city: Princeton

first: Namit

last: Kumar

state: NJ

address: 3551 lawrenceville

department: Informatics & Predictive Sciences

institute: Bristol-Myers Squibb

summary: Epithelial-to-mesenchymal transition (EMT) is associated with tumor initiation, metastasis, and drug resistance. However, the mechanisms underlying these associations are largely unknown. We studied several tumor types to identify the source of EMT gene expression signals and a potential mechanism of resistance to immuno-oncology treatment. Across tumor types, EMT-related gene expression was strongly associated with expression of stroma-related genes. Based on RNA sequencing of multiple patient-derived xenograft models, EMT-related gene expression was enriched in the stroma versus parenchyma. EMT-related markers were predominantly expressed by cancer-associated fibroblasts (CAFs), cells of mesenchymal origin which produce a variety of matrix proteins and growth factors. Scores derived from a 3-gene CAF transcriptional signature (COL1A1, COL1A2, COL3A1) were sufficient to reproduce association between EMT-related markers and disease prognosis. Our results suggest that CAFs are the primary source of EMT signaling and have potential roles as biomarkers and targets for immuno-oncology therapies.

overall_design: Resected tumors and adjacent normal tissues were procured from BioIVT (BioIVT, Westbury, NY) from 14 treatment-naive patients with colorectal or renal cell carcinoma. Tissue samples were enzymatically dissociated and single cells were sorted for live, nucleated CD45+ and CD45− cells to enrich for immune and non-immune cells, followed by generating single-cell sequencing libraries.

first: Mohan

last: Bolisetty

first: James

middle: L

last: Holloway

first: Ryan

last: Golhar

first: Brian

last: Kidd

first: Philip

last: Hull

first: Jeff

last: Houser

first: Logan

last: Vlach

first: Nathan

middle: O

last: Siemers


title: ERK inhibitor, ulixertinib induces transcriptomic changes in NGP cells

status: Public on Mar 01 2023

city: Washington

first: Yang

last: Yu

state: DC

address: 111 Michigan Ave NW

country: USA

institute: Children's national hospital

type: Expression profiling by high throughput sequencing

summary:
To investigate the effect of ERK inhibitor, ulixertinib, on NB cell proliferation and delineate the mechanisms of ulixertinib-mediated ERK pathway inhibition in NB.
We treated human neuroblastoma cell line, NGP with ulixertinib and performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design:
We compared the transcriptomic change between ulixertinib-treated groups and the control groups.  Differential gene expression (DGE) analysis of RNA-Seq was conducted with the R statistical package DESeq2 (v1.28.1).
We performed gene set analysis on DGEs by over-representation test on the ConsensusPathDB  web-portal. Genes detected in our experiments are selected on the background list.

first: Yanling

last: Zhao

first: Chunchao

last: Zhang

first: Jianhua

last: Yang


title: The polymethoxyflavone Sudachitin modulates the circadian clock to enhance energy metabolism and remodel liver physiology

city: Tokushima-City

first: KAZUAKI

last: MAWATARI

state: Tokushima

address: 3-18-15 KUROMOTO-CHO

country: Japan

institute: Tokushima University

summary: Polymethoxylated flavones (PMFs) are a group of natural compounds known to display a wide array of beneficial effects to promote physiological fitness. Recent studies revealed circadian clocks as an important cellular mechanism mediating the preventive efficacy of the major PMF Nobiletin against metabolic disorders. Sudachitin is a PMF enriched in Citrus sudachi, and its functions and mechanism of action are poorly understood. Using circadian reporter cells, we showed that Sudachitin modulated circadian amplitude and period of Bmal1 promoter-driven reporter rhythms, and real-time qPCR analysis showed that Sudachitin altered expression of core clock genes, notably Bmal1, at both transcript and protein levels. Mass-spec analysis revealed systemic exposure in vivo. In mice fed with high-fat diet with or without Sudachitin, we observed increased nighttime activity and daytime sleep, accompanied by significant metabolic improvements in a circadian time-dependent manner, including respiratory quotient, blood lipid and glucose profiles and liver physiology. Focusing on the liver, RNA-sequencing and metabolomic analyses revealed prevalent diurnal remodeling in both gene expression and metabolite accumulation. Taken together, our study elucidates Sudachitin as a new clock-modulating PMF with hepatic remodeling functions to improve systemic metabolic homeostasis, and highlights the circadian clock as a fundamental mechanism to safeguard physiological well-being.

overall_design: Examination of transcriptomics by RNA-sequencing using RNA samples from livers isolated from control and sudachitin treated mice at ZT6 and ZT18 (daytime and nighttime, respectively).

first: Kazuaki

last: Mawatari

first: Nobuya

last: Koike

first: Akira

last: Takahashi

first: Seung-Hee

last: Yoo

first: Zheng

last: Chen


title: Multi-Omics Biomarkers of Response to Immunotherapy in Combination with Epigenetic Modulators

city: Milan

first: Andrea

last: Anichini

address: Via Venezian 1

department: Research

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: Epigenetic immunomodulation by association of guadecitabine with ipilimumab  (NIBIT-M4 Phase Ib trial, NCT02608437) has been shown to be safe and tolerable in advanced melanoma and to have significant immunomodulatory and antitumor activity [Di Giacomo et al. Clin Cancer Res. 2019 Dec 15;25(24):7351-7362].   Here we carried out a multi-omics assessment of pre-therapy (week 0, w0) and on-treatment (week 4, w4 and week 12, w12) tumor biopsies from enrolled patients looking at the specific parameters that could explain clinical benefit vs treatment failure. Available whole exome sequencing, reduced-representation bisulfite sequencing and RNA sequencing data, together with focused analysis of immune-related signatures by custom NanoString panels, were integrated with existing information on tumor immune contexture data by immunohistochemistry. Results indicated that clinical benefit vs progressive disease could be explained, even at the single patient level, by applying a multifactorial code integrating information from a variety of parameters investigated on sequential biopsies. Crucial parameters included: tumor genomic/transcriptomic landscape, immune structure of the tumor microenvironment (inferred by deconvolution of gene expression data or assessed by immunohistochemistry), profile of genes and molecules relevant for antigen processing and presentation (immunoproteasome subunits, HLA class I molecules on tumor cells), tumor classification by the immunological constant of rejection (Bertucci et al. British Journal of Cancer 2018; 119:1383–1391), genetic immunoediting score (the ratio between the observed versus the expected number of neoantigens), enrichment for differentiation-, metabolism-, proliferation- and immunity-related pathways as well as analysis for signatures related to  B cell content and differentiation, TLS formation, follicular T helper cells, TEX subsets, tumor-associated endothelial cells, ICB response and guadecitabine-specific gene upregulation.

overall_design: RNA was extracted from two 12m-thick sections from FFPE blocks of tumor biopsies surgically removed from enrolled patients at three time points: W0 (pre-therapy), W4 and W12 (week 4 and week 12 on-treatment). The custom-designed NanoString panel allowed to test for expression of 364 genes that define the following signatures (numbers identify the signature ID replicated in header 5 of the data matrix): 1. Tertiary lymphoid structures (Cabrita et al., Nature 2020;577:561–565); 2. B cells (Patil et al., Cancer Cell 2022;40:1–12); 3. Follicular B cells (Patil et al., Cancer Cell 2022;40:1–12); 4. Plasma cells (Patil et al., Cancer Cell 2022;40:1–12); 5. Germinal center B cells (Patil et al., Cancer Cell 2022;40:1–12); 6. Germinal center B cellls (Cui et al., Cell 2021;184:1–18); 7. T follicular helper cells (Cui et al., Cell 2021;184:1–18); 8. Antibody secreting cells (Cui et al., Cell 2021;184:1–18); 9. B cells (Zhang, Cancer Cell 2021;39:1578–1593); 10. Tertiary lymphoid structures (Meylan et al., Immunity  2022;55:1–15); 11. Guadecitabine-specific gene signature (Anichini et al. Research Square  https://doi.org/10.21203/rs.3.rs-1918233/v1); 12. IFN-gamma-induced ICB response signature (Grasso et al.,Cancer Cell 2020;38:500–515); 13. IFN-gamma-related ICB response signature (Ayers et al., J Clin Invest. 2017;127:2930-2940); 14. ICB response signature (Rodig et al., Sci. Transl. Med. 2018;10:eaar3342); 15. Tumor-associated endotelial cells (Asrir et al., Cancer Cell 2022; 40:318–334); 16. CD8+ exhausted T cells (Zheng et al., Science 2021;374:1462); 17. CD8+ GZMK+ Tex cells (Zheng et al., Science 2021;374:1462); 18. CD8+ terminal Tex (Zheng et al., Science 2021;374:1462); 19. CD8+ OXPHOS+ Tex cells (Zheng et al., Science 2021;374:1462); 20. CD8+ TCF7+ Tex cells (Zheng et al., Science 2021;374:1462).

first: ANDREA

last: ANICHINI

first: MICHELE

last: MAIO


title: Epigenetic reprogramming of intestinal stemness by dietary arachidonic acid [Organoid]

city: Cold Spring Harbor

first: Aybuke

last: Alici

state: NY

address: 1 Bungtown Rd.

institute: Cold Spring Harbor Laboratory

summary: Single cell transcriptomic profiling (sc RNA-seq)  of  arachidonic acid (AA) induced  gene expression pogram associated with regeneration in intestinal organoids.

overall_design: Single cells (from intestinal organoids treated with vehicle, arachidonic acid or 6,16-dimethyl PGE2) were flow-sorted  and then  loaded into 10X Chromium platform.

first: Onur

last: Eskiocak

first: Semir

last: Beyaz

first: Cem

last: Meydan

last: Alici-Garipcan

first: Vyom

last: Shah


title: Epigenetic reprogramming of intestinal stemness by dietary arachidonic acid [In_vivo]

summary: Single cell transcriptomic profiling (sc RNA-seq)  of  diatery arachidonic acid (AA) induced  gene expression pogram associated with regeneration in intestinal organoids.

overall_design: Single cells of intestinal crypts from mice fed with control or AA-Rich (AR) diet were flow-sorted  and then  loaded into 10X Chromium platform.


title: Wnt-Activating Human Skin Organoid Model of Atopic Dermatitis Induced by Staphylococcus aureus and Its Protective Effects by Cutibacterium acnes

city: Seoul

first: Min-Ji

last: Kim

address: Gwanak-gu

country: South Korea

institute: Seoul National University

summary: We investigated transcriptional changes associated with S. aureus infection by performing RNA sequencing. the goal of this transcriptome analysis was to confirm ALI-skin organoids can capture the host cellular responses against bacterial infection including bacterial recognition and inflammatory signaling.

