title: Comprehensive analysis of pathological changes in hip joint capsule of patients with developmental dysplasia of the hip

city: Changsha

first: Xi

middle: Yu

last: Zhou

state: Hunan Province

address: No. 72 Xiangya Road, Changsha City, Hunan Province

institute: Xiangya Stomatological Hospital

summary:
Aims: Developmental dysplasia of the hip (DDH) is a complex musculoskeletal disease that occurs mostly in children. This study aimed to investigate the molecular changes in the hip joint capsule of patients with DDH.
Results: More than one thousand genes were differentially expressed in hip joint capsules between healthy controls and DDH. Both gene ontology (GO) and Kyoto encyclopedia of genes and genome (KEGG) analyses revealed that extracellular matrix (ECM) modifications, muscle system processes, and cell proliferation were markedly influenced by the differentially expressed genes.
Conclusion: DDH is associated with the loss of collagen fibers and fibroblasts, which may cause loose joint capsule formation. However, the degree of differentiation of fibroblasts to myofibroblasts needs further studies.

overall_design: Methods: High-throughput sequencing was used to identify genes that were differentially expressed in hip joint capsules between healthy controls and DDH patients. Patients with DDH (n=6) and control subjects (n=6) were enrolled in this study.  The diagnosis of the patients with DDH was confirmed by expert medical examination with nuclear magnetic resonance and radiographic evidence, and they all had unilateral or bilateral DDH. Control subjects are enrolled from patients with femoral neck fracture due to falling accidence.

first: Chuan

last: Li

first: Zhi

last: Peng

first: You

first: Yongyue

last: Su

first: Pengfei

last: Bu

first: Xuhan

last: Meng

first: Bo

first: Yongqing

last: Xu


title: Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [RNA-seq]

status: Public on Mar 21 2022

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

country: USA

institute: NIH

type: Expression profiling by high throughput sequencing

summary: To gain insight into hemogen function during human erythropoiesis, RNA-seq was performed in different type of erythroid cells, such as WT and hemogen KD CD34+ cells, WT and hemogen KD HUDEP2 cells, WT and hemogen KO K562 cells. Notably, depletion of hemogen in these human erythroid cells significantly reduced the expression of genes associated with heme and hemoglobin synthesis, such as ALAS2, HMBS, GYPA, EPOR, and HBB, supporting a positive role of hemogen in erythroid maturation. To further explore hemogen function in mouse embryonic erythropoiesis, RNA-seq was performed in WT and hemogen KO E14.5 fetal liver cells and the data indicated hemogen play a consistently positive role in erythroid maturation-related genes as shown in the human cells, suggested hemogen is conserved activator during the mammalian erythropoiesis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq were performed using WT and KD hemogen CD34 cells at differentiation day 8, 10,12,14 and 16, and WT and KD HUDEP2 cells before differentiation (day0) and after differentiation day 3,5 and 7 to identify the key genes regulated by hemogen during erythrocyte maturation. RNA-seq was also perfromed in human K562 cells to further validate hemogen targets during the differentiation. RNA-seq in embryonic day E14.5 fetal liver cells between control and hemogen knockout mice to identify the differentially expressed genes which are essential for mouse  erythropoiesis.

first: Ann

last: Dean


title: Fight or flight cardiac responses require augmentation of Ca2+ influx via Rad phosphorylation [RNAseq]

status: Public on Mar 20 2022

city: New York

first: Steven

last: Marx

state: NY

address: 622 W168 Street

institute: Columbia University

summary: One of the most recognizable physiological phenomena is the adrenergic-induced fight-or-flight increase in heart rate and cardiac contraction. For the β-adenergic agonist-induced enhancement of calcium influx and transients, and contractility in the heart, we identify the dual requirement of a subpopulation of Rad-bound calcium channels under basal conditions and PKA phosphorylation of Rad. In mice expressing a non-phosphorylatable Rad mutant, basal cardiac contractility is reduced and adrenergic-augmentation of the calcium current and contractility are disabled. Expression of mutant calcium channel β-subunits that cannot bind the mutant Rad restored contractility, revealing a highly specific therapeutic approach to mimic the contractility imparted by adrenergic agonists. Our findings place Rad and its modulation of calcium channels at the nexus of adrenergic modulation of cardiac responses.

overall_design: Left ventricular tissues were collected from 4SA-Rad knock-in and wild-type control mice (n=3 per group). For RNA-seq analysis, total RNAs were isolated.


title: Transcriptome analysis of PRRSV Nsp1 overexpressed 3D4/31 cells

city: Seoul

first: In byung

last: Park

address: 145, Anam-ro, Seongbuk-gu, Seoul

country: South Korea

institute: Korea University

summary: This study investigated the immunological function of PRRSV Nsp1 by ectopic expression of PRRSV Nsp1 in 3D4/31 cell line. Identifying the functional role of PRRSV Nsp1 associated with host cell modulation may provide better knowledge about the pathogenesis of PRRS (Porcine reproductive and respiratory syndrome).

overall_design: A macrophage cell line, 3D4/31, was transfected with pBabepuro (Mock), PRRSV NSP1-pBabepuro (PRRSV NSP1), PRRSV NSP1 alpha-pBabepuro (PRRSV NSP1a), or PRRSV NSP1 beta-pBabepuro (PRRSV NSP1b). Cloned PRRSV NSP1, NSP1 alpha, and NSP1 beta is derived from PRRSV VR2332 (GenBank accession U87392) (Cheng Song et al, Virology, 2010). To identify differentially mRNAs in the PRRSV NSP1, PRRSV NSP1 alpha, PRRSV NSP1 beta transfectants and mock, three cDNA libraries from each transfectant group were generated and sequenced using the Illumina NovaSeq 6000 sequencer.

first: In

middle: B


title: Differential gene expression upon ADAR3 expression in U87 glioblastoma cells

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

address: 1001 E 3rd St

department: Medical Sciences

institute: Indiana University Bloomington

summary: The genes that are differentially expressed in ADAR3 expressing cells compared to control U87 cells were identified.

overall_design: Total RNA from three biological replicates of ADAR3 expressing and control U87 cells were isolated and subjected to PolyA RNA sequencing followed by differential gene expression analysis.

first: Reshma

middle: R

last: Kurup

middle: A


title: Aire suppresses CTLA-4 expression from thymic stroma to control autoimmunity

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

summary: We show that thymic epithelial cells in the medulla (mTECs) that present self-antigens (self-Ags) to developing thymocytes for establishing immunological self-tolerance also express CTLA-4 if Aire, loss of which is responsible for the hereditary autoimmunity, is nonfunctional. Upon binding with its ligand, CD80 and CD86, expressed on thymic DCs, CTLA-4/ligand complex was internalized by Aire-deficient mTECs. This attenuated the ability of DCs to provide costimulatory signals and to present self-Ags, resulting in the reduced production of Tregs.

overall_design: FACS-sorted CD45-EpCAM+ TECs from Aire-KO at eight weeks of age were prepared for scRNA-seq analyses. In brief, cell suspensions were loaded onto a Chromium instrument (10× Genomics) to generate a single‑cell emulsion. scRNA-seq libraries were prepared using Chromium Single Cell 3′ Reagent Kits v3 Chemistry and sequenced in multiplex on the Illumina NovaSeq platform. FASTQ files were processed using Fastp, and reads were demultiplexed and mapped to the mm10 reference genome via Cell Ranger (v3.0.0). Processing data by the Cell Ranger pipeline was performed using the HOKUSAI supercomputer at RIKEN and the NIG supercomputer at ROIS National Institute of Genetics. Expression count matrices were prepared by counting unique molecule identifiers.

first: Junko

last: Morimoto

first: Minoru

last: Matsumoto

first: Ryuichiro

last: Miyazawa

first: Koichi

last: Tsuneyama

first: Mitsuru


title: Chromatin landscape associated with sexual differentiation in a UV sex determination system

city: ROSCOFF

first: Olivier

last: GODFROY

address: Place Georges Teissier CS90074

department: Station Biologique de Roscoff

country: France

institute: CNRS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, we set out to understand the extent and nature of epigenomic changes associated with sexual differentiation in the brown alga Ectocarpus, which has a well described UV system. Five histone modifications, H3K4me3, H3K27Ac, H3K9Ac, H3K36me3, H4K20me3, were quantified in near-isogenic male and female lines, leading to the identification of 13 different chromatin states across the Ectocarpus genome that showed different patterns of enrichment at transcribed, silent, housekeeping or narrowly-expressed genes. Chromatin states were strongly correlated with levels of gene expression indicating a relationship between the assayed marks and gene transcription. The relative proportion of each chromatin state across the genome remained stable in males and females, but a subset of genes exhibited different chromatin states in the two sexes. In particular, males and females displayed distinct patterns of histone modifications at sex-biased genes, indicating that chromatin state transitions occur preferentially at genes involved in sex-specific pathways. Finally, our results reveal the unique chromatin landscape of the U and V sex chromosomes compared to autosomes. Taken together, our observations reveal a role for histone modifications in sex determination and sexual differentiation in a UV sexual system, and suggest that the mechanisms of epigenetic regulation of genes on the U/V sex chromosomes may differ from those operating on autosomal genes.

sample_organism:
Ectocarpus sp. Ec460
Ectocarpus sp. Ec457

overall_design: Examination of 6 different histone modifications between male and female brown algae Ectocarpus.

first: Josselin

last: Gueno

first: Michael

last: Borg

first: Simon

last: Bourdareau

first: Guillaume

last: Cossard

last: Godfroy

first: Agnieszka

last: Lipinska

first: Leila

last: Tirichine

first: Mark

last: Cock

first: Susana

last: Coelho


title: Activation of β-adrenoceptor signaling inhibits extracellular matrix deposition of human bladder smooth muscle cells

city: Chengdu

first: Junyu

last: Lai

address: No. 37 Guo Xue Xiang, Chengdu, Sichuan

country: China

institute: Sichuan University

summary: To extensively explore its underlying mechanism, our study aims to investigate the effect of β-adrenoceptor (ADRB) signaling on the ECM of human bladder smooth muscle cells (hBSMCs) exposed to pathological hydrostatic pressure.

overall_design: hBSMCs were exposed to the pathological hydrostatic pressure (100 cm H2O) for 6 h, RT-PCR and western blotting were employed, and combined with the microarray analysis of 3-weeks rat pBOO model to investigate the effect of ADRB signaling on the deposition of hBSMCs ECM.

first: Tong-Xin

last: Yang


title: Regulation of the Hippo pathway by phosphoinositol transfer protein (PITP) and phosphoinositides

city: La Jolla

first: Fulong

last: Li

state: CA

address: 2880 Torrey Pines Scenic Dr, SCRM 4805

institute: UC San Diego

summary: The Hippo pathway plays a key role in development, organ size control, and tissue homeostasis, and its dysregulation contributes to cancer. The LATS tumor suppressor kinases phosphorylate and inhibit the YAP/TAZ transcriptional co-activators to suppress gene expression and cell growth. Through a screen of marine natural products, we identified microcolin B (MCB) as a Hippo activator. Structure-activity optimization yielded more potent MCB analogs, which led to identification of PITP  as the direct molecular targets. We established a critical role of PITP in regulating LATS and YAP. Moreover, we showed that PITP influences the Hippo pathway via cellular PI4P. This study uncovers a previously unrecognized role of PITP in Hippo pathway regulation and as potential cancer therapeutic targets.

