title: Transcriptional, chromatin, and metabolic landscapes of LDHA inhibitor–resistant pancreatic ductal adenocarcinoma

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Metabolic reprogramming, due in part to the overexpression of metabolic enzymes, is a key hallmark of cancer cells. Lactate dehydrogenase (LDHA), a metabolic enzyme that catalyzes the interconversion of lactate and pyruvate, is overexpressed in a wide variety of cancer types, including pancreatic ductal adenocarcinoma (PDAC). Furthermore, the genetic or pharmacological inhibition of LDHA suppresses cancer growth, demonstrating a cancer-promoting role for this enzyme. Therefore, several pharmacological LDHA inhibitors are being developed and tested as potential anti-cancer therapeutic agents. Because cancer cells are known to rapidly adapt and become resistant to anti-cancer therapies, in this study, we modeled the adaptation of cancer cells to LDHA inhibition. Using PDAC as a model system, we studied the molecular aspects of cells resistant to the competitive LDHA inhibitor sodium oxamate. We performed unbiased RNA-sequencing (RNA-seq), assay for transposase-accessible chromatin with sequencing (ATAC-seq), and metabolomics analyses of parental and oxamate-resistant PDAC cells treated with and without oxamate to identify the transcriptional, chromatin, and metabolic landscapes of these cells. We found that oxamate-resistant PDAC cells were significantly different from parental cells at the levels of mRNA expression, chromatin accessibility, and metabolites. Additionally, an integrative analysis combining the RNA-seq and ATAC-seq datasets identified a subset of differentially expressed mRNAs that directly correlated with changes in chromatin accessibility. Finally, functional analysis of differentially expressed metabolic genes in parental and oxamate-resistant PDAC cells treated with and without oxamate, together with an integrative analysis of RNA-seq and metabolomics data, revealed changes in metabolic enzymes that might explain the changes in metabolite levels observed in these cells. Collectively, these studies identify the transcriptional, chromatin, and metabolic landscapes of LDHA inhibitor resistance in PDAC cells. Future functional studies related to these changes remain necessary to reveal the direct roles played by these changes in the development of LDHA inhibitor resistance and uncover approaches for more effective use of LDHA inhibitors in cancer therapy.

overall_design: RNA-seq analysis was done in Miapaca2 parental and LDHA inhibitor resistant cells.

first: Vipin

last: Rawat

first: Parmanand

last: Malvi

first: Romi

last: Gupta


title: Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features in Ductal Carcinoma In Situ of the Breast

status: Public on Aug 02 2022

city: Chuo-ku

first: Jun

last: Nakayama

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center

type: Expression profiling by high throughput sequencing

summary: This sample was collected to conduct spacial transcriptome analysis of breast cancer. We analyzed heterogeneity of HER2+ ducal cacinoma in situ (DCIS). We obtained transcriptome data from 1,521 distinct spots. By an unsupervised dimensionality reduction approach through UMAP, the data were decomposed into 5 clusters (Clusters 0 to 4). The 2 luminal epithelial clusters were identified, however ERBB2/HER2 expression level was different in these clusters. Unsupervised clustering analysis showed clear separation of the cells from the 2 clusters. Analysis of canonical pathways and upstream regulators by IPA indicated functionally distinct luminal epithelial populations in one HER2+ DCIS sample.

overall_design: Spacial transcriptome profiling from 1 human breast cancer tissues (DCIS).

first: Momoko

last: Tokura

first: Yusuke

last: Yamamoto


title: Genome-wide maps of chromatin state in mouse small intestinal intraepithelial lymphocytes.

city: Shanghai

first: haohao

last: zhang

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: We performed CUT&Tag-Seq against histone H3K27me3 in mouse small intestinal TCRβ+CD8αα+ intraepithelial lymphocytes (IELs) of wild-type mice to analyze epigenetic modifications.

overall_design: Examination of H3K27Me3 modifications in mouse small intestinal TCRβ+CD8αα+ IELs.

first: Haohao

last: Zhang

first: Yiming

last: Hu

first: Dandan

last: Liu

first: Xiaoren


title: Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid flux

city: Durham

first: Jarrett

last: Bliton

address: 6 Davis Drive

country: USA

institute: Altis Biosystems

summary:
Background & Aims: Absorption, metabolism, and secretion of lipids occurs in the small intestinal epithelium. Caco-2 and organoids have been used to study these processes but are limited in physiological relevance or preclude simultaneous apical and basal access. Here, we develop a dynamic and flexible planar absorptive enterocyte (AE) monolayer system, investigate how fatty acid oxidation (FAO) regulates FA mobilization mechanisms and probe a role for metformin in FA mobilization.
Methods: Single-cell RNA-sequencing (scRNAseq) was performed on primary human jejunum. Transcriptomic signatures and trajectory analysis defined in vivo AE maturational signatures, which informed culture methods to differentiate ISCs and mimic in vivo AEs. The system was scaled for high-throughput drug screening and FAO was pharmacologically modulated. BODIPY (B)-labelled fatty acids (FAs) were used to easily and sensitively evaluate FA handling via fluorescence, and thin layer chromatography (TLC).
Results: scRNAseq shows increasing expression of lipid-handling genes as AEs mature. In vitro, ISCs differentiate into AEs that mimic the in vivo maturational program, exhibit strong barrier function and express FA-handling genes. FA synthase inhibitor, C75, increased apical to basolateral mobilization of B-C16. Short-chain FA (B-C5) was unaffected and diffused freely through AEs. FAO inhibitor, etomoxir, decreased apical to basolateral mobilization of medium and long chain FAs (B-C12, B-C16) whereas anti-diabetic drug, metformin, augmented this mobilization.
Conclusions: Primary human ISCs in culture undergo programmed maturation in vitro to generate a sensitive culture system of absorptive epithelium to investigate FA-handling. Modulating FAO impacts mobilization of FAs across absorptive epithelium and FAO enhanced by metformin increases basolateral mobilization pointing to an intestine-specific role.

overall_design:
One entire human intestine, hashtagged and called for the six regions. Only Jej and Ile are analyzed in this dataset
Also see jejunum and ileum data from GSE185224.

first: Ismael

last: Gomez-Martinez

first: R

middle: J

first: Keith

middle: A

last: Breau

first: Michael

last: Czerwinski

first: Ian

last: Williamson

first: Jia

last: Wen

first: John

middle: F

last: Rawls

first: Scott

middle: T

last: Magness


title: Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection

city: New York

first: Julia

last: Brown

state: New York

address: 413 E 69th Street, 1252A

institute: Weill Cornell Medicine

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

overall_design: Refer to individual Series


title: Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL


title: Captopril treatment in rats with DEN-induced cirrhosis and hepatocellular carcinoma

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

summary: Hepatocellular carcinoma (HCC) is one of the leading cause of cancer-related mortality worldwide. Liver cirrhosis is well-established risk factor of HCC development, although prevention of HCC in cirrhosis patients is challenging. By utilizing bioinformatic compound screening based on a clinical HCC-risk-predicitve gene signature, we identified captopril as a potential HCC chemoprevention agent. We tested the drug in rats with diethylnitrosamine (DEN)-induced cirrhosis and HCC, and confirmed its HCC-preventive effect.

overall_design: To evaluate effect of captopril for hepatocellular carcinoma (HCC) chemoprevention, rats with diethylnitrosamine-induced liver cirrhosis and HCC were treated with the drug or vehicle. Liver tissues were harvested for transcriptome profiling by RNA-Seq.

first: Emilie

last: Crouchet

first: Shen

last: Li

first: Yujin

last: Hoshida

first: Bryan

last: Fuchs

first: Thomas

last: Baumert


title: Chip of BRD4 in Neurofibromatosis type 2

city: Sioux Falls

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Background:  Neurofibromatosis type 2 (NF2) is an autosomal dominant genetic disease characterized by the development of multiple Schwannomas, usually occurring on both VIIIth (vestibular) cranial nerves.  Bromodomain and extra-terminal domain (BET) proteins regulate gene transcription and their activity is required in a variety of cancers including malignant peripheral nerve sheath tumors (MPNST).  The use of BET inhibitors as a therapeutic option to treat NF2 schwannomas has not been explored and is the focus of this study.     Methods:  A panel of normal and NF2-null Schwann cell and schwannoma cell lines were used to characterize the impact of the BET inhibitor JQ1 in vitro and in vivo.  The mechanism of action was explored by chromatin immunoprecipitation (ChIP) of the BET BRD4, phospho-kinase arrays and immunohistochemistry of BRD4 in human vestibular schwannomas.   Results:  JQ1 inhibited the proliferation of NF2-null schwannoma and Schwann cell lines in vitro and in vivo.  Further, loss of NF2 by CRISPR deletion or siRNA knockdown increased the sensitivity of cells to JQ1.  Knock-down experiments identified BRD4 as the BET family member mediating the majority of JQ1 effects on cell proliferation. Immunohistochemistry demonstrated elevated levels of BRD4 protein in human vestibular schwannomas.  BRD4 ChIP experiments identified the small G-protein Rac1 and PI3K signaling pathways as sensitive to JQ1.     Conclusions:  NF2 deficient Schwann cell and schwannoma cells are sensitive to BET inhibition, primarily mediated by BRD4, which is overexpressed in human vestibular schwannomas.  BRD4 regulates Rac/Ras and PI3K signaling pathways and inhibition of these pathways by JQ1 impedes NF2 Schwannoma growth. These findings implicate BET inhibition as a therapeutic option for NF2-deficient schwannomas.

overall_design: 2 biological replicates from Jq1-treated or mock (DMSO)-treated human NF2 cell lines

first: Joanne

last: Doherty

middle: S

first: Joseph

middle: L

last: Kissil


title: Next Generation Sequencing Facilitates Quantitative Analysis of Human Pluripotent Stem Cell-Derived Neutrophil-like Cell Transcriptomes

city: West Lafayette

first: Xiaoping

last: Bao

state: Indiana

address: 480 Stadium Mall Drive

department: Chemical Engineering

institute: Purdue University

summary: Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for different cell lineage formation from human pluripotent stem cells (hPSCs). We report here the application of RNA-sequencing technology for transcriptome profile of human primary and hPSC-derived neutrophils, and compare to those of hPSCs. Thirteen neutrophil samples from H9 hESCs were performed in IIIumina HiSeq2500. The resulting sequence reads were mapped to human genome (hg19) using HISAT, and the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py. Our RNA-seq data confirmed the stable expression of key neutrophil markers including ITGAM, FUT4, FCGR3A, CEACAM8 and ITGB2. This study shows a detailed analysis of neutrophil transcriptomes generated by RNA-seq technology, providing insight into the mechanisms underlying the differentiation of hPSCs into neutrophils.

overall_design: Neutrophil transcriptome profiles of human primary and hPSC-derived neutrophils were generated by RNA-seq technology using IIIumina NextSeq500

first: Yun

last: Chang


first: Narendra

last: Wajapeyee

overall_design: ATAC-seq analysis was done in Miapaca2 parental and LDHA inhibitor resistant cells.

