title: Intellicage analysis of Cpa3+/+ and Cpa3Cre mice

city: Heidelberg

first: Robin

last: Thiele

address: Im Neuenheimer Feld 280

department: Immunology

institute: German Cancer Research Center

summary:
We investigated antigen-specific avoidance behavior in mice, and found that is critically dependent on mast cells. We interrogated potential signaling routes between mast cells and the brain using mutant mice, pharmacological inhibition of serotonin receptor 3, neural activity recordings, and vagotomy.
We analyzed gene expression comparing naive versus immunized wild type mice, and versus mast cell-deficient mice at different times following antigen exposure

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cpa3+/+ (wild type) and Cpa3Cre/+ (mast cell-deficient) mice

first: Thomas

last: Plum

last: Binzberger

first: Nathalie

last: Stakenborg

first: Candice

last: Fung

first: Anke

last: Tappe-Theodor

first: Zheng

last: Wang

first: Marina

last: Fortea

first: Daniel

last: Postrach

first: Fuwei

last: Shang

first: Tanja

last: Poth

first: Duncan

last: MacLaren

first: Guy

last: Boeckxstaens

first: Pieter

last: Vanden Berghe

first: Rohini

last: Kuner

first: Satoshi

last: Tanaka

first: David

last: Voehringer

first: Jessica

last: Strid

last: Monyer

first: Thorsten

last: Feyerabend

first: Hans-Reimer

last: Rodewald


title: Single-cell analysis of megakaryopoiesis in peripheral CD34+ cells: insights into ETV6-related thrombocytopenia

status: Public on Jun 15 2023

city: Marseille

first: Timothée

middle: Jean-Rémi

last: Bigot

address: 27 Bd Jean Moulin

department: Equipe 2

country: France

type: Expression profiling by high throughput sequencing

summary: Using single-cell RNA sequencing (scRNAseq), we investigated ETV6-variant (P214L and F417LTer4) carriers who are affected by constitutional thrombopenia. We demonstrate that ETV6-variant carriers presented transcriptomic aberrant populations of megakaryocytes (MK) and mega-erythroid progenitors (MEP) with affected pathways. We confirmed this bioinformatic analyzes by functional assays. We also demonstrate a bypass of common myeloid progenitors (CMP) during physiologic differentiation from hematopoietic stem/progenitors cells (HSPC) to MK and we identified a new population of MK-primed CMP in our culture model. We raise this analysis as a new exploratory modus operandi for constitutional diseases.

overall_design: Single cell RNA-seq study of ETV6-variant carriers cells compared to controls at two time points (Day 6 and 11 of culture).

first: Elisa

last: Gabinaud

first: Laurent

last: Hannouche

first: Véronique

last: Sbarra

last: Andersen

first: Delphine

last: Bastelica

first: Céline

last: Falaise

first: Manal

last: Ibrahim-Kosta

first: Marie

last: Loosveld

first: Paul

last: Saultier

first: Dominique

last: Payet-Bornet

first: Marie-Christine

last: Alessi

last: Potier

first: Marjorie

last: Poggi


title: Sirtuin 2 inhibition selectively induces senescence in ATRX-deficient malignant gliomas by modulating chromatin landscapes genome-wide

city: Houston

first: Prit Benny

last: Malgulwar

state: TX

address: 2130 W Holcombe Blvd

department: Translational Molecular Pathology

country: USA

institute: U.T. M.D. ANDERSON CANCER CENTER

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq of mutant delta POX01387after transfer from glucose medium to Avicel medium for 24 hours

city: Nanning

first: Shuai

last: Zhao

state: Guangxi

address: 100 Daxue Road

country: China

institute: Guangxi University

summary: To explore the effect of transcription factor POX01387 on transcription levels of plant-biomass-degrading enzyme-encoding genes in Penicillium oxalicum

overall_design: mutant delta POX01387 and the parental strain delta ku70 with three replicates for each strain

first: Cheng-Xi

last: Li

first: Ting

last: Zhang


title: miRNA expression analysis of breast cancer tissue and matched nomal tissue

city: Seoul

first: Yesol

last: Kim

address: Cheongpa-ro 47-gil 100, Yongsan-gu

country: South Korea

institute: Sookmyung Women's University

summary: Breast cancer can classify molecular subtype, luminal A, B, and HER2-positive and triple-negative breast cancer. Especially TNBC, there is no therapeutic target compared to other molecular subtypes. To investigate dysregulated miRNAs in TNBC, we performed miRNA microarray using breast cancer tissue with matched normal tissue in each subtype.

overall_design:
The RNA were extracted from human cancer tissues and adjacent normal tissues using TRIzol (Life Technologies). miRNA microarray were performed by a SurePrint G3 miRNA Microarray Kit, 8x60K (Agilent, G4872A)
-------------
*** Submitter declares the raw data are not available.

first: Jong-Hoon

last: Park

first: Hyun-Kyung

last: Kong


title: RNA-seq of mutant delta POX07277 after transfer from glucose medium to Avicel medium for 24 hours

summary: Effect of phospholipase on cellulase production

overall_design:
6 Samples, 3 Samples for each treatment
Relevant sequences in process data have been uploaded in GSE80076.

first: Shi-huan


title: Characterisation of a hybrid histidine kinase controlling acetate metabolism in Acinetobacter baumannii

city: North Ryde

first: Ian

last: Paulsen

state: New South Wales

address: 14 Eastern Road

department: Molecular Sciences

country: Australia

institute: Macquarie University

summary: RNA sequencing transcriptomics was performed on a highly multidrug resistant A. baumannii strain belonging to international clone I, AB5075_UW and a transposon insertion inactivated mutant of ABUW_0182 (acmS), which encodes a hybrid histidine kinase.Transcriptomics suggests that AcmS controls expression of the genes involved in short-chain fatty acid metabolism in A. baumannii. Biophysical analyses showed ABUW_0182 binds acetic and propionic acid with affinities in a low micromolar range, suggesting they represent the physiological ligands for this hybrid histidine kinase system.

overall_design: Global transcriptomic profiles of the acmS mutant and the parental A. baumannii strain were compared. The parental and mutant cells were grown to mid exponential phase at 37°C, with shaking. Cell pellets were harvested and the total RNA was extracted from three biological replicates. Ribosomal RNA was depleted using Ribozero magnetic kit (Bacteria) (Illumina, Inc., USA) and the cDNA library was generated using Truseq stranded RNA preparation kit (Illumina, Inc., USA). RNA libraries were prepared for sequencing using standard Illumina protocols.

first: Alaska

last: Pokhrel

first: Bhumika

last: Shah


title: Spatio-temporal adaptation of DOT1L-mediated transcriptional control within defined cell lineages during cortical development

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

summary:
Purpose:Transcriptional regulation of cell fate determination is cortical development. The goals of this study were to determine the role of the histone methyltransferase DOT1L neurogenesis during cortical development in mouse, effect of DOT1L inhibition on lineage progression, and gene regulatory alterations mediated by DOT1L inhibition
Methods: Neural progenitor cells in the ventricular zone of E14.5 organotypic brain slices from mouse embryos were labelled via microinjection (Taverna et al., 2012) and treated with DOT1L inhibitor EPZ5676 (Pinometostat) or vehicle for 24 h. Labelled cells and progeny were processed for single cell RNA sequencing (scRNA-seq) using the CEL-Seq2 (Hashimshony, 2016) with modifications as descried in the mCEL-seq2 protocol (Herman et al., 2018). Libraries were sequenced (paired-end) on Illumina Hi-seq 2500 at a depth of ~150,000 reads per cell. Reads were aligned to the mouse transcriptome (GRCm38/mm10) using bwa (version 0.6.2-r126) (H. Li & Durbin, 2009) with default parameters. Cells from two microinjection experiments were pooled for sequencing.
Results:710 cells expressing 34,205 genes were recovered. Analysis was performed with Seurat v3.0. The top 800 higjly variable genes were used for clustering recovering 5 cell types: apical progenitors, basal progenitors, transitory cells, neurons I, and neurons II, which were observed in both inhibition and control conditions. Slingshot pseudotime analysis revealed alterations to differentiation trajectories in inhibition condition compared to control. In addition, gene regulatory network analysis revealed alterations in transcription factor activities which were important for metabolic regulation of neurogenesis.
Conclusions: This study revealed a novel cell state, transitory cells, which arises after apical progenitor mitoses. It showed that methyltansferase activity of DOT1L is crucial for cortical neurogenesis.

overall_design: Samples from two microinjection experiments were pooled for sequencing. EPZ treated and control cells were pooled to generate one single cell gene expression matrix.

first: Bismark

last: Appiah

first: Camila

last: Fullio


title: Molecular analysis in imiquimod (IMQ)-induced psoriasis model

city: Guangzhou

first: Xueting

last: Liu

address: Changgangdong 250

institute: The Second Affiliated Hospital of Guangzhou Medical University

summary: The mechanisms underlying pruritus of imiquimod (IMQ)-induced psoriasis remain poorly understood. In this study, we investigated whether there are certain key signaling molecules downstream of the recently identified peptides mediating itch in the spinal cord. We investigated the changes in the trascriptome by performing RNAseq of cervical spinal cords in control and IMQ-induced psoriasis. Our study represents the detailed analysis of transcriptomes of spinal cord in chronic itch model with biologic replicates, generated by RNA-seq technology.

overall_design: six mice (3 controls and 3 psoriasis) were sacrificed. Cervical spinal cord isolation is followed by RNA extraction of single samples, library preparation and sequencing.

first: Yanmei

last: Wang

first: Yuhuan

last: Wen

first: Ailin

last: Tao


title: RNA-seq Analysis of mRNA profiles in β-Gal-overexpressing, and HuR-overexpressing primary hepatocytes

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
Purpose: The goal of this study is to investigate how HuR regulates hepatocyte death.
Methods: mRNA profiles of β-Gal-overexpressing, and HuR-overexpressing primary hepatocytes were generated by deep sequencing using an Illumina HiseqX platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.83) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1).
Conclusion: Our study represents the first detailed analysis of mRNA profiles in HuR-overexpressing primary hepatocytes, generated by RNA-seq technology. Our results show that 258 genes were upregulated and 357 genes were downregulated following HuR overexpression. GO analysis indicated that the upregulated genes were primarily related to cell death, death, apoptotic process, programmed cell death and intrinsic apoptotic signaling pathway. These data indicate that upregulation of HuR leads to hepatocyte death.

overall_design: mRNA profiles in β-Gal-overexpressing, and HuR-overexpressing primary hepatocytes were generated by deep sequencing, in a single test, using Illumina HiseqX platform.

