title: Transcriptomic Landscape of Human iPSCs-derived Osteogenic Differentiation Identifies a Key Regulator, KLF16

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: The osteogenic differentiation process is essential for bone development and metabolism, but the underlying gene regulatory networks have not been well investigated. In this study, we performed RNA-seq analysis of mesenchymal stem cell differentiation to preosteoblasts and osteoblasts, derived from normal human induced pluripotent stem cell (iPSC) lines. Systematic analyses revealed potential transcription factor (TF) - TF regulatory networks, regulatory roles of long noncoding RNAs (lncRNAs), and differential splicing of extracellular matrix, TF, lncRNA, and splicing factor genes. TF-TF regulatory and gene co-expression network analyses predicted a key role for KLF16 in osteogenesis. In vitro and in vivo biological functional studies further established the inhibitory role of Klf16 in osteogenesis. Our model system and transcriptomic approach identify novel osteogenic genes and highlight the regulatory complexity of osteogenesis.

overall_design: Cells at three osteogenic differentiation stages of mesenchymal stem cell (MSC) at day 0, preosteoblast (preOB) at day 7 and osteoblast (OB) at day 21 were harvested. Total RNA was isolated, converted to RNA-seq libraries, and sequenced on the Illumina HiSeq 2500 platform. Comparisons between MSC to preOB, and preOB to OB stages were performed to identify differentially expressed genes. Global TF-TF regulatory network and gene co-expression network was used to indentify key regulators of osteogenesis.

first: Ying

last: Ru

first: Meng

last: Ma

first: Xianxiao

last: Zhou

first: Divya

last: Kriti

first: Ninette

last: Cohen

first: Dalila

last: Pinto

first: Sunita

last: D’Souza

first: Eric

last: Schadt

first: Christoph

last: Schaniel

first: Susan

last: Motch Perrine

last: Wu

first: Greg

last: Holmes

last: van Bakel

first: Bin

last: Zhang

first: Ethylin

last: Wang Jabs


title: Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes

status: Public on Mar 06 2024

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.

sample_organism:
Danio rerio
Macaca fascicularis
Homo sapiens
Canis lupus familiaris
Sus scrofa domesticus
Capra hircus
Oryctolagus cuniculus
Cricetulus griseus
Mesocricetus auratus
Mus musculus
Rattus norvegicus
Cavia porcellus

overall_design: Profiling small RNAs and mRNA in oocytes from 12 animals.

first: Li

last: Hou

first: Ligang


title: Biallelic null variants in PNPLA8 cause microcephaly through the reduced abundance of basal radial glia

status: Public on Mar 05 2024

city: Nagoya

first: Yuji

last: Nakamura

address: Kawasumi 1, Mizuho-cho, Mizuho-ku

department: Department of Pediatrics and Neonatology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

summary: PNPLA8, one of the calcium-independent phospholipase A2 enzymes, is involved in various physiological conditions through the maintenance of membrane phospholipids. However, little is known about its role in brain development. Here, we report 14 individuals from 12 unrelated families with biallelic ultra-rare variants in PNPLA8 presenting with a wide spectrum of clinical features ranging from developmental and epileptic-dyskinetic encephalopathy (DEDE) to progressive movement disorders and no phenotype depending on the variants and their positions. Complete loss of PNPLA8 was associated with the severe end of the spectrum showing DEDE manifestations and congenital or progressive microcephaly. Using cerebral organoids generated from human induced pluripotent stem cells (iPSCs), we found that loss of PNPLA8 reduces the abundance of basal radial glial cells (bRGCs) and upper-layer neurons. By spatial transcriptomic analysis targeting apical radial glial cells (aRGCs), we found the downregulation of bRGC-related gene sets in patient-derived cerebral organoids. Lipidomic analysis revealed a decrease in the amount of lysophosphatidic acid, lysophosphatidylethanolamine, and phosphatidic acid, indicative of the disturbed phospholipid metabolism in PNPLA8 knockout neural progenitor cells. Our data suggest that PNPLA8 has a critical role in the bRGC-mediated expansion of the developing human cortex by regulating the fate commitment of aRGCs.

overall_design: We performed PIC analysis to isolate expression profiles of neural progenitor cells in the subventricular zone of cerebral organoids derived from patient and control induced pluripotent stem cells.

first: Issei

middle: S

last: Shimada

first: Reza

last: Maroofian

first: Masanori

last: Fujimoto

first: Emi

last: Sato

first: Hiroshi

last: Takase

first: Shiho

last: Aoki

first: Akihiko

last: Miyauchi

first: Eriko

last: Koshimizu

first: Satoko

last: Miyatake

first: Yuko

last: Arioka

first: Mizuki

last: Honda

first: Takayoshi

last: Higashi

first: Fuyuki

last: Miya

first: Yukimune

last: Okubo

first: Isamu

last: Ogawa

first: Mohammad

last: Miryounesi

first: Sahar

last: Alijanpour

first: Farzad

last: Ahmadabadi

first: Peter

last: Herkenrath

first: Hormos

last: Salimi Dafsari

first: Mohammed

last: Balwi

first: Antonio

last: Vitobello

first: Anne-Sophie

last: Denommé-Pichon

first: Médéric

last: Jeanne

first: Antoine

last: Civit

first: Maha

last: Zaki

first: Hossein

last: Darvish

first: Somayeh

last: Bakhtiari

first: Michael

last: Kruer

first: Christopher

middle: J

last: Carroll

first: Ehsan

last: Ghayoor Karimiani

first: Rozhgar

middle: A

last: Khailany

first: Talib

last: Adil Abdulqadir

last: Bauer

first: Giovanni

last: Zifarelli

first: Mina

last: Zamani

first: Tahere

last: Seifi

first: Chadi

last: Al Alam

first: Henry

last: Houlden

first: Kazuhiro

last: Haginoya

first: Tamihide

last: Matsunaga

first: Hitoshi

last: Osaka

first: Naomichi

last: Matsumoto

first: Norio

last: Ozaki


title: Acetyl-CoA Carboxylase Obstructs CD8+ T-Cell Lipid Utilization in the Tumor Microenvironment

city: Chapel Hill,

first: Jessica

last: Thaxton

state: NC

address: 5229 Marsico Hall

department: Department of Cell Biology and Physiology

country: USA

institute: The University of North Carolina at Chapel Hill

summary: The solid tumor microenvironment (TME) imprints a compromised metabolic state in tumor infiltrating T cells (TILs) hallmarked by the inability to maintain effective energy synthesis for antitumor function and survival. T cells in the TME must catabolize lipids via mitochondrial fatty acid oxidation (FAO) to supply energy in nutrient stress, and it is established that T cells enriched in FAO are adept at cancer control.However, endogenous TILs and unmodified cellular therapy products fail to sustain bioenergetics in tumors. Using patient samples and mouse models, we reveal that the solid TME imposes perpetual acetyl-CoA carboxylase (ACC) activity, invoking lipid biogenesis and storage in TILs that directly opposes FAO. Using metabolic, lipidomic, and confocal imaging strategies, we find that restricting ACC rewires T cell metabolism, enabling energy maintenance in TME stress. Moreover, limiting ACC activity potentiates a gene and phenotypic program indicative of T cell longevity, engendering T cells with increased survival and polyfunctionality, with the ability to control solid cancer.

overall_design: Experiment 1: Conducted using vehicle or ACCi-treated splenocytes grown in  CD8+ differentiation conditions for 7 days (n=4). Experiment 2: Conducted using CD8+ T cells isolated from spleens and d14 subcutaneous MCA205 fibrosarcomas established in C57bl/6 mice (n=3).


title: Employing totipotent cells to reconstruct embryogenesis [scRNA-seq]

city: beijing

first: yuxin

last: luo

address: NO.49 Huanyuanbei Road Haidian District

institute: Peking University Third Hospital

summary: Blastoids, a structure similar to blastocysts in morphological and molecular level, can be applied to regeneration research. Using totipotent cells to construct blastoids will extend the information of early development to an earlier stage, and explore clues of regeneration. Totipotent blastomere-like cells (TBLCs) are a novel type of stably cultured mouse totipotent cell line generated by inhibiting spliceosomes. Here, we constructed blastoids (TBL-blastoids) in a new three-dimensional culture system using TBLCs. Morphological and transcriptomic analysis revealed TBL-blastoids contained typical morphology and key cell lineages of blastocysts and had higher degree of consistency in developmental rate and morphology compared to other blastoids. Moreover, TBL-blastoids implanted into uterus, induced decidua and even developed to embryonic tissues, indicating their in vivo developmental potential. The expansion and structures of TBL-blastoids in the IVC system also showed their in vitro developmental potential. The efficiency of generating TBL-blastoids and implantation rate suggest the necessity of TE-like component formation. Meanwhile, TBLCs can differentiate into extraembryonic cell lines directly, which provides an alternative strategy for evaluating totipotency. Furthermore, we explored the impacts of senescence, a central role in regeneration, on TBLCs and found that cellular senescence impaired the totipotency of TBLCs and the efficiency of generating blastoids. Also, the in vivo and in vitro developmental potential of TBL-blastoids were declined. In conclusion, the induction of TBLCs into blastoids and extraembryonic cells is valuable for promoting regeneration, early embryonic development study and evaluating totipotency.

overall_design:
We constructed blastoids (TBL-blastoids) in a new three-dimensional culture system using TBLCs. Morphological and transcriptomic analysis revealed TBL-blastoids contained typical morphology and key cell lineages of blastocysts and had higher degree of consistency in developmental rate and morphology compared to other blastoids.
Sample 1 is the TBLC cell line derived from miPSCs treated with spliceosomal inhibitor. TBLCs are the totipotent-like cells which resembles 2-cell embryonic cells and possesses totipotent features.  Sample 2 and Sample 3 are synthetic embryos and constructed by TBLCs. TBL-blastoids have the typical morphology and key cell lineages of blastocysts and are blastocyt-like structures. Sample 2 and Sample 3 are the biological replicates to perform scRNA-seq.  Sample 4 are also the TBL-blastoids and were derived from the TBLCs treated with 1 mM H2O2 for 1 h.

first: Yang

last: Yu

first: Yong

last: Fan

first: Zheying

last: Min

first: Yuxin

last: Luo

first: Ke

last: Zhong


title: Common modes of ERK induction resolve into context specific signalling via a combination of signal duration and cell type specific transcriptional repression [ESC_RNA]

