title: RELA is required for CD271 expression and stem-like characteristics in hypopharyngeal cancer.

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

country: Japan

institute: Miyagi Cancer Center


title: RELA is required for CD271 expression and stem-like characteristics in hypopharyngeal cancer [dataset 2]

status: Public on Oct 26 2022

summary: To investigate the RELA-induced CD271 signaling, RELA-binding sequence of CD271 promoter region was deleted and performed microarray analysis

overall_design: RELA-binding sequence of CD271 promoter region of HPCM2 cells was deleted by CRISPR-Cas9 method

first: Akira

last: Nakazato

first: Mai

last: Mochizuki

first: Haruna

last: Fujimori


title: Single-cell transcriptional profiling reveals low-level tragus stimulation improves septic myocardial dysfunction by promoting M2 macrophage polarization.

city: Changsha, Hunan

first: Yufan

last: Yang

state: China

address: No. 86 Ziyuan Road

country: China

institute: Hunan Children's Hospital

type: Expression profiling by high throughput sequencing

summary: Background: Sepsis can lead to multiple organ damage, and the heart is one of the most vulnerable organs. Vagal nerve stimulation can reduce myocardial injury in sepsis and improve survival rate. However, the relative effect of disparate cell populations on sepsis induced myocardial dysfunction and the low-level tragus stimulation on it, remain unclear.  Methods: We used the cardiac single-cell transcriptomic strategy to characterize the cardiac cell population and the network of cells that forms the heart. And we selected all cardiac macrophage from CD45+ cells using single-cell mRNA sequencing data. Then we used echocardiography performing, western blot and immunofluorescence and immunohistochemical technology to verify the data of the single-cell mRNA sequencing results.  Results: In single-cell mRNA sequencing data, our analysis provides a comprehensive map of the cardiac cellular landscape uncovering multiple cell populations that contribute to sepsis induced myocardial dysfunction under low-level tragus stimulation. Pseudo timing analysis in single-cell sequencing showed that low level vagal nerve stimulation could induce the transformation of cardiac monocytes into M2 macrophages and play an anti-inflammatory role. After low-level tragus stimulation, the expression of α7nAChR in the heart tissue increased significantly. Echocardiography showed that low-level tragus stimulation could improve the cardiac function of septic myocardial injury of the mice. Comparing with the sepsis group, the expression of interleukin-1β in heart tissue of the mice in sepsis with low-level tragus stimulation group is significantly lower.   Conclusion: Low-level tragus stimulation can improve sepsis-induced myocardial dysfunction by promoting cardiac monocytes to M2 macrophages.  Goal of the study: In the present study, we aimed to screen macrophages, their crosstalk with other cells, and macrophages associated with cardiac injury and further verify their origins and roles in the septic myocardial injury process and low-level tragus stimulation (LL-TS) to treat septic myocardial dysfunction.

overall_design: Four sample from mice heart tissue

first: Longlong

last: Xie

first: Yinghui

last: Peng

first: Haipeng

last: Yan

first: Jiaotian

last: Huang

first: Zhenghui

last: Xiao

first: Xiulan

last: Lu


title: RELA is required for CD271 expression and stem-like characteristics in hypopharyngeal cancer [dataset 1]

summary: To investigate the mechanisms of CD271 transcription, we analyzed the difference between sorted CD271-low and CD271 expression-recovered cells.

overall_design: HPCM2 cells were sorted according to CD271 expression, and CD271-low HPCM2 cells were cultured for 3 days


title: Perinatal morphine exposure and the offspring prefrontal cortex

city: Highland Heights

first: Brittany

middle: L

last: Smith

state: KY

address: Founders Hall

country: USA

institute: Northern Kentucky University

summary:
To investigate how exposure to morphine during the prenatal and early postnatal period affects the offspring prefrontal cortex in a mouse model
We performed gene expression profiling analysis using data obtained from RNA-seq of offspring prefrontal cortical brain samples at postnatal day 21

overall_design: Comparative gene expression profiling analysis of RNA-seq data for prefrontal cortical samples of male and female offspring with perinatal morphine (MO) vs. saline (SAL) exposure

first: Teresa

last: Reyes


title: Tristetraprolin Limits Age-related Expansion of Myeloid-Derived Suppressor Cells

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

summary: Aging results in enhanced myelopoiesis, which is associated with an increased prevalence of myeloid leukemias and the production of myeloid-derived suppressor cells (MDSCs). Tristetraprolin (TTP) is an RNA binding protein that regulates immune-related cytokines and chemokines by destabilizing target mRNAs. As TTP expression is known to decrease with age in myeloid cells, we used TTP-deficient (TTPKO) mice to model aged mice to study TTP regulation in age-related myelopoiesis. Both TTPKO and myeloidspecific TTPKO (cTTPKO) mice had significant increases in both MDSC subpopulations M-MDSCs (CD11b+Ly6ChiLy6G-) and PMN-MDSCs (CD11b+Ly6CloLy6G+), as well as macrophages (CD11b+F4/80+) in the spleen and mesenteric lymph nodes; however, no quantitative changes in MDSCs were observed in the bone marrow. In contrast, gain-of-function TTP knock-in (TTPKI) mice had no change in MDSCs compared with control mice. Within the bone marrow, total granulocyte-monocyte progenitors (GMPs) and monocyte progenitors (MPs), direct antecedents of M-MDSCs, were significantly increased in both cTTPKO and TTPKO mice, but granulocyte progenitors (GPs) were significantly increased only in TTPKO mice. Transcriptomic analysis of the bone marrow myeloid cell populations revealed that the expression of CC chemokine receptor 2 (CCR2), which plays a key role in monocyte mobilization to inflammatory sites, was dramatically increased in both cTTPKO and TTPKO mice. Concurrently, the concentration of CC chemokine ligand 2 (CCL2), a major ligand of CCR2, was high in the serum of cTTPKO and TTPKO mice, suggesting that TTP impacts the mobilization of M-MDSCs from the bone marrow to inflammatory sites during aging via regulation of the CCR2-CCL2 axis. Collectively, these studies demonstrate a previously unrecognized role for TTP in regulating age-associated myelopoiesis through the expansion of specific myeloid progenitors and M-MDSCs and their recruitment to sites of injury, inflammation, or other pathologic perturbations.

overall_design: Bone marrow scRNA-transcriptomic profile of 3-month-old wildtype (WT), tristetraprolin knock-out (TTPKO) and myeloid-specific TTPKO (cTTPKO) mice. Bulk-RNA sequencing of 6 month (BM_Y1,2,5,6,9,10) and 24 month WT bone marrow (BM_O1,2,4,5,6,7)

first: Kyu

middle: H

last: Kwack

first: Lixia

last: Zhang

first: Elliot

middle: D

last: Kramer

first: Ramkumar

last: Thiyagarajan

first: Natalie

middle: A

last: Lamb

first: Yukitomo

last: Arao

first: Kenneth

last: Seldeen

first: Bruce

middle: R

last: Troen

first: Perry

last: Blackshear

first: Scott

middle: I

last: Abrams

first: Keith

last: Kirkwood


title: Metabolic labeling of cardiomyocyte-derived small extracellular-vesicle (sEV) miRNAs identifies miR-208a in cardiac regulation of lung gene expression

city: Birmingham

first: Chaoshan

last: Han

state: Alabama

address: VH G100H 1670 University Blvd

department: Biomedical Engineering

institute: University of Alabama at Birmingham

type: Non-coding RNA profiling by high throughput sequencing

summary: Toxoplasma gondii uracil phosphoribosyltransferase (UPRT) converts 4-thiouracil (4TUc) into 4-thiouridine (4TUd), which is incorporated into nascent RNAs and can be biotinylated, then labeled with streptavidin conjugates or isolated via streptavidin-affinity methods. Here, we generated mice that expressed T. gondii UPRT only in cardiomyocytes (CMUPRT mice) and tested our hypothesis that CM-derived miRNAs (CMmiRs) are transferred into remote organs after myocardial infarction (MI) by small extracellular vesicles (sEV) that are released from the heart into the peripheral blood (PBsEV). We found that 4TUd was incorporated with high specificity and sensitivity into RNAs isolated from the hearts and PBsEV of CMUPRT mice six hours after 4TUc injection. In PBsEV, 4TUd was incorporated into CM-specific/enriched miRs including miR-208a, but not into miRs with other organ or tissue-type specificities. 4TUd-labeled miR208a was also present in lung tissues, especially lung endothelial cells (ECs), and CM-derived miR-208a (CMmiR-208a) levels peaked 12 hours after experimentally induced MI in PBsEV and 24 hours after MI in the lung. Notably, miR-208a is expressed from intron 29 of alpha myosin heavy chain (a-MHC), but a-MHC transcripts were nearly undetectable in the lung. When PBsEV from mice that underwent MI (MI-PBsEV) or sham surgery (Sham-PBsEV) were injected into intact mice, the expression of Tmbim6 and NLK, which are suppressed by miR-208a and cooperatively regulate inflammation via the NF-kappa B pathway, was lower in the lungs of MI-PBsEV-treated animals than the lungs of animals treated with Sham-PBsEV or saline. In MI mice, Tmbim6 and NLK were downregulated, whereas endothelial adhesion molecules and pro-inflammatory cells were upregulated in the lung; these changes were significantly attenuated when the mice were treated with miR-208a antagomirs prior to MI surgery. Thus, CMUPRT mice enables us to track sEV-mediated transport of CMmiRs and identify an miR-208a-mediated mechanism by which myocardial injury alters the expression of genes and inflammatory response in the lung.

overall_design: two troup : 1, small extracellular vesicle from peripherial blood 12 h after sham surgery, 2,   small extracellular vesicle from peripherial blood 12 h after myocardial infarction surgery. Each group contain 2 replicate.

first: Qin

last: Gangjian

first: Han

last: Chaoshan


title: Intestinal epithelial cells

city: Philadelphia

first: Joshua

middle: .H

last: Rhoades

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Effect of  depletion of the Gne gene in Sol8 murine muscle cells

city: Jerusalem

first: Stella

last: Mitrani-Rosenbaum

address: Ein Karem

country: Israel

institute: Hadassah -The Hebrew University Medical Center

summary: GNE myopathy is an adult onset neuromuscular disorder characterized by slowly progressive distal and proximal muscle weakness, caused by missense recessive mutations in the GNE gene. Although the  encoded bifunctional enzyme is well known as the limiting factor in the biosynthesis of sialic acid, no clear mechanisms have been recognized to account for the muscle atrophic pathology, and novel functions for GNE have been hypothesized.  No reliable animal model is available for the disease and cellular models from GNE myopathy patients' muscle cells (expressing the mutated protein) are less informative than expected.  In order to broaden our knowledge on GNE functions in muscle, we have generated a Gne knock out murine muscle cell lineage to identify the events resulting from the total lack of the protein. A thorough multi-omics analysis of both systems including transcriptomics, proteomics, phosphoproteomics and ubiquitination,  unraveled novel pathways for Gne, in particular its involvement  in cell cycle control and in the DNA damage/repair pathway.The elucidation of fundamental mechanisms of Gne in normal muscle may contribute to the identification of the disrupted functions in GNE myopathy, thus, to the definition of novel  biomarkers and possible therapeutic targets for this disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Sol8 Gne KO and  WT cells

first: Nili

last: Ilouz

first: Miriam

last: Guttman

first: Shmuel

last: Ruppo


title: Single cell transcriptomics of bulk and Chga-CreER marked intestinal epithelial cells.

