title: Gene expression profile at single cell level of CD4 T cells from the spleens of wildtype (WT) and Interferon regulatory factor 5 (IRF5) knockout (KO) C57BL6/J mice following 6 hour anti-CD3/anti-CD28 stimulation

city: Manhasset

first: Zarina

last: Brune

state: New York

address: 350 Community Drive

institute: The Feinstein Institutes for Medical Research

summary: The precise mechanisms by which IRF5 regulates CD4 T cell support of the adaptive immune response is still unknown. Here, we used scRNAseq to analyse the impact of loss of Irf5 expression on CD4 T cells following T cell receptor (TCR) stimulation.

overall_design: Splenic CD4 T cells from WT and Irf5-/- mice were isolated by Flourescence-activated cell sorting (FACS) then stimulated with anti-CD3/anti-CD28 Dynabeads per manufacturer protocols for 6 hours followed by scRNAseq analysis.

first: Betsy

last: Barnes


title: STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1

status: Public on Sep 18 2024

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cohesin complexes carrying STAG1 or STAG2 organize the genome into chromatin loops. STAG2 loss-of-function mutations promote metastasis in Ewing sarcoma, a pediatric cancer that is driven by the fusion transcription factor EWS-FLI1. We have integrated transcriptomic data from patients and cellular models to identify a STAG2-dependent gene signature associated with worse prognosis. Subsequent genomic profiling and high-resolution chromatin interaction data from Capture Hi-C indicate that cohesin-STAG2 facilitates the communication between EWS-FLI1-bound long GGAA repeats acting as neoenhancers and their target promoters. Changes in CTCF-dependent chromatin contacts, unrelated to EWS-FLI1 binding, also contribute to the aggressive phenotype. STAG1 is unable to compensate for STAG2 loss and chromatin-bound cohesin is severely decreased, while levels of the processivity factor NIPBL remain unchanged, resulting in altered DNA looping dynamics. These results illuminate how STAG2 loss rewires the Ewing sarcoma chromatin interactome to promote metastasis and provide a list of potential biomarkers and therapeutic targets.

overall_design: ChIP-Seq for H3K27me in WT ans STAG2ko A673 cells

last: Giménez-Llorente

first: Ana

last: Cuadrado

first: María

middle: J

last: Andreu

first: Inmaculada

last: Sanclemente

first: Maria

last: Solé

first: Miriam

last: Rodríguez-Corsino

last: Losada


title: Expression data from mouse embryo

city: Suita-shi

first: Manami

last: Nakai

state: Osaka-fu

address: 1-6 Yamadaoka

country: Japan

institute: Osaka University

summary:
Normal mouse development is regulated through dynamic changes in gene expression.
Changes in RNA modification-related enzymes were confirmed using microarrays.

overall_design: Mouse embryos were selected at some development stages for RNA extraction and hybridization on microarrays. After inducing superovulation, natural mating was performed, and the day the vaginal plug was confirmed in the female mouse was designated as E0.5. Early embryos, including pronuclear (E0.5), 2-cell (E1.5), and morula (E2.5) stages, were collected and pooled. E10.5 and E16.5 embryos were collected whole-body from three individuals each.


title: single cell RNA-seq on FACS purfied murine paneth cells

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

type: Expression profiling by high throughput sequencing

summary: The small intestinal crypts harbour secretory Paneth cells (PCs) which express bactericidal peptides that are crucial for maintaining intestinal homeostasis. Considering the diverse environmental conditions throughout the course of the small intestine, multiple subtypes of PCs are expected to exist. We applied single cell RNA-sequencing of PCs combined with deep bulk RNA-sequencing on PC populations of different small intestinal locations and discovered several expression-based PC clusters. Some of these are discrete and resemble tuft cell-like PCs, goblet cell (GC)-like PCs, PCs expressing stem cell markers, and atypical PCs. Other clusters are less discrete but appear to be derived from different locations along the intestinal tract and have environment-dictated functions such as food digestion and antimicrobial peptide production

overall_design: Paneth cells were purfied from the small intestine of mice using FACS, using positive markers c-KIT and CD24. Purified cells were used to perform single cell transcriptomics using 10X genomics, cellrangerd and seurat.

first: Timmermans

last: Steven

first: Wallaeys

last: Charlotte

first: Polaris

last: Lotte

first: Garcia-Gonzalez

last: Natalia

first: Saeys

last: Yvan

first: Libert

last: Claude


title: Transcriptomic analysis of rhabdomyolysis induced kidney injury

city: Berlin

first: Robert

last: Labes

address: Charitéplatz 1

department: Institute of Translational Physiology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Acute kidney injury (AKI) represents a syndrome seldom characterized by a single, distinct pathophysiological cause. Rhabdomyolysis-induced acute kidney injury (RIAKI) constitutes roughly 15% of AKI cases, yet its underlying pathophysiology remains poorly understood. Using a murine model of RIAKI induced by muscular glycerol injection, we aimed to analyse transcriptomic alterations by RNAseq.

overall_design: We analysed kidneys lysates following 24 hours of AKI induction by rhabdomyolysis (N=6) to obtain a transcriptomic profile at a stage of beginning kidney failure (significant raise of creatinine).

first: Vera

middle: A

last: Kulow

first: Michael

last: Fähling


title: Methylation and Transcriptomic Profiling Reveals Short Term and Long Term Regulatory Responses in Polarized Macrophages [RNA-Seq]

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Macrophage plasticity allows the adoption of distinct functional states in response to environmental  cues. While unique transcriptomic profiles define these states, focusing solely on transcription neglects  potential long-term effects. The investigation of epigenetic changes can be used to understand how  temporary stimuli can result in lasting effects. Moreover, epigenetic alterations play an important role  in the pathophysiology of macrophages, including phenomena related to the trained innate immunity,  which allow faster and more efficient inflammatory responses upon subsequent encounters with the  same pathogen. In this study, we used a multi-omics approach to elucidate the interplay between gene  expression and DNA-methylation, unravelling the long-term effects of diverse polarizing environments  on macrophage activity. We identified a common core set of genes that are differentially methylated  regardless of exposure suggesting a potential mechanism for rapid adaptation to various stimuli. These  conserved epigenetic modifications might represent a fundamental state that allows for flexible  responses to various environmental cues. Functional analysis revealed that processes requiring rapid  responses displayed transcriptomic regulation, whereas functions critical for long-term adaptations  exhibited co-regulation at both transcriptomic and epigenetic levels. Our study unveils a novel set of  genes critically linked to the long-term effects of macrophage polarization. This discovery underscores  the potential of epigenetics in elucidating how macrophages establish long-term memory and influence  health outcomes.

overall_design: We studied how the macrophage polarization leads to long-term reprogramming. We did this by first turning monocytes into macrophages using a chemical trigger (phorbol 12-myristate 13-acetate), and then exposing them to various signaling molecules (LPS, INFgamma, IL13, IL14) at different time points.

first: Giorgia

last: Migliaccio

first: Jack

last: Morikka

first: Giusy

last: Del Giudice

first: Maaret

last: Vaani

first: Lena

last: Mobus

first: Angela

last: Serra

first: Antonio

last: Federico


title: Expression data from  SQ-diEG treated mice

city: Tsukuba

first: Yaman

middle: (Yaman

last: Zhang

state: Ibaraki

address: Amakubo 2-4-1

department: Comprehensive human science

institute: University of Tsukuba

summary:
Global gene expression profiling reveals a potential anti-melanoma effect of SQ-diEG in B16F10 lung colonization mice model. Squalene (SQ) was considered as a promising natural agent in anti-cancer treatment due to its strong antioxidant and anti-inflammatory activity; however, its pharmacological value has been largely underestimated because of its poor solubility and bioavailability. To adress this problem, a novel amphiphilic SQ derivative which bearing ethylene glycol oligomers was synthesized and was used as a permeation enhancer in this study to check its potential effect on anti-melanoma metastasis using B16F10 lung colonization mice model.
Total 40 six years old male C57BL/6J mice were randomly divided into five groups (8 mice per group), including the control "(-)B16F10 injected and water treated"; the model "(+) B16F10 injected and water treated"; the positive control "(+) B16F10 injected and DTIC treated (Dacarbazine, 70 mg/kg/day)"; the SQ-diEG treatment "(+) B16F10 injected and SQ-diEG treated (5 mg/kg/day)"; the SQ-diEG treatment "(+) B16F10 injected and SQ-diEG treated (25 mg/kg/day)". After one week of acclimatization, B16F10 were murine melanoma cells line which intravenously injected (200000 tumor cells in 100 μl PBS, 0.2 ml/mouse) through the tail vein of mice. Mice was orally administrated with Dacarbazine (DTIC, positive control, 70mg/kg), and SQ-diEG (5mg/kg and 25mg/kg) for 20 days. On the last day of administration, mice was sacrificed and its lung was washed and collect for the further RNA extraction. Finally, the mice microarray gene expression profiling was conducted for two biological replicates.

overall_design: RNA from the lung tissue was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). The mouse genome array strips were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Single-cell transcriptomics reveals subset-specific metabolic profiles underpinning the bronchial epithelial response to flagellin

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

summary: Airway epithelial cells represent the first line of defense against respiratory pathogens. Flagellin drives the motility of many mucosal pathogens and has been suggested as an immune enhancing adjunctive therapeutic in infections of the airways. This study leveraged single-cell RNA sequencing to determine cell-specific effects of flagellin in primary human bronchial epithelial cells growing in air-liquid interface. Seven cell clusters were identified, including ciliated cells, ionocytes and several states of basal and secretory cells, of which only inflammatory basal cells and inflammatory secretory cells demonstrated a proportional increase in response to flagellin. Inflammatory secretory cells showed evidence of metabolic reprogramming toward aerobic glycolysis, whilst in inflammatory basal cells transcriptome profiles indicated enhanced oxidative phosphorylation. Inhibition of mTOR prevented the shift to glycolysis and reduced inflammatory gene transcription specifically in inflammatory secretory cells. This data demonstrates the functional heterogeneity of the human airway epithelium upon exposure to flagellin.

overall_design: HBE cells were derived from healthy tracheobronchial tissue obtained from a lobectomy in a patient with lung cancer at the Amsterdam University Medical Centers in the Netherlands, as previously reported. The Institutional Review Board of Amsterdam UMC approved the study protocol (2015-122#A2301550) and written informed consent was obtained from the donor before sampling.