overall_design: mRNA profiles of HEK293A cells treated with vehicle ctrl or 20nM VT01454 for 2 hours

first: Fu-Long

first: Kun-Liang

last: Guan


title: RNAseq analysis of Trichoderma reesei QM6a and Δace1 transferred to MA medium containing 1% D-mannitol as carbon source

city: Vienna

first: Nadine

middle: Elpida

last: Tatto

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences

summary: We report the gene expression of T. reesei QM6a and Δace1. Both strains were cultivated for 24 h on Mandels-Andreotti medium containing D-glucose as carbon source. Mycelia were then transferred to Mandels-Andreotii medium containin D-mannitol (1%) as carbon source for three hours.

overall_design: Comparison of the differential gene expression of T. reesei QM6a and Δace1 upon transfer to D-mannitol as carbon source.

first: Theresa

last: Radebner

first: Bernhard

last: Seiboth


title: Overall reduction in 5hmC levels during the S phase of DNMT1-deficient mouse embryonic stem cells

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

institute: Osaka University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an essential for genome stability and mammalian embryonic development. DNA methyltransferase 1 (DNMT1) maintains cellular DNA methylation profile and its loss causes embryonic lethality. In this study, immunofluorescence staining, which can compare the difference between sister chromatids, were performed in mouse embryonic stem cells (ESCs) and suggest that the timing and region of de novo methylation by DNMT3 are restricted in DNMT1-deficient ESCs. To reanalyze the timing of de novo methylation by DNMT3, we collected cells from G1 to early S phases (called G1), cells in the mid-S phase, and cells in late S, G2, and M phases (called G2) by FACS, respectively. Among them, two cell populations, G1 and G2, were used for Me/hMeDIP-seq. As a result, the 5mC and 5hmC were globally decreased in the G2 cells.

overall_design: MeDIP-seq and hmeDIP-seq were performed on DNMT1 KO mESCs in G1 and G2, respectively.

first: T

first: L

last: Lefebvre

first: M

last: Tada


title: RNA sequencting of CLL cells treated by BTK degrader

status: Public on Mar 19 2022

city: Bethesda

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: BTK plays a critical role in B cell malignancies survival. BTK inhibitor was successfully used as first line treatment for CLL in clinical. The emerging unmet needs is new segments are needed for ibrutinib R/R patients. The purpose of this study is to investigate genomic changes and signaling pathway differences after  CLL cells were treated with BTK inhibitor (ibrutinib) or degrader (NRX0492).

overall_design: 4 IGHV unmutated primary CLL samples were selected for drug treatment. CLL cells were purified (negtive selection) using CD3+ MACS Cell Separation Columns following manufacturer’s protocol (Miltenyi Biotec). Cells were treated with DMSO, 1 µM ibrutinib, 2 nM hook, or 2 nM NRX-0492 for 18 hours .After treatment, cells were seperated into two groups, treatment verification group and RNA extraction group, for stimulation. For treatment verification group, cells were stimulated by 20 µg/mL F(ab’)2 anti-human IgM (Jackson ImmunoResearch Laboratories) at 37°C  for 15 min  and were detected by flow to make sure drug and stimulation work well. For RNA extration group, cells were harvest for RNA extration after 6 hours anti-IgM stimulation. Purified RNA was sequenced, and data was analyzed by bioinfomatics scientist.

first: Deyi

last: Zhang

first: Adrian

last: Wiestner

first: Yuesheng

last: Piroozia


title: Mapping global miR-29a targets in pancreatic cancer adenocarcinoma (PDAC) cells using Next Generation Sequencing approach

city: Indianapolis

first: Janaiah

last: Kota

state: Indiana

address: 975 W. Walnut Street, IB 244C

department: Medical & Molecular Genetics

institute: Indiana University School of Medicine

summary: In this study, we aim to understand the regulatory role of miR-29a in differential expression of genes and pathways associated with PDAC. Functional validation of the top candidate miR-29a targets identified from the RNASeq data delineates novel PDAC pathways paving the way for the development of de novo therapeutic strategies for PDAC treatment.

overall_design: Comparison of the transcriptional status of control vs. miR-29a overexpressing (OE) cells in two different PDAC cell lines (Panc-1 and MIA PaCa-2) identifies differentially expressed genes in each dataset. Overlapping targets from the two datasets were then considered for further analyses.

first: Jun

last: Wan


title: Single-cell and spatially resolved analysis uncovers cell heterogeneity of breast cancer

city: Wuhan

first: Si-Qing

last: Liu

address: No.9 Zhang Zhidong Road

institute: Wuhan university

summary: The heterogeneity and the complex cellular architecture have a crucial effect on breast cancer progression and response to treatment. However, deciphering the neoplastic subtypes and their spatial organization is still challenging. Here we combine single-nucleus RNA sequencing (snRNA-seq) with a microarray-based spatial transcriptomics (ST) to identify cell populations and their spatial distribution in breast cancer tissues. Malignant cells are clustered into distinct sub-populations. These cell clusters not only have diverse features, origins and functions, but also emerge to the crosstalk within subtypes. Furthermore, we find that these sub-clusters are mapped in distinct tissue regions, where discrepant enrichment of stromal cell types are observed. We also inferred the abundance of these tumorous subpopulations by deconvolution of large breast cancer RNA-seq cohorts, revealing differential association with patient survival and therapeutic response. Our study provides a novel insight for the cellular architecture of breast cancer and potential therapeutic strategies.

overall_design:
We performed single-nucleus RNA sequencing (10X Genomics) on 2 primary tumors of breast cancer, and spatial transcriptomics on one of the primary tumor sample.
NOTE FROM SUBMITTER: Considering the privacy of our patients, we do not plan to public the raw data for now.

first: Qi

last: Wu

first: Xiang-Yu

last: Meng

first: Zhi-Jie

last: Gao


title: Impact of Bisphenol-A on the Spliceosome and Meiosis of Sperm in the Testis of Adolescent Mice

city: Fayetteville

first: Yongjie

last: Wang

state: Arkansas

address: 400 N Coral Canyon Loop, Apt 402

institute: University of Arkansas

summary:
Background：Bisphenol-A (BPA) has estrogenic activity and adversely affects humans and animals' reproductive systems and functions. There has been a disagreement with the safety of BPA exposure at Tolerable daily intake (TDI) (0.05 mg/kg/d) value and non-observed adverse effect level (5 mg/kg/d). The current study investigated the effects of BPA exposure at various doses starting from Tolerable daily intake (0.05 mg/kg/d) to the lowest observed adverse effect level (50 mg/kg/d) on the testis development in male mice offspring. The BPA exposure lasted for 63 days from pregnancy day 0 of the dams to post-natal day (PND) 45 of the offspring.
Results：The results showed that BPA exposure significantly increased testis and serum BPA contents of PND 45 mice. The spermatogenic cells became loose, and the lumen of seminiferous tubules enlarged when BPA exposure at 0.05 mg/kg/d TDI. BPA exposure at a low dose (0.05 mg/kg/d) significantly reduced the expression of Scp3 proteins and elevated sperm abnormality. The significant decrease in Scp3 suggested that BPA inhibits the transformation of spermatogonia into spermatozoa in the testis. The RNA-seq proved that the spliceosome was significantly inhibited in the testes of mice exposed to BPA. According to the RT-qPCR, BPA exposure significantly reduced the expression of Snrpc and Hnrnpu.
Conclusions：This study indicated that long-term BPA exposure at Tolerable daily intake (0.05 mg/kg/d) is not safe because low-dose long-term exposure to BPA inhibits spermatogonial meiosis in mice testis impairs reproductive function in male offspring.

overall_design: Examination of BPA on testicular gene expression in mice, 3 samples in each group were mixed then sequencing.

first: Shilei

first: Yanyan


title: Transcriptome analysis by RNA-seq of gastric cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

institute: Japanese Foundation For Cancer Research

summary: We performed the RNA-seq experiments for mRNA of gastric cancer tissue.

overall_design:
Messenger RNA were extracted from primary and Metastases tumor of 60 samples from 50 gastric cancer patients, prepared with ilumina True Seq RNA Access sample Preparation Kit and sequenced  on the illumina HiSeq

>>Raw data are not available for this series due to patient privacy concerns. Furthermore, the raw data will not be available through controlled-access resources such as dbGaP or EGA. The IRB prohibits public access to the raw data.<<

first: Toshiharu

last: Yamaguchi


title: Next generation sequencing analysis of fetal brown adipose tissue in response to maternal fish oil intake

city: Amherst

first: Soonkyu

last: Chung

state: MA

address: 100 Holdsworth Way Chenoweth Buld Rm211

department: Nutrition

institute: University of Massachusetts

summary: We report the impact of maternal fish oil intake during gestation and lactation on the fetal brown fat development and metabolic health in later life

overall_design:
Mothers were fed either Control or Fish oil-containing diet during pregancy and lactation in C57BL/6 mice. Fetus were collected at 3 different timelines below
Fetus brown fat (BAT) collected born in mothers with either control diet (FC) or fish oil diet (FF)
Weaned brown fat samples collected born in mothers fed with with either control diet (WC) or fish oil diet (WF)
After weaning pups have received either control (AC) and fish oil (AF) diet were fed for high fat for 8 weeks.

first: Tomas

last: Helikar

first: Bhanwar

middle: L

last: Puniya


title: Next Generation Sequencing of MCF7 cells exposed to conditioned media from growing or senescent fibroblasts

status: Public on Mar 18 2022

first: Jorge

last: Morales-Valencia

address: 430 East 29th st.

institute: NYU Langone

summary: MCF7 cells were exposed for 48 hours to conditioned media from growing or senescent fibroblasts before harvesting of cell pellets for RNA extraction.

overall_design: mRNA profiles of MCF7 cells exposed to conditioned media from growing or senescent fibroblasts.

first: Lena

last: Lau

first: Gregory

last: David


title: Genome-wide analysis of differentially expressed genes in Fbw7 mutant cells [RNA-seq]

city: Seattle

first: Heshani

middle: Nayanga

last: Thirimanne

state: WA

address: 1100 Fairview AV N, D2-213

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: Fbw7 is one of the most highly mutated tumor suppressor genes in human cancers. Several Fbw7 mutation types have been found in cancers (e.g. Fbw7Arg/+, other missense mutations and Fbw7-/-). Fbw7Arg/+ missense mutation is the most commonly observed mutation type, however the tumorigenic mechanisms led by Fbw7Arg/+ are as of yet poorly understood. Fbw7 targets almost thirty proteins to degradation, out of many are transcription factors. We performed an integrative study to understand global transcriptional regulation by Fbw7. We investigated the deregulation of two well-studied oncogenic Fbw7 substrates: cMyc and cJun in wild-type and Fbw7 mutant colorectal cancer cell lines and neural stem cells. Our study revealed context-specific transcriptional regulation by Fbw7.

overall_design: We sequenced RNA from Hct116 colorectal cancer cell lines (wild-type, Fbw7-/- and Fbw7R505C/+) , and U5 neural stem cells (Fbw7+/+ and Fbw7-/-). Three replicates per cell condition were included.

