title: Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro [bulkRNA-seq]

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

summary:
Rationale: Although epithelial-mesenchymal transition (EMT) is a common feature of fibrotic lung disease, its role in fibrogenesis is controversial. Recently, aberrant basaloid cells were identified in fibrotic lung tissue as a novel epithelial cell type displaying a partial EMT phenotype. The developmental origin of these cells remains unknown.
Objectives: To elucidate the role of EMT in the development of aberrant basaloid cells from human bronchial epithelium by mapping EMT-induced transcriptional changes at the population and single-cell level.
Methods: Human bronchial epithelial cells (HBECs) grown as submerged or air-liquid interface (ALI) cultures with or without EMT induction were analyzed by bulk and single-cell RNA-Sequencing.
Measurements and Main Results: Comparison of submerged and ALI cultures revealed differential expression of 9,868—protein coding (PC) and long non-coding RNA (lncRNA)—genes and revealed epithelial cell-type-specific lncRNAs. Similarly, EMT induction in ALI cultures resulted in robust transcriptional reprogramming of 6,927—PC and lncRNA—genes. While there was no evidence for fibroblast/myofibroblast conversion, cells displayed a partial EMT gene signature and an aberrant basaloid-like cell phenotype.
Conclusions: The substantial transcriptional differences between submerged and ALI cultures highlights that care must be taken when interpreting data from submerged cultures. This work supports that lung epithelial EMT does not generate fibroblasts/myofibroblasts and confirms ALI cultures provide a physiologically relevant system to study aberrant basaloid-like cells and mechanisms of EMT. We provide a catalog of PC and lncRNA genes and a data visualization package for further exploration for potential roles in the lung epithelium in health and lung disease.

overall_design: 8 individual donor bronchial epithelial cells were used for RNA sequencing analysis; of which 4 were from diseased and 4 were from normal lung.

first: Dinesh

last: Uthaya Kumar

first: Efthymios

last: Motakis

first: Vivek

last: Kohar

first: Jan

last: Martinek

first: Mingyang

last: Lu

first: Karolina

last: Palucka

first: Jonathan

last: Koff

first: Adam

last: Williams


title: Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro

status: Public on Apr 21 2022

country: USA

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The FACT complex facilitates expression of lysosomal and antioxidant genes through binding to TFEB and TFE3 [RNA-seq]

city: Bethesda

first: Jose

last: Martina

state: Maryland

address: 50 South Dr., Building 50, Room 3533

department: NHLBI, CDBC

institute: NIH

summary: The transcription factors TFEB and TFE3 orchestrate the cellular response to a variety of stressors, including nutrient deprivation, oxidative stress, and pathogens. Here we describe a novel interaction between TFEB/TFE3 and FACT, a heterodimeric histone chaperone consisting of SSRP1 and SPT16 that mediates nucleosome disassembly and assembly, thus facilitating transcription. Extracellular stimuli, such as nutrient deprivation or oxidative stress, induce nuclear translocation and activation of TFEB and TFE3, which then associate with the FACT complex to regulate stress-induced gene transcription. Depletion of FACT does not affect TFEB activation, stability, or binding to the promoter of target genes. In contrast, reduction of FACT levels by siRNA or treatment with the FACT inhibitor curaxin, severely impair induction of numerous antioxidant and lysosomal genes, revealing a crucial role of FACT as a regulator of cellular homeostasis. Furthermore, upregulation of antioxidant genes induced by TFEB over-expression is significantly reduced by curaxin, consistent with a role of FACT as a TFEB transcriptional activator. Together, our data show that chromatin remodeling at the promoter of stress-responsive genes by FACT is important for efficient expression of TFEB/TFE3 targets, thus providing a link between environmental changes, chromatin modifications and transcriptional regulation.

overall_design: Analysis of mRNA expression under different stress conditions in HeLa cells depleted of FACT complex.

first: Eutteum

last: Jeong

first: José

middle: A

first: Pablo

middle: S

last: Contreras

first: Rosa

last: Puertollano


title: Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro [scRNA-seq]

overall_design: 3 individual healthy donor bronchial epithelial tissue samples were used for single-cell RNA sequencing analysis. The single-cell RNA-seq data were generated in two ALI libraries, AW20003 and AW21001, and one submerged cultures library, SC2100310. (1) AW20003 contained the data of donor ID 34 (11 years old Caucasian male). Hashtag-oligos (HTOs) 5 and 6 labelled the Day 0 cells, HTOs 3 and 4 the Day 1 cells and HTOs 1 and 2 the Day 5 cells. (2) AW21001 combined the data of donor IDs 27 (60 years old black male) and 54 (19 years old black female) in different HTOs. HTOs 1 and 4 labelled the Day 0 cells of each donor respectively. Similarly, HTOs 2 and 5 and HTOs 3 and 6 held the data of Days 1 and 5. (3) SC2100310 combined the data of all three donors with HTO 1 marking the cells of donor IDs 27, HTO 2 the cells of donor ID 34 and HTO 3 the cells of donor ID 54.

middle: B

middle: L


title: The FACT complex facilitates expression of lysosomal and antioxidant genes through binding to TFEB and TFE3.

type: Genome binding/occupancy profiling by high throughput sequencing


title: Gene expression profile at Ptpmt1 cardiomyocytes-specific Knockout mcie, Eif2a mutant mice, Gcn2 Knockout mice, and Hri Knockout mice

city: la jolla

first: Siting

last: Zhu

state: california

address: 9500 Gilman Drive, University of California San Diego

department: Medicine

institute: UCSD

summary: To study the mitochondrial stress response HRI-eIF2a-ATF4 signaling pathway in mitochondrial cardiomyopathy , we generated Ptpmt1 cardiomyocytes-specific Knockout mcie, Eif2a mutant mcie, Gcn2 Knockout mcie, and Hri Knockout mcie

overall_design: We  performed gene expression profiling analysis using data obtained from RNA-seq of 4 different mice line.

first: Jun

last: Zhao

first: Xi

last: Fang


title: Cloning and variation of adult renal tubular progenitors

status: Public on Apr 22 2022

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

country: China

institute: University

summary: Kidney damage involves the progressive and inexorable destruction of tubular and glomerular system. However, it is known that the patients survive AKI often recover renal structure and function. Correspondingly, previous studies demonstrated tubular regeneration in mice after massive kidney injury and linked mouse Sox9+ renal progenitor cells to this process. Here we show that renal progenitor cells can be cloned from renal needle biopsy sample of CKD patients. Progenitor cells can readily assembly into “kidney organoids” expressing proximal/distal tubular cell markers in 3D culture.

overall_design: Tissue sample from CKD patients, isolated human Sox9+ renal tubular progenitors, and in vitro differentiated kidney organoids were prepared for RNA-sequencing. Duplicate experiments were taken from 2 biological samples.

first: Daniel

middle: W

last: Henry


title: Cloning and transplantation of adult renal tubular progenitors

summary: Kidney damage involves the progressive and inexorable destruction of tubular and glomerular system. However, it is known that the patients survive AKI often recover renal structure and function. Correspondingly, previous studies demonstrated tubular regeneration in mice after massive kidney injury and linked mouse Sox9+ renal progenitor cells to this process. Here we show that progenitor cells can be cloned from mouse medulla and cortex. Clones can be grown from a single cell and indefinitely passaged. Progenitor cells derived from renal medulla can readily assembly into “kidney organoids” expressing proximal/distal tubular cell markers in 3D culture.

overall_design: Tissue sample of mouse cortex and medulla, progenitor cells derived from mouse cortex and medulla, and organoids derived from mouse cortex and medulla were characterized by microarrays to study their gene expression profiles. Duplicate experiments were taken from 2 biological samples.


title: Targeting Krebs-cycle-deficient renal cell carcinoma with Poly ADP-Ribose Polymerase inhibitors and low-dose alkylating chemotherapy

city: New Haven

first: Ranjit

last: Bindra

state: CT

address: 15 York Street

department: Therapeutic Radiology

institute: Yale University

summary: In this study, we evaluated novel treatment approaches in newly generated models of FH- and SDHB-deficient RCC. CRISPR/Cas9 was used to engineer isogenic Fh1- and Sdhb-deficient murine models of RCC. RNA-Seq was used to profile this model.

overall_design: RNA-Seq was performed on RENCA parental cells in comparison to FH1 & SDHB knockout cells.  Two biological replicates were performed for each cell line.

first: Daiki

last: Ueno

first: Juan

middle: C

last: Vasquez

first: Amrita

last: Sule

first: Jaiyu

last: Liang

first: Jinny

last: van Doorn

first: Ranjini

last: Sundaram

first: Sam

last: Friedman

first: Randy

last: Caliliw

first: Xun

last: Bao

first: Jing

last: Li

first: Huihui

last: Ye

first: Karla

last: Boyd

first: Rong-Rong

last: Huang

first: Jack

last: Dadson

first: Paul

last: Boutros

first: Brian

last: Shuch


title: ZFP91 and IKZF1 Cooperatively Promote IMiD Resistance in T-Cell Lymphomas

city: Guangzhou

first: Wenchao

last: Wu

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District,

institute: Sun Yat-sen University Cancer Center

summary: The immunomodulatory (IMiD) agents, such as lenalidomide, are highly effective treatment for several B cell lymphomas but have poor efficacy in T cell lymphomas (TCLs). Here, we show that IKZF1 is a key drug target and vulnerability in lenalidomide sensitive TCL cells. However, TCLs are largely resistant and become less dependent on IKZF1. Instead, ZPF91 functions as a transcription factor (TF) and coregulates cell survival with IKZF1 in TCL cells that develop resistance to lenalidomide. Aberrant upregulation of CSNK2B, which leads to c-Jun inactivation, contributes to an enhanced TF activity of ZFP91 and suppresses immune activation triggered by lenalidomide. Although ZFP91 can be better targeted by pomalidomide compared to lenalidomide, an inefficient degradation of IKZF1 and ZFP91 widely exists among IMiD-resistance TCLs. A novel CELMoD agent CC-92480, with markedly increased potency and similar substrate selectivity, can overcome IMiD-resistance across multiple TCL subtypes by near complete degradation of IKZF1 and ZFP91.

overall_design: We generated three independent pools of lenalidomide-resistant SU-DHL-1 cells by long-term culture in the presence of increasing concentrations of lenalidomide. We then cultured these resistant cells in the absence of lenalidomide for at least 2 months to generate lenalidomide-regrown lines.  RNA-seq, ChIP-seq and PRO-seq were performed in SU-DHL-1 parental and len-regrown cells.  RNA-seq were also performed in SUDHL1 parental (P) and len-regrown (RG) cells with ZFP91 knockout cells, and in SUDHL1 and KIJK cells with CSNK2B overexpression cells.   ZFP91 and Histone marks ChIP-seq were also performed in some other T-cell lymphoma cell lines.

first: Kristen

middle: E

last: Stevenson

first: Tayla

last: Heavican

first: Marcus

middle: K

last: Jones

first: Geoffrey

middle: M

last: Nelson

first: Karen

last: Adelman

first: David

last: Weinstock


title: Next-generation interaction screening to discover AVRA1 related protein-protein interactions regulating barley powdery mildew disease immunity and susceptibility.

