC differentiation by comparing the expression of genes between control and AVP treatment neutrophils.We demonstrated that AVP treatment increased the expression of a variety of cytokine genes, especially IL36G, and the augmentation of bone marrow myelopoiesis involves IL36G-IL1RL2 axis.

overall_design: We performed transcriptional profiling using RNA-seq in flow cytometry sorted neutrophils from blood of control and AVP-treated mice


title: Salidroside Mitigates Oligoasthenospermia by Attenuating Ferroptosis-mediated Lipid Peroxidation via NF-κB Pathway Inhibition

city: Xi'an

first: Xiaolong

last: Zhao

address: 127 West Changle Road

department: Urology

institute: Xijing Hospital

summary: Aims: Oligoasthenozoospermia (OAS) causes male infertility. However, the etiology and pathogenesis of OAS are unclear, and specific therapy is lacking. Ferroptosis contributes to the progress of various diseases; however, its role in OAS is unknown. This study aimed to explore the mechanism of OAS and to find effective treatments. Results: Human OAS sperm exhibits biochemical and morphological hallmarks of ferroptosis. Ferroptosis represents a crucial role in OAS induced by cyclophosphamide (CP) of mice in vivo, and inhibiting ferroptosis can effectively improve OAS. Further search for safe, stable and clinically applicable of natural compounds found Salidroside （Sal）improved the sperm quality of OAS by attenuates ferroptosis-mediated lipid peroxidation in germ cells by increasing the expression of GPX4, and thus ameliorates OAS in vivo. To further investigate at which stage of spermatogenesis Sal acts, the result revealed that Sal increases the expression of GPX4 starting from primary spermatocytes gradually by immunohistochemistry. In vitro, we verified the above results in vivo using a mouse spermatocytes cell line, GC-2 cells. Mechanistically, integrated RNA-Seq and bioinformatic analysis showed that Sal likely promotes GPX4 expression by inhibiting NF-κB Pathway, thereby inhibiting ferroptosis. Innovation: Our findings support the view that ferroptosis plays an important role in patients with OAS, and provide convincing evidence that Sal ameliorates OAS by inhibiting ferroptosis-mediated lipid peroxidation via NF-κB pathway suppression. Conclusions: Thus, ferroptosis plays an important role in OAS, and Sal could ameliorate OAS by attenuating ferroptosis-mediated lipid peroxidation via NF-κB pathway inhibition.

overall_design: To clarify the mechanism by which Sal upregulates the expression of GPX4, RNA-Seq of GC-2 cells was carried out and the data analyzed.


title: Rac1 impairs retinal axon degeneration via Kif2a in a mouse model of chronic ocular hypertension

city: shanghai

first: Hong

last: Zhou

state: shanghai

address: dongan road 130

department: Institutes of Brain Science

summary: Rac1, a member of the small G protein Rho family, has been implicated in neurodegenerative diseases. However, its role in axon degeneration is not fully understood. Here we found that activation of Rac1 exacerbated axonal transport damage in an experimental glaucoma model. Inhibiting Rac1 activity by genetic or pharmacological methods alleviated the dysfunction of axonal transport and improved the integrity of microtubule by upregulating the expression of β-III tubulin and myelin basic protein. Rac1 interacted with Sirt1, a key molecule of Wallerian degeneration, which regulated the activity of PAK1, a downstream molecule of Rac1. Furthermore, Rac1 modulated Kif motors at the transcriptional level, among which Kif2a, a lysosome-location regulator, was negatively regulated by Rac1. Intravitreal injection of Kif2a siRNA reversed the improvement of Rac1 inhibition-mediated axonal transport through reducing autophagolysosomes. Our results suggest that Rac1/Kif2a accelerates the process of RGC axon degeneration by impairing the autophagic flux in glaucoma, which may be an intriguing therapy target for glaucoma.

overall_design: CUT&Tag sequencing from retinal cells of control and COH 1w retinas to search for Rac1-related genes and transcription factors.