middle: N

first: Feinan

first: Derek

last: Janssens

first: Patrick

last: Paddison

first: Steven

last: Henikoff

first: Bruce

middle: E

last: Clurman


title: Transcriptome profiling of WT and Hbxip-KO E14 ESCs in pluripotent condition and during differentiation

city: Tianjin

first: Ni

last: Peiling

address: Weijin Road

institute: nankai university

summary: To gain more insights about the role of Hbxip in mESC, we performed RNA-Seq for WT and Hbxip-KO E14 ESCs in pluripotent condition and during differentiation. The goals of this study are to compare the transcriptome changes upon Hbxip knockout in pluripotent condition and during differentiation.

overall_design: RNA-seq analysis of the transcriptome profiling of WT and Hbxip-KO E14 ESCs in pluripotent condition and  during differentiation

first: P

last: Ni

first: L

last: Chen


title: Next Generation Sequencing of LCN2+/+ and LCN2 -/- MCF7 exposed to conditioned media from senescent fibroblasts

city: New York

summary: MCF7 cells were exposed for 48 hours to conditioned media from senescent fibroblasts before harvesting of cell pellets for RNA extraction.

overall_design: mRNA profiles of LCN2+/+ or LCN2-/- MCF7 cells exposed to conditioned media from senescent fibroblasts.


title: MCF7 cells exposed to conditioned media from growing or senescent fibroblasts

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

overall_design: Refer to individual Series


title: The dual role of Irf1 in maintaining epithelial identity while enabling EMT

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel


title: OFCD (Occulofciocardiodental) patient's PDL (peridontal ligament cells) and Healthy control PDL cells

city: Tokyo

first: Kyaw Min

last: Soe

department: Orthognathics

institute: TMDU

summary:
Transcriptional profiling of mouse embryonic stem cells comparing Mutant PDL cells and healthy PDL cells to study Radiculomegaly (excessive dental root elongation)
Two-condition experiment, Mutant vs. Healthy PDL cells, technological triplicate

overall_design: KYAW, M,SOE

first: OGAWa

last: TAKUYA


title: Determination of system level alterations in host transcriptome due to Zika virus (ZIKV) infection in retinal pigment epithelium

city: Atlanta

first: Manoj

last: Bhasin

state: GA

address: Woodruff Memorial Research Building, Room 4107, 101 Woodruff Circle, 4th Floor East

institute: Emory

summary: Zika Virus (ZIKV) induces ocular complications in infants born from ZIKV infected mothers during pregnancy. We previously reported that ZIKV is permeable to cells lining the blood-retinal barrier. In this study, we measure the alteration of host transcriptome by ZIKV using primary retinal pigmented epithelial (RPE) cells.

overall_design:
Human primary retinal pigmented epithelial (RPE) cells (Lonza, Walkersville, MD) were cultured in RtEGM™Bulletkit® media as per the manufacturer’s instruction (Lonza). Pr. RPE cells were infected with ZIKV (PRVABC59, NR-50240) for 48 and 96h at MOI 1. Cells were harvested and RNA was isolated using a Qiagen RNA extraction kit. The host transcriptome was analyzed using an RNAseq.
*** Submitter states raw data were never received from the core facility (now closed).

first: Singh

last: Pawan Kumar

first: Khatri

last: Indu

first: Jha

last: Alokkumar

first: Pretto

last: Carla D.

first: Spindler

last: Katherine R.

first: Arumugaswami

last: Vaithilingaraja

first: Giri

last: Shailendra

first: Kumar

last: Ashok

first: Bhasin

last: Manoj K.


title: Gene expression-based, astrocyte treatments

first: Cristian

last: Lasagna-Reeves

address: 320 West 15th Street

department: Anatomy & Cell Biology

summary:
Astrocytes, a major cell type found throughout the central nervous system have general roles in neuronal development, blood-brain barrier function, regulation of neuroimmune responses as well as metabolic support of other brain resident cells. Here we show that a distinct subtype of reactive astrocyte is induced by activated endothelial cells and is distinct from astrocytes classically activated by neuroinflammatory microglia. We show that activated endothelial cells strongly induce C3 + astrocytes that retain their phagocytic capacity while exhibiting a gain of neurotoxic function decreasing neuronal cell survival. We show that endothelial activated astrocytes have increased A1-astrocytic genes and exhibit a distinctive extracellular matrix remodeling profile. Finally, we show that endothelial activated astrocytes are Decorin positive and are associated to vascular amyloid deposits but not amyloid plaques in mouse models and AD/CAA patients. Taken together these findings show the existence of potentially extensive and subtle functional diversity of A1-reactive astrocytes.
Astrocytes treated with Control or Activated Microglia or Endothelial Conditioned media

overall_design: To compare the transcriptional profiles for glial activation in Astrocytes to Microglia vs Endothelial Stimuli

first: Xavier

last: Taylor


title: The dual role of Irf1 in maintaining epithelial identity while enabling EMT [ChIP-seq]

summary: To investigate the context-dependent function of Irf1 in maintaining epithelial identity while enabling TGFbeta-induced EMT in NMuMG/E9 cells, we performed chromatin immunoprecipitation with Irf1-specific antibodies in NMuMG cells treated for 2 days with TGFbeta or left untreated (0d TGFbeta). Intersection with RNA-sequencing after downregulation of Irf1 with or without treatment with TGFbeta for two days revealed genes that are directly regulated by Irf1 and that could contribute to the dual role of Irf1 in EMT.

overall_design: ChIP sequencing of NMuMG/E9 cells with or without TGFbeta treatment (0d, 2d TGFb) was performed with Irf1-specific antibodies.

first: Nathalie

last: Meyer-Schaller

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: The dual role of Irf1 in maintaining epithelial identity while enabling EMT [mRNA-seq]

first: DBM Bioinformatics

last: Core Facility

summary: To investigate the context-dependent function of Irf1 in maintaining epithelial identity while enabling TGFbeta-induced EMT in NMuMG/E9 cells, we downregulated Irf1 by siRNA and analyzed differentially regulated genes and pathways upon EMT induction (2 days TGFbeta) or in the absence of EMT (0 day TGFbeta). Intersection with Irf1 ChIP-sequencing after 2 days of TGFbeta treatment or in untreated cells revealed genes that are directly regulated by Irf1 and that could contribute to the dual role of Irf1 in EMT.

overall_design: RNA sequencing of NMuMG/E9 cells transfected with Irf1-specific or control siRNA with (2 days) or without TGFbeta treatment to induce EMT.


title: Genome-wide mapping of histone modifications and transcription factor occupancy in Fbw7 mutant cells [CUTandRUN]

first: Heshani

last: Thirimanne

overall_design: We used Cleavage Under Targets and Release Using Nuclease (CUTandRUN), a chromatin profiling strategy to map the genome-wide histone modifications and transcription factors in wild-type and Fbw7 mutant cells (Fbw7-/- and Fbw7R505C/+). Three replicates per cell condition and an IgG negative control were included for each experiment.

first: Feinan

last: Wu

first: Derek

last: Janssens

first: Patrick

last: Paddison

first: Steven

last: Henikoff

first: Bruce

last: Clurman


title: Microglia and the immune response to a human temporal lobe seizure

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: Inflammatory processes and cells of the immune system including brain-resident microglia are activated in the epilepsies. We examined shape, transcriptomic profile and expression of microglial markers in tissue from the temporal lobe of epileptic patients. In the basal state, transcripts and pathways associated with the anti-inflammatory cytokine IL10, were up-regulated in the tissue from more sclerotic regions.  We found that seizures also induce dynamic immune responses and change microglial phenotype. A pseudo-temporal ordering of the delay between the last seizure and tissue and analysis, based on immediate early gene expression, indicated an initial and local, innate immune response. At longer pseudo-time delays, infiltration of extra-cerebral cells, principally T-cells, contributed to the immune response. Ictal-like activity or ADP application in slices reproduced microglial activation including changes in motility and the liberation of inflammatory cytokines.

overall_design: Comparison of 4 hippocampus regions from 13 human patients with MTLE (temporal lobe epilepsy with hippocampal sclerosis)

first: Mélanie

last: Morin-Brureau

first: Giampaolo

last: Milior

first: Juliette

last: Royer

first: Farah

last: Chali

first: Caroline

last: Le Duigou

first: Etienne

last: Savary

first: Corinne

last: Blugeon

first: Laurent

last: Jourdren

first: David

last: Akbar

first: Franck

last: Bielle

first: Sophie

last: Dupont

first: Vincent

last: Navarro

first: Michel

last: Baulac

first: Bertrand

last: Mathon

first: Stéphane

last: Clemenceau

first: Richard

last: Miles


title: Massive Organ Inflammation in Experimental and in Clinical Meningococcal Septic Shock

status: Public on Mar 17 2022

city: Oslo

first: Ole

middle: Kristoffer

last: Olstad

address: Kirkeveien 166

department: Medical Biochemistry

country: Norway

institute: OUS

summary:
The aims of the present study were to investigate the inflammatory responses in various organs as compared with the systemic circulation in an experimental porcine model of meningococcal sepsis
using wild-type N. meningitidis; to study the role of LPS versus non-LPS microbial molecules as triggers of organ inflammation in meningococcal sepsis

overall_design: Healthy Norwegian landrace pigs (n = 19) (30 ± 2.5 kg) were investigated. The biological samples used in the present study were from a larger project to define the pathogenic role of LPS versus non-LPS molecules in N. meningitidis sepsis. 4 organs were investigated in duplicates at three differen doses of Meningococci: Liver, lungs, spleen and kidney.

first: Bernt

middle: C

last: Hellerud

middle: K

first: Erik

middle: W

last: Nielsen

first: Anne-Marie

middle: S

last: Trøseid

first: Øyvind

last: Skadberg

first: Ebbe

last: Thorgersen

first: Åshild

last: Vege

first: Tom

last: Mollnes

first: Petter

last: Brandtzæg


title: Sterol scarcity primes p38 immune defenses through a TIR-1/SARM1 phase transition

city: Worcester

first: Read

last: Pukkila-Worley

state: Massachusetts

address: 55 N Lake Ave

department: Medicine

institute: University of Massachusetts Medical School

summary: Intracellular signaling regulators are concentrated into membrane-free, higher-ordered protein assemblies to initiate protective responses during stress — a process known as phase transition. Here, we show that a phase transition of the C. elegans Toll/interleukin-1 receptor domain protein (TIR-1), a homolog of the mammalian sterile alpha and TIR motif-containing 1 (SARM1), primes host immune defenses when dietary sterols are limited to handle subsequent bacterial infection. TIR-1/SARM1 is an upstream component of the p38 PMK-1 pathway in intestinal cells, an innate immune defense and stress response pathway in metazoans. Under conditions of low cholesterol availability, multimerization and precipitation of TIR-1/SARM1 potentiates the intrinsic NAD+ glycohydrolase activity of this protein complex, increases p38 PMK-1 phosphorylation, and promotes pathogen clearance from the intestine. Dietary cholesterol is required for C. elegans to survive infection with pathogenic bacteria and to support development, fecundity, and lifespan. Thus, activation of the p38 PMK-1 pathway in sterol-deficient animals is an adaptive response that allows a metazoan host to anticipate environmental threats under conditions of essential metabolite scarcity.