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

summary: The barley powdery mildew avirulence effector (AVRA1) dataset was part of a larger Y2H screen (GEO GSE150396) to identify novel proteins involved in barley immune responses. Yeast-two-hybrid (Y2H) screening was coupled with next-generation sequencing to identify and quantify interacting proteins. An AVRA1 bait was mated to a cDNA prey library derived from a 0-48 hour time course of infected leaf tissue. Screens were performed in batch liquid culture to enrich yeast populations for cells expressing positive interactions. After two rounds of enrichment under selective (Histidine absent) and non-selective (Histidine present) conditions, yeast cells were collected. Y2H plasmids were extracted and prey cDNA amplicons were generated via low-cycle PCR. Fragmented amplicons were used as input to generate sequencing libraries and processed on the HiSeq 3000 platform. Reads were mapped to the barley and Blumeria graminis genomes and read counts were analyzed using a custom data processing and scoring pipeline. Putative interactors were cloned and binary Y2H was used to confirm interactions.

sample_organism:
Hordeum vulgare
Blumeria hordei

platform_organism:
Hordeum vulgare
Blumeria hordei

overall_design: Y2H screening of a cDNA library was coupled to next-generation sequencing to identify and rank positive protein-protein interactions. Screening for the AVRA1 bait was conducted in triplicate with yeast cells grown in selective and non-selective conditions. NuGEN’s AnyDeplete technology was used to deplete HORVU3Hr1G072260 (zinc finger protein) from the samples. Two constructs of luciferase were used as bait negative controls. Samples were run on three lanes of Illumina’s HiSeq 3000.

first: Sagnik

last: Banerjee

first: Valeria

last: Velasquez-Zapata

first: James

last: Elmore

first: Gregory

last: Fuerst

middle: P


title: ATAC-seq chromatin accessibility profiling in pancreatic islets isolated from Arid1aFl/Fl ; MIP-rtTA control and Arid1aFl/Fl; MIP-rtTA; TRE-Cre mice (Arid1a βKO) with/without pancreatectomy

city: Dallas

first: Hao

last: Zhu

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

summary: To determine how ARID1A loss might regulate genes that were preferentially regulated on the gene expression level, we performed an assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) on islets isolated from control and Arid1a β-cell knockout (βKO) mice at baseline and 6 days after 50% pancreatectomy (PPx).

overall_design: In vivo ATAC-Seq on islets isolated from 3-month-old male control and Arid1a βKO mice at baseline and 6 days after PPx (Pre-PPx: 4 Arid1aFl/Fl; MIP-rtTA control and 3 Arid1aFl/Fl; MIP-rtTA; TRE-Cre mice, Post-PPx: 4 Arid1aFl/Fl; MIP-rtTA control and 4 Arid1aFl/Fl; MIP-rtTA; TRE-Cre mice, all males).

first: Cemre

last: Celen

first: Yuemeng

last: Jia

first: Tianshi

last: Lu


title: Next-generation interaction screening to discover CSEP0491 related protein-protein interactions regulating barley powdery mildew disease immunity and susceptibility.

summary: The barley powdery mildew effector (CSEP0491) dataset was part of a larger Y2H screen (GEO GSE150396) to identify novel proteins involved in barley immune responses. Yeast-two-hybrid (Y2H) screening was coupled with next-generation sequencing to identify and quantify interacting proteins. The CSEP0491 bait was mated to a cDNA prey library derived from a 0-48 hour time course of infected leaf tissue. Screens were performed in batch liquid culture to enrich yeast populations for cells expressing positive interactions. After two rounds of enrichment under selective (Histidine absent) and non-selective (Histidine present) conditions, yeast cells were collected. Y2H plasmids were extracted and prey cDNA amplicons were generated via low-cycle PCR. Fragmented amplicons were used as input to generate sequencing libraries and processed on the HiSeq 3000 platform. Reads were mapped to the barley and Blumeria graminis genomes and read counts were analyzed using a custom data processing and scoring pipeline. Putative interactors were cloned and binary Y2H was used to confirm interactions.

overall_design: Y2H screening of a cDNA library was coupled to next-generation sequencing to identify and rank positive protein-protein interactions. Screening for the CSEP0491 bait was conducted in triplicate with yeast cells grown in selective and non-selective conditions. NuGEN’s AnyDeplete technology was used to deplete HORVU3Hr1G072260 (zinc finger protein) from the samples. Two constructs of luciferase were used as bait negative controls. Samples were run on three lanes of Illumina’s HiSeq 3000.


title: RNA-Seq in pancreatic islets isolated from Arid1aFl/Fl control and Arid1aFl/Fl; UBC-CreERT2 mice (Arid1a KO) with/without pancreatectomy

summary: To determine how ARID1A loss might regulate gene expression, we performed RNA-sequencing (RNA-seq) on islets isolated from control and Arid1a knockout (KO) mice at baseline and 6 days after 50% pancreatectomy (PPx).

overall_design: In vivo RNA-Seq on islets isolated from 3-month-old male control and Arid1a KO mice at baseline and 6 days after PPx (Pre-PPx: 2 Arid1aFl/Fl control and 5 Arid1aFl/Fl; UBC-CreERT2 mice, Post-PPx: 2 Arid1aFl/Fl control and 2 Arid1aFl/Fl; UBC-CreERT2 mice).

first: Jen

last: Chuang

first: Xin

last: Luo


title: Blocking Fra-1 sensitizes triple-negative breast cancer to olaparib

city: Stockholm

first: Dandan

last: Song

address: Tomtebodavägen 23

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Fra-1 (FOSL1) is overexpressed in triple-negative breast cancer (TNBC). Fra-1 is a member of the activator protein 1 (AP-1) transcription factor complex, which plays crucial roles in tumor progression and treatment resistance. We have previously identified 118 proteins that interact with endogenous chromatin-bound Fra-1 in TNBC cells in a large screen, and these included PARP1(Poly (ADP-ribose) polymerase 1). PARP1 inhibitor olaparib is currently in clinical use for treatment of BRCA-mutated TNBC breast cancer. Here, we demonstrate that this interaction impacts the efficacy of olaparib treatment. We corroborate that PARP1 interacts with Fra-1, and we show that PARP1 downregulates Fra-1 and consequently reduces AP-1 transcriptional activity. Inhibition of PARP1, on the other hand, increases Fra-1 levels and enhances its transcriptional activity, which in turn can increase treatment resistance. However, by inhibiting Fra-1, we found that TNBC cells became sensitized to olaparib treatment. We compared Fra-1 chromatin binding sites with the Fra-1 and PARP1 regulated transcriptomes, and found that a large fraction of PARP1-regulated genes was dependent on Fra-1. We further show that PARP1 protein levels significantly correlate with Fra-1 in clinical breast cancer tumors, and we identify that high PARP1 expression is indicative of a poor clinical outcome in breast cancer patients overall, but not in basal-like tumors. In conclusion, by exploring the functionality of the Fra-1 and PARP1 interaction, we propose that targeting Fra-1 could serve as a therapeutic approach to improve olaparib treatment outcome for TNBC patients.

overall_design: mRNA profiles of BT549 upon olaparib treatment and/or AP-1 knockdown

first: Cecilia

last: Williams


title: Single Cell RNA sequencing of TLR9 ligand (CpG oligonucleotide) and TLR2/4 ligand (LPS)-treated mouse gingiva

city: Los Angeles

first: Ichiro

last: Nishimura

state: CA

department: Dentistry

institute: UCLA

summary: Purpose: The goal of this study was to characterize the gingival oral barrier immunity of TLR9 ligand (CpG oligonucleotide) and TLR2/4 ligand (LPS)-treated mouse maxilla. Method: TLR9 ligand or TLR2/4 ligand was topically applied to the mouse palatal gingiva. Mouse palatal gingiva was harvested at 4 days after topical application. Gingival cells were harvested and subjected to 10X Genomix scRNA-seq. Cell Ranger processed data were analysed.

overall_design: Gingival oral barrier cells were compared between TLR9 ligand and TLR2/4 ligand-treated group.

first: Takeru

last: Kondo


title: Changes in hepatic transcriptome profile in α4β7 mAb-treated Western diet-fed mice

city: Pittsburgh

first: Reben

last: Raeman

state: PA

address: 200 Lothrop St, S408 South BST

department: Pathology

institute: University of Pittsburgh

summary: Hepatic transcriptome of junctional adhesion molecule A knockout, F11r–/– mice fed a Western diet (WD) for eight weeks. A cohort of WD-fed mice were treated with IgG or α4β7 mAb for four weeks starting at week four following initiation of the WD.

overall_design: Liver samples were collected at the end of study.

first: Ravi

last: Rai


title: An innate IL-25-ILC2-MDSC axis creates a cancer-permissive microenvironment for Apc-mutation-driven intestinal tumorigenesis

status: Public on Apr 20 2022

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

summary: Interleukin-25 and group 2 innate lymphoid cells (ILC2s) defend the host against intestinal  helminth infection, and are associated with inappropriate allergic reactions. Recently, it was  reported that IL-33-activated ILC2s augment protective tissue-specific pancreatic cancer  immunity. Here we show a diametrically opposite role for intestinal IL-25-activated ILC2s  where they create an innate cancer-permissive microenvironment. Colorectal cancer (CRC)  patients with higher tumor IL25 expression have reduced survival, and increased IL-25 Rexpressing tumor-resident ILC2s and myeloid-derived suppressor cells (MDSCs) associated with impaired anti-tumor responses. Ablation of IL-25-signalling reduced tumors, virtually doubling life-expectancy in an Apc-mutation-driven model of spontaneous intestinal  tumorigenesis. Mechanistically, IL-25 promotes tumor ILC2s, which sustain MDSCs to  suppress anti-tumor immunity. Therapeutic blockade of IL-25-signalling decreased ILC2s,  MDSCs and adenoma/adenocarcinoma, while increasing anti-tumor IFNg and adaptive T cell  immunity. Thus, the roles of innate epithelium-derived cytokines IL-25 and IL-33, and ILC2s in cancer cannot be generalized, and instead offer differential pathways for therapeutic  intervention.

