title: Jiedu Xiaozheng Yin extract targets cancer stem cell signaling and inhibits patient-derived organoid and xenograft tumor growth in colorectal cancer

status: Public on Nov 23 2023

city: Fuzhou

first: Zhiyun

last: Cao

state: 福建Fujian

address: 1# Qiu Yang Road

institute: Fujian university

summary: We used RNA-sequencing (RNA-Seq) to analyze gene expression in CRC cells treated with JXY. Next, we confirmed these findings on the protein level using western blot and immunofluorescence. Finally, we analyzed the stemness of CRC cells treated with JXY using matrigel spheroid assay and verified it with CRC patient-derived organoids (PDOs) and xenograft mice models.

overall_design: CRC cell line HCT116 was treated byJXY for 48 h and then performed RNA-Sequencing (RNA-Seq) by sequencing company.

first: Hailan

last: Feng

first: Jian

last: Du

first: Hong


title: ATM Loss and Therapeutic Vulnerabilities in Bladder Cancer

status: Public on Nov 24 2023

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

type: Expression profiling by high throughput sequencing

summary: ATM plays a central role in the cellular response to DNA damage and ATM alterations are common in several tumor types including bladder cancer.  However, the specific impact of ATM alterations on therapy response in bladder cancer is uncertain. Here, we combine preclinical modeling and clinical analyses to comprehensively define the impact of ATM alterations in bladder cancer.  We show that ATM loss is sufficient to increase sensitivity to DNA damaging agents including cisplatin and radiation.  Furthermore, ATM loss drives sensitivity to DNA repair targeted agents including PARP and ATR inhibitors.  ATM loss alters the immune microenvironment and improves anti-PD1 response in preclinical bladder models but is not associated with improved anti-PD1/PD-L1 response in clinical cohorts. Finally, we show that ATM expression by IHC is strongly correlated with response to chemoradiotherapy.  Together these data define a potential role for ATM as a predictive biomarker in bladder cancer.

overall_design: RNA-seq of bladder tumors from BBN and BBN-ATM-KO tumor-bearing mice. When tumors reached 500 mm3 in size, mice were sacrificed and tumors harvested with half of the tumor snap-frozen for RNA sequencing (RNA-seq).

first: Yuzhen

last: Zhou

first: Kent

last: Mouw


title: FANC1 affects R-loop distribution resulting in tumor progression in LUAD

city: Guiyang

first: Fuzhou

last: Tang

state: Guizhou

address: Dangwu Town

country: China

institute: Guizhou Medical University

summary: To plot the R-loop landscape of LUAD cells, we conducted DRIP-seq using S9.6, an anti-DNA/RNA hybrid antibody.We next tested the effect of FANCI deficiency on R-loop distribution and found that FANCI knockout clearly altered the R-loop landscape, showing a strong loss trend.Our analysis revealed that changes in R-loop distribution mediated by FANCI deficiency blocks the activity of the Ras signaling pathway, thereby suppressing tumor-cell proliferation and dissemination. Importantly, our study highlights the causal role of FANCI-mediated changes in R-loop distribution that leads to LUAD development

overall_design: R-loop profiles of FANCI knockdown PC-9 cells

first: Yan

last: Gu

first: Xianpeng

last: Wei


title: Hepatocyte growth factor(HGF) and insulin-like growth factor-1(IGF-1) for repair of bone-cartilage defects in bone marrow mesenchymal stem cells in a rabbit model of postmenopausal

city: Weifang

first: Jiaqi

last: Guan

address: Shandong Second Medical University, No. 7166 Baotong West Street, Weicheng District, Weifang City (Fuyanshan Campus)

department: School of Clinical Medical

institute: Weifang Medical University

summary: In postmenopausal osteoporosis (PMOP), the differentiation of bone marrow mesenchymal stem cells (BMSCs) is unbalanced,because of the lack estrogen, that is, osteogenic differentiation is reduced, adipogenic differentiation is increased.To investigate the mechanism of aberrant differentiation of BMSCs in PMOP, we performed transcriptome sequencing of Bone marrow mesenchymal stem cells in a postmenopausal osteoporosis model(PMOP-BMSCs)and Bone marrow mesenchymal stem cells in a healthy control model(Normal-BMSCs).In this analysis, the reference transcriptome sequencing of 6 samples was completed, and the genome alignment of each sample was obtained by aligning the reads to the reference genome, and the expression of protein-coding genes was analyzed based on the alignment results. According to the expression of protein-coding genes in different samples, differential screening was performed, and a total of 1 differential group was set up.

overall_design: We established an induced postmenopausal osteoporosis model using the method of removing bilateral ovaries;Then, the bone marrow mesenchymal stem cells of the osteoporosis rabbit model and the bone marrow mesenchymal stem cells of normal control rabbits were analyzed by RNA-seq for gene expression profiling；Comparative gene expression profiling of RNA-seq data from bone marrow mesenchymal stem cells for osteogenic, chondrogenic and adipogenic differentiation

first: Yahui

last: Wang

first: Feifan

last: Chen

first: Yilin


title: RILseq of VP882 phage activation in V. cholerae

city: Jena

first: Marcel

last: Sprenger

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

summary: Many, if not all, bacteria use quorum sensing (QS) to control gene expression and collective behaviours, and more recently QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or “listen in” on the host’s communication processes, in order to switch between lytic and lysogenic modes of infection. In this project, we studied the interaction of Vibrio cholerae, the causative agent of cholera disease, with the lysogenic vibriophage VP882. The lytic cycle of VP882 is induced by the QS molecule DPO (3,5-dimethylpyrazin-2-ol), however, the global regulatory consequences of DPO-mediated VP882 activation have remained unclear. Using a combination of transcriptomic, genetic, and biochemical approaches, we discovered that induction of VP882 results in binding of phage transcripts to the major RNA chaperone Hfq, which in turn outcompete and down-regulate host-derived Hfq-dependent small RNAs (sRNAs). VP882 itself also encodes Hfq-binding sRNAs and we demonstrate that one of these sRNAs, named VpdS, modulates the expression of multiple host and phage mRNAs through a base-pairing mechanism and thereby promotes phage replication. We further show that host-derived sRNAs can affect phage replication by interfering with the translation of phage mRNAs and thus might be part of the phage defence arsenal of the host. Taken together, our data draw a complex picture of post-transcriptional interactions occurring between host- and phage-derived transcripts that together determine the phage-mediated lysis program.

overall_design: To investigate the RNA-RNA interactome on Hfq upon VP882 activation, V. cholerae ∆tdh + JSP-1269 (VP882::kanR) and ∆tdh hfq::3XFLAG + JSP-1269 (VP882::kanR) were cultivated in M9 medium to OD600 of 0.2 and VP882 phage was activated by 25 µM DPO and 0.035% arabinose to induce the lytic cycle. Cells were subjected to RNA crosslinking, coimmunoprecipitation and ligation followed by chimeric cDNA synthesis and high-throughput sequencing. Three biological replicates for each condition are provided.

first: Malte

last: Siemers

first: Kai

last: Papenfort


title: RIPseq of VP882 phage activation in V. cholerae

overall_design: To idenity Hfq-binding RNAs in Vibrio cholerae during VP882 activation, we used RNA co-immunoprecipitation followed by RNA-sequencing (RIP-seq). V. cholerae ∆tdh + JSP-1269 (VP882::kanR) and ∆tdh hfq::3XFLAG + JSP-1269 (VP882::kanR) were cultivated in M9 medium to OD600 of 0.2 and VP882 phage was activated by 25 µM DPO and 0.035% arabinose to induce the lytic cycle. Cells were subjected to RNA-seq analysis. Three biological replicates for each condition are provided.


title: RNAseq of VP882 and VP882 ∆vpdS phage activation in V. cholerae

overall_design: To investigate the impact of the phage sRNA VpdS on transcriptional changes during VP882 activation, V. cholerae ∆tdh + JSP-1269 (VP882 Wt) and ∆tdh + JSP-1269 (VP882 ∆vpdS) were cultivated in M9 medium to OD600 of 0.2 and VP882 phage was activated by 25 µM DPO and 0.035% arabinose to induce the lytic cycle. Cells were harvested before induction (pre) and 30 min, 60 min post induction. Three biological replicates for each condition are provided.


title: RNAseq of VP882 phage activation in V. cholerae

summary: Many, if not all, bacteria use quorum sensing (QS) to control gene expression and collective behaviours, and more recently QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or “listen in” on the host’s communication processes, in order to switch between lytic and lysogenic modes of infection. In this project, we studied the interaction of Vibrio cholerae, the causative agent of cholera disease, with the lysogenic vibriophage VP882. The lytic cycle of VP882 is induced by the QS molecule DPO (3,5-dimethylpyrazin-2-ol), however, the global regulatory consequences of DPO-mediated VP882 activation have remained unclear.

overall_design: To investigate the transcriptional changes upon VP882 activation, V. cholerae ∆tdh + JSP-1269 (VP882::kanR) were cultivated in M9 medium to OD600 of 0.2 and VP882 phage was activated by 25 µM DPO and 0.035% arabinose to induce the lytic cycle. Cells were subjected to RNA-seq analysis. Three biological replicates for each condition are provided. To identify transcriptional start sites (TSS) of the VP882 phage, RNA samples of each time point were pooled and treated with terminator exonuclease to enrich primary transcripts.


title: Single cell transcriptomic analysis of skeletal muscle cells

city: Nuthetal

first: Tim

middle: Julius

last: Schulz

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition

summary: Single cell RNA-sequencing was used to analyze the cellular heterogeneity of mononucleated, non-myofiber cell populations and their transcriptional states in post-injury skeletal muscle

overall_design: Droplet-based scRNA-sequencing of non-myofiber mononucleated cells purified by fluorescence-activated cell sorting (FACS) from muscle samples of aged and young control female mice at 4 days post injury was performed.

middle: J

first: Marina

last: Leer


title: Transcriptomic analysis of muscle-resident fibro-adipogenic progenitor cells

summary: We used single cell RNA-sequencing analysis to analyze the transcriptomic heterogeneity of fibro-adipogenic progenitors in skeletal muscle

overall_design: To assess cellular functions in regenerating muscles we performed single cell-RNA sequencing (scRNA-seq) of fibro-adipogenic progenitors isolated from muscle samples of post-injury male mice at different ages.