overall_design: RNA-seq of C. elegans wild-type (N2),  nhr-8(hd117), and nhr-8(ok186) animals exposed to Escherichia coli (OP50) or Pseudomonas aeruginosa (PA14)

first: Nicholas

middle: D

last: Peterson


title: COPD is Associated with Epigenome-wide Differential Methylation in BAL Lung Cells

city: Stockholm

first: Simon

last: Merid

state: Stockholm

address: Sjukhusbacken 10

country: Sweden

institute: Karolinska Institutet

type: Methylation profiling by genome tiling array

summary: DNA methylation patterns in chronic pulmonary obstructive disease (COPD) might offer new insights into disease pathogenesis. To assess methylation profiles in the main COPD target organ, we performed an epigenome-wide association study on bronchoalveolar lavage (BAL) cells. Bronchoscopies were performed in 18 COPD subjects and 15 controls (ex- and current smokers). DNA methylation was measured with Illumina MethylationEPIC BeadChip covering >850,000 CpGs. Differentially methylated positions (DMPs) were examined for 1) enrichment in pathways and functional gene relationships using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology; 2) accelerated aging using Horvath’s epigenetic clock; 3) correlation with gene expression; and 4) colocalization with genetic variation. We found 1,155 Bonferroni significant (P < 6.74 × 10-8) DMPs associated with COPD, many with large effect sizes. Functional analysis identified biologically plausible pathways and gene relationships, including enrichment for transcription factor activity. Strong correlation was found between DNA methylation and chronological age, but not between COPD and accelerated aging. For 79 unique DMPs, DNA methylation correlated significantly with gene expression in BAL cells. Thirty-nine percent of DMPs were co-localized with COPD-associated SNPs. To the best of our knowledge, this is the first EWAS of COPD on BAL cells, and our analyses revealed many differential methylation sites. Integration with mRNA data showed a strong functional readout for relevant genes, identifying sites where DNA methylation might directly impact expression. Almost half of DMPs were co-located with SNPs identified in previous GWAS of COPD, suggesting joint genetic and epigenetic pathways related to disease.

overall_design: Bisulphite converted DNA from the 33 samples were and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

first: Simon Kebede

first: Jonas Eriksson

last: Ström

first: Annelie F

last: Behndig

last: Melén


title: RNA-Sequencing of Astrocytes Stimulated with Activated Endothelial conditioned media (ECM) and Activated Microglia conditioned media (MCM)

first: Cristian

last: Lasagna-Reeves

summary: The goal of this study is to compare the mRNA transcriptome of astrocytes treated with Activated Microglia and Endothelial conditioned media

overall_design: Astrocyte mRNA profiles after Activated ECM and MCM treatments

first: Xavier

last: Taylor

first: Hongyu

last: Gao


title: Variation in CRABS CLAW (CsCRC) contributes to fruit length modulation in cucumber

city: Beijing

first: xiaofeng

last: Liu

address: No.2 Yuanmingyuan Xi Lu

institute: China Agricultural University

summary: Fruit length is a key domestication trait that affects crop yield and appearance quality. Cucumber fruits vary from 5~60 cm in length. Despite multiple fruit length QTLs have been identified, the underlying genes and regulatory mechanisms are poorly understood. Map-based cloning identified a nonsynonymous SNP (G to A) in CRABS CLAW (CsCRC) confers the major effect fruit length QTL FS5.2. CsCRCA is a rare allele only exist in Xishuangbanna cucumber with round fruits. Construction of near-isogenic line (NIL) of CsCRCA led to 34~39% reduction in fruit length. Introduction of CsCRCG into the NIL rescued the short-fruit phenotype, and knockdown of CsCRCG resulted in reduced fruit length and decreased cell size. RNA-seq results showed that an auxin responsive protein CsARP1 expressed decreased in CsCRC-RNAi lines. Further, an auxin responsive protein Further, CsARP1 is the downstream target gene of CsCRCG, instead of CsCRCA. Knockout of CsARP1 produced decreased fruit length with smaller cells. Hence, our work suggested that CsCRCG positively regulates fruit elongation through transcriptional activation of CsARP1 and thus enhanced cell expansion. Utilization of CsCRC alleles provides a new strategy to manipulate fruit length in cucumber breeding.

overall_design: Fruits at anthesis from R1461 and Ci transgenic plants were used as samples for RNA sequencing. Two biological replicates were prepared for each sample

first: Gen

last: Che

first: Yupeng

last: Pan

first: Xiaofeng

first: Jianyu

last: Zhao

first: Shuangshuang

last: Yan

first: Zhihua

last: Cheng

first: Junjun

last: Shen

first: Zhongyi

last: Wang

first: Weiyuan

last: Song

first: Zhaoyang

last: Zhou

first: Yiqun

last: Weng

first: Xiaolan

last: Zhang


title: TRF2 cooperates with CTCF for controlling the oncomiR-193b-3p in colorectal cancer.

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

summary: Background: The Telomeric Repeat binding Factor 2 (TRF2), a key protein involved in telomere integrity, is over-expressed in several human cancers and promotes tumor formation and progression. Recently, TRF2 has been also found outside telomeres where it can affect gene expression. Here we provide evidence that TRF2 is able to modulate the expression of microRNAs (miRNAs), small non-coding RNAs altered in human tumors. Among the miRNAs regulated by TRF2, we focused on the miR-193b-3p, an oncomiRNA that positively correlates with TRF2 expression in human colorectal cancer patients. At the mechanistic level, the control of miR-193b-3p expression requires the cooperative activity between TRF2 and the chromatin organization factor CTCF. We found that CTCF physically interacts with TRF2, thus driving the proper positioning of TRF2 on a binding site located upstream the miR-193b-3p host-gene. The binding of TRF2 on the identified region is necessary for promoting the expression of miR-193b3p which, in turn, inhibits the translation of the onco-suppressive methyltransferase SUV39H1 and promotes tumor cell proliferation. The translational relevance of the oncogenic properties of miR-193b-3p was confirmed in patients, in whom the association between TRF2 and miR-193b-3p has a prognostic value.

overall_design: Evaluation of effects mediated by the telomeric protein TRF2 on miRNAs expression. Colorectal cancer HCT116 cells were stable silenced for TRF2 by using shTRF2 vector and its relative control vector (shControl). The two samples (shControl and shTRF2) were performed in triplicate and the reference sample used for the analysis was the shControl.

first: Roberto

last: Dinami

first: Eleonora

last: Petti

first: Manuela

last: Porru

first: Angela

last: Rizzo

first: Federica

last: Ganci

first: Andrea

last: Sacconi

first: Paola

last: Ostano

first: Giovanna

last: Chiorino

first: Livio

last: Trusolino

first: Giovanni

last: Blandino

first: Gennaro

last: Ciliberto

first: Pasquale

last: Zizza

first: Annamaria

last: Biroccio


title: Carbonic Anhydrase 2 is Required for Maintaining Metabolic Homeostasis  of Human Articular Chondrocytes

city: St. Louis

first: Brian

last: DeBosch

state: Missouri

address: 660 South Euclid Avenue

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

summary:
Objective: To examine the role of carbonic anhydrase II (CA2 gene), the most efficient isoform in the CA family of zinc-containing metalloenzymes, in chondrocyte metabolism.
Methods: CA2 expression was measured in human and mouse osteoarthritic cartilage. RNA-seq was performed in C28/I2 cells in which CA2 was silenced. Normal human chondrocytes were cultured under normoxia (21% oxygen) or hypoxia (2% oxygen) following CA2 knockdown. Cell metabolism was studied by measuring extracellular lactate production, glucose consumption, intracellular ADP/ATP, intracellular pH, and ROS production. Glycolysis was measured using Seahorse XF96 analyzer. The effect of CA2 knockdown on anabolic and catabolic markers was measured following treatment with IL-1. Effects of CA2 was examined on cell proliferation, cell-cycle distribution, colony-formation, and migration.
Results: CA2 was highly elevated in human and murine osteoarthritic cartilage. RNA-seq analysis revealed that processes related to glycolysis, apoptosis and TNF signaling were perturbed in cells lacking CA2. CA2 expression was 10-fold higher under hypoxia and its knockdown caused decreased extracellular lactate production, increased ADP/ATP ratio, impaired glycolysis, decreased glycolytic capacity and lowered the expression of glycolysis rate-limiting enzymes, but did not affect intracellular pH and ROS production. CA2 deficiency disturbed chondrocyte anabolic and catabolic equilibrium. CA2 knockdown suppressed chondrocyte migration and proliferation and induced cell-cycle arrest.
Conclusion: This study unravels a novel role of CA2 in chondrocyte metabolism and inflammation. These findings indicate that CA2 is required for the maintenance of chondrocyte metabolic homeostasis. Future work is needed to further illuminate the mechanistic and functional role of CA2 in osteoarthritis development.

overall_design: RNA-Seq analysis of cells transduced with CA2 shRNA

first: Muhammad

middle: F

last: Rai

first: Mingming

last: Yan

first: Eric

last: Tycksen

first: Xin

last: Duan

first: Lei

last: Cai


title: RNA-sequencing analysis of the KYSE150 cells overexpressing caspase-8 mutants (M4, M6, M10, M13) or wild-type caspase-8

city: beijing

first: li

last: lei

address: 17 Panjiayuan Nanli

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using RNA sequencing analysis to test the effects of overexpressing caspase-8 mutants or wild-type caspase-8 on the mRNA of KYSE150 cells.  Methods: KYSE150 cells were transfected with caspase-8 mutants or wild-type caspase-8 for 48 hours in 1640 medium plus 10% serum. Two independent replicates were plated, transfected in parallel for each caspase-8 mutants or wild-type caspase-8. Results: Log-fold changes of mRNAs between caspase-8 mutants and wild-type caspase-8 group were selected with a significance threshod of p<0.05. There are 3974 overlapping differentially expressed genes in the caspase-8 mutant cells compared to the wild-type caspase-8 cells. Conclusions: Our study determined the mRNA changes of caspase-8 mutant KYSE150 cells compared to the wild-type caspase-8 cells.

overall_design: KYSE150 cells mRNA profiles of WT (transfected with wild-type caspase-8), M4 (transfected with caspase-8 M4 mutant), M6 (transfected with caspase-8 M6 mutant), M10 (transfected with caspase-8 M10 mutant), M13 (transfected with caspase-8 M13 mutant) were generated by RNA sequencing.

first: Li

last: Lei


title: Influence of form of Se supplementation and tall fescue endophyte toxicity on the kidney transcriptome of grazing beef steers

city: Lexington

first: James

last: Matthews

state: Kentucky

address: 325 Cooper Drive

department: Animal and Food Sciences

institute: University of Kentucky

summary: To test the hypothesis that average daily gain (ADG) and clinical parameters of steers grazing novel non-toxic (NTE) or toxic KY-31 (TE) endophyte-infected tall fescue would be improved by ad libitum intake of vitamin-mineral mixes (V-M) that contain 27 ppm Se as a 1:1 blend of SELPLEX:sodium selenite (MIX) vs. sodium selenite (ISe), 32 fescue-naïve beef steers depleted of Se were randomly assigned to ad libitum consumption ISe vs MIX for 35 d and fed enough of a NTE/alfalfa/grain diet to achieve 0.57 kg BW gain/d. Within Se-form treatments, 2 steers were randomly assigned to each of 4 NTE (ISe = 316 ± 31 kg, MIX = 315 ± 22 kg) or TE (ISe = 316 ± 37 kg, MIX = 314 ± 39 kg) paddocks for 84 d and had ad libitum access to their respective V-M. Steers were slaughtered over a 23-d period from day 90 to day 113 (August 27, 2019 to September 19, 2019) of the study and the left kidney removed.