summary: The intestinal epithelium exhibits a rapid and efficient regenerative response to injury. Emerging evidence supports a model where plasticity of differentiating(ed) cells, particularly those in the secretory lineages, contributes to epithelial regeneration upon ablation of injury-sensitive stem cells. However, such facultative stem cell activity is rare within secretory populations. Here we ask whether specific functional properties predict facultative stem cell activity. We utilize in vivo labeling combined with ex vivo organoid formation assays to evaluate how cell age and autophagic state contribute to facultative stem cell activity within secretory lineages.  Strikingly, we find that cell age (time elapsed since cell cycle exit) does not correlate with secretory cell plasticity. Instead, high autophagic activity predicts plasticity and resistance to DNA damaging injury independently of cell lineage. Our findings indicate that autophagic status prior to injury serves as a lineage-agnostic proxy for the prospective identification of facultative stem cells.

overall_design: Single cell RNA sequencing on intestinal epithelial cells from a ChgaCreER-tdTomato::Rosa26LSL-eYFP mouse. After 5 daily 1mg tamoxifen injections, eYFP+ and bulk epithelial cells were sorted from small intestinal crypts and incubated with BioLegend Hashtag antibodies to distinguish sample origin.

first: Christopher

middle: J

last: Lengner

first: Nicolette

middle: M

last: Johnson


title: Single cell transcriptomics of Autophagy high and low intestinal epithelial cells.

overall_design: Single cell RNA sequencing of intestinal epithelial cells with high and low autophagic flux. Cells were stained with the autophagic vesicle tracker dye, CytoID, and the brightest (CytoID_High) and dimmest (CytoID_Low) 15% of cells were sorted out and processed for sequencing. CytoID cells from high and low cells were pooled from N=2 mice with each mouse identified using BioLegend Hashtag antibodies.


title: The genomic response of human granulosa cells (KGN) to melatonin and specific agonists/antagonists to the melatonin receptors

city: Québec

first: Asma

last: Arjoune

state: Québec

address: 3326,rue de la monnerie, Appertement 1

department: Animal sciences

country: Canada

institute: Laval University

summary: Melatonin is a known modulator of follicle development, it acts through several molecular cascades via binding to its two high-affinity, G-protein coupled receptors MT1 and MT2. Even though it is believed that melatonin can modulate granulosa cell (GC) functions, there is still limited knowledge of how it can act in human GC through MT1 and MT2 and which one is the major receptor implicated in the effects of melatonin on the metabolic processes in the dominant follicle. To better characterize the roles of the MT1 and MT2 receptors on the effects of melatonin on follicular atresia and the regulation of proliferation and differentiation of granulosa cells during the antral stage, human granulosa-like tumor cells (KGN) were treated with specific melatonin receptor agonists and antagonists, and gene expression was analyzed with RNA-seq technology. Following appropriate normalization and the application of a fold change cut-off of 1.5 (FC 1.5, p ≤ 0.05) for each treatment, lists of the principal differentially expressed genes (DEGs) are generated. Analysis of major upstream regulators suggested that the MT1 receptor may be involved in the melatonin antiproliferative effect by reprogramming the metabolism of human GC by activating the PKB signaling pathway. Our data suggest that melatonin may act complementary through both MT1 and MT2 receptors to modulate human GC steroidogenesis, proliferation, and differentiation. However, MT2 receptors may be the ones implicated in transducing the effects of melatonin on the prevention of GC luteinization and follicle atresia at the antral follicular stage through stimulating the PKA pathway.

overall_design: 28 samples were analysed, 4 control compared to 4 melatonin treatments  (10 -7M),then compared to 4 melatonin treatments (10-9 M), then compared to 4 melatonin (10-9 M) + N-acetyl serotonin treatments , then  compared to 4 melatonin (10-9 M) + IIK7 treatments, then compared to 4 melatonin (10-9 M) + S26131 treatments, then compared to  4 melatonin (10-9 M) + 4P-PDOT treatments (total of 4 replicates)

first: A

first: M

last: Assidi

last: Sirard


title: Bulk transcriptomics of Hopx-CreER and Lgr5-CreER marked intestinal epithelial cells.

overall_design: RNA sequencing on intestinal epithelial cells from HopXCreER::Rosa26LSL-tdTomato and Lgr5eGFP-IRES-CreER::Rosa26LSL-tdTomato mice. We injected N=3 mice/genotype with 1mg of tamoxifen and harvested small intestinal crypts 16h later. We extracted RNA from sorted tdTomato+ cells from HopXCreER::Rosa26LSL-tdTomato mice and eGFP/tdTomato double + cells from Lgr5eGFP-IRES-CreER::Rosa26LSL-tdTomato mice.


title: Analysis of Drosophila melanogaster nascent transcription start sites

city: La Jolla

first: Nathaniel

last: Delos Santos

state: CA

address: 9500 Gilman Drive MC 0640

institute: University of California San Diego

summary: To identify TF binding motifs with position-dependent functions associated with transcription initiation, we performed csRNA-seq to map initiating transcripts in Drosophila melanogaster embryos. We started with cell culturing and csRNA-seq for data acquisition. This was followed by a csRNA-seq bioinformatics analysis comparing TSS with more vs. less nascent transcription.

overall_design: Fly cell culture and treatment      Canton S wild-type Drosophila melanogaster flies were grown at 25˚C at 70-80% humidity in population cages. The embryos were collected on molasses-agar plates covered with yeast.  Library prep and csRNA-seq on fly cells      CsRNA-seq was performed on embryonic (0-12h) Drosophila melanogaster cells as previously described  (Duttke et al., 2019).  TSS quantification from csRNA-seq      First, 3’ adapters were cut using the the following command:  homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20 {reads.fastq.gz}      Where {reads.fastq.gz} stands in for the actual read file.  Then the trimmed reads were aligned to the dm6 reference genome using the STAR aligner, with splice junctions informed by the corresponding Ensemble Genes GTF file available from UCSC  (Dobin et al., 2013; Howe et al., 2021). The read alignments were converted into tag directories using HOMER. A HOMER script, getTSSfromReads.pl, was then used to identify individual TSS from the assay from the 5’ ends of the aligned reads, and score them by their coverage.  The resulting TSS file was converted to a scored bed file using awk, and coverage scores were transformed using the function log2(x+1), where x was the original score.

first: Sascha

last: Duttke

middle: P

last: Santos

first: Sven

last: Heinz

last: Benner


title: TE-derived small RNA  analysis of human and chimpanzee iPS cells

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: Small RNA-seq were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2).  The human samples were mapped to the human genome (hg38) and the chimpanzee samples were mapped to the chimpanzee genome (panTro5).  The mapped reads for individual TE copies (in the repeatmasker tables downloaded from UCSC genome browser) were counted, and those for the same subfamily were summed up.  The counts were normalized by RPM (reads per million genome-mapped reads).

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Two human and two chimpanzee iPS cell lines (all are females and 36 to 43 years old) were cultured in the same condition.  RNAs were then extracted, and small RNA sequencing libraies were made for HiSeq sequencing in the 50-bp single-end mode.

first: Tomoko

first: Takuma

last: Hashimoto

first: Masanori

last: Imamura


title: ChIP-seq analysis of human and chimpanzee iPS cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq for H3K4me3 and H3K27me3 were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2).  The reads were  mapped to the respective genomes (hg38 for human and panTro5 for chimpanzee).

overall_design: Two human and two chimpanzee iPS cell lines (all are females and 36 to 43 years old) were cultured in the same condition.  Native chromatins were prepared by the micrococcal nuclease treatment, and incubated with antibodies against H3K4me3 and H3K27me3, respectively.  Input and IP libraries were sequenced on HiSeq X Ten in the 150-bp paired-end mode.

first: Mayu

last: Hirata


title: Transcriptome analysis of human and chimpanzee iPS cells

summary: mRNA-seq were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2).  To compare gene expression levels, the reads were first mapped to the chimpanzee genome (panTro5), and mapped reads were then mapped to the human genome (hg38).  Gene expression was anlyzed based on the hg38 annotation.

overall_design: Two human and two chimpanzee iPS cell lines (all are females and 36 to 43 years old) were cultured in the same condition.  RNAs were then extracted, and strand-specific poly(+) RNA sequencing libraies were made for HiSeq sequencing in the 150-bp paired-end mode.


title: ChIP-seq and Transcriptome analysis of human and chimpanzee iPS cells


title: HCP5 inhibits apoptosis via c-Myc transcriptional regulation mediated by UTP3 based chromatin-RNA-binding protein interaction [ATAC-Seq]

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

summary: This study demonstrates that HCP5/UTP3/c-Myc/VAMP3 axis plays important role in inhibition of cancer cell apoptosis and HCP5 can be targeted to contribute to cell apoptosis induced by cytotoxic agents.

overall_design: ATAC-seq of HCP5-silenced and control KYSE150 and KYSE510 cells

first: Yabing

first: Qingyu

last: Luo


title: HCP5 inhibits apoptosis via c-Myc transcriptional regulation mediated by UTP3 based chromatin-RNA-binding protein interaction


title: In vivo expansion of a functionally different CD9 decidual-like NK cell subset following autologous hematopoietic stem cell transplantation

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: Autologous hematopoietic stem cell transplantation (autoHSCT) is a treatment option for hematological disorders and pediatric solid tumors. Natural killer (NK) cells are the first lymphocyte subset returning to normal levels. To uncover global changes during NK cell reconstitution after autoHSCT, we performed for the first time RNA-sequencing on NK cells before and after autoHSCT. Results showed profound changes in gene expression profile of NK cells immediately after autoHSCT. Several biological processes including cell cycle, DNA replication and the mevalonate pathway were enriched. Significantly, we observed that following autoHSCT, NK cells acquired a decidual-like gene expression profile. By using multiparametric flow cytometry, we confirmed the expansion of NK cells expressing CD9 immediately after autoHSCT, and we observed that these decidual-like NK cells exhibited lower degranulation besides higher granzyme B and perforin expression than CD9- NK cells. These results provide new insights on the physiopathology of NK cells during their reconstitution after autoHSCT.

overall_design: We performed RNA sequencing using RNA from NK cells obtained from blood of Multiple Myeloma patients treated with Autologous Hematopoietic Steam Cell Transplantation (AutoHSCT) at 3 time point (T1 = pre-transplantation; T2 = after recovery of > 1000 leukocytes/ul, around 15 days after transplantation; T3 = 03 days after transplantation).