first: Xinzhi


title: Bulk RNA-seq on human pluripotent stem cell-derived type 2 alveolar cell-like cells

city: Beijing

first: Shuyu

address: Shuang Qing Road 18

institute: Research Center for Eco-Environmental Sciences

summary: We reportWe used bulk RNA sequencing technology to profile gene expression in human pluripotent stem cell-derived type 2 alveolar cell-like cells. By obtaining over 15,000 genes, we compared the derived alveolar cell-like cells to H9 embryonic stem cells. We found significant down-regulation of several pluripotency genes whereas activation of lung or alveolus marker genes, and thus suggested successful induction. We treated the derived cells with nano carbon black and sequenced the samples in order to obtain differentially expressed genes due to the treatment. From KEGG analysis, we concluded that expression of most genes inferring lung or alveolus identities were not affected by the treatment. However, pathways such as chemical carcinogenesis and xenobiotic metabolism were significantly promoted. Finally, since organoid culture is trendy, we compared monolayer-derived alveolar cell-like cells to organoid-based derived ones. Results showed overall similarity in gene expression yet organoid culture yielded morphologically and structurally better cells. This study uses bulk RNA sequencing to confirm the alveolar induction from human pluripotent stem cells and provides insights for nano carbon black toxicities in alveolar cells.

overall_design: RNA profiling of H9 human embryonic stem cell-derived type 2 alveoalr cell-like cells induced in monolayer fashion or organoid system, and derived cells subjected to nano carbon black treatment

first: Renjun

last: Yang

first: Francesco

last: Faiola


title: The transcriptional alteration and non-invasive biomarker potential of peripheral blood microRNAs in patients with early-onset pre-eclampsia

status: Public on Jun 14 2023

city: Wenzhou

first: Meng

last: Zhou

address: 270 Xueyuan Xi Road

institute: Wenzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Early-onset preeclampsia (EOPE) is a severe pregnancy complication associated with significant maternal and fetal morbidity and mortality. Currently, there is a critical need for accurate, non-invasive biomarkers to facilitate early diagnosis and effective management of EOPE. In this study, we aimed to investigate the transcriptional alterations and non-invasive biomarker potential of peripheral blood microRNAs in patients with EOPE. Through our research, we successfully identified two reliable plasma miRNA biomarkers and proposed a circulating two-miRNA panel for the non-invasive early detection of EOPE. Additionally, we independently validated our findings in different patient cohorts using various technological platforms.

overall_design:
To investigate non-invasive biomarker potential of peripheral blood microRNAs in early-onset pre-eclampsia, we conducted a two-phase discovery and validation study.
We then performed miRNA expression profile analysis using data from RNA-seq of 17 plasma samples (5 EOPE, 5 LOPE, and 7 non-disease controls) to identify potential miRNA biomarkers and validate them in external independent cohorts.

first: Zhangye

last: Xu


title: The organismal landscape of clock cells and circadian gene expression in Drosophila

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

department: Biology department

institute: Brandeis University

summary: Circadian rhythms time physiological and behavioral processes to 24-hour cycles. It is generally assumed that most cells contain self-sustained circadian clocks that drive circadian rhythms in gene expression that ultimately generating circadian rhythms in physiology. While those clocks supposedly act cell autonomously, current work suggests that in Drosophila some of them can be adjusted by the brain circadian pacemaker through neuropeptides, like the Pigment Dispersing Factor (PDF). Despite these findings and the ample knowledge of the molecular clockwork, it is still unknown how circadian gene expression in Drosophila is achieved across the body . Here, we used single-cell and bulk RNAseq data to identify cells within the fly that express core-clock components.  Surprisingly, we  found that less than a third of the cell types in the fly are enriched for core-clock genes. Moreover, we identified Lamina wild field (Lawf) and Ponx-neuro positive (Poxn) neurons as putative new circadian neurons. In addition, we found several cell types that don’t express core clock components but are highly enriched for cyclically expressed mRNAs. Strikingly, these cell types  express the PDF receptor (Pdfr),  suggesting that PDF drives rhythmic gene expression in many cell types in flies. Other cell types express both core circadian clock components and Pdfr, suggesting that in these cells, PDF regulates the phase of rhythmic gene expression. Together, our data suggest three different mechanisms generate daily gene expression in cells and tissues: an endogenous canonical molecular clock, PDF signaling-driven expression, or a combination of both.

overall_design: w1118 flies were entrained for at least 3 days 25 °C and dissected at six different timepoints (ZT3, ZT7, ZT11, ZT15, ZT19, and ZT23). RNA from the fly brains was extracted using TRIzol reagent (Sigma, T9424) and treated with DnaseI (NEB, M0303L). We used 150 ng of RNA as input for preparing 3' RNA sequencing libraries following CelSeq2 protocol (97,98), changing the UMI to 6 bases. Sequencing was performed on Illumina NextSeq 500 system

first: Ines

last: Patop

first: Ane

last: Martin Anduaga


title: Single-cell RNA-seq data of parathyroid gland (PTG) cells

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: The University of Tokyo

summary: We have performed single-cell RNA-seq to evaluate whether Gcm2 KO affects chimerism of PTG cell lineages.

overall_design: Adult Gcm2-/- mice complemented with mESCs showing 50‒70% chimerism of peripheral blood cells were used (three for para10_215 and five for para10_222). Single-cell gel beads-in-emulsion were generated using the Chromium Controller (10x Genomics). Libraries were generated using the Single Cell 3’ Reagent Kit v.3.1 for dual index (10x Genomics) according to manufacturer’s instructions.

first: Mayuko

last: Kano

first: Naoaki

last: Mizuno

first: Eiji

last: Mizutani


title: Bulk RNA-seq data of parathyroid gland (PTG) cells

summary: To examine the gene expression profile essential for the development and maintenance of PTGs, we performed bulk RNA-seq.

overall_design: Under fluorescent-light illumination, 10–20 tdTomato-expressing PTG cells were manually collected using a micromanipulator. The SMART-Seq HT Kit was used to synthesize cDNA from total RNA derived from PTG  cells.


title: Gene expression changes in cerebellum induced by dietary restriction

city: Utrecht

first: Wilbert

last: Vermeij

state: Utrecht

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: The beneficial effects of dietary restriction (DR) are associated with a rearrangement of gene expression that modulate metabolic and cytoprotective pathways. However, the effect of DR on the cerebellar transcriptome remained to be fully defined. Therefore we analyzed the effect of 30% DR on the transcriptome of cerebellar cortex of young-adult male mice using RNAseq.

overall_design: Cerebellar cortex of mice on different diets were examined by gene expression profiling

first: Rutger

middle: A

last: Ozinga

first: Ákos

last: Gyenis

first: Jan

middle: H

last: Hoeijmakers

middle: P


title: Gene profile of human monocyte-derived macrophages treated with MTX

city: Amsterdam

first: Ittai

middle: Bernardo

last: Muller

address: De Boelelaan 1118

institute: Amsterdam UMC

summary: Comparison of the transcriptome macrophages derived from CD14+ human monocyte-derived macrophages generated in the presence of M-CSF (M-Mphage) or GM-CSF (GM-Mphage) and MTX.

overall_design: mRNA profiles of monocyte-derived macrophages generated by culturing monocytes for 7 days in the presence of M-CSF (10 ng/ml) to generate M-Mphage, or in the presence of GM-CSF (1000 U/ml) to generate GM-Mphage, while treated with 50nM MTX.

middle: B

first: Gerrit

last: Jansen

first: Amaya

last: Puig Kröger


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [14D, 15B, 15C, 16A]

status: Public on Jun 16 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (14D_210401, 15B_210805, 15B_210810, 15C_210408, 15C_210415, 16A_210805).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

middle: M

last: Behrens


title: Bulk RNA-seq and Single-cell RNA-seq data of parathyroid gland (PTG) cells

first: Takaharu

last: Kimura


title: mRNA expressiom profiling of breast cancer cell line MCF-7 and its endocrine-resistant lines

first: Jing

last: Zhou

state: Guang Dong

address: Yanjiang West Road 107#

institute: Sun Yat-sen University

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

summary: To explore the mechanism of endocrine resistance development in estrogen receptor positive breast cancer,  transcriptome analysis of MCF-7 and its endocrine resistant derivatives, including tamoxifen resistant (TAMR) sub-lines and long-term estrogen deprivation (LTED) sub-lines, were performed using microarray.

overall_design: Total mRNA of MCF-7, MCF-7-LTED and MCF-7-TAMR were analyzed,  and a single replicate was analyzed for each sample.

first: Yujie

first: Qiang


city: shijiazhuang

first: jiaojiao

last: bai

address: huaizhong road No.286

institute: UCAS

summary: To identify potential ubiquitin ligases that regulate BIK1 homeostasis,A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. We using an optimized data analysis workflow,

overall_design: RNA isolated from seedlings of 12-day old wild type arabidopsis plants(Col-0) treated with H2O and flg22,and with 3 repeats of each sample

first: Jiaojiao

last: Bai

first: Dongping

last: Lu


title: Exploring the functional roles of telomere maintenance 2 in the tumorigenesis of Glioblastoma multiforme and drug respon-siveness to temozolomide

city: Taipei

first: Yi-Lin

last: Chiu

address: No.161, Minquan E. Road 6th Sec., Neihu dist.,

department: Biochemistry

country: Taiwan

institute: National Defense Medical Center

summary: Glioblastoma multiforme (GBM) is a grade IV human glioma and is the most malignant primary central nervous system tumor in adults, accounting for around 15% of intracranial neoplasms and 40–50% of all primary malignant brain tumors. However, the median survival time of GBM patients is still less than 15 months, even after treatment with surgical resection, concurrent chemoradiotherapy, and adjuvant chemotherapy with temozolomide (TMZ). Telomere mainte-nance 2 (TELO2) mRNA is highly expressed in high-grade glioma patients, and its expression correlates with shorter survival outcomes. Hence, it is urgent to address the functional role of TELO2 in the tumorigenesis and TMZ treatment of GBM. In this study, we knocked down TELO2 mRNA in GBM8401 cells, a grade IV GBM, compared with TELO2 mRNA overexpression in hu-man embryonic glial SVG p12 cells and normal human astrocyte (NHA) cells. We first analyzed the effect of TELO2 on the Elsevier pathway and Hallmark gene sets in GBM8401, SVG p12, and NHA via an mRNA array analysis. Later, we further examined and analyzed the relationship between TELO2 with fibroblast growth factor receptor 3, cell cycle progression, epithelial–mesenchymal transient (EMT), reactive oxygen species (ROS), apoptosis, and telomerase activity. Our data showed that TELO2 is involved in several functions of GBM cells, including cell cycle progression, EMT, ROS, and apoptosis, telomerase activity. Finally, we examined the crosstalk between TELO2 and the responsiveness of TMZ or curcumin mediated through the TE-LO2-TTI1-TTI2 complex, the p53-dependent complex, the mitochondrial-related complex, and signaling pathways in GBM8401 cells. In summary, our work provides a new insight that TELO2 might modulate target proteins mediated through the complex of phosphatidylinositol 3‑kinase‑related kinases in its involvement in cell cycle progression, EMT, and drug response in GBM patients.