title: Chromosomal integrons are genetically and functionally isolated units of genomes

city: Madrid

first: José

middle: Antonio

last: Escudero

state: Madrid

address: Av Puerta de Hierro s/n

department: Sanidad Animal

country: Spain

institute: Universidad Complutense de Madrid

summary: Integrons are genetic elements that enable bacterial adaptation by collecting new genes encoded in integron cassettes (ICs) to create a reservoir of adaptive functions. These cassettes typically lack their own promoters and rely on the integron platform for their expression. Integrons, well-known for spreading antibiotic resistance genes in clinically relevant Gram-negative species, include Mobile Integrons (MIs), that transport over 170 resistance genes. In contrast, Sedentary Chromosomal Integrons (SCIs), ubiquitous in Vibrio species, are primarily found within bacterial chromosomes. However, their functions are not related to antimicrobial resistance and are largely unexplored. SCIs, typified by the Superintegron (SI) in Vibrio cholerae, represent ancient and highly variable regions in bacterial genomes. The SI is extensive, housing 179 integron cassettes, mostly with unknown functions. Although 19 cassettes encode toxin-antitoxin (TA) systems, which stabilize the array, the intricacies of the SI are challenging to study due to its size and unique integrase. To investigate the SI's impact on V. cholerae, we developed the SeqDelTA approach, enabling the gradual deletion of the SI. This deletion facilitates the use of standard genetic tools without SI interference. Our in-depth analysis of the resulting ∆SI strain, covering various aspects, demonstrated no significant alterations in V. cholerae's physiology. Despite their extended coevolution, SCIs appear to be genetically isolated from the host genome.

overall_design: Gene expression analysis of RNA-seq data at exponential (OD600 0.8) and stationary (OD600 2.8) growth phase at 37˚C in LB medium of Vibrio cholerae N16961 (A001) and a V. cholerae ∆SI, where the superintegron has been deleted (B522) Three biological replicates per condition and strain are included.

first: Paula

last: Blanco

first: Filipa

last: Trigo da Roza

first: Laura

last: Toribio-Celestino

first: Lucía

last: García-Pastor

first: Niccolò

last: Casselli

first: Francisco

last: Ojeda

first: Baptiste

last: Darracq

first: Ester

last: Vergara

first: Álvaro

last: San Millán

first: Ole

last: Skovgaard

first: Didier

last: Mazel

first: Céline

last: Loot

middle: A


title: Lysine 117 residue is essential for the function of the hepatocyte nuclear factor 1α in pancreas

city: Beijing

first: Xian

last: Liu

address: 38 Life Science Park Street

institute: Beijing Institute of Life Omics

summary:
To determine the impact of K117E mutation on HNF1α functions, we generated a C57BL/6J knock-in mouse model wherein the lysine 117 (K117) was replaced with glutamic acid (E117) in the endogenous murine HNF1α locus by CRISPR/Cas9.
We then performed gene expression profiling analysis using data obtained from RNA-seq of pancreas of WT and HNF1αK1117E Hom mice of 9 weeks old (n=3/group)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pancreas of WT and HNF1αK1117E Hom mice of 9 weeks old (n=3/group).

first: Miao

last: Yu


title: α-Synuclein promotes H4R3me2s through interacting with BAF-PRMT5 complex

city: Sendai

first: Takaaki

last: Nakamura

address: 1-1 Seiryomachi, Aobaku

department: Department of Neuroscience and Organs

country: Japan

institute: Tohoku university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We conducted a screening for nuclear proteins which interact with α-synuclein by mass-spectrometry. As a result, we found that α-synuclein interact with BAF complex. Furthermore, overexpressed α-synuclein increased global H4R3me2s by promoting interaction between BAF complex and PRMT5 in cultered cells. In this study, we explored the influence of overexpressed α-synuclein on H4R3me2s by ChIP-seq using anti-H4R3me2s antibody.

overall_design: SH-SY5Y cells were neuronally differentiated over 10 days by culturing in 3%FCS DMEM supplemented wiith 10 µM RA for 6 days and DMEM without FCS supplemented with 50 ng/ml BDNF for following 4 days. α-synuclein was inducted for 3 days by 1 µg/ml doxycyline (Tet-on system). ChIP was conducted using H4R3me2s antibody.

first: Naoto

last: Sugeno

first: Kensyo

last: Ikeda


title: Time-dependent specific molecular signatures of inflammation and remodelling are associated with Trimethylamine-N-oxide (TMAO)-induced endothelial cell dysfunction

city: Singapore

first: Meyammai

last: Shanmugham

address: 8 Somapah Road

department: Science, Mathematics, and Technology

country: Singapore

institute: Singapore University of Technology and Design

summary: Cardiovascular diseases (CVDs) are leading causes of death worldwide. Endothelial dysfunction is a critical initiating factor contributing to CVDs, which progression involves the gut microbiome-derived metabolite Trimethylamine N-oxide (TMAO). Here, we aim to clarify the time-dependent pathways by which TMAO mediates endothelial dysfunction.

overall_design: We performed transcriptomics and metabolomics analyses on human microvascular endothelial cells (HMEC-1) treated with TMAO. Differentially expressed genes (DEG) and gene set enrichment analysis (GSEA) followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses allowed the identification of specific molecular pathways. Cell viability and reactive oxygen species (ROS) generation were also evaluated.

first: Arun

middle: G

last: Devasia

first: Yu

middle: L

last: Chin

first: Kang

middle: H

last: Cheong

first: Eng

middle: S

last: Ong

first: Sophie

last: Bellanger

first: Adaikalavan

last: Ramasamy

first: Chen

last: Leo


title: Droplet-based forward genetic screening of astrocyte-microglia communication mechanisms

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

country: USA

institute: Dana Farber Cancer Institute

summary: SPEACC-seq is a novel high-throughput method which enables forward genetic screens to identify cell-cell interaction mechanisms that uncovered an astrocyte-microglia regulatory circuit mediated by amphiregulin and IL33-ST2. signaling. Cell-cell interactions in the central nervous system (CNS) play central roles in neurologic diseases. However, little is known about the specific molecular pathways involved, and methods for their systematic identification are limited. For example, several factors mediate microglia-astrocyte interactions that promote CNS pathology, but less is known about regulatory interactions that limit tissue pathology. Here we report the development of SPEACC-seq (Stimulation, Perturbation, and Encapsulation of interACting Cells followed by Sequencing), a forward genetic screening platform which combines genome-wide CRISPR/Cas9 perturbations, cell co-culture in picoliter droplets, and microfluidic-based fluorescence activated droplet sorting to identify mechanisms of cell-cell communication. Using SPEACC-seq in combination with an in vivo perturb-seq screen, we identified microglia-produced amphiregulin as a suppressor of disease promoting astrocyte responses in experimental autoimmune encephalomyelitis (EAE), a pre-clinical model of multiple sclerosis (MS). The production of microglial amphiregulin was induced via ST2 signaling by IL-33 released from astrocytes during EAE. Indeed, the genetic inactivation of ST2 or amphiregulin in microglia, or IL-33 or amphiregulin signaling in astrocytes resulted in the worsening of EAE, suggesting that IL-33-induced microglial amphiregulin limits disease-promoting astrocyte responses associated with CNS pathology. This regulatory loop was also detected in human astrocytes and microglia both in vitro and in MS patient CNS samples. In summary, we developed SPEACC-seq, a high-throughput, droplet-based forward genetic screening platform for the identification of cell-cell interaction mechanisms, which identified a novel microglia-astrocyte negative feedback loop that limits CNS pathology.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Studying the effects of AREG, IL-33, and ST2 in astroyctes and microglia in vivo and in vitro.

first: Hong-Gyun

last: Lee

first: Iain

last: Clark

first: Francisco

last: Quintana

first: Michael

last: Wheeler


title: Differential Gene Expression of Field Pea Genotypes After Peyronellaea pinodes infection

city: Bundoora

first: Yvonne

middle: Oby

last: Ogaji

state: VIC

address: 5 Ring Road

department: Department of Jobs, Precincts and Regions.

country: Australia

institute: AgriBio, Centre for AgriBioscience

summary:
Ascochyta blight (AB) is a devastating and aggressive disease of field peas caused by multiple pathogens and the occurrence of the combinations of these pathogens forms a disease complex of which Peyronellaea pinodes, is the most aggressive. AB symptoms include necrotic lesions on all above ground parts of the plant, which can reduce crop yield by up to 70% and result in major economic losses globally. Crop resistance to the disease is reported to be quantitative and, although several genes have been reported to be AB response genes in Spanish pea genotypes, the lines or genotypes of the Australian field pea breeding program have not been investigated.
Plants have specialized defence mechanisms that enable them respond to pathogen invasion, and this involves a cascade of genes which are differentially regulated upon infection. In this study, the time-course gene expression profiles of four Australian field pea genotypes including commercial varieties, known to have varying levels of AB resistance were investigated in response to P. pinodes infection.  Infected and control plants at 0, 6, 24, 48, 72 and 96HPI were sampled for RNA seq.  Mapping of transcriptome sequencing data against the field pea genome resulted in about the identification of c. 6,700 differentially expressed genes. Of the 21 AB resistance genes reported in previously published studies, only seven were present on the list of DEGs generated in this study. No significant pattern was identified in gene expression for the seven genes to differentiate resistant from susceptible genotypes. However, four key genes i.e., disease response protein, malate dehydrogenase, isoflavone 2 hydrogenase and Isoflavone reductase were shown to be associated with suppression of AB disease phenotype after 96HPI. Furthermore, GO functional annotation revealed several genes associated with defence including genes associated with the Salicylic acid pathway, reactive oxygen species, programmed cell death and hypersensitive response.
Although the overall result showed a lack of strong resistance in the Australian pea genotypes as well as the fact that disease suppression does not directly equal resistance, we however were able to identify potential candidates that could be pyramided from exotic material into the breeding program to assess for improved resistance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for field pea genotypes (11HP302-12HO-1, PBA WHARTON, PBA TWILIGHT, and OZP1604) at 0hpi, 6hpi, 48hpi, 72hpi and 96hpi (hours post infection)

middle: O

first: Sameer

last: Joshi

first: Garry

middle: M

last: Rosewarne

first: Hans

last: Daetwyler

first: Tim

middle: I

last: Sawbridge

first: Sukhjiwan

last: Kaur


title: Transcriptome data of different pathogenic stages in Cytospora chrysosperma

city: Being

first: Li

last: Xueyan

address: No.35, Qinghua Eastern Road, Haidian

department: The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry

institute: Beijing Forestry University

summary: To analyze whether the 22 SNAREs in C. chrysosperma were required for the fungal virulence, we performed a transcriptomic analysis during the infection processes, we planned to make a transcriptomic analysis at the infection stages 0d,1d, 3d,  which might result from the tissue necrosis during the infection process.