overall_design: Single cell RNA-seq anallysis of the DN1 population from E15.5 embryoninc thymus of the 5x polychromILC mice

first: Eric

last: Jou

first: Noe

last: Rodriguez-Rodriguez

first: Ana-Carolina

middle: F

first: Helen

last: Jolin

first: Paula

last: Clark

first: Kovilen

last: Sawmynaden

first: Michelle

last: Ko

first: Jane

last: Murphy

first: Jonathan

last: Mannion

first: Christopher

last: Ward

first: David

middle: J

last: Matthews

first: Simon

last: Buczacki

first: Andrew

middle: N

last: McKenzie


title: Increase genome editing efficiency by Cas9 transcriptional activator and histone acetyltransferase activator

city: QingDao

first: Qilai

last: Huang

address: Binhai road 72#

institute: Shandong University

summary: The CRISPR/Cas9 system shows diverse levels of genome editing activities on eukaryotic genomic DNA targets, and experiments desire high-efficiency targets. Here we show that chromatin open status is a pivotal determinant of the Cas9 editing activity in mammalian cells, and increasing chromatin accessibility can efficiently improve Cas9 genome editing activity. However, the strategy that fusing the VP64 transcriptional activation domain at the C-terminus of Cas9 can only promote genome editing activity slightly at most tested CRISPR/Cas9 targets in Lenti-X 293T cells. Because histone acetylation increases eukaryotic chromatin accessibility, we further improve genome editing by elevating histone acetylation. We demonstrate that promoting histone acetylation using histone acetyltransferase (HAT) activator YF-2 can improve genome editing from Cas9 and more robustly from the Cas9 transcriptional activator. This provides a strategy to improve CRISPR/Cas9 genome editing activity and enables broader gRNA target choices in eukaryotes.

overall_design: Qilai Huang

first: Junhao

last: Liu

first: Bo

last: Li

first: Lele

last: Yang

first: Naixia

last: Ren

first: Meichen

last: Xu


title: Transcriptome of full-length cDNAs from human glioma stem cells

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

summary:
These data correspond to one SMRT cell sequencing run (performed on Sequel II, PacBio) of full length cDNAs from 3 pooled glioma stem cell line libraries.
No tag was added to distinguish the 3 different samples

overall_design: Glioma stem cell lines were established as previsouly described from human glioblastoma tumors by the group of Pr L Karayan-Tapon (Poitiers) (Villalva et al., 2011; Villalva et al., 2012; Guichet et al., 2018).

first: Catherine

last: VAURS-BARRIERE


title: Effect of O-GlcNAc Transferase (OGT) siRNA in trophoblastic BeWo cells

city: Milwaukee

first: Stephanie

last: Olivier Van-Stichelen

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Every year, about 18 million babies are born from mothers with gestational diabetes mellitus (GDM). While diabetic symptoms usually resolve after delivery, lasting complications can occur for both mother and child, including fetal overgrowth, type 2 diabetes (T2D), cardiovascular diseases, and obesity. The rapid progression of GDM is unique to pregnancies, and likely arises from placental dysfunction. Indeed, stress, nutrition and fetal gender are thought to trigger changes in placental endocrine function, including metabolic hormones and inflammatory cytokines, potentially causing GDM. Nutrient-sensing O-GlcNAcylation and its enzyme O-GlcNAc Transferase (OGT, X-linked) has been previously identified as a placental biomarker of maternal stress particularly deleterious for male offspring. Thus, we wondered whether O-GlcNAcylation participate in GDM development in a sex-dependent manner. After demonstrating that OGT is largely downregulated in male GDM compared to healthy placentas, we knocked down OGT in male trophoblastic cells. We observed changes in placental hormones, cytokines and nutrient-sensing pathways, correlating with previously demonstrated disruption in GDM placentas.  Altogether, this study demonstrates that OGT and O-GlcNAcylation are partly responsible for changes observed in GDM placenta and might be the cause of sexual dimorphism observed in this pathology.

overall_design: siRNA against O-GlcNAc Tansferase(siOGT) was transfected for 72h in BeWo Cells. siCtrl cells were transfected with negative scramble siRNA. Each condition was performed in biological replicates. mRNA was purified and RNA-sequencing was performed by GeneWiz.inc

last: Olivier-Van Stichelen

first: Yiwen

last: Cui


title: DNA methylome and transcriptome profiles in carboplatin-sensitive and -resistant ovarian cancer cell lines [methylation array]

city: Vejle

first: Silvia

middle: Regina

last: Rogatto

address: Beriderbakken 4

department: Clinical Genetics

country: Denmark

institute: Vejle Hospital

type: Methylation profiling by genome tiling array

summary: Genetic and epigenetic changes contribute to intratumor heterogeneity and chemotherapy resistance in several tumor types. LncRNAs have been implicated, directly or indirectly, in the epigenetic regulation of gene expression. We investigated lncRNAs that potentially mediate carboplatin-resistance of cell subpopulations, influencing the progression of ovarian cancer (OC). Four carboplatin-sensitive OC cell lines (IGROV1, OVCAR3, OVCAR4, and OVCAR5), their derivative resistant cells, and two inherently carboplatin-resistant cell lines (OVCAR8 and Ovc316) were subjected to RNA-sequencing and global DNA methylation analysis. Integrative and cross-validation analyses were performed using external (The Cancer Genome Atlas, TCGA dataset, n=111 OC samples) and internal datasets (n=39 OC samples) to identify lncRNA candidates. A total of 4,255 differentially expressed genes (DEGs) and 14,529 differentially methylated CpG positions (DMPs) were identified comparing sensitive and resistant OC cell lines. The comparison of DEGs between OC cell lines and TCGA-OC dataset revealed 570 genes, including 50 lncRNAs, associated with carboplatin resistance. Eleven lncRNAs showed DMPs, including the SNHG12. Knockdown of SNHG12 in Ovc316 and OVCAR8 cells increased their sensitivity to carboplatin. The results suggest that the lncRNA SNHG12 contributes to carboplatin resistance in OC and is a potential therapeutic target. We demonstrated that SNHG12 is functionally related to epigenetic mechanisms.

overall_design: Global DNA methylation analysis was performed in four ovarian cancer cell lines with in vitro acquired resistance to carboplatin (IGROV1-R1, OVCAR3-R1, OVCAR3-R2, and OVCAR5-R1), four sensitive cell lines (IGROV1, OVCAR3, OVCAR4, and OVCAR5), and two inherently carboplatin-resistant cell lines (Ovc316   and OVCAR8). Differentially methylated CpG positions were determined by comparing the sensitive with the resistant cell lines.

first: Cecilie

last: Abildgaard

first: Naiade

last: Calanca

middle: R


title: Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells (CUT&RUN)

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave., room E251

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

summary: Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN-stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat (Myotis lucifugus) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN. We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional upregulation in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NRLC5, SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN. Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting potential candidate loci that contribute to bat-specific immune function.

overall_design: Epigenomic (CUT&RUN) profiling of bat embryonic fibroblast cells that were either untreated or stimulated with 1000U/mL universal interferon alfa (IFNa) for 4hrs.

first: Giulia

last: Pasquesi


title: Optimized ATAC-seq library preparation from Drosophila neurons

city: Salt Lake City

first: Adrian

last: Rothenfluh

state: UT

institute: University of Utah

summary: We optimzed ATAC-seq library preparation for use with Drosophila melanogaster. The protocol addresses factors specific to fruit flies, such as the insect exoskeleton and smaller genome size. The optimized protocol provides guidelines for sample input, nuclei isolation, and enzymatic reaction times. The data included here were generated using our optimized library preparation workflow.

overall_design: Examination of dopaminergic and GABAergic neurons from adult Drosophila brains.

first: Collin

last: Merrill


title: Transcriptomics analysis of bisphenol A induced injury on human normal ovarian epithelial cells at human-relevant levels

city: Chengdu

first: Xiaomeng

address: Renmin South Road, 16#

institute: Sichuan University

summary: After a 28-day exposure to BPA on human normal ovarian epithelial cells (IOSE80), the differentially expressed genes were mainly enriched in the KEGG pathway of ribosome biogenesis in eukaryotes, RNA transport, cell cycle, cellular senescence, progesterone-mediated oocyte maturation, etc. which were possible key signaling pathways.

overall_design: mRNA profiles of 12 samples with triple duplication from BPA/DMSO/E2 exposure on human normal ovarian epithelial cells (IOSE80)


title: Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells (RNA-Seq)

overall_design: Transcriptional profiling (RNA-seq) of primary bat embryonic fibroblasts that were either untreated or stimulated with 1000U/mL universal interferon alfa (IFNa) for 24hrs or 4hrs.


title: Protozoan predation drives rapid adaptive divergence by selecting for tuned cellulose production and amyloid fibrils in Pseudomonas fluorescens SBW25

city: Christchurch

first: Heather

last: Hendrickson

department: Biological Sciences

country: New Zealand

institute: University of Cantebury

summary:
Purpose: Protozoan predators affect the structure of bacterial communities, but investigations into how predation influences bacterial evolution and antagonistic behaviours are scarce. We performed a 20-day predator-prey evolution experiment on solid media to investigate the adaptive traits that arise in bacterial prey under continuous protozoan predation.
Methods: Pseudomonas fluorescens SBW25 and a wild Acanthamoeba sp. isolate as a predator prey pair co-evolved for 20 days yielded both previously described (Wrinkly Spreader; WS) and novel colony morphotype (Wrinkly Fried Egg; WFE) isolates with conferred grazing resistance. These isolates were subjected to RNAseq profiling with and without predation to determine transcriptional changes contributing to grazing resistance.
Results: For differential gene expression the WT SBW25 without predation was used as a baseline. For the WS condition, a total of 881 differentially expressed genes (DEGs) were identified, of which 424 were upregulated and 457 were downregulated. In the WFE condition, a total of 908 DEGs were identified, of which 475 were upregulated and 434 were downregulated. Among all DEGs, 335 upregulated and 313 downregulated genes were shared between the WS1 and WFE conditions
Conclusions: Our findings suggest that protozoan predation can profoundly influence the course of genetic and phenotypic evolution in a short period of time. Together, the differential expression results suggest expression of features that would be expected to increase biofilm formation in WFE according to previous studies. However, increased expression of these traits may not lead to a stronger biofilm, but may still provide predation resistance. For example, fibrils may increase the effective profile size of a bacterial cell. Increased Fap-mediated biofilm formation also induces increased alginate synthesis in P. aeruginosa PA01, an exopolysaccharide that protects mucoid P. aeruginosa against macrophage killing. Interestingly, we found increased expression of alginate biosynthesis genes in both WFE and WS1 (algA, algF), suggesting alternate mechanisms leading to increased alginate production in these two strains.

sample_organism:
Pseudomonas fluorescens
Acanthamoeba sp.