first: Ane

last: Orrantia

last: Vázquez de Luis

first: Gabriel

last: Astarloa-Pando

first: Iñigo

last: Terrén

first: Ainhoa

last: Amarilla-Irusta

first: Carmen

last: Gonzalez

first: Alasne

last: Uranga

first: Tomás

last: Carrascosa

first: Juan

last: Mateos-Mazón

middle: C

last: García-Ruiz

first: Ana

last: Quintas

last: Dopazo

first: Olatz

last: Zenarruzabeitia

first: Francisco

last: Borrego


title: HCP5 inhibits apoptosis via c-Myc transcriptional regulation mediated by UTP3 based chromatin-RNA-binding protein interaction [RNA-Seq]

last: Yabing Nan

overall_design: RNA-seq of HCP5-silenced and control KYSE150 and KYSE510 cells


title: Characterization of a new genetic signature associated with copy number variation that determines outcome in lung adenocarcinoma patients

city: Guangzhou

first: Gong

last: Zhang

state: Guangdong

address: 601,Huangpu Avenue West,Tianhe District

department: College of Life Science and Technology

institute: Jinan University

summary: Background: The occurrence of lung adenocarcinoma (LUAD) is a complicated process, involving the genetic and epigenetic changes of proto-oncogenes and oncogenes. The objective of this study was to establish new predictive signatures of lung adenocarcinoma based on copy number variation (CNVs) and gene expression data.  Methods: Next-generation sequencing was implemented to obtain gene expression and CNV information. According to univariate, multivariate survival Cox regression analysis and Lasso analysis, the expression profiles of lung adenocarcinoma patients were screened and a risk score formula was established and experimentally validated in a local cohort. The model was evaluated by three independent cohorts, and then validated by clinical samples from LUAD patients.  Results: A total of 844 CNV-related differential expressed genes (CNV related DEGs) were identified. An CNV associated-six gene signature was dramatically linked to overall survival in lung adenocarcinoma samples from both training and validation groups. Functional enrichment analysis further revealed involvement of genes in p53 signaling pathway and cell cycle, as well as the mismatch repair pathway. Risk score is an independent marker considering clinical parameters and had better prediction in clinical sub-population.  The same signature also classified tumors tissues of clinical patients those with CNV detected from their corresponding non-tumorous tissues with an accuracy of 0.92.  Conclusions: In conclusion, we identified a new class of 6 CNV-related gene markers that may act as efficient prognostic predictors of lung adenocarcinoma, thus contributing to individualized treatment decisions in patients.

overall_design: In total, 20 pairs of  tumor and matched adjacent tumor-free tissues were collected during the surgery from LUAD patients admitted to The Maoming People’s Hospital between 2020 and 2021. None of the patients had preoperative chemotherapy or preoperative radiotherapy. Tumor staging was determined according to AJCC TNM system. All tumor infomations were histologically classified based on World Health Organization criteria. Pathologic, clinical and follow-up patient informations were obtained from hospital medical records

first: Yisheng

last: Huang


title: Genome-wide maps of ALKBH1 binding sites in mouse primary hepatocytes

city: Chengdu

first: Liping

last: Luo

state: Sichuan

address: 783#，Xindu Avenue

department: School of Bioscience and Technology

institute: Chengdu Medical College

summary: AlkB homolog 1 (ALKBH1) has been reported to act as a DNA 6mA demethylase to remove 6mA modification in eukaryotic genomes. Our previous data showed downregulated ALKBH1 in mouse and human fatty liver and increased DNA 6mA levels in mouse fatty liver. We developed liver-specific ALKBH1 knockout (AKO) mice to directly study the role of ALKBH1 mediated DNA 6mA modification during the development of hepatic steatosis. Deletion of liver ALKBH1 promoted hepatic steatosis and insulin resistance. Overexpression of ALKBH1 resulted in opposite phenotypes. To investigate the mechanism of ALKBH1 in regulating target gene expression. We performed ChIP-seq for identifying ALKBH1 binding sites on mouse hepatocytes genomes and validated its demethylase activity for DNA 6mA modification on the target genes via ChIP-qPCR assays.

overall_design: Examination of ALKBH1 binding sites in mouse primary heaptocytes

first: Haiyan

last: Zhou


title: Regulation of Liver metabolism by ALKBH1

summary: AlkB homolog 1 (ALKBH1) has been reported to act as a DNA 6mA demethylase to remove 6mA modificatione in ukaryotic genomes. Our previous data showed downregalted ALKBH1 in mouse and human fatty liver and increased DNA 6mA levels in mouse fatty liver. We hypothesize that ALKBH1 may be involved in hepatic lipid metabolism. To test this hypothesis, we generated liver-specific ALKBH1 knockout (Alkbh1 f/f, Albumine-cre; AKO) mice and used high-throughput RNA sequence and other assays to directly study the role of ALKBH1 during the development of hepatic steatosis.

overall_design: Examination of differential expressed genes between control (Alkbh1 f/f ) and AKO hepatocytes.


title: Discovery and validation of circulating miRNAs for the clinical prognosis of severe dengue

city: Bangkok

first: Umaporn

last: Limothai

state: Thailand

address: 1873 Rama IV Rd, Pathum Wan, Pathum Wan District, Faculty of Medicine, Chulalongkorn University

country: Thailand

institute: Chulalongkorn University, Faculty of Medicine

summary:
Background:  dengue is a potentially life-threatening viral infection. Early prognostic markers of severe complications may improve case management and reduce dengue-related mortalities. This study aimed to identify circulating microRNAs (miRNAs) as biomarkers for predicting severe dengue.
Methods: Serum samples from dengue-infected patients were collected on the first day of admission. Patients were followed up for 14 days after admission to determine the final diagnosis. Participants were divided into non-severe and severe dengue, as defined by WHO 2009 criteria. Circulating microtranscriptome analysis was performed using the NanoString miRNA Expression Assay. The expression level of candidate miRNAs were then validated by quantitative reverse transcription-PCR (qRT-PCR) method.
Findings: The discovery cohort (N=19) lead to the identification of 37 differentially expressed miRNAs between the two groups. Six miRNAs (miR122-5p, miR1246, miR1303, miR574-5p, miR30d-5p, and miR424-5p) were selected and further validated in the larger cohort (N=135). The qRT-PCR analysis confirmed that the six miRNAs expression levels were significantly higher in the severe dengue group compared to the non-severe group. Based on receiver operating characteristic (ROC) analysis, miR574-5p and miR1246 displayed the highest diagnostic performance in discriminating between severe from non-severe dengue (AROC curve =0·83). Additionally, miR574-5p and miR1246 had high sensitivity and high negative predictive value for detecting severe dengue. Multivariate analysis suggested that serum miR574-5p was an independent predictor of severe dengue (odds ratio 3·30, 95% CI 1·81-6·04; p<0·001).
Interpretation: Circulating miRNAs, especially miR-574-5p and miR-1246, could be promising diagnostic and prognostic biomarkers for severe dengue.

overall_design: A total of 19 serum samples were selected to investigate the expression profile of 798 human miRNAs using the nCounter1Human v3 miRNA Expression Assays (NanoString Technologies, Seattle, USA). The patients were divided into two groups based on their final diagnosis, including non-severe (N=11) and severe dengue groups (N=8).

first: Nattawat

last: Jantarangsi

first: Natthasit

last: Suphavejkornkij

first: Sasipha

last: Tachaboon

first: Janejira

last: Dinhuzen

first: Watchadaporn

last: Chaisuriyong

first: Supachoke

last: Trongkamolchai

first: Mananya

last: Wanpaisitkul

first: Chatchai

last: Chulapornsiri

first: Anongrat

last: Tiawilai

first: Thawat

first: Terapong

last: Tantawichien

first: Usa

last: Thisyakorn

first: Nattachai

last: Srisawat


title: Modeling Synaptic Mechanisms of Autism-associated Neuroligin-3 R451C Mutation Using Human Neurons

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Synaptic dysfunction represents a key pathophysiology in neurodevelopmental disorders such as autism spectrum disorder (ASD). Rare mutation R451C in human Neuroligin 3 (NLGN3, encoded by X-linked gene NLGN3), a cell adhesion molecule essential for synapse formation, has been linked to ASD. Despite success in recapitulating the social interaction behavioral deficits and the underlying synaptic abnormalities in mouse model, the impact of NLGN3 R451C on the human neuronal system remains elusive. Here, we generated isogenic knock-in human pluripotent stem cell lines harboring NLGN3 R451C allele and examined its impact on synaptic transmission. Analysis of co-cultured excitatory and inhibitory induced neurons (iNs) with mutation revealed an augmentation in excitatory synaptic strength comparing to isogenic control, but not in inhibitory synaptic transmission. Consistently, the augmentation in excitatory transmission was confirmed in iNs transplanted into mouse forebrain. Using single-cell RNA seq on co-cultured excitatory and inhibitory iNs, we identified differential expression genes (DEGs) and found NLGN3 R451C alters gene networks associated with synaptic transmission. Gene ontology and enrichment analysis revealed convergent gene networks associated with ASD and other mental disorders. Our finding suggests that the NLGN3 R451C mutation could preferentially impact excitatory neurons, which causes overall network properties changes and excitation-inhibition imbalance related to mental disorders.

overall_design: Three samples of mixed excitatory and inhibitory human neurons cultured on primary mouse glia were harvested and run through the 10X Genomics Chromium device for scRNAseq.  One sample was prepared from unedited H1 hESC and two were isolates of CRISPR/Cas9-edited H1 cells with NLGN3 R451C introduced.  Libraries were prepared using the 10X Genomics 3' GEM Reagent Kit v3.1. After aligning reads with a mixed human and mouse reference index in cellranger, and merging samples in Seurat, mouse-specific clusters were removed, leaving only human cell data for analysis.

first: Le

last: Wang

first: Vincent

last: Mirabella

first: Azadeh

last: Jadali

first: Kelvin

middle: Y

last: Kwan

first: Zhiping

last: Pang


title: Knockdown of Ror2 in lineage-depleted tumor cells were derived from 2153L basal-like TP53null mammary tumor models

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We elucidated the function of the alternative Wnt receptor Ror2 in lineage-depleted tumor organoid cells, using lentiviral short hairpin RNA (shRNA)-mediated depletion.

overall_design: two group comparison

first: Fengju

last: Chen

first: Kevin

last: Roarty


title: A new LKB1 activator, Piericidin Analogue S14, attenuates tubular cell senescence and renal fibrosis through promoting AMPK-induced autophagy and mitochondrial homeostasis pathway [II]

first: canzhen

last: liu

address: Jingxi Street  Guangzhou Baiyun District China

department: Nanfang Hospital

institute: Southern Medical University

summary: AMP-activated protein kinase (AMPK) stabilizes tubular cell metabolism and protects against renal fibrosis through promoting autophagy and mitochondrial homeostasis. Liver kinase B1 (LKB1) is the key regulator for AMPK activation. However, the direct activators of LKB1 are scarce in commercial. In this study, we report a novel LKB1 activator, the piericidin analogue S14 (PA-S14), which was isolated from the culture broth of a marine-derived Streptomyces strain by our group. PA-S14 binds with residue D176 in LKB1 kinase domain, and then induces LKB1 phosphorylated activation and its complex formation with MO25 and STRADα. Furthermore, PA-S14 promotes AMPK activation to enhance LC3B-II/LC3B-I ratio, trigger autophagosome formation and increase autophagic flux. PA-S14 exhibits perfect protective effects on stabilizing mitochondrial homeostasis, inhibiting tubular cell senescence, and retarding fibrogenesis in various CKD models (UUO, UIRI and adriamycin nephropathy models) and TGF-β-stimulated tubular cell culture. Transcriptomics sequencing and site-specific mutation analysis further prove that PA-S14 is a novel lead compound of LKB1 activator, which perfectly protects against renal fibrosis through inducing AMPK-mediated autophagy and mitochondrial homeostasis.