overall_design: The expression of SNARE protein in different pathogenic stages in Cytospora chrysosperma

first: Xueyan


title: Next generation sequencing of circular and lnc RNAs in diabetes mellitus rats after sleeve gastrectomy

city: Jinan

first: Linchuan

state: Shandong

address: 16766# Jingshi Road

institute: Shandong University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next generation sequencing of long non-coding RNAs in diabetes mellitus rats after sleeve gastrectomy

summary: Sleeve gastrectomy (SG) could improve diabetes mellitus dramatically. However, the mechanisms remain largely undetermined. With the advancement of in-depth bioinformatic analysis, non-coding RNAs especially long non-coding RNAs(lncRNAs), have been implicated in many biological processes. To explore whether lncRNAs mediate the amelioration of diabetes mellitus condition after SG, we subjected liver samples of diabetic rats after SG and shame operations for RNA sequencing. Further, interaction network between lncRNAs and mRNAs/microRNAs(miRNAs) were constructed to infer the function of lncRNAs in diabetic remission, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Through RNA sequencing, we identified more than 9000 lncRNAs with a dramatically differentially expressed profile of 147 lncRNAs. Some of these specific lncRNAs were only expressed in diabetic rats after SG, which may be promising biological markers of diabetic remission and SG prognosis. Through co-analysis between lncRNAs and mRNAs, 20 potential target genes of lncRNAs were screened out. Further bioinformatic analysis indicated the differentially expressed lncRNAs harbored various miRNAs binding sites and three representative lncRNA-miRNA networks of lnc50 and lnc136 were constructed. The KEGG analysis revealed that differential expressed lncRNAs were mainly related to mitogen-activated protein kinase (MAPK) pathway. These results demonstrated that SG dramatically altered expression profile of lncRNAs on diabetes mellitus, and altered lncRNAs expression may contribute to the improvement on diabetic remission through MAPK pathway by interaction with mRNA/miRNA. Our findings provide valuable resources for molecular mechanism of diabetic remission after SG and is benefit for development of lncRNAs-based diagnostic and therapeutic interventions of diabetes mellitus.

overall_design: Expression profile of long non-coding RNAs in diabetes mellitus rats after sleeve gastrectomy

first: Sanyuan

last: Hu


title: Next generation sequencing of circular RNAs in diabetes mellitus rats after sleeve gastrectomy

summary: Sleeve gastrectomy (SG) can improve diabetes mellitus dramatically. However, the mechanisms remain largely undetermined. With the advancement of in-depth bioinformatic analysis, non-coding RNAs especially circular RNAs(circRNAs), have been implicated in many biological processes. To explore whether circRNAs mediate the amelioration of diabetes mellitus after SG, we subjected liver samples of diabetic rats after SG and shame operations for RNA sequencing. Through RNA sequencing, we identified a dramatically differentially expressed profile of 107 circRNAs. Some of these specific circRNAs were only expressed in diabetic rats after SG, which may be promising biological markers of SG prognosis.

overall_design: Expression profile of circular RNAs in diabetes mellitus rats after sleeve gastrectomy


title: Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder

status: Public on Nov 22 2023

city: St Louis

first: Tiandao

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: Purpose The function of FAM177A1 and its relationship to human disease is largely unknown. Recent studies have demonstrated FAM177A1 to be a critical immune-associated gene. One previous case study has linked FAM177A1 to a neurodevelopmental disorder in four siblings. Methods We identified five individuals from three unrelated families with biallelic variants in FAM177A1. The physiological function of FAM177A1 was studied in a zebrafish model organism and human cell lines with loss-of-function variants similar to the affected cohort.  Results These individuals share a characteristic phenotype defined by macrocephaly, global developmental delay, intellectual disability, seizures, behavioral abnormalities, hypotonia, and gait disturbance. We show that FAM177A1 localizes to the Golgi complex in mammalian and zebrafish cells. Intersection of the RNA-seq and metabolomic datasets from FAM177A1-deficient human fibroblasts and whole zebrafish larvae demonstrated misregulation of pathways associated with apoptosis, inflammation, and negative regulation of cell proliferation. Conclusion Our data sheds light on the emerging function of FAM177A1 and defines FAM177A1-related neurodevelopmental disorder as a new clinical entity.

overall_design: RNA profile comparison of 8dp fam177a1a 700 homozygote, fam177a1a/b 700;746 double homozygote and WT

first: Lilianna

last: Solnica-Krezel

first: Jimann

last: Shin

first: Anthony

middle: R

last: McAdow

first: Zhang

last: Bo


title: Effect of AATF silencing on gene expression of BIU-87 [RNA-seq]

city: Shenyang

first: Shutao

last: Tan

address: No.36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary: Differentially expressed genes were identified by comparing the gene expression profiling of BIU-87 of AATF silencing with that of control. Results provide important information to indicate Effect of AATF silencing on BIU-87.

overall_design:
To investigate the effect of AATF on bladder cancer, we established BIU-87 cell lines in which AATF has been silenced by si_AATF.
Then, we added si_nc to another cell line of the same generation as a control and performed the gene expression profiling analysis of these two different cells.
Comparative gene expression profiling analysis using data for BIU-87 with AATF silencing.


title: Z-RNA drives Tau-mediated neurodegeneration of Alzheimer’s disease [RIP-Seq]

city: Hangzhou

first: Songang

last: Wu

state: Zhejiang

address: West Wenyi Road

institute: Zhejiang University School of Medicine

summary: Tau aggregates lead to progressive neurodegeneration in Alzheimer’s disease (AD). Neuron death is one of the hallmarks of neurodegeneration.However, the pathological influence of neuronal death is undetermined, and the connection between Tau aggregates and neuronal death remains elusive. Here we demonstrated the essential role of neuron death in Tau-related neurodegeneration. Tau-neurons died in necroptosis, dependent on ZBP1 sensitized by Z-RNAs (an unusual left-handed conformation). Those endogenous Z-RNAs were transcripts of reactivated transposable elements (TEs) originally silenced in heterochromatin.

overall_design: ZBP1 or ZNA from 9-month-old PS19 and WT mice were pull down by corresponding antibodies.The immunoprecipitated RNA was purified for RNA sequencing.

first: Fan

last: Hong

first: Wei

last: Liu


title: Z-RNA drives Tau-mediated neurodegeneration of Alzheimer’s disease [RNA-Seq]

summary: Tau aggregates lead to progressive neurodegeneration in Alzheimer’s disease (AD) (ref). Neuron death is one of the hallmarks of neurodegeneration (ref). However, the pathological influence of neuronal death is undetermined, and the connection between Tau aggregates and neuronal death remains elusive. Here we demonstrated the essential role of neuron death in Tau-related neurodegeneration. Tau-neurons died in necroptosis, dependent on ZBP1 sensitized by Z-RNAs (an unusual left-handed conformation). Those endogenous Z-RNAs were transcripts of reactivated transposable elements (TEs) originally silenced in heterochromatin.

overall_design: The gene expression profiling analysis for the hippocampus of 10-month-old WT, PS19 and PS19 Zbp1+- mice.


title: Z-RNA drives Tau-mediated neurodegeneration of Alzheimer’s disease [lncRNA-Seq]

overall_design: The expression profiling analysis of long noncoding RNAs for 9-month-old WT vs PS19 mice.(Three samples for each genotype)


title: Z-RNA drives Tau-mediated neurodegeneration of Alzheimer’s disease


title: Knocking down the eIF4E gene in HaCaT cells, which M5 stimulates to establish the in vitro psoriasis cell model.

first: Wang

last: Ruijie

address: Jinan, China

institute: Qilu Hospital of Shandong University, Jinan, China

summary: We transfected keratinocytes cell line (HaCaT cells) with si-NC and si-eIF4E, and added M5 into the cell culture medium to reveal the function of eIF4E in the in vitro psoriasis cell model.

overall_design: We set up si-NC+M5 (n=3) and si-eIF4E+M5 groups (n=3) in HaCaT cells, extracting total RNA after 48 hours, and sent the obtained samples for transcriptome sequencing to reveal the function of eIF4E in psoriatic keratinocytes.

first: Ruijie

last: Wang


title: Characterization of 3D-Organotypic Culture of Mouse Adipose-Derived Stem Cells

city: Busan

first: Tae Gen

last: Son

address: 40 Jwadong-gil, Jang-an eup, Gijang-gun

country: South Korea

institute: Dongnam Institute of Radiological and Medical Sciences

summary: This study explored the use of three-dimensional (3D) cultures to preserve the regenerative potential of adipose-derived stem cells (ADSCs) and investigated their cellular properties

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 2D cultured adipose stem cells and 3D cultured adipose stem cells .

first: TaeGen

first: Yoojin

last: Seo

first: Hyung-Sik

last: Kim


title: A zebrafish model of Ifih1-driven Aicardi-Goutières syndrome reproduces the interferon signature and the exacerbated inflammation of patients

city: Elche

first: Alicia

last: Martinez Lopez

state: Alicante

address: Avenida Candalix 42, 5A

institute: IMIB

summary: Type I Interferonopathies are a heterogenic group of rare diseases associated with an increase of type I interferon (IFN). The main challenge for the study of Type I interferonopathies is the lack of a well-founded animal model in which better characterize the phenotype as well as to perform fast and large drug screenings to offer the best treatment options. In this study, we report the development of a transgenic zebrafish model of Type I interferonopathy overexpressing ifih1 carrying the mutation p.Arg742His (Tg(ifih1_mut)), corresponding to the human mutation p.Arg779His. RNA sequence analysis from Tg(ifih1_mut) larvae revealed a systemic inflammation and IFN signature upon a suboptimal poly I:C induction compared with wild type larvae, confirming the phenotype observed in patients suffering from Type I interferonopathies. More interestingly, the phenotype was manifested in the zebrafish inflammation and Type I IFN reporters nfkb:eGFP and isg15:eGFP, respectively, making this zebrafish model suitable for future high throughput chemical screening (HTS). Using the unique advantages of the zebrafish model for gene editing we have generated Tg(ifih1_mut) knocked down for mavs and ikbke, that completely abrogated the Poly I:C induction and activation of the GFP of the reporters. Finally, we used an FDA approved drug, Baricitinib (Jak1/Jak2 inhibitor), which was able to reduce the inflammation and the ISGs expression. Our results demonstrate the potential of this model to further understand AGS pathological mechanisms and to identify novel therapeutic drugs by HTS.

overall_design: To investigate the difference in the gene expression between zebrafish larvae control vs Tg(ifih1_mut) with and without Poly I:C stimulation, we sent to analyze 3dpf larvae of each group by RNAseq.


title: Proenkephalin deletion in hematopoietic cells induces intestinal barrier failure resulting in clinical feature similarities with irritable bowel syndrome in mice

city: Toulouse

first: Eric

last: Espinosa

state: France

address: IRSD  INSERM U1220 105 Avenue de Casselardit

department: IMMUNOLOGY

country: France

institute: INSERM

summary: Opioid-dependent immune-mediated analgesic effects have been broadly reported upon inflammation. In preclinical mouse models of intestinal inflammatory diseases, the local release of enkephalins (endogenous opioids) by colitogenic T lymphocytes alleviate inflammationinduced pain by down-modulating gut-innervating nociceptor activation in periphery. In this study, we wondered whether this immune cell-derived enkephalin-mediated regulation of the nociceptor activity also operates under steady state conditions. Here, we show that chimeric mice engrafted with enkephalin-deficient bone marrow cells exhibit not only visceral hypersensitivity but also an increase in both epithelial paracellular and transcellular permeability, an alteration of the microbial topography resulting in increased bacteriaepithelium interactions and a higher frequency of IgA-producing plasma cells in Peyer’s patches. All these alterations of the intestinal homeostasis are associated with an anxiety-like behavior despite the absence of an overt inflammation as observed in patients with irritable bowel syndrome. Thus, our results show that immune cell-derived enkephalins play a pivotal role in maintaining gut homeostasis and normal behavior in mice. Because a defect in the mucosal opioid system remarkably mimics some major clinical symptoms of the irritable bowel syndrome, its identification might help to stratify subgroups of patients.