overall_design: The total RNA was extracted from three biological replicates of ALI-skin organoids after treatment with S. aureus (10⁶ CFU) for 18 hrs

first: Song-yi

last: Jung

first: Hyun

middle: J

last: You

first: Kyung-Sun

last: Kang


title: Intracellular angiopoietin-1 promotes TKI-resistance via activation of JAK/STAT5 pathway in chronic myeloid leukemia [RNA-seq_12]

city: Guiyang

first: Yunsheng

last: Ran

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

country: China

institute: Guizhou Medical University

summary: Drug resistance from BCR-ABL tyrosine kinase inhibitors (TKIs) and other chemotherapeutics results in treatment failure and disease progression in chronic myeloid leukemia (CML). However, the mechanism is still uncertain. In this study, we investigated the role of angiopoietin-1 (ANG-1) as a potential prognostic factor for drug resistance in CML. Both intracellular and secretory ANG-1 (iANG-1 and sANG-1) were overexpressed in multidrug-resistant CML samples. The IC50 value was higher in primary CD34+ CD38– cells with more ANG-1. Silencing ANG-1 significantly sensitized three TKI-resistant CML cell lines to imatinib (IM) while recombinant human ANG-1 failed to retain cell survival in vitro. This indicated the important role of iANG-1 as opposed to sANG-1 in CML drug resistance. Moreover, a similar effect was observed in xenograft mice models bearing ANG-1-silenced CML cells. Subsequently, pathway analysis and protein validation experiments showed activation of the JAK/STAT pathway and augmentation of STAT5a phosphorylation in ANG-1 restored CML cells. Upstream Src phosphorylation, which plays a crucial role in CML drug resistance, was also upregulated as a key event in iANG-1-related JAK/STAT pathway activation. In conclusion, our study elucidated a new BCR-ABL independent molecular mechanism induced by intracytoplasmic ANG-1 overexpression as a potential strategy for overcoming CML resistance.

overall_design: BM mononuclear cells derived from the newly diagnosed/relapsed patients with CML without drug treatment were collected for RNA-seq.

first: Dan

last: Ma

first: Ping

last: Liu

first: Chujiao

last: Hu

first: Zhen

last: Zhou

last: Wang

first: Yan

first: Yaming

last: Zhang

first: Pinghao

last: Li

first: Jiangyuan

last: Zhao

first: Jishi

first: Chengliang

first: Lei

last: Tang


title: Effect of loss of lymphocytes in Rag2-/- mice on gene expression of glial cells

city: Los Angeles

first: Ye

state: CA

address: 635 Charles E Young Dr S

institute: UCLA

summary: To investigate the influence of peripheral lymphocytes on cells in the brain, we purified four major classes of brain cells and performed RNA sequencing from mice lacking lymphocytes

overall_design: Glial cells were purified from the cerebral cortex of adult Rag2-/- mice and their immune-competent littermates.

first: Mitchell

middle: C

last: Krawczyk

first: Alice


title: Intracellular angiopoietin-1 promotes TKI-resistance via activation of JAK/STAT5 pathway in chronic myeloid leukemia

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

overall_design: Refer to individual Series


title: A screen for histone mutations that affect quiescence in S. cerevisiae.

city: Los Alamos

first: Eric

middle: M

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

summary: Quiescence is a distinct cell cycle phase, termed G0, in which growth, transcription, translation, and replication are suppressed. Yeast cells enter G0 following glucose exhaustion but remain viable for an extended period and can re-enter the cell cycle when returned to glucose-rich medium. Quiescence is a feature of all organisms and is essential for the maintenance of stem cells and tissue renewal. Quiescence is also related to chronological lifespan (CLS) - or the capacity of post-mitotic quiescent cells to survive over time - and thus contributes to longevity. However, important questions remain to be answered regarding the mechanisms that control entry into quiescence, the maintenance of quiescence, and the re-entry of quiescent cells into the cell cycle. Histone acetylation is lost during the formation of quiescent yeast cells, and chromatin becomes highly condensed. This unique chromatin landscape plays a key role in supporting quiescence-specific transcriptional repression and has been linked to the formation and maintenance of quiescent cells. To ask if other chromatin features regulate quiescence, we conducted a comprehensive screen of histone H3 and H4 mutants. We identified several mutants that show altered quiescence entry and have characterized their chromatin phenotypes. None of these mutants retain histone acetylation, while several have altered chromatin condensation. Additionally, a screen for H3 and H4 mutants with altered chronological lifespan showed that CLS is highly correlated with quiescence entry.

overall_design: The H3/H4 mutant library was pooled for co-culturing. Proliferating (Log), isolated quiescent, stationary phase, and released stationary phase cells were collected from the pooled culture, gDNA isolate, and subjected to Bar-seq analysis to quantify the number of mutants in the pooled population.

first: Mary

middle: A

last: Osley


title: A Parathyroid Hormone/Salt Inducible Kinase Signaling Axis Controls Renal Vitamin D Activation and Organismal Calcium Homeostasis

city: Dallas

first: Jialiang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center


title: Intracellular angiopoietin-1 promotes TKI-resistance via activation of JAK/STAT5 pathway in chronic myeloid leukemia [RNA-seq_14]

first: Yunsheng

first: Dan


title: Effect of mechanically responsive miRNAs on biomechanical properties of airway smooth muscle cells and their related drug development studies [mRNA-Seq]

city: Changzhou City

first: kang

last: wen

state: Jiangsu Province

address: Changzhou University, HUTANG Town, Wujin District

department: Institute of Biomedical Engineering and Health Sciences

institute: Changzhou University

summary: In the short two decades since microRNAs (miRNAs) were discovered, scientists have focused more attention on the biological field of miRNAs. A deeper understanding of the role of miRNAs in development and disease has made miRNAs a powerful tool and target for new therapeutic approaches. However, whether miRNAs are involved in the response of ASMCs to high stretch and high matrix stiffness and their underlying mechanisms remain unclear, especially the relationship between the expression of miRNAs and the biomechanical behavior of ASMCs remains unclear. In this study, we combined bioinformatics and cell mechanics approaches to screen stretch-sensitive and matrix stiffness-sensitive miRNAs and investigate their effects on the biomechanical behaviors of ASMCs.

overall_design: Comparative gene expression profiling of RNA-seq data from hASMCs in the stretch, static and control groups

first: Luo

last: Zhi

first: Wen


title: Effect of mechanically responsive miRNAs on biomechanical properties of airway smooth muscle cells and their related drug development studies [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing


title: Epigenomic profiling in fetal brain after prenatal stress

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

summary: Prenatal stress is one of the risk factors for the development of mental disorders in offspring, but its underlying mechanism remains elusive. To perform epigenomic profiling of prenatal stress effects on fetal brains, ATAC-seq and RNA-seq were used to explore the changes of chromatin accessibility and gene expression on embryonic brains at E15.5 of offspring from pregnant mice, which were exposed to chronic mild unpredictable stress between E5.5 to E14.5.

overall_design: Whole brain from stressed and control mice

first: Yuhao

last: Dong

first: Yueyan

last: Zhu


title: Overexpression of TIPARP

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

summary: TIPARP-overexpression alter the gene expression profiles associated with remodeling of extracelluar matrix.

overall_design: Comparison of the gene expression profiles between TIPARP-overexpressing A549 cells and control cells.

first: Kenji

last: Miura

first: Takashi

last: Aoi


title: Lamina propria Interleukin 17 A aggravates natural killer T cells activation in autoimmune hepatitis

city: Hangzhou

first: Jianing

last: Chen

address: Qingchun Road 79#

institute: Zhejiang university

summary: Autoimmune hepatitis is an interface hepatitis characterized by the progressive destruction of the liver parenchyma, the cause of which is still obscure. Interleukin (IL)-17A is a major driver of autoimmunity, which can be produced by innate immune cells against several intracellular pathogens. Here, we investigated the involvement of IL-17A in a mice model of immune-mediated hepatitis with the intestine exposed to Salmonella typhimurium. Our results showed more severe Concanavalin (Con) A-induced liver injury and gut microbiome dysbiosis when the mice were treated with a gavage of S. typhimurium. Then the Natural Killer (NK) T cells were over-activated by the accumulated IL-17A in the liver in the Con A and S. typhimurium administration group. IL-17A could activate NKT cells by inducing CD178 expression via IL-4/STAT6 signaling. Furthermore, via the portal tract, the laminae propria mucosal-associated invariant T (MAIT) cell-derived IL-17A could be the original driver of NKT cells’ over-activation in intragastric administration of S. typhimurium and Con A injection. In IL-17A deficient mice, Con A-induced liver injury and NKT cells activation was alleviated. However, when AAV-sh-mIL-17a was used to specifically knock down IL-17A in liver, it seemed that hepatic IL-17a knock down did not significantly influence the liver injury. Our results suggested that, under Con A-induction, laminae propria MAIT-derived IL-17A activated hepatic NKT, and this axis could be a therapeutic target in autoimmune liver disease.

overall_design: Total genome DNA from murine luminal samples from ileocecus was extracted for amplification using the V4 regions (Qiagen, USA) (20). Sequencing libraries were prepared using the TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, USA) following the manufacturer's recommendations. The library quality was evaluated on the Qubit@ 2.0 Fluorometer (Thermo Scientific, USA) and Agilent Bioanalyzer 2100 system (Agilent Technologies, USA). At last, the library was sequenced on an Illumina platform (Illumina, USA), and 250 bp paired-end reads were generated. The 16S rDNA gene sequence data were processed using the QIIME (V1.7.0) with default parameters (21). Sequences analysis was performed by Uparse software (Uparse v7.0.1001) (22). Sequences with ≥97% similarity were assigned to the same operational taxonomic units (OTUs). The representative sequence for each OTU was screened for further annotation. The output data were further analyzed using Statistical Analysis of Metagenomic Profiles (STAMP) software version 2.1.3

first: Xuehui

first: Hongyan

last: Diao


title: RNA Sequencing of peripheral blood mononuclear cells (PBMCs) isolated from epilepsy patients treated with vagus nerve stimulation and not treated with vagus nerve stimulation.

city: Portland

first: Supender

last: Kaur

state: Oregon

address: 3181 SW Sam Jackson Park Road L220

department: Molecular Microbiology and Immuno

institute: Oregon health and science university

summary:
Purpose: To decipher the mechanisms responsible for the protective function of vagus nerve stimulation.
Methods: Blood was collected from Control and Treated patients followed by isolation of PBMC'S. Total RNA was extracted and RNA sequencing was done following standard protocols
Results:  Detailed analysis of the transcriptomic data show that anti-inflammatory responses were upregulated in the treated samples.
Conclusions: This study showed the protective role of vagus nerve stimulation in epilepsy patients.

overall_design: Human PBMC's RNA seq of 4 control and treated 4 patients, using Illumina platform

first: Alejandro

last: Aballay


title: RNA-seq of primary tumor-derived human gastric cancer stem cells (GCSCs) and differentiated cells (GCSCs treated with serum)

city: Shenzhen

first: Jixian

last: Xiong

state: Guangdong

address: Xueyuan Ave 1066

institute: Shenzhen University

summary: We performed RNA-seq analysis of human gastric cancer stem cell treated with or without serum to analyze the differentially expressed genes between GCSCs and differentiated cells, and find the potential key factors in GCSCs.