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary: Fibroblast Growth Factor (FGF) signalling via ERK exerts diverse roles in development and disease. In mammalian preimplantation embryos and naïve pluripotent stem cells ERK promotes differentiation, whereas in primed pluripotent states closer to somatic differentiation ERK sustains self-renewal. How can the same pathway produce different outcomes in two related cell types? To explore context-dependent ERK signalling in embryonic development and differentiation we generated cell and mouse lines that allow for tissue- and time-specific cell intrinsic ERK activation. Using these tools, we find variations in response to ERK are mostly mediated by repression of transcriptional targets that occur in tandem with reductions in chromatin accessibility at regulatory regions. Furthermore, immediate early ERK responses are largely shared by different cell types but become refined producing cell-specific programs as increasing durations of signalling interface with cell specific gene regulatory networks. Induction in naïve pluripotency is accompanied by chromatin changes, whereas in later stages it is not, suggesting that chromatin context doesn’t shape signalling response. Altogether, our data suggest that cell-type specific responses to ERK signalling exploit the same immediate early response, but then sculpt it to specific lineages via repression of distinct cellular programs and downstream indirect stimulation of available enhancer networks.

overall_design:
To map the transcriptional response to ERK in pluripotent cell types, we targeted mESCs with a version of the cRAF inducible model in Hamilton et al., 2019. The construct allows for rapid and homogeneous ERK induction upon tamoxifen supplementation.
We collected samples for RNA-seq before induction (0h), after 2h and 4h of ERK induction, and then treated for an additional 2h with MEK inhibitor (rev), to explore reversion of ERK targets.
For each condition, 2 replicates were collected from 2 biological clones (clone 4 and 8), as a total of 4 replicates per condition.

first: Marta

last: Perera

first: Joshua


title: Common modes of ERK induction resolve into context specific signalling via a combination of signal duration and cell type specific transcriptional repression [EpiLC_RNA]

overall_design:
To map the transcriptional response to ERK in pluripotent cell types, we targeted mESCs with a version of the cRAF inducible model in Hamilton et al., 2019. The construct allows for rapid and homogeneous ERK induction upon tamoxifen supplementation.
We differentiated ESCs towards RSCs for 2 passages, then towards EpiLCs for 48h, then collected samples for RNA-seq before induction (0h), after 2h and 4h of ERK induction, and finally treated for an additional 2h with MEK inhibitor (rev), to explore reversion of ERK targets.
For each condition, 2 replicates were collected from 2 biological clones (clone 4 and 8), as a total of 4 replicates per condition. 1 sample of 0h was discarded during Quality Control.


title: High-throughput transcriptomics of water extracts detects reductions in biological activity with water treatment processes

city: RTP

first: Logan

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: The presence of numerous chemical contaminants from industrial, agricultural, and pharmaceutical sources in water supplies poses a potential risk to human and ecological health. Current chemical analyses suffer from limitations including chemical coverage and high cost, and broad-coverage in vitro assays such as transcriptomics may further improve water quality monitoring by assessing a large range of possible effects. Here, we used high-throughput transcriptomics to assess the activity induced by field-derived water extracts in MCF7 breast carcinoma cells.

overall_design: Wastewater, surface water, drinking water, and reclaimed water samples were collected from four sites in the United States and Australia and prepared via solid phase extraction. Samples were generally collected as pairs: surface and drinking water (as conventional water supply) and wastewater and reclaimed water (as purified recycled water). Resulting extracts were exposed to MCF7 breast carcinoma cells in an eight-point dilution series (concentration factor 0.01-50) for 6 h using three independent cultures per dose.

first: Jesse

middle: D

last: Rogers

first: Frederic

last: Leusch

first: Bryant

last: Chambers

first: Kevin

last: Daniels

first: Richard

last: Judson

first: Keith

last: Maruya

first: Alvine

middle: C

last: Mehinto

first: Peta

last: Neale

first: Katie

last: Paul-Friedman

first: Russell

last: Thomas

first: Shane

last: Snyder

last: Harrill


title: Epitope-specific T cell responses after SARS-2 vaccination, including for a hypervaccinated individual

city: Erlangen

first: Kilian

last: Schober

state: Bavaria

address: Maximiliansplatz 2

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: Universitätsklinikum Erlangen

summary: Prime-boost vaccinations tailor adaptive immunity. However, chronic antigen exposure can also lead to immune dysfunction. Overall, the benefits and limits of repetitive antigen exposure for vaccinations in humans remain poorly understood. Here we performed in-depth immune profiling in an individual that reports 217 vaccinations (including 134 certified doses) against SARS-CoV-2 in less than two years (Hypervaccinated Individual from Magdeburg, HIM). Antigen-specific antibody and T-cell responses were of higher quantity, while quality was preserved, compared to a three-dose mRNA vaccine control cohort. Hyperimmunization did not lead to adverse events and HIM remains SARS-CoV-2 infection-free. Insights from extreme settings like the one reported here instruct our understanding on the consequences of repetitive antigen exposure on adaptive immunity in humans.

overall_design: Antigen-specific T cells (as well as unspecific T cells as a control) were identified by DNA-baroded pMHC multimers (Dextramers) including the SARS-CoV-2 specificity LTD as well as the EBV specificity RAK. Dextramer+ and - cells were sorted by FACS and subjected to 5' scRNAseq on a 10x Genomics platform including CITEseq for Dextramers and, for some samples, 130 surface proteins; different samples from different donors were labelled with hasthag antibodies

first: Katharina

last: Kocher

first: Carolin

last: Moosmann

first: Felix

last: Drost

first: Christine

last: Schülein

first: Pascal

last: Irrgang

first: Philipp

last: Steininger

first: Jahn

first: Johannes

last: Träger

first: Bernd

last: Spriewald

first: Christoph

last: Bock

first: Dirk

last: Busch

first: Christian

last: Bogdan

first: Benjamin

last: Schubert

first: Thomas

last: Winkler

first: Matthias

last: Tenbush

first: Ev-Marie

last: Schuster


title: Gene-environment interaction elicits dystonia-like features and impaired translational regulation in a DYT-TOR1A mouse model

city: Würzburg

first: Chi Wang

last: Ip

address: Josef-Schneider-Strasse 11

department: Neurology

institute: Neurologische Klinik und poliklinik

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

overall_design: Refer to individual Series


title: Gene-environment interaction elicits dystonia-like features and impaired translational regulation in a DYT-TOR1A mouse model (RNA-Seq)

summary:
To elicit a dystonia-like phenotype in a genetically predisposed DYT-TOR1A mouse model (DYT1KI) by performing a right sciatic nerve crush injury.
To identify novel pathophysiological pathways and possible biomarker, we performed a multi-omic analysis of three dystonia-relevant brain regions

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the cortex, striatum and cerebellum of naive and nerve-injured wildtype and DYT1KI mice

first: Colette

last: Reinhold

first: Susanne

last: Knorr

first: Rhonda

last: McFleder

first: Panagiota

last: Arampatzi

first: Tom

last: Gräfenhan

first: Thorsten

last: Bishler


title: Gene-environment interaction elicits dystonia-like features and impaired translational regulation in a DYT-TOR1A mouse model (miRNA-Seq)

overall_design: Comparative miRNA expression profiling analysis of miRNA-seq data for the cortex, striatum and cerebllum of naive and nerve-injured wildtype and DYT1KI mice


title: Nuclear Receptor Coactivator 6 is a Critical Regulator of NLRP3 Inflammasome Activation and Gouty Arthritis

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

country: South Korea

institute: Catholic University of Korea

summary: Transcriptional coactivators regulate the rate of gene expression in the nucleus, but their role in the extranuclear sites is largely unknown. Here, we demonstrated that nuclear receptor coactivator 6 (NCOA6) translocated to the cytoplasm, then was incorporated to NLRP3 inflammasome complex, and acquired a new function of “activation of inflammation and innate immune response”, beyond its original function of nuclear coactivation, in monocytes and macrophages. Mechanistically, cytoplasmic NCOA6 directly interacted with NACHT domain of NLRP3 and then promoted NLRP3 activity. Genetic ablation of Ncoa6 substantially attenuated severity of mouse models of two NLRP3-dependent diseases, folic-induced acute tubular necrosis and crystal-induced arthritis in mice. Consistent with these findings, NCOA6 was highly expressed in macrophages of gout patients and its signature was significantly enriched in the gout macrophages in transcriptome profiling. Conclusively, NCOA6 is a critical regulator of the NLRP3 inflammasome activation and therefore a promising target for NLRP3-dependent diseases, including gout.

overall_design: To systematically understand function of NCOA6 in monocytes/macrophages, we conducted global transcriptome profiling of bone marrow-derived macrophages (BMDMs) isolated from Ncoa6-KO (Ncoa6^(fl/fl)LysM^CRE) mice, whose macrophages specifically do not express Ncoa6, and Wild type (WT, Ncoa6^(fl/fl)) mice, which express Ncoa6, and compared the resulting profiles.

first: Kang-Gu

last: Lee

first: Saseong

first: Naeun

first: Saeung-Whan

last: Kim

first: Jennifier

first: Donghyun

first: Wan-Uk


title: Gene expression profile of adult Drosophila foregut

city: Baltimore

first: Haolong

last: Zhu

state: Maryland

address: 3520 San Martin Drive

institute: Carnegie Institution for Science

summary: Adult Drosophila foregut contains a diverse set of tissue and cell types. We applied single cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) to delineate the cellular composition and molecular profile of the foregut and its associated physiological functions.

overall_design: Adult Drosophila proventriculus and associated tissues within the foregut were collected and examined using scRNA-seq. Adult Drosophila proventriculus, crop, and salivary gland tissues were collected and examined using bulk RNA-seq.

first: William

middle: B

last: Ludington

first: Allan

last: Spradling


title: ESRG regulates alternative splicing of TCF3 to maintain hESCs self-renewal and pluripotency

city: Changsha

first: caiping

last: ren

address: 110 Xiangya Road,

institute: Central South University

summary: Elucidating the mechanism of self-renewal and pluripotency maintenance of human embryonic stem cells (hESCs) is of great significance in basic research and clinical applications. Long non-coding RNAs (lncRNAs) have been shown to play a key role in the self-renewal and pluripotency maintenance of hESCs. We previously reported that the lncRNA ESRG, which is highly expressed in undifferentiated hESCs, can interact with the replication licensing factor MCM2 and inhibit the p53 pathway to maintain the self-renewal and pluripotency of hPSCs. In addition to MCM2, RNA pull-down mass spectrometry showed that ESRG could also bind to other proteins, among which heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) attracted our attention. In this study, we show that HNRNPA1 can maintain self-renewal and pluripotency of hESCs. ESRG binds to and stabilizes HNRNPA1 protein through the ubiquitin-proteasome pathway. In addition, knockdown of ESRG or HNRNPA1 resulted in alternative splicing of TCF3, which originally and primarily encodes E12, to mainly encode E47 and inhibit CDH1 expression. HNRNPA1 could rescue the biological function changes of hESCs caused by ESRG knockdown or overexpression. Our results suggest that ESRG regulates the alternative splicing of TCF3 to affect CDH1 expression and maintain hESCs self-renewal and pluripotency by binding and stabilizing HNRNPA1 protein. This study lays a good foundation for exploring the new molecular regulatory mechanism by which ESRG maintains hESCs self-renewal and pluripotency.

