title: Studies on the R595H hydrocephalus-associated mutation on Trim71

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

country: USA

institute: Mayo Clinic

summary: We studies on how a hydrocephalus-associated mutation (R595H) on Trim71 alters Trim71's substrate mRNA binding

overall_design: Transcriptome-wide Trim71 (R783H) target mRNAs were identified through CLIPseq in mouse embryonic stem cells)

first: Qiuying

last: Liu

first: Mariah

last: Novak

first: Rachel

middle: M

last: Pepin


title: Manipulating Cholesterol Metabolism by oncolytic virus suppresses metastasis of triple-negative breast cancer [ChIP-Seq]

status: Public on May 06 2022

city: Nanjing

first: Jie

last: Dong

address: Hankou road 22

country: China

institute: Nanjing University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Investigate the role of FOXO3a in the ApoA1 induced KRT14 suppression.

overall_design: 4T1 with ApoA1-over expression were cultured for 24h. CHIP-seq was performed in 4T1ApoA1 lysis by using Anti-FOXO3a.

first: Dong

last: Jie

first: Kong

last: Likai


title: Effect of overexpression of miR130a-3p and miR130b-3p on gene expression on mesenchymal stem cells

city: Shanghai

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

type: Expression profiling by high throughput sequencing

summary:
To investigate the reprogramming roles of miR130a-3p and miR130b-3p  on mesenchymal stem cells, we transefected miRNA minics to overexpress them.
We then performed gene expression profiling analysis using data obtained from total RNA-seq of 3 different treatment after 3 days transfection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data regulated by miR130a-3p or miR-130b-3p in mesenchymal stem cells (miR130a-3p and miR130b-3p).

first: Zheng

last: Wang

first: Ke

last: Sui


title: Effect of Disulfiram on T cell activation

first: Qinlan

address: Chongqingnan R.280

institute: Shanghai Jiaotong University

summary: To determine the effect of DSF on T cell activation ,we treated T cells with DSF and analyzed their functions.

overall_design: Comparative gene expression profiling analysis of RNA-seq for T cells after treated with DSF.

first: Feng


title: Transcriptome analysis for CT mRNA treated MDA-MB-468 cells and negative control cells

city: Seoul

first: Hyeon-Cheol

last: Lee

address: 136, Changgyeonggung-ro,Jongro-gu

department: Research center

country: South Korea

institute: BPgene Co., Ltd.

summary: We report the altered metabolite changes by processing CT mRNA in the TNBC cell line, MDA-MB-468. It was confirmed that the treatment of CT mRNA disrupted the synthesis of dTTP during nucleic acid metabolism, increasing the signal related to DNA damage in the cell, and that the energy metabolism and NADPH metabolism in the cell were changed for its recovery. The main energy sources, glucose metabolism and glutamine metabolism, are closely linked to the mitochondrial TCA cycle products. In the CT mRNA treatment group, intracellular nucleic acid depletion was observed to increase glutamine metabolism as a source of N source, and the pathway of aspartate utilization was observed. It was confirmed that it was expanded. As a result, a significant increase in the cysteine influx was observed according to the occurrence of ROS, and an effort to regulate the intracellular NADPH balance was observed through the change of metabolites over time. Finally, it was observed that the oncogenic pathway was significantly reduced in the CT mRNA-treated group compared with all untreated groups or controls with other substrate specificities. This study characterizes changes in intracellular metabolites caused by specific dTTP biosynthesis disturbances.

overall_design: Examination of T001 mRNA, 2 different nucleotidase and untreated cells

first: Bong-Seong

last: Koo

first: Jin-Sook

last: Kim

first: Dae-Ho


title: Effect of restoring endogenous ZFP36L1 expression in CORL47 SCLC Cells that are CRISPR activated for ZFP36L1 (sgZFP36L1-1 and sgZFP36L1-2) or a non-targeting sgRNA (sgControl)