overall_design: Fresh isolated, primary tumor-derived GCSC cells were cultured with or without serum for 6 days, and then were collected for TRIzol lysed for RNA extraction. 6 RNAseq samples across 2 conditions:SP (sphere, without serum) (n=3) and AD (adhering, with serum) (n=3)


title: Next Generation Sequencing Facilitates Quantitative Analysis of antidepressants stressed E. coli K-12 MG1655 Transcriptomes

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 MG1655 and its mutants, and their mRNA response under the exposure of five antidepressants, including sertraline, duloxetine, bupropion, escitalopram and agomelatine. The concentrations were 50 mg/L for the treatment. For sertraline, in addition to 50 mg/L, 1 mg/L was also applied. The group without dosing antidepressants was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these five antidepressants on transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli MG1655 reference genome (NC_000913.3) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Bacterial mRNA profiles of wild-type E. coli K-12 MG1655 in response to 50 mg/L of antidepressants for 2 hours. Bacteria without dosing drugs are the control group, in triplicate, using Illumina HiSeq 2500

first: Yue

last: Wang

first: Zhigang

last: Yu

first: Likai

last: Mao


title: A Parathyroid Hormone/Salt Inducible Kinase Signaling Axis Controls Renal Vitamin D Activation and Organismal Calcium Homeostasis [SK]

first: Jialiang

summary: The renal actions of parathyroid hormone (PTH) promote 1,25-vitamin D generation; however, the signaling mechanisms in renal epithelial cells downstream of the PTH receptor that control vitamin D metabolism remain unknown. Here we demonstrate that Salt Inducible Kinases (SIKs) control renal 1,25-vit D production downstream of PTH signaling via regulating Cyp27b1 expression. As PTH inhibits the cellular activity of SIKs by cAMP-dependent PKA phosphorylation in bone, we hypothesized that SIKs would also work as an essential mediator of PTH doownstream signaling in kidney, thus regulate vitamin D metabolism. Whole tissue and single cell transcriptomics in kidney demonstrates that both PTH and pharmacologic SIK inhibitors regulate a vitamin D gene module in specific proximal tubule cells. Moreover, small molecule SIK inhibitors directly increase 1,25-vit D production and renal Cyp27b1 mRNA expression in mice and in human embryonic stem cell-derived kidney organoids. Global- and kidney-specific Sik2/Sik3 mutant mice show Cyp27b1 upregulation, elevated serum levels of 1,25-vit D, and PTH-independent hypercalcemia. The SIK substrate CRTC2 shows PTH and SIK inhibitor-inducible binding to key Cyp27b1 regulatory enhancers in the kidney, which are also required for SIK inhibitors to increase Cyp27b1 in vivo. Lastly, in a podocyte injury mouse model of chronic kidney disease (CKD) characterized by low 1,25-vit D levels, SIK inhibitor treatment stimulates both renal Cyp27b1 expression and 1,25-vit D production.

overall_design: C57BL6 male mice were treated with a single IP injection of either the vehicle (15% 2-Hydroxypropyl-beta-cyclodextrin) or SK-124 (IP) and total kindney mRNA profiles were generated by deep sequencing (n= 6 per treatment).

first: Sung-Hee

middle: S

last: Yoon

first: Marc

middle: N

last: Wein


title: A Parathyroid Hormone/Salt Inducible Kinase Signaling Axis Controls Renal Vitamin D Activation and Organismal Calcium Homeostasis [SIK]

overall_design: Kidney mRNA profiles from Ctrl and Six2 Cre-SIK1f/f;SIK2f/f,SIK3f/f mice (n= 4 per genotype) were generated by deep sequencing


title: Intracellular angiopoietin-1 promotes TKI-resistance via activation of JAK/STAT5 pathway in chronic myeloid leukemia [array]

first: Yunsheng

last: Ran

overall_design: We detected the difference in transcription between the CML parent cell line K562 and its multidrug-resistant cell line K562R without mutations in the BCR-ABL region using a Clariom S transcriptome chip.

first: Dan

last: Ma

first: Ping

last: Liu

first: Chujiao

last: Hu

first: Zhen

last: Zhou

first: Yan

first: Yaming

last: Zhang

first: Pinghao

last: Li

first: Jiangyuan

last: Zhao

first: Jishi

first: Chengliang

first: Lei

last: Tang


title: Effect of mechanically responsive miRNAs on biomechanical properties of airway smooth muscle cells and their related drug development studies

first: kang

last: wen


title: Human keratinocyte transcriptome response to KLK5 and KLK7

city: South San Francisco

first: Jason

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

summary: To determine how KLK5 and KLK7 can impact keratinocyte responses we treated human primary keratinocytes with recombinant KLK5 and KLK7 for 4 hours.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Primary keratinocytes (Gibco, C-020-5C) were cultured in basal medium and treated with recombinant and active KLK5 (6 µg/mL), KLK7 ( 5 µg/mL) and an inhibitory antibody against KLK5 and KLK7 (180 µg/mL).

first: Joseph

last: Chavarria-Smith

first: Tangsheng

last: Yi


title: Therapeutic effect of anti-KLK5 and KLK7 in a mouse model of atopic dermatitis

summary: To investigate the effect of blocking the activity of KLK5 and KLK7 in the skin in a model of atopic dermatitis, we treated mice inhibitory antibodies against KLK5 and KLK7.

overall_design: shaven  back skin of mice was treated with SDS and Protein A for 7 days. Therapeutic intervention included  inhibitory antibodies (IP) against KLK5 and KLK7 (500ug and 250ug every other day)  or oral antibiotics (amp., vanco, neo., metron.)


title: Targeting senescent hepatocytes using the THBD-PAR1 inhibitor Vorapaxar ameliorates NAFLD progression.

city: Raleigh

first: Raquel

last: Maeso-Diaz

state: United States

address: 3901 Sue Lane

institute: Duke University

summary:
Background: Senescent hepatocytes accumulate in parallel with fibrosis progression during NASH.  The mechanisms that enable progressive expansion of nonreplicating cell populations and the significance of that process in determining NASH outcomes are unclear. Many types of senescing cells upregulate the THBD-PAR-1 signaling axis to remain viable. Vorapaxar, an FDA-approved PAR-1 inhibitor, blocks the activity of that pathway. We used vorapaxar to determine if and how THBD-PAR1 signaling promotes fibrosis progression in NASH.
Methods: We evaluated the THBD-PAR1 pathway in liver biopsies from NAFLD patient cohorts with a spectrum of liver fibrosis. Chow fed mice were treated with viral vectors to over-express p16 specifically in hepatocytes and induce replicative senescence. Effects on the THBD-PAR-1 axis and regenerative capacity were assessed; the transcriptome of p16 over-expressing hepatocytes was characterized and we examined how conditioned medium from senescent but viable (dubbed ‘undead’) hepatocytes reprograms hepatic stellate cells. A genetically obese mouse model of NASH with little liver fibrosis, and a diet-induced mouse model of NASH with advanced fibrosis were treated with vorapaxar to determine effects on hepatocyte senescence and liver damage.
Results: Inducing senescence up-regulates the THBD-PAR1 signaling axis in hepatocytes and induces their expression of fibrogenic factors, including hedgehog ligands.  Hepatocyte THBD-PAR1 signaling increases in NAFLD and supports sustained hepatocyte senescence that limits effective liver regeneration and promotes maladaptive repair. Inhibiting PAR-1 signaling with vorapaxar interrupts this process, reduces the burden of ‘undead’ senescent cells, and safely improves NASH and fibrosis despite ongoing lipotoxic stress
Conclusion:  The THBD-PAR1 signaling axis is a novel therapeutic target for NASH because blocking this pathway prevents accumulation of senescing but viable hepatocytes that generate factors that promote maladaptive liver repair.

overall_design: Global transcriptome profiling was performed by RNA-seq using freshly isolated hepatocytes from P16-overexpressing hepatocytes or its control, GFP,  mice  before and at 48 h after PH (n=3wild type mice/group/time point).

last: Maeso-Díaz

first: Kuo

last: Du

first: Christopher

last: Pan

first: Cynthia

middle: D

last: Guy

first: SehHoon

last: Oh

first: Tianyi

last: Chen

first: Linda

first: Liuyang

last: Wang

first: Rajesh

middle: K

last: Dutta

first: Ayako

last: Suzuki

first: Manal

middle: F

last: Abdelmalek

first: Xiao-Fan

first: Anna Mae

last: Diehl


title: Epigenetic function during heroin self-administration controls future relapse-like behaviors in a cell type-specific manner

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary:
Opioid abuse produces enduring associations between the drug euphoria and features of the drug-taking experience, and these powerful associations can trigger relapse in individuals recovering from opioid use disorder. We show here that the epigenetic enzyme, histone deacetylase 5 (HDAC5), functions in the nucleus accumbens (NAc) during active heroin use to limit future relapse-like behavior. Moreover, enhancing HDAC5 function in NAc dramatically suppresses context-associated and reinstated heroin seeking behaviors, but it does not impact sucrose seeking. We also find that HDAC5 functions within dopamine D1 receptor-expressing medium spiny neurons (MSNs) to suppress cue-induced heroin seeking, but within dopamine D2 receptor-expressing MSNs to suppress drug-primed heroin seeking. Using cell type-specific transcriptomics analysis, we found that HDAC5 reduces expression of numerous genes linked to ion transport, and it decreases intrinsic excitability of NAc MSNs, suggesting that HDAC5 limits relapse vulnerability by suppressing NAc MSN firing rates during active heroin use.
We used microarrays to define genes differentially expressed in the presence or absence of AAV2-DIO-HDAC5-3SA in both D1 and D2 cell-types derived from Nucleus accumbens following vTRAP.

overall_design: Testing the transcriptomic effects of overexpressing a nuclear form of HDAC5 in the nucleus accumbens selectively in medium spiny neurons that expressed either dopamine receptor D1R or D2R.

first: Ethan

last: Anderson

last: Cowan


title: seq-RNA analysis of PBMC in stroke patients with severe atherosclerosis and healthy donors

city: 广州

first: Xiaohong

last: Cen

address: 1838, Guangzhou Avenue North

institute: Southern Medical University

summary: The goals of this study are to evaluate the gene expression of PBMC in stroke patients with atherosclerosis compared with healthy donors. PBMC mRNA profiles of stroke patients and healthy donors were generated by sequencing using Illumina. We detected 60613 transcripts, and there are there are 470 significant genes expression upregulated (fold change > 2 and p value < 0.05) and 355 downregulated (fold change < 0.5 and p value < 0.05) in atherosclerotic patients versus healthy individuals. We found that differentially expressed genes were significantly enriched among immune response and virus defense categories by functional KEGG analysis, including TNF signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway, NOD-like receptor signaling pathway, RIG-like receptor signaling pathway and apoptosis.