overall_design: Gene Expression Profiling of human embryonic stem cells (H9) treated by siControl and siHNRNPA1 for 48h were characterized using RNA-seq.

first: Wen

last: Xie

first: Weidong

last: Liu

first: Lei

last: Wang

first: Bin

first: Shasha

last: Li

first: Ziling

last: Liao

first: Hongjuan

last: Xu

first: Yihan

first: Xingjun

last: Jiang

first: Caiping

last: Ren


status: Public on Mar 04 2024

city: San Francisco

first: Jaymin

last: Kathiriya

state: CA

address: 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

summary: BCL-2 modulates IRE1a activation to attenuate ER stress and pulmonary fibrosis. Mice were treated with Bleomycin + Vehicle or Bleomycin + Navitoclax. Lungs were harvested 21 days after bleomycin injury followed by enzymatic digestion of the lungs to create single cell suspension and flow-sorting based isolation of total epithelial and stromal cells

overall_design: Mice were treated with Bleomycin + Vehicle or Bleomycin + Navitoclax. Lungs were harvested 21 days after bleomycin injury followed by enzymatic digestion of the lungs to create single cell suspension and flow-sorting based isolation of total epithelial and stromal cells. The cells were then mixed in 1:1 ratio to perform single cell RNA-sequencing.

first: Claude

last: Le Saux

first: Tsung-Che

last: Ho

first: Alexis

last: Brumwell

first: Ying

last: Wei

first: Vincent

last: Auyeung

first: Ferroz

last: Papa

first: Harold

last: Chapman


title: Spatial Transcriptomics reveals brain regional gene expression profiles in murine model of Periventricular Heterotopia

city: Bethesda

first: Yuanyi

last: Feng

state: MD

address: 4301 Jones Bridge Road

institute: UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES

summary: Periventricular Heterotopia (PH) is a malformation of cerebral cortical development characterized by the presence of neurons along the wall of lateral ventricles. The most notable neurological symptoms are seizures that usually first appear when PH becomes evident during the teenage years. Heterozygous loss of function mutations within the FLNA gene in Xq28 are the most frequent cause of familial PH, while the genotype-phenotype correlation has not been well established. We generated a mouse model of PH by conditionally deleting Flna in neural progenitors along with a Flnb null mutation. In this mouse model, periventricular neurons are predominantly generated in postnatal ages. To understand the pathogenesis of PH and the mechanism of postnatal- adult neurogenesis, we assessed transcriptomic alterations resulting from Flna and Flnb double loss of function in the ventricular/subventricular zone (V-SVZ), upper cortical layers, and periventricular neurons, respectively. This dataset reveals spatially-dependent differential gene expressions between PH and their normal control counterparts at 3 months of age.

overall_design: Brains of 3 Flna-Flnb double mutant (referred to as FlnKO) and 3 control mice at 3 months of age were fixed by transcardial perfusion with nuclease-free PBS and 4% paraformaldehyde. From the fixed brains cryosections of 7-μm thickness were placed on a microscope slide. The slide was analyzed by GeoMx Digital Spatial Profiler to assess whole transcriptome profiles in selected regions of interests (ROIs) that were identified by staining with fluorescent-conjugated antibodies to NeuN and Gfap.


title: Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage [Ad_RNA-seq]

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: To investigate the function of IRF1 in chondrocytes, we performed transcriptome analysis in priamry mouse articular chondrocytes. Using adenovirus expressing mouse Irf1 (Ad-Irf1) or expressing eGFP (Ad-eGFP), Irf1 was overexpressed in mouse chondrocytes.

overall_design: RNA sequencing data using samples from Ad-Irf1 or Ad-eGFP infected primary mouse articular chodnorcytes

first: Yongsik

last: Cho

first: Hyeonkyeong

first: Geunho

last: Yook


title: Employing totipotent cells to reconstruct embryogenesis

first: yuxin

last: luo


title: Common modes of ERK induction resolve into context specific signalling via a combination of signal duration and cell type specific transcriptional repression [ATAC-seq]

first: Josh

last: Brickman

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
To map the chromatin accessibility changes in response to ERK in pluripotent cell types, we targeted mESCs with a version of the cRAF inducible model in Hamilton et al., 2019. The construct allows for rapid and homogeneous ERK induction upon tamoxifen supplementation.
We differentiated targeted ESC towards RSC and EpiLCs, then collected samples for ATAC-seq before induction (0h) and after 4h of ERK induction with tamoxifen (4OHT).
For each condition, 2 replicates were collected, from 2 biological clones (clone 4 and 8).

first: Marta

last: Perera

first: Joshua


title: Epigenomic profiles of Brachypodium distachyon mutants deficient in RNA polymerase IV (Pol IV)

city: Strasbourg

first: Todd

middle: L

last: Blevins

address: 12 Rue du Général-Zimmer

country: France

institute: CNRS

summary: Monocot grass species (Poaceae) express a diverse set of multisubunit RNA polymerase enzymes, including Pol II, Pol IV and Pol V. To better understand this functional diversity, we have charted Pol IV function in the model Brachypodium distachyon. Intriguingly, pol IV null mutations in Poaceae crops disrupt growth, reproductive development and seed set. In order to investigate how Pol IV controls vegetative growth and TE activity in these grasses, we have isolated B. distachyon mutant alleles for Pol IV’s largest subunit, NRPD1. We obtained the germplasm in which to screen for these pol IV mutations from the B. distachyon community's sodium azide (NaN) and T-DNA insertion collections.

overall_design: Transcriptomic analysis of NRPD1 wild-type and nrpd1 null mutant Brachypodium distachyon lines, sampling RNA from young emerging leaves of 4-week-old plants, including triplicate biological replicates.

first: Christophe

last: Himber

first: Michael

last: Thieme

first: Calvin

last: Matteoli

first: Wenbo

last: Xu

first: John

last: Vogel

first: Debbie

last: Laudencia-Chingcuanco

first: Richard

last: Sibout

first: Bart

last: Rymen

first: Anne

last: Roulin


title: Spatial Multi-omics Reveals the Heterogeneity of Tumor Microenvironment in the OSF-Associated OSCC

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

summary: Oral submucous fibrosis (OSF) is one of the most common precancerous malignant orders (PMO) with high rates exacerbating into oral squamous cell carcinoma (OSCC), mostly occurred in patients with chewing betel-nut habits in Southeast Asia and Pacific region. However, the spatial characteristics and heteogeneities of tumor microenvironment (TME) in OSF-associated OSCC still remains unclear. Here, we characterized the spatiotemporal  changes of OSF-associated OSCC at different malignant states by performing  10x Visium Spatial Transcriptomics (ST) sequencing  and airflow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI) analysis.

overall_design: Samples from 4 OSF-associated OSCC patients were analysed by Spatial Transcriptomics sequencing (ST) and airflow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI)

first: Zhaoyang

last: Zeng


title: Enhancer-activated RET confers protection against oxidative stress to KMT2A-rearranged acute myeloid leukemia.

city: Little Rock

first: Kimberly

middle: E

last: Stephens

state: AR

address: 4301 W. Markham St Slot 510

department: Neuroscience

institute: University of Arkansas for Medical Sciences

summary: KMT2A-MLLT3, a fusion protein formed by the t(9;11) translocation in acute myeloid leukemia, is an epigenetic transcription factor that is known to regulate a unique leukemic gene expression profile. We show that rearranged during transfection (RET) proto-oncogene is highly overexpressed in the KMT2A-MLLT3 subgroup. In addition to biochemical studies, the RNA-seq and ATAC seq analyses have been performed in KMT2A-MLLT3 positive MOLM-13 AML cell line, compared to the umbilical cord blood-driven CD34+ hematopoietic stem progenitor cells.

overall_design: and libraries were sequenced using150  bp paired end reads on a NextSeq500 (Illumina).

first: Samrat

middle: R

last: Choudhury


title: Employing totipotent cells to reconstruct embryogenesis [RNA-seq]

first: yuxin

last: luo

overall_design:
We transferred ctrl TBL-blastoids and H2O2 TBL-blastoids into uterus of pseduo-pregnant mice at 2.5 dpc, individually. After 6 days, the surrogate mice wwere dissected and got out the wombs.
The DEC were the deciduas derived from the uteruses and the old or ctrl referred to the H2O2 TBL-blastoids or ctrl TBL-blastoids, respectively.
The ctrl EMB were the embryonic-like tissues in the deciduas triggered by ctrl TBL-blastoids.
Every group contained three biological replicates.

first: Yang

last: Yu

first: Yong

last: Fan

first: Zheying

last: Min

first: Yuxin

last: Luo

first: Ke

last: Zhong


title: The mechanosensory channel Piezo1 Triggers Angiopoietin-Tie Signaling in the Lymphatics

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E. Superior St,

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Angiopoietin-Tie1 signaling is required for lymphatic vascular integrity and both ANGPT2 and TIE1 genetic variants have been associated with lymphedema in patients1, 2.  Concurrent with growth-factor signaling, mechanical forces sensed by lymphatic endothelial cells (LECs) are also needed to regulate lymphatics3, 4.  How these two pathways might interact in the lymphatic system is unknown.  Here, we identified a regulatory network in LECs linking activation of the mechanosensory channel, PIEZO1 to Angiopoietin-Tie signaling and repression of a downstream FOXO1 transcriptional response. RNAseq analysis of dermal LECs from Tie1-deficient embryos showed persistent FOXO1 activity with downregulation of LEC-associated genes including Ccl21a, Foxc2, Gata2 and Gja4, as well as increased expression of the mechanosensory channel, Piezo1.  Activation of PIEZO1 in human dermal LECs (HDLECs) by the small molecule agonist, Yoda1, triggered exocytosis of the Tie ligand, Angiopoietin-2 (ANGPT2), activation of Tie/AKT/PI3K signaling and export of FOXO1 out of the nucleus. Our data identify a novel molecular pathway linking mechano-transduction to ANGPT2-Tie1 activity and dynamic modulation of FOXO1 activity needed for patterning and function of the lymphatic system

overall_design: RNA-seq of dermal lymphatic endothelial cells (WT, Tie1 KO).

first: Jing

last: Du

first: Pan

last: Liu

first: Benjamin

last: Thomson

first: Phoebe

last: Leeaw


title: Common modes of ERK induction resolve into context specific signalling via a combination of signal duration and cell type specific transcriptional repression [E3.5_RNA]

first: Josh

last: Brickman

overall_design:
To map the transcriptional response to ERK in pluripotent cell types, we targeted mESCs with a version of the cRAF inducible model in Hamilton et al., 2019. The construct allows for rapid and homogeneous ERK induction upon tamoxifen supplementation.
We then created a mouse line by injecting ESCs with this construct to morulas. We collected samples for RNA-seq from pre-implantation Epiblast (E3.5), before (0h) and after 4h of ERK.
For each condition, 2 replicates were collected from 2 biological clones (clone 4 and 8), as a total of 4 replicates per condition. 1 sample of 0h was discarded during Quality Control

first: Marta

last: Perera

first: Joshua


title: Identification of AtALKBH1A and AtALKBH1B as DNA N6-adenine demethylases in Arabidopsis thaliana

first: Chongsheng

last: He

address: 27 Tianma road

institute: Hunan university

summary:
Wild type and alkbh1a/1b seeds were stratified for two days, dry and stratified seeds were collected to extract total RNA for mRNA-seq.
We then performed gene expression profiling analysis using data obtained from mRNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dry and stratified wild type and atalkbh1a/1b seeds.