overall_design: mRNA profiles of Co-evolved predator (Acathamoeba sp.) and prey (Pseudomonas fluorescens SBW25)

first: Farhad

last: Golzar

first: Michael

last: Miller


title: Analysis of whole transcriptome RNA-seq data reveals the involvement of alternative splicing in the drought response of Glycyrrhiza uralensis

city: Shihezi

first: li

middle: guo

last: zhi

state: xinjiang

address: Xiangyang Street

department: College of Life Sciences

institute: Shihezi University

summary: we performed a genome-wide analysis of AS events in G. uralensis at different time points under drought stress using a high-throughput RNA sequencing approach. We detected 2479 and 2764 AS events in the aerial part (AP) and underground part (UP), respectively, of drought-stressed G. uralensis. Of these, last exon variable shear and exon skipping were the main types of AS. Overall, 2653 genes undergoing significant AS regulation were identified from the AP and UP of G. uralensis exposed to drought for 2, 6, 12, and 24 h. Gene Ontology analyses indicated that AS plays an important role in the regulation of nitrogen and protein metabolism in the drought response of G. uralensis. Notably, the spliceosomal pathway and basal transcription factor pathway were significantly enriched with differentially spliced genes (DSGs) under drought stress. Genes related to splicing regulators in the AP and UP of G. uralensis responded to drought stress and themselves underwent AS under drought conditions. In summary, our data suggest that drought-responsive AS directly and indirectly regulates the drought response of G. uralensis. Further in-depth studies on the functions and mechanisms of AS during abiotic stresses will provide new strategies for improving plant stress resistance.

first: Guozhi

last: Li

first: Haitao

last: Shen

first: Hailiang

last: liu

first: Dengxian

first: Gang

last: Huang

first: Quan

last: Bi

first: Mao

last: Yang


title: Endocrine, immune and renal toxicity in Largemouth bass after chronic exposure to glyphosate and Rodeo

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Glyphosate is the herbicide most used worldwide, with no historic comparison. It is used for genetically modified crops, and particularly in Florida, it is used as a sugar cane ripener. It is also formulated to treat aquatic weeds in waterbodies as Rodeo®. Because of its extended use, it can run off or be sprayed directly into waterbodies and aquatic wildlife can be chronically exposed. Exposure in animal models has been associated with kidney and liver damage and it has been suggested as an endocrine disruptor. We exposed adult male largemouth bass for 21 days to two doses of glyphosate and Rodeo (chemically equivalent concentration of glyphosate) including 0.5 mg/L and 10 mg/L and to clean water as a control (n=4/tank in quadruplicate). Concentrations during the experiment were corroborated with LC-MS/MS. Total RNA was isolated from the trunk kidney and head kidney. RNA-seq was performed for the high doses compared to controls (n=4/treatment). Transcripts were analyzed with fish and mammalian pathway analyses. Transcripts mapped to Zebrafish metabolic pathways using Paintomics showed the most significantly enriched pathway was steroid hormone biosynthesis in the trunk kidney. Steroid hormones were measured in plasma by LC-MS/MS. Total androgens were significantly reduced at 0.5 mg/L of glyphosate and Rodeo compared to control. While 11-ketotestosterone and estrone concentration was significantly reduced in all doses. Our results show a possible down regulation of the conversion of testosterone to 11-ketotestosterone by glyphosate and Rodeo at concentrations that are allowed in U.S drinking water. Using the mammalian pathway analysis algorithm, cellular processes associated with T-cell activation/development and intracellular pH were significantly enriched in the trunk kidney after glyphosate and Rodeo exposure. Glyphosate and Rodeo produce endocrine disruption corroborated at the hormone and gene expression level. Rodeo and glyphosate share gene expression pathways, however, Rodeo had more pronounced effects in largemouth bass.

first: Maite

last: Maria

first: Kevin

last: Kroll

first: Fahong

last: Yu

first: Mohammad-Zaman

last: Nouri

first: Cecilia

last: Silva-Sanchez

first: Juan

last: Perez

first: David

last: Moraga

first: Yanping

last: Zhang

first: Mike

last: Walsh

first: Nancy

last: Denslow


title: The Lys-motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in Arabidopsis thaliana

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary: Microbes of the root-associated microbiome contribute to improve resilience and fitness of plants. In this study, the interaction between the salt stress tolerance-inducing beneficial bacterium Enterobacter sp. SA187 and Arabidopsis was investigated with a special focus on the plant immune system. Among the immune signalling mutants, the Lys-motif receptors LYK4  strongly affected the beneficial interaction. Overexpression of the chitin receptor components LYK4 compromised the beneficial effect of SA187 on Arabidopsis.  Transcriptome analysis revealed that the role of LYK4 in immunity is intertwined with a function in remodeling defense responses. Overall, our data indicate that components of the plant immune system are key elements in mediating beneficial metabolite-induced plant abiotic stress tolerance.

overall_design: Examination of the effect of the beneficial bacterium Enterobacter sp. SA187 on Arabidopsis thaliana plants under control conditions and salt stress in WT, lyk4 and LYK4-OE genotypes

first: Eleonora

last: Rolli

first: Axel

last: de Zélicourt

first: Hanin

last: Alzubaidy

first: Michael

last: Karampelias

first: Sabiha

last: Parween

first: Naganand

last: Rayapuram

first: Baoda

last: Han

first: Katja

last: Froehlich

first: Aala

last: Abufaraj

first: Hanna

last: Alhoraibi

first: Kiruthiga

last: Mariappan

first: Cristina

last: Andrés Barrao

first: Jean

last: Colcombet

first: Heribert

last: Hirt


title: Single-Cell transcriptomics comparison of nasal polyps in patients with AERD and CRSwNP.

city: Vienna

first: Christine

last: Bangert

address: Waehringer Guertel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Objective: We sought to obtain detailed information about transcriptional differences in epithelial cells and immune cell subsets present in polyps of aspirin-exacerbated respiratory disease and chronic rhinosinusitis with nasal polyps.
Methods: After enrichment for various immune subsets by flow cytometric sorting of polyp-derived cells, we performed transcriptomic profiling by employing single-cell RNA sequencing of all patients.
Results: Transcriptomic profiling revealed that epithelial and mast cells not only complement one another in terms of gene expression associated with the 15-lipoxygenase pathway, but also show a clear type 2 associated inflammatory phenotype as identified by the upregulation of POSTN, CCL26 and IL13 in patients with aspirin-exacerbated respiratory disease.

overall_design:
Cells sorted from AERD and CRSwNP biopsies after mechanical and enzymatic isolation were used to generate libraries for scRNA-seq. Such libraries were generated using the 10X Chromium Controller and Single Cell 3’ Library & Gel Bead Kit v2 (samples 1-9) and v3 (samples 10-19) according to the manufacturer’s protocol.
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*** Authors state "Raw sequencing data is unavailable due to patient privacy concerns."

first: Sergio

middle: V

last: Merino

first: Martin

last: Fahrenberger

first: Thomas

last: Krausgruber

first: Wolfgang

last: Bauer

first: Victoria

last: Stanek

first: Nicholas

last: Campion

first: Tina

last: Bartosik

first: Tamara

last: Quint

first: Guenther

last: Regelsberger

first: Verena

last: Niederberger-Leppin

first: Christoph

last: Bock

first: Sven

last: Schneider

first: Julia

last: Eckl-Dorna


title: Transcriptomic and long-term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

summary: Transcriptomic data for 48 and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation.

overall_design: Two treatments - Controls and RFR-exposed (referred to as "5G"). Controls were exposed to no radiation. RFR-exposed were exposed to 3.5 GHz, ~30 dBm radiation from 6-48 h post fertilization (hpf). Embryos collected at 48 and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq-G50 platform, with 100 bl PE.

first: Subham

last: Dasgupta

first: Connor

last: Leong

first: Michael

last: Simonich

first: Lisa

last: Truong

first: Huaping

last: Liu

first: Robyn

last: Tanguay


title: Transcriptional changes of precision-cut liver slices after 3 days of cultures in the absence or presence of 2.5 mM valproic acid sodium salt.

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

summary: Transcriptional changes of mouse precision-cut liver slices (PCLS) after three days of culture were determined using RNA sequencing. PCLS were cultured for three days in the absence or presence of 2.5 mM valproic acid sodium salt (VPA). Illumina NovaSeq SP was used for sequencing.

overall_design: Bulk RNA sequencing of mouse precision-cut liver slice (PCLS) cultures. PCLS were cultured for 3 days in the absence (REG) or presence 2.5 mM valproic acid sodium salt (VPA).

first: Liza

last: Dewyse

first: Vincent

last: De Smet

first: Leo

last: van Grunsven


title: The FACT complex facilitates expression of lysosomal and antioxidant genes through binding to TFEB and TFE3 [ChIP-seq]

city: Bethesda

first: Jose

last: Martina

address: 50 South Dr., Building 50, Room 3533

institute: NIH

summary: The transcription factors TFEB and TFE3 orchestrate the cellular response to a variety of stressors, including nutrient deprivation, oxidative stress, and pathogens. Here we describe a novel interaction between TFEB/TFE3 and FACT, a heterodimeric histone chaperone consisting of SSRP1 and SPT16 that mediates nucleosome disassembly and assembly, thus facilitating transcription. Extracellular stimuli, such as nutrient deprivation or oxidative stress, induce nuclear translocation and activation of TFEB and TFE3, which then associate with the FACT complex to regulate stress-induced gene transcription. Depletion of FACT does not affect TFEB activation, stability, or binding to the promoter of target genes. In contrast, reduction of FACT levels by siRNA or treatment with the FACT inhibitor curaxin, severely impair induction of numerous antioxidant and lysosomal genes, revealing a crucial role of FACT as a regulator of cellular homeostasis. Furthermore, upregulation of antioxidant genes induced by TFEB over-expression is significantly reduced by curaxin, consistent with a role of FACT as a TFEB transcriptional activator. Together, our data show that chromatin remodeling at the promoter of stress-responsive genes by FACT is important for efficient expression of TFEB/TFE3 targets, thus providing a link between environmental changes, chromatin modifications and transcriptional regulation.

overall_design: Analysis of TFEB binding to promoter of oxidative stress genes under different stress conditions in HeLa cells depleted of FACT complex.

first: Eutteum

last: Jeong

first: José

middle: A

first: Pablo

middle: S

last: Contreras

first: Rosa

last: Puertollano


title: Metformin in the ileum

city: Gifu

first: Hiroshi

last: Takemori

state: Gifu

address: Yanagido 1-1

department: Chemistry and Biomolecular Science

country: Japan

institute: Gifu University

summary: C57BL/6J male mice were treated with or without metformin

first: Momoka

last: Mizoguchi


title: The developmental origin and the specification of the adrenal cortex in humans and cynomolgus monkeys