middle: M


title: Role of Lamin A/C on dendritic cell function in antiviral immunity

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

institute: CNIC

summary: Dendritic cells (DCs) play a crucial role in orchestrating immune responses, particularly in promoting IFNγ-producing-CD8 cytotoxic T lymphocytes (CTLs) and IFNγ-producing -CD4 T helper 1 (Th1) cells, which are essential for defending against viral infections. Additionally, the nuclear envelope protein lamin A/C has been implicated in T cell immunity. Nevertheless, the intricate interplay between innate and adaptive immunity in response to viral infections, particularly the role of lamin A/C in DC functions within this context, remains poorly understood. In this study, we demonstrate that mice lacking lamin A/C in myeloid LysM promoter-expressing cells exhibit a reduced capacity to induce Th1 and CD8 CTL responses, leading to impaired clearance of acute primary Vaccinia virus (VACV) infection. Remarkably, in vitro-generated granulocyte macrophage colony-stimulating factor bone marrow-derived DCs (GM-CSF BMDCs) show high levels of lamin A/C. Lamin A/C absence on GM-CSF BMDCs does not affect the expression of costimulatory molecules on the cell membrane but it reduces the cellular ability to form immunological synapses with naïve CD4 T cells. Lamin A/C deletion induces alterations in NFκB nuclear localization, thereby influencing NFκB-dependent transcription. Furthermore, lamin A/C ablation modifies the epigenetic signature of BMDCs, predisposing these cells to mount a less effective antiviral response upon TLR stimulation. This study highlights the critical role of DCs in interacting with CD4 T cells during antiviral responses and elucidates the molecular mechanisms through which lamin A/C modulates DC function via epigenetic and transcriptional regulation.

overall_design: We performed ATAC sequencing using BMDCs of WT and Lmna-/- mice. Samples are processed in biological duplicates, all 4 samples processed in paralel to avoid technical bias. For the peak identification all peaks included in both replicates of each condition are used.

first: Beatriz

last: Herrero-Fernandez

first: Raquel

last: Gómez Bris

first: Marina

last: Ortega Zapero

last: Saez

first: Salvador

last: Iborra

first: Virginia

last: Zorita

first: Ana

last: Quintas

last: Vazquez

last: Dopazo

first: Francisco

last: Sánchez-Madrid

first: Silvia

last: Magdalena Arribas

first: Jose

last: Gonzalez Granado


title: Interleukin-12 sustained release system promotes hematopoietic recovery after radiation injury

city: Chongqing

first: chuanchuan

last: lin

state: China

address: Shayang Road, Shapingba distract,

country: China

institute: Chongqing University

summary: The continuous production of all mature blood cell lineages is maintained by Hematopoietic stem cells (HSCs), but they are highly susceptible to damage by ionizing radiation (IR) that induces death. Therefore, devising the therapeutic strategies that can mitigate hematopoietic toxicity caused by IR would benefit acute radiation syndrome (ARS) victims and radiation therapy patients. Here, we prepared an injectable hydrogel based on RGD-alginate and Laponite by a simple mixing method to release IL-12 (RGD-Alg/Laponite@IL-12) slowly and locally. The localization administration of RGD-Alg/Laponite@IL-12 substantially increased the survival and promoted the hematopoietic recovery of mice following sublethal-dose irradiation. These results suggested that local intra-bone marrow injection of RGD-Alg/Laponite@IL-12 hydrogel can effectively stimulate IL12R-PI3K/AKT signaling axis, which promotes proliferation and hematopoietic growth factors (HGFs) secretion of bone marrow mesenchymal stem/stromal cells (BM-MSCs). This signaling axis facilitates hematopoietic microenvironment repair and plays a pivotal role in hematopoietic reconstitution. In conclusion, our study attempted a biomaterial-sustained release of IL-12 for the treatment of irradiated hematopoietic injury and provided a new therapeutic strategy for hematopoietic acute radiation syndrome (H-ARS).

overall_design: After co-culturing with different gels(IR-Con, RGD-Alg, RGD-Alg/IL-12, RGD-Alg/Laponite, RGD-Alg/Laponite@IL-12) for 48 h, RNA-seq was conducted to examine the transcriptome profile of BM-MSCs.

first: Chuanchuan

last: Lin

first: Yang

last: Xiang

first: Zhongjun

last: Li

first: Qian

last: Ran


title: 5-Fluorouracil Treatment Represses Pseudouridine-Containing miRNA Export into Extracellular Vesicles

city: Nashville

first: Hua-Chang

last: Chen

state: TN

address: 2525 West End Avenue, Suite 1100

department: Department of Biostatistics

country: USA

institute: Vanderbilt University Medical Center

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptome expression profile from lungs of mice infected with H7N9 between control and TFF2 treatment groups

city: Shanghai

first: Wei

middle: hui

last: Fu

address: No. 2901 Callang Road,Jinshan District

institute: Shanghai Public Health Clinical Center

summary: To further validate the protective mechanism of TFF2 in influenza infection, we used whole genome microarray expression profiling as a discovery platform to screen and identify differentially expressed genes in host immune response. The results indicate that TFF2 downregulates the expression of NF kB signaling pathway related genes and inflammatory cytokine genes.

overall_design: 6-8 week-old female C57/BL6 mice were given TFF2 protein via aerosol inhalation 2 hours before infection, and then infected with H7N9 virus. TFF2 protein was administered again 1 and 3 days after infection. On the 1st, 3rd, and 7th day after infection, mouse lung tissues were collected and RNA was extracted. After mixing total RNA of three mice in each group, transcriptome microarray analysis was performed.

first: Weihui


first: Daniel

last: Gimenez

overall_design: RNA-Seq in WT and STAG2ko A673

last: Giménez-Llorente

last: Cuadrado

first: María

last: Andreu

first: Inmaculada

last: Sanclemente

first: Maria

last: Solé

first: Miriam

last: Rodríguez-Corsino

last: Losada


title: 5-Fluorouracil Treatment Represses Pseudouridine-Containing miRNA Export into Extracellular Vesicles (RNA-seq)

summary: 5-Fluorouracil (5-FU) has been used for chemotherapy for colorectal and other cancers for over 50 years.  The prevailing view of its mechanism of action is inhibition of thymidine synthase leading to defects in DNA replication and repair.  However, 5-FU is also incorporated into RNA causing defects in RNA metabolism, inhibition of pseudouridine modification, and altered ribosome function.  We examined the impact of 5-FU on the expression and export of small RNAs into small extracellular vesicles (sEVs) and regulation of post-transcriptional small RNA modifications (PTxMs).  EVs are secreted by all cells and contain a variety of proteins and RNAs that can function in cell-cell communication.  PTxMs on cellular and extracellular small RNAs provide yet another layer of gene regulation.  We found that treatment of colorectal cancer (CRC) cells with 5-FU represses sEV export of miRNA and snRNA-derived RNAs, but promotes export of snoRNA-derived RNAs.  Strikingly, 5-FU treatment significantly decreased the levels of pseudouridine on both cellular and sEV small RNA profiles.  In contrast, 5-FU exposure led to increased levels of cellular small RNAs containing a variety of methyl-modified bases.  Our results suggest that 5-FU exposure leads to altered expression, base modification, and mislocalization of sEV small RNAs.

overall_design: Human DLD-1 colorectal cancer cells were treated or not with 10uM 5-FU for 48 hours

first: James

middle: G

last: Patton


title: Maternal high-fat diet alters Tet-mediated epigenetic regulation during heart development

city: Houston

first: Yun

last: Huang

state: TX

address: 2121 W HOLCOMBE blvd, Room 429

department: Health Science Center

institute: Texas A&M University

summary: Maternal exposure to balanced nutrition is critical for supporting embryonic development. Exposure to imbalanced nutrition during pregnancy, such as a high-fat diet (HFD), has been reported to negatively impact offspring, leading to conditions such as congenital heart disease. One possible mechanism is that metabolic stress from imbalanced food intake alters the function of epigenetic regulators, leading to abnormal transcriptional output in embryos. In this study, we observed that maternal exposure to a high-fat diet led to noncompaction cardiomyopathy (NCC) in embryos at E15.5. At the molecular level, maternal HFD exposure resulted in significantly reduced 5hmC production and chromatin remodeling in embryonic heart tissue collected from E15.5 embryos. Interestingly, maternal vitamin C treatment countered the negative impact of HFD exposure and restored the metabolic changes observed in pregnant mice, as well as the NCC phenotype observed in E15.5 embryos. This restoration is possibly due to the replenishment of iron, a co-factor of the Tet enzyme, in its reduced form. We further used a cardiac-specific Tet-triple knockout mouse model to confirm that the cardioprotective outcomes of maternal vitamin C treatment in HFD conditions are attributable to the enhanced activity of TET enzymes. Collectively, our results suggest a crosstalk between maternal nutrition exposure, such as HFD or vitamin C, and epigenetic rewriting during embryonic heart development。

overall_design: Nuclei were isolated from E15.5 normal diet treated embryonic hearts and E15.5 high-fat diet treated embryonic hearts, and then analyzed by assay for transposase-accessible chromatin with sequencing (ATAC-Seq). We performed three biological repeats for each condition.

first: Yuhan

last: Yang

first: Logan

last: Rivera

first: Shaohai

last: Fang

first: Maryn

last: Cavalier

first: Ashely

last: Suris

first: Yubin

last: Zhou


title: The effect of adipose tissue-specific overexpression of adrenomedullin 2 on the regulation of adipocyte function

city: Beijng

first: Pengcheng

last: Wang

address: Huanyuan Road 49

institute: Peking University Third hospital

summary: To investigate the effect of adipose tissue-specific overexpression of adrenomedullin 2 on the regulation of adipocyte function, the transgenic mouse line with adipocyte-specific overexpression of the ADM2 gene (aADM2-tg mice) was generated on a C57BL/6J background with the human ADM2 gene driven by the adiponectin (Adipoq) gene promoter (H11-Adipoq-hADM2-Wpre-PolyA mice, Strain NO. T059304). The mice were purchased from GemPharmatech (Nanjing, China). We then performed gene expression profiling analysis using data obtained from RNA-seg of visceral adipose tissue from aADM2-Tg and WT group.

overall_design: We  performed gene expression profiling analysis using data obtained from RNA-seg of visceral adipose tissue from 5 mice per group. Comparative gene expression profiling analysis of RNA-seg data for aADM2-Tg and WT group.

first: Song-Yang

last: Zhang

first: YongQiang

last: Dong


last: Gimenez

last: Giménez-Llorente

first: Ana

last: Cuadrado


title: Expression of genes involved in glycosylation pathway in mouse denrtic cells.

city: Boston

first: Pankaj

last: Sharma

state: MA

address: 220 Longwood Ave.

institute: Boston Childrens Hospital

summary: These datasets uncover the regulation of glycosylation genes by TGF-beta in DC2.4 cells and dendritic cells (DCs) isolated from mice harboring MCA101 fibrosarcoma tumors.

overall_design: Single cells suspensions from spleen and tumor (MCA101) were stained with antibodies directed against CD11c, MHC-II, CD103, CD8, F4/80, CD11b and CD45, and CD103-pos/CD8-pos DC1 cells  purified using FACS sorting. DC2.4 cells were collected upon trypsinization after 4 days of 2.5 ng/ml TGF-beta stimulation. Expression of genes involved in glycosylation were quantified by quantitative real-time PCR (qRT-PCR) using the glycosylation RT2 Profiler PCR Array according to the manufacturer’s instructions (PAMM-046Z, Qiagen). Briefly, RNA was isolated using the RNeasy Kit (Qiagen), and 50-100 ng RNA was converted to cDNA using the RT2 First Strand Kit (Qiagen). The cDNAs were subjected to amplification using gene-specific primers and SYBR Green (RT2 SYBR Green Master Mix, Qiagen) in an Ab7100 Real-Time PCR System (Thermo Fisher Scientific).