first: Shao-Wei

last: Feng

first: Zih-Syuan

last: Wu

first: Shih-Ming

last: Huang


title: Causal linkage of presence of mutant NPM1 to efficacy of novel therapeutic agents against AML cells with mutant NPM1 [ChIP-Seq]

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: In AML with NPM1 mutation causing cytoplasmic dislocation of NPM1, treatments with menin inhibitor (MI) and standard AML chemotherapy yield complete remissions. However, the causal and mechanistic linkage of mtNPM1 to the efficacy of these agents has not been definitively established. Utilizing CRISPR-Cas9 editing to knock-out (KO) or knock-in a copy of mtNPM1 in AML cells, present studies demonstrate that KO of mtNPM1 from AML cells abrogates sensitivity to MI, selinexor (exportin inhibitor) and cytarabine. Conversely, the knock-in of a copy of mtNPM1 markedly sensitized AML cells to treatment with MI or cytarabine. Following AML therapy, most elderly patients with AML with mtNPM1 and co-mutations in FLT3 suffer AML relapse with poor outcomes, creating a need for novel effective therapies. Utilizing the RNA-Seq signature of CRISPR-edited AML cells with mtNPM1 KO, we interrogated the LINCS1000-CMap data set and found several pan-HDAC inhibitors and a WEE1 tyrosine kinase inhibitor among the top expression mimickers (EMs). Additionally, treatment with adavosertib (WEE1 inhibitor) or panobinostat (pan-HDAC inhibitor) exhibited synergistic in vitro lethal activity with MI against AML cells with mtNPM1. Treatment with adavosertib or panobinostat also reduced AML burden and improved survival in AML xenograft models sensitive or resistant to MI.

overall_design: Paired-end ChIP-Seq of 4 Cultured AML Cell Lines with genomic input

first: Christopher

last: Mill

first: Kapil

middle: N

last: Bhalla


title: Mitochondrial OGG1 expression reduces age-associated neuroinflammation by regulating cytosolic mitochondrial DNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary:
Aging is accompanied by a decline in DNA repair efficiency, which leads to the accumulation of different types of DNA damage. Age-associated chronic inflammation and generation of reactive oxygen species exacerbate the aging process and age-related chronic disorders. These inflammatory processes establish conditions that favor accumulation of DNA base damage, especially 8-oxo-7,8 di-hydroguanine (8-oxoG), which in turn contributes to various age associated diseases. 8-oxoG is repaired by 8-oxoG glycosylase1 (OGG1) through the base excision repair (BER) pathway. OGG1 is present in both the cell nucleus and in mitochondria. Mitochondrial OGG1 has been implicated in mitochondrial DNA repair and increased mitochondrial function. Using transgenic mouse models and cell lines that have been engineered to have enhanced expression of mitochondria-targeted OGG1 (mtOGG1), we show that elevated levels of mtOGG1 in mitochondria can reverse aging-associated inflammation and improve functions. Old male mtOGG1Tg mice show decreased inflammation response, decreased TNFα levels and multiple pro-inflammatory cytokines. Moreover, we observe that male mtOGG1Tg mice show resistance to STING activation. Interestingly, female mtOGG1Tg mice did not respond to mtOGG1 overexpression. Further, HMC3 cells expressing mtOGG1 display decreased release of mtDNA into the cytoplasm after lipopolysacchride induction and regulate inflammation through the pSTING pathway. Also, increased mtOGG1 expression reduced LPS-induced loss of mitochondrial functions. These results suggest that mtOGG1 regulates age-associated inflammation by controlling release of mtDNA into the cytoplasm.
To understand what metabolism-related gene expression changes are altered  in mice overexpressing a mitochondrial OGG1 enzyme. Hippocampi tissues were collected from 13 month old control and transgenic mouse and subjected to RNA isolation.

overall_design: We analyzed a total of 12 samples of mouse hippocampus: controls (n=6 , 3 female and 3 male), mtOGG1 (n=6, 3 female and 3 male). Analysis employed nCounter Advanced Analysis Suite of tools.

first: Vilhelm

last: Bohr


title: Identify the effects of miR-19a-3p miRNA mimic overexpression in mouse calvarial osteoblast primary cultures

city: Rochester

first: David

last: Monroe

address: 200 1st St SW

institute: Mayo Clinic

summary: We used a primary calvarial osteoblast cell line (CalOB) to transfect either a negative control or miR-19a-3p miRNA mimic to understand the effects on global gene expression using bulk RNA-seq.

overall_design: We then performed mRNA gene profiling between the negative control and miR-19a-3p transfected CalOBs.

first: Monroe

last: David

first: Khosla

last: Sundeep


title: Causal linkage of presence of mutant NPM1 to efficacy of novel therapeutic agents against AML cells with mutant NPM1 [RNA-Seq]

city: Houston

overall_design: Paired-end RNAseq of 4 Cultured AML Cell Lines


title: Microfluidic Device Facilitates In Vitro Modeling of Human Neonatal Necrotizing Enterocolitis-on-a-Chip

city: Chapel Hill

first: Misty

last: Good

state: NC

address: 101 Manning Drive 4th Floor CB 7596

department: Pediatrics

institute: University of North Carolina at Chapel Hill

summary: Necrotizing enterocolitis is an intestinal disease induces rapid destruction of the epithelial monolayer of the neonatal intestine. Clinically relevant models of this disease are lacking. Using our novel microfluidic model of  necrotizing enterocolitis,  we characterized the response of intestinal epithelial cell-derived organoids to intestinal bacteria isolated from a neonate with fatal NEC. We subsequently used RNA-sequencing to determine the gene expression profile of these cells after 24 or 72 hours of incubation.

overall_design: Gene expression analysis was performed on RNA isolated from epithelial cells derived from a neonatal small intestine that were cultured on a microfluidic device. These cells were either untreated or exposed to polymicrobial enteric bacteria isolated from a neonate who died from necrotizing enterocolitis for 24 or 72 hours.

first: Wyatt

middle: E

last: Lanik

first: Cliff

middle: J

last: Luke

first: Lila

middle: S

last: Nolan

first: Qingqing

last: Gong

first: Lauren

middle: C

last: Frazer

first: Jamie

last: Rimer

first: Sarah

last: Gale

first: Raymond

last: Luc

first: Shay

last: Bidani

first: Carrie

last: Sibbald

first: Angela

last: Lewis

first: Belgacem

last: Mihi

first: Pranjal

last: Agrawal

first: Martin

last: Goree

first: Marlie

last: Maestas

first: Elise

last: Hu

last: Peters


title: Circular RNA hsa_circ_0064559 is identified to affect the progression of colorectal cancer [PrimeView]

city: Jinan

first: Ya'nan

last: Zhen

state: Shandong

address: No.38 Wuyinshan Road

department: Department of Gastrointestinal Surgery

institute: The Third Affiliated Hospital of Shandong First Medical University

summary:
A series of circular RNAs (circRNAs) play a pivotal role in the pathogenesis of CRC.We found that hsa_circ_0064559 knockdown had the most significant reduction in the proliferation of CRC cells.
The expressed genes(DEGs) between shEV group (n=3) and shCIRC group (n=3) from RKO cells were analyzed on Affymetrix GeneChip primeview human gene expression array (Affymetrix, CA, USA).

overall_design: We identified DEGs between shEV group and shCIRC group  from RKO cells, using  Affymetrix GeneChip primeview human gene expression array.The DEGs were uploaded to Ingenuity Pathway Analysis (IPA, Ingenuity Systems) and enrichment pathway analysis was performed to identify genes related to proliferation and apoptosis in CRC.

first: YA’NAN

last: ZHEN

first: GUODONG

last: SUN

first: CUNBAO

last: CHEN

first: JIANQI

last: LI

first: RUIXUE

last: XIAO

first: ZHONGFA

last: XU


title: TCF7L1 controls tuft cell differentiation

city: Mainz

first: Natalia

last: Soshnikova

address: Langenbeckstr. 1

department: Institute for Molecular Medicine

institute: University Medical Centre of the Johannes Gutenberg University

summary: To study the functions of Tcf7l1 during gut development, we have ablated Tcf7l1 specifically in the intestinal epithelium using Shh-Cre. To determine transcriptional changes upon loss of Tcf7l1, we have isolated EpCAM-positive epithelial cells from mouse embryos using fluorescence activated cell sorting (FACS) and performed RNA-sequencing analysis.

overall_design: Samples: Shhcre-Egfp:Tcf7l1lox/lox and wild type. Cell type: epithelial cells from the small intestine of mouse embryos. Stage of embryogenesis: embryonic day 13.5 (E13.5). Replicates: three biological replicates.

first: Nastasja

last: Kreim


title: Cardiac miRNA profiling in mouse heart failure that is rescued by estrogen treatment .

city: Los Angeles

first: Mansoureh

last: Eghbali

address: 10833 Le Conte Ave

institute: UCLA David Geffen School of Medicine

summary: End-stage heart failure has long been regarded as a terminal state of cardiac pathological remodeling that is almost impossible to be reversed by any available therapies.We discovered that short term estrogen (E2) treatment rescues preexisting severe heart failure (HF) induced by trans-aortic constriction (TAC) in mice by restoring ejection fraction (EF) from 30% to 55% and cardiac fibrosis (Iorga A, Li J, Sharma S, Umar S, Bopassa JC, Nadadur RD, et al. Rescue of Pressure Overload‐Induced Heart Failure by Estrogen Therapy. Journal of the American Heart Association [Internet]). Given the role of microRNAs in wide spectrum of physiological and pathological processes in HF and fibrosis, we explored whether E2 rescues HF and fibrosis by controlling the expression of specific microRNAs (miRs). RNA isolated from cardiac left ventricle of mice  in sham (n=4), HF (n=5) and E2-rescued (n=5) groups  was sent to Ocean Ridge Biosciences for miR microarray analysis. Comparison of E2-Rescued group versus HF and sham groups revealed a subset of 158 miRs significantly regulated by E2.