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

summary: Development of the adrenal cortex, a vital endocrine organ, originates in the adrenogonadal primordium, a common progenitor for both the adrenocortical and gonadal lineages in rodents. In contrast, we find that in humans and cynomolgus monkeys, the adrenocortical lineage originates in a temporally and spatially distinct fashion from the gonadal lineage, arising earlier and more anteriorly within the coelomic epithelium. The adrenal primordium arises from adrenogenic coelomic epithelium via an epithelial-to-mesenchymal-like transition, which then progresses into the steroidogenic fetal zone via both direct and indirect routes. Notably, we find that adrenocortical and gonadal lineages exhibit distinct HOX codes, suggesting distinct anterior-posterior regionalization. Together, our assessment of the early divergence of these lineages provides a molecular framework for understanding human adrenal and gonadal disorders.

overall_design: Urogenital organs at 3–8 wpf were obtained from donors who had provided informed consent and underwent elective abortion at the University of Pennsylvania, Ohkouchi Obstetrics and Gynecology Clinic and Fukuzumi Obstetrics and Gynecology Clinic. Embryo ages were determined through ultrasonographic measurement of the crown lump length. All experimental procedures were approved by the IRBs at the University of Pennsylvania (#832470) and Hokkaido University (19-066).

first: Keren

last: Cheng

first: Yasunari

last: Seita

first: Taku

last: Moriwaki

first: Kiwamu

last: Noshiro

first: Yuka

last: Sakata

first: Young

last: Hwang

first: Toshihiko

last: Torigoe

first: Mitinori

last: Saitou

first: Hideaki

last: Tsuchiya

first: Chizuru

last: Iwatani

first: Masayoshi

last: Hosaka

first: Toshihiro

last: Ohkouchi

first: Hidemichi

last: Watari

first: Takeshi

last: Umazume

first: Kotaro

last: Sasaki


title: DNA methylome and transcriptome profiles in carboplatin-sensitive and -resistant ovarian cancer cell lines

first: Silvia

last: Rogatto

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

overall_design: Refer to individual Series


title: RNASeq PROFILES RELATED TO ENDOMETRIAL HEALTH

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

institute: INRAE

summary: In postpartum dairy cows, subclinical endometritis (SCE) is characterized by persistent endometrial inflammation, which exerts profound detrimental effects on subsequent reproductive performance. So far, transcriptomic studies related to this condition were either based on biopsy-derived whole endometrium tissue or endometrial swab/cytobrush samples, thus neglecting cell type-specific variations in gene expression. This study tested the hypothesis that different endometrial health statuses are associated with distinct transcription profiles of endometrial stromal, glandular and luminal epithelial cells.  In conclusion, this study evidences that endometrial inflammation recovery or persistence is associated with gene expression patterns involved in immune function, tissue remodelling, and uterine receptivity in a cell type-specific manner. Identifying these signatures may prove instrumental to developing novel diagnostic and therapeutic targets, either to prevent persistence or speed recovery from endometrial inflammation, thus restoring the fertility of postpartum dairy cows.

overall_design: At 44 days postpartum, endometrial biopsies were taken from dairy cows (n = 24) classified as healthy (H), recovered from SCE (R), and affected by persistent SCE (PE), according to endometrial cytology taken at 21 and 44 days postpartum. Stromal, glandular and luminal epithelial cells were isolated from the whole tissue biopsy by laser capture microdissection, and the cell-specific transcription profiles were determined by RNAseq. Differential gene expression was analyzed with DESeq2.

first: Gonçalo

last: Pereira

first: Yongzhi

last: Guo

first: Elisabete

last: Silva

first: Marta

first: Claudia

last: Bevilacqua

first: Gilles

last: Charpigny

first: Luís

last: Lopes-da-Costa

first: Patrice

last: Humblot


title: The anti-aging protein Klotho affects early postnatal myogenesis by down-regulating Jmjd3 and the canonical Wnt pathway

city: Los Angeles

first: James

middle: G

last: Tidball

address: 610 Charles E Young Drive E

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: Modulating the number of muscle stems cells, called satellite cells, during early postnatal development produces long-term effects on muscle growth. We tested the hypothesis that high expression levels of the anti-aging protein Klotho in early postnatal myogenesis increase satellite cell numbers by influencing the epigenetic regulation of genes that regulate myogenesis. Our findings show that elevated klotho expression caused a transient increase in satellite cell numbers and slowed muscle fiber growth, followed by a period of accelerated muscle growth that resulted in larger fibers. Klotho also transcriptionally down-regulated the H3K27 demethylase Jmjd3, increased H3K27 methylation and decreased expression of genes in the canonical Wnt pathway, which was associated with a significant delay in muscle differentiation. In addition, Klotho stimulation and subsequent Jmjd3 down-regulation produced similar but not additive reductions in the expression of Wnt4, Wnt9a and Wnt10a in myogenic cells, indicating that inhibition occurred through a common pathway. Together, our results identify a novel pathway through which Klotho influences myogenesis by reducing expression of Jmjd3, leading to reductions in the expression of Wnt genes and inhibition of canonical Wnt signaling.

overall_design: H3K27me2/3 ChIP-seq experiment in either vehicle or Klotho treated C2C12 myoblasts.


title: Heterogeneous fates of simultaneously-born neurons in the cortical ventricular zone

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: Neocortical excitatory neurons belong to diverse cell types, which can be distinguished by their dates of birth, laminar location, connectivity and molecular identities. During embryogenesis, apical progenitors (APs) located in the ventricular zone first give birth to deep-layer neurons, and next to superficial-layer neurons. While the overall sequential construction of neocortical layers is well-established, whether multiple neuron types are produced by APs at single time points of corticogenesis is unknown. To address this question, here we used FlashTag to fate-map simultaneously-born (i.e. isochronic) cohorts of AP-born neurons at successive stages of corticogenesis. We reveal that early in corticogenesis, isochronic neurons differentiate into heterogeneous laminar, hodological and molecular cell types. Later on, instead, simultaneously-born neurons have more homogeneous fates. Using single-cell gene expression analyses, we identify an early postmitotic surge in the molecular heterogeneity of nascent neurons during which some early-born neurons initiate and partially execute late-born neuron transcriptional programs. Together, these findings suggest that as corticogenesis unfolds, mechanisms allowing increased homogeneity in neuronal output are progressively implemented, resulting in progressively more predictable neuronal identities.

overall_design: Patch-Seq of E13.5 born cells marked with FlashTag technology collected at P7 in Primary somatosensory area of the mouse brain.

first: Elia

last: Magrinelli

first: Natalia

last: Baumann

first: Robin

last: Wagener

first: Christelle

last: Glangetas

first: Camilla

last: Bellone

first: Esther

last: Klingler


title: Integrative analysis of the pharmaceutical active ingredient and transcriptome of the aerial parts of Glycyrrhiza uralensis under salt stress reveals liquiritin accumulation via ABA-mediated signaling

first: li

last: zhi

summary: The aerial parts of Glycyrrhiza uralensis supply substantial raw material for the extraction of active pharmaceutical ingredients comprehensively utilized in many industries. Liquiritin is the unique and most abundant flavonoid active component in G. uralensis. It has a wide range of pharmacological activities and high economic value. Our previous study indicated that moderate salt stress increased the content of active ingredients. However, the regulatory mechanism remains unclear. In this study, RNA-sequencing (RNA-seq) of the aerial parts of G. uralensis treated with 150 mM NaCl for 0, 2, 6, and 12 h was performed to identify the key genes and metabolic pathways regulating pharmacological active component accumulation. The main active component detection showed that liquiritin was the major ingredient and exhibited more than a 10-fold significant increase in the 6-h NaCl treatment. Temporal expression analysis of the obtained 4245 differentially expressed genes (DEGs) obtained by RNA-seq revealed two screened profiles that included the significant up-regulated DEGs (UDEGs) at different treatment points. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these UDEGs identified phenylpropanoid metabolism and flavonoid biosynthesis as the most significantly enriched pathways in 2-h treated materials. Interestingly, the carotenoid biosynthesis pathway that is related to ABA synthesis was also discovered, and the ABA content was significantly promoted after 6-h NaCl treatment. Following ABA stimulation, the content of liquiritin demonstrated a significant and immediate increase after 2-h treatment, with the corresponding consistent expression of genes involved in the pathways of ABA signal transduction and flavonoid biosynthesis, but not in the pathway of glycyrrhizic acid biosynthesis. Therefore, salt stress might promote liquiritin accumulation through the ABA-mediated signaling pathway in G. uralensis. Our study provides candidate genes and pathways controlling liquiritin synthesis, and would drive progress in genetic improvement and promote the comprehensive utilization of the aerial part of G. uralensis.

first: Quan

last: Bi

first: Hailiang

last: Liu

first: Haitao

last: Shen

first: Hongbin

last: Li

first: Hua

last: Yao

first: Fei

last: Wang

first: Dajun

last: He

first: Wenbin

last: Xu

first: Shuangquan

last: Xie

first: Xifeng

last: Chen

first: Yuxia


title: Differential gene expression in HFD-fed mouse liver

city: Hong Kong

first: Chi Bun

last: Chan

address: 5N10, SBS, HKU

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: Hepatic expression of genes in chow-fed and HFD-fed mice were compared.

overall_design: Female C57BL/6 mice (3-month-old) were fed with chow or high fat-diet (HFD) for 20 weeks, and the expression of genes in liver were measured.

first: Chi

middle: B


title: Comparative transcriptome analysis provides insights into the molecular mechanisms of high-frequency hearing differences between the sexes of Odorrana tormota

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

summary: Males of the concave-eared frog (Odorrana tormota) have evolved an ultrasonic communication capacity to avoid masking by the widespread background noise of local fast-flowing streams, whereas females exhibit no ultrasonic sensitivity. However, the molecular mechanisms underlying the high-frequency hearing differences between the sexes of O. tormota are still poorly understood. In this study, we sequenced the brain transcriptomes of male and female O. tormota, and compared their differential gene expression. A total of 4,605 differentially expressed genes (DEGs) between the sexes of O. tormota were identified and eleven of them were related to auditory based on the annotation and enrichment analysis. Most of these DEGs in males showed a higher expression trend than females in both quantity and expression quantity. The highly expressed genes in males were relatively concentrated in neurogenesis, signal transduction and ion transport, whereas the up-expressed genes in females were mainly related to energy metabolism, the growth and development regulation of specific auditory cells. This is the first research to reveal the molecular mechanisms of sex differences in ultrasonic hearing between the sexes of O. tormota and will provide new insights into the genetic basis of the auditory adaptation in amphibians during their transition from water to land.

overall_design: Identification of different sexes  O. tormota in brain transcriptome for auditory-related.