overall_design: A completely randomized design with a 2 × 2 factorial arrangement of treatments. 32 total samples were analyzed (n=8 for ISeTE, n=8 for ISeNTE, n=8 for MIXTE, and n=8 for MIXNTE ).

first: Chloe

middle: G

last: DeGiorgio

first: Kuey

last: Chen


title: Multi-dimensional modeling disrupted synapse formation underlying psychiatric disorders of Wolfram syndrome reveals essentiality of astrocytes

city: shanghai

first: Yana

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, China

department: Computational Biology

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: Dysregulated neurite outgrowth and synapse formation underlie many psychiatric disorders. Wolfram syndrome (WS) mainly caused by WFS1 deficiency is a monogenic genetic disease manifested by severe psychiatric disorders. Due to athe lack of proper human disease models, the underlying mechanism is poorly understood. Particularly, whether and how WFS1 deficiency affects synapse formation remain elusive. By mirroring the complexity of human brain development with cerebral organoids derived from human embryonic stem cells (hESCs) harboring WFS1 loss of function (LOF), we found that WFS1-deficient cerebral organoids not only recapitulated the neuronal loss phenotype in WS patients, but also exhibited significantly impaired synapse formation associated with reduced astrocytes, suggesting a defective structural basis for psychiatric disorders elicited by WFS1 deficiency. To further unravel the complexity of interplay between neurons and astrocytes, each neural cell type was respectively differentiated from hESCs harboring WFS1 LOF. WFS1 deficiency in neurons autonomously delayed neuronal differentiation with altered expressions of genes associated with psychiatric disorders, and impaired neurite outgrowth and reduced synapse formation associated with elevated cytosolic calcium. Interestingly, WFS1 deficiency in astrocytes decreased the expression of glutamate transporter EAAT2 and compromised glutamate uptake, causing reduced neurite outgrowth with increased cytosolic calcium when co-cultured with wildtype (WT) neurons, highlighting pathogenic role of WFS1-deficient astrocytes. Importantly, restoring EAAT2 expression in astrocytes by riluzole treatment significantly alleviated reduced neurite outgrowth phenotype in WT neurons co-cultured with WFS1-deficient astrocytes. Altogether, our study provides novel insights into how WFS1 deficiency affects neurite outgrowth and synapse formation, potentially contributing to predisposition of psychiatric disorders, and offers a potential strategy of therapy.

overall_design: Single-cell RNA sequencing (scRNA-seq) data of neurons and astrocytes derived from both WT and WFS1-/- HuES8-NPCs.

first: Rui

last: Hu

first: Yuan

last: Fei


title: Influence of form of Se supplementation and tall fescue endophyte toxicity on the adrenal gland and kidney transcriptome of grazing beef steers

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

overall_design: Refer to individual Series


title: Single-cell RNA sequencing of non-hematopoietic cells from mouse thymus spanning embryonic and adult stages

city: Shenzhen

first: Lisha

last: Mou

state: Guangdong

address: Room 604, Building 1, Yinxingzhijie 1 Qi Guanlan, Longhua District

institute: Shenzhen Second People's Hospital

summary: Here we constructed a single-cell transcriptional landscape of non-hematopoietic cells from mouse thymus spanning embryonic and adult stages, producing transcriptomes of 30,959 TECs. We resolved transcriptional heterogeneity of developing TECs, and highlighted the molecular nature of early TEC lineage determination and cortico-medullary thymic epithelial cell lineage divergency.

overall_design: We purified non-hematopoietic cells from thymi at embryonic day 11.5 (E11.5, n=30) and E12.5 (n=30), E13.5 (n=23), E14.5 (n=26), E15.5 (n=25), E16.5 (n=26), newborn (n=14), 5-week old (n=4) from C57BL/6 mice. And we performed single-cell transcriptomics by droplet-based 10X Genomics.

first: Pengfei


title: Influence of form of Se supplementation and tall fescue endophyte toxicity on the adrenal gland transcriptome of grazing beef steers

summary: To test the hypothesis that average daily gain (ADG) and clinical parameters of steers grazing novel non-toxic (NTE) or toxic KY-31 (TE) endophyte-infected tall fescue would be improved by ad libitum intake of vitamin-mineral mixes (V-M) that contain 27 ppm Se as a 1:1 blend of SELPLEX:sodium selenite (MIX) vs. sodium selenite (ISe), 32 fescue-naïve beef steers depleted of Se were randomly assigned to ad libitum consumption ISe vs MIX for 35 d and fed enough of a NTE/alfalfa/grain diet to achieve 0.57 kg BW gain/d. Within Se-form treatments, 2 steers were randomly assigned to each of 4 NTE (ISe = 316 ± 31 kg, MIX = 315 ± 22 kg) or TE (ISe = 316 ± 37 kg, MIX = 314 ± 39 kg) paddocks for 84 d and had ad libitum access to their respective V-M. Steers were slaughtered over a 23-d period from day 90 to day 113 (August 27, 2019 to September 19, 2019) of the study and the left adrenal gland removed.

first: Phillip

middle: J

last: Bridges


title: Validation of a DNA methylation microarray for 285,000 CpG sites of the mouse genome

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: We report the technical and biological validation of the newly developed Infinium Mouse Methylation BeadChip microarray that covers over 285,000 methylation sites.

overall_design: The Infinium Mouse Methylation BeadChip interrogates > 285k methylation sites per sample at single-nucleotide resolution. It provides balanced coverage of CpG islands, transcription start sites, enhancers, imprinted loci and other regions.

first: Carlos

last: Garcia-Prieto


title: APOE4 genotype confers transcriptomic and functional alterations to primary mouse microglia

first: Alison

last: Goate

state: NY

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Relative to E3 microglia, E4 microglia exhibit altered morphology, increased numbers of endosomes and lysosomes, increased cytokine/chemokine production, and increased lipid accumulation at baseline. These changes were accompanied by increased activation of kinases that mediate global repression of translation. In a subsequent phagocytosis assay, E4 microglia exhibited increased accumulation of a variety of substrates when compared to E3 microglia. While transcriptomic profiling of myelin-challenged microglia revealed a largely overlapping response profile across genotypes, differential regulation of several pathways including interferon-related signaling, translation-related processes was identified in E4 versus E3 microglia both at baseline and following myelin challenge. Here we identify and describe several important functional alterations in E4 relative to E3 microglia. Together, our results suggest E4 genotype confers elevated levels of baseline stress to microglia relative to E3 genotype, even prior to treatment with exogenous stimuli. This work provides insight into the molecular mechanisms by which E4 genotype may increase risk for AD.

overall_design: The major genetic risk factor for AD is Apolipoprotein E (APOE) genotype, with the ε4/ε4 genotype increasing risk for AD by ten fold compared to the most common ε3/ε3 genotype. However, the impact of APOE genotype on microglial function has not been thoroughly investigated. To address this, we cultured primary microglia from mice in which both alleles of the mouse Apoe gene have been humanized to encode either human APOE ε3 (E3) or APOE ε4 (E4). Using a combination of immunocytochemistry, immunoblotting, and flow cytometry we profiled functional differences in the endolysosomal system, lipid accumulation, phagocytosis, and cytokine secretion across E3 and E4 microglia both at baseline and in response to an acute (~3 hour) myelin challenge. RNA sequencing was used to assess differences in transcriptional profiles across genotypes and treatment conditions.

first: Saima

middle: I

last: Machlovi

middle: M

first: Yiyuan

last: Liu

first: Edoardo

last: Marcora


title: Genome-Scale Analysis of Transcriptional Regulation by the Fbw7 Ubiquitin Ligase

city: Seattle

first: Heshani

last: Thirimanne

address: 1100 Fairview AV N, D2-213

institute: Fred Hutchinson Cancer Research Center


title: Expression of SWI/SNF subunits BRG1 and BRM in C33A cells

first: Ann-Kristin

last: Östlund-Farrants

address: Svante Arrheniusväg 20 C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

institute: Stockholm University

summary: We exogenously expressed the SWI/SNF ATPase catalytic subunits BRG1 and BRM in the lacking cell line C33A, and compared the differences with mock transfected cell at gene expression and alternative splicing level.

overall_design: Exogenous expression of SWI/SNF subunits BRG1 and BRM in C33A cells.

first: Antoni

last: Gañez Zapater

first: Sebastian

last: Mackowiak

first: Ann


title: RIP-sequence of IGF2BP3 in Ishikawa cells

status: Public on Mar 16 2022

city: Shenyang

first: Cuicui

last: Wang

state: Liaoning

address: Sanhao Street

institute: China Medical University

summary: To explain the possible molecular mechanism underlying the oncogenic roles of IGF2BP3 in EC, we employed RNA immunoprecipitation (RIP) assays to identify the lncRNAs involved in the regulation of IGF2BP3 function. RIP experiments, high-throughput sequencing and data analysis were performed by Seqhealth Tech (Wuhan, China). RIP assays were carried out on Ishikawa cells. The cells were lysed, and the lysis samples for immunoprecipitation reactions were incubated with anti-IGF2BP3 antibody (ab177477, Abcam, USA) or rabbit IgG (Cell Signaling Technology). The library products were enriched, quantified and finally sequenced on the Illumina PE150 platform.One hundred ninety-one candidates as IGF2BP3-interacting lncRNAs were identified in the RIP-seq results.

overall_design: Identifing IGF2BP3-interacting lncRNAs by RIP-seq.

first: Xiaoxin

last: Ma

first: Jian

first: Fanfei

last: Kong


title: RNA sequencing of LINC00958 silenced and LINC00958 non-silenced Ishikawa cells

summary: To confirm the downstream genes of LINC00958, we employed RNA sequencing (RNA-seq) to identify the differentially expressed genes when LINC00958 was silenced in Ishikawa cells. The sample of LINC00958-silenced Ishikawa cells (sh-LINC00958, n=3) and negative control cells (sh-NC, n=2) were sent to Shanghai Sangon Biotech of China for library construction, sequencing, data preprocessing and gene mapping. Sequencing was performed on an DNBSEQ-T7 platform for the generation of raw data. Genes were considered significantly differentially expressed if the P value < 0.05 and |log2FC| > 1.The results showed that a total of 305 mRNAs were regulated after LINC00958 knockdown (fold change>2, P<0.05)

overall_design: Examination of transcriptome level changes in LINC00958 silenced ishikawa cells


title: ERa-related enhancers driven by BAP18-induced chromatin accessibility with CTCF/NURF complex enrichment contributes to aromatase inhibitor non-response in breast cancer (ChIP-seq)

city: Wuhan

first: Ge

last: Sun

state: Hubei

address: Shizi Mountain Street No.1

institute: Huazhong Argriculture University

summary: Endocrine therapy is the preferred therapeutic strategy for estrogen receptor alpha (ERa)-positive breast cancer, but intrinsic endocrine resistance leads a significant challenge. CCCTC binding factor (CTCF)-mediated hyperactivation of ERa-associated enhancers have been recognized as important molecular mechanism leading to endocrine resistance, yet the underlying molecular mechanism of this process still remains unclear. Here, we found a critical enhancer modulator, Bromodomain PHD Finger Transcription Factor (BPTF) associated protein of 18kDa (BAP18), had a global recruitment on gene enhancer combining with CTCF. Consistently, ERa-related enhancer transactivation was highly correlated with increasing BAP18 enrichment. BAP18 interacted with SMARCA1, another nucleosome remodeling factor (NURF) complex subunit, participating modulating CTCF and ERa recruitment on enhancers. Interestingly, BAP18 globally advantaged chromatin accessibility of enhancer regions, especially the sites with CTCF binding, thereby increasing targeted enhancer-promoter looping (E-P looping) by facilitating CTCF recruitment. Our functional studies in multiple culture and aromatase inhibitor (AI)-nonresponse models reveal a critical role of BAP18 in regulating drug tolerance of breast cancer cells and patients. Collectively, our study suggested that BAP18 coordinated with CTCF in transactivating ERa-related enhancers, and exhibited a better understanding about chromatin remodeling and E-P looping mechanism of AI therapy resistance.