first: Donghao

last: Li

first: Jun

first: Ming

last: Gao


title: Single-cell RNA sequencing reveals myeloid and T cell co-stimulation mediated by IL-7 anti-cancer immunotherapy

first: Hye Hyeon

last: Eum

address: 222, Banpo-daero, Seocho-gu

institute: The Catholic University of Korea

summary: Immune checkpoint inhibitors unleash inhibitory signals on effector T cells inflicted by tumor and surrounding stromal cells. Despite the great success of PD-1 inhibitors in a fraction of cancer patients, lack of checkpoint molecule expression and persistence of immunosuppressive cells limit the effects of the therapy. To overcome the limitations, combination therapies or direct stimulation of myeloid cells are being investigated. Nonetheless, combination therapies increase the incidence of side effects, and a single agent co-stimulating T cell and myeloid populations might be a better strategy. Exploring single cell RNA sequencing data from multiple human cancers and mouse tumor model, we found pleiotropic expression of interleukin 7 receptor on T cells, macrophages, and dendritic cells. Treatment of recombinant IL7 induced expansion of effector CD8 T cells along with pro-inflammatory activation of macrophages and dendritic cells. Spatial transcriptomic data revealed strengthen of anti-tumoral interactions between macrophages and T cells by IL7 treatment. Altogether, our results suggest that IL7 therapy is applicable to a broad range of cancer patients.

overall_design: The CT26 colon carcinoma cells (2x10^5 cells) were subcutaneously (s.c.) injected to the Balb/c mice. For the rIL7 treatment group, 10ug of recombinant mouse IL7 (rIL7) was intraperitoneally (i.p.) treated at day 11 and day 13 post-transplantation. Tissue specimens were obtained at day 14-15 then analyzed by flowcytometry, tissue immunostaining, scRNAseq, and spatial transcriptomics platform (Visium, 10x genomics).


title: Interleukin 7 therapy changes tumor immune environment to pro-inflammatory through myeloid and T cell interactions [Visium]

first: Hae-Ock

last: Lee

first: Hye

middle: H


title: Natural polymorphisms in ZMET2 encoding a DNA methyltransferase modulate the number of husk layers in maize

city: Beijing

first: Wang

last: Zi

address: NO2 Yuanmingyuan West Road, Haidian

department: ational Maize Improvement Center  of China

institute: China Agricultural University

type: Methylation profiling by high throughput sequencing

summary: The goals of this study are to investigate the effect of ZMET2 on genome-wide DNA methylation and gene expression.

overall_design: RNA sequencing (RNA-seq) and bisulfite sequencing(BS-seq) was performed using ear samples at the early growing stage of wild type and zmet2 mutant plants.

first: Zi

last: Wang


title: Dendritic cell-targeted therapy expands CD8 T cell responses to bona-fide neoantigens in lung tumors

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: Cross-presentation by type 1 DCs (cDC1) is critical to induce and sustain antitumoral CD8 T cell responses to model antigens, in various tumor settings. However, the impact of cross-presenting cDC1 and the potential of DC-based therapies in tumors carrying varied levels of bona-fide neoantigens (neoAgs) remains unclear. We develop a hypermutated model of non-small cell lung cancer, encoding genuine MHC-I neoepitopes to study neoAgs-specific CD8 T cell responses in spontaneous settings and upon Flt3L+CD40 (DC-therapy). We find that cDC1 are required to generate broad CD8 responses against a range of diverse neoAgs. DC-therapy promotes immunogenicity of weaker neoAgs and strongly inhibits the growth of high tumor-mutational burden (TMB) tumors. In contrast, low TMB tumors respond poorly to DC-therapy, generating mild CD8 T cell responses that are not sufficient to block progression. scRNA transcriptional analysis, immune profiling and functional assays unveil the changes induced by DC-therapy in lung tissues, which comprise accumulation of cDC1 with increased immunostimulatory properties and decreased exhaustion in effector CD8 T cells. We conclude that boosting cDC1 activity is critical to broaden the diversity of anti-tumoral CD8 T cell responses and to leverage neoAgs content for therapeutic advantage.

overall_design: Briefly, KP cells were transiently transfected with pZac2.1-U6sgRNA-CMV-ZsGreen and (pSpCas9(BB)(PX458) using Lipofectamine 3000 (Invitrogen), following the manufacturer´s instructions. ZsGreen+ cells were cell sorted. Mlh1 knockout clones were generated by Crispr Cas9 based technology using 2 single guide RNAs (sgRNA) targeting Mlh1 exon 5 as described previuosly.  and single clones were tested for Mlh1 expression. KPctrl cells derive from cells transiently transfected with only (pSpCas9(BB)(PX458). Then, RNA extraction was performed in triplicates using RNeasy Mini kit (Qiagen).

first: Federica

last: Benvenuti

first: Lucía

last: López

first: Giuseppe

last: Rospo

first: Roberto

last: Amadio

first: Giovanni

last: Germano


title: Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage

first: Jin-Hong

last: Kim

overall_design: Refer to individual Series


title: Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage [ATAC-seq]

summary: To investigate the mechanisms of IRF1 in the development of OA, we characterized regulatory elements accessible to IRF1 via DNA footprinting analysis in chondrocytes by employing the assay for transposase-accessible chromatin with sequencing (ATAC-seq).

overall_design: ATAC sequencing data using samples from primary mouse articular chondrocytes

first: Yongsik

last: Cho

first: Hyeonkyeong

first: Geunho

last: Yook


title: Chromatin contacts within a fountain-like structure

first: Yang

last: Liu

address: Yiheyuan Road, No. 5

institute: School of life sciences, Peking University

summary: Hundreds of DNA replication forks functioning simultaneously are essential for timely DNA duplication, but the organization of replication forks are poorly understood in mammalian cells. Here, we developed a replication-enriched in situ HiC (Repli-HiC) method to capture chromatin contacts located adjacent to replication forks and found two types of fountain-like chromatin contacts at thousands of loci. Interactions within fountain-spanning regions are confirmed by q3C-seq analysis of different stages of S phase cells.

overall_design: Three primers, two located within a fountain (Proximal and Distal) and one located outside the fountain, are used to clone the chromatin interaction in the G1, S1, S2, S3, S4, S5, and S6 phase cells.

first: Zhengrong

last: Zhangding

first: Xuhao

first: Jiazhi

last: Hu


title: Effects of PCB 52 Exposure Via Sub-Acute Nose-Only Inhalation on Gene Expression in Fat Depots of Adolescent Rats

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

summary: Polychlorinated biphenyls (PCBs) are persistent environmental toxicants that pose a variety of health risks in humans. PCB 52 has been found in the indoor air of schools where adolescent students and staff are being actively exposed. This study examined the three different fat depots, namely, brown adipose tissue (BAT), subcutaneous adipose tissue (SAT), and visceral adipose tissue (VAT), of adolescent Sprague-Dawley rats after sub-acute exposure to PCB 52 via nose-only inhalation. Rats were exposed for 4 hours daily for 28 consecutive days. RNA extracted from both male and female fat depots were submitted for RNA sequencing to compare the effects of PCB 52 on the expression of genes in the fat depots.

overall_design: To determine the gene expression alterations following PCB 52 inhalation exposure in adolescent rats, samples from male and female fat depots (BAT, SAT, and VAT) were processed for RNA sequencing. (N = 6 per sex; Samples were excluded if RNA RINs were below 8).

first: Francoise

last: Gourronc

first: Amanda

last: Bullert

first: Hui

first: Brynn

middle: K

last: Helm-Kwasny

first: Michael

last: Chimenti

first: Andrea

last: Adamcakova-Dodd

first: Xuefang

last: Jing

first: James

last: Ankrum

first: Peter

last: Thorne

first: Hans-Joachim

last: Lehmler


title: Interleukin 7 therapy changes tumor immune environment to pro-inflammatory through myeloid and T cell interactions [scRNAseq]

first: Hye Hyeon

last: Eum

overall_design: The CT26 colon carcinoma cells (1~2x10^5 cells) were subcutaneously (s.c.) injected to the Balb/c mice. For the rIL7 treatment group, 10ug of recombinant mouse IL7 (rIL7) was intraperitoneally (i.p.) treated at day 11 and day 13 post-transplantation. Tissue specimens were obtained at day 14-15 then analyzed by flowcytometry, tissue immunostaining, scRNAseq, and spatial transcriptomics platform (Visium, 10x genomics).

first: Hae-Ock

last: Lee

first: Hye


title: Enhancer-activated RET confers protection against oxidative stress to the MLL-rearranged acute myeloid leukemia cells

first: Kimberly

last: Stephens

summary: RET expression is upregulated in AML subtypes harboring genetic fusions of MLL-1 genes compared to age-matched healthy donors and other AML subtypes. In addition, we identify a novel epigenetic mechanism of RET overexpression in MLL-rearranged AML.

overall_design: examination of  chromatin accessibility in CD34 and MOLM13 cells

first: Samrat

last: Choudhury


title: Replication timing for the replication fountains

first: Yang

last: Liu

summary: This dataset includes replication timing of WT K562 cells and cells with or without 600 nM Aphidicolin treatment.

overall_design: Cells were treated with or without 600 nM treatement for 16 hours, BrdU for 1 or 3 hours, Hochest33342 for 30 minutes, and then sorted into 6 fractions, according to the DNA content. After that, genomic DNA was isolated and applied for Repli-seq analysis.

first: Zhengrong

first: Xuhao

first: Jiazhi


title: Evolutionary and Functional Insights into the Ski2-like helicase Family in Archaea: A Comparison of Thermococcales ASH-Ski2 and Hel308 Activities

city: Toulouse

first: Marta

last: Kwapisz

address: 118, route de Narbonne

department: MCD

institute: CNRS-UT

summary:
RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The
Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having
specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been
established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those
in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that,
in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions.
Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5′-3′ aRNaseJ exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3′-5′ polarity. To gain insights into
the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ASH-Ski2 mutant strain and provide evidence of the
importance of ASH-Ski2 in cellular metabolism pathways related to translation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T.barophilus MP (∆TERMP_00517; UBOCC-M-3300) and its derivative ΔASH-Ski2 (UBOCC-M-3315).