overall_design: PBMC mRNA profiles of stroke patients with severe atherosclerosis (n=4) and healthy donors (n=3)

first: Kui

last: Cheng


title: Epigenetic reprogramming of intestinal stemness by dietary arachidonic acid [intestinal organoids]

city: Cold Spring Harbor

first: Aybuke

last: Alici

address: 1 Bungtown Rd.

institute: Cold Spring Harbor Laboratory

summary: We evaluated the effects of  arachidonic acid (AA) on intestinal stem cell regeneration by RNA-seq and found that AA treatment led to strong upregulation of genes that are associated with stem cell reprogramming across the time points. AA elicits a conserved stem cell regeneration program in mouse intestinal organoids.

overall_design: mRNA profiles of  mouse intestinal organoids during time course of treatment with vehicle, arachidonic acid or 6,16-dimethyl PGE2.

first: Onur

last: Eskiocak

first: Cem

last: Meydan

last: Alici-Garipcan

first: Vyom

last: Shah

first: Hannah

last: Meyer

first: Semir

last: Beyaz


title: Linking erythropoietin to regulatory T-cell-dependent allograft survival through myeloid cells

city: New York

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: Erythropoietin (EPO) has multiple functions beyond stimulating erythrocytosis, including modulation of T cell immunity.  Effects EPO in transplantation and associated mechanisms remain incompletely understood. We analyzed outcomes and performed cellular and molecular mechanistic assessments in murine wild type (WT) and conditional EPO receptor (EPOR) knockout recipients of cardiac allografts.  In translational studies, we tested EPO’s effects in a non-human primate system.

overall_design: B6 mice were immunized with 20x106 BALB/c splenocytes. Recipient mice were treated with CTLA4-Ig (150µg i.p. once on day 2) (Abatacept, Bristol-Myers Squibb, New York, NY) ± recombinant EPO (5000 U/kg i.p. daily) (epoetin alfa, Amgen, Thousand Oaks, CA). On day 7, splenic CD11b+ myeloid cells were isolated by positive selection (kit #18970, STEMCELL, Vancouver, BC, Canada). RNA was isolated using TRIzol (Thermo Fisher Scientific, Waltham, MA) and cleaned using RNeasy Mini Kit (Qiagen, Hilden, Germany). Gene expression profiling was then performed using the nCounter® Myeloid Innate Immunity Panel (NanoString Technologies, Seattle, WA).

first: Julian

last: Horwitz

first: Zhengzi

last: Yi

first: Peter

last: Heeger


title: P53 is a direct regulator of the immune co-stimulatory molecule CD80

first: Gurkan

last: Mollaoglu

state: New York

address: Hess Center for Science and Medicine 5th Floor 302

department: Immunology and Immunotherapy

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Increasing evidence indicates oncogenes and tumor suppressors not only influence cell fitness but can also control the immunophenotype of cells. Here, we examined how 34 commonly mutated genes in colorectal cancer (CRC) may influence the expression of 8 key immunomodulatory proteins. To do this, we employed a functional genomics approach utilizing Pro-Code/CRISPR libraries for high-dimensional analysis. We introduced a library of 102 Pro-Code/gRNA combinations, targeting each of the 34 genes, in CT26 cells, a CRC cell model, and measured the expression of each of the immunomodulatory proteins by CyTOF mass cytometry. Notably, cells carrying a Pro-Code/CRISPR targeting the Trp53 lost expression of the immune co-stimulatory molecule CD80. Validation confirmed that Trp53 knockout resulted in the loss of CD80 and that activation of P53, through DNA damage or stabilization, resulted in CD80 upregulation. P53 ChIP-seq identified the CD80 promoter as a direct target of P53. CD80 regulation by P53 was identified in other cells, including normal epithelial cells and macrophages. Functionally, CD80 reduction caused by P53 loss led to a reduced capacity for CRC to prime antigen-specific T cells. These studies establish CD80, a canonical co-stimulatory molecule, as a direct target of the tumor suppressor and DNA damage response gene, P53.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-Seq) of TP53 targets in the genomes of CT26 mouse colorectal adenocarcinoma cell line and normal mouse gut epithelium.

first: Eziwoma

last: Alibo

first: Royce

last: Zhou

first: Ramon

last: Parsons

first: Brian

last: Brown


title: Histopathology and transcriptome analysis reveals the gills mucosa injury and immunotoxicity in gibel carp following acute deltamethrin exposure

city: changsha

first: Hao

last: Wu

address: shaunghe Road 728

institute: Hunan Fisheries Science Institute

summary: More and more evidence prove that deltamethrin (Del) exposure induced the adverse effect and damaged immune function to the aquatic animals in the parasite killing process with increasing insecticide application. However, little is currently known of the negative effect on mucosal immunity, especially in gills tissue. In this study, the LC50 of deltamethrin on gibel carp at 96h was determined to be 6.194 μg/L, and then juvenile gibel carp (Carassius auratus gibelio) (8.8 ± 1.0 g) were exposed to four Del exposure groups (0.61, 1.22, 2.44, and 4.88 μg/L) for 12h and 24h. To evaluate the innate immune-related enzymes in gills tissue, we measured the lysozyme (LYZ) and myeloperoxidase (MPO) contents and found that with increased concentration of Del exposure, the LYZ content was found to increase in the 1.22 μg/L Del group initially significantly and then gradually significantly decrease in the 4.88 μg/L Del group. And the activity of MPO was significantly lifted in a dose-dependent manner. The histological analysis showed that Del exposure serious desquamation and necrosis in the surface of epithelial cells are often found, accompanied by interlamellar cellular mass degenerative. In addition, the mucous cells were significantly decreased in the high Del concentration group (2.44 μg/L and 4.88 μg/L Del group) by AB-PAS staining. Importantly, totally 2857 DEGs (including 1624 up-regulated and 1233 down-regulated genes) were identified in the gill between the control group and 4.88μg/L Del exposure group using comparative transcriptional analysis. Among these, some genes involved in innate immune molecules, complement activation, apoptosis-related molecules, cytokine, and adaptive immune molecules, were also down-regulated. Importantly, we found several signal pathways related to immune response were downregulated, such as immune system process and tumor necrosis factor receptor (superfamily) binding pathways based on the GO and KEGG enrichment analysis. Consistently, we detect the expression of pro-inflammatory cytokines (TNF-α, IFN-γ, IL-1β, and IL-8), anti-inflammatory cytokines (TGF-β), LYZ, IgM, and Hsp70 in the gills tissue at 12h and 24h after Del exposure, which were consistent with our sequencing results. Collectively, these results demonstrated that the gills mucosa injury and immunotoxicity was induced by Del exposure and provided novel insight for explaining to some extent why Del-exposure fish and are more susceptible to concurrent or secondary viral or bacterial infections.

overall_design: Histopathology and transcriptome analysis of juvenile gibel carp (Carassius auratus gibelio) (8.8 ± 1.0 g)  exposed to four Del exposure groups (0.61, 1.22, 2.44, and 4.88 μg/L) for 24h


title: A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation

city: Aachen

first: Zhijian

last: Li

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen University

summary: Dendritic cells (DC) are professional antigen presenting cells that develop from multipotent progenitors (MPP) and DC committed common DC progenitors (CDP) and further differentiate into different subsets: classical DC type 1 and 2 (cDC1 and cDC2, respectively) and plasmacytoid DC (pDC). In this study MPP, CDP, cDC1, cDC2 and pDC were obtained in a two-step in vitro culture system according to Felker et al., J. Immunol. 185, 5326-5335, 2010. Briefly, mouse bone marrow cells were first amplified with a specific cytokine cocktail and then induced to differentiate into DC with Flt3 ligand. MPP, CDP, cDC1, cDC2 and pDC were obtained by FACS sorting as follows: MPP: Gr1- CD117hi CD135low/-; CDP: Gr1- CD117int CD135+ CD115+; cDC1: CD11c+ CD11blow/- XCR1+; cDC2: CD11c+ CD11b+ XCR1- and pDC: CD11c+ CD11b- B220+. FACS sorted cells were then subjected to Omni-ATAC-seq, nuclear-titrated (NuTi) Capture-C targeting Irf8 promoter, and RNA-seq analysis. ATAC-seq data of cDC1 and pDC are published (Li et al., Genome Biol. 20, 45, 2019; GSE118221). ATAC-seq data of MPP, CDP and cDC2, NuTi Capture-C and RNA-seq data of MPP, CDP, cDC1, cDC2 and pDC are published here. CD11c+ CD11b+ B220- cDC and CD11c+ CD11b- B220+ pDC were obtained by FACS sorting and subjected to ChIP-seq analysis of IRF8 and are published here.

overall_design: ATAC-seq analysis of mouse multipotent progenitors (MPP) and DC committed common DC progenitors (CDP), classical dendritic cells type 1 and type 2 (cDC1 and cDC2, respectively) and plasmacytoid dendritic cells (pDC) was performed by Omni-ATAC-seq according to Corces et al., Nat. Methods. 14, 959-962, 2017 with minor modifications as described in Li et al., Genome Biol. 20, 45, 2019 (GSE118221). NuTi Capture-C analysis (MPP, CDP, cDC1, cDC2 and pDC) was performed with a protocol modified from Downes et al., Nat. Commun. 12, 1-15, 2021 and Downes et al., Nat. Protoc. 17, 445-475, 2022. Design of Irf8 promoter viewpoint was with the design tool Oligo (https://oligo.readthedocs.io/en/latest/index.html) and resulted in 2 oligonucleotide probes targeting Irf8 promoter. Oligonucleotide probes were positioned adjacent to the DpnII cut sites on a restriction fragment spanning the Irf8 promoter (chr8:123,259,948-123,260,530). RNA-seq analysis (MPP, CDP, cDC1, cDC2 and pDC) and ChIP-seq analysis (cDC and pDC) was done as described in Allhoff et al., Nucleic Acids Res. 44, e153, 2016 (GSE73143).

first: Huaming

last: Xu

first: Chao-Chung

last: Kuo

first: Katrin

last: Götz

first: Thomas

last: Look

first: Marcelo

last: Toledo

first: Kristin

last: Seré

first: Ivan

middle: G

last: Costa

first: Martin

last: Zenke


title: Derivation of human salivary epithelial progenitors from pluripotent stem cells

city: Beijing

first: Siqi

last: Zhang

address: 22# Zhongguancun South Avenue, Haidian District

department: Department of Oral and Maxillofacial Surgery School and Hospital of Stomatology

institute: Peking University

summary: We described, for the first time, a robust protocol for direct differentiation of hPSCs into SGEP by mimicking the activity of retinoic acid and WNT signaling. These hPSC-derived SGEP expressed SOX9, KRT5 and KRT19, which were the important progenitor markers of developing salivary glands. The CD24 and α-SMA positive cells that are capable to restore the function of injured salivary glands were also present in SGEP cultures. Importantly, RNA-seq was performed to examine the similarity of SGEP to human fetal and mature salivary glands. The result revealed the SGEP resemble the transcript profile of human fetal submandibular glands. Therefore, we successfully induced hPSCs into SGEP and demonstrated that these SGEP potentially serves as models for studying mechanism underling salivary development, and as cell sources for clinical use.