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Healthy mice with an ejection fraction of ˜60% were randomly subjected to sham or transaortic constriction (TAC) surgery as described previously. HF was achieved 6 to 8 weeks after the TAC surgery with an ejection fraction of ˜35%. Once TAC mice reached HF, mice were randomly euthanized (HF group, n=5), or were assigned to treatment of estradiol (E2, n=5) via a subcutaneous 10-day continuous-release pellet of 0.03 mg E2/kg per day (Innovative Research of America,). Sham-operated mice (n=4) served as control.


title: Causal linkage of presence of mutant NPM1 to efficacy of novel therapeutic agents against AML cells with mutant NPM1

first: Xiaoping

last: Su

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

overall_design: Refer to individual Series


title: HPV-positive murine oral squamous cell carcinoma: development and characterization of a new mouse tumor model for immunological studies

city: Ljubljana

first: Maja

last: Cemazar

address: Zaloska 2

department: Department of Experimental Oncology

country: Slovenia

institute: Institute of Oncology Ljubljana

overall_design: Comparative gene expression profiling analysis of RNA-seq data for parental MOC1 cell line and transduced cell lines MOC1-HPV K1 and MOC1-HPV K3 that express HPV-16 E6 and E7 oncogenes.

first: Ziva

last: Modic

first: Bostjan

last: Markelc

first: Andrej

last: Cör

first: Gregor

last: Sersa

first: Simona

last: Kranjc Brezar

first: Tanja

last: Jesenko


title: Histone H3 dopaminylation in nucleus accumbens, but not medial prefrontal cortex, contributes to cocaine-seeking following prolonged abstinence

city: New York

first: Sasha

middle: Leilani

last: Fulton

state: NY

address: 3227 Broadway

institute: Columbia University

summary: Enduring patterns of epigenomic and transcriptional plasticity within the mesolimbic dopamine system contribute importantly to persistent behavioral adaptations that characterize substance use disorders (SUD). While drug addiction has long been thought of as a disorder of dopamine (DA) neurotransmission, therapeutic interventions targeting receptor mediated DA-signaling have not yet resulted in efficacious treatments. Our laboratory recently identified a non-canonical, neurotransmission-independent signaling moiety for DA in brain, termed dopaminylation, whereby DA itself acts as a donor source for the establishment of post-translational modifications (PTM) on substrate proteins (e.g., histone H3 at glutamine 5; H3Q5dop). In our previous studies, we demonstrated that H3Q5dop plays a critical role in the regulation of neuronal transcription and, when perturbed within monoaminergic neurons of the ventral tegmental area (VTA), critically contribute to pathological states, including relapse vulnerability to both psychostimulants (e.g., cocaine) and opiates (e.g., heroin). Importantly, H3Q5dop is also observed throughout the mesolimbic DA reward pathway (e.g., in nucleus accumbens/NAc and medial prefrontal cortex/mPFC, which receive DA input from VTA). As such, we investigated whether H3Q5dop may similarly be altered in its expression in response to drugs of abuse in these non-dopamine-producing regions.  In rats undergoing extended abstinence from cocaine self-administration (SA), we observed both acute and prolonged accumulation of H3Q5dop in NAc, but not mPFC. Attenuation of H3Q5dop in NAc during drug abstinence reduced cocaine-seeking and affected cocaine-induced gene expression programs associated with altered dopamine signaling and neuronal function. These findings thus establish H3Q5dop in NAc, but not mPFC, as an important mediator of cocaine-induced behavioral and transcriptional plasticity during extended cocaine abstinence.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for virally transduced male rat nucleus accumbens (NAc) and medial prefontal cortex (mPFC) tissue. Following 10 days of extended-access cocaine self-administration animals were pseudorandomly assigned to two groups per brain region and underwent bilateral intra-NAc or intra-mPFC injection of either lenti-pCDH-H3.3WT or lenti-pCDH-H3.3Q5A. Following 30 days of viral expression and forced abstinence animals underwent cocaine-associated cue-seeking.

middle: L

first: Andrew

middle: F

last: Stewart

first: Ian

last: Maze


title: Cooperativity between H3-K27M and PDGFRA poses multiple therapeutic vulnerabilities in human iPSC-derived diffuse midline glioma avatars (CUT&RUN)

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

summary: PDGFRA and H3.3 mutations cooperate in an iPSC-based model of diffuse midline glioma to alter tumor biology.

overall_design: Cleavage Under Targets & Release Using Nuclease of iDMG tumor cells

first: Kasey

last: Skinner

first: Tomoyuki

last: Koga

first: Shunichiro

last: Miki

first: Robert

last: Gruener

first: Florina-Nicoleta

last: Grigore

first: Emma

last: Torii

first: Davis

last: Seelig

first: Yuta

last: Suzuki

first: Daisuke

last: Kawauchi

first: Benjamin

last: Lin

first: Sriram

last: Venneti

first: Denise

last: Malicki

first: Clark

last: Chen

first: Etty

last: Benveniste

first: Rakesh

last: Patel

first: Braden

last: McFarland

first: R

last: Huang

first: Chris

last: Jones

first: Alan

last: Mackay

first: C

first: Frank

last: Furnari


title: Dynamic Patterns of Mammalian Mitochondrial DNA  Replication Uncovered Using SSiNGLe-5′ES

city: Xiamen

first: Dongyang

last: Xu

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

summary: The proper replication of mitochondrial DNA is key to the maintenance of this crucial organelle. Multiple studies aimed at understanding the mechanisms of replication of the mitochondrial genome have been conducted in the past several decades; however, while highly informative, they were conducted using relatively low-sensitivity techniques. Here, we established a high-throughput approach based on next-generation sequencing to identify replication start sites with nucleotide-level resolution and applied it to the genome of mitochondria from different human and mouse cell types. We found complex and highly reproducible patterns of mitochondrial initiation sites, both previously annotated and newly discovered in this work, that showed differences among different cell types and species. These results suggest that the patterns of the replication initiation sites are dynamic and might reflect, in some yet unknown ways, the complexities of mitochondrial and cellular physiology. Overall, this work suggests that much remains unknown about the details of mitochondrial DNA replication in different biological states, and the method established here opens up a new avenue in the study of the replication of mitochondrial and potentially other genomes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Established a next-generation sequencing based approach for identification of mitochondrial replication start sites

first: Philipp

last: Kapranov


title: Epigenomic profiling of EHMT1/2 depletion in PARPi-resistant HGSOC

city: Aurora

first: Lily

last: Nguyen

state: CO

address: 1635 Aurora Ct

institute: UNIVERSITY OF COLORADO DENVER

summary: Euchromatin methyltransferase1/2 (EHMT1/2) have been correlated with tumorigenesis and therapy resistance through unknown mechanisms of action. Using a combination of experimental and bioinformatic analyses in several PARP inhibitor resistant ovarian cancer models, we demonstrate that combinatory EHMT and PARP inhibition is effective in treating PARP inhibitor resistant ovarian cancers. Our in vitro studies show that combinatory therapy reactivates transposable elements and increased immunostimulatory dsRNA formation and several immune signaling pathways. Our in vivo studies show that single EHMT and combinatory EHMT and PARP inhibition reduces tumor burden and that this reduction is dependent on CD8 T cells. Together, our results show a direct mechanism by which transposable elements are regulated and how an epigenetic therapy can be used as a fine tune agent to treat cancers with specific genetics.

overall_design: Epigenomic profiling (RNA-seq) of PEO1-R cells that were treated with DMSO, a PARP inhibitor (olaparib), an EHMT1/2 inhibitor (UNC0642 or EZM8266) or combinatory PARP/EHMT inhbitors.

first: Zachary

last: Watson

first: Edward

last: Chuong

last: Bitler


title: Effect of KI696 treatment on gene expression in CALU6 cells

city: Charlestown

first: Maolin

last: Ge

state: Massachusetts

address: 149 13th Street

department: MGH Cancer Center

institute: Harvard Medical School

summary: To investigate the role of NRF2 in gene expression regulation, we treated CALU6 cell line with KI696 to activate NRF2 expression.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of CALU6 cells treated with DMSO/KI696.

first: Liron

last: Bar-Peled


title: ERdj5 protects goblet cells from endoplasmic reticulum stress-mediated apoptosis under inflammatory conditions

city: Chuncheon

first: Hyun-Jeong

last: Ko

address: Kangwondaehak-gil 1

department: Department of Pharmacy

institute: Kangwon National University

summary: Endoplasmic reticulum stress is closely associated with the onset and progression of inflammatory bowel disease. ERdj5 is an endoplasmic reticulum-resident protein disulfide reductase that mediates the cleavage and degradation of misfolded proteins. Although ERdj5 expression is significantly higher in the colonic tissues of patients with inflammatory bowel disease than in healthy controls, its role in inflammatory bowel disease has not yet been reported. Hence, in the current study, we utilized ERdj5-knockout mice to investigate the potential roles of ERdj5 in inflammatory bowel disease. ERdj5 deficiency causes severe inflammation in mouse colitis models and weakens gut barrier function by increasing NF-κB-mediated inflammation. ERdj5 may not be indispensable for goblet cell function under steady-state conditions, while its deficiency induces goblet cell apoptosis under inflammatory stimuli.

overall_design: 8-week-old female ERdj5 KO mice and their corresponding WT mice were administered 2% DSS in drinking water for 5 days. Mice were sacrificed, RNA from colon tissues were isolated for RNA-seq analysis. Each groups contain 2-3 replicates.

first: Hyunjin

last: Jeong

first: Eun-Hye

last: Hong

first: Sun-Young

last: Chang


title: Associations of miRNAs with blood phenotypes and ICU admission in COVID-19 patients [miRNA-seq]

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary: Individuals infected with SARS-CoV-2 vary greatly in their symptomatology and disease progression, likely as a result of numerous genetic, biological and environmental factors and their complex interactions. Meanwhile, the potential roles of microRNAs (miRNAs) in SARS-CoV-2 infection have not been fully described. MiRNAs have emerged as key post-transcriptional regulators of gene expression, and their dysregulation can be indicative of aberrant immune function. In this study, we characterize the potential roles of mIRNAs in early COVID-19 disease progression.  We studied a diverse cohort of 259 patients admitted to hospitals in Abu Dhabi, United Arab Emirates to understand the clinical and biological factors associated with ICU admission during COVID-19 treatment, integrating electronic health records (EHR), global miRNA and RNA expression, and genotyping data. Using EHR, we identified 26 factors correlated with ICU admission, including 8 blood phenotypes such as neutrophil-to-lymphocyte ratio,  Interleukin-6, and C-reactive protein levels. Using genome-wide miRNA expression data for a subset of 96 individuals from Southeast Asia and the Middle East and North Africa, we identified 27 miRNAs significantly associated with ICU admission (p < 0.01), and 97 miRNAs associated with at least one of the 8 blood phenotypes. [cross-cor] Integrating expression data for 632 miRNAs and genotyping data for ~260,000 SNPs, we identified 168 significant cis-expression quantitative trait loci (cis-eQTLs), of which 59 were associated with either ICU admission or one of the 8 blood phentoypes. Overall, our findings characterize the miRNA architecture of blood phenotypes during the early stages of COVID-19 infection, identify miRNAs associated with ICU admission and therefore COVID-19 disease severity, and suggest a potential genetic control of miRNA expression during early COVID-19 disease progression.

overall_design: Blood samples from patients with SARS-CoV2 infection were collected into tempus tubes at time of diagnosis (i.e. 1st timepoint). Total RNA was extracted from whole blood samples of the 96 patients where miRNA-seq was performed, and mRNA sequencing was performed on the same samples.

first: T

last: Gjorgjieva

first: A

last: Chaloemtoem

first: M

last: AlShaikh

last: Shahin

first: O

last: Bayara

middle: A

last: AlBaqi

first: J

middle: D

last: Monte

first: G

last: Begum

last: Dieng

last: Leonor

first: N

last: Drou

last: Arshad

first: Y


title: Associations of miRNAs with blood phenotypes and ICU admission in COVID-19 patients [mRNA-seq]

first: C


title: Liver metastases originating from 4 colorectal cancer patients (CRC-LM).