overall_design: Transcriptome profiling was performed on total RNAs (extracted as described below) of colonic biopsies originating from 4 animals in each group of penk+/+ and penk-/- chimeric mice. The corresponding RNA-seq paired-end libraries were prepared according to Illumina’s 18 protocol with some adjustments, using the TruSeq Stranded mRNA library prep Kit (Illumina, San Diego, USA). Briefly, mRNAs were first selected from 10 µg total RNA using poly-T beads. Then, RNAs were fragmented during 2 minutes and retrotranscribed to generate double stranded cDNA. Compatible adaptors were ligated, allowing the barcoding of the samples with unique dual indices. Twelve cycles of PCR were applied to amplify libraries, and a final purification step allowed to obtain 280-1000 pb fragments. Libraries quality was assessed using the HS NGS kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA). Libraries quantification and sequencing were performed at the GeT-PlaGe core facility (INRAe, Toulouse, France). Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche, Basel, Switzerland) to obtain an accurate quantification.

first: Xavier

last: Mas-Orea

first: Lea

last: Rey

first: Louise

last: Battut

first: Cyrielle

last: Bories

first: Camille

last: Petitfils

first: Anne

last: Abot

first: Nadine

last: Gheziel

first: Eve

last: Wemelle

first: Catherine

last: Blanpied

first: Jean-Paul

last: Motta

first: Claude

last: Knauf

first: Frederick

last: Barreau

first: Meryem

last: Aloulou

first: Nicolas

last: Cenac

first: Matteo

last: Serino

first: Lionel

last: Mouledous

last: Fazilleau

first: Gilles

last: Dietrich


title: METTL3-dependent m6A modification programs human neural progenitor cell proliferation [RNA-seq]

city: Shanghai

first: Li

last: Jianguo

address: 1239 Siping Road

institute: Tongji University

summary: To investigate whether the role of METTL3 in hNPCs is dependent on its m6A activity,samples form neural progenitor cell (NPC) differentiation in the small molecule-assisted shut-off (SMASh) tagged hESC groups were collected. Gene expression levels were quantitated by RNA-seq analysis, and the potential target genes were identified by MeRIP-seq analysis and RIP-seq.

overall_design: Examination of the potential target genes regulated by the METTL3 in hNPCs.

first: Yuan

last: Zhao


title: METTL3-dependent m6A modification programs human neural progenitor cell proliferation


title: Chromatin conformation maps in human kidney cortex and medulla from a diabetic donor

city: Freiburg

first: Stefan

last: Haug

address: Hugstetter Str. 49

institute: Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg

summary: We report chromatin conformation (Hi-C) maps from macro-dissected human kidney cortex and medulla from 1 individual

overall_design: Hi-C on macro-dissected kidney cortex and medulla from 1 individual

first: Shreeram

last: Akilesh

first: Anna

last: Köttgen

first: Yong

last: Li

first: Selvaraj

last: Muthusamy


title: Biofilm Heterogeneity-Adaptive Photoredox Catalysis Enables Red Light-Triggered Nitric Oxide Release for Combating Drug-Resistant Infections

city: Hefei

first: jian

last: cheng

address: JINZHAI ROAD 96

institute: USTC

summary: The formation of biofilms is closely associated with persistent and chronic infections, and physiological heterogeneity such as pH and oxygen gradients renders biofilms highly resistant to conventional antibiotics. To date, effectively treating biofilm infections remains a significant challenge. Herein, we report the fabrication of micellar nanoparticles adapted to heterogeneous biofilm microenvironments, enabling nitric oxide (NO) release through two distinct photoredox catalysis mechanisms. The key design feature involves the use of tertiary amine (TA) moieties, which function as sacrificial agents to avoid the quenching of photocatalysts under normoxic and neutral pH conditions and proton acceptors at acidic pH to allow deep biofilm penetration. This biofilm-adaptive NO-releasing platform shows excellent antibiofilm activity against ciprofloxacin-resistant Pseudomonas aeruginosa (CRPA) biofilms both in vitro and in a mouse skin infection model, providing a strategy for combating biofilm heterogeneity and biofilm-related infections.

overall_design: Ciprofloxacin-resistant Pseudomonas aeruginosa were mixed with PBS or G1, and then exposed to light to study the impact of NO release on bacterial gene expression through RNA sequencing.

first: Jian

last: Cheng

first: Guihai

last: Gan


title: Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks [CUT&RUN control and SOX9/TEA1-VPR over-expressing]

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

summary: Embryonic cells engage in diverse types of metabolism to execute specialized tasks in the developing embryo. Recent studies have demonstrated that metabolic reprogramming can also drive changes in cell identity and behavior by affecting the expression of developmental genes. However, the connection between cellular metabolism and differential gene expression is still not well understood. Here we report found that histone lactylation, an epigenetic mark derived from glycolysis-derived lactate, couples the metabolic state of embryonic cells with gene expression and the activation of gene regulatory networks. Embryonic tissues with high glycolytic flux, like the neural crest and the pre-somitic mesoderm, display high levels of lactylation. The lactylation mark is dynamically deposited in the loci of neural crest genes as these cells transition to a state of enhanced glycolysis. This process promotes accessibility of active enhancers and is necessary for proper deployment of the neural crest gene regulatory network. When we reduced the deposition of the mark by targeting LDHA and LDHB, lactylated genes were downregulated, and neural crest migration was impeded. Lactylation of neural crest enhancers is controlled by transcription factors SOX9 and YAP/TEAD, which are necessary and sufficient for the deposition of the mark. These findings define an epigenetic mechanism that integrates cellular metabolism with the gene regulatory networks that orchestrate embryonic development.

overall_design: Examination of the genomic deposition of lactylation using CUT&RUN in control and SOX9/TEA1-VPR over-expressing chicken embyros at the HH6 stage of development in tissue enriched for neural plate border (NPB) cells.

first: Fjodor

last: Merkuri

first: Megan

last: Rothstein


title: Comparison of CNV in 6 ostosarcoma cell lines

city: Tampa

first: Chia-Ho

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

type: Genome variation profiling by genome tiling array

summary: We evaluated 6 established ostesarcoma cell lines. Copy Number Variation and loss-of-heterozygosity status were explored to look for similar patterns across cell lines

overall_design: 6 cell lines were compared, overall and specifically at genes of interest.

first: Darcy

last: Welch

first: Brooke

last: Fridley

first: Ling

last: Cen

first: Jamie

last: Teer

first: Sean

last: Yoder

first: Fredrik

last: Pettersson

first: Liping

last: Yu

first: Yonghong

last: Zhang

first: Mark

last: Alexandrow

first: Shengyan

last: Xiang

first: Makr

last: Robertson-Tessi

first: Joel

last: Brown

first: Jonathan

last: Metts

first: Andrew

last: Brohl

first: Damon

last: Reed


title: METTL3-dependent m6A modification programs human neural progenitor cell proliferation [RIP-seq]

first: Li

last: Jianguo

first: Yuan

last: Zhao


title: Spatial profiling of a unique cancer-associated fibroblast population in the tumor microenvironment in sporadic early-onset colon cancer [eocc_pip]

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: The incidence of sporadic early-onset colon cancer (EOCC) has increased worldwide. The molecular mechanisms in the tumor and the tumor microenvironment in EOCC are not fully understood. The aim of this study is to unravel unique spatial transcriptomic and proteomic profiles in tumor epithelial cells and cancer-associated fibroblasts (CAFs). Sporadic colon cancer FFPE tissue samples were divided into patients diagnosed with EOCC (<50 yrs) and late-onset colon cancer (LOCC, ≥50 yrs). A total of 13 LOCC and 13 EOCC patients that were analyzed using HTG EdgeSeq Precision Immuno-Oncology Panel. The data generated was combined with in silico analysis and functional assays to characterize FAP(+) CAFs at the EOCC tumor invasive margin.

overall_design: Twenty six colon cancer FFPE tissue samples were analyzed by HTG EdgeSeq Precision Immuno-Oncology Panel.  Thirteen FFPE tissue samples were from EOCC, and thirteen samples were from LOCC patients. For each FFPE tissue, a total of 12 µm2 area was collected for each tissue sample.

first: Satoru

last: Furuhashi

first: Matias

last: Bustos

first: Shodai

last: Mizuno


title: METTL3-dependent m6A modification programs human neural progenitor cell proliferation [MeRIP-seq]


title: Effect of ceftriaxone treatment on gene expression of MYCN-amplified RB170

city: Bangkok

first: Rossukon

last: Kaewkhaw

address: 270 Rama VI Road Ratchathewi

country: Thailand

institute: Mahidol University

summary: To study the gene expression response of RB170 to ceftriaxone treatment. We performed gene expression profiling analysis using data obtained from RNA-seq of 3 different ceftriaxone concentration cells at two days of treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ceftriaxone treatment on RB170 at different concentration (vehicle, 2mM, and 8mM) for 2 day.

first: Kaewkhaw

last: Rossukon


title: Modeling Phenotypic Heterogeneity Towards Evolutionary Inspired Osteosarcoma Therapy

first: Chia-Ho

last: Cheng

summary: Osteosarcoma is the most common bone sarcoma in children and young adults. While chemotherapy is universally delivered, benefit from chemotherapy is limited to roughly half of localized patients.  Increasingly, intratumoral heterogeneity is being appreciated as a source of therapeutic resistance.  In this study we developed and evaluated an in vitro model of osteosarcoma heterogeneity, characterizing phenotype (growth in varying environments, sensitivity to chemotherapy) and genotype. We present the genotypic and phenotypic characterization of an osteosarcoma cell line panel with a focus on coculture of the most phenotypically divergent cell lines, 143B and SAOS2. The extent of phenotypic heterogeneity can be altered with relatively modest environmental (pH, glutamine) or chemical perturbations.  We demonstrate that in nutrient rich in vitro culture conditions 143B outcompetes SAOS2, but with selection pressure from nutrient variations or conventional chemotherapy, SAOS2 growth can be favored in spheroids.  Importantly, perturbations that affect the faster growing cell line have only a modest effect on final spheroid size when the simplest heterogeneity state (a two-cell line coculture) is evaluated, and thus the only evaluated therapies to eliminate the spheroids were by switching therapies from a first strike to a second strike. This extensively characterized, widely available system can be modeled and scaled to allow for improved strategies to anticipate resistance in osteosarcoma due to phenotypic heterogeneity.

overall_design: In this study we evaluated 6 established osteosarcoma cell lines (U2OS, MG-63, OS252, SAOS2, 143B, MNNG).  U2OS, MG-63, SAOS2, 143B, and MNNG were obtained from ATCC. OS252 was a gift from Richard Gorlick at MD Anderson{Wang, 2022 #5303}. The identities of the lines were confirmed using STR analysis. Cells were maintained in DMEM+15% FBS and antibiotics. Basic growth characteristics and kinetics including doubling time and log-phase were determined at several starting cell concentrations. Cell lines at 80% confluence were subjected to RNA-sequencing for gene expression analysis.

first: Darcy

last: Welch

first: Brooke

last: Fridley

first: Ling

last: Cen

first: Jamie

middle: K

last: Teer

first: Sean

last: Yoder

first: Fredrik

last: Pettersson

first: Liping

last: Yu


title: Spatial profiling of a unique cancer-associated fibroblast population in the tumor microenvironment in sporadic early-onset colon cancer

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

overall_design: Refer to individual Series


title: H3K27me3 modulates aberrant transcription and apoptosis in cyclophosphamide-induced ovarian granulosa cell injury [CUT&Tag]

city: Changchun

first: Tongjian

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

summary: Chemotherapy-induced ovarian damage and infertility are significant concerns for women of childbearing age with cancer, but the underlying mechanisms are still not fully understood. Our study revealed a close association between H3K27me3 and cyclophosphamide (CTX)-induced ovarian damage, especially in granulosa cells.

overall_design: To determine whether the up-regulation of selected genes induced by CTX treatment were associated with loss of H3K27me3 on specific gene regions, we performed an anti-H3K27me3 CUT&Tag experiment of GCs from the CTX-treated and the control groups using PBS (phosphate buffered saline) at 6 h after CTX or PBS treatment (or labeled as NT).

first: Yingyan

last: Chen

first: Yan

last: Rong

first: Songying

last: Zhang


title: Gene expression profiling of rat postnatal 4 cortex following gestational exposure to 4-Methylimidazole (4-MeI) and maternal seizures.