overall_design: Analysis of global transcriptomes of human embryonic stem cell (H1) derived salivary gland epithelial progenitors.There are two  replicates. Control group are published RNA-seq datasets.

first: Zhang

last: Siqi

first: Wei

last: Shicheng


title: A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: Goals:  1) To analyse amyloid-b aggregation and proteomic and transcriptomic changes in 2, 5 and 8 months old 5xFAD mice   2) To determine differentially expressed proteins correlating and anti-correlating with aggregate formation  3) To analyse whether correlating or anti-correlating proteins change at transcriptional or posttranscriptional level  4) To determine differentially expressed or correlating and anti-correlating proteins which overlap with proteomic changes found in human AD brains  5) To analyse, whether Arl8b, which is an Ab aggregate correlating protein, show significant changes in CSF of AD patients  Summary: Our study revealed that Ab42 driven aggregate formation leads to distinct brain region-specific proteome changes in 5xFAD mouse brains. We detected 195 dysregulated proteins correlating or anti-correlating with Ab-aggregation in hippocampus and cortex of 5xFAD mice. Most of these protein changes were caused by posttranscriptional mechanisms, only a minor part was associated with transcriptional dysregulation. A fraction of the Ab-correlated and anti-correlated DEPs was conserved in post-mortem brains of AD patients revealing that proteome changes in 5xFAD mice recapitulate disease-relevant changes in AD patient brains. Among the group of Ab42-correlating proteins, we have found the lysosome associated protein Arl8b, which is present in increased levels in CSF samples of AD patients and might have potential as an AD biomarker.

overall_design: In total 34 brain samples (cortex and hippocampus) of 2, 5 and 8 months old 5xFAD and WT (control) mice were analysed. Per age and tissue 2-3 biological replicates were used for the analysis (see table below).

first: Christin

last: Suenkel

first: Agnieszka

last: Rybak-Wolf

first: Eric

last: Blanc

first: Annett

last: Boeddrich

first: Christian

last: Haenig

first: Erich

middle: E

last: Wanker


title: The RNA seq of cytomatrix and cytosol

city: Houston

first: Tattym

last: Shaiken

address: One Baylor Plaza

department: Medicine

institute: Baylor College of Medicine

summary: We report separation of the viscous fluid component of the cytoplasm, the cytosol, from the elastic solid, the cytomatrix and describe distinct molecular pathways of each compartment.

overall_design: mRNA profiles of the cytosol (Cyt) and cytomatrix (CMX) at normal growth condition and under the treatment of mTOR-KI, pp242 with 2 replicates for each condition

first: Sandra

last: Grimm

first: Cristian

last: Coarfa

first: Matthew

last: Robertson

first: Daniel

last: Kraushaar

first: Emily

last: Ricco


title: Transcription factor GATA4 regulates RNA splicing [RNA-seq]

city: san francisco

first: Lili

last: Zhu

address: 1650 owens street

institute: Gladstone Institutes

summary: RNA-seq data indicated that Knockdown of GATA4 in human cardiomyocytes resulted in differential alternative splicing changes in genes involved in cytoskeleton organization and calcium ion import. Enhanced crosslinking and immunoprecipitation (CLIP) assay demonstrated that GATA4 directly binds to defined mRNAs motifs in a sequence-specific manner

overall_design: 4 replicates of GATA4-Knockdown in d7 hiPSC derived hCPCs by siRNA(48h after siRNA transfection). RNA-seq in D7 hiPSC derived hCPCs.

first: Deepak

last: Srivastava


title: Transcription factor GATA4 binds to RNA [eCLIP-seq]

summary: eCLIP-seq data indicated that GATA4 binds to RNAK

overall_design: 3 replicates of GATA4-eCLIP in d7 hiPSC derived hCPCs by siRNA(48h after siRNA transfection). Triplicates of eCLIP in D7 hiPSC derived hCPCs.


title: Changes in miRNA expression profile upon treatment with plumbagin or menadione in SW-620 colorectal cancer cells

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: To elucidate the mode of actions of Plumbagin and Menadione, miRNA-profilling was performed after treating cells with vehicle (DMSO), Plumbagin (10uM), and Menadione (10uM) for 24 hours. Threel replicates for control and Menadione and two replicates for Plumbagin were subjected to miRNA-microarray.

overall_design: Agilent one-color experiment,Organism: Homo sapiens, Agilent Human miRNA 8x60k Arrays AMADID: 070156

first: Priyanka

last: Samji

first: Priyadharshini

last: Mayalagu

first: Chandra

last: Kishore

first: Devarajan

last: Karunagaran


title: Insight into the potential candidate genes and signaling pathways involved in lymphoma progression in dogs using a comprehensive whole blood transcriptome analysis

city: Wanju

first: Kyung-Tai

last: Lee

state: JeonBuk

address: 1500 Kongjwipatjwi

department: Animal Genomics and Bioinformatics Division

institute: National Institute of Animal Science

summary:
Purpose: This goal of this study was to explore the important genes and pathways involved in canine lymphoma progression and understand the underlying molecular using RNA-Sequencing.
Methods: RNAs acquired from seven pairs of lymphoma and non-lymphoma blood samples were sequenced from different breeds of dogs. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches.
Result: A total of 625 differentially expressed genes (DEGs) were identified between lymphoma and non–lymphoma samples, including 347 up–regulated DEGs such as SLC38A11, SCN3A, ZIC5 etc. and 278 down–regulated DEGs such as LOC475937, CSMD1, KRT14 etc. Especially, the pathway of PI3K-Akt signaling, which was directly related to the lymphoma, was enriched in KEGG analysis. In the protein-protein interaction network, CDK1 was found to be a top hub gene with highest degree of connectivity in lymphoma samples.
Conclusion: We found important candidate genes and pathways for further testing in canine lymphoma.

overall_design: Blood transcriptome profiles of lymphoma and non-lymphoma disease of canine

first: Kyoung-Won

last: Seo


title: Transcriptomic evaluation of age-associated CNS-resident CD8 memory T cells identifies CD200R1 as an important regulator of T cell entry and activation

city: Bar Harbor

first: Gareth

last: Howell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: We report a novel role for the CD200-CD200R1 pathway in regulating the basal entry and activation of resident memory phenotype CD8 T cells in the brain and other non-lymphoid tissues.

overall_design: Brain and spleen CD8 T cells (CD44HiCD62LLo)  were isolated by FACS, Cells were stimulated with or without PMA/ionomycin for 2 hours to were subjected to RNA-sequecing

first: Rodney

last: Ritzel

first: Meaghan

last: Roy-O’Reilly

first: Hongtian

last: Yang

middle: R

first: Louise

last: McCullough


title: GwEEP - A comprehensive approach for the profiling of DNA modifying enzymes

city: Saarbrücken

first: Jörn

last: Walter

state: Saarland

address: Campus A2.4

department: Genetics and Epigenetics

institute: Saarland University

type: Methylation profiling by high throughput sequencing

summary:
A precise understanding of DNA methylation dynamics on a genome wide scale is of great importance for the comprehensive investigation of a variety of biological processes such as reprogramming of somatic cells to iPSCs, cell differentiation and also cancer development. To date, a complex integration of multiple and distinct genome wide data sets is required to derive the global activity of DNA modifying enzymes.
We present GwEEP - Genome-wide Epigenetic Efficiency Profiling as a versatile approach to infer dynamic efficiency changes of DNA modifying enzymes at base pair resolution on a genome wide scale. GwEEP relies on genome wide oxidative Hairpin Bisulfite sequencing (HPoxBS) data sets, which are translated by a sophisticated hidden Markov model into quantitative enzyme efficiencies with reported confidence around the estimates. GwEEP in its present form predicts de novo and maintenance methylation efficiencies of Dnmts, as well as the hydroxylation efficiency of Tets but its purposefully flexible design allows to capture further oxidation processes such as formylation and carboxylation given available data in the future.
Applied to a well characterized ES cell model, GwEEP precisely predicts the complex epigenetic changes following a Serum-to-2i shift i.e., (i) instant reduction in maintenance efficiency (ii) gradually decreasing de novo methylation efficiency and (iii) increasing Tet efficiencies. In addition, a complementary analysis of Tet triple knock-out ES cells confirms the previous hypothesized mutual interference of Dnmts and Tets. GwEEP is applicable to a wide range of biological samples including cell lines, but also tissues and primary cell types.

overall_design: In total we generated eight hairpin libraries (BS and oxBS, respectively) for WT ES cells at three distinct time points - Serum/Lif(d0), 2i 72h (d3) and 2i 144h (d6); four libraries for TetTKO cells (BS only) - Serum/LIF, 2i 48h (d2), 2i 96h (d4) and 168h (d7), as well as two low-input libraries for WT ES cells 72h 2i (BS and oxBS).

first: Charalampos

last: Kyriakopoulos

first: Karl

last: Nordström

first: Paula Linh

last: Kramer

first: Judith

last: Gottfreund

first: Abdulrahman

last: Salhab

first: Julia

last: Arand

first: Fabian

last: Müller

first: Ferdinand

last: von Meyenn

first: Gabriella

last: Ficz

first: Wolf

last: Reik

first: Verena

last: Wolf

first: Pascal

last: Giehr


title: RNA-seq to find the most related genes with Wdr62 expression in HL-1 cells

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

summary: To explain molecular mechanism of WDR62 functions in myocardial cell mitosis, RNA-seq was performed to analyze the differential expression genes (DEGs) among three HL-1 cell groups: control (CON), Wdr62 knock-down (KD) and rescued KD by overexpressing WDR62-WT (RE)

overall_design: Experiments were done on quadruplicate for each group including CON, KD and RE.