first: Manon

last: Batista

first: Petra

last: Langendijk-Genevaux

first: Isabelle

last: Canal

first: Duy

last: Phung

first: Laura

last: Plassart

first: Régine

last: Capeyrou

first: Yann

last: Moalic

first: Mohamed

last: Jebbar

first: Didier

last: Flament

first: Gwennaele

last: Fichant

first: Marie

last: Bouvier

first: Beatrice

last: Clouet d'Orval


title: Polysaccharides from Sargassum fusiforme protect mice against Citrobacter rodentium infection through intestinal microbiota-drived microRNA-92a-3p

city: Dalian

first: Hong

middle: xu

address: 1 Light Industry Garden, Ganjingzi District, Dalian City, Liaoning Province, China

institute: Dalian Polytechnic University

summary: To explore the regulatory mechanism of intestinal flora in Citrobacter rodentium -induced intestinal infection by transcriptome analysis at miRNA molecular level.

overall_design: The feces from three groups (Control, Model and LSFP group) underwent miRNA-seq.

first: Hongxu

first: Ningbo

last: Qin


title: Venous plexus-associated lymphoid hubs support meningeal humoral immunity

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: There is increasing interest in how immune cells in the meninges, the membranes that surround the brain and spinal cord, contribute to homeostasis and disease in the central nervous system (CNS)1,2. The outer layer of meninges, the dura mater, has recently been described to contain both innate and adaptive immune cells, and function as a site for B cell development. Here, we identified organised lymphoid structures protecting fenestrated vasculature in the dura mater that we term dural-associated lymphoid tissue (DALT). We found the most elaborate immune organization, including lymphatic vessels, surrounding the rostral_x0002_rhinal confluence of sinuses. We termed this structure that interfaced with the skull bone marrow and a comparable venous plexus at the skull base, the rostral-rhinal venolymphatic hub. Immune aggregates were present in DALT during homeostasis and expanded with age or following challenge with systemic or nasal antigens. DALT contained germinal centre (GC) B cells, and supported the generation of somatically mutated, antibody-producing cells in response to a nasal pathogen challenge. Inhibition of lymphocyte entry into the rostral-rhinal hub at the time of nasal viral challenge abrogated the generation of germinal centre B cells and class-switched plasma cells, as did perturbation of B-T cell interactions. These data demonstrate lymphoid architecture around vasculature in dura mater that can sample antigens and rapidly support humoral immune responses following local pathogen challenge.

overall_design: Rostral rhinal hubs isolated from the dorsal meninges were analyzed by scRNAseq in two groups of mice (uninfected vs day 8 post-VSV infection) in two independent experiments.  Experiment#1: uninfected (Men_Naive), d8 VSV (Men_VSV); Experiment#2: uninfected (PBS_HUB), d8 VSV (VSV_HUB)

first: Zachary

last: Fitzpatrick

first: Nagela

middle: G

last: Zanluqui

first: Jared

last: Rosenblum

first: Zewen

last: Tuong

first: Colin

middle: Y

last: Lee

first: Vikram

last: Chandrashekhar

first: Maria

last: Negro-Demontel

first: Andrew

middle: P

last: Stewart

first: David

last: Posner

first: Monica

last: Buckley

first: Kieren

last: Allinson

first: Panagiotis

last: Mastorakos

first: Prashant

last: Chittiboina

first: Dragan

last: Maric

first: Danielle

last: Donahue

first: Adel

last: Helmy

first: Tamara

last: Tajsic

first: John

last: Ferdinand

first: Anais

last: Portet

first: Ana

last: Peñalver

first: Eleanor

last: Gillman

first: Zhengping

last: Zhuang

first: Menna

last: Clatworthy

first: Dorian

last: McGavern


title: Genome-wide gene expression profiling  of macrophages treated with novel 1,2,4-oxadiazole scaffold-based compounds

city: Paris

first: Ludovic

last: Tailleux

state: non-US Resident

address: 25-28 rue du Dr Roux, 75015 Paris, France

institute: Institut Pasteur

summary:
Background: Anti-tuberculosis drugs, mainly developed more than 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multi-resistant strains of Mycobacterium tuberculosis are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy (HDT) has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, we evaluated the impact of two host-directed compounds, namely MC3465 and MC3209, on the response of human monocytes-derived macrophages infected with Mycobacterium tuberculosis (MTB).
Results: The expression of 181 genes was differentially regulated following MC3465 treatment (p-value < 0.05, log FC ≥ 0.5 and ≤ -0.5) after 4 h, with 53 being upregulated and 128 being downregulated. The expression of more genes was affected after 24h of treatment. 224 genes were upregulated and 652 genes downregulated.  (p value < 0.05, log FC ≥ 0.5 and ≤ -0.5). We classified those differentially expressed genes by performing gene-set enrichment analysis using ClueGO cluster analysis. The gene set downregulated by MC3465 at 4 h was significantly enriched for genes associated with chemotaxis and cellular zinc ion homeostasis and cell chemotaxis. At 24 h, most of the downregulated genes belongs to the innate immune response and the cytokine response, with many genes belonging to the type I IFN pathway.
Conclusions: Our results indicate that MC3465 alters zinc homeostasis in human macrophages.

overall_design: CD14+ monocytes were isolated from 4 blood donors (named D1, D2, D3 and D4) by positive selection using CD14 microbeads (Miltenyi Biotec). Cells were cultured at 37°C and 5% CO2 in RPMI-1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Dutscher), and 2 mM L-glutamine (Gibco) with macrophage colony stimulating factor (M-CSF, 20 ng/mL; Miltenyi Biotec). After six days of differentiation, the resulting macrophageswere infected with Mycobacterium tuberculosis (H37Rv strain, multiplicity of infection: one bacterium-per two cell). Naive macrophages and M. tuberculosis infected macrophages were treated  with MC3465 (40) or MC3209 (a1). After 4 h and 24 h of treatment, we characterized the genome-wide gene expression profiles of macrophages by RNAseq, with DMSO-treated cells serving as a control.

first: Alexandra

last: Maure


title: Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

city: Exeter

first: Akshay

last: Bhinge

state: Devon

address: Stocker Road

country: United Kingdom

institute: Living Systems Institute, University of Exeter

summary: RNA processing is a fundamental mode of gene regulation that is perturbed in a variety of diseases including cancer and neurodegenerative disorders. RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions such as CLIP rely on purifying single proteins at a time. Methods to identify transcriptome wide binding of RBPs without purifying individual RBPs are gaining interest. We have developed a new method (ePRINT) to map RBP-RNA interaction networks on a global scale in an RBP agnostic manner. Our method allows precise mapping of the 5’ end of the RBP binding site and uncovers RBPs that are differentially activated during cell fate transitions.

overall_design:
ePRINT analysis of HEK293T cells transfected with an siRNA against FUS or a scrambled control siRNA.
ePRINT analysis of motor neuron progenitors and differentiated motor neurons.

first: Sophie

last: Hawkins

first: Seema

last: Namboori

first: Alexandre

last: Mondaini

first: Asif

last: Javed


title: Short Noncoding RNAs as predictive biomarkers for the development from Inflammatory Bowel Disease Unclassified to Crohn’s Disease or Ulcerative Colitis

city: Herlev

first: Jaslin

last: James

address: Borgmester Ib Juuls vej 1

department: Department of Pathology

institute: Herlev hospital

summary: To find predictive biomarkers for the development from inflammatory bowel disease unclassified (IBDU) to Crohn's disease(CD) or ulcerative colitis (UC), we performed short non-coding RNA profiling on IBDU patient samples at the time of diagnostic endoscopy.

overall_design:
Mucosal tissue biopsies from IBDU patients(35) who were reclassified to CD (IBDU-CD, 12), UC (IBDU-UC, 15) or remained as IBDU (IBDU-IBDU, 8)), and 8 IBD patients were used in the study.
*** NOTE FROM SUBMITTER: Raw data generated during the current study can not be made publicily available, which is in accordance with the rules concerning processing of personal data set out in the EU General Data Protection Regulation (GDPR) and the Danish Data Protection Act. Nonetheless, may a researcher have an interest in our data they are welcome to contact us and collaborate. The data that support the findings of this study can be requested from The National Secretariat for Bio- and Genome Bank Denmark, RBGB.sekretariat.herlev-og-gentofte-hospital@regionh.dk, Herlev Hospital, Borgmester Ib Juuls Vej 73, 2730 Herlev, Denmark. ***

first: Lene

last: Buhl Riis

first: Mikkel

last: Malham

first: Estrid

last: Høgdall

first: Ebbe

last: Langholz

first: Boye

middle: S

last: Nielsen


title: Development of gene expression signatures in whole spectrum of leprosy

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To further development of our gene expression approach in different groups of leprosy, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish leprosy reactions and relapse cases from healthy controls. Human biopsy and skin slit were collected from reaction cases, PB cases, MB cases, relapse cases and healthy contacts. Total 1891,1384, 1134, 475 and 762 no of genes were overexpressed in PB, T1R, T2R, LL and relapse cases respectively. Expression of seven genes (glcB, infB, ftsH, ppgk,relA, rpsR and atpB) from relapse cases was quantified in the same RNA samples by real-time PCR confirming role of theses genes in relapse cases.

overall_design: Agilent one-color experiment,Organism: Mycobacterium leprae  Agilent Microarray Gene Expression 8x15K Arrays AMADID: 84765

first: Itu

last: Singh

first: Mallika

last: Lavania


title: Phase separation-competent FBL shapes nucleolar function and translation in leukemogenesis

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

institute: Zhejiang University

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


title: The TET-Sall4-BMP regulatory axis controls craniofacial cartilage development

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

summary: Craniofacial microsomia (CFM) is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However, the molecular basis of CFM pathogenesis is largely unknown. Here, we employ the zebrafish model to investigate mechanisms of CFM pathogenesis. In early embryos, tet2 and tet3 are essential for pharyngeal cartilage development. Single-cell RNA sequencing reveals that loss of Tet2/3 impairs chondrocyte differentiation due to insufficient BMP signaling. Moreover, biochemical and genetic evidence reveals that the sequence-specific 5mC/5hmC-binding protein, Sall4, binds the promoter of bmp4 to activate bmp4 expression and control pharyngeal cartilage development. Mechanistically, Sall4 directs co-phase separation of Tet2/3 with Sall4 to form condensates that mediate 5mC oxidation on the bmp4 promoter, thereby promoting bmp4 expression and enabling sufficient BMP signaling. These findings suggest the TET-BMP-Sall4 regulatory axis is critical for pharyngeal cartilage development. Collectively, our study provides insights into understanding craniofacial development and CFM pathogenesis.