first: Shu-Min

last: Zhong

first: Yun-Hui

last: Guo

first: Guo-Li

first: Wenwen

last: Ding

first: Fang

last: Li

first: Yong-Chen

last: Wang

first: Bo

last: Lei

first: Zhongfeng

first: Yanying

last: Miao


title: A novel pancreatic ductal adenocarcinoma organoid recapitulating tumor microenvironment reveals macrophage-driven enhanced cancer cell survival [scRNA-Seq]

first: Shunsuke

last: Tabe

overall_design:
The fused pancreatic cancer organoid (FPCO) generated by patient-derived pancreatic cancer organoids(PCOs), hiPSC-derived mesenchymal cells (hiPSC-MC) and vascular endothelial cells (hiPSC-EC) previously described. In addition, THP-1 derived macrophages were introduced into this organoid.
We analyzed only M0-FPCO at day14 in this experiment.

first: Kenta

last: Takeuchi

first: Yuya

last: Yamamoto

first: Ryotaro

last: Eto

first: Megumi

last: Matsuo

first: Yasuharu

last: Ueno

first: Takanori

last: Konishi

first: Yoichi

last: Furukawa

first: Kiyoshi

last: yamaguchi

first: Soichiro

last: Morinaga

first: Yohei

last: Miyagi

first: Masayuki

last: Ohtsuka

first: Naoki

last: Tanimizu

first: Hideki

last: Taniguchi


title: The effect of age on crystalline silica-induced pulmonary toxicity

first: Pius

last: Joseph

summary: The effect, if any, of age on the pulmonary toxicity induced by Min-U-Sil 5 crystalline silica exposure was investigated in rats. As part of the study, the changes in global gene expression profiles in the blood and lungs of the animals were determined.  To conduct these studies, to determine if age influences the pulmonary response to crystalline silica exposure, two different age groups of healthy, male F344 rats were used.  In this study the young age group of rats (6 months old at the time of exposure) was exposed to either air or crystalline silica (Min-U-Sil 5) (15 mg/m3, 6 hours/day, 5 days) by whole body inhalation. The young age group of rats simulates a group of workers who would be 18 to 20 years old.  At two crystalline silica post-exposure time periods (1-day and 6-months) animals were euthanized and pulmonary inflammatory, cytotoxic, and oxidant responses were determined.  Analysis of bronchoalveolar lavage parameters of toxicity such as oxidant generation and inflammation revealed significant changes in pulmonary toxicity in the crystalline silica exposed rats compared with the time-matched, air exposed control rats. The blood gene expression profiles showed only minimal changes, at both the time points, in the crystalline silica exposed rats compared with the controls. Specifically, there were a total of 5 genes significantly differentially expressed (fold change >1.5 and FDR p<0.05) in the one-day post-exposure group and no significantly differentially genes in the 6-month post-exposure group. However, the lung gene expression profiles showed substantial changes in the crystalline silica exposed animals at both one-day and 6-month post-exposure.  Specifically, there were a total of 385 genes significantly differentially expressed (fold change >1.5 and FDR p<0.05) at the one-day post-exposure group and 317 genes significantly differentially expressed at the 6-month post-exposure. The data obtained from the present study demonstrated that crystalline silica inhalation exposure, under the conditions employed in the present study, resulted in significant changes in lung toxicity parameters and lung gene expression profile in the rats at both 1-day and 6-month post-exposure.

first: Tina

last: Sager


title: miRNomes of caprine adipose tissue

city: Saint Genès-Champanelle

first: christine

last: Leroux

address: Route de Theix

institute: INRAE

summary: The aim is to determine the miRNomes of goat adipose tissue and identify the effects of feed deprivation on adipose miRNA profile.

overall_design: Eleven lactating Alpine goats were studied at peak of lactation (48 ± 2 days postpartum, at the beginning of the experiment), a period during which AT lipids are strongly mobilized. For a 2-wk pre-experimental period, the goats were fed a standard diet of orchardgrass hay with a 35:65 forage-to-concentrate ratio. During the 48 h before slaughter, five goats received the standard diet ad libitum (control) while the others six were food deprived.