city: Boston

first: Matthew

last: Oser

state: MA

address: 450 Brookline Avenue, Mayer 457

institute: Dana-Farber Cancer Institute

summary:
To investigate the impact of restoring endogenous ZFP36L1 expression in CORL47 SCLC Cells on neuroendocrine cell state
We performed RNA-sequencing on CORL47 SCLC Cells that are CRISPR activated for ZFP36L1 (sgZFP36L1-1 and sgZFP36L1-2) or a non-targeting sgRNA (sgControl)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CORL47 CRISPR activated sgZFP36L1-1, sgZFP36L1-2, or sgControl cells

middle: G


title: Effect of LSD1 Inhibitor ORY-1001 on NCI-H1876 small cell lung cancer cells that are CRISPR-inactivated for ZFP36L1 (sgZFP36L1) or ZFP36L1-WT (sgControl)

summary:
To investigate the impact of inactivating ZFP36L1 on the transcriptional response to the LSD1 inhibitor ORY-1001
We performed RNA-sequencing on NCI-H1876 sgZFP36L1 or sgControl cells treated with ORY-1001 or DMSO

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NCI-H1876 sgZFP36L1 or sgControl cells treated with ORY-1001 or DMSO


title: Translatome profiling of cortical layer5a neurons using S100a10 bacTRAP mice

city: NY

first: Revathy

middle: Uthaiah

last: Chottekalapanda

state: NY

address: 1230 York Avenue

department: Laboratory of Molecular and Cellular neuroscience

institute: The Rockefeller University

summary: Translational profiling of cortical layer5a neurons in response to stress and normalization by SSRI, Fluoxetine (Flx). Some Flx-treated animals were anxious.

overall_design: Polysome-bound mRNAs from TRAP immumoprecipitations were compared to whole tissue mRNAs from the whole cortex. We collected four replicates each for IP and inputs.

middle: U

first: Eric

middle: F

last: Schmidt

first: Evelyn

last: Lambe


title: ZFP36L1

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

overall_design: Refer to individual Series


title: Inhibition of Toll-like receptor 4 and Interleukin-1 receptor prevent SARS-CoV-2 mediated kidney injury in vitro

city: Sapporoshi kitaku

first: Daigo

last: Nakazawa

state: Hokkaido

address: kita15 nishi7

country: Japan

institute: Hokkaido University

summary: to explore the underlying mechanisms and therapeutic targets of renal SARS-CoV-2, we performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells treated with SARS-CoV-2

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUEhT and HK2 cells treated with SARS-CoV-2

first: Masatoshi

last: Kanda


title: Transcriptome changes associated with M9T337 root defense response after 6S-2 colonization and MR5 infection

city: Tai，an

first: Haiyan

state: Shandong

address: 61 Daizong Street

institute: Shandong Agricultural University

summary: To study the transcriptional level of M9T337 roots induced by T. asperellum 6S-2, and the mechanism of defense against MR5.

overall_design: We then performed gene expression profilling analysis using data obtained from RNA-seq of 4 different treatments (CK, Ta, Fp,TaFp) at three repetitions

first: Zhiquan

last: Mao


title: CRISPR/Cas9 screening targeting the deregulated metabolic genes in Huh 7 cells

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

summary: The exact functional roles of most of the dysregulated metabolic genes in tumorigenicity are still unclear. We report the application of CRISPR/Cas9 knockout screen technology in hepatocellular carcinoma cells. By an in vivo CRISPR/Cas9 knockout screen that targets 1,121 differentially expressed metabolic genes in HCC, we identified 67 metabolic genes as oncogenic candidates for HCC.

overall_design: A pooled sgRNA library, which contained 6,726 sgRNAs targeting 1,121 metabolic genes, 12 sgRNAs targeting two validated oncogenes and 500 control sgRNAs, was constructed and transduced into HUH7 cells stably expressing Cas9-GFP-Luc at a multiplicity of infection (MOI) of 0.3. The transduced cells were selected with puromycin, propagated and subcutaneously transplanted into NOD/SCID mice. After we harvested genomic DNA from the primary tumors at 4 weeks after transplantation and HUH7 cells, the sgRNA sequences were PCR-amplified and measured by next-generation sequencing to determine the enrichment in day 28 (T28) cells relative to day 0 (T0) cells.