first: Xiaolong

first: Kevin

last: Ly

first: Ji

last: Kim

first: Qi

last: Wan

first: Jessica

first: Mumeng

last: Lou

first: Lisa

last: Kain

first: Luc

last: Teyton

first: Florian

last: Winau


title: Gene expression of P. putida KT2440 cultivated in an anoxic bioelectrochemical system

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

institute: Saarland University

summary: To get insights in the electrogenic anaerobic lifestyle of P. putida KT2440 cultivated in a bioelectrochemical system (BES), we employed whole genome microarray expression profile.

overall_design: Samples were taken from aerobic pre-culture (4 replicates) as control, and during anaerobic bioelectrochemical system cultivation after 24 h (4 replicates) and 100 h (4 replicates).

first: Anna

last: Weimer

first: Christoph

last: Wittmann


title: Effect of depletion of Sas10 in pre-rRNA processing

city: Hangzhou

first: Shuyi

last: Zhao

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

summary: Ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied, however, how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins, namely MPP10, UTP25, EMG1 and two UTP-B components UTP12 and UTP13, and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0-site while loss-of-function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the 5′ETS, supporting the crucial role of UTP3 in mediating the 5′ETS processing and degradation. Moreover, UTP3 directly interacts with and delivers EXOSC10 into the nucleolus, suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed 5′ETS. These findings lay the ground for studying the mechanism of cytoplasm-to-nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre-rRNA processing.

overall_design: To validate pre-rRNA processing defect in zebrafish sas10, tbl3 mutants and human UTP3 knock-down cells, we performed 3'RACE-seq of these samples.

first: Jiayang

last: Bao

first: Baochun

last: Su


title: Disruption of HSD17B12 in mouse hepatocytes leads to reduce body weight and defect in the lipid droplet expansion associated with microvesicular steatosis

city: Turku

last: Gabriel

address: Kiinamyllynkatu 10

institute: University of Turku

summary: Hepatocyte-specific knockout mice of Hydroxysteroid dehydrogenase 12 (LiB12cKO) show significant fat accumulation in their liver. As they age, they also show a reduced whole-body fat percentage. However, liver fat accumulation does not result in the typical formation of large lipid droplets; instead, small droplets were more prevalent in the LiB12cKO liver. This indicates a failure in the lipid droplet (LD) expansion. This was associated with liver damage, presumably due to lipotoxicity. The increase in the CIDEC expression further supported the deficiency in LD expansion in the LiB12cKO liver, and the downregulation of several members of the MUP family of proteins suggests the presence of endoplasmic reticulum stress LiB12cKO liver.

overall_design:
To investigate the disruption of HSD17B12 in mouse liver, we generated hepatocyte specific Hsd17b12 knockout mouse model using Cre-Lox technology.
A floxed Hsd17b12 mouse strain (Am J Physiol Endocrinol Metab. 2020 Sep 1;319(3):E494-E508) was crossed with Albumin-Cre mouse strain (. J Biol Chem. 1999;274(1):305-315). The albumin-promoter directs the Cre recombination in hepatocytes, from the time when hepatocytes begin to replace hematopoietic cells in the fetal liver., and the genotypes used for the experiment were HSD17B12lox/lox;Alb-CreCre/WT (knockout) and HSD17B12lox/lox;Alb-CreWT/WT  (wild type) mice.
Comparative gene expression analyses were conducted by comparing the WT male mice with KO male at age of eight weeks.

first: Hanna

last: Heikela

first: Matti

last: Poutanen


title: Maternal SMARCA5 is required for major ZGA in mouse [RNA-seq]

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Zygotic genome activation in mice happens in two waves, a minor wave in the 1 cell embryo, and a major wave at the two-cell stage, both accompanied by global transcriptional and epigenetic reprogramming. However, the orchestration of these reprogramming events by maternal factors deposited in the oocyte is not yet entirely understood. We and others have recently shown that epigenetic modifiers such as SMARCA5 (the main ATPase in ISWI complexes), can initiate the ZGA transcriptional programme in vitro. So far, the role of SMARCA5 in ZGA in vivo has not been addressed, as constitutive knock-out mice lacking SMARCA5 are not viable. We have overcome this issue by using the targeted protein-depletion system Trim-Away. Degradation of SMARCA5 in early zygotes in combination with single cell multi-omics methods allow us to investigate its role in transcription, DNA methylation and chromatin accessibility during ZGA, as well as the wider impact of the lack of maternal SMARCA5 on embryonic development. We show that in absence of SMARCA5, major ZGA transcription is downregulated, whereas maternal and other genes are upregulated. Our results show that the global accessibility at the two-cell stage is higher than in a wild-type context, and that major ZGA gene promoters are not following that global trend but remain less accessible in SMARCA5 depleted embryos. Moreover, while the accessibility of repeat elements like MERVL increases, so does the methylation level in these regions, suggesting that SMARCA5 might indirectly influence more than just the chromatin accessibility during these stages.

overall_design: RNA-seq libraries were generated from Smarca5 Heterozygous 2 cell stage embryos (Smarca5 mat KO x WT male) (2 technincal replicates, each replicate containing embryos from multiple matings, pooled). Same type of libraries generated from WT 2 cell stage embryos in which SMARCA5 was degraded at the zygotic stage, using the TrimAway system (libraries generated at least 24 hours post-injection). The Trim Away embryos libraries were also in 3 technical replicates (each replicate representing a different pool of injected embryos). The same samples were used to generate NOME-seq libraries (as part of the scNMT-seq protocol);

first: Oana

last: Kubinyecz

first: Deborah

last: Drage

first: Fatima

last: Santos

first: Hanneke

last: Okkenhaug

first: Christel

last: Krueger

first: Jasmin

last: Taubenschmid-Stowers

first: Wolf

last: Reik


title: Replication licensing regulated by an intrinsically disordered region of origin recognition complex

city: Hong Kong

first: Yuanliang

last: Zhai

address: Kadoorie Biological Sciences Building, The University of Hong Kong, Pok Fu Lam Rd

country: Hong Kong

institute: The University of HongKong

summary: In eukaryotes, the hetero-hexameric origin recognition complex (ORC) is responsible for assembling Mcm2-7 complex into a head-to-head double hexamer (DH), forming pre-replicative complex (pre-RC) that licenses origin DNA for replication initiation. This process is tightly controlled throughout the cell cycle to ensure accurate duplication of the genome. Here we show that the N-terminal intrinsically disordered region (IDR) of the yeast Orc2 subunit plays a critical role in promoting pre-RC assembly. We found that removing a short segment (residues 175-200) from Orc2-IDR or mutating a key isoleucine (194) in this region significantly inhibits replication initiation across the genome and causes cell death. Although the Orc2-IDR mutants can still assemble the ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) intermediate on DNA, the assembled mutant OCCM exhibits impaired ATP hydrolysis, preventing its conversion into Mcm2-7-ORC (MO) complex and subsequent DH formation. Interestingly, our in vitro assays showed that adding the Orc2-IDR peptide in the pre-RC reactions can rescue this defect. Furthermore, phosphorylation of this Orc2-IDR motif by S-cyclin dependent kinase (S-CDK) blocks its binding to Mcm2, leading to defective pre-RC assembly. Our findings provide crucial mechanistic insights into the multifaceted roles of ORC in modulating MCM loading to support origin licensing during the G1 phase and its regulation to restrict origin firing within the S phase.

overall_design: To gain insights into the underlying mechanism of replication initiation defects associated with Orc2-NTD mutants, we utilized a synchronization-sequencing (syn-seq) assay to examine the broader context of chromatin replication. Syn-seq is a whole-genome sequencing (WGS) method used to measure the efficiency of origin firing. In this method, the genome is divided into small segments, and the sequencing data of the relevant genome isolated at a particular time point provides of the exact copy number of each segment during DNA replication. We included the following three strains in this analysis: ORC2-WT, orc2∆N200, and orc2-I194E. We generated two datasets for each strain at 0 min (G1-phase) and 30 min (S-phase), representing non-replicative and replicative cells, respectively. We then plotted the ratio of copy number between replicative and non-replicative ones against the genomic locus to obtain a genome-wide landscape of replication initiation.

first: Yuhan

last: Lin

first: Qiongdan

last: Zhang

first: Yue

last: Wu


title: Identification of genes regulated by human HSF1, chicken HSF1 and chicken HSF3

city: Ube

first: Ryosuke

last: Takii

state: Yamaguchi

address: minami-kogushi, 1-1-1

department: Biochemistry and Molecular Biology

institute: Yamaguchi university

summary: To examine whether human HSF1, chicken HSF1 and chicken HSF3 regulates the  expression of different genes, we performed DNA microarray analysis.

overall_design: mRNA levels in wild-type OUMS-36T-3F, HSF1-knockout OUMS-36T-3F, chicken HSF1-overexpressed HSF1-knockout and chicken HSF3-overexpressed HSF1-knockout OUMS-36T-3F.

first: Mitsuaki

last: Fujimoto

first: Akira

last: Nakaki


title: Biodegradable oxygen-evolving metalloantibiotics for spatiotemporal sono-metalloimmunotherapy against orthopaedic biofilm infections

first: Wanbo

last: Zhu

state: None Selected

address: No600, Yishan road, Shanghai, China

institute: Shanghai Sixth Peoples Hospital Affiliated to Shanghai Jiao Tong University

summary: Pathogen-host competition for manganese and intricate immunostimulatory pathways  severely attenuates the efficacy of antibacterial immunotherapy against biofilm  infections associated with orthopaedic implants. Herein, we introduce an unprecedented spatiotemporal sono-metalloimmunotherapy (SMIT) strategy aimed at efficient biofilm ablation by custom design of ingenious biomimetic metal-organic framework (PCN-224)-coated MnO2-hydrangea nanoparticles (MnPM) as a metalloantibiotic. Upon reaching the acidic H2O2-enriched biofilm microenvironment, MnPM can convert abundant H2O2 into oxygen, which is conducive to significantly enhancing the efficacy of ultrasound (US)-triggered sonodynamic therapy (SDT), thereby exposing bacteria-associated antigens (BAAs). Moreover, MnPM disrupts bacterial homeostasis, further killing more bacteria. Then, the Mn ions released from the degraded MnO2 can recharge immune cells to enhance the cGAS-STING signaling pathway sensing of BAAs, further boosting the immune response and suppressing  biofilm growth via biofilm-specific T cell responses. Following US withdrawal, the  sustained oxygenation promotes the survival and migration of fibroblasts, stimulates  the expression of angiogenic growth factors and angiogenesis, and neutralizes excessive inflammation. Our findings highlight that MnPM may act as an immune costimulatory metalloantibiotic to regulate the cGAS-STING signaling pathway, presenting a promising alternative to antibiotics for orthopaedic biofilm infection treatment and pro-tissue repair.