overall_design:
10× library construction and sequencing
Single-cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer’s instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.
Bulk RNA-seq library construction and sequencing
Total RNAs were purified using TRIzol reagent (Life Technologies, 343702). Libraries were constructed using a VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme) according to the manufacturer’s instructions and then sequenced on the MGISEQ-2000 platform.
5hmC hMeDIP-seq library construction and sequencing
DNA was purified from tissues according to the manufacturer’s instructions. 5hmC DNA immunoprecipitation (hMeDIP) was performed as previously described. Briefly, genomic DNA was digested with proteinase K at 55°C overnight and then with RNase A at 37°C for 1 h. Genomic DNA was purified by phenol/chloroform extraction and recovered by ethanol precipitation. Purified genomic DNA was sonicated to an average size of 200–400 bp and heat-denatured (95°C, 10 min). Then, 5 μg of fragmented genomic DNA was diluted in 500 μL DNA-IP buffer [10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100] and pre-cleared with 50 μL protein A/G beads at 4°C for 3 h. Five percent of the pre-cleared genomic DNA was saved as an input sample. The DNA-IP sample was incubated with 5 μg 5hmC antibody (Active Motif, 39769) at 4°C overnight and then with 50 μL protein A/G beads for 4 h at 4°C. Three washes for a total of 30 min were then performed to remove non-specifically bound antibodies. The beads were then treated with 200 μL TE buffer (pH 8.0) plus proteinase K for at least 3 h at 1000 rpm, 55°C in a thermomixer. The DNA was then purified by phenol/chloroform extraction followed by ethanol precipitation. Purified DNA was dissolved in ultrapure H2O, and libraries were constructed using a VAHTS Universal DNA Library Prep Kit for MGI (Vazyme) according to the manufacturer’s instructions. Libraries were then sequenced on the MGISEQ-2000 platform.


title: Gene expression analysis in murine muscle stem cells after denervation

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Background: Skeletal muscle function crucially depends on motor innervation and after injury on the resident muscle stem cells (MuSCs). However, it is poorly understood how innervation affects MuSC properties.  Methods: We investigated the alterations of MuSCs and their immediate niche, the myofiber, after denervation in a surgery-based mouse model of unilateral sciatic nerve transection. FACS-isolated MuSCs were subjected to transcriptomics and proteomics analyses to investigate which changes occur after denervation. We performed Cardiotoxin-induced muscle injury, MuSC transplantation and floating myofiber cultures to assess MuSC functionality after denervation in addition to bioinformatics and histological analyses.  Results: We observed a significant increase in the number of MuSCs (Pax7 positive; p-value= 0.0441), proliferating MuSCs (Pax7/Ki67 positive; p-value= 0.0023), activated MuSCs (MyoD positive; p-value= 0.0016) and differentiating MuSCs (Myog positive; p-value= 0.0057) after denervation. This aberrant activation and premature commitment of MuSCs to the myogenic lineage was accompanied by profound alterations on the mRNA (2613 differentially expressed genes, adj. p-value <0.05) and protein (1096 differentially abundant proteins, q-value <0.05) level after denervation. MuSCs from denervated hosts still engrafted and fused to form new myofibers irrespective of the innervation status of the recipient, suggesting the MuSC niche is driving alterations in MuSCs after denervation. The myofiber transcriptome after denervation showed massive changes in the general expression profile (10492 DEGs, p-value <0.05) and in several predicted secreted factors. Incubation of myofiber-associated MuSCs with supernatant from denervated myofibers increased cluster formation, reinforcing myofibers as a source of secreted factors driving MuSC alterations after denervation. Opn and Tgfb1 showed an increased secretion by denervated myofibers (30-fold and 6000-fold, respectively), and incubation with Tgfb1 alone induced Junb expression in myogenic cells, one of the genes highly upregulated in MuSCs after denervation (p-value= 1.85e-18, log2fc= 3.27), demonstrating that myofiber-secreted ligands influence MuSC gene expression. A combination of skeletal muscle injury and denervation led to reduced numbers of proliferating MuSCs (Sham: 47 vs DEN: 19.75 cells per cross section 10 days post-injury) and sustained high levels of developmental myosin heavy chain (Sham: 1 % vs DEN: 40 % of all myofibers 21 days post-injury), indicating hampered MuSC functionality due to changes in the microenvironment.  Conclusion: Denervation of skeletal muscle causes alterations in myofiber secretion, leading to activation and profound changes of MuSCs, ultimately resulting in a reduced regenerative capacity. As these alterations are partially reversible, MuSCs are a promising target for novel treatment options for neuromuscular disorders and peripheral nerve injuries.

overall_design: 8 samples in 2 groups: 4 samples per group (DEN, sham)

first: Henriette

last: Henze


title: Phase separation-competent FBL shapes nucleolar function and translation in leukemogenesis (RNA-Seq)

summary: Exploring the mechanism of transformation and propagation of acute myeloid leukemia is still the key to solving its refractory and relapse-prone problems. Phase separation refers to the process of specific aggregation of biological macromolecules through multivalent binding, and then leads to the functional sectorization in cell. Despite the fact that phase separation has been related to the dysregulation of various cellular processes, its role in the malignant transformation and development of AML is still less characterized. Nucleolus, as a multilayer condensate formed by phase separation, is an important place for the initiation of ribosome formation, and its function is directly related to protein translation. High-resolution imaging and fluorescence recovery after photo-bleaching experiments decode the positive regulatory relationship between the phase separation of FBL and the structure and function of nucleoli. Here, we used polysome profiling coupled with RNA-seq to depict transcriptome of AML cells with or without FBL knockdown.

overall_design: Polysome profiling coupled with RNA-seq to depict transcriptome of AML cells with or without FBL knockdown.

first: Lin

last: Yang

first: Penglei

last: Jiang

first: Pengxu

last: Qian


title: Phase separation-competent FBL shapes nucleolar function and translation in leukemogenesis (rRNA 2'-O-me modification)

summary: Exploring the mechanism of transformation and propagation of acute myeloid leukemia is still the key to solving its refractory and relapse-prone problems. Phase separation refers to the process of specific aggregation of biological macromolecules through multivalent binding, and then leads to the functional sectorization in cell. Despite the fact that phase separation has been related to the dysregulation of various cellular processes, its role in the malignant transformation and development of AML is still less characterized. Nucleolus, as a multilayer condensate formed by phase separation, is an important place for the initiation of ribosome formation, and its function is directly related to protein translation.High-resolution imaging and fluorescence recovery after photo-bleaching experiments decode the positive regulatory relationship between the phase separation of FBL and the structure and function of nucleoli. Here, we used RiboMeth-seq to examine rRNA 2’-O-me modification changes influenced by FBL knockdown in AML cells.

overall_design: Examination of rRNA 2’-O-me modification changes influenced by FBL knockdown in AML cells.


title: Gene expression profile of alveolar macrophages (AM) from bleomycin treated mice.

city: Durham

first: Mari

last: Shinohara

address: 207 research drive

department: Immunology

institute: Duke University Medical School

summary: Osteopontin (OPN, Spp1-/-)  is considered detrimental in pulmonary fibrosis. However, effect of OPN produced by AMs during pulmonary fibrosis is not known. We used bulk RNA sequencing to analyze the effect of OPN in AMs from bleomycin treated mice.

overall_design: Alveolar macrophages of wild type (WT) and osteopontin knock-out (Spp1-/-) mice were isolated by Fluorescence-activated cell sorting (FACS) according to the cell surface markers and analyzed using scRNAseq.

first: Aggarwal

last: Nupur


title: Gene expression analysis in murine muscle fibers and whole muscle after denervation

overall_design: 16 samples in 4 groups: 4 samples per group (whole muscle DEN, whole muscle sham, muscle fiber DEN, muscle fiber sham)


title: Analysis of exosomal miRNAs in MCF7 cells regulated by LSD1

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

summary: Lysine specific demethylase 1 (LSD1) is an important histone demethylase that mediates metastasis in luminal breast cancer. Exosomes play a major role in cell-to-cell communication. Thus, the characterization of miRNAs of exosome in MCF7 cells regulated by LSD1 is imperative in clarifying intercellular signaling.

overall_design: miRNA-seq in exosomes isolated from scrambled control siRNAs transfected MCF7 cells (NC), LSD1-specific siRNAs transfected MCF7 (KD), MCF7 cells transfected with LSD1-specific siRNAs and LSD1 rescue plasmid (RE). Each cell type have 3 biological replicates.

first: Ziyu

last: Liu


title: Analysis of miRNAs in MCF7 cells regulated by LSD1

summary: Lysine specific demethylase 1 (LSD1) is an important histone demethylase that mediates metastasis in luminal breast cancer. Thus, the characterization of miRNAs in MCF7 cells regulated by LSD1 is imperative in clarifying intercellular signaling.

overall_design: miRNA-seq in scrambled control siRNAs transfected MCF7 cells (NC), LSD1-specific siRNAs transfected MCF7 (KD), MCF7 cells transfected with LSD1-specific siRNAs and LSD1 rescue plasmid (RE). Each cell type have 3 biological replicates.


title: Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage [RNA-seq]

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: To investigate the function of IRF1 in chondrocytes, we performed transcriptome analysis in priamry mouse articular chondrocytes. Using control and Irf1 siRNA, gene expression profiles were analyzed in depletion of Irf1

overall_design: RNA sequencing data using samples from control and Irf1-knockdown primary mouse articular chodnorcytes

first: Yongsik

last: Cho

first: Hyeonkyeong

first: Geunho

last: Yook


title: RNA Sequencing of npr-15(tm12539) and  wild type (WT) N2 C elegans

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

summary:
Purpose: To uncover immune genes and pathways that are modulated by the GPCR/NPR-15
Methods: RNA was extracted from synchronized L4 stage npr-15(tm12539) and WT animals grown at 20 C using Qiagen extraction kits and following standard methods
Results: RNA seq analyses shows enriched and signficant upregulated immune, neuropeptide, synaptic signaling and metabolism genes and pathways that are dependent on NPR-15
Conclusions: Our study uncovered NPR-15 to be modulator of the innate immunity in C. elegans

overall_design: RNA seq  profiles of L4-stage npr-15(tm12539) and wild type (WT) C elegans animals were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000 platform.

first: Alejandro

last: Aballay


title: Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors

city: Tampere

first: Kirsi

last: Rautajoki

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere university

summary: Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness, exceptionally low mutation rate, and aberrant but still unresolved epigenetic regulation. To evaluate methylation associated regulation in AT/RTs, we compared them to medulloblastomas and choroid plexus tumors by integrating DNA methylation (507 samples), gene expression (120 samples), and public transcription factor (TF) binding data. We showed that elevated DNA methylation masks the binding sites of TFs driving neural development and is associated with reduced transcription for specific neural regulators in AT/RTs. Hypermethylated sites largely behaved similarly in AT/RTs and pluripotent stem cells, revealing DNA methylation -driven halted cell differentiation. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 members, like EZH2, and linked to suppressed genes with a role in neural development and tumorigenesis. The obtained results highlight and characterize these DNA methylation programs as drivers of AT/RT malignancy.

overall_design:
The cohort has material from 2 AT/RT patients, 3 MB patients and 5 Coroid plexus tumor (PLEX) patients. It consists of 10 RNA-seq samples and 10 RRBS samples from the same tumours, but due to ethical reasons, the raw material cannot be published. Processed files (Gene counts and the methylation percentages in regional level (1000bp regions) are provided.