first: Hongquan

last: Li

first: Zhiao

last: Chen


title: Mature human iPS- and NMP-derived motor neurons in alginate neural ribbons [Alg60]

city: Albany

first: Janet

middle: L

last: Paluh

address: CNSE, Nanofab East, 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

summary: Unpublished findings related to iScience 2021 article: Fully characterized mature human iPS- and NMP-derived motor neurons thrive without neuroprotection in the spinal contusion cavity

overall_design:
RNA-Seq of; Day  32 Spinal Motor Neurons of humanAfrican American hiPSC line F3.5.2 in alginate neural ribbons

The Paluh-HKYW5AFXY.featureCounts.tsv contains processed data for both GSE178600 and GSE178601.

first: Zachary

middle: T

last: Olmsted


title: CRISPR/Cas9 screens reveal that hexokinase 2 enhances cancer stemness and tumorigenicity

summary: We identified that HK2 facilitate the maintenance and self-renewal of liver cancer stem cells (CSCs). Moreover, HK2 exerts its function by enhancing the accumulation of acetyl-CoA and epigenetically activating the transcription of acyl-CoA synthetase long chain family member 4 (ACSL4), leading to an increase in fatty acid β-oxidation (FAO) activity.

overall_design: Huh 7 cells were transfected with siRNA targeted indicated genes using Lipofectamine RNAiMAX or were transfected with shRNA targeted indicated genes lentivirus. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed using indicated antibodies to study the H3K27ac status and binding sites of transcription factor in Huh 7 cell.


title: Regulation of flowering time by autophagy in rice

city: Beijing

first: Zhi

last: Hu

address: No.20, Nanxin Village, Xiangshan, Haidian District, Beijing

institute: Institute of Botany, Chinese Academy of Sciences

summary: This study investigated the effect of autophagy on flowering time in rice. Results provide important information of the response of flowering time to autophagy, such as specific flowerig time genes, up- or down-regulated specific flowering time functions.

overall_design: We examined gene expression by RNA-seq in wide-type and mutant osatg5-1 at the tellering stage.WT and osatg5-1 were growth on a faddy field under natural long-day conditions. the mature leaves were frozen in liquid nitrogen before mRNA extraction for sequencing at the tillering stage. There are 3 replicates per sample.

first: Lu

middle: C

last: Ming

first: Hu

last: Zhi


title: Intron Mutations and Early Transcription Termination in Duchenne and Becker muscular dystrophy

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

summary:
Purpose: DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated in 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis.
Methods: Reverse transcription PCR (RT-PCR) or high-throughput RNA sequencing (RNA-Seq) methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations.
Results: In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3’-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD.
Conclusions: We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches.  Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients.

overall_design: Skeletal muscle mRNA profiles of patients with intronic mutations in the dystrophin gene.


title: A combined human gastruloid model of cardiogenesis and neurogenesis

summary: Here we extend our previous EMLO gastruloid technology to cardiac (EMLOC) with the generation of interconnected neuro-gut-cardiac interconnected multilineages. The contractile EMLOCs recapitulate numerous developmental features of heart tube formation and specialization, cardiomyocyte differentiation and remodeling phases, epicardium, ventricular wall morphogenesis, and formation of the putative outflow tract. Cardiogenesis in EMLOCs originates anterior to the gut tube primordium and we observe neurons that progressively populate the cardiogenic region in a pattern that mirrors the spatial distribution of neurons in heart innervation. The EMLOC mode represents the first multi-lineage advancement  of neuro-cardiac lineages in a gastruloid model that parallels human cardiogenesis with neurogenesis.

overall_design: single cell combined RNA-Seq of day 7 and day 16 EMLOC gastrulids drom human Hispanic-Latino hiPSC line H3.1.1


title: Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [RNA-seq]

city: Daejeon

first: Taemook

last: Kim

address: 291 Daehak-ro, Yuseong-gu

department: Biological sciences

institute: Korea Advanced Institute of Science and Technology

summary: Triple-negative breast cancer (TNBC) is malignant cancer with a high risk of recurrence. To date, the underlying 3D chromatin organizations of TNBC have remained unclear. Here, using in situ Hi-C, we characterized the 3D chromatin organizations in cells representing five distinct subtypes of breast cancer (including TNBC) and TNBC tissues, compared to normal cells/tissues. We found that the global and local 3D architectures are severely disrupted in TNBC cells. Importantly, we detected CTCF-dependent TNBC-susceptible loss/gain of 3D chromatin organizations and found that these changes were strongly associated with perturbed chromatin accessibility and transcriptional dysregulations. Although some discrepancies exist between TNBC cell lines and tissues, we observed that perturbed local 3D architectures found in TNBC cells are partially conserved in TNBC tissues. Furthermore, we discovered distinct tissue-specific chromatin loops by comparing normal and TNBC tissues. Collectively, our findings provide important features of 3D chromatin organization in TNBC.