first: Christine

first: Yannick

last: Faulconnier

first: Tao

last: Ye


title: Used of transcriptomics to identify molecular signatures of utero-placenta tissues

city: Newcastle Upon Tyne

first: Michael

last: Taggart

state: Tyne And Wear

address: International Centre for Life,

department: Biosciences Institute,

institute: Newcastle University

summary: Tissues throughout the human body exert finely-tuned specific functions even when there is considerable overlap in the cellular constituents. Even when the major cellular component of tissues is the same – for example in the case of smooth muscle-rich tissues - discrete phenotypes are evident.  Yet, the molecular expression profiles underpinning such specialised functionality is often unclear.  This presents a challenge for introducing new medicinal therapies for pathophysiologies: can one target what makes tissue functionality unique without producing unwanted effects on the features that are similar. Such a scenario can be considered for the human uteroplacental unit.  Ideally, one would like to target complications of pregnancy like pre-eclampsia (hypertension and proteinuria) or spontaneous preterm birth (early activation of parturition) by targeting particular types of smooth muscle tissues (e.g. arteries versus myometrium) without adversely affecting others.  This situation is further complicated by the need to consider maternal and fetoplacental circumstances.  Three smooth muscle-rich tissues of importance here are myometrium, maternal uterine (myometrial) arteries and placental arteries.  Indeed, each display subtly distinct phenotypes suggesting that distinct molecular signatures may underlie these differences. Hence, we aimed to compare expression profiles of these three tissues to identify the underpinning molecular signatures using multi-omics approaches.

overall_design: To study transcriptome-wide expression of three smooth-muscle rich human utero-placental tissues, paired uterine biopsies and placentas were obtained, following written informed consent (LREC 10/H0906/71), from normal pregnant women undergoing elective Caesarean section at term (39-40 weeks gestation, n=9). Myometrial strips (M), myometrial arteries (MA) and placental chorionic plate arteries (PA) were each isolated, and cleaned of surrounding material, by careful microdissection, snap frozen in liquid N2 and stored at -80oC until further use. Comparative gene expression profiling analysis was carried using next generation RNA-seq data generated from these three utero-placental tissues.

first: Huei Teng

last: Ng

first: Florence

last: Burté

first: Julie

first: Paul

last: Ayk

first: Stephen

last: Robson


title: Adaptive anoikis resistance promotes ovarian cancer metastasis

city: Birmingham

first: Mythreye

last: Karthikeyan

state: Alabama

address: 1824 6th avenue south

department: pathology

institute: university of alabama

summary: Anoikis resistance or evasion of cell death triggered by cell detachment is a hallmark of cancer that is concurrent with cell survival and metastasis. Phenotypes of anoikis resistant cancer cells have been extensively investigated, however, how exposure to suspension stress may lead to acquisition of a anoikis resistance phenotype has not been previously described in detail.  Here we show using a spectrum of ovarian cancer cells, that cycles of suspension stress followed by attached growth, leads to adaptation and acquisition of resistance to cell death in suspension . Comparing the stepwise transcriptomic changes as cells acquire resistance, we find strong transcriptional reprogramming in the population with a majority of differentially expressed genes being downregulated during progressive acquisition of anoikis resistance. Adapted anoikis resistant cells display an enhanced dependency on oxidative phosphorylation and are capable of evasion from T cell-mediated immune surveillance. We find that such acquired anoikis resistance is not genetic. However, transcriptional reprogramming is essential to this process as acquisition of such adaptive anoikis resistance invitro and invivo are both exquisitely sensitive to specific inhibition of transcriptional reprogramming. Our data demonstrate that recovery from the verge of anoikis leads to adaptation that promotes metastasis in ovarian cancer, but can be therapeutically prevented by specific inhibitors to transcriptional reprogramming.

overall_design: To assess the effects of exposure to cycles of  matrix detachment stress, cells were grown in attached conditions and subject to a 24 hr period of suspension cultures followd by expansion in attached cultures. Tis cycle was repeated for 7-8 rounds. P0 refers to the parental cell line and P1 refers to cells from suspension cultures. RNA seq was performed from RNA collected from the cells ( three independent biological trplcaites) over time alternating between suspension stress and expansion in attached cultures.  For WES, DNA was collected at baseline, at mid point and after cells had adapted to the suspension stress and was conducted on DNA collected from two biologiccal trials

first: Mehri

last: Monavarian

first: Emily

last: Page

first: Felipe

last: Massicano

first: Lara

last: Ianov

first: Elizabeth

last: Worthey


title: A Mitochondrial-Based Transfer and Metabolic Remodeling Hydrogel with Immune Responsiveness to Augmented Bone Regeneration