Additionally, CUT&RUN data from 4 cell lines (3 AT/RT, 1 MB) with two technical replicates each. The processed MACS3 peaks are provided.

CUT&RUN sequencing for NEUROD1 for 3 AT/RT cell lines as well as 1 MB cell lines.

***The submitter declares that Raw data cannot be published due to ethical reasons***

first: Meeri

last: Pekkarinen

first: Kristiina

last: Nordfors

first: Joonas

last: Uusi-Mäkelä

first: Ville

last: Kytölä

first: Anja

last: Hartewig

first: Laura

last: Huhtala

first: Minna

last: Rauhala

first: Henna

last: Urhonen

first: Sergei

last: Häyrynen

first: Ebrahim

last: Afyounian

first: Olli

last: Yli-Harja

first: Wei

last: Zhang

first: Pauli

last: Helen

last: Lohi

first: Hannu

last: Haapasalo

first: Matti

last: Nykter

first: Juha

last: Kesseli

middle: J


title: Transcriptional responses of fission yeast to DNA damage.

city: Hefei

first: Bingbing

last: Ren

state: Anhui

address: University  of  Science  and  Technology  of  China,  443  Huangshan  Road, Hefei, Anhui

summary: We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to DNA damage. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in response to four DNA damage agents: Camptothecin, Hydroxyurea, Methyl methanesulfonate, Phleomycin.

overall_design: Examination expression profiles of lncRNAs and mRNAs in response to four DNA damage agents in fission yeast.

first: Tianyi

last: Yu

first: Ruikun

last: Wu

first: Ge

last: Shan


title: Extensive transcriptome alteration in response to acute heat stress in porcine immature Sertoli cells

city: jingzhou

first: wu

middle: zi

last: wei

state: Hubei

department: Animal Science

institute: yangtze university

summary: Heat stress (HS) could damage animal reproduction, while the mechanisms are still required to be better understood. Here, we showed that incubation of porcine immature Sertoli cells (iSCs) at 43 °C for 30 minutes followed 36h recovery under normal culture could inhibit the proliferation, promote apoptosis and increase the lactate production. Then, we profiled mRNA expression by RNA sequencing on Control (before HS), HS0.5 (0h after HS) and HS0.5-R36 (36h recovery after HS) groups of iSCs. We identified 126 (92 up- and 64 down-regulated), 3372 (2076 up- and 1296 down-regulated) and 3096 (1772 up- and 1324 down-regulated) differentially expressed (DE) mRNAs respectively in HS0 vs. Control, HS0-R36 vs. HS0 and HS0-R36 vs. Control comparisons. Gene ontology (GO ) enrichment found multiple significantly enriched biological pathways involved in different comparisons, including cellular response to heat, heat shock protein binding, regulation of cellular response to stress, RNA polyadenylation, sterol biosynthetic process, positive regulation of stress-activated MAPK cascade, chaperone-mediated protein folding, ATPase activity, cell cycle process and DNA replication etc. KEGG analysis showed the changed pathways, including cell cycle, MAPK, P53, PI3K-AKT, GnRH, HIF1, Wnt, cAMP signal pathways and Glycolysis/Gluconeogenesis etc. RT-qPCR validation of 9 DEGs (DNAJB1, TRAF6, INSIG1, GADD45G, HDAC6, FKBP4, SERPINE1, PFKP and GALM) showed the expression change trend of most DEGs (except TRAF6) consistent with the RNA-seq. Moreover, 6 of HSPs (HSPA6, HSPB1, HSPD1, HSP90AA1, HSP90AB1 and HSPH1) were validated by RT-qPCR and 5 of 6 (except HSP90AB1) showed the similar expression trend to RNA-seq results. Further validation of HSP90AA1 on protein level via immunostaining and westernbloting showed similar expression trend to RT-qPCR and RNA-seq. Taken together, HS could extensively change the global transcriptome, especially HSPs, to affect proliferation, apoptosis and metabolite production of pig iSCs.

overall_design: The important mRNAs on Control (before HS), HS0.5 (0h after HS) and HS0.5-R36 (36h recovery after HS) groups of  porcine immature Sertoli cells.

first: Cai-Xia

last: Yang

first: Zhi-Qiang

last: Du


title: Expression profiles of lncRNAs and mRNAs in fission yeast.

institute: University of Science and Technology of China

summary: We explored transcriptional profiles of the fission yeast Schizosaccharomyces pombe. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in wild type cells.

overall_design: Examination expression profiles of lncRNAs and mRNAs in fission yeast.


title: Expression profiling of Hsf5 WT and Hsf5 KO testes in mouse on postnatal day 16

status: Public on Mar 03 2024

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

institute: WuHan University

summary: To investigate the role of HSF5 protein in mouse reproduction, We collected WT or Hsf5+/- (control) and Hsf5-/- testes at postnatal day 16 (P16) for RNA sequencing.

overall_design: To investigate the role of HSF5 protein in mouse reproduction, We collected WT or Hsf5+/- (control) and Hsf5-/- testes at postnatal day 16 (P16) for RNA sequencing, three replication for every group.

first: Mengcheng

last: Luo

first: Rong

last: Liu

first: Qi

last: Sun

first: Zhiyi

last: Chen


title: Establishment of epithelial inflammatory injury model using adult kidney organoids [RNA-seq]

city: 山东省

first: Haoran

state: 山东省

address: wenhuaxi road 44

institute: shandong university

summary: Kidney organoids are emerging as an increasingly applied model system to hold great promise for transplantation to individuals with end-stage renal disease and as a useful tool for kidney research. Multiple iPSC-derived renal organoids have been established to understand kidney development and disease. However, few disease models originated from adult renal tissue with fully mature cell fates have been set up to recapitulate kidney inflammation or fibrosis. Here we created a novel organoid model that faithfully representing the cellular state of inflammatory response during the progression of renal disease upon TNFα exposure. scRNA-seq showed signatured inflammatory chemokines, cytokines and inflammation-associated signaling pathways were activated in TNFα-treatment organoids together with injury-associated markers such as LCN2 and CLU. Donor age is associated with TNFα-induced inflammatory reaction in organoids. Kidney organoids from young donors showed more transcriptional changes by down-regulation of TGFβ and extracellular matrix genes. In summary, we established an in vitro TNFα-treated kidney organoid model that representing the cellular state of the inflammatory response during renal disease progression and provided a novel tool for studying inflammation-related kidney disease and drug discovery.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for kidney organoids.

first: Liqiang

last: Guo

first: Jiabei

last: Lian

first: Huili

last: Hu


title: Establishment of epithelial inflammatory injury model using adult kidney organoids [scRNA-seq]

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for kidney organoids.


title: The effect of high fat diet on mouse prostate development

city: Boston

first: Christina

last: Sharkey

state: MA

address: 99 Brookline Ave Rm 389

department: Urology

institute: Beth Israel Deaconess Medical Center

summary: Steroid 5α reductase 2 (SRD5A2) is the predominant enzyme responsible for prostatic development and growth. Despite the introduction of steroid 5α-reductase inhibitors (5ARI) for benign prostatic hyperplasia (BPH), the progression of LUTS is only slowed by 34% with 5ARI-response. Previous literature establishes link between obesity and BPH progression. We hypothesize that high fat diet is associated with prostate development.

overall_design: Single-cell RNA sequencing of fresh mouse prostate samples

first: Sharkey

last: Christina

first: Xingbo

last: Long

first: Ra'ad

last: Al-Faouri

first: Douglas

last: Strand

first: Aria

middle: F

last: Olumi

first: Zongwei

last: Wang


title: Type 1 immunity enables neonatal thymic ILC1 production

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

summary: We used scRNA seq to analyze mice organ cells (liver, spleen, thymus and bone marrow) as well as neonatal thymus organ cultures that were treated cytokines IL-12 and IL-18.

overall_design: Two sets of scRNAseq samples were created. The first set consists of four samples, all derived from supernatant of neonatal thymus organ cultures (Control, IL-18 treated, IL-12 treated, IL-12 + IL-18 treated); the second set consists of eight samples, one for every combination of organs (Thymus, Spleen, Bone Marrow, Liver) and mice age (Neonate, Adult).

first: Peter

last: Tougaard

first: Mario

last: R Pérez

first: Wolf

last: Steels

first: Jelle

last: Huysentruyt

first: Jessica

last: Vetters

first: Tatyana

last: Divert

first: Amanda

last: Gonçalves

first: Ria

last: Roelandt

first: Nozomi

last: Takahashi

first: Sophie

last: Janssens

first: Terkild

last: B Buus

first: Georges

last: Leclercq

last: Vandenabeele


title: PRPF19 Inhibition Attenuates Non-Small Cell Lung Cancer Progression through Impairing Citron Kinase-controlled Cytokinesis and Enhancing Anti-tumor Immune Responses [Prpf19_KP-1_RNAseq]

city: XuHui

first: Shuaihu

last: Li

state: ShangHai

address: No.131 Dongan Road

institute: Fudan University

summary: Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related death, primarily due to limited therapeutic targets and the emergence of drug resistance. In this study, we conducted CRISPR knockout screens to identify the pre-mRNA processing factor 19 (PRPF19) as a potential therapeutic target for NSCLC. Our findings revealed that PRPF19 is highly expressed in NSCLC, and its expression is negatively correlated with the clinical outcomes. Through functional validation, we confirmed that genetic ablation of PRPF19 significantly attenuated cancer progression both in vitro and in vivo. Mechanistically, we discovered that PRPF19 plays a crucial role in regulating the precise location of Citron Kinase (CIT) within the contractile ring, thereby sustaining the normal cytokinesis processes. Inhibition of PRPF19 resulted in cytokinesis failure, leading to micronuclei formation and activating the anti-tumor immune response through the TBK1-IFNs pathway. Taken together, our results demonstrate the critical involvement of the PRPF19-CIT axis in NSCLC progression and suggest that targeting PRPF19 represents a promising therapeutic approach for NSCLC patients.

overall_design: To investigate the signaling pathway regulated by PRPF19 in our model, we established KP-1-shPrpf19 stable cell lines utilizing a doxycycline (Dox)-inducible short hairpin RNA (shRNA) system. And then, we performed gene expression profiling analysis for control cell lines (KP-1-shLacZ) and it’s KD cell lines (KP-1-shPrpf19).

first: Tian

last: Xu

first: Xinlei

last: Cai

first: Yan

last: Shang


title: FTO suppresses cardiac fibrosis after myocardial infarction via m6A-mediated epigenetic modification [MeRIP-seq]

city: Shanghai

first: Jian

last: Wang

address: Pujian Load 160th, Pudong New Aera

institute: Shanghai Jiao Tong University School of Medicine

summary: Cardiac fibrosis is common in cardiovascular diseases. N6-methyladenosine (m6A) is one of the most common modifications in eukaryotic mRNAs. Previous research has suggested that m6A modification is vital in cardiovascular diseases. The underlying targets of FTO were selected through transcriptome sequencing (RNA-seq) combined with methylated RNA immunoprecipitation sequencing (MeRIP-seq). According to MeRIP-seq and RNA-seq, FTO inhibited collagen synthesis in CFs.