first: Vipin

last: Rawat

first: Parmanand

last: Malvi

first: Romi

last: Gupta


title: Genome wide distribution of dH1K27me2 in Wild Type Drosophila melanogaster S2 cells

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

overall_design: ChIP-Seq peak calling of dH1K27me2 against Input sample in Drosophila melanogaster S2 cells

first: Jordi

last: Bernués

first: Andrea

last: Izquierdo-Bouldstrigde

last: Reina

first: Fernando

last: Azorín


title: Transcriptomic profiling identifies CD8+ T-cells in the brain of aged and Alzheimer’s disease transgenic mice as tissue-resident memory T-cells

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

summary: Immune cell infiltration to the brain is a prominent feature in aging and in various neurodegenerative diseases such as Alzheimer´s disease (AD). For example, a specific subpopulation of CD8+ T-cells clonally expands in the CSF of AD patients. Also, with AD progression that typically includes amyloid-beta plaque formation, neuronal damage and microglia-associated neuroinflammation, CD8+ T-cells infiltrate into the AD brain parenchyma and tightly associate with neuronal and microglia structures. The functional properties of CD8+ T-cells in the brain are largely unknown, besides the fact that experimental ablation in a transgenic AD animal model (APP-PS1) leads to changes in the expression of neuronal- and synapse-related genes. To gain further insights into the putative functional role of CD8+ T-cells in the brain, we explored and compared the transcriptomic profile of these cells in blood and brain of aged and transgenic AD mice.  Surprisingly, CD8+ T-cells isolated from brains of aged APP-PS1 and WT animals had a similar transcriptomic profile, but they substantially differed from blood circulating CD8+ T-cells. The gene expression signature of brain CD8+ T-cells from APP-PS1 mice identified these cells as tissue-resident memory T-cells (Trm) indicated by specific regulation of genes such as Klf2/3, Ccr7, Sell, and Cxcr6. Immunohistochemical analysis confirmed the Trm identity of CD8+ T-cells at sites of amyloid-plaques. Gene ontology enrichment analysis on the significantly up-regulated genes showed an overrepresentation of biological processes as “response to virus”, “T-cell mediated immunity” and “response to interferon-beta” suggesting similarities to virus-responding T-cells. This is also supported by KEGG analysis, which highlighted upregulation of several pathways for “virus infections”, “cellular senescence” and “antigen processing and presentation”. In addition, the transcriptome of APP-PS1 brain CD8+ T-cells overlapped with gene microarray data of brain Trm CD8+ T-cells derived from an acute virus infection mouse model, suggesting similar functions of CD8+ T-cells in the brain either after viral infections or in AD. In conclusion, our herein presented data give new insights on the transcriptome of brain CD8+ T-cells and demonstrate adaptive immune responses in transgenic AD mice. This might open the door for immunotherapy as potential treatment option for AD.

overall_design: Two different strains were used: Seven APP Swedish PS1 dE9 (APP-PS1) mice and ten wild type (WT) mice. Whole transcriptome analysis of CD8+ T-cells in blood and brain was compared between aged and transgenic AD mice and wild type strain

first: Michael

last: Unger


title: Next generation sequencing showing miRNA profiles of exosomes derived from DHT-treated CAFs and matched ETOH-treated CAFs

first: Yu

last: Zhang

address: Xinsongjiang Road 650, Shanghai, China

institute: Shanghai Jiaotong University, School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Androgen deprivation therapy (ADT) is the backbone of therapy for advanced prostate cancer (PCa). Despite the good initial response, castration resistance and metastatic progression will inevitably occur. Cancer-associated fibroblasts (CAFs) may be implicated in promoting metastasis of PCa after ADT. Our aim is to investigate the role and mechanism of CAF-derived exosomes involving in metastasis of PCa after ADT.   Methods: PCa cells were co-cultured with exosomes derived from DHT-treated or ETOH-treated CAFs, and their migration and invasion differences under castration condition were examined both in vitro and in vivo. The miRNA profiles of exosomes derived from DHT-treated CAFs and matched ETOH-treated CAFs were analysed via next generation sequencing. The transfer of exosomal miR-146a-5p from CAFs to PCa cells was identified by fluorescent microscopy. The function and direct target gene of exosomal miR-146a-5p in PCa cells were confirmed through Transwell assays, luciferase reporter, and western blot.  Findings: Compared with DHT-treated CAFs, exosomes derived from ETOH-treated CAFs dramatically increase migration and invasion of PCa cells under castration condition. MiR-146a-5p level in exosomes from ETOH-treated CAFs was significantly reduced. The loss of miR-146a-5p may strengthen the epithelial-mesenchymal transition (EMT) to accelerate cancer cells metastasis by modulating epidermal growth factor receptor (EGFR)/ERK pathway.   Interpretation: CAFs-derived exosomal miR-146a-5p confers metastasis in PCa cells under ADT through the EGFR/ERK pathway and it may present a new treatment for PCa.

overall_design: Examing 2 conditions, each with 3 replicates

first: Jing

last: Zhao

first: Mao

last: Ding


title: Effect of CTNS downregulation by siRNA on fertile human caput epididymis (FHCE) cell line in vitro for 48 hours

city: Leuven

first: Ahmed

last: Reda

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: We report that CTNS downregulation in FHCE cells in vitro for 48 hours had minimal effect on the transcriptional profile clustring

overall_design: FHCE cells were transfected in vitro with either CTNS siRNA or scrambled siRNA, cell pellets were collected after 48 hours, RNA was isolated, followed by RNA sequencing

first: Elena

last: Levtchenko


title: Kdm6b is required for the maturation and function of intestinal TCRβ+CD8αα+ intraepithelial lymphocytes

first: haohao

last: zhang

summary: To under the role of Kdm6b in the regulation of intestinal TCRβ+CD8αα+ intraepithelial lymphocytes (IELs), Kdm6b was conditionally deleted in mouse T cells. Small intestinal TCRβ+CD8αα+ IELs were sorted by flow cytometry and RNA-seq was conducted to identify the differentially expressed genes.

overall_design: RNA-seq on control and Kdm6b-deficient mouse intestinal TCRβ+CD8αα+ IELs.

first: Haohao

first: Yiming

last: Hu

first: Dandan

last: Liu

first: Xiaoren


title: Genome-wide high-throughput sequencing analysis of TLR4-overexpressing ovarian cancer cells treated with taxol and curcumin

city: Taoyuan

first: Nian Kang

last: Sun

address: No.261, Wenhua 1st Rd.Guishan Dist

department: Division of Biomedical Sciences

country: Taiwan

institute: Chang Gung University of Science and Technology

summary: The purpose of this study is to approach overexpression of TLR4 which contributes the drug resistance in ovarian cancer cells. However, curcumin overcomes this effects. Comparison of the transcriptional regulated genes were performed: (1) analysis of TLR4-overexpressing (T4) and mock (MCS) SKOV3 cells by taxol treatment; (2) assay of taxol alone and combined with curcumin treatments in TLR4-overexpressing (T4) SKOV3 cells. Differential expression analysis was performed with ≥ 2-fold or ≤0.5-fold (p<0.05) changed expression for pathway enrichment analysis.

overall_design: TLR4-overexpressing (T4) and mock (MCS) SKOV3 cells were treated with taxol. In addition, treatment of taxol combined with curcumin was performed in TLR4-overexpressing cells as well. All samples were prepared in duplicates.

first: Nian-Kang

first: Shang-Lang

last: Huang


title: Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis I

first: Evarist

last: Planet

summary: Tumors occasionally express oncogenes via aberrant activation of transposable elements (TE), but a role for this process in oncogenesis was seldom demonstrated. Here, we identify expression of the hominid-restricted retrogene POU5F1B through aberrant activation of an endogenous retroviral promoter as a strong negative prognostic marker in colorectal cancer (CRC). We further determine that POU5F1B is membrane-enriched and interacts with ERBB2 and associated effectors, and fosters the proliferation and metastatic potential of CRC cells through intracellular signaling events and release of trans-acting molecules involved in cell growth, angiogenesis and cell adhesion. As POU5F1B is apparently non-essential and only lowly expressed in normal tissues, and as POU5F1B-containing TE-driven transcripts are detected in other tumors besides CRC, these data provide interesting leads for the development of cancer therapies.

overall_design: RNA-sequencing analysis of POU5F1B- and GFP-overexpressing SW480 cells.

first: Laia

last: Simo-Riudalbas


title: Expression of the host and pathogen genes during sugarcane - S. scitamineum interaction

city: Fuzhou

first: Ning

state: Fujian

address: Cangshan Distrc,Shangxia Dian Road 15

institute: Fujian Agriculture and Forestry University

summary: According to the key words, the gene set, including oxidation-reduction, RNA silence, disease resistance, phytohormone, phosphorylation, dephosphorylation, transcription factor, receptor, kinase, ubiquitination and RNA binding,etc. from sugarcane and the whole CDS sequence from smut genome, was achieved and used  as targets in the present microarray assay. Based on smut infection samples from smut-susceptible sugarcane genotype YC71-374 and smut-resistant sugarcane genotype NCo376, the hybridization was conducted and validated by real-time fluorescent quantitative PCR. It would provide a basic data for the study on sugarcane-smut interaction mechanism, which referred to sugarcane smut resistance and smut pathogenesis.

overall_design: Samples injected with S. scitamineum were consisted of three biological replicates and the bud samples were collected at 0 day, 3 days, 5 days and 7 days post inoculation (dpi).

first: Hui

last: Ling

first: Youxiong

last: Que


title: HERV1-env dependent unfolded protein response activation is a potential initiator of T cell autoreactivity in autoimmune liver disease.

city: New Haven

first: Udeme

middle: D

last: Ekong

state: CT

address: 333 Cedar Street

department: Pediatrics

institute: Yale University

summary: Here we report Human Endogenous Retrovirus 1 (HERV1-env) induction of endoplasmic reticulum (ER) stress with Unfolded Protein Response (UPR) activation, through its interaction with ATF6.ATF6α up-regulates RORC, STAT3 and TBX21 and induces IL-17A and INF-γ production in Tregs by binding to promoter sequences.

overall_design: ChIP-DNA from FACS-sorted memory Tregs from 5 subject groups

first: Sameet

last: Mehta


title: Single-Cell RNA Sequencing Reveals Novel Genes Regulated by Hypoxia in the Lung Vasculature

status: Public on Aug 01 2022

city: Columbus

first: Brenda

middle: J.