overall_design: six sample are analyzed, replicates are included, there are 3 UIRI groups and 3 UIRI+PA-S14 groups. For UIRI model, BALB/c mice were subjected to unilateral IRI. At 4 days after IRI, mice were subjected to daily intraperitoneal injections of vehicle or PA-S14 for 7 days.

first: Canzhen

last: Liu


title: A new LKB1 activator, Piericidin Analogue S14, attenuates tubular cell senescence and renal fibrosis through promoting AMPK-induced autophagy and mitochondrial homeostasis pathway [I]

overall_design: six sample are analyzed, replicates are included, there are 3 control groups and 3 PA-S14 groups. The difference between the two groups was the intraperitoneal injection of vehicle in the control group and the intraperitoneal injection of drug PA-S14 in the PA-S14 group


title: Knockdown of Ror2 in lineage-depleted tumor cells were derived from 2225L basal-like TP53 null mammary tumor models

overall_design: Two-group comparison.


title: A new LKB1 activator, Piericidin Analogue S14, attenuates tubular cell senescence and renal fibrosis through promoting AMPK-induced autophagy and mitochondrial homeostasis pathway

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

overall_design: Refer to individual Series


title: RNA-sequencing analysis reveals mitochondrial dysfunction in Akap1 Knockout mice exposed to hyperoxia

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Akap1 KO and Wt mice were exposed to normoxia or hyperoxia for 48h. Total RNA was extracted from lungs of Wt Normoxia (n=3), Wt hyperoxia (n=3), Akap1 KO (n=3) and Akap1 hyperoxia (n=3) mice. RNA-sequencing was carried out followed by differential expression of genes in the following groups. Wt Normoxia vs Wt Hyperoxia, Akap1 KO Normoxia versus Akap1 KO Hyperoxia, Wt Normoxia versus Akap1 KO Normoxia and Wt Hperoxia versus Akap1 Hyperoxia.

overall_design: RNA-sequencing of Akap1 knockout and Wt lungs exposed to normoxia or hyperoxia for 48h

first: Ramani

last: Soundararajan

first: Narasaiah

last: Kolliputi


title: Single cell sequencing of transgenic mouse model of PDAC

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: We report the application for high-throughput profiling of different cell types in PDAC.

overall_design: Examination of all cell types from two mice bearing pancreatic carcinoma

first: Jing

last: Xue


title: Intestinal epithelial inositol polyphosphate multikinase protects mice from experimental colitis via governing colonic tuft cell homeostasis

city: Daejeon

first: Hanseul

last: Yang

address: 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Intestinal homeostasis is dynamically coordinated by various types of epithelial cells fulfilling their specific functions. Tuft cells as chemosensory cells have emerged as key players of the host response, such as innate immunity. Tuft cells are also critical for the restoration of intestinal architecture upon damage, thereby contributing to inflammatory bowel diseases (IBDs) characterized by defective intestinal barrier integrity. However, the molecular mechanism of how tuft cell homeostasis is controlled remains obscure. Recent studies have identified single-nucleotide polymorphisms in the inositol polyphosphate multikinase (IPMK) gene associated with IBD predisposition. IPMK, an essential enzyme for inositol phosphate metabolism, has been known to mediate major biological events such as growth. To investigate the functional significance of IPMK in gut epithelium, we generated intestinal epithelial cell (IEC)-specific Ipmk knockout (IPMKΔIEC) mice. Whereas IPMKΔIEC mice developed normally and showed no intestinal abnormalities during homeostasis, Ipmk deletion aggravated dextran sulfate sodium (DSS)-induced colitis, with higher clinical colitis scores, and elevated epithelial barrier permeability. Surprisingly, no apparent defects in epithelial growth signaling pathway and inflammation were found in DSS-challenged, IPMK-deficient colons. Rather, Ipmk deletion led to a significant decrease in the number of tuft cells without influencing other intestinal epithelial cells. Ipmk deletion in the gut epithelium was found to reduce choline acetyltransferase but not cytokines (e.g., IL-25), suggesting selective loss of cholinergic signaling. Single-cell RNA-sequencing of mouse colonic tuft cells (EpCAM+/Siglec F+) and immunohistochemistry revealed three populations of tuft cells and further showed that, in IPMKΔIEC mice, a transcriptionally inactive tuft club cell population was markedly expanded, and neuronal-related tuft cells were relatively decreased, supporting the abnormal development of tuft cells without IPMK functions. Thus, IPMK acts as a physiological determinant of colonic tuft cell homeostasis, thereby mediating tissue regeneration upon injury.

overall_design: Mouse colonic tuft cells (EPCAM+/SIGLEC-F+) were FACS sorted from wild type and Villin-Cre; IPMKf/f mouse. The sorted cells were analyzed by single cell RNA sequencing

first: Seung

last: Park

first: Dongeun

last: Lee

first: Seyun

last: Kim


title: Single-cell RNA-seq Identifies Dynamic Cardiac Transition Program from Adipose Derived Cells Induced by Leukemia Inhibitory Factor

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Adipose-derived cells (ADCs) from white adipose tissue (WAT) are promising stem cell candidates due to large innate regenerative reserves and achievement of clinically meaningful cardiac regeneration. However, due to the heterogeneity of ADCs and unsolved molecular mechanism underpins of cardiac acquisition, the ADC-Cardiac transition efficiency remains low. Here, we found a population of ADCs reacted to leukemia inhibitory factor (LIF) and differentiated into functional beating cardiomyocyte-like cells. With single cells sequencing, we profiled 39,432 single cell transcriptomes at multiple time points throught the cardiac transition course. Combined with FACS, we identified three distinct pdgfra+ ADC populations that responded differently to the LIF signaling and transited to cardiomyocyte like cells. Dynamic trajectories derived from pseudotime analysis on ADCs navigate a trajectory with two branches that correspond to two alternative fate decisions. Analysis of starting branch revealed Nuclear factor erythroid 2-related factor 2 (Nrf2) signaling is the crucial event in initiation of myogenic program. The ending two branches represented activated myofibroblast and cardiomyocyte like cells. Collectively, our findings offer a high-resolution dissection of ADC heterogeneity and cell fate dynamics during ADCs-Cardiac transition, thus shed new insights into potential cardiac stem cells for future usage.

overall_design: single-cell RNA-seq of adipose-derived progenitor cells undergoing cardiac transition.

first: Jiayi

last: Yao

first: Matteo

last: Pellegrini

first: Kristina

last: Boström


title: Expression atlas of chickpea during development

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we aim to present a global view of transcriptome dynamics in different tissues/organs/developmental stage in chickpea. We generated about ~31-95 million reads from each of 94 libraries representing 32 different tissues/organs using Illumina platform. We generated a hybrid assembly of these data along with PacBio data to produce full-length transcriptome assembly. We mapped the reads to the transcriptome assembly for estimation of the abundance of coding and long non-coding transcripts in different tissue samples. The transcriptome dynamics was studied by differential and tissue-specific expression analyses, and co-expression network and transcriptional regulatory network analyses.

overall_design: We collected different tissues/organs from vegetative and reproductive stages of development. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to the chickpea transcriptome assembly using Bowtie and fragments per exon kilobase per million (FPKM) was calculated using RSEM for each gene in all the samples to measure their gene expression.

first: Jain

last: Mukesh

first: Garg

last: Rohini

first: Bansal

last: Juhi


title: Methyltransferase Inhibitors Restore SATB1 Protective Activity Against Cutaneous T cell Lymphoma

city: TAmpa

first: Yonghong

last: Zhang

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

summary: We report Chromatin Immunoprecipitation for the histone modifications H3K27ac, H3K27m3 and H3K9m3 in human leukemia and lymphoma cell lines HuT78, Jurkat, K562, and RAJI to ascertain the regulatory landscape of in regards to transcriptional repression and activation.

overall_design: Examination of two different histone markers in 4 human leukemia/lymphoma cell lines

first: Harro

last: Carly

first: Xiaoqing

last: Yu

first: Jose

last: Conejo-Garcia


title: Comprehensive analysis of immune parameters, mRNA/miRNA profiles, and immune genes expression in the gill of rainbow trout infected infectious hematopoietic necrosis virus

status: Public on Oct 25 2022

city: Lanzhou City

first: lu

last: zhao

state: Gansu Province

address: Yintan Road Street

institute: Gansu Agricultural University


title: The Nup98::Nsd1 fusion gene induces CD123 expression in 32D cells

city: Kyoto

first: Kenji

last: Okamoto

state: Kyoto

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

institute: Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine

summary: The NUP98::NSD1 fusion gene is associated with extremely poor prognosis in patients with acute myeloid leukemia (AML). NUP98::NSD1 induces self-renewal and blocks differentiation of hematopoietic stem cells, leading to leukemia development. Despite its association with poor prognosis, targeted therapy for NUP98::NSD1-positive AML is lacking, as the details of NUP98::NSD1 function are unknown. Here, we generated 32D cells (a murine interleukin-3 (IL-3)-dependent myeloid progenitor cell line) expressing mouse Nup98::Nsd1 to explore the function of NUP98::NSD1 in AML, including by comprehensive gene expression analysis. We identified two properties of Nup98::Nsd1+ 32D cells in vitro: first, Nup98::Nsd1 promoted blocking of AML cell differentiation, consistent with a previous report; second, Nup98::Nsd1 increased dependence on IL-3 for cell proliferation, due to overexpression of the alpha subunit of the IL-3 receptor (IL3-RA, also known as CD123). Consistent with our in vitro data, IL3-RA was also up-regulated in samples from patients with NUP98::NSD1-positive AML. These results highlight CD123 as a potential new therapeutic target in NUP98::NSD1-positive AML.

overall_design: We compared gene expression profiling of Nup98::Nsd1+ 32D and mock-transduced 32D cells using a GeneChip™ Mouse Genome 430 2.0 Array to explore the function of NUP98::NSD1 in AML, including by comprehensive gene expression analysis.