city: 武汉

first: Gilbert

last: Han

state: 湖北

address: 双林南路

institute: Wuhan University

summary: Intercellular mitochondrial transfer has recently been discovered as a strategy for local microenvironment regulation and repair. However, improving the efficiency of mitochondrial transfer and reducing immune rejection caused by implants is challenging for its application in bone regeneration tissue engineering. We found that bone marrow mesenchymal stem cells (BMSC)s can obtain mitochondria from macrophages through tunnel nanotubes (TNT)s. Mitochondria are crucial for the metabolism and function of BMSC. We further designed a composite hydrogel based on aldehyde sodium hyaluronate and chitosan as the network matrix, containing anti-inflammatory dimethyl itaconate (DMI) and macrophage-targeted zwitterionic nanoparticles (MDVNPs). The acidic bone injury microenvironment triggers a reversible Schiff base reaction in response to pH; further, the released DMI upregulates the M2 phenotype of macrophages by reducing the ROS level. Subsequently, MDVNPs with targeting, high transfection, and low immunogenicity accelerated the efficiency of mitochondrial transfer between macrophages and BMSC by increasing the expression of the mitochondrial transfer regulatory protein Rho GTPase 1 (Miro1). In vitro studies have confirmed that promoting mitochondrial transfer can effectively increase adenosine triphosphate (ATP) and oxidative phosphorylation (OXPHOS) levels in BMSC, promoting osteoblastic differentiation. In the mouse model of critical defect, the composite hydrogel (Gel@MDI) can reduce inflammatory reactions, improve energy metabolism, and enhance bone repair by promoting the balance between the immune system and bone metabolism. This study establishes a potential method for the immune microenvironment to enhance cellular mitochondrial bioenergy and achieve tissue regeneration by regulating mitochondrial transfer between cells.

overall_design: We designed and developed immune responsiveness and injectable fluidity composite hydrogel (Gel@MDI) based on a reversible dynamic crosslinked network (-N=CH-), incorporating dimethyl itaconate (DMI) and macrophage-targeted zwitterionic nanoparticles (MDVNPs). Based on the Schiff-based reaction by aldehyde sodium hyaluronate (OSH) and chitosan (CS), hydrogel could realize the recombination and decomposition of polymer networks under different pH environments, which effectively induced the release of anti-inflammatory drug (DMI), leading to enhanced polarization of macrophages towards the M2 phenotype, thereby significantly improving the inflammatory response. Moreover, the novel zwitterionic nanoparticles (MDVNPs) not only effectively adjusted the mechanical properties of composite hydrogel to suit the bone regeneration microenvironment but also were capable of fulfilling their gene carrier function with exceptional efficiency, resulting in superior gene transfection rates and reduced cytotoxicity[19]. Therefore, Rho GTPase 1 (Miro1) loaded MDVNPs with macrophage-targeted function facilitated the mitochondrial transfer process from macrophages to BMSC. This transfer of mitochondria from macrophages serves as a crucial source of energy required for successful bone regeneration, which influences the intracellular metabolic state of BMSC by regulating ROS, adenosine triphosphate (ATP), and oxidative phosphorylation (OXPHOS) levels, thus promoting the formation and growth of fresh bone tissues[20]. Our study further explains the importance of bone immune regulation in the initiation stage of bone defect repair and the discovery of mitochondrial transfer as an intercellular regulatory approach in tissue regeneration, providing new ideas for tissue regeneration engineering.

first: Wenjin

last: Cai

first: Shihua

last: Mao

first: Litian

first: Jiaying

last: Zhao

first: Yongzheng

last: Li

first: Bicong

last: Gao

first: Yani

last: Chen

first: Jintao

last: Yang

first: Guoli


title: Dual RNA-seq analysis of gene co-expression and immune response mechanisms in chickens infected by Eimeria tenella

city: Uppsala

first: Alma

last: Hansen

address: Ulls väg 2B

country: Sweden

institute: Statens veterinärmedicinska anstalt

summary: We have analyzed immune chickens undergoing a secondary E. tenella infection using dual RNA-seq. Samples were taken from caecal tissue where the parasites replicate at six timepoints between 0 and 10 days post infection. The results that immune chickens have a much faster response to E. tenella compared to that of naïve chickens, and that there is a clear IFN-signature

overall_design: mRNA profiles of chicken caeca infected with Eimeria tenella sporozoites, taken from 6 timepoints with 6 biological replicates each.

first: Robert

last: Söderlund

first: Eva

last: Wattrang