last: Lilly

state: OH

address: 700 CHILDREN'S DRIVE

institute: NATIONWIDE CHILDREN'S HOSPITAL

summary: Pulmonary arterial hypertension (PAH) is a chronic progressive disease with significant morbidity and mortality. The disease is characterized by vascular remodeling that includes increased muscularization of distal blood vessels and vessel stiffening associated with changes in extracellular matrix deposition. In humans, chronic hypoxia causes PAH, and hypoxia-induced rodent models of PAH have been used for years to study the disease. With the development of single-cell RNA sequencing technology, it is now possible to examine hypoxia-dependent transcriptional changes in vivo at a cell-specific level. In this study, we used single-cell RNA sequencing to compare lungs from wild-type mice exposed to hypoxia for 28 days to normoxia-treated control mice. We additionally examined mice deficient for Notch3, a smooth muscle-enriched gene linked to PAH. Data analysis revealed that hypoxia promoted cell number changes in immune and endothelial cell types in the lung, activated the innate immunity pathway, and resulted in specific changes in gene expression in vascular cells. Surprisingly, we found limited differences in lungs from mice deficient for Notch3 compared to wild-type controls. These findings provide novel insight into the effects of chronic hypoxia exposure on gene expression and cell phenotypes in vivo and identify unique changes to cells of the vasculature.

overall_design: single cell RNA-seq of mouse lung from wildtype normoxia, wild-type hypoxia, Notch3-deficient normoxia, and Notch3-deficient hypoxia

first: Aiman

last: Khan

first: Sathiyanarayanan

last: Manivannan


title: RNA-Seq of Ctrl, Myocd KO, Mrtfa/b DKO and TKO cardiomyocytes

city: Boston

first: Yangpo

last: Cao

address: 320 Longwood Ave

institute: Boston Children's hospital

summary: To characterize transcriptome changes uopn Myocd KO, Mrtfa/b DKO and  Mrtfa/b/Myocd TKO in maturing cardiomyocytes

overall_design: AAV-Cre or AAV-Myocd-sgRNAwere injected into P1 Rosa-Cas9GFP or Mrfta-/-; Mrtfb-F/F; Rosa-Cas9/Cas9 mice. The cardiomyocyets were isolated at 4wk old for FACS purification and RNA-seq analysis

first: Yuxuan

last: Guo


title: Integrin αEβ7+ T cells direct intestinal stem cell fate decision via adhesive signaling

first: Chen

last: Shiyang

address: Room 413, New biochemistry building, YueYang Road

institute: Shanghai Institute of Biochemistry and Cell Biology (CAS)

summary: Intestinal stem cells (ISCs) maintain gut homeostasis by differentiating into different epithelial cell types, which is precisely regulated by a niche of accessory cell types. In the niche, lymphocytes may interact with stem and transient amplifying (TA) cells in the intestinal crypts. However, it is unknown whether and how the lymphocyte- stem/TA cell contacts affect ISC differentiation. Here we discover and mechanistically dissect the role of T cell-stem/TA cell contacts in ISC fate decision. We found T cells are often seen in contact with ISCs and TA cells in the small intestinal crypts, whereas B cell-stem/TA cell interaction was hardly observed. Using single-cell RNA sequencing and immunostaining, we showed that depletion of intestinal lymphocytes resulted in aberrant ISC differentiation in mice, with decreased Paneth and goblet cells, increased enteroendocrine cells and impaired enterocyte maturation. Transferring T cells but not B cells into those mice efficiently restored normal ISC differentiation. Mechanistically, integrin αEβ7 on T cells binds to E-cadherin on ISCs and TA cells. Blocking this adhesion suppressed Wnt signaling in ISCs and TA cells and promoted Notch signaling in TA cells, leading to defective ISC differentiation. In vitro study using purified αEβ7 protein showed consistent effects on the intestinal organoid differentiation. Taken together, our study reveals that the gut-resident integrin αEb7+ T cells regulate the ISC differentiation through adhesion between αEβ7 on T cells and E-cadherin on ISCs and TA cells. The αEβ7-E-cadherin adhesive signaling is critical for the fate decision of ISCs and the maintenance of intestinal homeostasis.

overall_design: Using single-cell RNA-seq of  enriched crypt epithelial cells from C57BL/6J WT and integrin β7 knock out (Itgb7-/-) mice small intestines in triplicate, we found that lack of intestinal lymphocytes resulted in aberrant ISC differentiation in mice, with decreased Paneth and goblet cells, increased enteroendocrine cells and impaired enterocyte maturation.

first: Jianfeng

last: Chen

first: Shiyang


title: circRNA sequencing facilitates quantitative analysis of CUS mice hippocampus and Control mice hippocampus

city: Nanjing

first: Rongrong

state: Jiangsu

address: 87 Dingjiaqiao

institute: Southeast University

summary: The goal of this study is to seek the potential circular RNAs (circRNAs), which express differently between control group and chronic unpredictable stress (CUS) group mouse hippocampus, involved in major dipresssion disorder (MDD) by high-throughput sequencing. QPCR was preformed to identify the circRNAs trend. CircRNAs are a class of RNAs in the eukaryotic transcriptome. The function and explicit downstream mechanisms of circRNA regulated in maior depression disorser remain unclear. To further investigate the potential role of circRNAs in MDD, we performed human and mouse homology screening on circRNA sequences using the Basic Local Alignment Search Tool on the NCBI website. CircSTAG1, a homologous human and mouse circRNA, was found downregulated in circRNA high-throughput sequencing. Our study represents the first detailed analysis of circRNA expressing differently in CUS mouse hippocampus by high-throughput sequencing.

overall_design: CUS induced circular RNA expression in mice hippocampus  was measured, and their expression in healthy controls were set as comparison. Three independent samples from CUS group and three independent samples from control group were employed in high-throughput sequencing analysis.

first: Honghong

last: Yao


title: CircRNA-miRNA in anesthesia-induced permanent nerve injury during caesarean delivery

city: Guangzhou

first: Baisong

last: Zhao

state: Guangdong

address: No. 9 Jinsui Road, Tianhe District

department: Department of Anesthesiology

institute: Guangzhou Women and Children’s Medical Center

summary: Permanent nerve damage caused by anesthesia is a rare but critical issue, and the mechanism of it remains unclear. Large-scale analysis of changes in noncoding RNA such as circRNA and microRNA in anesthesia-related nerve damage may provide insight into the mechanism of anesthesia-induced nerve injury.

overall_design: Three patients with caesarean delivery under combined spinal and epidural anesthesia, who had neurological complications with a final diagnosis of post-anesthesia permanent nerve damage, were selected. Three patients undergoing the same operation and anesthesia process, but without neural damage were chosen as parallel control. All patients were followed up for 5 years, and venous blood was collected for whole transcriptome sequencing.

first: Bai-Song

first: Xing-Rong

last: Song


title: miR-145 transgenic mice develop cardiopulmonary complications leading to postnatal death

summary: Both downregulation and elevation of microRNA miR-145 has been linked to an array of cardiopulmonary phenotypes, and a host of studies suggest that it is an important contributor in governing the differentiation of cardiac and vascular smooth muscle cell types.

overall_design: Compared wild-type lungs with miR-145 transgenic lungs


title: Exposure of non-lethal doses of furfural drives genomic alterations and phenotypic evolution in Saccharomyces cerevisiae

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

summary: Using multiple genetic screening assays and high-throughput analysis approaches, this study explored the genotoxic and evolutional effects of nonlethal dosages of furfural in yeast model.

overall_design: To confirm the crossover events in the recombinants appeared on furfural plates, we selected 53 independent white colonies and 33 independent red colonies, and analyzed the T-LOH events among the these colonies using a custom chr IV-specific SNP microarray.

first: Lei

last: Qi

first: Dao-qiong


title: The effect of c-Myc over-expression on the sensitivity to Tipifarnib treatment in three cancer cell lines

city: Houston

first: Han

last: Liang

state: Texas

address: 1400 Pressler Street

department: Bipinformatics and computational biology

institute: MD Anderson Cancer Center

summary:
To investigate whether the over-expression of c-Myc gene can sensitize cancer cells of multiple tissue origins to Tipifarnib.
We performed differential gene expression analysis using RNA-seq profile of three c-Myc over-expressed and control cell lines with/without Tipifarnib treatment.

overall_design: We over-expressed c-Myc in three cancer cell lines without c-Myc amplification, SKOV3, A549, and MDA-MB-231, representing ovarian, lung, and breast cancer, respectively, using lentivirus. The over-expression cell lines and three control cell lines were treated with Tipifarnib or DMSO as control for 48 hours before RNA extraction. Differential gene expression analysis was performed using the RNA-seq data to identify genes associated with the change of Tipifarnib sensitivity between the c-Myc over-expressed cell lines and the control cell lines.

last: Han

first: Liang


title: Time-series of human LPS stimulated-monocyte derived macrophages

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: We studied the lipidome (236 individual lipid species including sphingolipids, ceramides, cholesterol, gangliosides, phosphatidylethanolamines) in basal and LPS-stimulated human monocyte derived macrophages (MDMs) over a time-course by LC-MS (30min, 3h, 8h, 16h; n=12 human donors). In order to explore how transcriptomic changes induced by LPS stimulation can correlate with changes in the lipidome, we performed RNAsequencing on MDMs from 4 donors over a time-course (30min, 3h, 8h, 16h)

overall_design: We carried out RNA-sequencing in MDMs from 4 donors at 4 time-points (30min, 3h, 8h, 16h).

first: Marta

last: Bagnati

first: Federico

last: Torta

first: Enrico

last: Petretto

first: Jacques

last: Behmoaras


title: 3,4-Dimethoxychalcone, a caloric restriction mimetic, enhances the TFEB-mediated autophagy and alleviates pyroptosis and necroptosis after spinal cord injury

city: wenzhou

first: zhang

middle: hao

last: jie

address: chashan

institute: wenzhou medical university

summary: This study investigated the therapeutic value of a candidate CRM, 3,4-dimethoxychalcone (3,4-DC), in functional recovery after SCI and its underlying mechanism.  RNA sequencing was used to identify the mechanisms of 3,4-DC in SCI.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCI group and SCI+3,4-DC group

first: haojie

last: zhang

first: junsheng

last: lou

first: huazi

last: xu

first: kailiang

last: zhou


title: LKB1/STK11 Is a Tumor Suppressor in the Progression of Myeloproliferative Neoplasms

city: New York

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

summary: The myeloproliferative neoplasms (MPN) frequently progress to blast phase disease, an aggressive form of acute myeloid leukemia. To identify genes that suppress disease progression, we performed a focused CRISPR/Cas9 screen and discovered that depletion of LKB1/Stk11 led to enhanced in vitro self-renewal of murine MPN cells. Deletion of Stk11 in a mouse MPN model caused rapid lethality with enhanced fibrosis, osteosclerosis, and an accumulation of immature cells in the bone marrow, as well as enhanced engraftment of primary human MPN cells in vivo. LKB1 loss was associated with increased mitochondrial reactive oxygen species and stabilization of HIF1α, and downregulation of LKB1 and increased levels of HIF1α were observed in human blast phase MPN specimens. Of note, we observed strong concordance of pathways that were enriched in murine MPN cells with LKB1 loss with those enriched in blast phase MPN patient specimens, supporting the conclusion that STK11 is a tumor suppressor in the MPNs.