first: Toshihiko

last: Imamura

first: Seiji

last: Tanaka

first: Hideki

last: Yoshida

first: Norio

last: Shiba

first: Tomoko

last: Iehara


title: Comprehensive analysis of immune parameters, mRNA/miRNA profiles, and immune genes expression in the gill of rainbow trout infected infectious hematopoietic necrosis virus [mRNA]

summary: Rainbow trout (Oncorhynchus mykiss) is a species of cold-water fish with important economic values, which is widely cultivated around the world. It is susceptible to infectious hematopoietic necrosis virus (IHNV), resulting in a large number of deaths. In this study, we measured the changes of immune parameters in different periods (6-, 12-, 24-, 48-, 72-, 96-, 120-, and 144 hours post infection (hpi)), transcriptome profiles of T48G/C48G and important immune-related genes expression patterns in rainbow trout gill following IHNV challenge through biochemical methods, RNA-seq and qRT-PCR. The results showed that AKP, ACP, T-SOD, ALT and AST activities, as well as MDA and LZM content decreased and then increased during infection, and reached to the lowest value at 48 hpi (P < 0.05), whereas CAT activity showed significant peaks at 48 hpi (P < 0.05). The mRNA and miRNA analysis identified 4343 differentially expressed genes (DEGs) and 11 differentially expressed miRNAs (DEMs), and numerous DEGs involved in immune responses, such as tlr3, tlr7, tlr8, traf3, ifih1, trim25, dhx58, ddh58, hsp90a.1, nlrc3, nlrc5, socs3, irf3, irf7, mx1, vig2, bcl2, casp3 and casp8。Integrated analysis identified four key miRNAs (miR-27d-3p, miR-124-5p, miR-301a-5p and miR-146-5p) that target important immune-related DEGs (tlr3, ifih1, vig2, irf8, socs3 and cox1). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs and target genes were significantly enriched in various immune-related terms including inflammatory response, DNA replication, cell adhesion and pathways of Toll-like receptor signaling, apoptosis, DNA replication, p53 signaling and MAPK signaling. The expression trends of 15 DEGs and 2 DEMs were further verified by quantitative real-time PCR, which confirmed the reliability of the transcriptome sequencing results. Expression analysis showed that tlr3, tlr7, traf3, ifih1, trim25, dhx58, hap90a.1, irf3, irf7 and mx1 genes increased significantly after 48 hpi during infection. This study contributes to the understanding of the immune response of rainbow trout against IHNV infection, and provides new insights into the immune regulation mechanisms for future studies.

first: Jinqiang

last: Huang

first: Lu

last: Zhao


title: Comprehensive analysis of immune parameters, mRNA/miRNA profiles, and immune genes expression in the gill of rainbow trout infected infectious hematopoietic necrosis virus [miRNA]

overall_design: In this study, we measured the changes of immune parameters in different periods (6-, 12-, 24-, 48-, 72-, 96-, 120-, and 144 hours post infection (hpi)), transcriptome profiles of T48G/C48G and important immune-related genes expression patterns in rainbow trout gill following IHNV challenge through biochemical methods, RNA-seq and qRT-PCR.


title: The role of macrophages extracellular traps on the biologic behaviors of FLSs from patients with RA

first: Weizhen

last: Weng

address: tianhe road 600

institute: the third affiliated hospital of SYSU

summary: Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammatory in joints. Macrophages are abundant in synovial tissue and fluid of RA. Macrophages extracellular traps (METs) are induced from macrophages and may generate a stable autoantigen-DNA complexes, leading to the generation of autoantibodies and development of autoimmunity. We aimed to investigate the role of METs on the biologic behaviors of FLSs from patients with RA. RA-FLS from 3 independent RA patients were treated with METs, and performed whole transcriptome sequencing on MET-treated and untreated groups in a total of 6 groups. Further, we performed bioinformatic analysis on the sequencing results (Novogene, China). The transcriptome was first explored for differentially expressed genes and the main results were visualized with a heatmap. Next, GO and KEGG enrichment analysis were performed on the differential genes. The results were visualized using dot plots to explore which functions of RA-FLS may be affected by MET and the potential pathways that affect RA-FLS function

overall_design: RA-FLS from 3 independent RA patients in medium containing 400ng/ml METs for 48 hours, and performed whole transcriptome sequencing on MET-treated and untreated groups.

first: Yunfeng

last: Pan


title: Post-transcriptional regulation in cranial neural crest cells expands developmental potential

first: Rachel

last: Keuls

address: One baylor plaza, Alkek N1020


title: Epigenetic inhibitors

summary: The project aims to looks at differential gene targets in the human Sezary syndrome HuT78 cell line when treated with epigenetic inhibitors romidepsin, F5446, and chaetocin compared to the vehicle treated cells (DMSO) for 72hrs.

overall_design: Cell line HuT78 treated with chaetocin, F5446, romidepsin, and DMSO for 72hrs


title: Post-transcriptional regulation in cranial neural crest cells expands developmental potential [I]

summary: Developmental potential is progressively restricted after germ layer specification during gastrulation. However, cranial neural crest cells challenge this paradigm, as they develop from anterior ectoderm yet give rise to both mesodermal derivatives of the craniofacial skeleton and ectodermal derivatives of the peripheral nervous system. How cranial neural crest cells differentiate into multiple lineages is poorly understood. Here, we demonstrate that cranial neural crest cells possess a transient state of increased chromatin accessibility; and that the earliest premigratory neural crest are biased towards either a neuronal or ectomesenchymal fate, with each lineage expressing distinct factors from the pluripotent state. We profile the spatiotemporal emergence of each neural crest population and demonstrate that the ectomesenchymal lineage forms prior to the neuronal progenitors. Expression of the pluripotency microRNA family miR-302 is maintained in cranial neural crest cells and genetic deletion leads to precocious specification of the ectomesenchymal lineage. We find that miR-302 directly targets Sox9 to slow the timing of ectomesenchyme induction and regulates multiple genes involved in chromatin condensation to maintain accessibility for neuronal differentiation. Loss of mir-302 results in reduced chromatin accessibility in the neuronal progenitor lineage of neural crest and a reduction in peripheral neuron differentiation. Our findings reveal a post-transcriptional mechanism governed by miRNAs from pluripotency as an important mechanism to expand developmental potential of cranial neural crest.

overall_design: The cranial region from TS16, 32-34 somite embryos were harvested for single cell mRNA sequencing using a 10X Genomics chromum controller

first: Ronald

last: Parchem


title: Hippocampal neurons’ cytosolic and membrane-bound ribosomal transcript profiles are differentially regulated by learning and subsequent sleep

city: Ann Arbor

first: Lijing

last: Wang

state: MI

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

summary: The hippocampus is essential for consolidating transient experiences into long-lasting memories. Memory consolidation is facilitated by postlearning sleep, although the underlying cellular mechanisms are largely unknown. We took an unbiased approach to this question by using a mouse model of hippocampally mediated, sleep-dependent memory consolidation (contextual fear memory). Because synaptic plasticity is associated with changes to both neuronal cell membranes (e.g., receptors) and cytosol (e.g., cytoskeletal elements), we characterized how these cell compartments are affected by learning and subsequent sleep or sleep deprivation (SD). Translating ribosome affinity purification was used to profile ribosome-associated RNAs in different subcellular compartments (cytosol and membrane) and in different cell populations (whole hippocampus, Camk2a+ neurons, or highly active neurons with phosphorylated ribosomal subunit S6 [pS6+]). We examined how transcript profiles change as a function of sleep versus SD and prior learning (contextual fear conditioning; CFC). While sleep loss altered many cytosolic ribosomal transcripts, CFC altered almost none, and CFC-driven changes were occluded by subsequent SD. In striking contrast, SD altered few transcripts on membrane-bound (MB) ribosomes, while learning altered many more (including long non-coding RNAs [lncRNAs]). The cellular pathways most affected by CFC were involved in structural remodeling. Comparisons of post-CFC MB transcript profiles between sleeping and SD mice implicated changes in cellular metabolism in Camk2a+ neurons and protein synthesis in highly active pS6+ (putative "engram") neurons as biological processes disrupted by SD. These findings provide insights into how learning affects hippocampal neurons and suggest that the effects of SD on memory consolidation are cell type and subcellular compartment specific.

overall_design: Translating ribosome affinity purification (TRAP) followed by analysis of ribosome-associated mRNAs [both membrane-bond (pellet fraction - PELL) and cytosolic (supernatant fraction - SUP)] in Camk2a+ neurons (HA-tagged), pS6+ neurons (S6-tagged), and input in CFC/HC and Sleep/SD mice.

first: James

last: Delorme

first: Varna

last: Kodoth

first: Yifan

first: Jingqun

last: Ma

first: Sha

last: Jiang

first: Sara

last: Aton


title: TNFα and IFNγ cooperate for efficient pro- to anti-inflammatory transition of macrophages during muscle regeneration

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia


title: Macrophage depletion blocks congenital SARM1-dependent neuropathy

city: St Louis

first: Jeffrey

last: Milbrandt

state: Missouri

address: 660 S Euclid Ave #5101

department: Genetics

institute: Washington University School of Medicine

summary: Axon loss contributes to many common neurodegenerative disorders. In healthy axons, the axon survival factor NMNAT2 inhibits SARM1, the central executioner of programmed axon degeneration. We identified two rare NMNAT2 missense variants in two brothers afflicted with a progressive neuropathy syndrome. The polymorphisms result in amino acid substitutions, V98M and R232Q, which reduce NMNAT2 NAD+-synthetase activity.  We generated a mouse model of the human syndrome and found that Nmnat2V98M/Nmnat2R232Q compound-heterozygous CRISPR mice survive to adulthood but develop progressive motor dysfunction, peripheral axon loss, and macrophage infiltration. These disease phenotypes are all SARM1-dependent. Remarkably, macrophage depletion therapy blocks and reverses neuropathic phenotypes in Nmnat2V98M/R232Q mice, identifying a SARM1-dependent neuroimmune mechanism as a key driver of disease pathogenesis. These findings demonstrate that SARM1 induces an inflammatory neuropathy and highlight the potential of immune therapy to treat this rare syndrome and other neurodegenerative conditions associated with NMNAT2 loss and SARM1 activation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NMNAT2(V98M/R232Q) transheterozygous mouse sciatic nerves at 2 and 6 months of age compared to WT age-matched controls.

first: Caitlin

middle: B

last: Dingwall

first: Amy

last: Strickland

first: Aldrin

middle: K

last: Yim

first: Joseph

last: Bloom

first: Aaron

last: DiAntonio


title: Apolipoprotein A-IV reduced metabolic inflammation in white adipose tissue by inhibiting IKK and JNK signaling in adipocytes

city: Shaanxi

first: Xiaoming

last: Li

address: Zhuque Street

institute: xian jiaotong univercity

summary: ApoA-IV produced by enterocytes as a major component of high-density lipoprotein plays a role in the satiation signal and also the transport of serum lipids. The present study aimed to investigate the effects of ApoA-IV on diet-induced obesity (DIO), metabolic inflammation and the underlying mechanisms. C57BL/6J ApoA-IV-/- (KO) and wildtype (WT) mice as well as KO mice stably transfected with ApoA-IV-green fluorescent protein (KO-A4-GFP) or solely GFP (KO-GFP) encoding adenoviruses were fed with standard 5% fat rodent chow (CD) or 60% high fat rodent chow (HFD) for 16 weeks.

overall_design: RNA-seq profiling of ApoA4 knockdown or WT mice, fed high fat diet or chow diet.  Total RNA was isolated from eWAT tissue samples taken from 21-week-old mice (n = 4 per group) . After fragmentation and conjugation with sequencing adapters, the cDNA libraries were sequenced on a BGI-seq 500 platform using the PE100 strategy

first: Xiaohuan

last: Liu

first: Yupeng

last: Zhang

first: Jingting

last: Zhou

first: Jing

last: Gao


title: The extraretinal photoreceptor OPSIN3 in the hypothalamus is involved in the regulation of water balance, body temperature and motor activity

city: Bristol

first: Ghadir

last: ElSamad

address: Whitson St.