overall_design: For RNA-seq experiment (cell lines) : Strand-specific mRNA-seq of Human mammary epithelial cell (HMEC, as a control) and the cell line of 5 breast cancer subtypes, The cell lines were performed the biological replicates. For RNA-seq experiment (Tissues) : Strand-specific mRNA-seq of Five Contralateral breast normal tissue, fourteen triple negative breast cancer (IDC) tissues.

first: Sungwook

last: Han

first: Yujin

last: Chun

first: Hyeokjun

last: Yang

first: Hyesung

last: Min

first: Sook Young

last: Jeon

first: Jang-il

first: Hyeong-Gon

last: Moon

first: Daeyoup

last: Lee


title: Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [ATAC-seq]

overall_design:
For ATAC-seq experiment (cell lines) : Genome-wide distribution of chromatin accessibility in Human mammary epithelial cell (HMEC, as a control) and the triple negative breast cancer B subtype cells (BT549)
Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.


title: Single-Cell Transcriptomics of hypothalamic CRH-expressing neurons informs mechanisms by which Early-Life Adversity sculpts stress-responses enduringly

city: Irvine

first: Seyed

middle: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3 519 Ring Rd

department: Developmental and Cellular Biology

institute: University of California, Irvine

summary: Mental and cognitive health, as well as vulnerability to neuropsychiatric disorders, involve the interplay of genes with the environment during sensitive developmental periods. Genetic and environmental factors contribute to the development and maturation of neurons, synapses, and the resulting brain circuits. Within the hypothalamus, early-life experiences cause changes in the number of excitatory synapses onto corticotropin-releasing hormone (CRH)-expressing neurons in the paraventricular nucleus (PVN). Further, such synaptic changes suffice to induce enduring epigenomic changes within these cells, influencing programs of gene expression. However, the epigenetic mechanisms by which early-life experiences orchestrate transcriptional programs within individual CRH-expressing neurons, with enduring functional consequences, remain unknown. We utilize animal models of an impoverished environment and unpredictable maternal care (in a limited bedding and nesting [LBN] paradigm), which provokes major alterations in cognitive and emotional outcomes. We are focused on the change in gene expression profiles of stress-sensitive CRH-neurons in the PVN following early-life adversity (ELA). Because of the known heterogeneity of CRH-expressing neuronal populations, we are using single-cell RNA sequencing (RNA-seq) to determine differential gene expression associated with early-life adversity and establish the upstream mechanisms and downstream consequences. We found that CRH-expressing populations of neurons in the PVN can be clustered by both their gene expression profiles as well as by their neurotransmitter phenotype. ELA significantly modified gene expression programs in some neuronal clusters more than others, reducing programs of neuronal development and differentiation and enhancing gene families involved in responses to stress and inflammation. The use of single-cell transcriptomics revealed that ELA impacts gene expression profiles in a cell-type specific manner, with distinctive influence on the different clusters and subpopulations of CRH neurons.

overall_design: Compare control vs early life adversity conditions in mice during a sensitive time in brain development

first: Christina

middle: W

last: Thai

first: Annabel

last: Short

first: Tallie

middle: Z

last: Baram

first: S

middle: A


title: PARP1 binds and regulates expression of extracellular matrix genes in renal tubular epithelial cells [RIP-Seq]

city: Wu Han

first: Jing

last: Ke

address: No. 17 High-tech 6th Road, East Lake High-tech Development Zone, Wuhan, Hubei 430200, China.