first: Zhuo

first: Yao


title: Folic acid treatment of colorectal cancer cell lines

city: Budapest

first: Sára

last: Zsigrai

state: --None--

address: Korányi Sándor utca 2/a

country: Hungary

institute: Semmelweis University

summary:
Folic acid is involved in DNA methylation, thereby it can potentially induce gene silencing.
We used microarrays to detect the transcripts that are showing different expressions after short-term folic acid (FA) treatment.

overall_design: Colorectal cancer (CRC) cells were kept in FA-free medium or treated with 10000 ng/mL folic acid, then harvested for gene expression analysis following 72 hours incubation period. HTA 2.0 microarray experiments were performed according to the manufacturer’s instructions. Firstly, 100 ng input total RNA samples were applied as starting material. For sscDNA synthesis 15 µg cRNA was used and 5.5 µg fragmented and labeled sscDNA sample was hybridized to HTA 2.0 microarrays (Affymetrix) for 16 hours at 45°C with 60 rpm rotation in the Hybridization Oven (Affymetrix). Microarrays were washed and stained with GeneChip® Hybridization, Wash, and Stain Kit reagents according to FS450_0001 protocol using the Fluidics Station 450 instrument (Affymetrix). Scanning was performed with GeneChip Scanner 3000 (Affymetrix).

first: Alexandra

last: Kalmár

first: Béla

last: Molnár


title: RNA-seq data from MDA-MB-231 cells

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

institute: Osaka University graduate school of dentistry

summary: To understand the role of GPR81 in cancaer malignancy, we generated silenced GPR81 using shRNA in MDA-MB-231 cells and performed RNA-seq analysis.

overall_design: Total RNA was isolated from shNT MDA-MB-231 cells and shGPR81 MDA-MB-231 cells. Total RNA library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA, USA), in accordance with the manufacturer’s protocol. Sequencing was performed on an Illumina HiSeq 2500 platform in 75-base single-end mode. Illumina Casava1.8.2 software was used for base-calling. Sequenced reads were mapped to the mouse reference genome sequence (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.


title: DNA methylome and transcriptome profiles in carboplatin-sensitive and -resistant ovarian cancer cell lines [RNA-seq]

city: Vejle

first: Silvia

last: Rogatto

address: Beriderbakken 4

institute: Vejle Hospital

summary: Genetic and epigenetic changes contribute to intratumor heterogeneity and chemotherapy resistance in several tumor types. LncRNAs have been implicated, directly or indirectly, in the epigenetic regulation of gene expression. We investigated lncRNAs that potentially mediate carboplatin-resistance of cell subpopulations, influencing the progression of ovarian cancer (OC). Four carboplatin-sensitive OC cell lines (IGROV1, OVCAR3, OVCAR4, and OVCAR5), their derivative resistant cells, and two inherently carboplatin-resistant cell lines (OVCAR8 and Ovc316) were subjected to RNA-sequencing and global DNA methylation analysis. Integrative and cross-validation analyses were performed using external (The Cancer Genome Atlas, TCGA dataset, n=111 OC samples) and internal datasets (n=39 OC samples) to identify lncRNA candidates. A total of 4,255 differentially expressed genes (DEGs) and 14,529 differentially methylated CpG positions (DMPs) were identified comparing sensitive and resistant OC cell lines. The comparison of DEGs between OC cell lines and TCGA-OC dataset revealed 570 genes, including 50 lncRNAs, associated with carboplatin resistance. Eleven lncRNAs showed DMPs, including the SNHG12. Knockdown of SNHG12 in Ovc316 and OVCAR8 cells increased their sensitivity to carboplatin. The results suggest that the lncRNA SNHG12 contributes to carboplatin resistance in OC and is a potential therapeutic target. We demonstrated that SNHG12 is functionally related to epigenetic mechanisms.

overall_design: RNA sequencing was performed in four ovarian cancer cell lines with in vitro acquired resistance to carboplatin (IGROV1-R1, OVCAR3-R1, OVCAR3-R2, and OVCAR5-R1), four sensitive cell lines (IGROV1, OVCAR3, OVCAR4, and OVCAR5), and two inherently carboplatin-resistant cell lines (Ovc316   and OVCAR8). Differentially expressed genes were determined by comparing the sensitive with the resistant cell lines.

first: Cecilie

last: Abildgaard

first: Naiade

last: Calanca


title: RNA-sequencing of sorted epidermal cells from murine dorsal skin

city: Goettingen

first: Nadine

last: Brandes

address: Heinrich-Düker-Weg 12

department: Institute of Human Genetics

country: Germany

institute: University Medical Center Goettingen

summary: Comparative transcriptome analyses confirmed the HF-SC identity of tdT+/tdTneg CD49fhigh CD34+ Sca-1neg cells and suggests and IFE identity of the tdT+/tdTneg CD49fhigh CD34+ Sca-1+ population

overall_design: mRNA profiles of sorted dorsal skin cells from adult CD4Cre R26-tdT lineage tracing mice were generated by RNA-sequencing

first: Anja

last: Uhmann


title: RNA-Seq analysis of wildtype Populus ussuriensis root in response to PEG stress

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

summary: Drought is one of the major environmental problem in terms of limiting the survival of plant. Roots are the first plant organ to sense drought stress, so it is important to understanding of the molecular machanisms of drought stress responses in the roots. Here we aim to characterized the gene expression profile in Populus ussuriensis roots at 0, 6, 12, 24, 48 and 120 h after the start of PEG-induced drought stress. A total of 2 μg RNA per sample was used to generate sequencing libraries using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA). Libraries were sequenced in 150 bp paired-end mode, using an Illumina HiSeq X Ten platform. Our results provide a global view of gene expression profile that contributes to drought resistance in Populus ussuriensis, and meaningful information for genetic engineering research in the future.

overall_design: Three-week-old Populus ussuriensis seedlings with uniform root growth were then further transferred to PEG liquid media containing 6% PEG 6000 for 0, 6, 12, 24, 48, and 120 h; includes 18 samples: 3 replicates each of  6 time points treated with 6% PEG

first: Wenlong


title: Mogrosisde V improves follicular development and ovulation in PCOS rats induced by letrozole and high-fat diet through promoting glycolysis

city: HengYang

first: Lan'e

last: Huang

state: Hunan

address: 28 Changsheng Xi Lu, Hengyang City, Hunan Province, China

department: Department of Histology and Embryology

institute: University of South China

summary:
Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine disorder characterized by hyperandrogenism, ovulatory dysfunction, and polycystic ovaries. In this study, we induced a PCOS rat model by oral administration of letrozole combined with a high-fat diet and then treated with mogroside V (MV) to evaluate the protective roles on endocrine and follicle development in PCOS rats and the underlying mechanisms.
Purpose: To detect the difference of ovary transcriptome profiling between PCOS model and Control rat and to evaluate the effect of mogroside V on the transcriptome profiling of ovaries of PCOS model rats.
Methods: Ovarian mRNA profiles of 15-week-old Control, PCOS and PCOS-MV group rats (4 rats per group) were generated by deep sequencing,using Illumina PE150.

overall_design: Ovarian mRNA profiles of 4 Control，4 PCOS and 4 PCOS-MV rats respectively.

first: Lan’e

first: Aihong

last: Liang

first: Tianlong

first: Xiaocan

last: Lei

first: Xi

first: Biyun

last: Liao

first: Jinru

last: Tang

first: Gang

first: Fengyu

first: Yiyao

last: Wang

first: Lin-Lin

last: Hu

first: Weiguo

first: Meixiang


title: Integrated mRNA and miRNA expression profile analyses reveal the potential roles of miRNA–mRNA pairs in skin color variation between wild-type and yellow mutant rainbow trout

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

summary: As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained.

overall_design: This study simultaneously analyzes mRNA and miRNA expression profiles and constructs miRNA-mRNA regulatory networks to identify key miRNA-mRNA pairs that may participate in skin color formation of WR and YR.

first: Jinqiang

first: Shenji

last: Wu


title: Comparative Transcriptome Analysis Uncovers the Regulatory Functions of MicroRNAs in Flower Development and Color Changes of Pink-flowered Strawberry

city: Shenyang

first: Jingyu

last: Yue

address: Dongling Road

institute: Shenyang Agricultural University

summary: The pink-flowered strawberry is very popular in China due to its appreciation and economic benefits and its flower has rich red petal with varying degrees, which is provided by anthocyanins accumulation. To better understand the functions of miRNAs, sRNAome, transcriptome and degradome sequencing were used to explore the target genes of miRNAs in flower development and coloring of pink-flowered strawberry. Nine small RNA libraries and a mixed degradome library from flower petals at different developmental stages were constructed and sequenced in this study. A total of 739 known miRNAs and 964 newly identified miRNAs were identified via small RNA sequencing, and their 2816 target genes were cleaved by 639 miRNAs based on the degradome data. There were 317 different expression miRNAs among flower development in pink-flowered strawberry regulated 2134 different expression target genes, which significantly enriched in the transcriptional regulation, phenylpropanoid biosynthesis and plant hormone signal transduction. Furthermore, integrated microRNAomic and transcriptomic analyses suggested that 98 miRNAs were targeted several transcription factors related to anthocyanin accumulation, in which 26 were targeted to MYBs, 12 bHLHs, 14 NACs, and 19 SPLs. And that, twenty seven different expression miRNAs may affect anthocyanin biosynthesis by regulating 23 targets participated in hormone signal transduction pathway in pink-flowered strawberry. The qRT-PCR analysis confirmed the expression changes of 21 miRNA-target pairs showed an opposite trend. Moreover, a co-expression regulatory network was constructed based on differentially expressed miRNA-targets according to the degradome data. Overall, we conducted a comparative analysis uncovered the regulatory functions of microRNAs in flower development and color changes of pink-flowered strawberry via multiple factors, including anthocyanin biosynthesis, hormone signaling and regulation factors. This work not only expands the knowledge of miRNAs affecting the coloration in strawberry, but also provides rich resources for future functional studies.

overall_design: Petals of three developmental stages with obviously different color (‘L’, ‘Z’ and ‘D’) were selected for miRNAsanalysis and three biological repetitions were set for each treatment.

first: Li

last: Xue

first: Jiajun


title: Radix Astragalus Polysaccharide Accelerates Angiogenesis by Activating AKT/eNOS to Promote Nerve Regeneration and Functional Recovery

city: Zheng Zhou

first: Geyi

last: Zhang

address: No. 1 Jianshe East Road

institute: The First Affiliated Hospital of Zhengzhou University

summary: Peripheral nerve injury (PNI) results in loss of neural control and severe disabilities in patients. Promoting functional nerve recovery by accelerating angiogenesis is a promising neuroprotective treatment strategy. Here, we identified a bioactive Radix Astragalus polysaccharide (RAP) extracted from traditional Chinese medicine (TCM) as a potent enhancer of axonal regeneration and remyelination. Notably, RAP promoted functional recovery and delayed gastrocnemius muscle atrophy in a rat model of sciatic nerve crush injury. Further, RAP treatment induced angiogenesis in vivo. Moreover, our in vitro results showed that the role of RAP in endothelial cell (EC) migration and tube formation was probably related to the activation of AKT/eNOS signaling pathway. Altogether, our results show that RAP can enhance functional recovery by accelerating angiogenesis, thereby providing a polysaccharide-based therapeutic strategy for PNI.