sample_organism:
Staphylococcus aureus
Mus musculus

platform_organism:
Staphylococcus aureus
Mus musculus

overall_design: We used Staphylococcus aureus as a study subject. The intervened bacteria were obtained through different studied nanomaterials and sequenced for transcriptomics.

first: Zheng

last: Su

first: Dongdong

last: Xu

first: Xianli

last: Hu

first: Lingtong

last: Kong

first: Zhengzheng

last: Qian

first: Jiawei

last: Mei

first: Ruixiang

last: Ma

first: Xifu

last: Shang

first: Wenpei

last: Fan

first: Chen


title: Design of antiviral AGO2-dependent short hairpin RNAs

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

institute: Wuhan institue of virology, CAS

summary: The increasing emergence and re-emergence of RNA virus outbreaks underlines the urgent need to develop effective antivirals. RNA interference (RNAi) is a sequence-specific gene silencing mechanism that is triggered by small interference RNAs (siRNAs) or short hairpin RNAs (shRNAs), which exhibit significant promise for antiviral therapy. AGO2-dependent shRNA (agshRNA) generates a single-stranded guide RNA effector and presents significant advantages over traditional siRNA and shRNA. In this study, we applied a logistic regression algorithm to a previously published chemically siRNA efficacy dataset and built a machine learning-based algorithm with high predictive power. Using this algorithm, we designed siRNA sequences targeting diverse RNA viruses, including human enterovirus A71 (EV71), Zika virus (ZIKV), dengue virus 2 (DENV2), mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and developed them into agshRNAs according to the rule of agshRNA design. These agshRNAs inhibited viral replication in infected cells and their efficiencies of antiviral effects displayed a consistent trend with the score ranking of siRNA sequences predicted by the algorithm. Using the agshRNA targeting EV71 as an example, we showed that the anti-EV71 effect of agshRNA was more potent compared with the corresponding siRNA and shRNA. Moreover, the antiviral effect of agshRNA is dependent on AGO2-processed guide RNA, which can load into the RISC. We also confirmed the antiviral effect of agshRNA in vivo. Together, this work develop a novel approach that combines machine learning-based algorithm and agshRNA design to custom design antiviral agshRNAs with high efficiency.

overall_design:
To investage sequence feature of processed agshRNA and the loading of agshRNA in AGO2 cell, 293T were transfected with different agshRNAs. Small RNA sequencing were performed to detect processed agshRNA in Input sample and IP sample.
To investage the influence of agshRNA designed by our resarch, 293T cell were transfected with agshRNA and agshNC. Transcriptome sequencing was performed to detect the change in cells.

first: Yuanyuan

last: Bie

first: Jieling

first: Jiyao

last: Chen

first: Yuming

first: Xiaobei

last: Xiong

first: Leike

first: Xi

last: Zhou


title: Clues to Drivers of Juvenile Dermatomyositis: Genetic Alterations after Type I Interferon and JAK Inhibitor Treatment in Pediatric Bioengineered Skeletal Muscle

city: Durham

first: Gregory

middle: A.

last: Taylor

state: NC

address: 182 GRECC VA Med Ctr, 508 Fulton St

department: Department of Medicine, Division of Geriatrics, and Center for theStudy of Aging and Human Development

institute: Duke University Medical Center

summary: To better understand the pathogenesis of juvenile dermatomyositis (JDM) we examined the genetic alterations that result from exogenous IFN I exposure in pediatric skeletal muscle. We compared untreated healthy pediatric donor-derived myobundles with those treated with IFN I as well as with JAKi baricitinib and tofacitinib. We used bulk mRNA sequencing to evaluate how IFN I and treatment with JAKi influence healthy and JDM skeletal muscle gene expression and show IFNβ leads to a greater pro-inflammatory gene response than IFNα in pediatric skeletal muscle. As a type I interferon gene signature is established in JDM, downregulated oxidative phosphorylation, myogenesis, and contractile protein gene expression is implicated in JDM pathology. These genetic changes are partially reversed by JAK inhibitors, baricitinib and tofacitinib, with baricitinib leading to greater genetic alteration than tofacitinib. Our findings show that analysis of differential gene expression in bioengineered pediatric skeletal muscle can inform our knowledge of JDM pathogenesis and therapeutic effects.

overall_design: We compared untreated healthy pediatric donor-derived myobundles with those treated with IFN I as well as with JAKi baricitinib and tofacitinib. Bulk mRNA sequencing to evaluate how IFN I and treatment with JAKi influence healthy and JDM skeletal muscle gene expression.

first: Lauren

middle: T

last: Covert

first: Joseph

last: Prinz

first: Jeffery

last: Dvergsten

first: George

last: Truskey


title: 5-Fluorouracil Treatment Represses Pseudouridine-Containing miRNA Export into Extracellular Vesicles (smallRNA seq)

first: Hua-Chang

first: James

last: Patton


title: Change of gene expression due to aging in the hypothalamus of mice: A DNA microarray analysis

city: Kyoto

first: Masataka

last: Narukawa

state: Kyoto

address: 35 Kitahiyoshicho, Imakumano, Higashiyama, Department of Food and Nutrition, Kyoto Women's University

department: Department of Food and Nutrition

institute: Kyoto Women's University

summary:
To investigate the gene expression changes in the hypothalamus due to aging, we performed a DNA microanalysis using the hypothalamus samples obtained from young and old mice.
We found that several neuropeptide genes, such as agouti-related neuropeptide, neuropeptide Y, and pro-melanin-concentrating hormone, that promote food intakes, were upregulated in old mice.

overall_design: mRNA expression in the hypothalamus was compared between 24-week-old (Young) and 138-week-old (Old) C57BL/6J male mice.

first: Yoshikazu

last: Saito

first: Yoichi

last: Kasahara

first: Tomiko

last: Asakura

first: Takumi

last: Misaka


title: Syndecan-1 inhibition promotes anti-tumor immune response and facilitates the efficacy of anti-PD1 checkpoint immunotherapy (kdSdc1 and mutant)

first: Liu

last: Yongzhong

institute: Shanghai Cancer Institute

summary: To investigate the function of SDC1 in the regulation of anti-tumor immunity, we established B16 and MC38 cell lines in which sdc1 or control RNA has been knocked down by shRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B16 and MC38 cell lines representing sdc1 knockdown, sdc1 knockdown+c30 mutant, sdc1 knockdown+ect mutant, sdc1 knockdown+sdc1 wt, that were stimulated with IFNr.

first: Yun

last: Liu

first: Chen

last: Xu

first: Zhang

last: Li

first: Yongzhong


title: Direct reprogramming of fibroblasts into functional macrophages

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

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

overall_design: Refer to individual Series


title: H3T11 phosphorylation by CKII is required for heterochromatin formation in Neurospora

city: BeiJing

first: Tian

last: Yuan

address: CAU

institute: CAU

type: Methylation profiling by high throughput sequencing

summary: Heterochromatin is a key feature of eukaryotic genomes. In the filamentous fungus Neurospora crassa, the mechanism leading to heterochromatin initiation is unknown. Here, we show that casein kinase II (CKII) are required for heterochromatin formation at the well-defined 5-kb heterochromatin of the 5H-cat-3 region. Similarly, mutation of the histone H3 phosphorylation site T11 also impairs heterochromatin formation at the same locus. The catalytic subunit CKA co-localizes with phosphorylated H3T11 (H3pT11) within the 5H-cat-3 domain and the deletion of cka results in a significant decrease in H3T11 phosphorylation. Furthermore, the loss of kinase activity of CKII results in a significant reduction of H3pT11, H3K9me3, and DNA methylation levels, suggesting that CKII regulates heterochromatin formation by promoting H3T11 phosphorylation. Together, our results establish that histone H3 phosphorylation by CKII is a critical event required for heterochromatin formation.

overall_design: Bisulfite-sequencing sample preparation was performed using the MGIEasy WGBS Library Prep Kit (1000005251;MGI) for DNBSEQ™ platform (MGI) and the EZ DNA Methylation-Gold Kit (Zymo Research). Raw reads that pass quality control were performed with Bismark software (version 0.23.1) for alignment and quantification. Clean reads were mapped to N. crassa OR74A (NC10) genome using Bowtie2 (version 2.4.4). Only unique mappers were retained for downstream analyses. The position and density of 5mC was evaluated by Bismark software with command bismark methylation extractor and visualized with the Integrative Genomics Viewer (IGV). The pipeline for WGBS data processing, quantification and visualization are available on GitHub.

first: Yuan

last: Tian

first: Tong

last: Yin

first: Lu

last: Zhang

first: Qun

last: He

first: YunKun

last: Dang


title: Direct reprogramming of fibroblasts into functional macrophages [scRNA-Seq]

summary: Macrophages derived from somatic cells by reprogramming technologies have the potential to enable the development of cell-based therapies for numerous malignant diseases. Here we report on the establishment of a novel methodology allowing for the conversion of fibroblasts into functional macrophages with pro-inflammatory phenotype just by c-Myc overexpression. Ectopic expression of c-Myc in fibroblasts in induced pluripotent stem cell (iPSC) culture medium induced the rapid appearance of CD45+ hematopoietic cell complex (HCC) intermediates with engraftment capacity as well as the repopulation of distant hematopoietic compartments. HCC intermediates were stably maintained in suspension culture and continuously generated functional and highly pure-induced macrophage (iMac) just by M-CSF cytokine stimulation. Single-cell transcriptomic analysis of HCC intermediates revealed that c-Myc up-regulates the expression of MafB, a major regulator of macrophage differentiation, to promote macrophage differentiation. Characterization of the macrophage activity showed NF-kB signaling activation and pro-inflammatory phenotype. iMac transplantation significantly reduced leukemia and breast cancer progression in animal xenograft models. Our finding indicates that reprogramming strategies of fibroblasts could help circumvent long-standing obstacles to gaining “off-the-shelf” macrophages for anti-cancer immunotherapy.

overall_design: A single-cell RNA sequencing of Myc-induced myeloid-cell-complex (MCC) was performed

first: Yanxin


title: Single cell RNA sequencing data of SNCA triplication cortical organoids

city: Jacksonville

first: Yunjung

last: Jin

email: Jin.Yunjung@mayo.edu, tcikezu@gmail.com

address: 4500 San Pablo Rd

institute: Mayo Clinic

summary: Aggregated α-synuclein (α-SYN) proteins, encoded by the SNCA gene, are hallmarks of Lewy body disease (LBD), affecting multiple brain regions. However, the specific mechanisms underlying α-SYN pathology in cortical neurons, crucial for LBD-associated dementia, remain unclear. Here, we generated human cortical LBD models by differentiating induced pluripotent stem cells (iPSCs) from SNCA triplication LBD patients into cerebral organoids and observed increased levels of pathological α-SYN in these organoids. Single-cell RNA sequencing revealed prominent expression of the SNCA gene in excitatory neurons, which exhibited synaptic and mitochondrial dysfunction, consistent with findings in the cortex of LBD human brains. Furthermore, screening 1280 FDA-approved drugs identified four candidates, which inhibited α-SYN seeding in RT-QuIC assay, reduced α-SYN aggregation and alleviated mitochondrial dysfunction in SNCA triplication iPSC models. Our findings provide valuable insights into the development of cortical LBD models and the discovery of potential drugs targeting α-SYN aggregation.