country: United Kingdom

institute: University of Bristol

summary: To explore the role of the light-sensitive protein OPSIN3 in the supraoptic nucleus (SON) of the hypothalamus, we knocked down the gene encoding this protein (Opn3) in one SON of sprague dawley rats by delivering a Opn3 short hairpin RNA (shRNA). A non-targeting ShRNA was delivered to the opppsite SON in the same rat as a contros.We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 different rats at one time point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Opn3 knock down SON samples in comparison to control SON samples.

first: Soledad

last: Bárez-López

last: Elsamad

first: Paul

last: Bishop

first: David

last: Murphy

first: Michael

last: Greenwood


title: Glomerular RNA-seq data of the kidney podocyte-specific Hdac1 and Hdac2 deficient mice

city: New Haven

first: Paulina

last: Medina Rangel

state: Connecticut

address: 333 Cedar St

department: Internal Medicine

institute: Yale University

summary: Podocyte histone deacetylases (HDAC) are essential in maintaining a normal glomerular filtration barrier by modulating podocyte quiescence. Podocyte-specific loss Hdac1 and 2 in mice results in severe proteinuria and sustained DNA damage, likely caused by epigenetic alterations and deficient DNA repair, that result in podocyte senescence. Through glomeruli isolation and RNA-seq profiling from the mutant mice, we demonstrated that senescent podocytes develop a senescence-associated secretory phenotype (SASP) that contribute to the loss of podocytes. The role of HDACs in senescence may provide important clues in our understanding of how podocytes are lost following injury.

overall_design: The freshly glomeruli samples were isolated from the Control mice and HDAC KO mice at 3 weeks of age for the RNAseq analysis. Each sample contained 2 mice in order to get the sufficient glomeruli samples, and 2 independent experiments were analyzed and summarized.

first: Shuta

last: Ishibe

middle: X

first: Xuefei

last: Tian

first: Jianlei

last: Gu


title: SCAPs Regulate DFSC Differentiation via the Osteoglycin-Hedgehog Pathway

city: Beijing

first: Xiaoyu

middle: yu

last: Lin

state: Beijing

address: You an men

summary: The developing root apical complex, including the Hertwig’s epithelial root sheath, apical papilla, and dental follicle (DF), is the germinal center of root development wherein the DF constantly develops into periodontal tissues. However, whether the DF development is regulated by the adjacent apical papilla is largely unknown. In this study, using a transwell system in vitro, we found that stem cells from the apical papilla (SCAPs) inhibited the differentiation but maintained the stemness of dental follicle stem cells (DFSCs). Furthermore, high-throughput transcriptome sequencing revealed that the Hedgehog (Hh) pathways were significantly downregulated in DFSCs when co-cultured with SCAPs. Upregulation or downregulation of the Hh pathway could activate or inhibit the multidirectional differentiation of DFSCs, respectively. By secreting osteoglycin (OGN), the SCAPs regulated the stemness and multidirectional differentiation of DFSCs via the OGN-Hh pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dental follicle (DF)/Co-culture DFSCs/Control DFSCs

first: Xiaoshan

last: Wu

first: Qiong

first: Songlin

last: Wang


title: DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression (microarray)

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

summary: Chronic myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed bulk transcriptome profiling accompanied by single cell RNA-sequencing on CD34+ stem/progenitor cells from serial patient samples obtained at the chronic MPN and sAML phases, identifying aberrantly increased expression of dual-specificity phosphatase 6 (DUSP6) underlying disease transformation. Genetic and pharmacologic targeting of DUSP6 led to inhibition of S6 and JAK/STAT signaling, resulting in potent suppression of cell proliferation, while also reducing inflammatory cytokine production in primary samples. Furthermore, ectopic DUSP6 expression augmented proliferation and mediated JAK2 inhibitor resistance, while DUSP6 inhibition reduced colony-forming potential of JAK2 inhibitor-persistent patient cells. Mechanistically, DUSP6 perturbation dampened S6 signaling via inhibition of RSK1, which we identified as a second indispensable candidate associated with poor clinical outcome. Ectopic expression of DUSP6 in patient-derived xenograft (PDX) models exacerbated disease severity and led to early lethality, whereas DUSP6 knockdown suppressed leukemic engraftment. Finally, pharmacological inhibition of DUSP6 potently and specifically suppressed disease development across Jak2 V617F and MPL W515L MPN mouse models, as well as sAML PDXs, without inducing toxicity in healthy controls. These findings underscore DUSP6 in driving disease transformation and therapeutic resistance, and highlight the DUSP6-RSK1 axis as a novel, druggable pathway in myeloid malignancies.

overall_design: Microarray analysis of sorted CD34+ HSPCs from MPN, sAML, and healthy donors

first: Stephen

middle: T

last: Oh


title: Research on mechanisms of miR-27a-3p on  Cisplatin sensitivity of hepatocellular carcinoma based on next generation sequencing

city: Changchun

first: Shui

last: Liu

state: Jilin Province

address: Ziqiang Stree No.218

department: The Second Hospital of Jilin University

institute: Jilin University

summary: Hepatocellular carcinoma (HCC) accounts for 75% of primary liver cancer, ranking seventh in the incidence rate of tumors worldwide, and second in the mortality rate of tumors. The 5-year survival rate after radical surgery is only 59%-68%, and due to the influence of proliferation, invasion, microvascular infiltration and inflammatory environment of hepatocellular carcinoma, Recurrence is still possible after surgical resection, local ablative therapy or liver transplantation. Systemic antitumor therapy can control disease progression and prolong patient survival, and a variety of kinase inhibitors are used in patients who cannot undergo surgery. However, due to the existence of acquired drug resistance to multikinase inhibitors, its effect is not good. Platinum-based FOLFOX4 is recommended, but its efficacy is limited by drug resistance. miR-27a-3p, located in the short arm of chromosome 19, has been found to be involved in inhibiting the activity, proliferation, angiogenesis, and invasion of liver cancer. Other studies have found that miR-27a-3p regulates the sensitivity of tumors (esophageal cancer and breast cancer) to Cisplatin by regulating the apoptosis of the Bcl-2 protein family. The cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimitotic solution. The HCC cell line Huh-7 was transfected using Lipofectamine 3000 reagent following the manufacturer’s protocol and incubated for 48h for further analysis. The gene expression profiles were analyzed of Huh-7 cells transfected with miR-27a-3p mimics or NC to assess effect of miR-27a-3p on Cisplatin sensitivity of HCC.

overall_design: High-throughput sequencing raw data for 6 samples, M1,M2 and M3 are three samples from experimental group (cells with miR-27a-3p mimics transfection), NC1, NC2,and NC3 are three samples from negative control group (cells with NC transfection).

first: Jinda

last: Bian


title: Nm-REP-seq Reveals 2’-O-Methylation Landscape at the 3'-end of Noncoding RNAs with Single-base Resolution

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary:
Many non-coding RNAs (ncRNAs),  such as piRNAs, miRNAs and siRNAs, contain Nm at the 3'-end nucleotides, protecting the 3’-ends form terminal nucleotide addition or exonucleolytic degradation, but whether other kinds of RNAs contain a 3'-terminal Nm remain unknown. Here, we developed Nm-REP-seq to globally profile the 3'end-Nm sites and we revealed several novel classes of Nm-containing ncRNAs in mice and drosophila. Importantly, we discovered that Nm distribute at the end of miRNA, snoRNA, snRNA, tRNA as well as fragments derived from them. Collectively, our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation.
Method: We developed Nm-REP-seq to globally profile the 3'-end Nm sites.
Results: We discovered that Nm distribute at the end of miRNA, snoRNA, snRNA, tRNA as well as fragments derived from them.
Conclusion:Collectively, our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Total RNA was extracted from mouse testis as well as drosophila Kc167 cell and subjected to modified Nm-REP-seq library construction protocol, in three biological repeats (rep1, rep2 and rep3).

first: Jianhua

first: Ping

last: Zhang


title: The Transcriptomic Landscape of Pediatric Astrocytoma

city: CIUDAD DE MEXICO

first: Abrahan

last: Hernandez-Hernandez

state: CIUDAD DE MEXICO

address: Dr.Márquez No.162, Col. Doctores, Delegación: Cuauhtémoc

country: Mexico

institute: Hospital Infantil de México Federico Gómez

summary: Tumors of the central nervous system are the most common solid neoplasia during human childhood, representing one of the leading causes of cancer-related mortality. Tumors that originate from astrocyte cells (astrocytoma) in the brain are the most frequently found. According to their histological and pathological features, these tumors are classified into four categories. However, recently an extra layer of molecular classification of the tumorigenesis-associated genes IDH1/2 and H3F3A has been incorporated into the classification guidelines. While mutations in H3F3A are exclusively found in a subtype of pediatric astrocytoma grade IV, mutations in IDH1/2 are very rare in children younger than 14 years old. The transcriptomic profiles of astrocytoma in adults and children have been extensively studied however focusing on the study of the transcriptomic profile of the different grades of astrocytoma (including the additional layer of molecular classification) in pediatric populations are scarce. Therefore, we have profiled the transcriptomic landscape of the four grades of pediatric astrocytoma by RNA sequencing.

overall_design: Next Generation Sequencing of total RNA from 15 biopsies of pediatric astrocytoma from cerebrum and cerebellum and five healthy matching tissues

last: Hernández-Hernandez

first: Tayde

last: López-Santaella

first: Aranxa

last: Torres-Caballero

first: Amarantha

last: Serrato

first: Ulises

last: Torres-Flores

first: Diego

last: Valencia

first: Fernando

last: Chico-Ponce de Leon

first: Vicente

last: González-Carranza

first: Samuel

last: Torres-García

first: Rosa

last: Rebollar-Vega

first: Inti

last: De la Rosa-Velázquez

first: Rosario

last: Ortiz

first: Monserrat

last: Ramírez

first: Normand

middle: G

last: Hernández

first: Antonio

last: Méndez

first: Francisco

last: Arenas-Huertero


title: Impact of iASPP knockout on p63 genome occupancy in mouse keratinocytes

city: Oxford, Oxfordshire

first: Xin

last: Lu

address: Roosevelt Drive

institute: Ludwig Institute for Cancer Research, University of Oxford

summary: iASPP (PPP1R13L) is an evolutionarily conserved regulator of p53 family members. In mice, iASPP deletion in keratin 14-expressing keratinocytes is sufficient to cause detrimental phenotypes with squamous epithelium abnormalities. In human skin, wild-type nuclear iASPP colocalizes with the key squamous differentiation regulatory factor, TP63, and iASPP mutations are associated with abnormalities in skin development. To clarify how iASPP modulates p63 genome occupancy, p63 ChIP-seq data from iASPP WT and iASPP KO primary mouse keratinocytes (MKC) were compared.

overall_design: Mouse keratinocytes (MKC) were isolated from mice with or without a Krt14-Cre+;Ppp1r13l-/- genotype, which causes a deletion of iASPP exon 8 in Krt14-expressing epithelial cells. ChIP-seq was performed on isolated keratinocytes from Krt14-Cre+;Ppp1r13l-/- (iASPP KO) or iASPP WT mice, using the H129 p63 antibody (Santa Cruz). KO and WT ChIP-seq profiles were then compared using a quantitative method for ChIP-seq sample comparison (MAnorm).