overall_design: Compared with the control group, the mRNA profile of Human umbilical vein endothelial cells (HUVEC) after 24 hours of rap treatment.

first: Jinsheng


title: RNA-seq reveals the role of miR-29c in regulating inflammation and oxidative stress of bovine mammary epithelial cells

city: Yinchuan

first: Xing-Ping

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

institute: Ningxia University

summary: Purpose: to detect expression profile of differentially expressed mRNAs during bovine mammary epithelial cells line (MAC-T) transfected with miR-29c inhibitor or negative control (NC) inhibitor in vitro.  Methods: bovine mammary epithelial cells were transfected with miR-29c inhibitor or negative control (NC) inhibitor to assess the expression profiles of mRNAs using RNA-seq.  Results: a total of 42 up-regulated and 27 down-regulated mRNAs were found in the miR-29c inhibitor transfected group compared with the NC inhibitor group.  Conclusion: the inhibition of miR-29c in MAC-T cells could lead to the up-regulation of 42 mRNAs and the down-regulation of 27 mRNAs. The functional enrichment of the differentially expressed mRNAs indicated that miR-29c might be a potential regulator of oxidative stress and inflammatory response in MAC-T through multiple genes, such as FOXO1, TNF-α and BoLA-DQA5, which enriched in stress-activated MAPK cascade, Epstein-Barr virus infection and inflammatory bowel disease signaling pathways. The above results imply that miR-29c plays an important role in the steady state of bMECs or bovine mammary glands and may be a potential therapeutic target for mastitis in dairy cows.

overall_design: Bovine mammary epithelial cells previously frozen in liquid nitrogen were thawed and cultured in in one 6-well plates. When bovine mammary epithelial cell monolayers reached 60%~70% confluence, three wells were transfected with NC inhibitor (100 nM), and the remaining three wells were transfected with miR-29c inhibitor (100 nM), which were used as the negative control group and the experimental group, respectively. Subsequently, all samples were used to perform the RNA-seq.

first: Jian

last: Yang

first: Qi-Chao

first: Zhuo-Ma

last: Luoreng

first: Jin-Peng

first: Qian-Qian

last: Ren

first: Da-Wei

last: Wei

first: Yun

last: Ma


title: Methylation profiling by array for Parkinson's disease using brain tissue

city: Royal Oak

first: Stewart

last: Graham

state: Michigan

address: 3811 West 13 Mile Road, Suite 415

department: OBGYN

institute: Corewell Health - Research Institute

summary:
Parkinson’s disease is second most prevalent neurodegenerative disorder. Parkinson’s disease is hypothesized to be caused by a multifaceted interplay between genetic and environmental factors. We profiled the DNA methylation using the frontal lobe from people who died from Parkinson’s disease and compared them with age-, and sex-matched controls. We hypothesized that the complex regulation of DNA methylation and metabolome leads to deficits that cause irregular motor function among Parkinson’s disease subjects and the metabolomic disparities may reflect the effect of these complex interactions. Herein, we aim to integrate quantitative metabolomics and DNA methylation of brain tissue from primary motor cortex (Brodmann area 4) from Parkinson’s disease sufferers to better understand the biochemistry associated with the onset of the disease.
Parkinson’s disease (PD) is second most prevalent neurodegenerative disorder following Alzheimer’s disease. Parkinson’s disease is hypothesized to be caused by a multifaceted interplay between genetic and environmental factors. Herein, and for the first time, we describe the integration of metabolomics and epigenetics (genome-wide DNA methylation; epimetabolomics) to profile the frontal lobe from people who died from PD and compared them with age-, and sex-matched controls. We identified 48 metabolites to be at significantly different concentrations (FDR q<0.05), 4,313 differentially methylated sites [5'-C-phosphate-G-3' (CpGs)] (FDR q<0.05) and increased DNA methylation age in the primary motor cortex of people who died from PD.  We identified Primary bile acid biosynthesis as the major biochemical pathway to be perturbed in the frontal lobe of PD sufferers, and the metabolite taurine (p-value = 5.91E-06) as being positively correlated with CpG cg14286187 (SLC25A27; CYP39A1) (FDR q = 0.002), highlighting previously unreported biochemical changes associated with PD pathogenesis. In this novel multi-omics study, we identify regulatory mechanisms which we believe warrant future translational investigation and central biomarkers of PD which require further validation in more accessible biomatrices.

overall_design: A total of 78 brain tissue samples were acquired from the NIH NeuroBioBank (40 brain tissue samples were from PD cases and 38 were from cognitively healthy subjects). The frozen brain tissues were obtained from the primary motor cortex (Brodmann area 4) and processed using Infinium MethylationEPIC Array following the manufacturer’s instructions (Illumina Infinium HD Methylation Assay Experienced User Card, Automated Protocol 15019521 v01). Raw signal intensity data were preprocessed from raw *.idat files using minfi Bioconductor package. The samples were normalized using Noob normalization. Methylation beta values were extracted for the remaining probes. Sample position effect on the EPIC array was adjusted using empiricalBayesLM function from WGCNA package. The effect of sample position was modeled as polynomial of second degree. Proportion of neuronal cells in each sample was then estimated using flow sorted PFC samples and estimateCellCount function from minfi package.

first: Sangeetha

last: Vishweswaraiah

first: Sumeyya

last: Akyol

first: Ali

last: Yilmaz

first: Zafer

last: Ugur

first: Juozas

last: Gordevicius

first: Kyung

last: Oh

first: Patrik

last: Brundin

first: Uppala

last: Radhakrishna

first: Viviane

last: Labrie


title: Dual checkpoint blockade of CD47 and PD-L1 using a novel affinity-tuned bispecific antibody maximizes anti-tumor immunity (scRNA-Seq)

city: San Diego

first: Wenjing

last: Yanf

state: CA

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

summary: A novel affinity-tuned dual-checkpoint bispecific antibody with potent PD-L1 and moderate CD47 affinity was designed to improve the selectivity to TME and thus enhance antitumor immunity and efficacy. The scRNAseq analysis was performed to examine the immune cell modulation in TME following the CD47/PD-L1 bispecific treatment.

overall_design: MC38 tumor-bearing C57/BL6 mice were treated with vehicle control, aCD47, aPD-L1 monotherapy, their combination, or the bispecific antibody every 3 to 4 days starting at day 10 post-tumor implant. Tumors were harvested at day 20 and preared for scRNAseq analysis (n = 4~5 mice/group).

first: Shih-Hsun

last: Chen

first: Nadia

last: Kurd


title: Expression data from Human PDAC SUIT-2 cells exposed to various periods of acidic pHe stress

city: Zhunan Town

first: Wun-Shaing

middle: Wayne

last: Chang

state: Miaoli County

address: 35, Keyan Road

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary:
Many solid tumors grow slowly, with an average volume doubling time of several months to multiple years. Yet, most studies to date have focused mainly on the short-term fate of cancerous cells upon exposure to acidic pHe (extracellular pH), a common hallmark of tumor microenvironment. Little is known about how solid tumors, such as intractable PDAC originated from pancreatic ductal cells that secrete alkaline fluids, evolve to tolerate and adapt to the sustained and prolonged exposure of acidic pHe stress.
We established a series of PDAC tumor cells exposed to prolonged periods of extracellular acidification. These biological materials were further subjected to microarray analysis to detail the genome-wide gene expression profiles and to identify the differential expressed genes related to the long-term adaptation of PDAC tumor cells to the extracellular chronic acidosis stress.

overall_design: A total of six groups in duplicates were established, including 1) control group (Ctrl), in which SUIT-2 cells were grown in control medium at physiological pHe 7.4; 2-3) two buffered group, in which tumor cells were incubated in control medium supplemented with non-volatile HEPES/PIPES buffer at pHe 7.4 for either a short period of 2-3 weeks (Buff_2W) or a long period of 10-12 months (Buff_12M); and 4-6) three acidic stress-treated groups, in which PDAC cells were cultured in control medium buffered with HEPES/PIPES at pHe 6.7 for either a short period of 2-3 weeks to reflect the initial stage of extracellular acidification (denoted hereafter as SA for short-term acidic exposure); a medium period of 4-5 months to mirror the previously reported median TVDT in pancreatic cancer patients (denoted hereafter as MA for mid-term acidic exposure); or a long period of 10-12 months to simulate the prolonged TVDT in early cancer patients with small localized tumors (denoted hereafter as LA for long-term acidic exposure).

middle: W


title: The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis [CUT&RUN]

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

summary: The purpose of this study was to decipher the molecular function of ARID3A. We leveraged gene expression (RNA-Seq) and chromatin profiling (ATAC-Seq and CUT&RUN) to evaluate gene expression changes upon restoring Arid3a expression in the context of the Gata1s mutation and miR-125b overexpression

overall_design: We induced Arid3a-FLAG protein using doxycycline in Gata1s-FLCs lentivirally expressing miR-125b

first: Oriol

last: Alejo-Valle


title: High-throughput Sequencing contributes to Quantitative Analysis of Renal Ischemic-Reperfusion-Injury Transcriptomes

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

summary: Purpose: The different ischemic time of Ischemia-reperfusion-injury (IRI) mouse models resulted in different outcomes, severe IRI led to chronic kidney disease, while mild IRI led to the recovery of kidneys. We isolated tubules from mice from each group. The goals of this study are to compare differentially expressed mRNAs, lncRNAs and circRNAs among severe IRI-injured tubules, mild IRI-injuried tubules and control mouse tubules.

overall_design: Methods: kidney tubular mRNA, lncRNA, circRNA profiles of severe IRI (40-min ischemia), mild IRI (20-min ischemia) and control mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.  qRT–PCR validation was performed using SYBR Green assays.

first: Peng

last: Wang


title: Stem Cell Factor Confers Protection against Retinal Degeneration

city: Beijing

first: Xi

address: 95 Yongan Rd

institute: Beijing Friendship Hospital

summary: The goals of this study are to compare the transcriptomics between SCF treated NMDA mice and controls.

overall_design: Retinal mRNA profiles of NMDA exposed WT mice and SCF treated NMDA exposed WT mice.


title: Single-cell RNA sequencing reveals testicular niche cells development  in pigs

city: Yangling

first: Lingkai

last: zhang

address: No. 3, Taicheng Road, Yangling District,  Xianyang 712100，Shaanxi Province，China.