overall_design: Single cell RNA sequencing of isolated cells from SNCA triplication and control cortical organoids. Three replicates per subclone, two subclones per cell line, and two cell lines per triplication or control group

first: Tadafumi

middle: C

last: Ikezu

last: Zhao


title: Interferon-lambda uniquely promotes CD8 T cell immunity against SARS-CoV-2 relative to type I interferon

city: Columbus

first: Emily

last: Hemann

state: OH

address: 460 W 12th Ave

institute: Ohio State University

summary: Optimization of protective immune responses against SARS-CoV-2 remains an urgent worldwide priority. In this regard, type III interferon (Interferon-lambda, IFNl) restricts SARS-CoV-2 infection in vitro and treatment with IFNl limits infection, inflammation, and pathogenesis in murine models. Further, IFNl has been developed for clinical use to prevent illness during COVID-19. However, whether endogenous IFNl signaling has an impact on SARS-CoV-2 antiviral immunity and long-term immune protection in vivo is unknown. In this study, we identified a requirement for IFNl signaling in promoting viral clearance and protective immune programming in SARS-CoV-2 infection of mice. Both IFN and IFN-stimulated gene (ISG) expression in the lungs was independent of IFNl signaling. Instead, IFNl promoted generation of protective CD8 T cell responses against SARS-CoV-2 by facilitating accumulation of CD103+ DC in lung-draining lymph nodes. Conversely, CD8 T cell immunity to SARS-CoV-2 is independent of type I IFN signaling, revealing a unique dependence on IFNl. Overall, these studies demonstrate that IFNl is critical for protective innate and adaptive immunity upon infection with SARS-CoV-2, and suggest that IFNl serves as an immune adjuvant to support CD8 T cell immunity.

overall_design: C57BL6/J WT or Ifnlr1-/- mice were infected with 10^5 TCID50 of SARS-CoV-2 MA10. Lungs were harvested from naïve mice, or on days 2 or 5 following infection. RNA was extracted from whole lung homogenates and RNAseq and gene expression analysis was performed

first: Abigail

last: Solstad

first: Parker

last: Denz

first: Adam

middle: D

last: Kenney

first: Najmus

middle: S

last: Mahfooz

first: Samuel

last: Speaks

first: Qiaoke

last: Gong

first: Richard

last: Robinson

first: Matthew

middle: E

last: Long

first: Adriana

last: Forero

first: Jacob

last: Yount


title: Single cells RNA sequencing of peripheral blood mononuclear cells reveals that hyperinflammatory monocytes are associated with Mycobaterium abscessus pulmonary disease

city: Milan

first: Federico

last: Di Marco

state: Outside U.S./Canada

address: Via Olgettina 60

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: Rationale: Nontuberculous mycobacteria (NTM) infection can promote progressive lung function decline and damage, a condition known as NTM Pulmonary Disease (NTM-PD). Mycobacterium abscessus complex (MABSC) is a common cause of infections in people with cystic fibrosis (pwCF). Here, we performed the first single-cell transcriptome characterization of circulating cellular transcripts in pwCF at risk of MABSC infections.  Objectives: To define the circulating immune transcriptional profiles of pwCF with MABSC colonization or MABSC pulmonary disease. Methods: We isolated peripheral blood mononuclear cell (PBMCs) and blood plasma of 12 pwCF including those displayed MABSC colonization or pulmonary disease and those with no history of NTM detection as control group. To identify immune signatures, we performed single cell (sc)RNA-sequencing and Luminex assay and validate our findings publicpublicly available datasets. Measurements and Main Results: We determined 10 cells populations annotated according to the expression levels and performed differentially expressed genes analysis among the three groups in each cellular population. We found out that pwCF with active MABSC pulmonary disease showed i) a set of transcripts specifically upregulated in CD14+ and CD16+ monocytes, ii) a downregulation of expression profiles related to NK and CD8 T cellular clusters, iii) the identified CD14+ monocytes characterized by IFNs signalling and pro-inflammatory pathways. In addition, we confirmed the highest CXCL10 levels in pwCF with pulmonary disease. Moreover, we validated our findings in a second publicpublicly available datasets from a cohort of pwCF infected by MABSC. Conclusions: Overall, we applyedapplied scRNAseq technologies to circulating blood cells and defined that circulating hyperinflammatory monocyte responses are associated to MABSC pulmonary disease in pwCF.

overall_design: We isolated peripheral blood mononuclear cell (PBMCs) and blood plasma of 12 pwCF including those that displayed M. abscessus colonization, M. abscessus pulmonary disease and those with no history of NTM detection as control group. To identify immune signatures, we performed single cell (sc)RNA-seq and Luminex assay and validate our findings with publicly available datasets.

first: Nicola

middle: I

last: Lorè

first: Stefano

last: de Pretis


title: Reduction of H3K9 methylation by G9a inhibitor improves development of mouse SCNT embryos

city: Tsukuba

first: Inoue

last: Kimiko

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

summary: Inefficient mammalian cloning can be improved by removal of somatic H3K9me3 from the embryonic genome. However, this strategy involves injection of histone demethylase mRNA into embryos, which itself is a limiting step due to the invasive and labor-consuming nature. Here we report that treatment with an inhibitor against G9a (G9ai), the major histone methyltransferase that introduces H3K9me1/2 in mammals, greatly improved development of cloned embryos in mice. Intriguingly, G9ai treatment resulted in immediate reduction of H3K9me1/2 and secondary loss of H3K9me3 in SCNT embryos. By G9ai treatment, the birth rate of cloned pups increased about fivefold (up to 3.9%) and, when combined with trichostatin A, a histone deacetylase inhibitor, it was further improved to 14.5%. Mechanistically, G9ai and TSA synergistically enhanced H3K9me3 demethylation and boosted zygotic activation of Obox family genes. Thus, we established an easy, highly effective SCNT protocol that would enhance future cloning research and applications.

overall_design: Comparative analysis of gene expression in embryos derived from IVF, non-treated SCNT, TSA-treated SCNT, G9a inhibitor-treated SCNT, and TSA&G9a inhibitor-treated SCNT.

first: Shogo

last: Matoba

first: Daiki

last: Shikata

first: Takaki

last: Tatebe


title: Single Cell RNA-Sequencing Identifies the Effect of Normothermic ex vivo Liver Perfusion on Liver-Resident T cells

city: New Orleans

first: Ruoxin

last: Lan

state: LA

address: 204 S Saratoga St, Apt 316

institute: Tulane University

summary: This is the first study to create an atlas of liver TRM T cells in a naïve liver and demonstrate the effects of NEVLP on liver TRM T cells at the single cell gene expression level. Furthermore, we show the potentially beneficial effects of adding anti-inflammatory cytokines to the NEVLP circuit on liver-resident TRM T cells.

overall_design: Rat livers were perfused for 4 hours at 37°C with or without the addition of IL-10 and TGF-β. Naïve and cold storage (4 hours at 4°C) livers served as controls. Following preservation, liver function, damage, and immune activation were assessed. TRM gene expression profiles were assessed through single cell RNA sequencing (scRNA-seq). Downstream analyses include T cell subset extraction, followed by differential expression analysis between various treatment groups. Gene set enrichment was then conducted on the identified differentially expressed genes to highlight the differentially regulated pathways and functional terms associated with treatment groups.

first: David

last: Al-Adra

first: Yao-Zhong

last: Liu


title: Maternal SMARCA5 is required for major ZGA in mouse

first: Laura

last: Biggins


title: Dual roles of ARID1A in both mucin production and secretion to restrain gastric signet ring cell carcinoma [ATAC-Seq]

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

summary: Signet ring cell carcinoma (SRCC) of the stomach is a subtype of gastric cancer with poor prognosis. It is characterized with unique large vacuoles of mucin and compressed nucleus, which resemble signet rings, while the underlying molecular mechanisms driving SRCC remain elusive. Here, we studied whether and how human gastric SRCC-associated ARID1A deficiency drove the disease.

overall_design: Gastric organoids and various mouse models of gastric cancer were applied to investigate the functions of ARID1A in SRCC tumorigenesis. Histological assays and transcriptome profiling were used to analyze the properties of SRCC models with Arid1a deficiency. Multi-omics analyses, including RNA-seq, CUT&Tag-seq and ATAC-seq, were performed to identify the molecular mechanisms of ARID1A loss in SRCC, which were further validated with in vitro and in vivo functional assays.

first: Hongyu


title: Maternal SMARCA5 is required for major ZGA in mouse [NOME-seq]

summary: Zygotic genome activation in mice happens in two waves, a minor wave in the 1 cell embryo, and a major wave at the two-cell stage, both accompanied by global transcriptional and epigenetic reprogramming. However, the orchestration of these reprogramming events by maternal factors deposited in the oocyte is not yet entirely understood. We and others have recently shown that epigenetic modifiers such as SMARCA5 (the main ATPase in ISWI complexes), can initiate the ZGA transcriptional programme in vitro. So far, the role of SMARCA5 in ZGA in vivo has not been addressed, as constitutive knock-out mice lacking SMARCA5 are not viable. We have overcome this issue by using the targeted protein-depletion system Trim-Away. Degradation of SMARCA5 in early zygotes in combination with single cell multi-omics methods allow us to investigate its role in transcription, DNA methylation and chromatin accessibility during ZGA, as well as the wider impact of the lack of maternal SMARCA5 on embryonic development. We show that in absence of SMARCA5, major ZGA transcription is downregulated, whereas maternal and other genes are upregulated. Our results show that the global accessibility at the two-cell stage is higher than in a wild-type context, and that major ZGA gene promoters are not following that global trend but remain less accessible in SMARCA5 depleted embryos. Moreover, while the accessibility of repeat elements like MERVL increases, so does the methylation level in these regions, suggesting that SMARCA5 might indirectly influence more than just the chromatin accessibility during these stages.