overall_design: RNA-seq of paired human patient samples of chronic phase myelofibrosis (MF) and blast phase disease (acute myeloid leukemia; AML)

first: John

last: Crispino

middle: P

first: Raajit

middle: K

last: Rampal


title: Dysregulated gene expression in human osteoarthritic (OA) and rheumatoid arthritis (RA) synovium

city: NEW YORK

first: Mukundan

last: Attur

state: NY

address: 301E, 17TH STREET

institute: NYU GROSSMAN SCHOOL OF MEDICINE

summary: Osteoarthritis (OA) causes pain and functional disability for over 500 million people worldwide and is characterized by progressive loss of cartilage and synovial hyperplasia from the articulating surfaces of diarthrodial joints. Although the etiology of the disease is unknown, it is widely accepted that these degenerative changes arise from an imbalance of synthetic and degradative pathways that control cartilage and synovium extracellular matrix metabolism. Genome-wide U133A Affymetrix oligonucleotide array set was used to comprehensively investigate the expression pattern in non-osteoarthritis (normal) and synovium obtained from OA and rheumatoid arthritis (RA) patients undergoing knee replacement surgery. This study was undertaken to understand the disease's molecular basis better and provide relevant insight into phenotypical alterations and mechanisms involved in OA pathogenesis.

overall_design: Analyzed 7 normal and 7 OA and 2 RA synovium samples.

first: Steven

middle: B

last: Abramson


title: Modeling PRPF31 retinitis pigmentosa using iPSC-derived retinal organoids and retinal pigmented epithelium and rescue by gene augmentation strategy

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

country: France

institute: CNRS-Universite Paris Sud

summary: Mutations in the ubiquitously expressed pre-mRNA processing factor (PRPF) 31, one of the most common cause of dominant form of Retinitis Pigmentosa (RP), lead to retina-specific phenotype. It is uncertain which retinal cell types are affected and animal models do not clearly present the RP phenotype observed in PRPF31 patients. Retinal organoids and retinal pigmented epithelial (RPE) cells derived from human induced pluripotent stem cells (iPSCs) provide potential opportunities for studying human PRPF31-related RP. We demonstrated that RPE cells carrying PRPF31 mutations present important morphological and functional changes and that PRPF31-mutated retinal organoids recapitulate the human RP phenotype, with a rod photoreceptor cell death followed by a loss of cones. The low level of PRPF31 expression may explain the defective phenotypes of PRPF31-mutated RPE and photoreceptor cells, which were not observed in cells derived from asymptomatic patients or after correction of the pathogenic mutation by CRISPR/Cas9. Transcriptome profiles revealed differentially expressed and mis-spliced genes belonging to pathways in line with the observed defective phenotypes. The rescue of RPE and photoreceptor defective phenotypes by PRPF31 gene augmentation, provide the proof of concept for future therapeutic strategies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from retinal organoids and retinal pigmented epithelial (RPE) cells derived from patient induced pluripotent stem cells (iPSCs). Human iPSCs were derived from control and  familly members carrying PRPF31 mutations who are asymptomatic or symprtomatic with photoreceptor degeneration.

first: Rodrigues

last: Amélie

first: Slembrouck-Brec

first: Nanteau

last: Céline

first: Terray

last: Angélique

first: Tymoshenko

last: Yelyzaveta

first: Zagar

last: Yvrick

first: Reichman

last: Sacha

first: Xi

last: Zhouhuan

first: Sahel

last: José-Alain

first: Orieux

last: Gael

first: Nandrot

last: Emeline F

first: Byrne

last: Leah C

first: Audo

last: Isabelle

first: Roger

last: Jérôme E

first: Goureau

last: Olivier


title: Epigenomic Features and Potential Functions of K+ and Na+   Favorable DNA G-Quadruplexes in Rice

first: huang

middle: ran

last: ran

address: weigang 1

institute: Nanjing Agricultural College

summary: We explores the effects of K+ and Na+ on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future.

first: Wenli

last: Zhang

first: Yilong

last: Feng

first: Zhenyu

last: Luo


title: Loss of Jagged1 in mature endothelial cells causes vascular dysfunction with alterations in smooth muscle phenotypes

first: Brenda

last: Lilly

summary: Notch signaling is an evolutionarily conserved pathway that functions via direct cell-cell contact. The Notch ligand Jagged1 (Jag1) has been extensively studied in vascular development, particularly for its role in smooth muscle cell maturation. Endothelial cell-expressed Jag1 is essential for blood vessel formation by signaling to nascent vascular smooth muscle cells and promoting their differentiation. Given the established importance of Jag1 in endothelial cell/smooth muscle crosstalk during development, we sought to determine the extent of this communication in the adult vasculature for blood vessel function and homeostasis.

overall_design: Comparative expression of EC-Jag1-deficient aortas with wild-type controls

first: Randa

last: Breikaa

first: Aiman

last: Khan


title: Polydatin Alters Proliferative Properties and Synergizes the Inhibitory Activity of Doxorubicin and Cisplatin in hepatocellular Carcinoma

city: Harbin

first: Guangyue

last: Li

state: heilongjang

address: No.26 Hexing Road Xiangfang District

department: College of Life Science

institute: Northeast Forestry University

summary: Polydatin (PD) is a natural compound associated with a wide-range of effects in cells and animals, including anticancer activity and lifespan extension capability. Ample research suggests the tumor suppressive effects of PD in hepatocellular carcinoma (HCC); however, the molecular mechanism underlying this activity is unclear. To determine differentially protein-coding expression genes inducted by PD treatment, we used 50 µM of PD and DMSO to treat HepG2 cells for 24 h, extracted the total RNAs, and then employed the RNA-seq approach to analyze the transcript profiles. The obtained dataset consisted of all Poly(A)-containing RNAs, including mRNAs.

overall_design: RNA-seq was constructed in HepG2 cells with Polydatin (PD)) and cells with DMSO treatment

first: Umar

last: Farooq

first: Shah

last: Jehan

first: Guangchao

last: Sui


title: Time-resolved in situ transcriptomics of mouse gastric pit cells during postnatal development reveals distinct features from those observed of the whole stomach

city: Shanghai

first: Ying

last: Wei

address: No.800 Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary:
Whole-organ transcriptomic analyses have emerged as a common method for characterizing developmental transitions in mammalian organs. However, it is unclear if all cell types in an organ follow the whole-organ defined developmental trajectory.
To investigate the developmental process of mouse postnatal gastric pit cells. Here, using laser capture microdissection to obtain in situ transcriptomic data ranging from postnatal week 1 to week 8.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for mouse gastric pit cells ranging from week 1, week 2, week 3, week 4, week 5 and week 8.
Every barcode represent a sample with about 10 cells which were processed with the Single-cell library method (SCRB-seq).  These data have 6 time points and each time point with 4 replicates.

first: Zeqian

last: Xu

first: Daniel

middle: M

last: Czajkowsky

first: Yan

last: Guo


title: Effect of imeglimin on mitochondrial function, AMPK activity and gene expression in hepatocytes

city: Kobe

first: Wataru

last: Ogawa

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

institute: Kobe University Graduate School of Medicine

summary: To further understand the pharmacological properties of imeglimin, we here investigated the effects of imeglimin in hepatocytes and compared those with metformin. We investigated the genes expression in the cultured human hepatoma HepG2 cells by RNA-seq. HepG2 cells were stimulated with 0.25 mM, 3 mM metformin or imeglimin, or 1 mM AICAR, or vehicle alone for 12 h.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells stimulated with metformin, imeglimin, AICAR or vehicle

first: Kaori

last: Hozumi

first: Kenji

last: Sugawara


title: SnRNA Transcriptome analysis reveals key miRNAs and pathways on adipocytes

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Our research is helpful to understand the physiological and pathological level changes caused by Chronic intermittent hypoxia

overall_design: In this study, the control group and the model  group subjected to miRNA sequencing.

first: Duan

last: Yanru


title: Age of the bone marrow dictates clonality of smooth muscle-derived cells in the atherosclerotic plaque [bulk RNA-seq]

first: Rihao

last: Qu

address: 300 George Street

institute: BBS Program, Yale University

summary: Purpose: The goal of this study is to investigate the gene expression in aged (18 month old) and young (3 month old) bone marrow-derived monocytes.     Methods: Bone marrow was harvested by flushing the femurs and tibias of young (3 month old) and aged (18 month old) mice in PBS with 2% fetal bovine serum (FBS) on ice. Cells were isolated from bone marrow by density gradient centrifugation using Lympholyte (Cedarlane, CL0531). After centrifugation at 1300 g for 20 min, bone marrow cells were collected from the interface and washed in Ca2+/Mg2+ - free HBSS. The cells were dissociated to a single-cell suspension by filtering through a 70-µm nylon mesh. For monocyte isolation, a suspension of bone marrow cells was stained with Alexa 700 anti-CD3 (1:100, BioLegend, 100215), PE-Cy7 anti-CD19 (1:100, BioLegend, 115520), FITC anti-CD11b (1:100, BD Pharmingen, 553310) and APC anti-Ly6c antibodies (1:100, BioLegend, 128015) in PBS with 0.5% FBS for 30 min. CD11b+Ly6c+CD3-CD19- monocytes were isolated with a BD FACSAria cell sorter. Total RNA was extracted and subjected to bulk RNA-seq using Illumina HiSeq 2000.    Results: Expression profiles of the transcriptome are compared between bone marrow-derived monocytes isolated from aged (18 month old) and young (3 month old) mice.    Conclusions: Significant differences in the expression levels of genes are noted between the two age groups.

overall_design: Total RNA extracted from FACS-isolated bone marrow-derived monocytes of young (3 month old) and aged (18 month old) mice was subjected to bulk RNA-seq to assess gene expression.

first: I

last: Kabir

first: D

last: Greif


title: Hematopoietic Loss of Y Chromosome Leads to Cardiac Fibrosis and Dysfunction and is Associated with Death due to Heart Failure

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

summary: Hematopoietic mosaic loss of Y chromosome (mLOY) is associated with increased risk of mortality and a variety of age-related diseases in men, but causal and mechanistic relationships have yet to be established. Here it is shown that mice reconstituted with bone marrow cells lacking the Y chromosome display increased mortality and age-related profibrotic pathologies including a progressive decline in cardiac function. Accelerated cardiac dysfunction and fibrosis were also observed in younger mice subjected to a pressure-overload model of heart failure. Bone marrow-derived, cardiac macrophages lacking the Y chromosome exhibited polarization toward a more fibrotic and less inflammatory phenotype. Treatment with a TGFb1  neutralizing antibody led to greater amelioration of heart failure in mice reconstituted with mLOY compared to wild-type bone marrow. Consistent with these data, a prospective study in men revealed that mLOY in blood is associated with an increased risk for cardiovascular disease and heart failure-associated mortality. Together, these results indicate that hematopoietic mLOY contributes to heart failure in men.

overall_design: Cardiac Leukocytes, Control BMT, TAC, scRNAseq and Cardiac Leukocytes, LOY BMT, TAC, scRNAseq

first: Anupreet

last: Kour

first: Hayato

first: Soichi

last: Sano

first: Kenneth

last: Walsh


title: Identification of smRNA-based cell-type markers for the stem cell manufacture system with a statistical scoring function