city: Montpellier

first: Andrei

last: Turtoi

address: 208 avenue des Apothicaires

institute: Inserm U1194

summary: Using liver metastases  from 4 colorectal cancer patients (CRC-LM), we explored one receptor: EGFR whose signaling triggers cell proliferation and is exacerbated in many tumors.

overall_design:
We performed Spatial Transcriptomics using 10X Genomics Visium in these four different cancer patients and focused on ligand receptor interactions.  For some patients, we were also able to perform validations by immunofluorescence.
All patients were treated with neo-adjuvant chemotherapy prior to surgery and sample collection.


title: RNA-seq of IL-13 activated human schwann cell compared with control human schwann cell

city: Henan

first: Wenhao

last: Zhang

address: 开封

institute: Henan University

summary: IL-13 activated human schwann cell and upregulated the transcription levels of cytokines,such as IL-6,IL-8,IL-24,CCL2 ,CCL7,etc.

overall_design: Examination of IL-13 activation in human primary schwann cell on the regulation of gene expression.  RNA sequencing of 6 human schwann cell samples was performed. They are 3 samples of IL-13-treated cells, and 3 samples from un-treated control cells

first: Jianghui

last: Meng


title: Associations of miRNAs with blood phenotypes and ICU admission in COVID-19 patients


title: Comparison of miRNA profiles between young (6 months) and old (24 months) male mouse vertebral samples

first: David

last: Monroe

summary: To understand the effect of age on miRNA profiles in male mouse vertebrae, we isolated L4-5 vertebral samples and digested with endotoxin-free collagenase (Liberase) twice for 30 minutes. The resulting bone was confirmed to be largely osteocyte-enriched and RNA was isolated using QIAzol reagent.

overall_design: We then performed miRNA gene profiling between the young (6 month) and old (24 month) vertebral samples.

first: Sundeep

last: Khosla


title: Delay Modulates the Immune Response to Nerve Repair

city: Ithaca

first: Jennifer

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: Effective regeneration after peripheral nerve injury requires macrophage recruitment.  We investigated activation of remodeling pathways within the macrophage population when repair is delayed and identified alteration of key upstream regulators of the inflammatory response. We then targeted one of these regulators, using exogenous IL10 to manipulate the response to injury at the repair site.  We demonstrate that this approach alters macrophage polarization, promotes macrophage recruitment, axon extension, neuromuscular junction formation and increases the number of regenerating motor units reaching their target. We also demonstrate that this approach can rescue the effects of delayed nerve graft.

overall_design: Comparison of Delayed vs Immediate repair in sciatic nerve branches of mice 5 and 14 days after injury.  Evaluated at 5 or 14 days after delayed or immediate graft repair

first: Jonathan

last: Cheetham

first: Masoud

last: Golshadi

first: Elaine

last: Claffey


title: MUC1-C INDUCES PBRM1-MEDIATED CHROMATIN REMODELING IN DRIVING CHRONIC INFLAMMATION AND DNA DAMAGE RESISTANCE IN TRIPLE-NEGATIVE BREAST CANCER [tet-MUC1 shRNA]

city: Buffalo

first: Qiang

last: Hu

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: STAT1 and IRF1 are essential effectors of the type I and II interferon (IFN) pathways. Here, we report that the oncogenic MUC1-C protein is necessary for inducing chromatin accessibility and activation of the STAT1 and IRF1 genes in triple-negative breast cancer (TNBC) cells. Our results demonstrate that MUC1-C activates the PBRM1 subunit of the SWI/SNF PBAF chromatin remodeling complex and forms a nuclear complex with PBRM1. We show that MUC1-C associates with PBRM1 and STAT1 on the IRF1 gene at (i) a proximal enhancer-like signature (PLS), and (ii) distal enhancer-like signatures (dELSs). We also show MUC1-C and PBRM1 are necessary for opening chromatin at these signatures and for the induction of IRF1 expression. In extending these results, we found that MUC1-C binds directly to IRF1 and forms nuclear complexes with PBRM1 and IRF1, which are necessary for inducing chromatin accessibility at PLS of the (i) STAT1 gene, (ii) type II IFN pathway IDO1 and WARS genes, and (iii) type I IFN pathway RIG-I, MDA5 and ISG15 genes. Consistent with involvement of chronic inflammation in promoting the cancer stem cell (CSC) state, we show that MUC1-C, PBRM1 and IRF1 are required for self-renewal of TNBC CSCs. Of translational relevance, we report that targeting MUC1-C, PBRM1 and IRF1 circumvents intrinsic DNA damage resistance of TNBC CSCs and that MUC1-C is necessary for acquired resistance to the PARP inhibitor olaparib. These findings demonstrate that MUC1-C activates PBRM1/IRF1 and thereby chromatin remodeling of IFN pathway genes that promote chronic inflammation, the CSC state and DNA damage resistance.

overall_design: MDA-MB-436 cells stably expressing a tet-MUC1 shRNA vector were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline. Total RNA from cells cultured in triplicates was isolated and used for library preparation.

first: Nami

last: Yamashita

first: Donald

last: Kufe

first: Mark

last: Long


title: MUC1-C INDUCES PBRM1-MEDIATED CHROMATIN REMODELING IN DRIVING CHRONIC INFLAMMATION AND DNA DAMAGE RESISTANCE IN TRIPLE-NEGATIVE BREAST CANCER [BT549_shPBRM1]

overall_design: BT-549 cells stably expressing a tet-PBRM1 shRNA vector were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline. Total RNA from cells cultured in triplicates was isolated and used for library preparation.


title: Stress-triggered hematopoietic stem cell proliferation relies on Primpol-mediated repriming

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Stem cell division is linked to tumorigenesis by yet-elusive mechanisms. The hematopoietic system reacts to stress by triggering stem and progenitor cell (HSPC) proliferation, which can be accompanied by chromosomal breakage in activated haematopoietic stem cells (HSCs). However, whether these lesions persist in their downstream progeny and induce a canonical DNA damage response (DDR) remained unclear. Inducing HSPC proliferation by simulated viral infection, we report that the associated DNA damage is restricted to HSCs and that proliferating HSCs rewire their DDR upon endogenous and clastogen-induced damage. Combining transcriptomics, single-cell and single-molecule assays on murine bone marrow cells, we found accelerated fork progression in stimulated HSPCs, reflecting engagement of Primpol-dependent repriming, at the expense of replication fork reversal. Ultimately, competitive bone marrow transplantation revealed the requirement of Primpol for efficient HSC amplification and bone marrow reconstitution. Hence, fine-tuning replication fork plasticity is essential to support stem cell functionality upon proliferation stimuli.

overall_design: Examination of 4 cell types LT-HSCs, ST-HSCs, MPPs and LIN cells with or without stimulation by pIpC, for a total of 8 samples per replicate. 3 replicates in total

first: Kurt

last: Jacobs

first: Cyril

last: Doerdelmann


title: MUC1-C INDUCES PBRM1-MEDIATED CHROMATIN REMODELING IN DRIVING CHRONIC INFLAMMATION AND DNA DAMAGE RESISTANCE IN TRIPLE-NEGATIVE BREAST CANCER [BT549_shIRF1]

overall_design: BT-549 cells stably expressing a tet-IRF1 shRNA vector were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline. Total RNA from cells cultured in triplicates was isolated and used for library preparation.


title: MUC1-C INDUCES PBRM1-MEDIATED CHROMATIN REMODELING IN DRIVING CHRONIC INFLAMMATION AND DNA DAMAGE RESISTANCE IN TRIPLE-NEGATIVE BREAST CANCER

overall_design: Refer to individual Series


title: Leptin-responsive dorsomedial hypothalamic neurons link circadian and metabolic systems to govern food anticipation [snRNA-seq]

city: Charlottesville

first: Lizzie

last: Godschall

state: Virginia

address: 1821 Jefferson park Ave, 12

institute: UVA

summary: In contrast to light-dependent entrainment of the central circadian pacemaker, the molecular and neural underpinnings of entrainment by non-photic cues, such as food, remain unclear. Using single-nucleus RNA-sequencing, we identified a leptin receptor (LepR) positive neuronal population in the dorsomedial hypothalamus (DMH) that is responsive to scheduled feeding (SF). During SF, DMH LepR neuron activity precedes an impending meal. Mis-timed exogenous leptin administration or chemogenetic activation of DMH LepR neurons inhibits both neuronal and behavioral food anticipatory activities. Further, repetitive chemogenetic activation of DMH LepR neurons partitions a secondary bout of circadian locomotor activity in phase with the stimulation. This work places DMH LepR neurons as an essential integrator of food entrainment, and positions leptin as a critical central mediator of this circadian response.

overall_design: We performed single nuclei RNA-seq of the dorsomedial hypothalamus and suprachiasmatic nucleus of Lepr-cre::tdTomato mice under either ad libitum, overnight fasted, of scheduled feeding diets.

first: Tang

last: Qijun

first: Godschall

last: Elizabeth

first: Brennan

last: Charles

first: Abraham-Fan

last: Ruei-Jen

first: Zhang

last: Qi

first: Williams

middle: P

last: Sydney

first: Onoharigho

last: Roberta

first: Salinas

last: Ricardo

first: Olivieri

last: Joey

first: Deppmann

last: Christopher

first: Campbell

last: John

first: Podyma

last: Brandon

first: Güler

last: Ali


title: Effec of lactic acid or HCl on the Lactiplantibacillus plantarum gene expression

city: GwangJu

first: JongHee

last: Lee

address: kimchi ro86

institute: World Institute of Kimchi

summary: To characterize the effect of lactic acid on the L. plantarum growth and adaptation, we investigated the transcriptome under hydrochloride (HCl) or lactic acid at the early stage of the growth.

overall_design: the bacteria was cultivated to OD=0.05 and further cultivated  3h in MRS pH 5.5 adjusted with lactic acid or HCl, respectively

first: Jong-Hee


title: microRNA-33 Deficiency in Macrophages Enhances Autophagy, Improves Mitochondrial Homeostasis, and Protects Against Lung Fibrosis

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

department: PCCSM

institute: Yale School of Medicine

summary: To investigate the effects of miR-33 inhibition on gene expression profile of IPF lung in an ex vivo model

overall_design: IPF Precision cut lung slices treated with miR-33 inhibitor or scramble control

first: Farida

last: Ahangari

first: Taylor

last: Adams

first: Ivan

last: Rosas


title: DNA hypomethylation restrains early antitumor immunity in prostate cancer [Nanopore]