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Compromised maternal health and specifically, the occurrence of maternal seizures can have adverse effects on the healthy development of offspring possibly via hypoxia-ischemia, disrupted programmed cell death, or GABA signaling. The current study examined cortical tissue from F2b postnatal day 4 offspring of female Harlan SD rats following a two-generation reproductive and continuous breeding (RACB) study design with daily oral exposure to the seizure genic compound 4-Methylimidazole (0, 750, or 2500 ppm 4-MeI). mRNA levels were determined by qRT-PCR for GABA related genes and by whole genome microarray for differential gene expression (DGE) profiles. While maternal seizures occurred at 2500 ppm, there was no indication of disrupted GABA or glutamatergic signaling.  At 750 ppm, DGE suggested adaptation or developmental delay. At 2500 ppm, DGE suggested an impact on critically timed structural events such as synaptogenesis and membrane stability/signaling. Pathways related to growth process and cell signaling showed a negative activation supporting an interpretation of disruption or delay in developmental processes. Further examination across multiple post-partum and preweaning ages for an evaluation of the temporal sequence of development will provide better foundation for biological interpretation.

overall_design: Young adult Hsd:Sprague Dawley SD rats were orally exposed to 4-MeI and breeding schedule followed a two-generation reproductive and continuous breeding (RACB) study design with continuous exposure over multiple breeding and generations.  Three biological replicates for each group were set up.

first: A

last: Massri

first: M

last: Fitzpatrick

first: H

last: Cunny

first: J

first: G

last: Harry


title: ZNF714 – a novel oncogene in lung cancer cells

city: Poznan

first: Marta

last: Machnik

state: Wielkopolska

address: Rokietnicka 8

department: Chair of Medical Biotechnology

institute: Poznan University of Medical Sciences

type: Methylation profiling by genome tiling array

summary: The emerging data indicate that many KRAB-ZNF factors belonging to a large gene family may be involved in carcinogenesis. Our previous study identified ZNF714, a KRAB-ZNF gene of unknown function, as commonly overexpressed in many tumors, pointing to its hypothetical oncogenic role. We knocked down ZNF714 gene expression in two lung cancer cell lines: H2073 (lung adenocarcinoma) and SKMES (squamous cell carcinoma), and subjected them to methylation microarray analysis. We identified 45k DMRs in H2073 and 75k DMRs in SKMES. In both cell lines, the majority of changes (both hypo- and hypermethylation) occurred within gene bodies and promoter regions (TSS1500 and TSS200). The only visible altered methylation pattern indicated more frequent hypomethylation within the promoter region in both shZNF714 cell lines. We correlated those results with our RNA-seq analysis and identified target genes simultaneously overexpressed and unmethylated in cells with knocked-down ZNF714 expression. We identified 54 genes in H2073 and 36 genes in SKMES that met our criteria. Interestingly, several of those genes have documented tumor-suppressive functions, further supporting our in vitro results demonstrating an oncogenic role of ZNF714.

overall_design: We analyzed 6 samples from two different lung cancer cell lines in biological triplicates (total 18 samples). For each cell line (H2073 and SKMES) we analyzed unmodified cells (WT), cells with knocked-down expression of ZNF714 (shZNF714) and cells carrying control shRNA sequence (shLUC).

first: Urszula

last: Oleksiewicz


title: Spatial profiling of a unique cancer-associated fibroblast population in the tumor microenvironment in sporadic early-onset colon cancer [eocc]

first: Dave

last: Hoon

summary: The incidence of sporadic early-onset colon cancer (EOCC) has increased worldwide. The molecular mechanisms in the tumor and the tumor microenvironment in EOCC are not fully understood. The aim of this study is to unravel unique spatial transcriptomic and proteomic profiles in tumor epithelial cells and cancer-associated fibroblasts (CAFs). Sporadic colon cancer FFPE tissue samples were divided into patients diagnosed with EOCC (<50 yrs) and late-onset colon cancer (LOCC, ≥50 yrs). Spatial transcriptomic analysis of 112 areas of interest (AOIs) were performed using Nanostring GeoMx digital spatial profiling. The data generated was combined with in silico analysis and functional assays to characterize FAP(+) CAFs at the EOCC tumor invasive margin.

overall_design: Eight CC FFPE tissue samples were analyzed by NanoString GeoMX Digital Spatial Profiling. Four FFPE tissue samples were from EOCC, and four samples were from LOCC patients. The regions of interest (ROI) were collected in each tissue samples and segmented in areas of interest (AOIs) based on the staining pattern of three fluorescently labeled cell type specific morphological markers: PanCK+, Vim, and FAP. In addition, histological regions in the FFPE tissues were pathology-defined as tumor center (TC), tumor invasive margin (TIM), and adjacent normal (AN) tissue areas.

first: Satoru

last: Furuhashi

first: Matias

last: Bustos

first: Shodai

last: Mizuno


title: TGF-β induces matrisome pathological alterations and EMT in patient-derived prostate cancer tumoroids

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

summary:
Extracellular matrix (ECM) tumorigenic alterations resulting in high matrix deposition and stiffening are hallmarks of adenocarcinomas and are collectively defined as desmoplasia.
Here, we thoroughly analysed primary prostate cancer tissues obtained from numerous patients undergoing radical prostatectomy to highlight reproducible structural changes in the ECM leading to the loss of the glandular architecture.
Starting from patient cells, we established prostate cancer tumoroids (PCTs) and demonstrated they require TGF-β signalling pathway activity to preserve phenotypical and structural similarities with the tissue of origin.
By modulating TGF-β signalling pathway in PCTs, we unveiled its role in ECM accumulation and remodelling in prostate cancer.
We also found that TGF-β-induced ECM remodelling is responsible for the initiation of prostate cell epithelial-to-mesenchymal transition (EMT) and the acquisition of a migratory, invasive phenotype.
Our findings highlight the cooperative role of TGF-β signalling and ECM desmoplasia in prompting prostate cell EMT and promoting tumour progression and dissemination.

overall_design: Comparative gene expression analysis of RNA-seq data obtained from prostate cancer organoids treated in the presence or absence of TGF-B signalling pathway inhibitor (A-83-01). Organoids isolated from 5 different donors were used for this study.

first: Soraia

last: Fernandes

first: Jorge

last: Oliver-De La Cruz

first: Marco

last: Cassani

first: Sofia

last: Morazzo

first: Helena

last: Ďuríková

first: Alessio

last: Caravella

first: Piergiuseppe

last: Fiore

first: Giulia

last: Azzato

first: Giuseppe

last: De Marco

first: Agostino

last: Lauria

first: Valerio

last: Izzi

first: Veronika

last: Bosáková

first: Jan

last: Fric

first: Petr

last: Filipensky

first: Giancarlo

last: Forte

first: Václav

last: Hejret


title: H3K27me3 modulates aberrant transcription and apoptosis in cyclophosphamide-induced ovarian granulosa cell injury

first: Tongjian

last: Zhao

summary: Chemotherapy-induced ovarian damage and infertility are significant concerns for women of childbearing age with cancer, but the underlying mechanisms are still not fully understood. Our study revealed a close association between the loss of H3K27me3 and cyclophosphamide (CTX)-induced ovarian damage.

overall_design: To determine whether the apoptosis of CTX-treated granulosa cells(GCs) was possibly related to alternations in gene expression and signaling pathways, we performed RNA-seq analyses of GCs from the CTX-treated and the control groups using PBS (phosphate buffered saline) at 6 h after CTX or PBS treatment.

first: Yingyan

last: Chen

first: Yan

last: Rong

first: Songying

last: Zhang


title: Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks [R-GNE-140 ATAC-seq]

city: Boston

first: Marcos

last: Simoes-Costa

overall_design: Examination of the accessibility of genomic regions upon lactate depletion in neural crest cell explants from HH9 embryos.

first: Fjodor

last: Merkuri

first: Megan

last: Rothstein


title: Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks [scATAC-seq]

overall_design: Examination of chromatin accessibility in single cells.


title: FoxK1 Associated Gene Regulatory Network in Hepatic Insulin Action and It’s Relationship to FoxO and Insulin Receptor Mediated Transcriptional Regulation

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: ChIP-seq analysis demonstrates FoxK1 binding to proximal promoters and enhancers, especially to genes containing a TGTTTAC motif, which is similar to the FoxA/FoxO motifs.

overall_design: Examination of FoxK1 binding in basal and insulin-stimulated HepG2 cells (ChIP-seq).

first: Prasanna

last: Allu

first: C

last: Kahn


title: Transcriptome analysis from wild type and nHOTAIRM1 knock-out iPSC-derived spinal motor neurons

city: Napoli

first: Francesco

last: Migliaccio

address: Via Pietro Castellino 111

department: DIETI / IAC

country: Italy

institute: Federico II / IAC

summary: In the central nervous system, motor neurons (MNs) are responsible for controlling essential body functions. Long noncoding RNAs have emerged overwhelmingly as gene expression regulators crucial at any step of MN differentiation and function. To uncover the function of the neuronal lncRNA nHOTAIRM1, abundantly expressed in spinal MNs, we generated, analysed and compared RNA-Seq data  from wild type (WT) and nHOTAIRM1 knock-out (KO) MNs derived from iPSCs through a differentiaton protocol of 12 days

overall_design: Three poliA+ RNA samples derived from nHOTAIRM1 KO spMNs and 3 control samples from WT spMNs were subjected to RNA-Seq analysis.