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: Cell-type biomarkers are useful in stem cell manufacture to monitor cell purification, cell quantity, and quality. However, the study on cell-type marker, specifically for stem cell manufacture, is limited. The emerging questions are which RNA transcripts can serve as biomarkers during stem cell culture, and what method can efficiently and accurately discover these biomarkers. We developed a scoring function system to  identify small RNA (smRNA) biomarkers with RNA-seq data. We applied the method to two data sets, one for extracellular smRNAs and the other for intracellular smRNAs. To get the RNA-seq data from intracellular smRNAs, we cultured four types of cells: human embryo stem cells (H9), neural stem cells (NSC), hESC-derived endothelial cells (EC) and conducted small RNA-seq to their intracellular smRNAs. Using these data, we identified a set of smRNAs as candidates of biomarkers for different types of cells.

overall_design: gene expression profiling analysis of small-RNA-seq data for  H9, EC, and NSC.

first: Yuguo

last: Lei

first: Yu

last: Shi

first: Haishuang

last: Lin


title: Single cell RNA-seq to delineate the gene expression of bone marrow cells

city: New Haven

summary: Purpose: The goal of this study is to investigate the role of integrin beta3 (Itgb3) deficiency on the gene expression of bone marrow cells.    Methods: Bone marrow was harvested by flushing the femurs and tibias of Apoe(-/-), Itgb3(+/+) and Apoe(-/-), Itgb3(-/-) mice in PBS with 2% fetal bovine serum on ice. Cells were isolated from bone marrow by density gradient centrifugation using Lympholyte (Cedarlane, CL0531). After centrifugation at 1300 g for 20 min, bone marrow cells were collected from the interface and washed in Ca2+/Mg2+ - free HBSS and dissociated to a single-cell suspension by filtering through a 70-µm nylon mesh. The cells were then subjected to 10X Genomics single cell 3’ RNA-seq libraries construction and sequencing. scRNA-seq data was processed with Cell Ranger v 3.1.0. Reads were aligned to a modified version of the mouse transcriptome mm10. The top cell barcodes selected by Cell Ranger were utilized for downstream analysis.    Results: Expression profiles of the transcriptome are compared between cell types isolated from the bone marrow of Apoe(-/-), Itgb3(+/+) and Apoe(-/-), Itgb3(-/-) mice.    Conclusions: Significant differences in the expression profile of genes are present in bone marrow cells of Apoe(-/-), Itgb3(+/+) and Apoe(-/-), Itgb3(-/-) genotypes.

overall_design: Bone marrow cells were harvested from Apoe(-/-), Itgb3(+/+) and Apoe(-/-), Itgb3(-/-) mice and subjected to 10X Genomics single cell 3’ RNA-seq library construction and sequencing. Identified cell clusters were annotated based on classical cell type-specific markers.


title: Non-toxic direct targeted therapy for MLL-fusion driven leukemias

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: Improving the poor prognosis of infant leukemias remains an unmet clinical need. This disease is a prototypical fusion oncoprotein-driven pediatric cancer, with MLL (KMT2A)-fusions present in most cases. Direct targeting of these driving oncoproteins represents a unique therapeutic opportunity. This rationale led us to initiate a drug screening with the aim of discovering drugs that can block MLL-fusion oncoproteins.   A screen for inhibition of MLL-fusion proteins was developed that overcomes the traditional limitations of targeting transcription factors. This luciferase reporter-based screen, together with a secondary western blot screen, was used to prioritize compounds. We characterized the lead compound, Disulfiram, based on its efficient ablation of MLL fusion proteins. The consequences of drug-induced MLL-fusion inhibition was confirmed by cell proliferation, colony formation, apoptosis assays, RT-qPCR, in vivo assays, RNA-seq and CHIP-qPCR and CHIP-seq analysis. All statistical tests were two-sided.  Drug-induced inhibition of MLL-fusion proteins by Disulfiram resulted in a specific block of colony formation in MLL-rearranged cells in vitro, induced differentiation and impeded leukemia progression in vivo. Mechanistically, Disulfiram abrogates MLL-fusion protein binding to DNA, resulting in epigenetic changes and down-regulation of leukemic programs setup by the MLL-fusion protein.    Disulfiram can directly inhibit MLL-fusion proteins and demonstrates antitumor activity both in vitro and in vivo, providing, to our knowledge, the first evidence for a therapy that directly target the initiating oncogenic MLL-fusion protein.

overall_design: RNA sequencing of THP-1 cells untreated or treated with DSF, combined with ChIP-seq data of MLL, H3K4me3 and H3K27ac

first: Sandra

last: Cantilena

first: Luca

last: Gasparoli

first: Deepali

last: Pal

first: Olaf

last: Heidenreich

first: Jan-Henning

last: Klusmann

middle: H

first: Alexandre

last: Faille

first: Alan

last: Warren

first: Mawar

last: Karsa

first: Ruby

last: Pandher

first: Klaartje

last: Somers

first: Owen

last: Williams

first: Jasper

last: de Boer


title: Dietary long-chain omega 3 fatty acids modify sphingolipid metabolism to facilitate asthmatic airway hyperreactivity

first: Simone

last: Caielli

address: 413 E 69th Street

department: Department of Pediatrics

institute: Weill Cornell Medicine

summary: We report the effects of dietary n-3 polyunsaturated fatty acids (PUFAs) on sphingolipid metabolism and airway reactivity in the lung. Mice were fed a n3-PUFA enriched fishoil diet or an isocaloric control coconut oil-enriched diet (CO) for 8 weeks. The n-3 PUFA diet affected pulmonary sphingolipid metabolism, and airway reactivity, independent of inflammation or allergic sensitization. These findings support a role for pulmonary sphingolipid homeostasis in asthma and could have implications for the use of n-3 PUFA dietary supplements in asthma.

overall_design: Female C57Bl/6 mice were fed a high-fat, semipurified diet (total 19% fat, 0.2% cholesterol, w/w) enriched in either n-3 PUFAs (91% menhaden fish oil and 9% corn oil; Harlan Teklad; TD. 07500; "FO") or saturated fat (SAT; 78% saturated fat from coconut oil, 13% monounsaturated fat from olive oil, and 9% polyunsaturated fat from corn oil; Harlan Teklad; TD. 08081; "CO") for 8 weeks. Weights and food consumption were checked weekly. After 8 weeks the animals underwent pulmonary function testing (airway reactivity), the lungs were perfused with PBS and RNA was extracted and RNA sequencing performed.

first: Stefan

last: Worgall

first: Emily

last: Wassermann

first: Uthra

last: Balaji

first: Jinghua

last: Gu


title: Age of the bone marrow dictates clonality of smooth muscle-derived cells in the atherosclerotic plaque

first: Rihao

last: Qu

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

overall_design: Refer to individual Series


title: RNA-seq of single cholangiocyte-derived organoids reveals high organoid-to-organoid variability

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

country: Germany

institute: Max Planck Institute

summary: Organoids have been established from the majority of tissue resident stem cells. In recent years, several reports hinted at intraculture organoid variability, but a systematic analysis of such a heterogeneity has not been performed before. Here, we used RNA-seq of individual organoids to address this question. Importantly, we find that batch-to-batch variation is very low, even when prepared by different researchers. On the other hand, there is organoid-to-organoid variability within a culture. Using differential gene expression, we did not identify specific pathways that drive this variability, pointing towards possible effects of the microenvironment within the culture condition.

overall_design:
Methods: Picking single organoids followed by bulk-RNA-seq with UMI libraries to assess heterogeneity. The impact of microenvironment (culturing method) on gene expression of organoid cultures by RNA-seq.The impact of passaging in gene expression.
Dataset 1: RNA-seq data of 35 cholangiocyte-derived organoids from liver tissue of four 3-months-old mice, only one liver for each set, Set 1: 8, Set 2: 10, Set 3: 5 , Set 4: 12 Dataset 2: RNA-seq data of three 3-months-old cholangiocyte-derived organoid from liver tissue cultures, generated by pooling digested material from different animals each (Pool A = 2 mice; Pool B = 4 mice; Pool C = 3 mice), cultured in either matrigel domes or shaking suspension (in total 6 samples). Dataset 3: RNAseq of 3 organoid sets (1, 3 and 4) in passage 4 and the same organoid sets in passage 11 (in total 6 samples- each sample consists of 2 technical replicates).

first: Kristin

last: Gehling

first: Swati

last: Parekh

first: Farina

last: Schneider

first: Marcel

last: Kirchner

first: Vangelis

last: Kondylis

first: Chrysa

last: Nikopoulou


title: Transcriptome analysis of Litchi chinensis under inoculated with P.litchii treatments

city: Guangzhou

first: Liu

last: Hailun

address: Tianhe District

institute: Guangdong Academy of Agricultural Sciences

summary: To investigate the potential mechanism of disease resistance in Litchi, a genome-wide transcriptomic analysis was carried out using 'Guiwei' and 'Yurong1' Litchi under inoculated with P.litchii treatments.

overall_design: The gene expression profiling analysis using data obtained from RNA-seq of 'Guiwei' and 'Yurong1'. The treated leaves were collected at 24 hpi. RNA sequencing was performed by the Allwegene Technologies Corporation (Beijing, China) using an Illumina NovaSeq platform.

first: Hailun

last: Liu


title: Transcriptional heterogeneity and cell cycle regulation as a central determinant of Primitive Endoderm priming

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary: During embryonic development cells acquire identity at the same time as they are proliferating, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to rates of cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single cell RNAseq in the contexts of self-renewal, priming and differentiation of embryonic stem cells (ESCs) towards the Primitive Endoderm lineage (PrE). Since ESCs are derived from the Inner Cell Mass of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing subfractions that are primed for either of the two ICM lineages, Epiblast and PrE. These subfractions represent dynamic states that can readily interconvert in culture, and the PrE subfraction is functionally primed for endoderm differentiation. Here we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naïve ESC culture conditions promote Epiblast-like expansion and PrE differentiation stimulates the selective proliferation of PrE-primed cells. In endoderm differentiation, we find that this change is accompanied by a counter-intuitive increase in G1 length that also appears replicated in vivo. While FGF/ERK signalling is a known key regulator of ESC and PrE differentiation, we find it is not just responsible for ESC heterogeneity, but also cell cycle synchronisation, required for the inheritance of similar cell cycles between sisters and cousins. Taken together, our results point to a tightly regulated relationship between transcriptional heterogeneity and cell cycle regulation in the context of lineage priming, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage specific fashion while allowing plasticity during early determination.

overall_design: The in vitro study contains double reported Sox2-GFP and Hhex-mCherry cell line sequenced in 2 batches.