overall_design: Neonatal rat cardiac fibroblasts (NRCFs) were collected from healthy Sprague-Dawley rats within 3 days post-birth. NRCFs were transfected with the plasmid of FTO and Vector and performed comparative m6A expression profiling between FTO and Vector groups.

first: Yanyan

first: Lijie

last: Deng

first: Yafang

last: Zha

first: Song

last: Zhang


title: Landscape of TFs binding in mouse early embryos [Bisulfite-seq]

first: Gran

last: Young

state: --- Select a state ---

address: 1239th, Siping Road, Yangpu district

institute: Tongji University

summary: In mammals, early lineage specification originates from the establishment of cell polarization in early embryos, before providing the foundation for all somatic development. Although there have been heated debates about whether transcription factors (TFs) or epigenetic information plays the dominant role in cell fate decisions, the precise annotation of TFs remains largely elusive in early embryos, restricting the functional study of developmentally important TFs. Here, we investigated the genome-wide landscapes of two known triggers of mouse embryo polarization: transcription factor AP-2 gamma (Tfap2c) and TEA domain transcription factor 4 (Tead4). We found that Tfap2c can bridge the connection between the promoter and the proximal enhancer, and further facilitate the functions of downstream Tead4 and Klf5 in boosting polarization. Our study also implicated that Rarg-initiated active demethylation might be a prerequisite for proper Tfap2c functioning. Furthermore, the results demonstrated that both genomic imprinting and nucleotide polymorphism can instruct TF binding, leading to allele-specific expression in early embryos. Overall, our study characterized TF dynamics during the peri-implantation stage and revealed their spatiotemporal interactions with the epigenetic environment in driving polarization and lineage specification.

overall_design: DNA methylation levels in early 2-cell stage between WT and LY2955303 samples.

first: Guang

last: Yang

first: Rui

last: Gao

first: Shaorong

first: Cizhong

last: Jiang

first: Jiayu

last: Chen


title: PRPF19 Inhibition Attenuates Non-Small Cell Lung Cancer Progression through Impairing Citron Kinase-controlled Cytokinesis and Enhancing Anti-tumor Immune Responses [PRPF19_H2009_RNAseq]

overall_design: To investigate the signaling pathway regulated by PRPF19 in our model, we established H2009-shPRPF19 stable cell lines utilizing a doxycycline (Dox)-inducible short hairpin RNA (shRNA) system. And then, we performed gene expression profiling analysis for control cell lines (H2009-shLuc) and it’s KD cell lines (H2009-shPRPF19).


title: Lamtor5 maintains immune homeostasis by regulating lysosomal activity via v-ATPase and mTOR signaling

city: chongqing

first: zhou

last: sha

address: 55 University City South Road, Shapingba District, Chongqing, China

institute: chongqing university

summary: Despite accumulating evidences linking defective lysosome function with autoimmune diseases, how the catabolic machinery is regulated for immune homeostasis remains largely unknown. Lamtor5 is a subunit of the Ragulator mediating mTORC1 activation in response to amino acids, but its action mode and physiological role are yet to be addressed. Here we unexpectedly found that myeloid Lamtor5 ablating mice developed spontaneous inflammation and systemic lupus erythematosus (SLE)-like manifestation. Loss of Lamtor5 in macrophages caused impaired vacuolar H⁺-ATPase (v-ATPase) activity, lysosome de-acidification, and aberrant mTORC1 activation, correlating with undesirable inflammatory responses. Mechanistically, we showed that Lamtor5 physically associated with ATP6V1A, an essential subunit of v-ATPase, and promoted the V0/V1 holoenzyme assembly for lysosome acidification. Notably, binding of Lamtor5 to v-ATPase substantially affected lysosomal tethering of Rag GTPase and weakened its interaction with mTORC1 for activation. Importantly, defective Lamtor5 expression, along with impaired lysosomal function and hyperactivation of mTORC1, was corroborated in peripheral blood mononuclear cells (PBMCs) of SLE patients and correlated with disease severity. Overall, our findings establish Lamtor5 as a new lysosome regulator, and elucidate an unappreciated mechanism that coordinates catabolic and anabolic pathways to bolster immune homeostasis preventing autoimmunity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDMs of HBXIPΔLysM mouse and wild type control

first: Liyun

last: Shi

first: Wei

first: Zhou

last: Sha


title: Effect of knockdown of Musashi-1 in Group 3/4 medulloblastomas cells

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

summary: Groups (Grp) 3 and 4 are aggressive molecular subgroups of medulloblastoma (MB), with high rates of leptomeningeal dissemination. To date, there is still a paucity of biomarkers for these subtypes of MBs. In this study, we investigated the clinical significance and biological functions of MSI1 in Grp3/Grp4-MBs. To that, we identified that the MSI1 knockdown sensitized D283 Med cells to cisplatin treatment by enhancing cell apoptosis and modulated cancer-related pathways. The results of the present demonstrate that MSI1 may play a role as biomarker for Grp3/Grp4-MBs. In addition, MSI1 knockdown combined with cisplatin may offer a potential strategy to be further explored in Grp3/Grp4-MBs.

overall_design: Gene expression profiles from medulloblastoma cell line samples (n=6) using high throughput sequencing.

first: L

last: Tone

first: C

middle: A

first: E

middle: T

last: Valera

last: Carlotti

first: R

last: Queiroz


title: Focal epilepsy human surgical samples

city: PARIS

first: Franck

last: Bielle

address: 83 Bd de l'Hopital

department: Paris Brain Institute

institute: Sorbonne Université

summary: We identified diffuse lesions made of BRAF V600E-mutant CD34-immunopositive stellar cells in human samples resected to cure drug-resistant focal epilepsy. We performed single-nuclei RNAseq 5' 10X on three human brain samples (two BRAF mutant samples and one BRAF wildtype sample as control) in order to identify the molecular phenotype of CD34+ cells.

overall_design: The three samples are: (i) as control, one BRAF wildtype medial temporal lobe epilepsy associated  hippocampal sclerosis (MTLE-HS), (ii) one BRAF mutant medial temporal lobe epilepsy associated  hippocampal lesion, (iii) one BRAF mutant epilepsy-associated  neocortical lesion

first: Muriel

last: Andrieu

last: Letourneur

first: Vincent

last: Navarro


title: Landscape of TFs binding in mouse early embryos [RNA-seq]

first: Gran

last: Young

overall_design: Gene expression comparison in 8-cell stage among samples w/ or w/o Tfap2c interference.

first: Guang


title: Landscape of TFs binding in mouse early embryos [HiCuT]

overall_design: HiCuT experiment on E9.5 placenta, mice crossed by c57(m) x pwk(p)

first: Rui

last: Yang


title: Landscape of TFs binding in mouse early embryos [CUT&RUN-seq]

overall_design: TFs binding dynamics in early embryos.

last: Gao

first: Shaorong

first: Cizhong


title: Landscape of TFs binding in mouse early embryos

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

overall_design: Refer to individual Series


title: lncRNA-seq analysis CARM1 knockdown effect on MDA-MB-231 cells

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

summary: Previous studies reported that NEAT1 and its partner p54nrb are necessary for CARM1 to associate with paraspeckles and H3R26 methylation. There are also reports that CARM1 is essential for LincGET's role in guiding the ICM lineage in mouse embryos. We speculate that there may be a connection between CARM1 and lncRNA. In order to verify our guess, we conducted lncRNA-seq experiments against CARM1 control or siRNA in MDA-MB-231 cells to explore the lncRNA that may be regulated downstream of CARM1. Here, we showed that CARM1 and HIF1A co-upregulates the expression of  MALAT1 in hypoxia pathway to promote carcinogenesis and metastasis in triple-negative breast cancer cells. These results indicate that there is a connection among CARM1, HIF1A and MALAT1 in triple-negative breast cancer.

overall_design: CARM1 siRNA or control were transfected into MDA-MB-231 cells (n=1 per group) for 48 hours. Total RNA was extracted using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.

first: Dandan

last: Feng

first: Yan

last: Wang


title: Maternal folic acid overconsumption in mice leads to sex-specific transcriptional alterations in cerebral cortex in offspring

city: Barcelona

first: Marta

last: Cosin Tomas

state: Spain

address: Dr. Aiguader, 88

department: Child Health and environment

country: Spain

institute: ISGlobal

summary:
Recent concerns have been raised regarding high folate intake during pregnancy and lactation, particularly following food fortiﬁcation and increased vitamin supplement use. Epidemiologic studies have shown that high folic acid (FA) intake can negatively impact motor and neurocognitive development in offspring.
We used microarray to investigate the mechanisms by which a supplemented diet containing 5-fold higher FA than recommended (FASD) affects brain function in both male and female offspring.

overall_design: At weaning, wild-type C57BL/6 female mice were placed for a month on a control diet or a FASD, and then mated to study offspring. Diets were maintained throughout pregnancy and lactation. We conducted several behavioral tests on pups before sacrificing them at weaning. Brains were collected to conduct gene expression analysis by microarray using Affymetrix Clariom S array_Mouse Chip.

last: Cosín-Tomás

last: Luan

first: Daniel

last: Leclerc

first: Olga

last: Maleysheva

first: Nidia

last: Lauzon

first: Renata

last: Bahous

first: Karen

last: Christensen

first: Marie

last: Caudill

first: Rima

last: Rozen


title: Variations of transcriptome along intestinal  of mice under two-month food arsenic exposure

city: Dongguan

first: Xin

last: Liu

state: Guangdong

address: No.1 Xincheng Blvd, Songshan Lake National High-tech Industrial Development Zone

department: School of Public Health

institute: Guangdong Medical University

summary: After 2 months arsenic exposure, among the 33,492 surveyed genes, 13,005 genes were detected with expression (mean FPKM > 1) in 27 samples of the intestinal tracts (ileum, cecum, and colon) of control and test mice. Among the detected genes, and in comparison to the control and test mice, 328, 579 and 90 dierentially expressed genes (DEGs) were obtained from ileum, cecum, and colon, respectively (FDR < 0.05, Log2 Fold Change > 1). To explore the potential functions of DEGs in the three intestines, we performed GO and KEGG pathway enrichment analysis. Analysis revealed by machine learning of the transcriptome results showed that significantly affected the gene network of pathways related to disease and immunity in the intestine. The results demonstrated that food arsenicals change the intestinal transcriptome significantly, suggest that the host genes might participate in arsenical biotransformation.

overall_design: Expression profile of the intestinal tracts in the rats after two-month food arsenic exposure

first: Lianxian

last: Guo