first: Thomas

last: Carroll

first: Zinaida

last: Dedeić

first: Martin

last: Oti

first: Artem

last: Smirnov

first: Evelyn

middle: N

last: Kouwenhoven

first: Michael

last: Tellier

first: Shona

last: Murphy

first: Huiqing

last: Zhou


title: Transcriptional impact of iASPP knockout in mouse keratinocytes

summary: iASPP (PPP1R13L) is an evolutionarily conserved regulator of p53 family members. In mice, iASPP deletion in keratin 14-expressing keratinocytes is sufficient to cause detrimental phenotypes with squamous epithelium abnormalities. In human skin, wild-type nuclear iASPP colocalizes with the key squamous differentiation regulatory factor, TP63, and iASPP mutations also show abnormalities in skin development. To clarify how iASPP influences the keratinocyte transcriptome, iASPP WT and iASPP KO primary mouse keratinocytes (MKC) were compared.

overall_design: Mouse keratinocytes (MKC) were isolated from mice carrying a tamoxifen-inducible iASPP deletion (Ppp1r13lflox/flox;Cre+ERT). For each of 3 batches, isolated keratinocytes were split in half and either treated with medium with or without tamoxifen to create iASPP KO and WT MKCs, respectively. Transcriptomes of these 3 replicates of iASPP KO and WT MKCs were then compared, and significant differentially expressed genes and enriched pathways were compared between the two conditions.


title: Effect of iASPP knockout in mouse keratinocytes

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

overall_design: Refer to individual Series


title: Evaluating the effects of bisphenol A alternatives and pendimethalin on the transcriptome profile of human mammary epithelial cells

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

institute: Kings College London

summary: Three different cell lines (MCF-7, MCF-10A, MCF-12A) were exposed to varying concentrations of BPA, BPA-analogues, pendimethalin and pendimethalin formulation.

overall_design: These cell lines were exposed to BPA and bisphenol alternatives (bisphenol AF (BPAF), bisphenol AP (BPAP), bisphenol B (BPB), bisphenol F (BPF), bisphenol S (BPS) and bisphenol Z (BPZ)). Besides bisphenols, the cells were also exposed to pendimethalin to test if the systems used can detect estrogenic properties of other chemical classes. Pendimethalin is a herbicide commonly used in the UK on arable crops and it is suspected to have endocrine-disrupting effects. The pure standard of pendimethalin, as well as its commercial formulation, were used.


title: Steroidogenic factor 1 (NR5A1) induces multiple transcriptional changes during differentiation of human gonadal-like cells

city: Helsinki

first: Kirsi

middle: Tuulia

last: Sepponen

address: Haartmaninkatu 8

department: Obstetrics and Gynecology

country: Finland

institute: University of Helsinki

summary: Nuclear receptor subfamily 5 group A member 1 (NR5A1) encodes steroidogenic factor 1 (SF1), a key regulatory factor that determines gonadal development and coordinates endocrine functions. Here, we have established a stem cell-based model of human gonadal development and applied it to evaluate the effects of NR5A1 during the transition from bipotential gonad to testicular cells. We combined directed differentiation of human induced pluripotent stem cells (46,XY) with activation of endogenous NR5A1 expression by conditionally-inducible CRISPR activation. The resulting male gonadal-like cells expressed several Sertoli cell transcripts, secreted anti-Müllerian hormone and responded to follicle-stimulating hormone by producing sex steroid intermediates. These characteristics were not induced without NR5A1 activation. A total of 2691 differentially expressed genetic elements, including both coding and non-coding RNAs, were detected immediately following activation of NR5A1 expression. Of those, we identified novel gonad-related putative NR5A1 targets, such as SCARA5, which we validated also by immunocytochemistry. In addition, NR5A1 activation was associated with dynamic expression of multiple gonad- and infertility-related differentially expressed genes. In conclusion, by combining targeted differentiation and endogenous activation of NR5A1 we have for the first time, been able to examine in detail the effects of NR5A1 in early human gonadal cells. The model and results obtained provide a useful resource for future investigations exploring the causative reasons for gonadal dysgenesis and infertility in humans.

overall_design: Total of 7 samples with 3 technical replicates each, collected at days 4, 6, 8, and 10 of differentiation of human induced pluripotent stem cells (HEL46.11-DDdCas9Vp192-SF1 clone 14)  into gonadal-like cells. At days 6, 8, and 10, samples were collected separately from both SF1 induced (ind) and non-induced (non ind) treatment conditions.

first: Karolina

last: Lundin

first: Dawit

last: Yohannes

first: Sanna

last: Vuoristo

first: Diego

last: Balboa

first: Matti

last: Poutanen

first: Claes

last: Ohlsson

first: Steinar

last: Hustad

first: Ersilia

last: Bifulco

first: Pauliina

last: Paloviita

first: Timo

last: Otonkoski

first: Olli

last: Ritvos

last: Sainio

first: Juha

middle: S

last: Tapanainen

last: Tuuri


title: RORa enforces stability of the T-helper-17 cell effector program (ATAC-Seq)

city: New York

first: Dan

last: Littman

state: NY

address: 430 East 29th St Room 403

institute: New York University School of Medicine

summary: Chronic inflammation is responsible for a number of debilitating human diseases including inflammatory bowel disease, multiple sclerosis, and rheumatoid arthritis. The Th17 subset of T lymphocytes is an important player in the development of these pathogenic conditions. The transcription factor, RORgt was initially coined the master regulator of the Th17 program, but targeting RORgt therapeutically is dangerous owing to an enhanced risk of thymoma upon its inhibition. Another ROR family member, RORa, has also been implicated in Th17 function.

overall_design: ATAC-Seq: To determine cis-regulatory regions involved in Rorc expression, we conducted ATAC-seq analysis of in vitro polarized and ex vivo isolated Th17 cells, and discovered previously unidentified open chromatin sites in Rorc locus.

first: June-Yong

last: Lee

first: Jason

last: Hall

first: Maria

last: Pokrovskii

first: Lina

last: Kroehling


title: RORa enforces stability of the T-helper-17 cell effector program (ChIP-Seq)

overall_design: ChIP-Seq: To ascertain whether RORa directly regulates Th17 lineage maintenance, ChIP-Seq of RORa was performed with in vitro differentiated Th17 cells generated from RORa -Twin Strep (RORA-TS) tag knockin-in mice. To further address the interdependency of RORa and RORgt in binding of target loci, RORa ChIP-Seq was also conducted on Th17-polarized CD4+ T cells isolated from RORA-TS mice in which RORgt activity was abolished (RORA-TS-TGKO).


title: RORa enforces stability of the T-helper-17 cell effector program (RNA-Seq)

overall_design: RNA-Seq: To investigate the molecular mechanism by which RORa regulates the Th17 program, TWT and TAKO Th17 cells were isolated from the DLN and SC of 3 separate cohorts of mixed chimeric mice based on their IL17AeGFP expression (see Figure 1G) at the peak of EAE disease, and their transcriptomes were sequenced (RNA-Seq)(Figures S3A-C).


title: RORa enforces stability of the T-helper-17 cell effector program


title: RORa enforces stability of the T-helper-17 cell effector program (ChIP-Seq (2))

overall_design: ChIP-Seq (2): To further address the interdependency of RORa and RORgt in binding of target loci, RORgt ChIP-Seq was also conducted on Th17-polarized CD4+ T cells isolated from wild-type, Rora knock-out (TAKO) and RORa/gt double knock-out (TDKO).


title: ENO1-IT1(ENSG00000236269.1) coordinates the acetylation of histone genome-wide in Colorectal Cancer

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

summary: LncRNA ENO1-IT1 has been found to be mainly located in the nucleus of colorectal mucosa epithelial cells, which indicates that this lncRNA may be responsible for regulating the expression of target gene. To address whether ENO1-IT1 modulates  epigenetic changes genome-wide, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) in HCT116 cells

overall_design: ChIP-seq was performed in HCT116  colorectal cancer cells after  knockdown of ENO1-IT1

first: Fangfang

last: Guo


title: Transcriptome profiling of control and Zmynd8-cKO mouse cardiomyocyte

status: Public on Oct 24 2022

city: Honolulu

first: Andrew

middle: Kekūpaʻa

last: Knutson

state: HI

address: 651 Ilalo St.

department: Center for Cardiovascular Research

institute: John A. Burns School of Medicine - University of Hawaiʻi

summary: Appropriate gene expression within cardiomyocytes is coordinated by chromatin factors and is essential for heart function. We investigated the role of the chromatin reader ZMYND8 in the mouse heart using null and conditional knockouts (Zmynd8-cKO). While full-length Zmynd8 is not required for cardiomyocyte development, Zmynd8-cKO mice develop cardiomegaly, decreased cardiac function, and premature death compared to controls. Transcriptome analysis of Zmynd8-cKO cardiomyocytes reveals illegitimate expression of transcripts and proteins normally limited to skeletal muscle and integration of TNNI2 skeletal troponin into cardiac sarcomeres of mutant mice. We conclude that ZMYND8 is necessary to maintain appropriate cardiomyocyte homeostasis and gene expression.

overall_design: Transcriptome profiles of 2 replicates of isolated cardiomyocytes from Myh6-CreTg/0 female mice, 2 replicates of isolated cardiomyocytes from Myh6-CreTg/0; Zmynd8fl/fl female mice, and 2 replicates of isolated cardiomyocytes from Myh6-CreTg/0; Zmynd8fl/fl male mice

first: Abigail

last: Avelar

first: Ralph

middle: V

last: Shohet


title: Chem-seq data from 5'-biotin-DRB-labelled human U2OS cells

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

summary: Confluent U2OS cells were released to serum-free medium, and continued to grow for 36 h (Per2-dLuc peak), then added biotin-DRB (40uM) treatment for 0.5, then fixed the cells, harvested genomic DNA by Strepavidin agarose beads, and conducted hi-seq sequencing

overall_design: To overcome the poor quality of commercial Abs against CDK9 for the ChIP assay, we apply the small molecule-bound hi-seq assay to evaluate the global CDK9 association on the chromatin

first: Wei

last: Xiong

first: Jiawen

last: Wang

first: Eric

middle: E

last: Zhang


title: Effect of haptoglobin (purified from human serum) on gene expression in monocyte-derived macrophages.

city: Marburg

first: Ho Ryun

last: Chung

address: Hans-Meerwein-Straße 6

department: Institute for Medical Bioinformatics and Biostatistics

country: Germany

institute: Philipps University of Marburg

summary: Haptoglobin is a major serum protein that sequesters free hemoglobin. Moreover, haptoglobin regulates the inflammatory response in the absence of hemoglobin. Conflicting functional outcomes are reported, whereas involvement of NFκB is suggested consistently. Our data indicate that purified haptoglobin induces NFκB-dependent transcription through toll-like receptor 4. Notably, haptoglobin itself is dispensable for this effect. We show here that haptoglobin binds lipopolysaccharides from different bacterial species with micromolar affinities. This finding explains previous divergent observations. Pro-inflammatory responses elicited by purified haptoglobin are caused by heterogeneous lipopolysaccharides associated with the protein. Given its abundance in human serum, haptoglobin constitutes a buffer for serum-borne lipopolysaccharide. Restricted lipopolysaccharide availability dampens inflammatory responses. Concordantly, NFκB activation in primary macrophages is delayed relative to stimulation with pure lipopolysaccharide. Our findings warrant evaluation of therapeutic benefits of haptoglobin for non-hemolytic conditions as well as re-evaluation of purification strategies and will furthermore allow to disentangle mechanisms of haptoglobin-dependent immunoregulation.