first: Marta

last: Perera

first: Silas

last: Nissen

first: Martin

last: Proks

first: Sara

last: Pozzi

first: Rita

last: Monteiro

first: Ala

last: Trusina

first: Joshua


title: FGFR inhibition reverses resistance to endocrine therapy by reducing expression of EMT-related genes

city: Oslo

first: Torbjørn

middle: Amundsen

last: Lien

state: OSLO

address: Ullernchausseen 64

department: Department of Cancer Genetics

country: Norway

institute: Institute for Cancer Research

summary:
Background: Up to 40% of patients with estrogen receptor positive (ER+) breast cancer experience treatment resistance and disease recurrence, often caused by the upregulation of growth factor receptors. Understanding the mechanisms of resistance, and the identification of novel therapeutic targets is, therefore, of vital importance if breast cancer prognosis is to be further improved. Fibroblast growth factor receptor 1 (FGFR1) is a potential driver of endocrine resistance; however, clinically successful attempts at targeting FGFR1 activity in breast cancer are rare and may result from an inability to correctly identify patients that could benefit from such treatment. The identification of additional genes associated with an FGFR1-mediated mechanism of resistance will provide a more precise classification scheme for FGFR1-dependency in breast cancer.
Methods: Live cell imaging and RNA sequencing of ER+ breast cancer cell lines (CAMA1, T47D, tamoxifen resistant T47D) were used to investigate FGFR1-dependency in breast cancer, mechanisms of endocrine resistance and the effects of treatment with tamoxifen and erdafitinib. An FGFR1-amplified ER+ breast cancer patient-derived xenograft (PDX) model was used to assess the effects of targeting FGFR1 in vivo. Gene expression analysis of human breast cancer from The Cancer Genome Atlas (TCGA) was used for clinical validation.
Results: We evaluated the effects of targeting FGFR1 in ER+/HER2- breast cancer with aberrant FGFR1 amplification and/or overexpression. We found that the FGFR tyrosine kinase inhibitor (TKI) erdafitinib inhibited cell proliferation of FGFR1-amplified CAMA1 cells in vitro. Additionally, erdafitinib significantly enhanced the anti-proliferative effect of 4-hydroxytamoxifen (4-OHT) and its anti-tumor effect was also demonstrated in vivo. Further, we demonstrated that the proliferation of FGFR1-overexpressing tamoxifen-resistant T47D (TR-T47D) cells is dependent on FGFR1 activity. Moreover, these TR-T47D cells are re-sensitized to tamoxifen upon treatment with erdafitinib. Finally, we found that upregulation of genes related to epithelial-mesenchymal-transition (EMT) correlates with FGFR1 overexpression, and is reversed by FGFR inhibition.
Conclusions: In this study we demonstrated that targeting FGFR1 in ER+/HER2- breast cancer with aberrant FGFR1 activity has the potential to inhibit tumor growth and to re-sensitize resistant tumors to tamoxifen. Furthermore, we identified a functional relationship between EMT, FGFR activity and endocrine resistance in breast tumorigenesis.

overall_design: Whole transcriptome sequencing of parental T47D cells (PAR01), and 4-hydroxytamoxifen resistant T47D cells (TR01). PAR01 cells were only treated with vehicle. TR01 cells were treated with the following four conditions: vehicle, erdafitinib, 4-OHT, and 4-OHT + erdaftinib. RNA was isolated from 3 biological replicates within each treatment condition, giving a total of 15 samples.

first: Anne-Marthe

last: Wium

first: Helga

last: Bergholtz

first: Daniel

last: Nebdal

first: Tonje

middle: G

first: Ellen

last: Haugsten

first: Jens

last: Norum

first: Jørgen

last: Wesche

first: Antoni

last: Hurtado

first: Therese

last: Sørlie


title: Knock-outs of TUT7 and 3’hExo show that they cooperate in histone mRNA maintenance and degradation

city: Chapel Hill

first: William

last: Marzluff

state: NC

address: 1 Medical Drive

department: Biology

institute: UNC Chapel Hill

summary: Metazoan histone mRNAs are the only cellular eucaryotic mRNAs that are not polyadenylated, ending instead in a conserved stemloop. SLBP is bound to the 3’ end of histone mRNA and is required for translation of histone mRNA. Their expression is tightly cell-cycle regulated. A major regulatory step is rapid degradation of histone mRNA at the end of S-phase or when DNA synthesis is inhibited in S-phase. 3’hExo, a 3’ to 5’ exonuclease, binds to the SLBP/SL complex, and trims histone mRNA to 3 nts after the stemloop.  Together with a terminal uridyl transferase, 3’hExo maintains the length of the histone mRNA during S-phase. 3’hExo is essential for initiating histone mRNA degradation on polyribosomes, initiating degradation into the 3’ side of the stemloop.  There is extensive uridylation of degradation intermediates in the 3’ side of the stem when histone mRNA is degraded.  Here we knocked out TUT7 and 3’hExo and we show that both modification of histone mRNA during S-phase and degradation of histone mRNA involve the interaction of 3’hExo, and a specific TUTase, TENT3B (TUT7, CHHC6).  Knockout of 3’hExo prevents initiation of 3’ to 5’ degradation, stabilizing histone mRNA, while knockout of TUT7 prevents uridylation of the mRNA degradation intermediates slowing the rate of degradation.  In synchronized 3’hExo KO cells, histone mRNA degradation is delayed but the histone mRNA is degraded prior to mitosis by a different pathway.

overall_design: CRISPR Cas9 Knock out and Rescue of TUT7 and 3'hExo in HCT116 Cells, with histone specific RNA sequencing to study the 3' termini via EnD-Seq

first: Christopher

last: Holmquist

first: Wenxia

last: He

last: Meganck


title: Arginine-derived polyketides are ubiquitous signals shaping cross-kingdom microbial interactions

city: Jena

first: Amelia

middle: E

last: Barber

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Fungal Informatics

institute: Leibniz-HKI

summary: To investigate the effect of bldA deletion on gene expression in Streptomyces iranensis with respect to secondary metabolite cluster genes

overall_design: We compared gene expression of S. iranensis wildtype and ΔbldA using data obtained from RNA-seq of samples pooled from three replicates, respectively, after 48 h of cultivation in TSB medium.

first: Volker

last: Schroeckh


title: ATAC-seq of bone marrow neutrophil treated PGE2 or Vehicle

city: La Jolla

first: Ye Ji

last: Shin

address: 9500 Gilman Dr

institute: University of California, San Diego

summary:
Purpose: Investigate the gene accessibility change of neutrophils from PGE2 stimulation and identify the posibility for PGE2 could induce lung neutrophil like characteristics.
Methods: Isolated bone marrow neutrophils with Percoll gradient are treated with 10 μM of PGE2 for 24 hours.
Conclusion: Chromatin accessibility for the genes that were upregulated in lung neutrophils and PGE2 treated neutrophils were increased, so PGE2 could induce lung neutrophil like characteristics with change chromatin accessibility.

overall_design: ATAC-seq analysis of neutrophils isolated bone marrow were treated with 10 μM PGE2 or vehicle.  3 biological replicates.

first: Geon

last: Bae

first: Ye

middle: J

first: Hong

last: Kim

first: Yoe


title: RNA-seq of bone marrow neutrophil treated PGE2 or Vehicle

summary:
Purpose: Investigate the neutrophils could exspress different mRNA de novo from PGE2 stimulation.
Methods: Isolated bone marrow neutrophils with Percoll gradient are treated with 10 μM of PGE2 for 24 hours.
Results: Qualified sequence reads per sample to the mouse genome (mm10) with Bowtie2 or STAR were processed with StringTie and identified genes.
Conclusion : 1,359 genes were significantly different in PGE2 treated bone marrow neutrophils from vehicle treated ones.

overall_design: RNA-seq analysis of neutrophils isolated from bone marrow treated 10μM PGE2 or DMSO vehicle for 24 hours.  3 biological replicates.

middle: S


title: Comparitive genomics of multiple backcross mouse populations identifies Sgcg as a novel potential obesity-modifier gene

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary: To nominate novel disease genes for obesity and type 2 diabetes (T2D) we recently generated two mouse backcross populations of obese and T2D- susceptible New Zealand Obese (NZO/HI) mice with the two lean mouse strains 129P2/OlaHsd and C3HeB/FeJ. Comparative linkage analysis of our two female backcross populations identified seven novel body fat-associated quantitative trait loci (QTL). Only the locus Nbw14 (NZO body weight on chromosome 14) showed linkage to obesity-related traits in both backcross populations, indicating that the causal gene variant is likely specific for the NZO strain as NZO allele carriers in both crosses displayed elevated body weight and fat mass. To nominate candidate genes for Nbw14, we used a combined approach of gene expression and haplotype analysis to filter for NZO-specific gene variants in gonadal white adipose tissue (gWAT), which appeared to be the most likely target tissue. Only two genes, Arl11 and Sgcg, fulfilled our criteria. In addition, expression QTL analysis revealed cis-signals for both genes within in the Nbw14 locus. Retroviral overexpression of Sgcg in 3T3-L1 adipocytes resulted in increased glucose uptake. In humans, mRNA levels of Sgcg correlated with BMI and body weight exclusively in diabetic subjects, suggesting that Sgcg represents a novel marker for metabolically unhealthy obesity in humans. In conclusion, our comparative-cross analysis could substantially improve the mapping resolution of the obesity locus Nbw14. Future studies will shine light on the mechanism by which Sgcg protects from the development of obesity.

overall_design: We used microarrays to enable the detection of candidate genes in the critical region in a combined approach of haplotype- and gene expression analysis to search for obesity related  gene variants in the white adipose tissue.

first: Tanja

last: Kuhn

first: Sandra

last: Lebek

first: Hadi

last: Al-Hasani

first: Alexandra

last: Chadt


title: RNA-seq of tissue neutrophil

summary:
Purpose: Neutrophils in lung at steady states seems have different characteristics from blood neutrophils even both of them located intravascular regions. The goals of this study are to identify what make lung neutrophils different from other neutrophils from bone marrow and peripheral blood.
Methods: Sorted CD11b+ Ly6G+ cells from bone marrow, blood, and lungs of C57BL/6 were investigated with RNAseq using Illumina.
Results: Qualified sequence reads per sample to the mouse genome (mm10) with Bowtie2 or STAR were processed with StringTie and identified genes. Neutrophil mRNA profiles from bone marrow, blood and lung of 8 weeks old wild type C57BL/6.
Conclusion : 2,032 genes were significantly different in lung neutrophils compared to blood neutrophils.

overall_design: RNA-seq analysis of neutrophil isolated from 3 different tissues : Bone marrow, Blood, Lung  3 biological replicates.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ocular Adnexal B-cell Lymphoma Transcriptomes (Control Group)

first: Jiahao

last: Shi

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District,

department: Department of Ophthalmology

institute: Shanghai 9th Peoples Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to describe NGS-derived  transcriptome profiling (RNA-seq)  of ocular adnexal B-cell lymphomas (OABLs). Gene expression profiling of RNA was performed on OAL samples to identify  pathway alterations and expression changes affected by clinical traits

overall_design: mRNA profiles of 8 idiopathic orbital inflammation, 3 reactive lymphoid hyperplasia, and 6 aesthetic orbital plastic surgery specimens were generated by deep sequencing using Illumina Novaseq 6000 according to the manufacturer's direction. RNA was extracted from cryopreserved lymphoma tumor specimens. The sequence reads that passed quality filters were analyzed at the transcript isoform level. These profiles were defined as controls to identify gene expression profile of OABLs.