first: Guoying

last: Hunag

first: Duan

last: Ma

first: Lili

last: Hao


title: The effect of circulating Klotho in response to nephrotoxic serum (NTS)-induced injury

city: Stockholm

first: Emmanuelle

last: Charrin

address: Alfred Nobels Alle 8

country: Sweden

institute: Karolinska Institute

summary: The goal of this study is to compare glomerular- and tubular-enriched fraction in transgenic mouse model overexpressing circulating human Klotho (Alb-hKL) vs WT mice seven days after nephrotoxic serum-induced injury

overall_design: 3 Alb-hKL and 4 WT mice were used. The glomerular (GLOM) fraction and the tubular (ROK) fraction were isolated for each mouse

first: Hannes

last: Olauson

first: Jaakko

last: Patrakka

first: Anastasios

last: Damdimopoulos


title: Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

summary: A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation from the start codon. Unlike programmable frameshifting during elongation, start codon-associated ribosome frameshifting (SCARF) stems from the slippage of the initiating ribosome. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra unannotated from human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity during the transition from initiation to elongation. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF products provide a degradative source to mitigate amino acid scarcity during starvation. Our findings illustrate the beneficial effect of divergent translation in nutrient stress adaptation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Ezra-seq in different cells or mouse tissues

first: Longfei

last: Jia

first: Shu-Bing

last: Qian


title: Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 512 B Preston Research Building

department: Biochemistry

institute: Vanderbilt University

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

overall_design: Refer to individual Series


title: Neutrophil S100A9 supports M2 macrophage niche formation in granulomas

city: Sapporo

first: Tatsuaki

last: Mizutani

address: N15W7, Kita-ku

institute: Hokkaido University

summary: Mycobacterium infection gives rise to granulomas predominantly composed of inflammatory M1-like macrophages, with bacteria-permissive M2 macrophages also detected in deep granulomas. Our histological analysis of Mycobacterium bovis bacillus Calmette-Guerin-elicited granulomas in guinea pigs revealed that S100A9-expressing neutrophils bordered a unique M2 niche within the inner circle of concentrically multilayered granulomas. We evaluated the effect of S100A9 on macrophage M2 polarization based on guinea pig studies. S100A9-deficient mouse neutrophils abrogated M2 polarization, which was critically dependent on COX-2 signaling in neutrophils. Mechanistic evidence suggested that nuclear S100A9 interacts with C/EBPβ, which cooperatively activates the Cox-2 promoter and amplifies prostaglandin E2 production, followed by M2 polarization in proximal macrophages. Since the M2 populations in guinea pig granulomas were abolished via treatment with celecoxib, a selective COX-2 inhibitor, we propose the S100A9/Cox-2 axis as a major pathway driving M2 niche formation in granulomas.

overall_design: Analyses of transcriptional profiles in S100a9 KO and WT neutrophils.

first: Keiko

last: Takemoto


title: Genome-widebinding maps of arabidopsis KYP

city: New Taipei City

first: FU-YU

last: HUNG

address: Singyi Rd. 17ave. 9s 8th 2F

country: Taiwan

institute: RIKEN

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of KYP in 10 days old KYPpro::KYP:3xFLAG arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide binding levels of KYP:3xFLAG. ChIP was performed using anti-FLAG antibody (sigma M2), and ChIP DNA were analyzed by Illumina NovoSeq.

overall_design: Chromatin immunoprecipitation was performed with KYPpro::KYP:3xFLAG arabidopsis. ChIP DNA was analyzed by Illumina NovoSeq.

first: Fu-Yu

last: Hung

first: Yun-Ru

last: Feng

first: Keqiang


title: scRNA-seq analysis of Msi2CreER-MycT58A Mouse Pre-cancer and Pancreas ASCP tumor

city: La Jolla

first: Michael

last: Hamilton

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

summary: scRNA-seq analysis evaluating transcriptional heterogeneity in mouse pre-cancer and pancreas tumors in an effort to model the progression of pancreas tumors.  Single cells were captured at t=0 (before tamoxifen induction), t=5 (5 weeks after tamoxifen induction) and t=12 (12 weeks after tamoxifen induction).

overall_design: Pancreas pre-cancer (5 weeks post-induction) and pancreas tumors cells (12 weeks post-induction) from the Msi2-CreER MycT58A mouse model were dissociated and single cells were processed according to 10x genomics instructions.

first: Tannishtha

last: Reya


title: Microarray analysis of glioma cell lines : Temozolomide Sensitive vs. Resistant

city: Seoul, Republic of Korea

first: Sunghyouk

last: Park

email: cmg8075@gmail.com, psh@snu.ac.kr

address: 1, Gwanak-ro, Gwanak-gu

institute: SNU

summary:
Transcriptional profiling of glioma cells comparing control U87(Temozolomide sensitive) cells with U87R(Temozolomide resistant).
The U87 cell line was given a low dose of temozolomide in culture media for 3 weeks, resulting in the formation of temozolomide-resistant cells made as U87R.

overall_design: Two-condition experiment, U87 vs. U87R cells. Biological replicates: 3 control (U87) replicates, 3 test (U87R) replicates.

first: Munki

last: Choo


title: scATAC-seq analysis of Msi2CreER-MycT58A Mouse Pre-cancer and Pancreas ASCP tumor

summary: scATAC-seq analysis evaluating epigenetic heterogeneity in mouse pre-cancer and pancreas ASCP tumor

overall_design: Pancreas pre-cancer (5 weeks post-induction) and ASCP tumors cells (orthotopic transplant of ASCP tumor) from the Msi2-CreER MycT58A mouse model were dissociated and single cells were processed according to 10x genomics instructions.


title: Bulk RNA-seq analysis of Msi2-MycT58A Mouse Pancreas Tumors

summary: RNA-seq comparative analysis of Msi2-MycT58A Mouse Pancreas Tumors

overall_design: Transcriptomic analysis of Epcam+ sorted pancreas tumors cells developed 12 weeks following tamoxifen induction in the Msi2-CreER MycT58A mouse model


title: Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [PRO-seq]

summary: Genetic models suggested that SMARCA5 was required for DNA templated events including transcription, DNA replication and DNA repair.  We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch (ISWI) complexes, in three different human cell lines to define the effects of rapid degradation of this key regulator.  Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6hr of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.

overall_design: PRO-seq was performed on biological replicates. Parental Kasumi-1 cells (wild type SMARCA5) or untreated Kasumi-1 cells expressing endogenous expressed SMARCA5-FKBP12F36V on both alleles as negative controls. Kasumi-1 SMARCA5- FKBP12F36V cells were harvested after 2hr, 6hr, and 24hr with 500nM dTAG-47 treatment. Nuclei were isolated to perform nuclear run-ons.

first: Monica

last: Bomber


title: miRNA expression profiling and identification of a miRNA regulator for  muscle regeneration in the ischemic limb with  proanthocyanidins treatment of adult mice

city: Luzhou city

first: Du

last: Chao

address: 25 Taiping Street, Jiangyang district

institute: The Affiliated Hospital of Southwest Medical University

summary: Using the highly sensitive miRNA array, we screened 411 differentially expressed genes microRNAs in the ischemic muscle with  proanthocyanidins treatment and we explored the functions of these miRNAs in the ischemic muslce by Gene Ontology and Kyoto Encyclopedia of Genes annotation. The enrichment results indicated that these miRNAs mainly participated in the muscle regeneration process. Furthermore, the quantitative real-time polymerase chain reaction, immunohistochemistry and dual luciferase reporter assay results showed that miR-133b-3p is a specific regulator of MKP1/ p38-MAPK signal axis, offering a novel therapeutic opportunity for limb ischemic injury.

platform_organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

overall_design: In this study, six samples from steady-state mice were used to acquire the miRNA expression profiling and the function of the abundant miRNAs in the ischemic muscle with  proanthocyanidins treatment were analyzed by bioinformatic methods,finally, miR-133b-3p was experimentally validated to be a regulator of MPK1.

first: Shi

last: Chen

first: Chao

last: Du


title: Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [RNA-seq]

summary: Genetic models suggested that SMARCA5 was required for DNA templated events including transcription, DNA replication and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch (ISWI) complexes, in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6hr of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.

overall_design: RNA-seq was performed on biological replicates. Parental Kasumi-1 cells (wild type SMARCA5) or untreated Kasumi-1 cells expressing endogenous expressed SMARCA5-FKBP12F36V on both alleles as negative controls. Kasumi-1 SMARCA5-FKBP12F36V cells were harvested after 2hr, 6hr, and 24hr with 500nM dTAG-47 treatment.


title: Gene expression profiling of adult Drosophila melanogaster prickle-spiny legs mutant brains

city: Iowa City

first: Krishna Madhav

last: Nukala

state: Iowa

address: 129 E Jefferson

department: Department of Biology

institute: University of Iowa

summary: Study of genome-wide differential gene expression of adult Drosophila melanogaster prickle-spiny legs mutant brains compared to control animals.

overall_design: Brains were dissected from prickle-spiny legs mutant and control adults. Total RNA was isolated and converted to cDNA for array hybridization. Each genotype was represented with two biological replicates, each with four technical replicates.

first: Krishna

first: John

last: Manak


title: Chromatin localization of nucleophosmin determines the sorting and compartmentalization of ribosome biogenesis

city: Memphis

first: Mario

last: Halic

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

summary: Assembly of eukaryotic ribosomes begins in the nucleolus, a compartmentalized membraneless  organelle. Although the two ribosomal subunits, 40S and 60S, assemble independently, it remains  unknown if these particles are physically sorted as they assemble and how they partition from the  central chromatin compartment into the outer nucleolar regions, where maturation occurs. In this  study, we show that nucleophosmin specifically mediates the assembly of nascent 60S subunits and  that this specificity is determined by its chromatin localization at the rDNA sites encoding for 60S  subunit rRNA. Nucleophosmin dissociates from chromatin to bind nascent 60S subunits, causing their  partitioning away from chromatin and from nascent 40S subunits through liquid-liquid phase  separation. This directs translocation of nascent 60S subunits towards the nucleophosmin-rich  granular component, where biogenesis continues. Notably, this compartmentalization increases the  efficiency of 60S subunit assembly, specifically the incorporation of the 60S domain III. Our data reveal  that the chromatin localization of nucleophosmin determines its specificity in sorting and coordinates  the movement of ribosomal subunits into specialized assembly compartments.

overall_design: ChIP sequencing, nascent and total RNA sequencing in wild type cells and different S. pombe mutants

first: Ilaria

last: Ugolini


title: Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [ATAC-seq]

first: Scott

last: Hiebert

overall_design: ATAC-seq was performed on biological replicates. Parental Kasumi-1 cells (wild type SMARCA5) or untreated Kasumi-1, HEL, OCI-LY1 cells expressing endogenous expressed SMARCA5-FKBP12F36V on both alleles as negative controls. Kasumi-1,  HEL, OCI-LY1 SMARCA5- FKBP12F36V cells were harvested after indicated time points with 500nM dTAG-47 treatment. Nuclei were isolated to Tn5 incubation.


title: Characterization of SETBP1-deficient hESCs in vitro differentiated towards cortical neuroprogenitors and neurons

city: Cardiff

first: Lucia

middle: Fernandez

last: Cardo

state: Wales

address: maindy road

country: United Kingdom

institute: Cardiff University

summary: Disruptions of SETBP1 (SET binding protein 1) on 18q12.3 by heterozygous gene deletion or loss-of-function variants cause SETBP1 disorder. Clinical features are frequently associated with moderate to severe intellectual disability, autistic traits and speech and motor delays. Despite SETBP1 association with neurodevelopmental disorders, little is known about its possible role during brain development. Using CRISPR/CAS9 genome editing technology, we generated SETBP1-deficient hESC lines and found that the derived cortical neural progenitors (NPCs) exhibit protracted proliferation and distorted layer-specific neuronal differentiation with overall decrease in neurogenesis. We analysed by genome wide transcriptome profiling the DEG and dysregulated pathways related  to SETBP1-deficiency.