overall_design: Monocyte-derived macrophages from three healthy female donors were treated with vehicle,  25 µg/ml mixed-type haptoglobin, or haptoglobin and 50 µM arachidonic acid for 2, 4, 6, and 8 hours for comparative RNA-seq.

first: Josina

last: Großmann

first: Andrea

last: Nist

first: Thorsten

last: Stiewe

first: Till

last: Adhikary

first: Ho

middle: R


title: The role of  keratinocyte DDX5 in IMQ-induced psoriatic mice

first: Yuping

last: Lai

address: No.500 Minhang Dongchuan Road

institute: East China Normal University

summary: To investigate whether DDX5 is involved in the development of psoriasis,we performed gene expression profiling analysis using data obtained from RNA-seq of ear skins from Ddx5f/f and K14Ddx5f/f  psoriatic mice

overall_design: A daily topical dose of 25 mg IMQ cream (5%) (Shichuan MedShine Pharmaceuticals Co.) per ear  for seven consecutive days. At day 8, ears were collected for RNA isolation.

first: Xinhui

last: Ni

first: Yi

last: Xu

first: Wang


title: Gene expression profile of human Th17 cells

city: München

first: Laurens

last: Lehner

address: Arcisstraße 21

institute: Technical University of Munich

summary: Adaptive immune responses are tailored to the invading microbial antigen and tissue microenvironment, resulting in diverse context-specific inflammatory signatures. There is emerging evidence that innate immune responses coopt adaptive properties such as memory. Whether T cells harness innate immune signaling pathways to diversify their repertoire of effector functions remains unknown. Here we show that human T cells can express gasdermin E (GSDME), a membrane pore forming molecule, which has recently been shown to execute pyroptotic cell death and thus to serve as a potential cancer checkpoint. In T cells, GSDME expression was, in contrast, associated with durable viability and was repurposed for the tunnelled release of the calpain-matured innate danger signal IL-1a. This property was restricted to a subset of human Th17 cells and regulated by the NLRP3 inflammasome and its engagement of a proteolytic cascade of successive caspase-8, caspase-3 and GSDME cleavage following T cell receptor stimulation. Autocrine IL-1a signaling enforced a pro-inflammatory Th17 cell fate through continuous IL-10 suppression and showed an association of this T cell subset with the autoinflammatory Schnitzler syndrome. Our results propose GSDME pore formation in T cells as a mechanism of unconventional cytokine release through harnessing of innate signaling platforms in response to adaptive stimuli. This diversifies the functional repertoire and mechanistic equipment of T cells and thus provides new therapeutic strategies for targeting the proinflammatory identity of human Th17 cells in various diseases.

overall_design: A library of human Th17 cells that were sorted ex vivo as CCR6+CCR4+CXCR3– memory Th cells using fluorescence-activated cell sorting (FACS) and then stimulated with anti-CD3 and anti-CD28 mAbs for 4 days (2 days plate-bound).

first: Christina

last: Zielinski


title: scRNA-sequencing reveals subtype-specific transcriptomic perturbations in DRG neurons of PirtEGFPf mice in neuropathic pain condition

city: Baltimore

first: Chi

state: MD

address: 720 Rutland Avenue

institute: Johns Hopkins University

summary: Functionally distinct subtypes/clusters of dorsal root ganglion (DRG) neurons may play different roles in nerve regeneration and pain. However, details about their transcriptomic changes under neuropathic pain conditions remain unclear. Chronic constriction injury (CCI) of the sciatic nerve represents a well-established model of neuropathic pain, and we conducted single-cell RNA-sequencing (scRNA-seq) to characterize subtype-specific perturbations of transcriptomes in lumbar DRG neurons on day 7 post-CCI. By using PirtEGFPf mice that selectively express an enhanced green fluorescent protein in DRG neurons, we established a highly efficient purification process to enrich neurons for scRNA-seq. We observed the emergence of four prominent CCI-induced clusters and a loss of marker genes in injured neurons. Importantly, a portion of injured neurons from several clusters were spared from injury-induced identity loss, suggesting subtype-specific transcriptomic changes in injured neurons. Moreover, uninjured neurons, which are necessary for mediating the evoked pain, also demonstrated cell-type-specific transcriptomic perturbations in these clusters, but not in others. Notably, male and female mice showed differential transcriptomic changes in multiple neuronal clusters after CCI, suggesting transcriptomic sexual dimorphism in DRG neurons after nerve injury. Using Fgf3 as a proof-of-principle, RNAscope study provided further evidence of increased Fgf3 in injured neurons after CCI, supporting scRNA-seq analysis, and calcium imaging study unraveled a functional role of Fgf3 in neuronal excitability.  These findings may contribute to the identification of new target genes and the development of DRG neuron cell-type-specific therapies for optimizing neuropathic pain treatment and nerve regeneration.

overall_design: We characterized perturbations of transcriptomes in DRG neurons at the single-cell level after chronic constriction injury (CCI) of the sciatic nerve. We have four groups: Male-CCI, Female-CCI, Male-Sham, and Female-Sham. Bilateral L4-5 DRGs were collected from male/female mice on day 7 after bilateral sciatic CCI or sham surgery for scRNAseq.

first: Ming-Wen

last: Hu

first: Xue-Wei

first: Xiang

last: Cui

first: Jing

last: Liu

first: Qian

last: Huang

first: Xu

last: Cao

first: Feng-Quan

last: Zhou

first: Jiang

last: Qian

first: Shao-Qiu

last: He

first: Yun

last: Guan


title: Keratinocyte DDX5 in response to IL-36γ

first: Yuping

summary: To compare how WT and DDX5-/- keratinocyte in response toIL-36γ, we performed gene expression profiling analysis using data obtained from RNA-seq of WT and DDX5-/- keratinocyte stimulated by IL-36γ

overall_design: To compare WT and DDX5-/- keratinocyte in response to IL-36γ, we generated DDX5-/- HaCat cell line by CRISPR/Cas9. WT and DDX5-/- keratinocyte were stimulated by 100ng/mL IL-36γ for 4 hours

last: Wang


title: Engineering human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia and solid tumor metastasis

city: Lund

first: Yuan

last: Li

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: Transcriptomic profiling of MSODB both before and after 21 days of chondrogenic differentiation

first: Ani

last: Grigoryan

first: Steven

last: Dupard

first: Paul

last: Bourgine


title: The role of  keratinocyte DDX5 in MC903-induced atopic dermatitis (AD) mice

last: Lai

summary: To investigate whether DDX5 is involved in the development of atopic dermatitis, we performed gene expression profiling analysis using data obtained from RNA-seq of ear skins from Ddx5f/f and K14Ddx5f/f  atopic dermatitis mice

overall_design: 1nmol MC903 (Sigma) dissolved in 10 μL ethanol was painted on each ear of 8-week-old Ddx5f/f and K14Ddx5f/f mice for 15 consecutive days. At day 16, ears were collected for RNA isolation.

first: Xinhui

last: Ni

first: Yi

last: Xu

first: Wang


title: microRNA high-throughput sequencing for Phellinus igniarius

city: shanghai

first: zhu

last: caibin

state: china

address: chenqiao road 2358#

institute: Cheermore Cosmetic Dermatology Laboratory

summary: We identified 5 novel microRNA expressed genes, and named them CM1~CM5

overall_design: total RNAseq for  for Phellinus igniarius


title: CRP and PepA RNAseq in V. cholerae

city: Boston

first: Jacob

last: Gibson

address: 25 Shattuck St

institute: Harvard University

summary: We found two DNA binding proteins, CRP and PepA, associate at the membrane. This study was performed to determine if their interaction affects transcription activity..

overall_design: To determine the transcriptional regulation by CRP and PepA in V. cholerae C6706 we performed RNAseq in WT, Δcrp, ΔpepA, and ΔcrpΔpepA mutants.

middle: A

first: Paula

middle: I

last: Watnick


title: Chi3l1 is a modulator of glioma stem cell states and a therapeutic vulnerability for glioblastoma [RNA-seq]

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

address: 1300 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine

summary: Chi3l1 (Chitinase 3-like 1) is a secreted protein highly expressed in glioblastoma. Here, we show that exposure of glioma stem cells (GSCs) to Chi3l1 reduces the CD133+/SOX2+ cells and increases the CD44+/Chi3l1+ cells. Single cell RNA-seq and RNA velocity following incubation of GSCs with Chi3l1 show significant changes in GSC state dynamics driving GSCs towards a mesenchymal expression profile and reducing transition probabilities towards terminal cellular states. ATAC-seq reveals that Chi3l1 increases accessibility of promoters containing MAZ transcription factor footprint. Inhibition of MAZ directly regulates genes with highest expression in cellular clusters exhibiting significant cell state transitions.

overall_design: To identify genes that are potentially directly regulated by MAZ following Chi3l1 treatment, we combined MAZ footprinting prediction from ATAC-seq data with RNA-seq data following MAZ knockdown.

first: Nikos

last: Tapinos

first: Charlotte

last: Guetta-Terrier

first: David

last: Karambizi

first: J


title: Effect of depletion of YAP1 on gene expression in triple negative breast cancer

city: ZHEJIANG

first: MISHA

last: MAO

state: Hangzhou

address: 3 Qingchun East road

institute: zhejiang university

summary:
To investigate the cooperative function HJURP/YAP1/NDRG1  in the regulation of  progression in triple negative breast cancer, we established MDA-MB-231 cell lines in which each target gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB-231 cells and its KD derivatives (shYAP1).

first: Linbo

first: Misha

last: Mao


title: CRP and PepA ChIPseq in V. cholerae

summary: We found two DNA binding proteins, CRP and PepA, associate at the membrane. This study was performed to determine if their interaction affects DNA binding.

overall_design: To determine the binding sites of CRP and PepA in V. cholerae C6706 we performed ChIPseq. To determine if CRP affected PepA binding, or vice versa, we also performed ChIPseq on PepA in a CRP mutant and on CRP in a PepA mutant.

first: Michael

middle: J

last: Gebhardt

first: Simon

middle: L

last: Dove


title: Chi3l1 is a modulator of glioma stem cell states and a therapeutic vulnerability for glioblastoma [scRNA-seq]

overall_design: To determine the effect of Chi3l1 on GCSs at the single cell level, we applied single cell RNA-seq (scRNA-seq) on glioma stem cells (GSC1 and GSC2) treated with or without Chi3l1 for 7 days using the 10x Genomics Chromium platform.


title: Single cell RNAseq of engineered human mini bones for the standarized modeling of healthy hematopoiesis, leukemia and solid tumor metastasis

first: Paul

state: Skane

summary: We have engineered human mesenchymal cell line-derived mini-bones as a model to study healthy hematopoiesis, leukaemia and solid tumor metastasis.

overall_design:
MSOD-B cells were used to engineer cartilage tissues in vitro followed by the subcutaneous implantation in mice for the bone formation.
***Raw data not available due to patient privacy concerns***

first: Ani

last: Grigoryan

last: Hidalgo Gil