first: Tianyu

last: Zhu

first: Renbing

last: Jia

first: Yixiong

last: Zhou

first: Xianqun

last: Fan


title: Effects of oxysterol Oxy186 and Oxy210 on A549 xenograft tumor growth

city: Bethesda

first: Ying

last: Zhang

state: Maryland

address: 37 Convent Dr., Bldg.37, Rm.2056

department: LCMB/CCR

institute: National Cancer Institute, NIH

summary: To examine the efficacy of oxysterols in inhibiting tumor growth in vivo, we tested Oxy186 and Oxy210 in subcutaneous xenograft tumor models constructed with A549 cells in nude mice.  After the tumor size reached an average of ~100 mm3, the compounds were administered daily via oral gavage at 50 mg/kg. We found that Oxy186 started to inhibit tumor growth at day 8, and significantly reduced the tumor volume from day 11 to day18 of treatment, compared to that of vehicle control.  Surprisingly, Oxy210 did not show such inhibitory effect.

overall_design: Total RNA from control and Oxy186-treated or Oxy210-treated xenografts were extracted, libraries were prepared with NEBNext UltraTM II RNA Librart Prep Kit from RNAs with RIN>8.0, and RNAseq were performed using Illumina Novaseq 6000 (Novogene).

first: Ting

last: Chen


title: Histone methyltransferases SlSDG33 and SlSDG34 mediate organ-specific nitrogen responses in tomato

city: New York

last: Li

address: 12 Waverly Place

institute: New York University

summary: Histone posttranslational modifications play an important role in regulating plant responses to environmental cues, however, few studies have focused on the role of histone lysine methylation in regulating plant responses to nutrient availability, especially in agriculturally important species. Here, we describe the functions of two paralogous histone lysine methyltransferases, SET Domain Group 33 (SDG33) and SDG34, in mediating nitrogen responses in tomato through genetic and transcriptome analyses. Our transcriptome analysis comparing  tomato lines demonstrated that SDG33 and SDG34 have overlapping yet distinctly regulated targets in tomato. Importantly, both SDG33 and SDG34 mediate gene regulation in response to changes in nitrogen level, with organ specificity. In roots, SDG33 and SDG34 are required for the regulation of a gene network that includes nitrate transporter NRT1.1, as well as auxin responsive SAUR genes. Consistently, mutations in sdg33 or sdg34 abolish the root growth response to N. In shoots, SDG33 and SDG34 affect the expression of photosynthesis genes and chlorophyll a/b ratio in response to nitrogen. Overall, we show that SDG33 and SDG34 regulate nitrogen responsive gene expression and hence physiological responses to nitrogen nutrients in an organ specific manner in the roots and shoots.

overall_design: This study includes 36 RNA-seq samples, including three genotypes (WT, sdg33, sdg 34) x two conditions (-N and +N) x two tissues (shoots and roots), in three biological replicates

first: Carol

last: Bvindi

first: Liang

last: Tang

first: Sanghun

last: Lee

first: Tesfaye

last: Mengiste


title: CSF1R-mediated myeloid cell depletion prolongs lifespan but aggravates distinct motor symptoms in a model of multiple system atrophy

first: Johannes

middle: Carolus Magnus

last: Schlachetzki

state: CA

address: 9500 Gilman Drive  #0651

department: Cellular and Molecular Medicine

institute: UCSD

summary: As the resident macrophages of the CNS, microglia fulfill manifold functions important for brain development and homeostasis. In the context of neurodegenerative diseases, they are crucial for de- and regenerative as well as immunological processes. The discovery of distinct activation patterns and increased phagocytosis indicated a damaging role of microglia in multiple system atrophy. This devastating, rapidly progressing atypical parkinsonian disorder is characterized by alpha-synuclein accumulation in the cytoplasm of oligodendrocytes. Alpha-synuclein aggregates have been related to myelin loss, severe neurodegeneration, and motor deficits accompanied by a region-specific myeloid immune response.  Analyzing the gene expression profile of microglia in a mouse model of multiple system atrophy, MBP29-hα-syn mice, we identified a disease-assoctiated expression profile with an upregulation of the colony-stimulating factor 1 (Csf1). Thus, we hypothesized that targeting the CSF1 receptor using the small-molecule inhibitor PLX5622 reduces myeloid cells and thereby modifies the disease progression and neuropathological phenotype in this mouse model. After validation of a widespread depletion of myeloid cells after CSF1R inhibition, we consequently analyzed the survival, motor functions, neuropathological characteristics, and gene expression of affected brain regions in MBP29-hα-syn mice. Intriguingly, we identified a two-faced outcome comprising (1) an improved survival rate (24%) accompanied by delayed onset of neurological symptoms in contrast to (2) severely impaired motor functions in beam walking, pole test, and RotaRod of PLX5622-treated MBP29-hα-syn mice. Gene expression analysis revealed that PLX5622 reversed myeloid cell activation, however, predominantly reduced the expression of genes related to transsynaptic signaling and signal release. While these transcriptional changes were accompanied by a reduction of dopaminergic neurons in the substantia nigra pars compacta (19%) of PLX5622-treated MBP29-hα-syn mice, an increase of the striatal neuritic density was observed without changes in alpha-synuclein levels or myelin lipids in the forebrain.  Together, our findings provide insight into the complex role of myeloid cell depletion in multiple system atrophy by demonstrating a two-faced outcome on the behavioral and neuronal phenotype of MBP29-hα-syn mice. Therefore, it is important to carefully balance the beneficial and adversive effects of CSF1R inhibition in different models of neurodegenerative disorders prior to clinical translation.

overall_design: RNA-seq from bulk brain tissue (Corpus Callosum, Cortex, Striatum) and Microglia from control and MBP29-haSyn mice. Mice received placebo or PLX5622, a CSF1R inhibitor.

first: Kristina

last: Battis

first: Jazmin

last: Florio

first: Michael

last: Mante

first: Addison

last: Lana

first: Isabel

last: Naumann

first: Isidoro

last: Cobo

first: Bethany

last: Fixsen

first: Ha

last: Kim

first: Eliezer

last: Masliah

first: Christopher

last: Glass

middle: C

first: Robert

last: Rissman

first: Jürgen

last: Winkler

first: Alana

last: Hoffmann


title: Intracellular free zinc mediates compressive stress-induced mechanotransduction in pancreatic cancer

city: Sapporo

first: Tatsuya

last: Nihei

state: Hokkaido

address: N10-W8, Kita-ku

institute: Hokkaido university

summary:
In this study, Nihei et al. show that unknown function of the intracellular free zinc in mechanical compressive stress-induced signaling and altered gene expression in pancreatic cancer cells, provide novel perspectives on zinc as a signal transducer and therapeutic target.
We explored the roles of compressive stress in pancreatic cancer progression by investigating the changes in gene expression induced by it using microarray.

overall_design: We performed microarray analysis on the AsPC-1 cells that were either uncompressed or subjected to compressive stress of 2.9 mmHg (compressed) for 24 h. After compression or uncompression, RNA were extracted. Gene expression profiling with the GeneChip Human Gene 2.0 ST expression array.

first: Seiichiro

last: Ishihara

first: Atsushi

last: Enomoto

first: Hisashi

last: Haga


title: Chemohormonal Therapy Remodels Prostate Cancer Immune Microenvironment and Enhances Checkpoint Inhibitor-based immunotherapy

city: Shanghai

first: Qi

last: Wang

address: 160 Pujian Road

institute: Shanghai Jiao Tong University

summary: Checkpoint blockade immunotherapy is a promising strategy in cancer treatment, depending on a favorable preexisting tumor immune microenvironment. However, prostate cancer is usually considered as an immune “cold” tumor with the poor immunogenic response and low density of tumor-infiltrating immune cells. This research uses samples from prostate cancer patients showing that docetaxel-based chemohormonal therapy reprograms the immune microenvironment and increases tumor-infiltrating T cells. Mechanistically, docetaxel treatment activates the cGAS/STING pathway and induces the type I interferon signaling, which may boost T cell-mediated immune response. In a murine prostate cancer model, chemohormonal therapy sensitizes tumor-bearing mice to PD1-blockade therapy. These findings demonstrate that docetaxel-based chemohormonal therapy activates prostate cancer immunogenicity and acts cooperatively with anti-PD-1 checkpoint blockade, providing a combination immunotherapy strategy that would lead to better therapeutic benefit for prostate cancer.

overall_design: mRNA profiles of 11 paired pre- and post-chemohormonal therapy prostate cancer samples

first: Zehua

last: Ma

first: Weiwei

last: Zhang

first: Zhixiang

last: Xin

first: Yiyi

last: Ji

first: Lei

last: Chen

first: Kai

last: Shen

first: Jiahua

last: Pan

first: Wei

last: Xue


title: scRNA-Seq and snRNA-Seq in human adipose tissue

city: Orlando

first: Lauren

last: Sparks

state: Florida

address: 301 E Princeton St, 301

institute: AdventHealth

summary: From subcutaneous adipsoe tissue from 2 particpants we performed scRNA-seq on the stromal vascular fraction, snRNA-seq on isolated adipocytes and snRNA-seq on frozen adipose tissue. We performed clustering analysis, differential gene expression analysis and over-representation analysis to decipher the different cell populations detectable with each technique. The SVF fraction was able to show more diverse immune cell populations. Whilst the snRNA-seq frozen adipose tissue showed diverse clusters of adipocytes that was not observable from a snRNA-Seq fraction

overall_design: Subcutaneous adipose tissue from two participants subjected to scRNA-seq on the stromal vascular fraction, snRNA-seq on isolated adipocytes and snRNA-seq on frozen adipose tissue

first: L

first: S

middle: R

last: Smith


title: RNAseq: Elacestrant demonstrates strong anti-estrogenic activity in PDX models of estrogen- receptor positive endocrine-resistant and fulvestrant-resistant breast cancer

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

country: United Kingdom

institute: Institute of Cancer Research

summary: We carried out a comparative study of the orally bioavailable investigational SERD elacestrant, versus fulvestrant, in models of endocrine sensitive and resistant BC harbouring varying genetic backgrounds. Both drugs showed comparable effects on tumour growth of ER+ patient-derived xenograft models harbouring several ESR1 mutations and elacestrant showed activity after acquired resistance to fulvestrant. Treatment with either drug showed similar impact on ER-cistrome, ER- interactome and suppression of estrogen-regulated genes, confirming the anti-estrogenic activity of elacestrant.