overall_design: NOME-seq libraries were generated from Smarca5 Heterozygous 2 cell stage embryos (Smarca5 mat KO x WT male) (1 technincal replicates, containing embryos from multiple matings, pooled). Same type of libraries generated from WT  2 cell stage embryos in which SMARCA5 was degraded at the zygotic stage, using the TrimAway system (libraries generated at least 24 hours post-injection). The Trim Away embryos libraries are in 3 technical replicates (each replicate representing a different pool of injected embryos). The same samples were used to generate RNA-seq libraries (as part of the scNMT-seq protocol)

first: Oana

last: Kubinyecz

first: Deborah

last: Drage

first: Fatima

last: Santos

first: Hanneke

last: Okkenhaug

first: Christel

last: Krueger

first: Jasmin

last: Taubenschmid-Stowers

first: Wolf

last: Reik


title: Effect of depletion of Sas10 on zebrafish gene expression at 5 days post fertilization

first: Shuyi

last: Zhao

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: In yeast, Upt3 overexpression caused a de-repression of the silenced genes at different loci, suggesting Utp3 might be involved in regulating gene expression. To this end, we extracted total RNA from the WT and sas10 (zebrafish homolg of yeast utp3) embryos, three biological repeats each, at 5dpf and carried out an RNA-seq analysis. Comparing the gene expression between the WT and sas10 using DESeq2 identified a total of 8574 differentially expressed genes (DEGs), including 4457 downregulated and 4117 upregulated DEGs in the sas10 mutant (criteria adopted: TPM>5 in at least one replicate, fold-change more than 1.5, p-adjust <0.05). We found that 150 out of 308 liver- and 185 out of 385 intestine-specific genes were identified to be among the downregulated DEGs. GO analysi of upregulated genes showed that these genes are related to protein transport and ribosome biogenesis and function. 64 genes encoding the SSU processome proteins, including wdr36, utp6, tbl3, pwp2h, and utp18 of the UTP-B genes, together with 17 genes encoding the RNA exosome proteins essential for ribosome biogenesis, including mtr4 and dis3 of the RNA Mtr4-exosome genes, were among the upregulated genes in sas10 mutant. By salmon we compared the expression levle of different regions across pre-rRNA transcript, and found that 18S rRNA was significantly decreased, and no obvious difference was observed for ITS1, 5.8S rRNA and 28S rRNA, while 5’ETS and ITS2 was significantly and drastically elevated.

overall_design: To investigate the influence of  depletion of sas10 in zebrafish gene expression, we extracted total RNA from the WT and sas10 embryos, three biological repeats each, at 5dpf and carried out an RNA-seq analysis. Gene expression profiling analysis was preformed. Differentially expressed genes were analysed. Transcripts per million (TPM) for each gene was obtained through featureCounts and was adopted to quantify the expression level. Reads of different regions across pre-rRNA was normalized by TPM regarding the 45S pre-rRNA transcript as the whole genome otherwise.

first: Jiayang

last: Bao

first: Baochun

last: Su


title: CFTR deficiency modulates the activity of endothelial mechanosensitive channels TRPV4 and PIEZO1; and drives endothelial barrier failure.

city: Los Angeles

first: Jean-Pierre

last: Amoakon

state: California

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-sinai Medical center

summary: Cystic fibrosis (CF) is a life-shortening genetic disease caused by a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Despite reports of CFTR expression on endothelial cells, pulmonary vascular perturbations, and perfusion deficit in CF patients, the mechanism of pulmonary vascular disease in CF remains unclear. Here, we describe loss of small pulmonary blood vessels in CF patients with severe lung disease. Using a vessel-on-a-chip model, we establish a shear stress-dependent mechanism of endothelial barrier failure in CF involving calcium-permeable mechanosensitive channel TRPV4. Furthermore, we demonstrate that CFTR deficiency downregulates the function of PIEZO1, another calcium-permeable mechanosensitive channel involved in angiogenesis and wound repair, and further exacerbates loss of small pulmonary blood vessels. We show that CFTR directly interacts with PIEZO1 and enhances its function, and that CFTR deficiency reduces PIEZO1 activity. Our study identifies key cellular targets to mitigate loss of small pulmonary blood vessels in CF.

overall_design: To investigate changes in gene expression and lipid metabolism when CFTR is knocked down by siRNA

first: Jesun

last: Lee

first: Pramodha

last: Liyanage

first: Kavisha

last: Arora

first: Anja

last: Karlstaedt

first: Goutham

last: Mylavarapu

first: Raouf

last: Amin

first: Anjaparavanda

last: Naren


title: Dual roles of ARID1A in both mucin production and secretion to restrain gastric signet ring cell carcinoma [Cut & Tag]

first: Ailing

last: Zhong

first: Hongyu

last: Liu


title: Syndecan-1 inhibition promotes anti-tumor immune response and facilitates the efficacy of anti-PD1 checkpoint immunotherapy

city: Shanghai

first: Yun

address: No. 2200, Xietu Road, Xuhui District, Shanghai, China


title: Direct reprogramming of fibroblasts into functional macrophages [RNA-Seq]

first: Guoyu

last: Chen

overall_design: We performed transcriptome analysis in PB CD45+ cells, bone marrow (BM), MCC, iPSC, and MEF using RNA-seq

first: Yanxin

last: Li


title: Single nucleus RNA sequencing data of Lewy Body Dementia (LBD) brains

first: Yunjung

last: Jin

overall_design: Single nucleus RNA sequencing of isolated nuclei from superior cortext region of LBD patients including SNCA duplication and SNCA triplication carriers and healthy individuals. Three brains from control individuals and five brains from LBD patients including one SNCA duplication and one SNCA triplication carrier were used.

first: Tadafumi

last: Ikezu


title: Self-Organized Generation Of Hepatic Cord Like Organoids (HCLOs) With Zonal Diversity (RNA-seq)

city: Cincinnati

first: Hasan Al

last: Reza

address: 3333 Burnet Ave

department: Developmental Biology

institute: CCHMC

summary: To investigate the efect of extracellular bilirubin and intracellular ascorbate on the development of zonal hepatocytes in human liver organoids

overall_design: We performed RNAseq on control HLOs compared to HLOs treated with extracellular bilirubin and genetically modified mGULO HLOs that express intracellular ascorbate

first: Hasa

first: Takanori

last: Takebe


title: Self-Organized Generation Of Hepatic Cord Like Organoids (HCLOs) With Zonal Diversity (snRNAseq)

summary: To investigate the efect of extracellular bilirubin and intracellular ascorbate on the development of zonal hepatocytes in human liver organoids.

overall_design: We performed snRNAseq on Hepatic Cord Like Orgnaoids (HCLOs) including Pericentral Organoids (PCO) and Periportal Organoids (PPO).

first: Hasan


title: Self-Organized Generation Of Hepatic Cord Like Organoids (HCLOs) With Zonal Diversity


title: RNA candidate screening in cell-to-cell contact-induced differentiation of human Pulmonary Artery Smooth Muscle Cells (hPASMC, Lonza)

city: Córdoba

first: Melina

middle: Mara

last: Musri

state: Córdoba

address: Friuli 2434

country: Argentina

institute: Instituto de Investigación Médica Mercedes y Martín Ferreyra

summary: Smooth muscle cells retain a high plasticity in adulthood, allowing them to change between a differentiated, contractile phenotype and a dedifferentiated, proliferative and migrative phenotype in response to microenvironmental cues. This plasticity is key to maintain the structure and function of vessel walls. When disregulated, it can lead to the onset of vascular pathologies related to vascular remodeling and excessive extracellular matrix deposition. This screening aims to find novel candidates involved in the regulation of this process, in particular long non-coding RNAs (lncRNAs).

overall_design: hPASMC were harvested at 70% confluency (undifferentiated) and at the beginning of the cell-to-cell contact-induced differentiation (100% confluence). Total RNA was extracted using TRIzol and Illumina RNA deep seq was performed.

first: Benjamin

last: de la Cruz-Thea

first: Lautaro

last: Natali


title: High-throughput sequencing of circRNA in human umbilical vein endothelial cells treated with high glucose

first: Hao

last: Lin

state: Shanghai

address: No. 389, Xincun Road

department: Department of Cardiology

institute: Tongji Hospital, School of Medicine, Tongji University,

summary: Atherosclerosis (AS) is a multiple factors-involved chronic inflammatory disease in the arterial wall, and is the dominant cause of cardiovascular disease (CVD). circRNAs can serve as competing endogenous RNA (ceRNA) to mRNAs and play function in multiple diseases. However, the molecular mechanisms underlying how circRNA regulates endothelial cells (ECs) abnormal transformation in AS remain unknown.Both clinical and basic studies have shown that HG-induced endothelial dysfunction is a crucial initiating factor in the development of diabetic vascular complications. In addition, studies have indicated that Ang Ⅱ is also involved in the process of atherosclerosis by inducing ECs dysfunction and regulating inflammatory responsesFor present study, therefore, we attempt to use circRNA microarray to indicate that the expression alters of circRNAs extracted from ECs treated with HG and Ang Ⅱ.

overall_design: Human umbilical vein endothelial cells were treated with high glucose (n=2) and Ang Ⅱ (n=2) and NC (n=1).

first: Haoran

last: Ding

first: Deqiang

last: Yuan

first: Jing

last: Tong

first: Fei

first: Xuebo


title: MicroRNA microarray related to circRNA in human umbilical vein endothelial cells

summary: Atherosclerosis (AS) is a multiple factors-involved chronic inflammatory disease in the arterial wall, and is the dominant cause of cardiovascular disease (CVD). Based on this hypothesis, several circRNAs are considered play crucial role in the regulation mRNA expression by competitive binding miRNA response elements. Meanwhile, our previous study found several circRNAs that may be involved in the pathogenesis of AS.However, the molecular mechanisms underlying how circRNA regulates endothelial cells (ECs) abnormal transformation in AS by miRNAs remain unknown.Thus, we indentified the miRNA and mRNA expression profiles and screened DE RNA species after overexpression of two above identified circRNAs through using microarray analysis.

overall_design: Human umbilical vein endothelial cells were treated with overexpression of hsa_circ_0122319 (n=2), hsa_circ_0002457 (n=2) and NC (n=1).


title: RNA sequencing of ovarian cancer cells treated by Paeonol

first: Jingchun

state: HUBEI

address: Zhangzhidong road

institute: Renmin Hospital of Wuhan University

summary: Traditional Chinese medicine (TCM) is widely used in clinics because of its beneficial features including multi-target effects, lower side effects, and safety, among which the anti-tumor effect has sparked wide attention. Paeonol (Pae; 2’-hydroxy-4’-methoxyacetophenone), a phenolic acid compound derived from the root bark of the Moutan Cortex, possesses properties with anti-inflammatory, antioxidant, immune regulatory activity and reverse chemoresistance, has been regarded as a potential anti-tumor drug. Our previous study have revealed that Pae activates autophagy by inhibiting the Akt/mTOR signaling pathway, suppressing the proliferation and inducing apoptosis in OC cells in a concentration- and time-dependent manner. Recently Pae was found to ameliorate glucose and lipid metabolism disorders in diabetic mice and improve acetylation of HK39 and HK412 through decreasing the expression of histone deacetylases. However, the detailed mechanism relevant for anti-tumor effects of Pae in EOC need to be explored.

overall_design: The assay was performed on three biological triplicates as well as three experimental triplictes of Pae treatment and control ovarian cancer cells(SKOV3 and SKOV3/DDP cells).