first: Paolo

last: Tollis

first: Annamaria

last: Carissimo

first: Pietro

last: Laneve

first: Elisa

last: Caffarelli


title: Rational design and development of selective BRD7 bromodomain inhibitors and their activity in prostate cancer

city: West Lafayette

first: Emily

last: Dykhuizen

address: 201 S University Street

institute: Purdue University

summary:
Bromodomain-containing proteins are readers of acetylated lysine and play important roles in cancer.1,2 Bromodomain-containing protein 7 (BRD7) has been implicated in multiple malignancies; however, there are no selective chemical probes to study its function in disease.3–13 Using crystal structures of BRD7 and BRD9 bromodomains (BDs) bound to BRD9-selective ligands, we identified a hydrophobic region unique to BRD7. We synthesized a series of ligands designed to occupy this binding region and identified two BRD7-selective inhibitors, 1-78 and 2-77, which show high affinity for the BRD7 BD and selectivity over the BRD9 BD using thermal shift assays and competitive fluorescence polarization.  Our binding mode analyses indicate that these ligands occupy the hydrophobic region in BRD7 and maintain key interactions with the Asn and Tyr residues critical for acetyllysine binding.  Finally, we validated the utility and selectivity of the compounds in cell-based models of prostate cancer.
We then performed gene expression profiling analysis using data obtained from RNA-seq of LNCaP cells with or without drug treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP cells with or without drug treatment (1µM 2-77, 10 µM ENZA, 0.2 µM ACBI, 2 µM BD98, 10 µM PB16 or DMSO) for 72 hours

first: Surbhi

last: Sood


title: Effect of depletion of TMT2 and addition of sugar on gene expression

city: Xi'an

first: Yanting

last: Cao

state: Shaanxi

address: Beilin district, North Taibai Road

institute: Yanting Cao

summary: To investigate the cooperative function  of TMT2 in sugar-auxin-TOR-energy metabolism pathway

overall_design: Wild-type and tmt2 mutant seedings on 1/2 MS media and 1/2 MS media with 1% sucrose, respectively, were analyzed. There are three replicates of each samples. The wild type seedlings on 1/2 MS media are controll samples.

first: Jinju

last: Hu


title: Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks [SOX9 MO ATAC-seq]

overall_design: Examination of the accessibility of genomic regions in control morpholino and SOX9 morpholino transfected neural crest cells from HH9 embryos.


title: Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks [NCC ATAC-seq]

overall_design: Examination of the accessibility of genomic regions in neural crest cells from HH9 embryos.


title: Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks [NCC CUT&RUN]

overall_design: Examination of the genomic deposition of pan lactylation, h3k18la, h3k27ac, and sox9 in embryonic cell types using CUT&RUN.


title: Transcriptome sequencing and microRNA–mRNA regulatory network construction in the lens from a Na2Se03-induced Sprague Dawley rat cataract model

city: Guangzhou

first: Li

last: Xinhui

address: Guangzhou

institute: Sun Yat-sen university


title: Transcriptome sequencing and microRNA–mRNA regulatory network construction in the lens from a Na2Se03-induced Sprague Dawley rat cataract model [RNA]

summary: To explore the regulatory mechanism of age-related cataract (ARC) formation and progression，we construct sodium selenite-induced rat cataract model and performed the high-throughput RNA sequencing (HTS) technology to identify the mRNA and miRNA expression profiles of the lens from Na2Se03-induced and saline - injected Sprague Dawley rats.

overall_design: Animals in the Na2SeO3 group were injected subcutaneously on the nape of the neck with 20umol/kg Na2SeO3 on days 3, 5, and 7, and animals in the control group were treated in the same way with the equivalent amount of saline. After extracting total RNA from six lens capsules (three rats from the control group and three rats from the Na2SeO3 group) using TRIzol reagent and quality inspection was performed, RNA was sequenced using novaseq illumina 6000 Platform with 150 bp paired-end Reads.

first: Rui

last: Fang

first: Pei-Lin

last: Yue

first: Hai-Long

last: Li

first: Xue-Fei

last: Ding

first: Yu-Xuan

last: Jia


title: Influence of metformin treatment during five days of bed rest and recovery in older adults

city: Salt Lake City

first: Micah

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

summary: The primary goal of this study was to determine the effect of metformin treatment during 5 days of bed rest in older adults and observe any residual effects of metformin treatment during recovery from this disuse period.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for older adult (>60 yr) skeletal muscle vastus lateralis muscle biopsy samples with 9-10 replicates per group

first: Jonathan

last: Petrocelli

first: Chris

last: Stubben


title: Cellular and molecular evidence that synaptic Schwann cells contribute to aging of mouse neuromuscular junctions

city: Providence

first: Gregorio

last: Valdez

state: RI

address: 70 Ship St

institute: Brown University

summary: Age-induced degeneration of the neuromuscular junction (NMJ) is associated with motor dysfunction and muscle atrophy. While the impact of aging on the NMJ pre- and postsynapse is well-documented, little is known about the changes perisynaptic Schwann cells (PSCs), the synaptic glia of the NMJ, undergo during aging. Here, we examined PSCs in young, middle-aged, and old mice in three muscles with different susceptibility to aging. Using light and electron microscopy, we found that PSCs acquire age-associated cellular features either prior to or at the same time as the onset of NMJ degeneration. Notably, we found that aged PSCs fail to completely cap the NMJ even though they are more abundant in old compared to young mice. We also found that aging PSCs form extensions that guide axon terminal sprouts away from innervated NMJs. We next profiled the transcriptome of PSCs and other Schwann cells (SCs) to identify mechanisms altered in aged PSCs. This analysis revealed that aged PSCs acquire a transcriptional pattern that promotes phagocytosis that is absent in other SCs. It also showed that aged PSCs upregulate unique pro-inflammatory molecules compared to other aged SCs. Interestingly, neither synaptogenesis genes nor genes that are typically upregulated by repair SCs were induced in aged PSCs or other SCs. These findings provide insights into cellular and molecular mechanisms that could be targeted in PSCs to stave-off the deleterious effects of aging on NMJs.

overall_design: S100B-GFP+ SCs and S100B-GFP+/NG2-dsRed+ PSCs collected from hindlimbs muscles of female young adult (4-5 months) and aged (23-24 months) S100B-GFP;NG2-dsRed mice.

first: Robert

last: Hastings

first: Mary

middle: F

last: Avila

first: Emma

last: Suneby

first: Devin

last: Juros

first: Anson

last: O'Young

first: Jason

last: Peres da Silva


title: Effect of miR-125b and its isomiRs on gene expression subjected to hypoxic challenge

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

institute: National University of Singapore

summary: To investigate the gene expresiion regulated by miR-125b and its isomiRs. We transfected H9C2 cells with respective mimics and performed gene expression profiling anlaysis using data from RNA-seq of mimic controls, miR-125b and its isomiRs mimics subjected to normoxia and hypoxia treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H9C2 cells subjected mimic control, miR-125b and its isomiRs mimic tranfection.

first: Lee

first: Azizah

middle: B

last: Fadzil

first: Qiying

last: Chen

first: Mark

last: Richards

first: Peipei

last: Wang


title: Transcriptome sequencing and microRNA–mRNA regulatory network construction in the lens from a Na2Se03-induced Sprague Dawley rat cataract model [miRNA]

first: Li

last: Xinhui

overall_design: Animals in the Na2SeO3 group were injected subcutaneously on the nape of the neck with 20umol/kg Na2SeO3 on days 3, 5, and 7, and animals in the control group were treated in the same way with the equivalent amount of saline. After extracting total RNA from six lenses (three rats from the control group and three rats from the Na2SeO3 group using TRIzol reagent and quality inspection was performed, RNA was sequenced using novaseq illumina 6000 Platform with 50 bp Single-ended Reads for microRNA.

first: Rui

last: Fang

first: Pei-Lin

last: Yue

first: Hai-Long

last: Li

first: Xue-Fei

last: Ding

first: Yu-Xuan


title: Hormone-regulated expansins - expression, localization and cell wall biomechanics in the control of Arabidopsis root growth

first: Core Facility

last: Bioinformatics

summary:
Expansins facilitate cell expansion by mediating pH-dependent cell wall (CW) loosening. However, the role of expansins in controlling CW biomechanical properties in specific tissues and organs remains elusive.
To characterize its potential importance in controlling CW biomechanical properties, we overexpressed EXPA1 and generated Dex-inducible lines (8-4 and 5-4).
We quantified the expression of genes from wild type and a Dex-inducible line (8-4). Total RNA was extracted from the roots of 7 days old seedlings.
The experiment comprises four replicates for plants grown in control condition, treated for 3 hours with Dex or treated for 7 days with Dex.

overall_design: Comparative gene expression analysis of RNA-seq data for wild type and Dex-inducible line under three conditions (control, 3h Dex treatment, 7 days Dex treatment).

first: Marketa

last: Samalova

first: Jan

last: Hejatko

first: Nicolas

last: Blavet


title: Gene Expression in Primary and Recurrent Oral Cancer Patient Samples

city: Milwaukee

first: Heather

last: Himburg

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: We report the results of RNAseq analysis using the NovaSeq platform of primary human cancer patient samples at diagnosis and following recurrence.

overall_design: Pairwise comparison of pre-treatment tumor specimens to matched recurrent tumor sample in the same patient. N=3 patients with oral squamous cell carcinoma and experienced local recurrence at the oral cavity site at a median of 13 months.

first: Joseph

last: Zenga

first: Musaddiq

last: Awan


title: Chromatin accessibility maps in human kidney cortex and medulla

city: Freiburg

first: Stefan

last: Haug

address: Hugstetter Str. 49

institute: Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg

summary: We report chromatin accessibility (ATAC-seq) maps from macro-dissected human kidney cortex and medulla from 3 individuals

overall_design: ATAC-seq on macro-dissected kidney cortex and medulla from 3 individuals

first: Shreeram

last: Akilesh

first: Anna

last: Köttgen

first: Yong

first: Selvaraj

last: Muthusamy


title: Mutant p53R211* specifically suppresses Th17 cell population and ameliorates the arthritic condition in AIA rat via direct binding of TBK1 and inhibition of TBK1-IRF3-STING signaling cascade

city: Macau

first: Yaling

last: Zeng

address: Avenida Wai Long, Taipa, Macau, China Avenida Wai Long, Taipa, Macau, China

institute: Macau university of science and technology

summary: In vivo studies were investigated using rat p53R211* overexpressing adjuvant-induced arthritis (AIA) rat model established by adeno-associated virus (AAV) injection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for P53R211*  in AIA rats.

first: Vincent

last: Wong


title: RNA-seq and Chromatin accessibility and conformation maps of human kidney cortex and medulla

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

overall_design: Refer to individual Series


title: Molecular and functional profiling of chemotolerant cells unveils nucleoside metabolism-dependent vulnerabilities in medulloblastoma

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
Chemotherapy resistance is considered one of the main causes of tumor relapse, still challenging researchers for the identification of the molecular mechanisms sustaining its emergence. Here, we setup and characterized chemotherapy-resistant models of Medulloblastoma (MB), one of the most lethal pediatric brain tumors, to uncover targetable vulnerabilities associated to their resistant phenotype.  Integration of proteomic, transcriptomic and kinomic data revealed a significant deregulation of several pathways in resistant MB cells, converging to cell metabolism, RNA/protein homeostasis, and immune response, eventually impacting on patient outcome. Moreover, resistant MB cell response to a large library of compounds through a high-throughput screening, highlighted nucleoside metabolism as a relevant vulnerability of chemotolerant cells, with peculiar antimetabolites demonstrating increased efficacy against them and even synergism with conventional chemotherapeutics.    Our results suggest that drug-resistant cells significantly rewire multiple cellular processes, allowing their adaptation to a chemotoxic environment, nevertheless exposing alternative actionable susceptibilities for their specific targeting.
In this study, we generated and characterized from a proteomic, transcriptional and kinomic point of view chemothrapy-resistant MB cells. Integrated data were then associated to the response of MB resistant cells to a large library of compounds through an high throughput screening approach identifying nucleoside metabolism as a peculiar targetable vulnerability emerged after chemotherapy adaptation.

overall_design: Gene expression was measured using Affymetrix platform in naive MB cells and their relative chemotherapy-resistant counterparts generated after several cycles of a chemotherapeutic cocktail, namely VECC.