overall_design: MCF7 cells were treated with estrogen(E2)  and equal EtOH for 1 hour

first: Baosheng

last: Zhou


title: RNA-seq of biotin-labelled-miR190b pulldown

city: Reykjavik

first: Maria

last: Bustos

address: Sturlugata 8

country: Iceland

institute: University of Iceland

summary: T-47d breast cancer cells were transfected in 6 test/control replicates with biotinylated miR-190b mimic or biotinylated mimic negative control by Qiagen. After 48h cells were lysed and miRNA:mRNA complexes were pulled-down by double precipitation. Firstly by pulling down Ago2 with Dynabeads G with rad Ago2 antibody and secondly via streptavidin coated magnetic beads. The precipitation was carried out according to manufacturer protocol. RNA from the eluted samples was then isolated using phenol-chloroform-isoamyl alcohol mixure and suspended in RNAse free water. This experiment was implemented to assess direct targets bound by miR-190b in the ER-positive breast cancer subtype T-47d.

overall_design: Examination of direct miR-190b targets in ER-positive breast cancer

first: Elisabet

middle: A

last: Frick

first: Stefan

last: Sigurdsson


title: ERa-related enhancers driven by BAP18-induced chromatin accessibility with CTCF/NURF complex enrichment contributes to aromatase inhibitor non-response in breast cancer (ATAC-seq)


title: ERa-related enhancers driven by BAP18-induced chromatin accessibility with CTCF/NURF complex enrichment contributes to aromatase inhibitor non-response in breast cancer


title: Platinum-sensitive HGOC residual tumors share joint expression of CRYAB, CEACAM6, SOX2 genes with tumors that acquired resistance

city: montpellier

first: stanislas

middle: P

last: du manoir

address: 280 rue des apothicaires

institute: IRCM

summary:
Purpose: Most High-Grade Ovarian Carcinomas (HGOCs) are sensitive to carboplatin (CBP)-based chemotherapy but frequently recur within 24 months. Recurrent tumors remain frequently CBP-sensitive and acquire resistance after several CBP cycles. We developed Patient-Derived Xenografts (PDXs) that allow the study of these different stages of CBP-sensitive recurrence and acquisition of resistance.
Experimental Design: We generated PDX models from CBP-sensitive HGOC. PDXs were CBP- or mock-treated and tumors were sampled, after treatment and at recurrence. We also isolated models with acquired-resistance from CBP-sensitive PDXs upon repeated CBP treatment. Tumors were characterized transcriptome levels by Affymetrix microarrays.
Results: All PDX models reproduced treatment response seen in the patients. CBP-sensitive residual tumors contained non-proliferating tumor cells clusters embedded in a fibrotic mesh. This was absent in CBP-resistant tumors. Residual tumors had marked differences in gene expression when compared to naïve and recurrent tumors, indicating downregulation of cell cycle and proliferation and upregulation of interferon response and epithelial–mesenchymal transition. This gene expression pattern resembled that seen in embryonal diapause and ‘drug-tolerant persister’ states. Residual and acquired-resistance tumors share the overexpression of three genes – CEACAM6, CRYAB, and SOX2.
Conclusions: In HGOC PDX, CBP-sensitive recurrences arise from a small population of quiescent, drug-tolerant, residual cells embedded in a fibrotic mesh.  These cells overexpress CEACAM6, CRYAB and SOX2, a signature also associated with acquired resistance and poor patient prognosis

overall_design:
design 1 : To analyze residual cells after treatment of 3 CBP-sensitive Patient-Derived Xenografts (PDX), using Affymetrix microarrays, for a total of 12 samples (2 mock-treated biological duplicates and 2 CBP-treated biological duplicates X 3 PDX models).
design 2:  Patient-Derived Xenografts (PDX) were analyzed using Affymetrix microarrays,in naive(nai),  after recurrence (regrowth=reg), or after acquired-resistance(resis) following several cycle of CBP treatments.

first: Stanislas

last: du Manoir

first: Charles

last: Theillet

first: Claude

last: Sardet


title: Immunostimulatory cancer-associated fibroblast subpopulations can predict immunotherapy response in head and neck cancer

city: Nashville

first: Young

last: Kim

state: TN

address: 2220 Pierce Ave PRB 654

institute: Vanderbilt University Medical Center

summary:
Purpose: Cancer-associated fibroblasts (CAF) have been implicated as potential mediators of checkpoint immunotherapy response. However, the extensive heterogeneity of these cells has precluded rigorous understanding of their immunoregulatory role in the tumor microenvironment
Experimental Design: We performed high dimensional single-cell RNA sequencing (scRNA-Seq) on four patient tumors pre- and post-treatment from a neoadjuvant trial of advanced-stage head and neck squamous cell carcinoma (HNSCC) patients that were treated with the aPD-1 therapy, nivolumab. The head and neck CAF (HNCAF) protein activity profiles, derived from this cohort of paired scRNA-Seq, were used to perform protein activity enrichment analysis on the 28-patient parental cohort of clinically annotated bulk transcriptomic profiles. Ex vivo coculture assays were used to test functional relevance of HNCAF subtypes
Results: Fourteen distinct cell types were identified with the fibroblast population showing significant changes in abundance following nivolumab treatment. Among the fibroblast subtypes, HNCAF-0/3 emerged as predictive of nivolumab response, while HNCAF-1 was associated with immunosuppression. Functionally, HNCAF-0/3 were found to reduce TGFβ-dependent PD-1+TIM-3+ exhaustion of CD8 T cells, increase CD103+NKG2A+ resident memory phenotypes, and enhance the overall cytolytic profile of T cells
Conclusions: Our findings demonstrate the functional importance of distinct HNCAF subsets in modulating the immunoregulatory milieu of human HNSCC. Additionally, we have identified clinically actionable HNCAF subtypes that can be used as a biomarker of response and resistance in future clinical trials

overall_design: Single cell and bulk RNA sequencing of Head and Neck Squamous Cell Carcinoma before and after treatment with nivolumab

first: Aleksandar

middle: Z

last: Obradovic

first: Diana

last: Graves

first: Michael

last: Korrer

last: Drake

first: Andrea

last: Califano


title: Expression data of knock down LOC441461 in MKN74 cell lines

city: Seongnam

first: JeongMan

last: Park

address: 689, Sampyeong-dong, Bundang-gu, Seongnam-si

institute: CHA university

summary: Stable knockdown of LOC441461 was achieved in MKN-74 Gastric Cancer cells. LOC441461 expression of which was negatively correlated with malignancy as assessed by TNM staging. Knockdown was achieved using siRNA targeting LOC441461. Gene expression was compared between knockdown and scrambled siRNA treated control cells.

overall_design: Two distinct cell lines were used in this study (all MKN-74 cells); (i) transfected with scrambled negative control siRNA (N.C) or (ii) si-LOC441461. After 24 h incubation, total RNA was extracted from cells and used for RNA sequencing analysis.

first: KyuBum

last: Kwack

first: Sang-soo

last: Lee

first: Sooyeon

last: Oh


title: The Interplay Between Translational Efficiency, Poly(A) Tails, MicroRNAs, and Neuronal Activation

city: Berkeley

first: Timothy

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

summary: Neurons provide a rich setting for studying post-transcriptional control. Here, we investigate the landscape of translational control in neurons and search for mRNA features that explain differences in translational efficiency (TE), considering the interplay between TE, mRNA poly(A)-tail lengths, microRNAs, and neuronal activation. In neurons and brain tissues, TE correlates with tail length, and a few dozen mRNAs appear to undergo cytoplasmic polyadenylation upon light or chemical stimulation. However, the correlation between TE and tail length is modest, explaining <5% of TE variance, and even this modest relationship diminishes when accounting for other mRNA features. Thus, tail length appears to affect TE only minimally. Accordingly, miRNAs, which accelerate deadenylation of their mRNA targets, primarily influence target mRNA levels, with no detectable effect on either steady-state tail lengths or TE. Larger correlates with TE include codon composition and predicted mRNA folding energy. When combined in a model, the identified correlates explain 38–45% of TE variance. These results provide a framework for considering the relative impact of factors that contribute to translational control in neurons. They indicate that when examined in bulk, translational control in neurons largely resembles that of other types of post-embryonic cells. Thus, detection of more specialized control might require analyses that can distinguish translation occurring in neuronal processes from that occurring in cell bodies.

overall_design: The experiments consist of 12 matched samples of ribosome profiling libraries (small RNA-seq and RPF reads, 24 files in total) from primary neuronal cortical culture or mouse tissues. These samples have matched PAL-seq V2 or TAIL-seq data. In addition, there are eight samples (light stimulated mouse visual cortex samples) that have PAL-seq V2 data but no matched ribosome profiling data.


title: Differential effects on the translation of immune-related alternatively polyadenylated mRNAs in melanoma and T cells by eIF4A inhibitors

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie

summary: We explored the regulation of intronic polyadenylation (IPA) isoforms by silvestrol in melanoma and T lymphocytes.

overall_design: We performed 3'-seq analyses on heavy polysomes and whole cytosol mRNAs of T lymphocytes (n=3) treated with silvestrol (in DMSO) or DMSO (control) alone.

first: Biswendu

last: BISWAS

first: Ramdane

last: GUEMIRI

first: Mandy

last: CADIX

last: LABBE

first: Alina

last: CHAKRABORTY

first: Martin

last: DUTERTRE

first: Caroline

last: ROBERT

first: Stéphan

last: VAGNER


title: Mutant glucocerebrosidase impairs alpha-synuclein degradation by blockade of chaperone-mediated autophagy

city: New York

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: The most common genetic risk factors for Parkinson’s disease (PD) are a set of heterozygous mutant (MT) alleles of the GBA1 gene that encodes Beta-glucocerebrosidase (GCase), an enzyme normally trafficked through the ER/ Golgi apparatus to the lysosomal lumen. We found that half of the GCase in lysosomes from post-mortem human GBA-PD brains was present on the lysosomal surface, and that this mislocalization depends on a pentapeptide motif in GCase used to target cytosolic protein for degradation by chaperone-mediated autophagy (CMA). Unfolded mutant GCase at the lysosomal surface inhibits CMA, causing accumulation of CMA substrates including -synuclein. Using single cell transcriptional analysis and comparative proteomics of brains from GBA-PD patients we confirmed reduced CMA activity and proteome changes comparable to those in CMA-deficient mouse brain. Loss of the MT GCase CMA motif is sufficient to rescue primary substantia nigra dopamine neurons from MT-GCase induced neuronal death. We conclude that MT GCase alleles block CMA function and produce -synuclein accumulation.