institute: Northwest A&F University

summary: Purpose: To understand the overall transcriptional profile changes in porcine testicular niche cells development.

overall_design: We profiled single cell RNA-seq to shed light on transcriptional changes in testicular niche cells development  in pigs (7-days old, 30-days old, 60-days old and 90-days old). The scRNA-seq analysis revealed three Sertoli cell types, five Leydig cell types and four peritubular myoid cell types. The functional enrichment analysis manifested these cell types played a diverse role in porcine testis development. The porcine testis development is complemented with comparative analyses performed on human species. Also, we calculated the transcription factors from these somatic cell types by pySCENIC . Taken together, our datasets and comparative analyses provide multiple insights into the development of porcine testis niche during puberty, while also providing a valuable data resource for the study of pig testis development.

first: Wenxian

last: Zeng

last: Zhang


title: Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through the epigenetic remodelling of genome-wide DNA methylation and transcription

city: Taipei

first: Pao-Yang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

type: Methylation profiling by high throughput sequencing

summary: Objective: Abdominal adiposity is strongly associated with diabetic and cardiovascular comorbidities. The long non-coding RNA HOTAIR (HOX Transcript Antisense Intergenic RNA) is an important epigenetic regulator, with fat depot-specific expression between abdominal subcutaneous adipose tissue (SAT) and gluteal SAT. HOTAIR locates closely with HOXC13, known to strongly associated with human fat distribution. Here, we examined the phenotypic effects of HOTAIR overexpression on abdominal adipogenesis, and hypothesized that HOTAIR-mediated DNA methylation is correlated with transcriptome changes, leading to the regulation of specific genes and the functional pathways.   Methods: The expression level of HOTAIR was compared among different fat-depots collected from six healthy, five severe obese, and five uremic subjects, and was correlated with dual-energy x-ray absorptiometry (DXA) defined regional adiposity. The human immortalized preadipocyte was used to assess the phenotypic effects of HOTAIR overexpression on abdominal adipogenesis. The integrative analysis of reduced representation bisulfite sequencing (RRBS) and RNA-sequencing was performed to identify putative genes that are epigenetically regulated by HOTAIR, and the associated signaling pathways. HOTAIR-repressed genes were further validated using RNA/chromatin immunoprecipitation with real-time qPCR and correlated with human body fat distribution.  Results: We found that the expression of HOTAIR was high in gluteal SAT, and low in arm/abdominal SAT and visceral (omental) adipose tissue. It could be aberrantly increased in uremic arm SAT. Notably, in severe obese subjects we found that HOTAIR is lowly expressed in abdominal SAT correlating with a higher abdominal adiposity, whereas in uremic patients HOTAIR is highly expressed in arm SAT correlating with lower arm adiposity. HOTAIR overexpression in human immortalized abdominal preadipocyte remarkably suppresses the in vitro adipogenesis. Overall the differentially methylated genes were functionally enriched for nervous system development. We specifically identified 10 HOTAIR-mediated genes showing strong changes of DNA methylation associated with gene expression during abdominal adipogenesis, suggesting potential epigenetic regulation. Two HOTAIR-repressed genes, SLITRK4 and PITPNC1, were further highlighted and validated; presenting an obesity-driven fat-depot specific expression pattern positively correlated with the central body fat distribution.  Conclusions: Our study indicated that HOTAIR is an important regulator for abdominal adipogenesis via intricate DNA methylation likely to associate with transcriptional regulation of specific genes, such as SLITRK4 and PITPNC1.

overall_design: Examination of HOTAIR overexpression during abdominal adipogenesis

first: Yu-Chun

last: Huang

first: Chien-Hsing

last: Lee

first: Kuo-Feng

last: Hsu

first: Hsiang-Yu

last: Yang

first: Li-Wei

last: Wu

first: Chieh-Hua

last: Lu

first: Yu-Juei

first: Ming-Ren

last: Yen

first: Feng-Chih

last: Kuo


title: Chromosome 21-encoded miR-125b cooperates with GATA1s in trisomy 21-associated megakaryoblastic leukemia by targeting the megakaryocytic transcription factor ARID3A III

first: Jan-Henning

summary: The purpose of this study was to decipher the gene expression changes in the ML-DS cell line CMK upon overexpression of ARID3A. For that, we used a doxycycline-inducible gene expression system to overexpress ARID3A

overall_design: We modulated levels of ARID3A in CMK cells


title: Chromosome 21-encoded miR-125b cooperates with GATA1s in trisomy 21-associated megakaryoblastic leukemia by targeting the megakaryocytic transcription factor ARID3A II

summary: The purpose of this study was to decipher the molecular network underlying the synergy between the GATA1s mutation and miR-125b. We used a doxycycline-regulated inducible system to determine gene expression changes associated with the expression of miR-125b.,

overall_design: We modulated levels of miR-125b in Gata1s-fetal liver cells

first: Oriol


title: GckPVT neuronal networks

city: Lausanne

first: Sophie

last: Croizier

state: Vaud

address: Building Genopode-Quartier Sorge

department: Center for integrative genomics

institute: University of Lausanne

summary: Transcriptomic characterization of the glucokinase-expressing neurons of the paraventricular thalamus in the mouse, using Transcribing Ribosome Affinity Purification (TRAP) sequencing.

overall_design: Transgenic mice expressing cre recombinase in the glucokinase-expressing cells were injected in the aPVT with an AAV-DIO-L10-GFP encoding a L10 ribosomal protein-GFP fusion protein that integrates in ribosomes. Ten days later, after an overnight fast, aPVT was dissected, lysed and the ribosomes were immunoprecipitated with an anti-GFP antibody. RNA-seq was then performed on the immunoprecipitated ribosomal fraction (output) and on the non-immunoprecipitated (input) material. 4 biological repricates were used.

first: Sevasti

last: Gaspari

first: Simon

last: Quenneville

first: Ana

last: Rodriguez Sanchez-Archidona

first: Bernard

last: Thorens


title: Distinct Patterns of Insulin response, sexual development, organ size regulation in postnatal developing Subcutaneous and Visceral fat of Bama Pig

city: Shanghai

first: zhang

middle: ying

last: ying

state: Shanghai

address: Beidi Road No.2901

department: Institute of Animal Husbandry & Veterinary Science

institute: Shanghai Academy of Agricultural Sciences

summary: In this study, the SAF and VAF development was characterized and compared in SAF and VAF of Bama pig during postnatal development (infancy, puberty and adulthood) using RNA sequencing technologies (RNA-Seq). We profiled the transcriptome of SAF and VAF isolated from 1-, 3- and 6-month-old pigs and identified 23636 expressed transcription units. Of the them, 1165 genes were differentially expressed between the despots and /or developmental stages. Upregulated gene in SAF of Bama pigs showed significant function and pathway enrichment in central nervous system development, lipid metabolism, oxidation-reduction process, cell adhesion while genes involved in immune system process, actin cytoskeleton organization, male gonad development, hippo signaling pathway preferentially expressed in VAF. Short time-series expression miner analysis demonstrated the differentiation in gene expression patterns between the two deposit was corresponding to their distinct responses in sextual development, hormone signaling pathway, lipid metabolism as well as hippo signaling pathway. Transcriptome analysis of SAF and VAF in Bama pigs suggested that the depot differences of the adipose tissue are not only related to lipid metabolism and endocrine function, but also closely associated with sextual development and organ size regulation.

overall_design: Subcutaneous fat (SAF) fand Visceral fat (VAF) mRNA profiles of Bama pig during postnatal development (infancy, puberty and adulthood; 1months, 3months and 6months) were generated RNA sequencing technologies (RNA-Seq). Nine cDNA libraries representing SAF-1, SAF-3, SAF6, VAF1, VAF3, VAF6 groups were constructed for mRNA transcriptome analysis.

first: Yingying


title: RNA sequence analysis to compare mouse breast CAFs  with and without targeted radiation at 6 day

city: Philadelphia

first: Andres

last: Blanco

state: PA

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

summary: Data generated shows that mouse CAFs from tumors with 6d TRT has several Wnt ligands upregulated

overall_design: Examination of mouse breast CAF (cancer fibroblasts) no RT(n=2) and CAF with 6GY RT (n=2)  from Dll1+ tumors with and without radiation

first: Rumela

last: Chakrabarti


title: Translational control of developmental potency and histone variant transcripts safeguards embryonic stem cell identity

city: New York

first: Jianlong

last: Wang

state: NY

department: Department of Medicine

institute: Columbia University Irving Medical Center

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

overall_design: Refer to individual Series


title: Chromosome 21-encoded miR-125b cooperates with GATA1s in trisomy 21-associated megakaryoblastic leukemia by targeting the megakaryocytic transcription factor ARID3A I

last: Klusmann

summary: The purpose of this study was to decipher the molecular network underlying the synergy between the GATA1s mutation and loss of Arid3a. We  used gene expression profiling (RNA-Seq) to evaluate gene expression changes upon gain and loss of Arid3a in the context of the Gata1s mutation

overall_design: We modulated levels of Arid3a in Gata1s-fetal liver cells

last: Alejo-Valle


title: RNA sequence analysis to compare Dll1+ mouse breast tumor cells with and without targeted radiation

summary: Data generrated shows that Dll1 has several genes upregulated after targeted radiation at day 30 inlcuding EMT, ROS etc

overall_design: Examination of Dll1+ no RT(n=2) and Dll1+RT(n=2) mouse breast tumor cells from MFP injection of PyMT-Dll1+ (with and without targeted radiation at day 30)


title: eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of embryonic and cancer stemness [Ribo-seq]

summary: Stemness is a defining feature in embryonic and cancer stem cells. How stemness is regulated at the mRNA translational initiation remains undefined. We carried out an RNAi screen for key translation initiation factors that maintain the stemness in mouse embryonic stem cells (ESCs). We identified eIF4A2 and defined its mechanistic action through Rps26-depleted and -containing ribosomes in translational initiation activation of mRNAs encoding pluripotency factors and H3.3 for embryonic and extraembryonic lineage repression, respectively. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent 2-cell (2C) transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Knockdown of eIF4A2 disrupts ESC proteome causing the loss of stemness in ESCs as well as in human glioblastomas where eIF4A2 is highly enriched. Collectively, our study establishes an eIF4A2-mediated translation initiation control of stemness and provides insight into cancer therapeutics targeting the translation initiation machinery.

overall_design: eIF4A2 ribosome profiling was investigated via Ribo-seq analysis in mouse embryonic stem cells.

first: Dan

last: Li

first: Jihong


title: eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of embryonic and cancer stemness [RNA-seq]

overall_design: eIF4A2 transcriptome profiling was investigated via RNA-seq analysis in mouse embryonic stem cells.

last: Yang