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: RNA-seq of human kidney cortex and medulla

summary: We report gene expression (RNA-seq) from macro-dissected human kidney cortex and medulla from 3 individuals

overall_design: RNA-seq on macro-dissected kidney cortex and medulla from 3 individuals

last: Li


title: Chromatin conformation maps in human kidney cortex and medulla

summary: We report chromatin conformation (Hi-C) maps from macro-dissected human kidney cortex and medulla from 1 individual

overall_design: Hi-C on macro-dissected kidney cortex and medulla from 1 individual


title: Serum neurofilament light reveals the contraction from widespread to lesion-bound neuroaxonal injury during autoimmune neuroinflammation

city: Mainz

first: Tobias

last: Brummer

state: Rheinland-Pfalz

department: Neurology

institute: Universitätsmedizin Mainz

summary: Blood-based neurofilament light (sNfL) indicates neuroaxonal injury in multiple sclerosis and is on the cusp of being implemented into clinical routine. However, anatomical origins and pathophysiological mechanisms of NfL release during acute relapses and later chronic disease stages are still poorly understood. Here, we applied immunohistochemistry, single molecule array, spatial transcriptomics and microglia/axon co-cultures to gain insight into spatio-temporal NfL release in experimental autoimmune encephalomyelitis (EAE). Results: Association of spinal cord white matter lesions and sNfL levels revealed a distinct, stage-dependent anatomical pattern of neuroaxonal damage: In chronic EAE, sNfL levels were predominately associated with anterolateral lumbar lesions, whereas in early EAE sNfL showed no correlation with lesions in any anatomical location. Furthermore, neuroaxonal damage in late EAE was largely confined to white matter lesions, but showed a widespread distribution in early EAE. Followingthis spatio-temporal pattern of neuroaxonal damage, spatial transcriptomics revealed a widespread cyto- and chemokine response at early disease stages, whereas late EAE was characterized by a prominent glial cell accumulation in white matter lesions. These findings were corroborated by immunohistochemistry and micro-glia/axon co-cultures, which further revealed a strong association between CNS myeloid cell activation and neuroaxonal damage both in vivo and in vitro. Interpretation: Our data demonstrate that sNfL release in EAE driven by CNS myeloid cells exhibits progress in a disease stage-dependent centripetal manner from normal-appearing white matter to focal white matter lesions. These findings may further aid the interpretation of elevated sNfL levels in multiple sclerosis patients at different disease stages.

overall_design: 3 animals for each disease stage, 2 for healthy control

first: Miriam

last: Schillner

first: Falk

last: Steffen

first: Flores

last: Kneilmann

first: Beatrice

last: Wasser

first: Timo

last: Uphaus

first: Frauke

last: Zipp

last: Bittner


title: Single cell RNA sequencing of human cortical organoids integrated with kirigami electronics.

city: Stanford

first: Xiao

last: Yang

address: 318 Campus Drive

institute: Stanford University

summary: We integrated human cortical organoids with kirigami electronics. We used single cell RNA sequencing to analyze how the integration affects corticogenesis.

overall_design: Human cortical organoids at day 100 of in vitro differentiation with and without the integration of kirigami electronics were dissociated and analyzed using single cell RNA sequencing.

first: Csaba

last: Forro

first: Thomas

first: Yuki

last: Miura

first: Tomasz

last: Zaluska

first: Ching-Ting

last: Tsai

first: Sabina

last: Kanton

first: James

middle: P

last: McQueen

first: Xiaoyu

last: Chen

first: Francesca

last: Santoro

first: Sergiu

last: Pașca

first: Bianxiao

last: Cui


title: CD45+ and CD45- cells of benign v/s metastatic mouse breast tumors

city: Trondheim

first: Miriam

middle: Soledad

last: Giambelluca

state: Sør-Trøndelag

address: NTNU, Kunnskapssenteret, Olav Kyrres gate 17, 7030 Trondheim

country: Norway

institute: NTNU

summary: Metastasis remains a leading cause of all cancer related mortalities and therapeutic challenges.   To successfully establish tumors and metastasiz, cancer cells must escape recognition and elimination by modulating immune cells during surveillance. Therapies that  mount anti-tumor response of the adaptive immune system and target the immune evasion mechanisms have entered the clinic. However, the number of patients that respond to these therapies remains humble. This is likely due to the pro-tumor and immunosuppressive mechanisms of innate immune system that remain elusive. Tumor immune cells demonstrate tremendous intra- and inter-tumoral heterogeneity. Presence of high neutrophil to lymphocyte ratio is typically associated with high risk of metastasis and poor patient outcome, which suggests that immune cells, specifically myeloid cells of metastatic tumors have distinct biological functions. We aim to identify these distinct biological functions and the candidates that may have prognostic and therapeutic potential using a non-metastatic and metastatic tumor from the 4T1 mouse breast cancer model.

overall_design:
67NR (non-metastatic) and 66cl4 (metastatic) tumors of the immunocpmpetent 4T1 mouse breast cancer model were indiced in mice by orthotopic injections. After development of tumors, they were resected and dissociated to form single cell suspension. The cells were sorted  based on CD45 expression into immune (CD45+) and non-immune (CD45-) cells. RNA was extracted from the sorted cell populations and transcriptome sequencing of immune and non-immune cells from both the tumors was done to understand the distinct biological functions associated with each subset.
contributor: Genomic Core Facility

first: Ansooya

last: Bokil


title: Pseudouridine-dependent ribosome biogenesis selectively regulates translation of polyglutamine proteins during Drosophila oogenesis [pulldown]

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

summary: Stem cells in many systems, including Drosophila germline stem cells (GSCs), have increased ribosome biogenesis and translation during terminal differentiation. Here, we show that pseudouridylation of ribosomal RNA (rRNA) mediated by the H/ACA box is required for ribosome biogenesis and oocyte specification. Reducing ribosome levels during differentiation decreased the translation of a subset of mRNAs that are enriched for CAG repeats and encodes polyglutamine-containing proteins, including differentiation factors such as RNA-binding Fox protein 1. Moreover, ribosomes were enriched at CAG repeats within transcripts during oogenesis. Increasing TOR activity to elevate ribosome levels in H/ACA box-depleted germlines suppressed the GSC differentiation defects, whereas germlines treated with the TOR inhibitor rapamycin had reduced levels of polyglutamine-containing proteins. Thus, ribosome biogenesis and ribosome levels can control stem cell differentiation via selective translation of CAG repeat-containing transcripts.

overall_design: Pseudouridine antibody was used to pulldown all RNAs present with pseudouridine and input was taken as a control. RNA was extracted, enriched for poly-A and sequenced.

first: Shane

last: Breznak

first: Yingshi

last: Peng

first: Limin

last: Deng

first: Noor

last: Kotb

first: Zachary

last: Flamholz

first: Elliot

middle: T

last: Martin

first: Ian

last: Rapisarda

first: Kara

last: LaBarge

first: Dan

last: Fabris

first: Elizabeth

last: Gavis


title: Pseudouridine-dependent ribosome biogenesis selectively regulates translation of polyglutamine proteins during Drosophila oogenesis [polysome-seq]

overall_design: Polysome-seq files of duplicate samples of ovaries from germline Nop60B and YWT, HsBam  as a  controls.


title: Immature brain cortical neurons lack the transcriptional competence to activate antiviral defences and control RNA virus infections

city: Parkville

first: Nagaraj

middle: Sundara

last: Moily

state: Victoria

address: Bio21 Institute, The University of Melbourne,

department: Biochemistry and Molecular Biology

institute: The University of Melbourne

summary:
Purpose: Virus infections of the CNS cause important diseases of humans and animals. As in other tissues, innate antiviral responses mediated by type I interferons (IFN) are crucially important in controlling CNS virus infections. Semliki Forest virus (SFV) infection of the mouse provides a well-characterised and tractable model to study the pathogenesis of virus encephalitis. The maturity of neuronal populations is an established critical factor determining the outcome of CNS virus infection. Using primary cultures of mouse cortical neurons, we investigated the relationships between neuronal maturation, type I IFN responses and the outcome of SFV infection.
Methods: mRNA profiles of immature and mature of primary mouse cortical neurons that were mock or iFNβ treated and mock or SFV infected were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. All 100-base-pair single-end reads were mapped to the reference mouse genome (GRCm38/mm10) using Salmon ultrafast aligner. Mapped reads were quantitated to the gene level estimates and genecount data was imported using the tximport package and differential expression analysis of RNA sequencing data was carried out using the edgeR  and limma-voom packages in Bioconductor.
Results: Using an optimized data analysis workflow, we mapped the 100 bp single end reads to the mouse genome (build mm10) and identified 14,933 genes in the immature and mature primary neurons with different treatments. Transcriptomic profiling revealed 3,666 genes differentially expressed between resting immature and mature cells. Multidimensional scaling plots revealed key differences between immature and mature neurons with different treatments. Immature neurons pre-treated with type I IFN and mock-infected or infected without prior IFN, clustered close to the basal (resting) control samples,indicating limited changes in gene expression under either condition. This was also the case for mature neurons treated with IFNβ. Whereas, immature neurons pre-treated with IFN and then infected, as well as mature neurons pre-treated or not with IFN and then infected underwent more dynamic changes in gene expression
Conclusions: Complete transcriptome analysis demonstrated that resting immature neurons lacked the transcriptional competence to mount antiviral responses. They had no detectable transcription of the genes Ddx58 and Ifih1 which encode the key RNA virus cytoplasmic sensors RIG-I and MDA5 and no, or very low, expression of genes encoding key regulators of downstream and associated signalling pathways. Upon infection, immature neurons failed to mount an antiviral response as evidenced by their failure to produce chemokines, IFNs and other cytokines. Treatment of immature neurons with exogenous IFNb prior to infection resulted in antiviral responses and lower levels of virus replication and infectious virus production. In contrast, resting mature neurons expressed Ddx58 and Ifih1 and upon infection generated a robust antiviral response. This was augmented by pre-treatment with IFNb. Infection of mature neurons derived from IFNAR-/- mice did not make an antiviral response and replicated virus to high levels.