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution single cell DNA methylation sequencing in prostate cancer, we identify 40 core hypomethylation domains, consistently hypomethylated across tumor cells and arising at early stages of malignancy. Transcriptionally silenced genes within these domains are enriched for immune-related genes; nested among repressive domains are small loci with preserved methylation, encoding cell proliferation genes that escape silencing. Prominent among hypomethylation-silenced genes is a gene cluster harboring all five CD1 genes that present lipid antigens to NKT cells, and four IFI16-related interferon-inducible genes implicated in innate immunity. Re-expression of CD1 or IFI16 murine orthologs in immunocompetent mice abrogates prostate tumorigenesis, accompanied by activation of anti-tumor immunity. Thus, early epigenetic changes in cancer may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for circulating tumor cells.

overall_design: CTCs are shed into the blood by invasive localized prostate cancers long before they establish metastases, raising the possibility that they may provide an orthogonal assay for early cancer detection. Given the specificity of DNA hypomethylation domains in prostate cancer cells and their large genomic size, we reasoned that they may provide high sensitivity and quantitative signal for cancer detection, following CTC enrichment in blood specimens. Oxford Nanopore long-read native sequencing typically produces sequencing reads up to 100 kb, and directly identifies methylated CpG residues, without requiring bisulfite conversion in library preparation. In contrast to the short Illumina sequencing reads (usually harboring <5 CpG sites per read), mathematical modeling indicates that the long reads generated by Nanopore sequencing would empower detection with significantly higher precision for rare signal. We therefore processed 10 ml blood specimens from patients with either localized or metastatic prostate cancer, using microfluidic enrichment to deplete leukocytes (10^4-fold depletion), but without further CTC purification or individual CTC micromanipulation.

first: Hongshan

last: Guo

first: David

middle: T

last: Miyamoto

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: DNA hypomethylation restrains early antitumor immunity in prostate cancer [ChIP-seq and CUT&RUN]

overall_design: To assess the repressive histine mark enrichment in prostate cancer, we performed H3K27me3 and H3K9me3 Cut and Run assay in mutiple prostate cancer cell lines and normal prostate epithelial cell lines. In addtion, we applied ultra-low-input native ChIP-seq procedure to the purified nuclei from microdissected normal prostate and from GS6 or GS8 prostate tumor specimens.


title: Effect of MKRN3 deletion on gene expression in hypothalamic neurons derived from human induced pluripotent stem cells (hiPSCs)

first: Ursula

last: Kaiser

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital/Harvard Medical School

summary: Makorin ring finger protein 3 (MKRN3) was identified as an inhibitor of puberty initiation with the report of loss-of-function mutations in association with central precocious puberty. To investigate the roles and mechanisms of action of MKRN3 within the human hypothalamus, we used hypothalamic neurons derived from human induced pluripotent stem cells (hiPSCs). MKRN3 deletion was introduced into hiPSCs using CRISPR interference (CRISPRi) technology. Three separated hypothalamic differentiation of MKRN3-wildtype hiPSCs (MKRN3-WT I, II and III) and MKRN3-deficient hiPSCs (MKRN3-KO I, II and III) were performed using an established hypothalamic neuron differentiation protocol. To identify hypothalamic targets of MKRN3, we performed comparative transcriptome analysis by RNA sequencing (RNA-seq) of MKRN3-WT and MKRN3-KO hypothalamic neurons after 30 days of differentiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MKRN3-WT and MKRN3-KO hypothalamic neurons derived from hiPSCs. Three replicates issued from three different hypothalamic differentiations of MKRN3-wildtype hiPSCs (MKRN3-WT I, II and III) and MKRN3-deficient hiPSCs (MKRN3-KO I, II and III) were analyzed.

first: Lydie

last: Naulé

first: Alessandra

last: Mancini

first: Sidney

last: Pereira

first: Brandon

last: Gassaway

first: Han

last: Kim

first: Joy

last: Liang

first: Cynara

last: Matos

first: Wade

last: Harper

first: Steven

last: Gygi

first: Florian

last: Merkle

first: Rona

last: Carroll

first: Ana

last: Abreu

middle: B


title: DNA hypomethylation restrains early antitumor immunity in prostate cancer [RNAseq]

first: Ben

last: Wittner

overall_design: To characterize genomewide DNA methylation features of single metastatic prostate cancer cells, we processed blood specimens from five patients using microfluidic-based enrichment of CTCs, followed by individual cell micromanipulation of 44 CTCs for sequencing analysis. For comparison, 40 single cells were analyzed from four prostate cancer cell lines (LNCaP, VCaP, PC3 and 22Rv1) and from two non-transformed prostate cell lines (HPrEC and BPH-1), together with 13 microfluidic-processed single leukocytes from four age-matched healthy men. To confirm the identity of single CTCs isolated from blood specimens, we adapted single-cell multiomics sequencing to enable separation of nucleus from cytoplasm in individual cells, subjecting the former to single-cell whole genome bisulfite sequencing (scBS-seq) and the latter to single-cell RNA-seq (SMART-seq2). On average, we detected 9 million CpG sites for each single-cell DNA methylation sequencing sample, and 5,790 genes (RPM>0) for each single-cell RNA-seq library.

first: Hongshan

last: Guo


title: Insplico: Effective computational tool for studying intron splicing order genome-wide with short and long RNA-seq reads

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: Investigation of the intron splicing order in different tissues , cell lines and conditions

overall_design: RNA seq from mouse tissues (Cerebellum, Cortex and Liver, Chromatin total RNA, Cytoplasmic polyA RNA) and human cell lines expressing GFP or SRRM4 (total RNA)

first: Andre

last: Gohr

first: Antonio

last: Torres-Mendez

first: Juan

last: Valcarcel

first: Sophie

last: Bonnal


title: Loss of cardiomyocyte CYB5R3 impairs redox equilibrium and causes sudden cardiac death

city: Pittsburgh

first: Adam

last: Straub

state: Pennsylvania

address: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: Sudden cardiac death (SCD) in patients with heart failure (HF) is allied with an imbalance in reduction-oxidation (redox) signaling in cardiomyocytes; however, the basic pathways and mechanisms governing redox homeostasis in cardiomyocytes are not fully understood. Here, we show that cytochrome b5 reductase 3 (CYB5R3), an enzyme known to regulate redox signaling in erythrocytes and vascular cells, is essential for cardiomyocyte function. Using a conditional cardiomyocyte-specific CYB5R3 knockout mouse, we discovered that deletion of CYB5R3 in male adult cardiomyocytes, but not female, causes cardiac hypertrophy, bradycardia, and SCD. The increase in SCD in CYB5R3 KO mice is associated with calcium mishandling, ventricular fibrillation, and cardiomyocyte hypertrophy. Molecular studies reveal that CYB5R3 KO hearts display decreased ATP, increased oxidative stress, suppressed coenzyme Q levels, and hemoprotein dysregulation. Lastly, from a translational perspective, we reveal that the high-frequency missense genetic variant rs1800457, which translates into a CYB5R3 T117S partial loss-of-function protein, associates with decreased event-free survival (~20%) in African Americans with HF with reduced ejection fraction (HFrEF). Together, these studies reveal a crucial role for CYB5R3 in cardiomyocyte redox biology and identify a new genetic biomarker for individuals in the African American population that may potentially increase the risk of death from HFrEF.

overall_design: Conditional cardiac muscle-specific CYB5R3 knockout mice (CYB5R3fl/fl, Myh6-CreERT2) and wild-type mice (CYB5R3wt/wt, Myh6-CreERT2) received tamoxifen injections between the age of 10-13 weeks. The whole heart of 6 knockout and wild-type mice (n=6) was collected for RNA sequencing analysis.

first: Nolan

last: Carew

first: Heidi

last: Schmidt

first: Shuai

last: Yuan

first: Joseph

last: Galley

first: Robert

last: Hall

first: Helene

last: Altmann

first: Scott

last: Hahn

first: Megan

last: Miller

first: Katherine

last: Wood

first: Beth

last: Gabis-Weber

first: Margaret

last: Stapleton

first: Sean

last: Hartwick

first: Marco

last: Fazzari

first: Yijen

last: Wu

first: Mohamed

last: Trebak

first: Brett

last: Kaufman

first: Charles

last: McTiernan

first: Francisco

last: Schopfer

first: Placido

last: Navas

first: Patrick

middle: H

last: Thibodeau

first: Dennis

last: McNamara

first: Guy

last: Salama


title: DNA hypomethylation restrains early antitumor immunity in prostate cancer [DNA methylation]

first: Ben

last: Wittner

first: Hongshan

last: Guo

first: David

last: Miyamoto

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: Global Epigenome and Transcriptome Maps of Human Trophoblast Cell Lineage Development [RNA-seq I]

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

summary: The extravillous trophoblast (EVT) cell lineage is a key feature of placentation and critical for spiral artery remodeling and successful pregnancy. Our knowledge of transcriptional regulation driving EVT cell development is limited. Here, we mapped the transcriptome and epigenome landscape as well as chromatin interactions of human trophoblast stem (TS) cells and their transition into the differentiated EVT cell lineage. We identified that chromatin accessibility in intergenic regions was more extensive in EVT cells than in TS cells in the stem state, which is indicative of increased enhancer-driven gene regulation. Using reference epigenome annotation, we noted that 18% of the chromatin landscape in EVT cells was uncharted.  We linked regulatory regions to their cognate target genes and characterized the three-dimensional organization of the TS cell functional genome by Hi-C. Integrational analysis of chromatin accessibility, long-range chromatin interactions, transcriptomic, and transcription factor binding motif enrichment enabled identification of transcription factors and regulatory mechanisms associated with EVT cell lineage development. Subsequent analyses elucidated functional roles for TFAP2C, EPAS1, SNAI1, and DLX6 in the regulation of EVT cell lineage development. EPAS1 was identified as an upstream regulator of EVT cell transcription factors, including SNAI1 and DLX6, and was found to be upregulated in idiopathic recurrent pregnancy loss. Collectively, we have revealed activation of a dynamic regulatory network that provides a framework for understanding EVT cell specification in trophoblast cell lineage development and human placentation.

overall_design: RNA-seq

first: Kaela

last: Varberg

first: Esteban

last: Dominguez

first: Ayelen

last: Moreno-Irusta

first: Ross

last: McNally

first: Emily

last: Wesley

first: Khursheed

last: Iqbal

first: Warren

last: Cheung

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Courtney

last: Marsh

first: Michael

last: Soares

first: Elin

last: Grundberg


title: Persistent Activation and Refractoriness of the Hepatic Interferon System in HBV-HDV Infection Determines Viral Dynamics and Therapeutic Response

city: Los Angeles

first: Meng

last: Li

state: CA

address: 2003 Zonal Avenue

institute: University of Southern California

overall_design: HBV and HDV infection of Terminally Differentiated Human Hepatocytes. In brief, Humanized Liver Chimeric Mice (HLCM)-derived human hepatocytes (HLCM-HH) were challenged with HBV or HDV as monoinfection or HBV-HDV coinfection, followed by the extraction of total cellular RNA for the subsequent poly-A based mRNA sequencing analysis.