first: Jiang

last: Yang

first: Li

last: Hong


title: Syndecan-1 inhibition promotes anti-tumor immune response and facilitates the efficacy of anti-PD1 checkpoint immunotherapy [kdSdc1_scRNAseq]

first: Yun

summary: To illustrate the effects of SDC1 depletion on the tumor immune microenvironment, we performed single-cell RNA sequencing (scRNA-seq) analysis to interrogate phenotypic and functional alterations of immune cells in sdc1-knockdown vs. control tumors.

overall_design: CD45+ population isolated from single cells pooled with six tumors per group were used for scRNA-seq.

first: Chen

last: Xu

first: Zhang

first: Guiqin

first: Zhaojuan

first: Lvzhu

last: Xiang

first: Kun

last: Jiao

first: Zehong

first: You

last: Zuo

first: Yongzhong


title: Dual roles of ARID1A in both mucin production and secretion to restrain gastric signet ring cell carcinoma [RNA-Seq]

first: Ailing

last: Zhong

first: Hongyu

last: Liu


title: Dual roles of ARID1A in both mucin production and secretion to restrain gastric signet ring cell carcinoma

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

overall_design: Refer to individual Series


title: Syndecan-1 inhibition promotes anti-tumor immune response and facilitates the efficacy of anti-PD1 checkpoint immunotherapy [kdSdc1_RNAseq]

summary: To investigate the function of SDC1 in the regulation of anti-tumor immunity, we established B16 cell lines in which sdc1 or control RNA has been knocked down by shRNA. Then the cells were stimulated with or without IFNγ. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different groups, each group included three replicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ShRFP control or Shsdc1 B16 cells with or without IFNr stimulation.

last: Li

last: Chen


title: Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments [EM-seq]

status: Public on Sep 17 2024

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: Long known as the site of ribosome biogenesis, the nucleolus is increasingly recognized for its role in shaping 3D genome organization. Still, the mechanisms governing the targeting of selected regions of the genome to nucleolus-associated domains (NADs) remain enigmatic. Here we reveal the essential role of ZNF274, a SCAN-bearing member of the Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFP) family, in sequestering lineage-specific gene clusters within NADs. Ablation of ZNF274 triggers transcriptional activation across entire genomic neighborhoods – encompassing, among others, protocadherin and KZFP-encoding genes – with loss of repressive chromatin marks, altered 3D genome architecture and de novo CTCF binding. Mechanistically, ZNF274 anchors target DNA sequences at the nucleolus and facilitates their compartmentalization via a previously uncharted function of the SCAN domain. Our findings illuminate the mechanisms underlying NADs organization and suggest that perinucleolar entrapment into repressive hubs constrains the activation of tandemly arrayed genes to enable selective expression and modulate cell differentiation programs during development.

overall_design: HiC of wild-type and ZNF274KO HEK293T cells with or without ZNF274 mutants expression. HiC of wild-type and ZNF274KO NPC cells. UMI-4C of wild-type and ZNF274KO HEK293T cells. EM-seqs of wild-type and ZNF274KO HEK293T cells.

first: Martina

last: Begnis

first: Didier

last: Trono


title: Evaluating the effect of secreted ribonucleases from Ustilago maydis on the extracellular RNA profile/repertoire of Zea mays during corn smut disease

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: The apoplast of host plants serves as a dynamic interface during invasion and subsequent establishment of disease by a microbial pathogen. In the recent past, host plant apoplasts have been demonstrated to harbour small membrane bound vesicles called extracellular vesicles (EVs) that contain both RNA and protein. EVs are considered to play a significant role in cell-cell communication between the host and the pathogen during infection. In this study the RNAs associated with EVs from the host plant Zea mays under infected and uninfected conditions were sequenced. Besides EV bound RNA, plant apoplasts also contain free RNA that are equally important for host pathogen interaction. We have also detected a pool of extracellular RNA (exRNA) in Z. mays located on leaf surfaces. In this experiment, we sequenced both the free apoplastic RNA and leaf surface RNA from Z. mays during U. maydis infection and under control uninfected conditions. The U. maydis genome codes for a number of secreted ribonucleases that are essential for the pathogenesis of the fungus. For three of these ribonucleases, we have also investigated their role in the regulation of cell:cell communication between Z. mays and U. maydis. Accordingly, this study includes comparative transcript profiling of all the three different forms of exRNA between Z. mays plants infected with either wild type U. maydis or U. maydis strains lacking one or more secreted ribonucleases.

overall_design: Z. mays plants of the variety B73 were infected at 7 days seedling stage with U. maydis strains SG200 WT, SG200Δnuc1Δnuc2 or SG200Δnuc3. The infected leaf samples were harvested at 5 days post infection (5 dpi). For isolation of leaf surface RNA, the leaf surfaces were sprayed   with vesicle isolation buffer (VIB) followed by RNA precipitation from the rinse buffer collected through centrifugation of the leaves. For isolating EV associated and free apoplastic RNAs, the harvested leaf samples were infiltrated with VIB followed by centrifugation to collect the apoplastic wash fluid (AWF). EVs were collected from the AWF by centrifugation at 40,000g for one hour and EV associated RNAs were isolated from the pellet. The supernatant was used for the isolation of the free apoplastic RNA. For uninfected samples, the seedlings were left uninfected and leaves were harvested at 12 days post sowing for RNA isolation. Thus, three different sets of RNAs were isolated and sequenced from four different conditions including one control uninfected and three infection conditions. Three biological replicates of the samples were sequenced.

first: Anupama

last: Ghosh

first: Roger

last: Innes

first: Madison

last: McGregor

first: Lucia

last: Borniego

first: Meenu

last: Singla-Rastogi

first: Megha

last: Hastantram Sampangiramaiah

last: Baldrich


title: Hypoxia limits  the tumor-suppressive effects of C/EBPδ in pancreatic cancer

city: Amsterdam

first: C.

middle: Arnold

last: Spek

address: Meibergdreef 9

department: CEMM

institute: Amsterdam UMC

summary: Pancreatic ductal adenocarcinoma (PDAC) is a horrid disease with a terrifyingly low 5- year survival rate of only 12%. While this rate has slightly increased over the past decade, the incidence of PDAC has risen faster, by about 1% every year. Pre-clinical models are being employed with the aim to better understand the underlying tumor biology but sadly, a translation into the clinic often fails due to unforeseen complications. In a previous study, we showed that the transcription factor C/EBPδ has tumor-suppressive effects on PDAC cells in vitro. In this study, we take those findings a step further and assess the effect of C/EBPδ in a preclinical PDAC model in mice. We establish that the lack of oxygen in vivo – hypoxia - counteracts the tumor-suppressive effects of C/EBPδ in PDAC cells and suggest that this is partly mediated by a reciprocal feedback loop between C/EBPδ and HIF-1α. Although RNA-sequencing shows that the tumor-suppressive effects of C/EBPδ are not entirely abrogated under hypoxia, our study demonstrates the importance of considering major physiological parameters in order to make clinically relevant propositions.

overall_design: MIA PaCa-2 cells were transduced with a doxycycline-inducible plasmid for CEBPD over-expression or with a control plasmid containing the doxycycline-inducible construct followed by a scrambled sequence. Cells were cultured under hypoxia (1% oxygen) and treated with 2 ug/ml doxycycline in triplicates for 48 hours prior to RNA extraction.

first: Leonie

last: Hartl

first: Marieke

last: ten Brink

first: Hella

last: Aberson

first: Jan

last: Koster

first: Danny

last: Zwijnenburg

first: Janwillem

last: Duitman

first: Maarten

middle: F

last: Bijlsma

first: C


title: Senescence-associated dysregulation of translation inhibits activation of the integrated stress response

city: Baltimore

first: Emmanouil

last: Maragkakis

state: MD

address: 251 Bayview Blvd, 10B133 Baltimore

department: Laboratory of Genetics and Genomics (LGG)

institute: National Institute on aging

summary: Senescence is a state of indefinite cell cycle arrest associated with aging, cancer, and age-related diseases. Here we find that translational deregulation and a corresponding maladaptive integrated stress response (ISR) is a hallmark of senescence that desensitizes senescent cells to stress. We present evidence that senescent cells maintain high levels of eIF2? phosphorylation, typical of ISR activation, but translationally repress production of the stress response transcription factor 4 (ATF4) by ineffective bypass of the inhibitory upstream open reading frames (uORFs). Surprisingly, ATF4 translation remains inhibited even after acute proteotoxic and amino acid starvation stressors, resulting in a highly diminished stress response. We also find that stress augments the senescence associated secretory phenotype with sustained remodeling of inflammatory factors expression that is suppressed by non-uORF carrying ATF4 mRNA expression. Our results thus show that senescent cells possess a unique response to stress that entails an increase in their inflammatory profile.

overall_design:
Differential gene expression and splicing analysis of long-read direct-RNA analysis for IMR-90 human fibroblasts induced to senescence through etoposide (Etop) or healthy cycling cells (Cyc).

Stress-induced effects on senescence were investigated by subjecting senescent cells to acute proteotoxic stress followed by recovery and then harvesting of bulk RNA.

first: Matthew

last: Payea

first: Showkat

last: Dar

first: Carlos

last: Anerillas

first: Jennifer

middle: L

last: Martindale

first: Cedric

last: Belair

first: Rachel

last: Munk

first: Sulochan

last: Malla

first: Jinshui

last: Fan

first: Yulan

last: Piao

first: Xiaoling

last: Yang

first: Abid

last: Rehman

first: Nirad

last: Banskota

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe

first: Manolis


title: The effect of Terc deficiency on differentiation and maturation of OCs during aging [bone slices]

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Aging alters the bone function and elevates osteoporosis disability in diseases such as fractures. Understanding how aging alters bone marrow cellular differentiation could help us identify potential anti-aging targets to restore cellular homeostasis.

overall_design: Unbiased RNA-sequencing was performed to test whether the osteoclasts (OCs) from different ages of wild typt (WT) mice or Terc-/- mice growing on bone slices have difference in gene expression.