overall_design: mRNA profiles of immature and mature of primary mouse cortical neurons that were mock or IFNβ treated and mock or SFV infected.

first: Divya

last: Narayanan


title: TGF-β1 induces bone marrow NK cells dysfunction

city: Hefei

first: Dongyao

last: Wang

state: Anhui

address: Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.

summary: TGF-β1 is a cytokine of the bone morphogenetic protein–activin family and commonly regarded as the most powerful immunosuppressive cytokine

overall_design: Here, 6 control, 6 cultured with active TGF-β, and 6 cultured with latent TGF-β were enrolled for analysis of the immunological characteristics of NK cells. We want to comprehensively characterize the transcriptional changes in the two groups by transcriptome sequencing.


title: Intestinal B cells license metabolic T-cell activation in NASH microbiota/antigen-independently and contribute to fibrosis by IgA-FcR signalling

city: Rehovot

first: Avital

last: Sarusi Portuguez

state: Select a State/Province/Region

address: 234 Herzl Street, POB 26

department: G-INCPM

country: Israel

institute: Weizmann Institute of Science

summary: Non-alcoholic steatohepatitis (NASH), which is increasing in incidence due to the obesity epidemic, is a T-cell mediated, auto-aggressive condition that can result in progressive liver disease and hepatocellular carcinoma (HCC). The gut-liver axis contributes to NASH, yet mechanisms underlying metabolic T-cell activation and NASH-related fibrosis have largely remained elusive. We found that gastrointestinal B-cells are activated and increased in number in mouse/human NASH, allowing metabolic T-cell activation to induce NASH antigen- and microbiota-independently. Genetic/therapeutic depletion of B-cells systemically or of gastrointestinal B-cells specifically, prevented or reverted NASH and fibrosis. Secretion of immunoglobulins was essential for NASH and fibrosis development. IgA secretion was necessary for fibrosis-induction by activating CD11b+CCR2+F4/80+CD11c-FCGR1+ hepatic myeloid cells through an IgA-FcRγ signaling-axis. Furthermore, clinical/molecular analyses from NASH-patients demonstrated IgA and activated FcRγ+ hepatic myeloid cells to correlate with the degree of liver-fibrosis. Thus, gastrointestinal B-cells and the IgA-FcRγ signaling-axis on hepatic myeloid cells represent potential therapeutic targets to treat NASH.

overall_design: Single-cell transcriptomic data are presented from sorted CD45+ cells of small intestines (after removal of Peyer's patches) of one WT normal diet fed mouse used as control, and one WT CD-HFD (choline-deficient high fat diet) mouse as model for NASH.

first: Elena

last: Kotsiliti

first: Valentina

last: Leone

last: Sarusi-Portuguez

first: Karsten

last: Rippe

first: Oren

last: Parnas

first: Mathias

last: Heikenwälder


title: Pseudouridine-dependent ribosome biogenesis selectively regulates translation of polyglutamine proteins during Drosophila oogenesis

first: Prashanth

last: Rangan


title: Whole transcriptome analysis of coding and non-coding RNAs associated with Spodoptera frugiperda feeding in Zea mays

status: Public on Nov 21 2023

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

summary: We report the application of whole transcriptome sequencing technology for high-throughput profiling of coding and non-coding RNAs associated with Spodoptera frugiperda feeding in Zea mays. 4,366 mRNAs and 233 lncRNAs were differentially expressed during Spodoptera frugiperda feeding in Zea mays. Our data contribute to the understanding of the function of coding and non-coding RNAs in the regulation of plant-insect interactions.

overall_design: Examination of coding and non-coding RNAs associated with Spodoptera frugiperda feeding in Zea mays


title: The browning and mobilization of subcutaneous white adipose tissue supports efficient skin repair

first: Juzi

last: Liu

state: --- Select One ---

address: North Guangzhou Avenue 1838, Nanfang Hospital

institute: Southern Medical University

summary: Adipocytes in dermis are considered to be important participants in skin repair and regeneration, but the role of subcutaneous white adipose tissue (sWAT) in skin repair is poorly understood. Here, we revealed the dynamic changes of sWAT during wound healing process. Lineage tracing mouse studies revealed that adipocytes from sWAT would migrate into the wound bed and participate in the formation of granulation tissue. Moreover, sWAT undergoes beiging after skin injury. Inhibition of sWAT beiging by genetically silencing PRDM16, a key regulator to beiging, hindered wound healing process. The transcriptomics results suggested beige adipocytes in sWAT abundantly express neuregulin 4 (Nrg4) which regulated macrophage polarization and the function of myofibroblasts. In diabetic wounds, the beiging of sWAT was significantly suppressed. Thus, adipocytes from sWAT regulate multiple aspects of repair and may be therapeutic for inflammatory diseases and defective wound healing associated with aging and diabetes.

overall_design: Inguinal subcutaneous white adipose tissue (sWAT) samples collected from C57BL/6 mice 7 days after skin injury and uninjured mice (n = 3 per group) were used to characterize the transcriptome of sWAT following injury. We also collected the sWAT beneath the wounds of Adipo-PRDM16 KO and C57BL/6 mice (n = 3 per group) 7 days after skin injury to characterize the transcriptome of sWAT after the inhibition of browning.

first: Junrong

last: Cai

first: Yuping

last: Quan

first: Shaowei

last: Zhu

first: Ting

last: Su

first: Jiayan

last: lin

first: Zhuokai

last: Liang

first: Qian

last: Zhang

first: Yunjun

last: Liao

first: Wenqing

last: Jiang

first: Yufei

last: He

first: Feng

last: Lu


title: Exploring the effects of rearing densities on epigenetic modifications in the zebrafish gonads

city: Barcelona

first: Laia

last: Ribas

address: Passeig Maritim 37-49

institute: Institut de Ciencies del Mar

type: Methylation profiling by high throughput sequencing

summary: The goal of this study was to determine whether there was a direct relationship between stress and DNA methylation changes in fish gonads.  During sex differentiation, we studied the sensitive window to density. Sex ratios were studied and methylation of canonical reproduction-related genes was analysed.

overall_design: Zebrafish were reared at high density conditions as described in Ribas et al., 2017 J. Exp. Biol. During 7-21 days post fertilization (dpf) and 18-45 dpf. At 90 dpf gonads were dissected and flash frozen with liquid nitrogen for further molecular analysis and sex ratios were recorded

first: A

last: Valdivieso

first: M

last: Caballero-Huertas

first: J

last: Moraleda-Prados

first: F

last: Piferrer

first: L


title: Assessing DNA methylation differences upon aquired Venetoclax resistance

city: Cologne

first: Christina

last: Grimm

address: Weyertal 115b

department: Translational Epigenetics

institute: University of Cologne, Medical Faculty and University Clinic Cologne

summary: We analyzed DNA methylation alterations upon acquired Venetoclax resistance using 8 different cell line pairs

overall_design: Examination of the DNA methylation by MeDIP-seq in cell line pairs before and after prolonged Venetoclax treatment which results in acquired Venetoclax resistance.

first: Matthias

last: Lienhard

first: Daniel

last: Thomalla


title: Identification of transcriptional changes after treatment with different Traditional Chinese Medicine (TCM) in pancreatic cancer mouse model

city: Shanghai

first: Libin

last: Song

address: 270 Dongan Road

institute: Fudan University Shanghai Cancer Center

summary:
Purpose: The goals of this study are to characterize the transcriptional changes of pancreatic cancer mouse model after TCM treatment. More importantly, the transcriptome differences betweeen different TCMs are compared to identify RNAs that may be targets of different TCMs.
Methods: High-throughput RNA sequencing (RNA-seq) was employed to capture the transcriptional changes in QYHJ treatment samples. StringTie was used to quantify gene expression and DESeq2 was utilized to compared expression changes between different sample groups.

overall_design: Tanscriptome-wide characterization of pancreatic cancer mouse model with different TCM treatment


title: Analysis of the transcriptomic profiles for HER2 CD8+ CAR T cells-overexpressed FOXO1WT

city: Shinjuku-ku

first: Makoto

last: Ando

state: Tokyo

address: 35 Shinanomachi

department: Department of Microbiology and Immunology

institute: Keio University School of Medicine

summary: T cell exhaustion and metabolic dysfunction induced by chronic antigen stimulation within the tumor microenvironment represent formidable obstacles in CAR T cell therapy for solid tumors. Previously, we developed a method to convert effector/exhausted CAR T cells that emerge from repeated antigen stimulation into stem cell memory-like CAR T (termed CAR-iTSCM) cells. These CAR-iTSCM cells exhibit expression of early memory markers and enhanced mitochondrial metabolism after quiescence under culture conditions containing IL-7, CXCL12, and the NOTCH-ligand. However, we noticed that this strategy was effective for CD19 CAR used for blood cancers, but not for HER2 CAR commonly used to treat solid tumors, due to tonic CAR signals. In this study, we developed a new culture condition for CAR iTSCM cells suitable for HER2 CAR and elucidated the mechanism of induction of stemness and mitochondrial fitness. We found that short-term resting condition with IL-7, CXCL12, and pan-tyrosine kinase inhibitor, Dasatinib can induce stem-like CAR T cells at the epigenetic level and enhance mitochondrial metabolism. We identified FOXO1 as a critical regulator in the process of epigenetic and metabolic reprogramming, and anti-tumor activity. We found that overexpression of FOXO1 leads to enhanced mitochondrial metabolism, efficient CAR T cell expansion, and potent anti-tumor effects through epigenetic modifications. These findings suggest that regulating the transcriptional activity of FOXO1 is a promising strategy for engineering effective CAR T cells for treating solid tumors. In this analysis, we aimed to investigate the effects of FOXO1WT overexpression on the transcriptomic profiles in 4-1BB-based HER2 CD8+ CAR T cells which exhibit tonic signals-induced exhaustion hallmarks.

overall_design: We performed bulk RNA-seq analysis using HER2 CD8+ CAR T cells under four different conditions (Empty, FOXO1WT, 7.12.I, and 7.12.I.Das). Each CAR T cells were generated from different three healthy donors (n=3).


title: miRNA expression-based, potential mechanism of a herbal medicine formula HTG in treating dyslipidaemia rats

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

summary:
Potential mechanism was discovered through expression profiling of a total of 3545 miRNAs in liver of rats fed with high fat diet after HTG treatment.
MiRNAs in liver of rats(3 group, normal fat diet group, 3, high fat diet group, 3, high fat diet + HTG treatment, 3) were detected, and differentially expressed miRNAs were analyzed to reveal potential mechanism of HTG in treating dyslipidaemia.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 9 rats were divided into 3 group(normal fat diet group: normal fat diet + 0.5% CMC-Na , high fat diet group:  high fat diet + 0.5% CMC-Na, HTG group: high fat diet + HTG treatment) and fed with different intervention for 12 weeks, at the end of the experiment, their liver tissues were harvested after anaesthetised for further detection.

first: Min

last: Li