overall_design: Droplet-based single nuclear RNA sequencing of Cyngulate Gyrus tissues from one non-pathological control, one Idiopatic and two Familiar PD patients.

first: Sheng-Han

last: Kuo

first: Inmaculada

last: Tasset

first: Melody

last: Cheng

first: Antonio

last: Diaz

first: Ming-Kai

last: Pan

first: Ori

last: Lieberman

first: Samantha

last: Hutten

first: Roy

middle: N

last: Alcalay

first: Sangjun

last: Kim

first: Pilar

last: Ximénez-Embún

last: Fan

first: Donghoon

first: Han

last: Ko

first: Talene

last: Yacoubian

first: Ellen

last: Kanter

first: Ling

last: Liu

first: Guomei

last: Tang

last: Muñoz

first: Sergio

last: Sardi

first: Aiqun

last: Li

first: Ana

last: Cuervo

first: David

last: Sulzer


title: Genome-Wide Investigation and Functional Analysis of RNA Editing Sites in Wheat

city: Islamabad

first: Muhammad Ramzan

last: Khan

state: pakistan

address: Park Road, National Agricultural Research Center (NARC)

department: National Institute Of Genomics And Advanced Bio-Technology (NIGAB)

country: Pakistan

institute: National Agricultural Research Centre

summary: The goals of this study were to compare the transcriptome of six genotypes of wheat grown under the normal conditions by RNA-Seq and to study the root architecture in drought sensitive and tolerant genotypes.

overall_design: Roots mRNA profiles of 35 days old six genotypes of wheat.

first: Khan

last: Ramzan

first: Ali

last: Naz

first: Jens

last: Léon

first: Fatima

last: Rasool


title: A single-cell transcriptomic landscape of innate and adaptive intratumoral immunity in triple negative breast cancer during chemo- and immunotherapies

city: Milan

first: Francesco

last: Bertolini

state: I am not in the U.S. or Canada

address: Via Giuseppe Ripamonti, 435

institute: European Institute of Oncology (IEO)

summary: Breast cancer (BC) constitutes a major health problem worldwide, making it the most common malignancy in women. Current treatment options for BC depend primarily on histological type, molecular markers, clinical aggressiveness and stage of disease. Immunotherapy, such as anti-PD-1, have shown combinatorial clinical activity with chemotherapy in triple negative breast cancer (TNBC) delineating some therapeutic combinations as more effective than others. However, a clear overview of the main immune cell populations involved in these treatments has never been provided.  Here, an assessment of the immune landscape in the tumour microenvironment (TME) of two TNBC mouse models (4T1 and EMT6 cell lines) has been performed using single-cell RNA sequencing (scRNA-seq) technology. Specifically, immune cells were evaluated in untreated conditions and after being treated with chemotherapy or immunotherapy used as single agents or in combination. A decrease of regulatory T cells, compared to the untreated TME, was found in treatments with in vivo efficacy as well as γδ T cells, which have a pro-tumoral activity in mice. Focusing on Cd8 T cells, across all the conditions, a general increase of exhausted-like Cd8 T cells was confirmed in pre-clinical treatments with low efficacy; on the other hand, an opposite trend was found for the proliferative Cd8 T cells. Regarding macrophages, M2-like cells were found enriched in treatments with low efficacy while opposite behaviour was associated with M1-like macrophages. For both cell lines, similar proportions of B cells were detected with an increase of proliferative B cells in treatments that involved cisplatin in combination with anti-PD-1. The fine-scale characterization of the immune TME in this work can lead to new insights on the diagnosis and treatment of TNBC for a possible application at the clinical level.

overall_design: Eight treatments and one untreated control for two murine tumoral cell lines (4T1 and EMT6).

first: Laura

last: Carpen

first: Paolo

last: Falvo

first: Stefania

last: Orecchioni

first: Giulia

last: Mitola

first: Roman

last: Hillje

first: Saveria

last: Mazzara

first: Patrizia

last: Mancuso

first: Stefano

last: Pileri

first: Alessandro

last: Raveane


title: Transcriptomic analysis of Steinernema nematodes highlights metabolic costs associated to Xenorhabdus endosymbiont association and rearing conditions

city: Tucson

first: Emilie

last: Lefoulon

state: AZ

address: 1117 E. Lowell Street

institute: University of Arizona

summary: We investigate the potential metabolic costs for Steinernema nematode in relation to the maintenance and vectoring of their Xenorhabdus endosymbionts. we performed a comparative dual RNA-seq analysis of infective juveniles (IJs) of two symbiotic partners: S. carpocapsae-X. nematophila and S. puntauvense-X. bovienii.

sample_organism:
Steinernema carpocapsae
Steinernema puntauvense

overall_design: For each association three conditions were study: 1) IJs reared in the insect (in vivo colonized), 2) colonized IJs reared on liver-kidney agar (in vitro colonized) and 3) IJs depleted by the bacteria reared on liver-kidney agar (in vitro aposymbiotic).

first: John

last: McMullen

first: S

last: Stock


title: Inhibition of HIV infection by structural proteins of the inner nuclear membrane is associated with reduced chromatin dynamics

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

summary: The human immunodeficiency virus (HIV) enters the nucleus to establish infection, but the role of nuclear envelope proteins in this process is incompletely understood. Inner nuclear transmembrane proteins SUN1 and SUN2 connect nuclear lamins to the cytoskeleton and participate in the DNA damage response (DDR). Increased levels of SUN1 or SUN2 potently restrict HIV infection through an unresolved mechanism. Here, we find that the antiviral activities of SUN1 and SUN2 are distinct. HIV-1 and HIV-2 are preferentially inhibited by SUN1 and SUN2, respectively. We identify DNA damage inducers that stimulate HIV-1 infection and show that SUN1, but not SUN2, neutralizes this effect. Finally, we show that chromatin movements and nuclear rotations are associated with the effects of SUN proteins and Lamin A/C on infection. These results reveal an emerging role of chromatin dynamics and the DDR in the control of HIV infection by structural components of the nuclear envelope.

overall_design: HeLa cells were transduced with a control lentivector or a lentivector expression human SUN1 or SUN2. RNA was extracted from resulting stable cell lines.

first: Anvita

last: Bhargava


title: Single cell RNA-seq for a mouse model of recessive dystrophic epidermolysis bullosa

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

summary: Recessive dystrophic epidermolysis bullosa (RDEB), intractable skin genetic disease, is caused by mutations in COL7A1. Most RDEB patients have mutations in a compound heterozygous manner. We established an RDEB model mouse with patient type mutations in a compound heterozygous manner. We selected two mutations, c.5818delC and E2857X, which is recurrently identified in human RDEB cohort, and introduced the mutations at corresponding locations of the mouse genome. We analyzed the established mouse by single cell RNA-seq to clarify how loss of functional type VII collagen impact on the integrity of skin.

overall_design: We collected back skins from mice (recessive dystrophic epidermolysis bullosa model). After isolating single cells by enzymatic dissociation, single cell RNA-seq analysis was performed.


title: ZNF207 promotes hepatocellular carcinoma by reprogramming kynurenine metabolism and inhibiting CD8+ T cell infiltration

city: Nanjing

first: Xu

last: Wang

state: Jiangsu

address: Longmian road 639

department: Center for New Drug Safety Evaluation and Research

institute: China pharmaceutical university

summary: Bioinformatic analysis identified ZNF207 as an immunosuppressive molecule in HCC. P53R249S mutation and hypoxia synergistically elevated ZNF207 expression. Silencing ZNF207 affected tumor growth in normal mice, but not in immunodeficient mice. Flow cytometry analysis showed increased proportion of CD8+ T cells in tumor tissues while exhaustion decreased after knocking down ZNF207. Mechanism studies showed that CX3CL1 was involved in the chemotaxis of CD8+ T cells, and ZNF207 regulated kynurenine production through transcriptional regulation of IDO1, then promoting the exhaustion of CD8+ T cells. High expression of ZNF207 showed a lower response rate to immunotherapy. In vivo experiments also confirmed the efficacy of ZNF207 knockdown combined with PD1 monoclonal antibody was better than PD1 alone.

overall_design: examine gene expression changes in ZNF207 knock down Hepa1-6

first: Yong

last: Yang

first: Xinying

last: Tang

first: Lutz

last: Birnbaumer


title: Pan-cancer predictions of transcription factors mediating aberrant DNA methylation

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

institute: IGBMC

summary:
Aberrant DNA methylation is a hallmark of cancer cells. However, the mechanisms underlying changes in DNA methylation remain elusive. Transcription factors initially thought to be repressed from binding by DNA methylation, have recently emerged as being able to shape DNA methylation patterns.
Here, we integrated the massive amount of data available from The Cancer Genome Atlas to predict transcription factors drivingAQ1 aberrant DNA methylation in 13 cancer types. We identified differentially methylated regions between cancer and matching healthy samples, searched for transcription factor motifs enriched in those regions and selected transcription factors with corresponding changes in gene expression. We predict transcription factors known to be involved in cancer as well as novel candidates to drive hypo-methylated regions such as FOXA1 and GATA3 in breast cancer, FOXA1 and TWIST1 in prostate cancer and NFE2L2 in lung cancer. We also predict transcription factors that lead to hyper-methylated regions upon transcription factor loss such as EGR1 in several cancer types. Finally, we validate that FOXA1 and GATA3 mediate hypo-methylated regions in breast cancer cells.
Our work highlights the importance of some transcription factors as upstream regulators shaping DNA methylation patterns in cancer.

overall_design: FOXA1 and GATA3 ChIP-seq (two replicates each) and corresponding input in HCC1954 breast cancer cells. WGBS in hTERT-HME1 normal cells and HCC1954 cancer cells as well as in FOXA1 and GATA3 KO clones (two replicates each) in HCC1954 cancer cells and with each a negative CRISPR clone.

first: Dylane

last: Detilleux

first: Yannick

last: Spill

first: Delphine

last: Balaramane

first: Michaël

last: Weber

first: Anaïs


title: A primate-specific alternative splicing of CCNE1 (pCCNE1) is an activator for evolutionally-gained enhancers [ChIP-seq]