first: Takeshi

last: Saito


title: Genome-wide DNA methylation analysis of normal and adult primary refractory immune thrombocytopenia samples

city: Xi 'an

first: Mengchang

last: Wang

state: Shaanxi Province

address: No.277, Yanta West Road, Yanta District

institute: The First Affiliated Hospital of Xi 'an Jiaotong University

summary:
Purpose:we'd like to provide the first DNA methylation profiling for ITP.
Methods:Peripheral blood CD4+ T lymphocytes samples were collected from 4 primary refractory ITP cases and 4 age-matched healthy controls, and DNA methylome profiling was performed using Illumina Human Methylation850K.
Results:The DNA methylome profiling identified a total of 260 differentially methylated CpG sites mapping to 72 hypermethylated and 64 hypomethylated genes.
Conclusions:we performed genome-wide DNA methylation profiling of primary refractory ITP and healthy controls, and identified a set of differentially methylated genes and pathways.

overall_design: CD4+ T lymphocytes from 4 patients with primary refractory ITP and 4 healthy individuals were randomly collected to genomic DNA

first: Hanzhi

last: Du

first: Qinghua

last: Tang

first: Jian

last: Yang

first: Bin

last: Yan

first: Lihong


title: Global Epigenome and Transcriptome Maps of Human Trophoblast Cell Lineage Development [ATAC-seq]

first: Boryana

last: Koseva

overall_design: ATAC-seq

first: Kaela

last: Varberg

first: Esteban

last: Dominguez

first: Ayelen

last: Moreno-Irusta

first: Ross


title: Clearance of a senescent macrophage-enriched niche ameliorates tumorigenesis in KRAS-driven murine lung cancer models

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: Understanding the important role of the tumour microenvironment on tumour initiation and progression is vital for a comprehensive understanding of cancer biology to design effective treatment strategies. Cellular senescence, while traditionally thought of as a cell autonomous tumour-suppressive response to potentially oncogenic insults, is now appreciated to have paracrine tumour promoting roles. We demonstrate a pro-tumourigenic effect of senescent microenvironmental cells on mouse lung tumour progression. To better understand the characteristics of these pro-tumourigenic senescent cells in the tumour microenvironment, we compare putatively senescent cells (reported by mCherry-expression) and non-senescent cells (mCherry-negative cells) from the lung microenvironment of mice induced to form lung tumours by oncogenic KrasG12D-expression in the lung epithelium. Putatively senescent cells are isolated by FACS, based on mCherry-expression which is expressed under the control of the Cdkn2a (p16) locus using a novel genetically engineered allele (p16FDR/+), along with their non-senescent counterparts for comparison by single cell RNA-sequencing.

overall_design: Comparison of senescent cells derived from the mouse lung tumour microenviroment with their non-senescent counterparts to understand their unique molecular characteristics and activated paracrine signaling pathways which promote tumourigenesis non-cell autonomously.

first: Scott

last: Haston

first: Juan

last: Martinez-Barbera

first: Daniel

last: Munoz-Espin

first: Alexander

last: Calderwood


title: Spatial transcriptomics combined with single-cell RNA-sequencing unravels the complex inflammatory cell network in atopic dermatitis [ST]

city: Davos Wolfgang

first: Yasutaka

last: Mitamura

state: Graubünden

address: Herman-Bruchard-Strasse 9

department: Immunology

institute: Swiss Institute of Allergy and Asthma Research

summary: Atopic dermatitis (AD) is the most common chronic inflammatory skin disease with complex pathogenesis. Using spatial and single-cell transcriptomics of whole skin biopsy and suction blister material, we investigated the cellular and molecular features of the leukocyte-infiltrated area in AD. We identified unique clusters of fibroblasts, dendritic cells, macrophages, and T cells in the lesional AD skin and molecular interactions between these cells. The leukocyte-infiltrated areas in lesional AD skin showed upregulation of COL6A5, COL4A1, TNC, IL32, CCL19 in COL18A1-expressing fibroblasts. Additionally, M2 macrophages expressed CCL13 and CCL18 in the same localization. Ligand–receptor interaction analysis of the spatial transcriptome identified a neighboring infiltration and interaction between activated COL18A1-expressing fibroblasts, activated CCL13- and CCL18-expressing M2 macrophages, CCR7- and LAMP3-expressing DCs, and T cells. As observed in skin lesions, serum levels of TNC and CCL18 were significantly elevated in AD and correlated with clinical disease severity.

overall_design: Spatial Transcriptomics (Visium Spatial Gene Expression; 10X Genomics) of human skin biopsy samples. 14 skin biopsy samples were collected from 7 atopic dermatitis patients, 1 from lesional and 1 from non-lesional skin per patient. In addition, 6 skin biopsy samples were collected from 6 healthy donors to serve as a control.

first: Matthias

last: Reiger

first: Juno

last: Kim

first: Yi

last: Xiao

first: Damir

last: Zhakparov

first: Ge

last: Tan

first: Arturo

middle: O

last: Rinaldi

first: Katja

last: Baerenfaller

first: Mübeccel

last: Akdis

first: Marie-Charlotte

last: Brüggen

first: Patrick

last: Brunner

first: Damian

last: Roqueiro

first: Claudia

last: Traidl-Hoffmann

first: Cezmi


city: beijing

first: di

last: zhao

address: 52 Fucheng Road, Haidian District, Beijing

institute: beijng cancer hospital

type: Genome binding/occupancy profiling by array

summary:
Stat3-binding promoters in human ESCC and CAFs
Investigation of the critical gene promoters binding by pStat3 between ESCC cells and cancer-associated fibroblasts (CAFs).

overall_design: We designed this experiment to screen for pSTAT3 directly binding promoters in human ESCC and cancer-associated fibroblasts (CAFs).

first: Di

last: Zhao

first: Qimin

last: Zhan


title: DNA hypomethylation restrains early antitumor immunity in prostate cancer

first: Ben

last: Wittner

address: 149 13th Street

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

overall_design: Refer to individual Series


title: Implications for Wnt Signaling in XLH Odontogenic Differentiation

city: Chicago

first: Elizabeth

last: Guirado

state: IL

address: 801 S. Paulina St. Room 421

department: Oral Biology

institute: University of Illinois Chicago

summary: X-linked hypophosphatemia (XLH) represents the most common form of familial hypophosphatemia. Although significant advances have been made in the treatment of the bone pathology, patients undergoing therapy continue to experience significantly decreased oral health-related quality of life. The following study addresses this persistent oral disease by further investigating the effect of DMP1 expression on the differentiation of XLH dental pulp cells. Dental pulp cells were isolated from the third molars of XLH and healthy controls and stable transduction of full-length human DMP1 was achieved. RNA sequencing was performed to evaluate the genetic changes following the induction of odontogenic differentiation using either an organic (beta-glycerophosphaet) or inorganic (sodium phosphate) phosphate source.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dental pulp cells from healthy and XLH patients, with or without constitutive expression of full-length human DMP1, undergoing odontogenic differentiation with either organic (beta-glycerophosphaet) or inorganic (sodium phosphate) phosphate sources.

first: Cassandra

last: Villani

first: Adrienn

last: Pethö

first: Yinghua

last: Chen

first: Mark

last: Maienschein-Cline

first: Zhengdeng

last: Lei

first: Nina

last: Los

first: Anne

last: George


title: Tex10 in spermatogenesis

city: New York

first: Jianlong

last: Wang

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Conditional Tex10 knockout compromises the spermatogenesis

overall_design: Examination of Tex10 in spermatogenesis in vivo by single cell RNA sequencing. Cells from testis of Tex10 conditional knockout mice and wildtype mice are used for single cell RNA sequencing.

first: Jihong

last: Yang


title: Tex10 in PGCLC specification and spermatogenesis


title: Tex10 in primordial gem cell-like cell (PGCLC) specification and spermatogenesis

summary: Tex10 depletion compromises the PGCLC specification and spermatogenesis

overall_design: Examination of Tex10 in PGC specification in vitro and spermatogenesis in vivo by RNA sequencing. Three batches of RNA samples are prepared: 1) RNA samples using Tex10 depletion treated by dTAG13 (500 nM) and control cells treated by DMSO during the in vitro PGC specification derived from epiblast-like cells (EpiLCs); 2) RNA samples using Tex10 overexpression and empty-vector control cells during the in vitro PGC specification derived from EpiLCs; 3) RNA samples from testis of Tex10 conditional knockout mice and wildtype mice.


title: Genome-wide maps of Tex10 and chromatin state in Day 2 primordial germ cell-like cells (PGCLCs)

summary: We report the Tex10 binding and genome-wide map of  H3K4me3 modification in Day 2 PGCLCs by chromatin immunoprecipitation sequencing.

overall_design: Examination of Tex10 binding and H3K4me3 modifications in Day 2 PGCLCs. In the cells, Tex10 is fused C-terminally to HA tag, so anti-HA tag antibody is used for identifying the Tex10 binding sites in Day 2 PGCLCs.


title: Expression data of 8 healthy people and 8 patients with coronary heart disease before and after 8 weeks treatment with Danlou tablets

city: Tianjin

first: Zhu

last: Li

state: Tianjin

address: No.10 PoYangHu Road, JingHai, District

institute: Tianjin university of TCM

summary:
The Danlou Tablets (DLT), a patented medicine, has been widely used to treat coronary heart disease (CHD) in China for several decades. Though the anti-inflammatory and anti-oxidation effect has been preliminarily proposed as one of the potential mechanisms of DLT for CHD treatment, the underlying mechanisms remain elusive.
We use microarray to explain the genome changes of patients with coronary heart disease and patients with coronary heart disease after treatment with Danlou tablets, so as to explore the potential mechanism of treating diseases with traditional Chinese medicine.

overall_design: Microarray gene expression analysis was used to identify the differentially expressed genes (DEGs) in peripheral blood mononuclear cells of healthy people and patients before and after DLT treatment.

first: C

middle: Q

last: Yu

first: Y

last: Bian

first: S

last: Gao

first: L

first: Z

first: Q

last: Cheng


title: Immune response to pathogens in diabetes

city: Bethesda

first: WeiPing

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: To investigate the differential gene expression by NGS technology in normal and diabetic corneas during Pseudomonas Aeruginosa (PA) infection, corneas from normal and diabetic mouse were gently scratched with 26‐gauge needles, followed by topical inoculation of PA. At 6 h, 1 and 3 days, the corneas were collected and processed for RNA sequencing. Bioinformatic analyses revealed an orderly activation of biological processes starting from pathogen pattern recognition, cytokine/chemokine expression, to innate immune cell infiltration (chemotaxis), and to the activation of TH2 and TH17 immunity in NL corneas. Diabetes disturbs these orderly innate and adaptive immune responses, leading to increased susceptibility and exacerbated progression of microbial keratitis. Completion of the proposed study should reveal novel insights into the molecular and cellular aspects of the proneness of diabetic patients to infection and may enable the development of new therapeutic modalities for enhancing mucosal innate immunity in diabetic patients, and for treating infectious keratitis in general.

overall_design: Examination of differential gene expression in normal and diabetic mouse corneas.