overall_design: 3 biological replicate samples each collected at 3 time points of cortical differentiation (days 15, 21, and 34,  n=9 each for SETBP1-/- and the isogenic control cells, respectively). 75bp paired-end sequencing was performed on a HiSeq 4000 sequencer (Illumina, USA) yielding 30 – 45 million reads per sample.

first: Meng

last: Li


title: Expression data in Heart Tissue associated with Tetralogy of Fallot

city: Zhengzhou

first: Lin

last: Liu

address: 7 Weiwu Road, Jinshui District

institute: Henan Provincial People’s Hospital


title: N-Myc overexpression leads to multiple types of acute leukemia in mice [WGS]

city: Tianjin

first: Haitao

last: Bai

state: Tianjin

address: 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

summary: The expression of the oncogene MYCN is upregulated in acute leukemia. However, the role of MYCN in leukemogenesis is poorly understood. We established multiple types of leukemia by retroviral overexpression of N-Myc in mice and studied the mechanism of leukemogenesis. Two types of hematopoietic stem cells and three types of hematopoietic progenitor cells highly purified from the bone marrow of adult C57BL/6 mice were transduced with N-Myc and transplanted into lethally irradiated mice. Acute leukemia developed from all these populations. Notably, not only B cell acute lymphoid leukemia, but also T cell acute lymphoid leukemia, acute myeloid leukemia, acute undifferentiated leukemia, and mixed phenotype acute leukemia developed, suggesting the multiple cells of origin, regardless types of leukemia. Moreover, leukemic stem cells were identified in Kit+Sca-1+Lin- bone marrow cells. RNA-seq data revealed the leukemia type-specific transcription profiles. Interestingly, acute undifferentiated leukemia appeared to be transcriptionally close to T cell acute lymphoid leukemia. Whole genome sequencing suggested that different types of leukemia arose associated with a large number of gene mutations induced by N-Myc overexpression but independent of retroviral integration sites. This study provides a new mouse model in which varying types of leukemia develop by only one oncogene.

overall_design: Examination of SNV, INDEL, CNV and integration sites of N-Myc for B-ALL, T-ALL, AML and AUL

first: Fang

last: Dong

first: Hideo

last: Ema


title: N-Myc overexpression leads to multiple types of acute leukemia in mice


title: N-Myc overexpression leads to multiple types of acute leukemia in mice [RNA-Seq]

overall_design: Examination of mRNA profile for B-ALL, T-ALL, AML and AUL


title: lncRNA and mRNA expression data in Heart Tissue associated with Tetralogy of Fallot

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

summary: The aim of the study is to identify the global messenger RNA (mRNA) and long noncoding RNA (lncRNA) expression profiling in tissue samples of the right ventricular outflow tract of 5 TOF children with no other intracardiac and extracardiac malformations and 5 normal fetuses.

first: Hongdan

last: Wang


title: MiRNA expression data in Heart Tissue associated with Tetralogy of Fallot

summary: The aim of the study is to identify the Micro RNA(miRNA) expression profiling in tissue samples of the right ventricular outflow tract of 5 TOF children with no other intracardiac and extracardiac malformations and 5 normal fetuses.


title: RTD-1 therapeutically normalizes synovial gene signatures in rat autoimmune arthritis and suppresses proinflammatory mediators in RA synovial fibroblasts

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

summary: Rhesus theta defensin-1 (RTD-1), a macrocyclic immunomodulatory host defense peptide from Old World monkeys, is therapeutic in pristane-induced arthritis (PIA) rat model.  RNA-sequence (RNA-seq) analysis was used to interrogate the changes in gene expression in PIA rats diseased model. To, study the anti-arthritic mechanisms of systemic RTD-1, the differentially expressed genes between synovial tissues of rats with pristane induced arthritis (PIA) and naïve animals were identified and the effect of RTD-1 treatment for 1, 3 or 5 days was then evaluated. The results indicate a regulation of arthritogenic gene networks in a manner that correlates temporally with clinical resolution of rat PIA.

overall_design: The differentially expressed genes between synovial tissues of rats with pristane induced arthritis (PIA) and naïve rats were identified and the effect of RTD-1 treatment for 1, 3 or 5 days was then evaluated.

first: Prasad

last: Tongaonkar

first: Akshay

last: Subramanian

first: Dat

middle: Q

last: Tran

first: Katie

last: Trinh

first: Justin

middle: B

last: Schaal

first: Teresina

last: Laragione

first: André

last: Ouellette

first: Percio

last: Gulko

first: Michael

last: Selsted


title: CircRNA expression data in Heart Tissue associated with Tetralogy of Fallot

summary: The aim of the study is to identify the  Circular RNA(circRNA) expression profiling in tissue samples of the right ventricular outflow tract of 5 TOF children with no other intracardiac and extracardiac malformations and 5 normal fetuses.

overall_design: CircRNA expression profiling in tissue samples of the right ventricular outflow tract of 5 TOF children with no other intracardiac and extracardiac malformations and 5 normal fetuses.


title: Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [CUT&RUN]

first: Scott

last: Hiebert

overall_design: CUT&RUN was performed on biological replicates. For anti-Flag CUT&RUN, untreated cells expressing endogenous expressed SMARCA5-FKBP12F36V-1xFLAG on both alleles was used as postivie control versus SMARCA5- FKBP12F36V-1xFLAG cells  treated for 18hrs with 500nM dTAG-47. For anti-CTCF CUT&RUN, untreated cells expressing endogenous expressed SMARCA5-FKBP12F36V-1xFLAG on both alleles was used as postivie control versus  SMARCA5- FKBP12F36V-1xFLAG cells  treated for 2hr, 6hr, and 24hr with 500nM dTAG-47. For anti-H2AZ and anti-H3K27me3, in untreated Kasumi-1 cells expressing endogenous expressed SMARCA5-FKBP12F36V-1xFLAG. For anti-RUNX1 and anti-ETOZnf CUT&RUN, untreated Kasumi-1 cells expressing endogenous expressed SMARCA5-FKBP12F36V-1xFLAG on both alleles was used as postivie control versus Kasumi-1 SMARCA5- FKBP12F36V-1xFLAG cells  treated for 24hr with 500nM dTAG-47.

first: Monica

middle: L

last: Bomber


title: Genome-wide maps of chromatin state in TAZ low/high GSCs

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

summary: Overexpression of TAZ in GSCs abrogated neuronal differentiation by re-alignment of the enhancer landscape and down-regulation of key master TFs associated with neurogenesis such as OLIG2 and ASCL1.

overall_design:
Examination of 5 different histone modifications in GSCs
Examination of H3K27Ac on GSC after HDACi treatment

first: Mayinuer

last: Maitituoheti

first: Kunal

last: Rai

first: Krishna

last: Bhat


title: MacroH2A1.2 inhibits prostate cancer-induced osteoclastogensis through cooperation with HP1a and H1.2

summary: Prostate cancer cells frequently metastasize to bone and secrete signaling factors that can lead to osteoclast differentiation.  However, the mechanism of regulation of ostecolastostogenesis by soluble secretory factors from prostate cancer is largely unknown. MacroH2A effect the chromatin function  and can potentially  attenuate the prostate cancer  induced  ostoclastogenesis. To study the effect of mH2A1.2 on osteclastogenesis , we used genome wide gene expression  studies in wild type and mH2A1.2 knockout DU154 – prostate cancer cells.

overall_design: Total RNA was isolated from DU154 cells in which mH2A1.2  gene  have been depleted along with the wild type cells to study the differenetial regulation of various genes in each case.

first: Jin-Man

last: Kim

first: Yonghwan

last: Shin

first: Sunyoung

last: Lee

first: Mi

middle: Y

first: Hong-In

first: Kyunghwan

first: Woojin

last: An


title: Optical Genome Mapping Identifies a Novel Pediatric Embryonal Tumor Subtype with a ZNF532-NUTM1 Fusion [methylation]

status: Public on Feb 28 2023

city: Washington

first: Miriam

last: Bornhorst

state: DC

address: 111 Michigan Ave

institute: Children's National Hospital

summary: Molecular characteristics of pediatric brain tumors have not only allowed for tumor subgrouping but have introduced novel treatment options for patients with specific tumor alterations. Therefore, an accurate histologic and molecular diagnosis is critical for optimized management of all pediatric patients with brain tumors, including central nervous system embryonal tumors. We present a case where optical genome mapping identified a ZNF532-NUTM1 fusion in a patient with a unique tumor best characterized histologically as a central nervous system embryonal tumor with rhabdoid features. Additional analyses including immunohistochemistry for NUT protein, methylation array, whole genome, and RNA-sequencing was done to confirm the presence of the fusion in the tumor. This is the first description of a pediatric patient with a ZNF532-NUTM1 fusion, yet the histology of this tumor is similar to that of adult cancers with ZNF-NUTM1 fusions and other NUTM1-fusion positive brain tumors reported in literature. Although rare, the distinct pathology and underlying molecular characteristics of these tumors separate them from other embryonal tumors. Therefore, the NUTM-rearrangement appears to define a novel subgroup of pediatric central nervous system embryonal tumors with rhabdoid/epithelioid features that may have a unique response to treatment. Screening for a NUTM1-rearrangement should be considered for all patients with unclassified central nervous system tumors with rhabdoid features to ensure accurate diagnosis so this can ultimately inform therapeutic management for these patients.

overall_design: Gene expression and Methylation analysis to determine presence of ZNF532::NUTM1 fusion and methylation clustering.

first: Augustine

last: Eze Jr

first: Surajit

last: Bhattacharya

first: Ethan

last: Putnam

first: M

middle: I

last: Almira-Suarez

first: Christopher

last: Rossi

first: Madhuri

last: Kambhampati

first: Miguel

last: Almalvez

first: Mariam

last: Barseghyan

first: Nicole

last: Del Risco

first: David

last: Dotson

first: Joyce

last: Turner

first: John

last: Myseros

first: Eric

last: Vilain

first: Roger

middle: J

last: Packer

first: Javad

last: Nazarian

first: Brian

last: Rood

first: Hayk


title: Transcriptome profiling of osteoblasts treated with uMSC-derived exosomes

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: To investigate the function and affected pathways of uMSC-derived exosomes on ossification, we used human and rat osteoblast cell line hFOB1.19 and ROS1728 treated with either exosomes or exosome-free supernatent (which is the  supernatent of exosome pelleting after ultracentrifugation) and a non-treated group as negative control. We take advantages of high through-put sequencing technology to fully reveal the transcriptome changes of the treated cells.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: we used human and rat osteoblast cell line hFOB1.19 and ROS1728 for the study. For exosome collection, umbilical cord were collected and washed with PBS and subjected to primary culture immediately. The samples were first depleted of blood vessels and minced to small pieces then put to culture flasks for primary culture. 10%FBS high-glucose DMEM were used as culture medium for primary cell culture. When cells reach 80% confluent, the cell were lysed with trypsin for passage. After 2 passages, the primary cells were ready to perform exosome collection. For exosome collection, we use 1% exosome-free FBS/DMEM for culture, the medium were collected at a 3-days interval, and the collected culture medium of  were subsequently subjected to ultracentrifugation. After the ultarcentrifugation, the pellet were washed with PBS and ultarcentrifugated again before use. The exosomes were measured for protein concentration using standard method, and 100ng/ml exosomes were used to treat the samples. 48h after treatment, the cells were collected for total RNA extraction.