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

summary: Divergence of protein and genetic function drives acquisition of novel phenotypes into organisms. Alternative splicing (AS) generates multiple proteins from a single gene and promotes the diversity of protein functions. The AS frequency has been increased throughout evolution and contributes to the complexity and the species specificity of cell and organ developmental programs. Retrotransposons (RTs) are major sources to configure the innovation and plasticity of the host genome and actively transcribed during human early development. However, it is not yet clear how the host genome responds to RTs in a reciprocal co-evolution. Here, we discovered that a primate-specific splicing variant of CCNE1 (pCCNE1) regulates primate-specific RTs to control human naïve pluripotency. Independent of the cell cycle regulatory function of ubiquitously-expressed CCNE1 (uCCNE1) with CDK2, we found that pCCNE1 competes with uCCNE1 in binding to the primate-specific RTs on a previously-uncharacterized DNA motif sequence. Especially, pCCNE1 preferentially activates hominid-specific SVA (SINE-VNTR-Alu) elements and synchronously upregulates their downstream host genes, which are uniquely expressed in human preimplantation embryos and naïve pluripotent stem cells (PSCs). Furthermore, pCCNE1 can activate dormant SVA (SINE-VNTR-Alu) enhancers and cooperatively activate their transcriptional regulatory activity with OCT4. Taken together, our results demonstrate that the evolutionary adaptation of human pluripotency via AS of CCNE1 contributes to the gain of novel molecular mechanisms for human-specific regulatory network, and how distinct phenotypes among species are created

overall_design: Chromatin binding profile of CCNE1 and OCT4

first: Kun-Yong

last: Kim

first: In-Hyun

last: Park


title: PP2A dependent modulation of c-Myc and p21 leads to differentiation and cell cycle control in Acute Myeloid Leukemia

city: Columbus

first: Pearlly

last: Yan

state: Ohio

department: Comprehensive Cancer Center

institute: The Ohio State University

summary: Aberrant kinase and phosphatase activity frequently contribute to Acute Myeloid Leukemia. Here we characterize the Protein Phosphatase 2A (PP2A) as a mediator of differentiation and cell cycle arrest in AML. Using a novel PP2A activator OSU-2S, we show that PP2A activation results in differentiation, growth arrest and cell death in AML, via depletion of c-Myc and upregulation of p21. Gene expression and mass cytometric profiling further show modulation of cell cycle regulators and differentiation factors, and importantly, decreased CD34+/CD38- stem cells in patient derived AML blasts treated with OSU-2S. Finally, we demonstrate in-vivo therapeutic efficacy of OSU-2S as seen by increased differentiation, decreased clonogenicity and improved survival in a Tet2-/-Flt3ITD murine AML model and human AML models.

overall_design: AML cultured cells were either treated with either by vehicle or OSU-2S, 3 replicates of each

first: Swagata

last: Goswami

first: Natarajan

last: Muthusamy


title: Expression data from Human Brain Cancer cell A172

city: SEOUL

first: Kyung-Chul

last: Choi

address: Sonpa-gu

department: Biomedical Sciences

institute: University of Ulsan college of Medicine

summary:
Histone Deacetylase (HDAC) is known as a key regulator of cell development and cancer through deacetylation of histones as well as other proteins. Recent studies have shown that HDAC class 1 expression is sometimes highly elevated in the diagnosis of patients who appear to have strongly proliferating cancer.
Among them, experiments were conducted to confirm the significance of the difference in the presence or absence of HDAC2.

overall_design: The expression of HDAC2 was induced in shHDAC2 using PLKO.1 Tet on vector in A172 cell line. Therefore, Doxycycline was treated in Tet on-shControl Cell and Tet on-shHDAC2 Cell through the presence or absence of HDAC2 expression in A172 cell line.

first: Sungmin

last: Kwak


title: A primate-specific alternative splicing of CCNE1 (pCCNE1) is an activator for evolutionally-gained enhancers [GRO-seq]

overall_design: Nascent RNA profiling in primed and naïve (5iLA or t2iGo) hESCs

first: Yoon

first: Tae-Hoon


title: Development of gene expression signatures for neonatal tissues of mice with Usp10 gene knockout

status: Public on Mar 15 2022

city: Beijing

first: hongchang

last: li

address: Changping District, Beijing

institute: State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing)

summary: To further explore gene expression in neonatal mice with Usp10 gene knockout, we have employed whole genome microarray expression profiling as a discovery platform to identify the pathways or biological processes with the potential to explain the cause of postnatal death of Usp10 knockout mice.  Kidney tissues from Usp10 knockout neonates and their littermates were used to be the samples to explore.

overall_design: Gene expression in neonatal mice was measured after birth about 6 hours. Three independent neonates for each genotype were performed.

first: Hongchang

last: Li


title: Maternal folic acid mild over consumption in mice leads to sex-specific transcriptional alterations in E17.5 embryonic cerebrum

city: Montreal

first: Rima

last: Rozen

state: Quebec

address: 1001 Decarie Blvd

department: Departments of Human Genetics and Pediatrics

institute: McGill University

summary:
Food fortification of folic acid (FA) and increased use of vitamin supplements have raised concerns over high folate intake periconceptionally. We reported that diet containing 5-fold higher FA than recommended for mice (5xFASD) during pregnancy, resulted in neurobehavioral abnormalities (hyperactivity and short-term memory impairment) in newborns. Our goal was to determine the origins of these changes and the underlying mechanisms by examing potential transcription changes in E17.5 embryonic cerebrum.
We used microarrays to compare the E17.5 cerebral gene expression changes by 5xFASD and indentified different transcription profiles due to diet or sex.

overall_design: At weaning, wild-type C57BL/6 female mice were placed on control diet (CD) or 5xFASD for a month before mating, and were maintained on the same diets until embryonic day 17.5 (E17.5). Cerebrums of both sexes from both diets were used for RNA extraction and were performed gene expression analysis by microarray using Affymetrix Clariom S array_Mouse Chip.

first: Yan

last: Luan

first: Marta

last: Cosín-Tomás

first: Daniel

last: Leclerc

first: Olga

middle: V

last: Malysheva

first: Marie

last: Caudill


title: A primate-specific alternative splicing of CCNE1 (pCCNE1) is an activator for evolutionally-gained enhancer

first: Yoshiaki

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

overall_design: Refer to individual Series


title: Maternal folic acid over consumption in mice leads to sex-specific transcriptional alterations in cerebral cortex in offspring

summary:
Recent concerns have been raised regarding high folate intake during pregnancy and lactation, particularly following food fortiﬁcation and increased vitamin supplement use. Epidemiologic studies have shown that high folic acid (FA) intake can negatively impact motor and neurocognitive development in offspring.
We used microarray to investigate the impact of a supplemented diet containing 5-fold higher FA than recommended (5xFASD) on cerebral transcription profile in both male and female postnatal day (P) 30 pups. We also studied gene expression changes due to sex.

overall_design: At weaning, wild-type C57BL/6 female mice were placed for a month on a control diet (CD) or 5x FASD, and then mated to study offspring. Diets were maintained throughout pregnancy and lactation until P30. We conducted several behavioral tests on pups before sacrificing them at P30. Cerebral cortices were collected to conduct gene expression analysis by microarray using Affymetrix Clariom S array_Mouse Chip.

last: Maleysheva


title: Gene expression analysis in high risk head and neck squamous cell carcinoma treated with post-operative radiotherapy

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

summary: Post-operative radiation therapy (PORT) is the standard treatment for patients with head and neck squamous cell carcinoma (HNSCC) having adverse pathological features. Despite PORT, many patients develop relapse causing morbidity and mortality. These specimens are from a high-risk cohort of such patients treated by PORT and are being used to develop gene signatures for therapeutic response.

overall_design: 102 specimens from surgically excised tumors. No replicates.

first: Michael

last: Story

first: K

last: Ang


title: Transcriptomics analysis of in vitro NASH models unveils potential adverse effect of elafibranor

city: Brussels

first: Joost

last: Boeckmans

address: Laarbeeklaan 103

department: In Vitro Toxicology & Dermato-Cosmetology (IVTD)

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

type:
Expression profiling by array
Third-party reanalysis

summary: Non-alcoholic steatohepatitis (NASH) is a life-threatening liver disease for which no drug has been approved. We have previously shown that human-derived hepatic in vitro models can be used to mimic key cellular mechanisms involved in the progression of NASH. In the present study, we first assess the predictive capacity of different in vitro models and then investigate how the reduction of NASH-specific parameters upon treatment with elafibranor, a PPAR-α/δ agonist, correlates with clinical NASH-resolution obtained through bariatric surgery.   Whole genome transcriptomics analyses revealed that in vitro NASH models based on primary human hepatocytes (PHH), HepaRG and human skin stem cell-derived hepatic progenitors (hSKP-HPC) exhibit up to 35% overlap with publicly available datasets of liver biopsies of 4 cohorts of NASH patients. Exposure of the in vitro NASH models to elafibranor partially reverses these human-specific transcriptional NASH signatures, with the hSKP-HPC-derived NASH model showing the most sensitive response. NASH-specific transcriptomic changes observed in patients that underwent bariatric surgery correlated with the changes observed in the in vitro NASH models exposed to the PPAR-α/δ agonist.   PPARGC1A, PPARA and SIRT1 are shared upstream regulators in the PHH-, HepaRG- and hSKP-HPC NASH models exposed to elafibranor. Activation of these upstream regulators increases the expression of ANGPTL4, PDK4 and PLIN2, while this does not occur in patients that underwent bariatric surgery, suggesting an adverse effect on lipid metabolism.   In conclusion, pathologic and therapeutic (anti-)NASH-specific transcriptional responses can be mimicked in PHH, HepaRG and hSKP-HPC, while the latter most sensitively responds to drug testing. PPAR-α/δ agonism adversely modulates pro-steatogenic genes which deserves attention in further studies.

overall_design: Hepatic in vitro models (human skin stem cell-derived hepatic progenitors (hSKP-HPC), primary human hepatocytes (PHH) and HepaRG cells) were exposed for 24h to lipogenic and inflammatory triggers in the abscence and presence of elafibranor (60 µM).

first: Anja

last: Heymans

first: Matthias

last: Rombaut

first: Vera

last: Rogiers

first: Joery

last: De Kock

first: Tamara

last: Vanhaecke

first: Robim

last: Rodrigues


title: Heterogeneity of tyrosine-based melanin anabolism regulates pulmonary and cerebral organotropic colonization microenvironment of melanoma cells

city: Shanghai

first: Xuefeng

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

summary: Dietary tyrosine regulating melanoma progression has been well-recognized. However, whether tyrosine-based melanin anabolism contributes to pulmonary and cerebral organotropic colonization of melanoma remains elusive. Furthermore, how to inhibit multi-organ metastasis by interfering tyrosinase activity of melanoma cells and function of immunocytes needs to be designed and validated. Patients derived melanoma cells and mouse B16 melanoma cells with different pigment were employed in this investigation. Tyrosine content dynamics in tumors and multiple organs during the melanoma progression were monitored, and tyrosine-based melanin synthesis ability of melanoma cells derived from multi-organ were detected. Additionally, we also adopted the RNA-seq, flowcytometry, real-time PCR and composite metastasis mouse model to analyze organotropic colonization and to design therapeutic strategies. B16 melanoma cells with high activity of tyrosinase and sensitivity of tyrosine utilization for melanin synthesis (Tyr-H cells) easily colonized in the lung, while B16 melanoma cells without above characteristics (Tyr-L cells) exhibited potent proliferation in the brain. Mechanistically, Tyr-H cells recruited and trained neutrophils and macrophages to build up the pulmonary metastatic niche dependent on highly secreted CXCL1 and CXCL2 and an excess melanosome accumulation-induced cell death. Tyr-L cells enhanced PD-L1 expression in tumor-infiltrated macrophages when they are progressing in the brain. Accordingly, intervention of tyrosinase activity (2-Ethoxybenzamide or hydroquinone), together with inhibitors to phagocytosis (GSK343) or chemotaxis (SB225002) suppress organotropic colonization and significantly improve the survival of immune checkpoint blockade (PD1 antibody) treated melanoma bearing mice. The heterogeneity of melanoma cells in utilization of tyrosine is associated with organotropic colonization, providing the basis for developing strategies to combat melanoma and prevent their metastasis.

overall_design: Six samples of B16 melanoma cells were analyzed by transcriptome sequencing

first: Yufang

last: Shi

first: Ying