first: Fushing


title: RNA-Seq and H3K27ac ChIP-Seq in the mouse seminal vesicles (SVs) and uterus (U) following neonatal DES exposure

city: RTP

first: Yin

state: NC

address: 111 TW alexander Drive

institute: NIEHS


title: Histone H3K27ac modification profiling by ChIP-Seq in the mouse seminal vesicles (SVs) and uterus (U) following neonatal DES exposure

summary: DES is a synthetic estrogen that is associated with adverse effects on reproductive organs. Our group has employed estrogen receptor (ER) α knockout (αERKO) mice to gain insight into the contribution of ER α in DES-induced toxicity following neonatal exposure

overall_design: Mice were neonatally exposed to DES. SVs were collected at weeks 5 and 10, and utures were collected at week 10. Histone H2K27ac profiling was performed using ChIP-Seq

first: Tianyuan


title: Genome-wide transcriptome in the mouse seminal vesicles (SVs) and uterus (U) following neonatal DES exposure

summary: DES is a synthetic estrogen that is associated with adverse effects on reproductive organs. Our group has employed estrogen receptor (ER) α knockout (αERKO) mice to gain insight into the contribution of ER a in DES-induced toxicity following neonatal exposure.

overall_design: Mice were neonatally exposed to DES. The SVs  were collected at week 5. Genome-wide transcriptome was performed by RNA-Seq.


title: Autoimmunity and infection give rise to distict inflammatory Th17 subsets [bulk RNA-seq]

status: Public on Jun 13 2023

city: Winston-Salem

first: Qianqian

last: Song

address: 1 Medical Center Boulevard

department: Cancer Genomics and Precision Oncology

institute: Wake Forest Baptist Comprehensive Cancer Center

summary: Th17 cells are a heterogeneous population that is critical for tissue homeostasis and inflammation during clearance of infections and autoimmunity. Despite substantial efforts distinguishing homeostatic and inflammatory roles of Th17 cells, the mechanism underlying the divergent functions of inflammatory Th17 cells is poorly understood. In this study, we show that the inflammatory Th17 engaged in autoimmune colitis and those involved in infection-induced colitis are two distinguishable populations illustrated by their distinct responses to a pharmacological molecule, clofazimine (CLF). Distinct from existing Th17 inhibitors, CLF selectively inhibits pro-autoimmune Th17 cells while preserving the functional state of infection-elicited Th17 cells through restricting Aldh1l2expression. Using bulk RNA sequencing, we explored transcriptional response to CLF on in vitro differentiated inflammatory and homeostatic Th17 cells. Notably, we identified a unique suppression in the transcription of signature inflammatory genes in Th17 cells with a marginal effect on those elicited by infection.

first: Ronald

last: Bouch

first: Jing

last: Zhang

first: Zhiheng

last: He


title: Autoimmunity and infection give rise to distict inflammatory Th17 subsets [single-cell RNA-seq]

summary: Th17 cells are a heterogeneous population that is critical for tissue homeostasis and inflammation during clearance of infections and autoimmunity. Despite substantial efforts distinguishing homeostatic and inflammatory roles of Th17 cells, the mechanism underlying the divergent functions of inflammatory Th17 cells is poorly understood. In this study, we show that the inflammatory Th17 engaged in autoimmune colitis and those involved in infection-induced colitis are two distinguishable populations illustrated by their distinct responses to a pharmacological molecule, clofazimine (CLF). Distinct from existing Th17 inhibitors, CLF selectively inhibits pro-autoimmune Th17 cells while preserving the functional state of infection-elicited Th17 cells through restricting Aldh1l2expression. Using single-cell RNA sequencing, we explored inflammatory Th17 transcriptional response to CLF from the colonic tissue of mice during autoimmune colitis and Citrobacter rodentiuminfection using Rorc gfp/+ reportor mice. Notably, we identified a unique suppression in the transcription of signature inflammatory genes in Th17 cells from autoimmune colitis with a marginal effect on those elicited by infection. Additionally, we illustrate with these data that the transcriptionally programming of pro-autoimmune Th17 cells are, indeed, unique compared to infection-elicited Th17 cells. Finally, we analyzed the impact of CLF on human inflammatory Th17 cells from the inflammed colon of a patient with IBD.

overall_design: Using single-cell RNA sequencing, we explored inflammatory Th17 transcriptional response to CLF from the colonic tissue of mice during autoimmune colitis and Citrobacter rodentiuminfection using Rorc gfp/+ reportor mice. Notably, we identified a unique suppression in the transcription of signature inflammatory genes in Th17 cells from autoimmune colitis with a marginal effect on those elicited by infection. Additionally, we analyzed the impact of CLF on human inflammatory Th17 cells from the inflammed colon of a patient with IBD.


title: Transcriptomic comparison of two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative responses

city: Baltimore

first: Kevin

last: Emmerich

address: 400 N Broadway

department: Human Genetics

institute: Johns Hopkins University

summary:
Retinal Müller glia (MG) can act as stem-like cells to generate new neurons in both zebrafish in mice. In zebrafish, retinal regeneration is innate and robust, resulting in the replacement of lost neurons and restoration of visual function. In mice, exogenous stimulation of MG is required to reveal a dormant and, to date, limited regenerative capacity. Zebrafish studies have been key in revealing factors that promote regenerative responses in the mammalian eye. Increased understanding of how the regenerative potential of MG is regulated in zebrafish may therefore aid efforts to promote retinal repair therapeutically. Developmental signaling pathways are known to coordinate regeneration following widespread retinal cell loss. In contrast, less is known about how regeneration is regulated in the context of retinal degenerative disease, i.e., following the loss of specific retinal cell types. To address this knowledge gap, we compared transcriptomic changes between two selective cell ablation paradigms, targeted loss of rod photoreceptors or bipolar cells. Our study spanned twelve time points encompassing the entire degenerative and regenerative process of each targeted cell type. 2,531 differentially expressed genes (DEGs) were identified. Interestingly, the majority of DEGs were paradigm specific, including during MG activation phases, suggesting the nature of the injury/cell loss informs the regenerative process from initiation onward. For example, early modulation of Notch signaling was implicated in the rod but not bipolar cell ablation paradigm. Components of JAK/STAT signaling were activated in both paradigms but were more strongly induced during rod cell regeneration. We functionally validated the role of JAK/STAT signaling during rod cell regeneration using CRISPR/Cas9-based knockdown of stat3 which inhibited both MG proliferation and rod cell regeneration kinetics. Additionally, although more than a third of all DEGs are implicated as immune-system regulators, individual immune-related factors were largely paradigm specific. These data support emerging evidence that discrete “fate-biased” regenerative processes follow from selective retinal cell loss.
Microarrays were used to follow gene expression changes in the eyes of fish following either rod or bipolar specific induced death.

overall_design: Larval fish were screened for transgenic expression and collected following ablation at times from 0-240h post ablation for RNA extraction and hybridization on Affymetrix microarrays.


title: Autoimmunity and infection give rise to distict inflammatory Th17 subsets


title: PCBP1 regulates LIFR through FAM3C to maintain BCSC self-renewal and invasiveness

city: Charleston

first: William

middle: Scott

last: Streitfeld

state: SC

address: 173 Ashley Ave BSB 510

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary:
The poly(rC) binding protein 1 gene (PCBP1) encodes the heterogenous nuclear ribonucleoprotein E1 (hnRNPE1), a nucleic acid binding protein that plays a tumor-suppressive role in mammary epithelium by regulating phenotypic plasticity and cell fate. Following loss of PCBP1 function, the FAM3C gene (encoding the Interleukin-like EMT inducer, or “ILEI” protein) and the leukemia inhibitory factor receptor (LIFR) gene are upregulated.
Interaction between FAM3C and LIFR in the extracellular space induces phosphorylation of the signal transducer and activator of transcription 3 (pSTAT3). The overexpression and/or hyperactivity of STAT3 has been detected in 40% of breast cancer cases and is associated with poor prognosis. Herein, we characterize feed-forward regulation of LIFR expression in response to FAM3C/LIFR/pSTAT3 signaling in mammary epithelial cells, and show that PCBP1 upregulates LIFR transcription through FAM3C, involving activity at the LIFR promoter.
Additionally, our bioinformatic analysis reveals a signature of transcriptional regulation associated with FAM3C/LIFR interaction and identifies the TWIST1 transcription factor as a downstream effector that participates in maintenance of LIFR expression.
Finally, we characterize the effect of LIFR expression in cell-based experiments that demonstrate promotion of invasion, migration, and breast cancer stem cell (BCSC) self-renewal, consistent with previous studies that link LIFR expression to tumor initiation and metastasis in mammary epithelial cells.

overall_design:
Comparative gene expression profiling of bulk RNA extracts from pooled cell populations. Comparisons made between normal murine mammary gland cells (NMuMG) and derivative cell lines, using two independent datasets.
Dataset 1: compares (A) NMuMG shPCBP1 with (B) NMuMG shPCBP1 FAM3C KO and (A) with (C) NMuMG shPCBP1 LIFR KO
Dataset 2: A pre-existing dataset that compares (D) NMuMG with (E) NMuMG shPCBP1

first: Annamarie

last: Dalton

first: Breege

last: Howley

first: Philip

last: Howe


title: Gene expression profiling on 2D vs 3D iPSC colonies

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: In this study, we aimed to investigate the influence of the local mechanical cell niche on mechano-responsive signaling activities and germ layer specification by engineering a unique 3D semispherical colony of human-induced pluripotent stem cells (iPSCs). To achieve this, we utilized a combination of an electrospun nanofibrous substrate and PDMS microwells. Specifically, we compared the gene expression profiles of iPSCs cultured on a plastic plate with those cultured on a PCL nanofibrous substrate  (19 kPa).

overall_design: In this study, we conducted gene expression profiling of four replicates of human-induced pluripotent stem cells (iPSCs) cultured on a plastic plate, and compared them to four replicates of iPSCs cultured on a soft PCL nanofibrous substrate  (19 kPa). The aim was to examine the differential gene expression patterns between these two culture conditions and investigate the potential effects of substrate stiffness on iPSC behavior.

first: Hung

last: Shih

first: Jin

last: Nam

first: Youyi

last: Tai


title: Gene expression profile at single cell level of cells from the murine colonic tumors

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cells within murine colonic tumors with genetic mutations.

overall_design: Cells from colonic tumors with either mutant Apc or mutant P53 with Notch1 activation were  harvested for analysis with scRNAseq

first: Noha-Ehssan

last: Mohammed

first: Tamsin

last: Lannagan

first: Owen

last: Sansom


title: Transcriptional profiling of Tissues, Tumors, and associated cells in mice with gene mutations relevant to colorectal cancer and macrophage infiltration

summary: A profile of gene expression differences in mouse colon tissue, colonic tumors, organoids from colon tumors and colonic macrophages with genetic changes and drug treatment.

overall_design: Expression data from the noted sample types, with the noted genetic changes and drug treatment.

last: Mohamed