first: Zicheng

last: Zhang

first: Wen

last: Yuan


title: Signatures and Molecular Mechanisms of N6-Methyladenosine circRNAs in Human Rheumatoid Arthritis from Microarray Data

city: Fuzhou

first: Hongbin

last: Luo

address: No.20,Chazhong road,Taijiang district

institute: Fujian medical university

summary: We used the m6A-circRNA epitranscriptomic microarray to measure the m6A methylated quantities and levels of circRNAs in the synovial tissues of human rheumatoid arthritis and osteoarthritis.

overall_design: Two-condition experiment, RA vs.  OA synovial tissues. Biological replicates: 3 control replicates, 3 test replicates.


title: Capture MRE-seq for methylation analysis of highly degraded DNA samples

city: St. Louis

first: Ting

last: Wang

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

summary: Understanding the impact of DNA methylation within different disease contexts often requires accurate assessment of these modifications in a genome-wide fashion. Frequently, patient-derived tissue stored in long-term hospital tissue banks have been preserved using formalin-fixation paraffin-embedding (FFPE). While these samples can comprise valuable resources for studying disease, the fixation process ultimately compromises the DNA’s integrity and leads to degradation.  Degraded DNA can complicate CpG methylome profiling using traditional techniques, particularly when performing methylation sensitive restriction enzyme sequencing (MRE-seq), yielding high backgrounds and resulting in lowered library complexity.  Here, we provide results using our new MRE-seq protocol (Capture MRE-seq),  tailored to preserving unmethylated CpG information when using samples with highly degraded DNA. The results using Capture MRE-seq correlate well (0.92) with traditional MRE-seq calls when profiling non-degraded samples, and can recover unmethylated regions in highly degraded samples when traditional MRE-seq fails, which we validate using bisulfite sequencing-based data (WGBS) as well as methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq).

overall_design: Data generated for this study include:   GM12878 traditional MRE-seq, GM12878 Capture MRE-seq, GM12878 (1 min degredation) Capture MRE-seq, GM12878 (10 min deg) Capture MRE-seq, GM12878 MeDIP-seq,   FFPE lung sample Capture MRE-seq, and FFPE lung sample MeDIP-seq

first: Xiaoyun

last: Xing

first: Jennifer

last: Flynn

first: Daofeng

last: Li

first: Hyo

last: Jang

first: Hyung

last: Lee


title: A novel reciprocal paracrine signaling loop mediated by transient expression of EphrinB2 in the myocardium regulates ventricular wall formation.

first: Vasu

last: Punj

summary: Genome-wide gene expression studies on EphB4 mutant over wild-type mice. We used microarray to show enrichment of neuregulin-1 pathway in EphB4 mutant mice

overall_design: A total of 6 mice were used, including 3 EphB4 mutant and 3 wild-type. Total RNA was isolated using Qiagen RNeasy kit (Qiagen, Valencia, CA) from mouse heart. Ten micrograms of total RNA was used to synthesize cDNA. T7 promoter introduced during the first strand synthesis was then used to direct cRNA synthesis, which was labeled with biotinylated deoxynucleotide triphosphate, following the manufacturer's protocol (Affymetrix, San Diego, CA). After fragmentation, the biotinylated cRNA was hybridized to Mouse 430.2 Array chips (Affymetrix,  San Diego, CA)

first: Jiang

last: Liu

first: Binyun

last: Ma

first: Sydney

last: Zaggar

first: Parkash

last: Gill

first: Henry

middle: M

last: Sucov

first: S

last: Kumar


title: Optical Genome Mapping Identifies a Novel Pediatric Embryonal Tumor Subtype with a ZNF532-NUTM1 Fusion [RNA-seq]

first: Miriam

last: Bornhorst

first: Augustine

last: Eze Jr

first: Surajit

last: Bhattacharya

first: Ethan

last: Putnam

first: M

last: Almira-Suarez

first: Christopher

last: Rossi

first: Madhuri

last: Kambhampati

first: Miguel

last: Almalvez

first: Mariam

last: Barseghyan

first: Nicole

last: Del Risco

first: David

last: Dotson

first: Joyce

last: Turner

first: John

middle: S

last: Myseros

first: Eric

last: Vilain

first: Roger

last: Packer

first: Javad

last: Nazarian

first: Brian

last: Rood

first: Hayk


title: Functional assessment of a new PBX1 variant through CRISPR-Cas9 gene editing

city: Rennes

first: Laura

last: Mary

address: Rue Henri Le Guilloux

department: Pôle de Biologie

country: France

institute: CHU de Rennes

summary:
To assess the role of a variant of unknown significance in PBX1 (p.(Arg107Gln) by generating a HEK293T-derived cell line knockdown for PBX1 (clone 22 cells) through CRISPR-Cas9.
We then transfected the KD cells or the WT HEK293T cells with a plasmid encoding either WT or Arg107Gln PBX1 proteins.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT HEK293T cells and clone 22 cells after transient transfection with plasmid encoding WT PBX1 (WT) or Arg107Gln PBX1 (MUT)

first: Delphine

last: Leclerc

first: Audrey

last: Labalme

first: Pascale

last: Bellaud

first: Séverine

last: Mazaud-Guittot

first: Stéphane

last: Dréano

first: Bertrand

last: Evrard

first: Antoine

last: Bigand

first: Aurélie

last: Cauchoix

first: Philippe

last: Loget

first: Anna

last: Lokchine

first: Laurence

last: Cluzeau

last: Gilot

first: Marc-Antoine

last: Belaud-Rotureau

first: Sylvie

last: Jaillard


title: Prognostic significance of integrin subunit alpha 2 (ITGA2) and role of mechanical cues in resistance to gemcitabine in pancreatic ductal adenocarcinoma (PDAC)

city: Amsterdam

first: Elisa

last: Giovannetti

address: de boelelaan

country: Netherlands

institute: Amsterdam UMC

summary: This study evaluate the role of the cell-adhesion molecule ITGA2 on PDAC resistance to gemcitabine.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Panc1 and Panc1 resistant to Gemcitabine cell lines

first: Alessandro

last: Gregori

first: Cecilia

last: Bergonzini

first: Giulia

last: Mantini


title: Isolated nuclei from frozen tissue are the superior source for single cell RNA-seq compared with whole cells

city: Auckland

first: Andrew

last: Jiang

address: 3 Symonds Street

country: New Zealand

institute: The University of Auckland

summary: The isolation of intact single cells from frozen tissue is a challenge due to the mechanical and physical stress inflicted upon the cell during the freeze-thaw process. Ruptured cells release ambient RNA into the cell suspension, which can become encapsulated into droplets during droplet based single cell RNA-seq library preparation methods. The presence of ambient RNA in droplets has been suggested to impact data quality, however there have been limited reports on single cell RNA-seq data from frozen tissue. Here, we compare the results of single cell RNA-seq derived from disaggregated cells from frozen brain tissue with single nuclei RNA-seq derived from purified nuclei of identical tissue using the 10X Genomics Chromium 3’ gene expression assay. Our results indicated that presence of ambient RNA in the cell suspension resulted in single cell RNA-seq data with a 25-fold lower gene count, a 5-fold lower UMI count per cell and a 2-fold lower fraction of reads per cell compared with single nuclei RNA-seq data. Cell clustering with the single cell RNA-seq data was unable to resolve the heterogeneity of brain cell types. Our conclusion is that nuclei from frozen tissue are the superior substrate for single cell transcriptome analysis.

overall_design: Single cell RNA-seq and single nuclei RNA-seq of frozen ovine striatal tissue


title: Hijacking a neurodevelopmental epigenomic program in metastatic dissemination of medulloblastoma

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

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

overall_design: Refer to individual Series


title: Nuclear myosin 1 regulates platelet activation and immune response in mice

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Here we suggest that NM1 regulation of oxidative phosphorylation in mitochondria has an effect on hematopoietic progenitor stem cells during their differentiation to terminal blood and bone marrow stromal cells. Deletion of NM1 in the bone marrow tissue leads to differential gene expression associated with platelet activation and blood coagulation; immune system response and osteoclast differentiation. The platelet activation gene programs which are dependent on glycolysis are upregulated in NM1 KO tissue, while lymphocyte and osteoclast differentiation which is dependent on oxidative phosphorylation is suppressed in NM1 KO bone marrow.

overall_design: RNA seq of bone marrrow tissue isolated from NM1 WT and KO mice

first: Tomas

last: Venit

first: Nizar

last: Drou


title: NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

city: Chicagp

first: Yaping

last: Liu

state: IL

address: 303 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Cis-regulatory elements coordinate the regulation of their targeted genes’ expression. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.

overall_design:
NOMe-HiC libraries were generated with 3 biological replicates at IMR-90 and GM12878 cell lines
Please note that the processed data files generated from all replicates are linked to the corresponding rep1 sample records.


title: Single-cell RNA sequencing of liver nonparenchymal cells from murine model of endotoxemia

city: Changsha

first: Xuejing

last: Sun

state: Hunan

address: Ton-zi po road

department: Department of Cardiology

institute: Third Xinagya Hospital

summary: Liver has a crucial role in the regulation of immune defense in systemic infections. During endotoxemia, the liver transits from an immune-tolerant towards an immune-active state and forms the first line of defense against invading microorganisms. the role of liver nonparenchymal cells in endotoxemia remains unintelligible. To characterize the liver nonparenchymal cells in endotoxemia liver, we performed single-cell RNA sequencing of liver nonparenchymal cells from healthy C57BL/6J mice and murine model of endotoxemia at early or late stage. The single-cell RNA-seq analyses revealed the heterogeneity of liver nonparenchymal cells in endotoxemia liver.

overall_design:
Single-cell RNA sequencing of liver nonparenchymal cells from healthy C57BL/6J mice (n=6, eight weeks-age) using MGISEQ-2000.
Single-cell RNA sequencing of liver parenchymal cells from murine model of endotoxemia at 3-hour time point (n=6, eight weeks-age) using MGISEQ-2000.
Single-cell RNA sequencing of liver parenchymal cells from murine model of endotoxemia at 12-hour time point (n=6, eight weeks-age) using MGISEQ-2000.

first: Yan

last: Tang

first: Yuanyuan

last: Chen

first: Suzhen

first: Lun

first: Youxiang

first: Yao

last: Lu

first: Hong

last: Yuan

first: Zhaoyang

first: Jingjing

last: Cai