first: Hao

last: Li


title: Investigation of oral microbiome composition in elderly Chinese patients with hypertension: A cross-sectional study

first: Xin

last: Chen

address: Zhangheng Rd

institute: SHUTCM

summary:
Background: Hypertension is one of the most common metabolic diseases in the elderly and its pathogenesis is associated with microbiota dysbiosis. Recent evidence suggests that oral microbiota dysbiosis is also an important factor in the development of hypertension. However, the relationship between hypertension and oral flora in the elderly has not been adequately investigated.
Objective: The aim of this cross-sectional study was to investigate the structure of the oral microbiota and its correlation with hypertension in elderly hypertensive patients. To provide new ideas for the prevention and treatment of hypertension.
Methods: 206 subjects aged 60 ~ 89 years were selected and divided into normal (CON) and hypertensive (HTN) groups, according to the 2018 Chinese Guidelines for the Management of Hypertension. The oral microbiome composition of saliva samples was determined by 16S rRNA gene sequencing.
Results: Although there was no significant difference in α and β diversity between the two groups, systolic and diastolic blood pressure were the most important factors influencing the structure of the oral microbiota. At the phylum level, the relative abundance of the spirochete phylum and the mutualistic bacterial phylum was higher in the HT group than in the CON group (p < 0.05).  Diastolic blood pressure was negatively correlated with Streptococcus. Furthermore, we analyzed HTN patients with 120 mmHg<systolic blood pressure<160 mmHg and systolic blood pressure>160 mmHg separately and found that the abundance of Saccharibacteria_(TM7) was significantly increased in the HTN_2 group.
Conclusions: Our study identified specific oral microbiota in elderly hypertensive patients, confirming the relationship between oral microbiota and hypertension. This enhances our understanding of the important role of oral microbiota in the pathogenesis of hypertension and accumulates more evidence for microbial involvement in the development of hypertension.


title: Self-Organized Generation Of Hepatic Cord Like Organoids (HCLOs) With Zonal Diversity (ChIPseq)

first: Hasan Al

last: Reza

overall_design: We performed EP300 ChIPseq on Hepatic Cord Like Orgnaoids (HCLOs) including Pericentral Organoids (PCO) and Periportal Organoids (PPO) to elucidate the epigenetic regulation behind zonal gene expression.

first: Hasan

first: Takanori

last: Takebe


title: Ezetimibe derivative L14-8 suppresses advanced prostate cancer by activating PLK1/TP53-SAT1-induced ferroptosis

first: Fuwen

last: Yuan

state: 上海

address: Cailun Road #1200, Pudong New area

institute: Shanghai University of Traditional Chinese Medicine

summary: Androgen receptor signaling inhibitors (ARSIs) have demonstrated a survival benefit in metastatic prostate cancer (PCa). However, patients taking these agents inevitably acquire resistance and even develop neuroendocrine prostate cancer (NEPC), in which stage, the AR signaling is inactive, and therapies are limited for these lethal cases. Therefore, there is an urgent need to develop novel treatments to improve patient outcomes. Here we report that L14-8, a small molecule derived and optimized from ezetimibe, significantly suppressed prostate cancer growth by inducing ferroptosis in vitro and in vivo without obvious toxicity. Further mechanism studies demonstrate that L14-8 bound to and enhanced the stability of PLK1 and promoted the phosphorylation and expression of TP53, which enhanced its enrichment at the promoter of SAT1, a ferroptosis inducer, and increased its transcriptional activity. Overall, our studies developed a novel anti-tumor agent for treating lethal prostate cancer in an AR-independent manner and provided mechanistic insights into its action by targeting the PLK1-mediated TP53-SAT1 axis-induced ferroptosis.

overall_design: mRNA profiles of C4-2B cells treated with vehicle, L14-8 were generated by deep sequencing, in triplicate, using Illumina HiSeq6000

first: Xiaowen

last: Song


title: RNA sequencing of mouse pancreas tissue

city: wenzhou

first: Tan

last: Zhang

address: Nanbaixiang street

institute: The First Affiliated Hospital of Wenzhou Medical University

summary: Pancreatic tissue sequencing results of wild-type(WT) mice and PFKFB3 pancreatic specific knockout(cKO) mice (Saline Group and FAEE-SAP Group)

overall_design: Acute alcoholic pancreatitis was established in wild-type (WT) and PFKFB3 pancreatic specific knockout (cKO) mice, and normal saline was injected as control. 24 h after modeling, RNA from mouse pancreas tissue was sequenced. The experiment had two biological replicates.

first: Shengchuan

first: Feng

last: Ma

first: Gang


title: mRNA microarray related to circRNA in human umbilical vein endothelial cells

last: Lin

first: Haoran

last: Ding

first: Deqiang

first: Jing

last: Tong

first: Fei

first: Xuebo

last: Liu


title: Silmitasertib in combination with cabozantinib impairs liver cancer cell cycle progression, induces apoptosis and delays tumor growth in a preclinical model

city: St. Louis

first: Michelle

last: Brennan

state: MO

address: 1100 South Grand Blvd

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

summary: The rising incidence of hepatocellular carcinoma (HCC) is a global problem. Several approved treatments, including immune therapy and multi-tyrosine kinase inhibitors, are used for treatment, although the results are not optimum. There is an unmet need to develop highly effective chemotherapies for HCC. Targeting multiple pathways to attack cancer cells is beneficial. Cabozantinib is an orally available bioactive multikinase inhibitor and has a modest effect on HCC treatment. Silmitasertib is an orally bioavailable, potent CK2 inhibitor with a direct role in DNA damage repair and is in clinical trial for other cancers. In this study, we planned to repurpose these existing drugs on HCC treatment.  We observed stronger antiproliferative effect of these two combined drugs on HCC cells generated from different etiologies as compared to the single treatment. Global RNA-seq analyses revealed a decrease in the expression of G2/M cell cycle transition genes in HCC cells following combination treatment, suggesting G2 phase cell arrest. We observed G2/M cell cycle phase arrest in HCC cells upon combination treatment compared to the single-treated or vehicle-treated control cells. The downregulation of CCNA2 and CDC25C following combination therapy further supported the observation. Subsequent analyses demonstrated that combination treatment inhibited 70-kDa ribosomal protein S6 kinase (p70S6K) phosphorylation, and increased Bim expression. Apoptosis of HCC cells were accompanied by increased poly (ADP-ribose) polymerase cleavage and caspase-9 activation. Next, we observed that a combination therapy significantly delayed the progression of HCC xenograft growth as compared to vehicle control. Together, our results suggested combining cabozantinib and silmitasertib would be a promising treatment option for HCC.

overall_design: To understand the global gene expression pattern induced by the combination treatment of cabozantinib and silmitasertib, RNA-Seq analysis was performed to determine genes differentially expressed in THH cells treated with 10 μM cabozantinib and 10 μM silmitasertib compared with vehicle-treated THH cells.

first: Yuki

last: Haga

first: Ranjit

last: Ray

first: Ratna

middle: B


title: miRNA and mRNA array related to circRNA in human umbilical vein endothelial cells

first: Hao

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


title: Inositol polyphosphates regulate resilient mechanisms in the green alga Chlamydomonas reinhardtii to adapt to extreme nutrient conditions

city: Sevilla

first: Rodrigo

last: Bedera-García

state: Sevilla

address: Américo Vespucio 49

department: Plant Biochemistry and Molecular Biology

institute: Universidad de Sevilla

summary: In the actual context of climate changing environments, photosynthetic organisms need to adapt to more extreme conditions. Microalgae can be excellent organisms to understand molecular mechanisms that activate survival mechanisms under stress. Chlamydomonas reinhardtii signaling mutants are extremely useful to decipher which strategies they use to cope with changeable environments. In this study, we conducted prolonged starvation in wild type and vip1-1 Chlamydomonas cells. The mutant vip1-1 has an altered profile of pyroinositol polyphosphates (PP-InsPs) which are signaling molecules present in all eukaryotes. These molecules have been connected to P signaling in other organisms including plants but their implications in other nutrient signaling is still under evaluation. After prolonged starvation, WT and vip1-1 showed important differences in the levels of chlorophyll and PSII activity. We also performed a metabolomic analysis under these conditions and found an overall decrease in different organic compounds such as amino acids including arginine and its precursors and tryptophan which is considered as a signaling molecule itself in plants. In addition, we observed significant differences in RNA levels of genes related to nitrogen assimilation that are under the control of NIT2 transcription factor. Overall our data indicate an important role of PP-InsPs in the regulation of nutrient starvation especially regarding N assimilation and C distribution. These data are of great importance for the generation of resilient strains to be used in open ponds and high capacity bioreactors.

overall_design: To investigate the signaling role of the inositol pyrophosphates in the response to nutrient limitation in Chlamydomonas reinhardtii, we performed a gene expression comparative analysis of wild-type and  an inositol pyrophosphates-deficient strain (vip1-1) cells in nutrient sufficiency (control) and nutrient limitation (nutritional stress) conditions. We generated RNA-seq data from 3 biological replicates for each condition.

first: Bedera-Garcia

last: Rodrigo

first: García-Gómez

last: María Elena

first: Personat

last: Jose María

first: Couso-Liáñez

last: Inmaculada


title: Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal [RNA-seq]

city: Seattle

first: Michael

last: Emerman

state: Washington

address: 1110 Fairview Ave N

institute: Fred Hutch Cancer Research Center

summary: The latent HIV reservoir is a major barrier to HIV cure. Combining latency reversal agents (LRAs) with differing mechanisms of action such as AZD5582, a non-canonical NF-kB activator, and I-BET151, a bromodomain inhibitor are appealing towards inducing HIV reactivation. However, even this LRA combination needs improvement as it is inefficient at activating proviruses in cells from people living with HIV (PLWH). We performed a CRISPR screen in conjunction with AZD5582 & I-BET151 and identified a member of the Integrator complex as a target to improve this LRA combination, specifically Integrator complex subunit 12 (INTS12). Integrator functions as a genome-wide attenuator of transcription that acts on elongation through its RNA cleavage and phosphatase modules. Knockout of INTS12 in both cell line models and in CD4 T cells from virally suppressed PLWH improves reactivation at the transcriptional level and is more specific than AZD5582 & I-BET151 treatment alone. INTS12 is present on chromatin at the promoter of HIV and therefore its effect on HIV may be direct. Additionally, we observe more RNAPII in the gene body of HIV only with the combination of INTS12 knockout with AZD5582 & I-BET151 indicating the combination may specifically overcome an elongation block to reactivation. We also observe viral RNA in the supernatant from CD4 T cells of all three virally suppressed PLWH tested upon INTS12 knockout suggesting that INTS12 controls full-length HIV RNA and virus production ex vivo.

overall_design: To investigate the effect of INTS12 knockout on HIV and host gene transcription we knocked out INTS12 or control AAVS1 in J-lat 10.6 cells in three independent experiments and concurrently treated them with no treatment (DMSO) or LRAs (AZD5582 & I-BET151 or PMA & Ionomycin). We performed total RNA-seq on samples and compared total HIV transcription between samples, but also compared global transcription changes with conditions compared to the DMSO treated AAVS1 knockout cells.

first: Gray

last: Carley

first: Emerman

last: Michael


title: Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal [AutoCUT&Tag]

overall_design: To take a look at if INTS12 is located at the HIV promoter and how RNAPII is affected by various treatments, we knocked out INTS12 or control AAVS1 in J-lat 10.6 cells and treated them with no treatment (DMSO) or LRAs (AZD5582 & I-BET151) to stimulate transcription and reactivation of HIV. We performed CUT & Tag with three different antibodies: INTS12 Ab #1, INTS12 Ab #2, or RPB3 on samples and compared binding profiles on HIV as compared to the DMSO treated AAVS1 knockout cells.

first: Carley

last: Gray