overall_design: overall design includes 5 biological replicates of cell lines treated with estradiol (e2), e2 + elacestrant and e2 + fulvestrant

first: Lesley-Ann

last: Martin


title: Elacestrant demonstrates strong anti-estrogenic activity in PDX models of estrogen- receptor positive endocrine-resistant and fulvestrant-resistant breast cancer

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

overall_design: Refer to individual Series


title: Citric acid, an ovarian cancer metabolite, induces pyroptosis via caspase-4/TXNIP-NLRP3-GSDMD pathway in ovarian cancer

city: nanjing

first: xiaogang

last: wang

address: Hankou road 22

institute: nanjing university

summary: Malignant tumors display profound changes in cellular metabolism, yet how these altered metabolites affect the development and growth of tumors is not fully understood. Here, we used metabolomics to analyze the metabolic profile differences in ovarian cancer, and found that citric acid (CA) is the most significantly downregulated metabolite. Recently, CA has been reported to inhibit the growth of a variety of tumor cells, but whether it is involved in pyroptosis of ovarian cancer and its potential molecular mechanisms still remains to be further investigated. Here, we demonstrated that CA inhibits the growth of ovarian cancer cells in a dose-dependent manner. RNA-seq analysis revealed that CA significantly promoted the expression of thioredoxin interacting protein (TXNIP) and caspase-4 (CASP4). Morphologic examination by transmission electron microscopy indicated that CA-treated ovarian cancer cells exhibited typical pyroptosis characteristics. Further mechanistic analyses showed that CA facilitates pyroptosis via CASP4/TXNIP-NLRP3-Gesdermin-d (GSDMD) pathway in ovarian cancer. This study elucidated that CA induces ovarian cancer cell death through classical and non-classical pyroptosis pathways, which may be beneficial as an ovarian cancer therapy.

overall_design:
We performed RNA-seq for A2780 cells with 8mM citric acid (CA) treatment. CA treatment resulted in 899 DEGs, including 585 up-regulated genes and 314 down-regulated genes.
CTL-1, CTL-2, CTL-3, CA-1, CA-2,CA-3
[contributor] LC-BIO TECHNOLOGIES


title: ChIP-seq: Elacestrant demonstrates strong anti-estrogenic activity in PDX models of estrogen- receptor positive endocrine-resistant and fulvestrant-resistant breast cancer

overall_design: overall design includes 2 biological replicates of cell lines treated with estradiol (e2), e2 + elacestrant and e2 + fulvestrant


title: The major urinary protein gene cluster knockout mouse as a novel model for translational metabolism research [RNAseq]

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

summary: Scientific evidence suggests that not only murine scent communication is regulated by major urinary proteins, but that their expression may also vary in response to metabolism via a yet unknown mechanism. Major urinary proteins are expressed mainly in the liver, showing a sexually dimorphic pattern with substantially higher expression in males. Here, we investigate the metabolic implications of a major urinary protein knockout in twelve-week-old male and female C57BL/6N mice during ad libitum feeding. Despite both sexes of major urinary protein knockout mice displayed numerically increased body weight and visceral adipose tissue proportions compared to sex-matched wildtype mice, the main genotype-specific metabolic differences were observed exclusively in males. Male major urinary protein knockout mice exhibited plasma and hepatic lipid accumulation accompanied by a hepatic transcriptome indicating an activation of lipogenesis. These findings match the higher major urinary protein expression in male compared to female wildtype mice, suggesting a more distinct reduction in energy requirements in male compared to female major urinary protein knockout mice. The observed sex-specific anabolic phenotype confirms a role of major urinary protein in metabolism and, since major urinary proteins are not expressed in humans, suggests the major urinary protein knockout mouse as a potential alternative model for translational metabolism research which needs to be further elucidated.

overall_design: Differential gene expression analysis in male and female major urinary protein knockout mice and their wildtype littermates

first: Sarah

last: Greve

first: Ferdinand

last: von Meyenn

first: Katrin

last: Giller


title: A Minimal Subset of Seven Genes Associated with Tumor Hepatocyte Differentiation Predicts a Poor Prognosis in Human Hepatocellular Carcinoma

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary:
An integrative transcriptomics analysis was performed to evaluate the clinical relevance of genes associated with hepatocyte differentiation in human hepatocellular carcinoma (HCC). The well-established HepaRG cell line model was used to define a gene expression signature reflecting the status of tumor hepatocyte differentiation. This signature was able to stratify HCC patients into clinically relevant molecular subtypes. Then, a minimal subset of 7 differentiation-associated genes was identified to predict a poor prognosis in several cancer datasets.
Hepatocellular carcinoma (HCC) is a deadly cancer worldwide as a result of a frequent late diagnosis which limits the therapeutic options. Tumor progression is correlated with a dedifferentiation of hepatocytes, the main parenchymal cells in the liver. Here, we hypothesized that the level of expression of genes reflecting the differentiation status of tumor hepatocytes could be clinically relevant in defining subsets of patients with variable clinical outcomes. To test this hypothesis, an integrative transcriptomic approach was used to stratify a cohort of 139 HCC patients based on a gene expression signature established using a well-controlled in vitro model of tumor hepatocyte differentiation in HepaRG cell line. First, we validated the HepaRG model by identifying a robust gene expression signature associated with hepatocyte differentiation and liver metabolism. This signature was able to distinguish specific developmental stages in mice. More importantly, the signature identified a subset of human HCC associated with a poor prognosis and cancer stem cell features. By using an independent HCC dataset (TCGA), a minimal subset of 7 differentiation-related genes was shown to predict a reduced overall survival, not only in patients with HCC but also in other types of cancers (e.g. kidney, pancreas, skin). In conclusion, the study demonstrates that genes reflecting the differentiation status of tumor hepatocytes are clinically relevant for predicting the prognosis of HCC patients.

overall_design: Gene expression profiling was performed to identify genes significantly differentially expressed between differentiated (n=3) and progenitor (n=3) HepaRG cells. Briefly, HepaRG cells were grown in William's E medium supplemented with 10% FBS, 100 U/mL penicillin, 100 mg/mL streptomycin, 5 mg/mL insulin, and 50 mmol/L hydrocortisone hemisuccinate. Differentiation of HepaRG from progenitors to mature well-differentiated hepatocytes was achieved in 4 weeks by culturing the cells in the supplemented medium in presence of 2% dimethyl sulfoxide (DMSO) for the last 2 weeks.


title: The major urinary protein gene cluster knockout mouse as a novel model for translational metabolism research

type: Methylation profiling by high throughput sequencing


title: The major urinary protein gene cluster knockout mouse as a novel model for translational metabolism research [RRBS]

overall_design: Differential methylation analysis in male and female major urinary protein knockout mice and their wildtype littermates


title: Transcriptome Array of IECs isolated from VEH/CBD treated EAE

city: COLUMBIA

first: Nicholas

last: Dopkins

state: SC

address: 1825 Saint Julian Pl 18A

institute: University of South Carolina

summary: The goal of this project was to define the changes observed in the intestinal IECs of EAE mice treated with CBD vs VEH

overall_design: 10 samples per group, grouped into 2 arrays of 5 biological replicates per group

first: Mitzi

last: Nagarkatti


title: microRNA-6126 downregulates NTCP expression through decreasing stability of its messenger RNA in hepatocyte

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: miR-6126 downregulated expression level of sodium taurocholate cotransporting polypeptide (NTCP), a host cell receptor required for hepatitis B virus (HBV) entry.

overall_design: The experiment was tetraplicated; one was transfected by miR-6126 and the other by negative control.

first: Koji

last: Fujita

first: Tsutomu

last: Masaki


title: Transcriptomic analysis of third instar larval wing imaginal discs of Drosophila melanogaster corto and uL11 mutants

city: Paris

first: Frédérique

last: Peronnet

address: 9, quai saint-Bernard

department: UMR7622-Developmental biology

institute: CNRS-SU

summary: We report here the transcriptomic analysis of Drosophila melanogaster wing imaginal discs from third instar female larvae mutant for corto (cortoL1/corto420)  The reference line was the w1118 genetic background of the mutant lines.

overall_design: Imaginal wing disc mRNA profiles of female  Drosophila melanogaster third instar larvae were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000.

first: Héloïse

last: Grunchec


title: Ribosome collisions in bacteria promote ribosome rescue by triggering mRNA cleavage by SmrB

city: Baltimore

first: Allen

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes. In a genetic screen in E. coli, we discovered a novel rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNA) to rescue upstream ribosomes. SmrB is recruited by ribosome collisions. Cryo-EM structures of collided disomes from E. coli and B. subtilis reveal interactions between the 30S subunits and a possible SmrB binding site. These findings show that ribosome collisions trigger ribosome rescue in bacteria and reveal the mechanism by which this occurs.

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

overall_design: Ribosome profiling of four strains expressing a reporter construct with a short SecM stalling motif from the plasmid "IRAGP_reporter" in four strains: Wild-type MG1655, delta-ssrA, delta-smrB, and the double knockout delta-ssrA delta-smrB.


title: Post-transcriptional regulation of proliferation and quiescence

city: Glasgow

first: Bashir

middle: Abdirahman

last: Mohamed

state: Glasgow

address: Switchback Road

institute: Beatson Institute for Cancer Research

summary: Several studies have reported that functionally related genes exhibit similar codon usage, which has been shown to impact protein production by the control of mRNA decay or translation. However, codon-mediated control and their relationship to growth conditions have been intensely debated and remain unclear. Here, we investigate the post-transcriptional gene expression control mechanisms employed in cells in proliferation or quiescence. These investigations show that in proliferative conditions we see that subsets of mRNAs with increased mRNA stability are associated with enhanced translation. However, this is not the case in quiescence, where mRNA stability is not linked to changes in translation. In addition, we observe that while G/C-ending codons are more frequently used in both conditions, there is a shift towards A/U-ending codons in proliferation, and this is accompanied by corresponding changes in tRNAs and translational output.

overall_design: tRNA profiles of proliferating and quiescent human fibroblasts

first: Holly

last: Hall

middle: A


title: Perfluorooctanoic acid toxicity on zebrafish embryonic development and mechanism exploration with single-cell RNA sequencing

city: Nanjing

first: Wu

last: Bing

address: No.163 Xianlin Avenue

department: School of the Environment

institute: Nanjing university

summary: The aquatic environment is an important site for perfluorooctanoic acid (PFOA) deposit and induced a high risk for aquatic organisms. Nevertheless, the current toxicity assessment was rarely reported the heart effect of PFOA. The exact mode of action and its resulting heterogeneity toxicological effects in aquatic organisms also remain largely unknown. In this study, the heart effects were investigated with a series of assays. The scRNA-seq showed nine cells populations were significantly altered with PFOA exposure. Heart was the mostly influenced cells and the function of cardiac muscle contraction, gas transport and oxygen binding was significantly changed. Moreover, the hatching gland cells, macrophages and lens cells were also significantly influenced with the altered function of apoptosis, endocrine and nervous and immune system. In addition, a significantly decreased swimming behavior and heart morphogenesis were verified.

first: Bing

last: Wu

first: Jing

last: Yu