institute: Renmin Hospital of Wuhan University

summary: To exploit the potential function of PARP1 during renal IRI by binding target RNA to regulate its expression, we obtained PARP1 bound peaks in proximal tubular epithelial cell (HK-2) by iRIP-seq for the first time, which showed that the bind peaks of PARP1_IP group is more enriched at GGUAA-rich motifs and PARP1 preferentially bound to the downstream of TSS (transcription start site) and upstream of TTS (transcription termination site). iRIP-seq analysis was used to decipher RBP binding sites and revealed the RNA that interacts with PARP1 within the genome of HK-2 cells.

overall_design: RIP-seq analysis of PARP1 IP versus input in HK-2 cells

first: Xiongfei

last: Wu


title: Comparative Characterization of 3D Chromatin Organization in Triple-Negative Breast Cancers [ChIP-seq]

overall_design:
For ChIP-seq experiment (cell lines) : Genome-wide distribution of CTCF and H3K27ac in Human mammary epithelial cell (HMEC, as a control) and the cell line of 5 breast cancer subtypes, The cell lines were performed the biological replicates.
Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.


title: Cord blood methylation profiles of bronchopulmonary dysplasia in preterm infants

status: Public on May 05 2022

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

type: Methylation profiling by genome tiling array

summary: Bronchopulmonary dysplasia (BPD) is a lung disease in premature infants characterized by impaired pulmonary development which persists into later life. While advances in neonatal care have improved survival rates of premature infants, cases of BPD haves been increased. Therapeutic options are limited for prevention and treatment. This study was designed to explore the relationship between gestational age (GA), birth weight and estímate blood cell-type composition in premature infants and to elucidate early epigenetic biomarkers associated with BPD. Cord blood DNA from preterm neonates that went on to develop BPD (n = 14) or not (nonBPD, n = 93)  was applied to Illumina 450K methylation arrays. Using DNA methylation analysis of cord blood DNA, we investigated association of GA and birth weight with the estimated distribution of cord blood cell types, particularly the nucleated red blood cell (NRBC) in a pilot-size cohort of preterm infants with or without BPD. We describe changes in methylation-based estimates of blood cell-type composition in relation to GA and birth weight. After adjusting for covariates (GA, birth weight, cell type proportions, etc.) we identify differentially methylated CpGs and genes associated with BPD.

overall_design: Cord blood DNA from preterm neonates that went on to develop BPD (n = 14) or not (nonBPD, n = 93)  was applied to Illumina 450K methylation arrays. We identify differentially methylated CpGs associated with BPD.

first: Douglas

last: Bell


title: Response of aspen cell cultures to combinatorial feeding of methyl jasmonate and AOPP.

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: Department of Genetics

institute: The University of Georgia

summary: To better understand the role of phenylpropanoid pathway perturbation in plant metabolism, Populus tremuloides cell cultures previously established from leaf mesophyll tissue were fed with methyl jasmonate, alpha-aminooxy-beta-phenylpropionic acid (AOPP), or both approximately 5 days after transfer to fresh medium.  Methyl jasmonate is an elicitor that activates a suite of defense responses including phenylpropanoid metabolism.  In contrast, AOPP acts as an inhibitor of phenylalanine ammonia lyase (PAL).  Samples were harvested 48 hrs after initiation of the experiment.  Total RNA was extracted and gene expression measured using Affymetrix poplar genome microarrays.

overall_design: Populus tremuloides cells suspended in liquid culture were fed methyl jasmonate in DMSO (MJ), alpha-aminooxy-beta-phenylpropionic acid in DMSO (AOPP), each compound in DMSO (MJ_AOPP), or with DMSO alone (C).  Two replicates of total RNA were utilized for microarray analysis from a total of six replicates generated per treatment.

first: L

middle: K

last: Tuominen

first: Raja

last: Payyavula

first: Lei

last: Du

first: Scott

last: Harding


title: Cord blood gene expression profiles of bronchopulmonary dysplasia in preterm infants

summary: Bronchopulmonary dysplasia (BPD) is a lung disease in premature infants characterized by impaired pulmonary development which persists into later life. While advances in neonatal care have improved survival rates of premature infants, cases of BPD haves been increased. Therapeutic options are limited for prevention and treatment. This study was designed to explore differentially expressed genes associated with BPD. Cord blood mRNA from preterm neonates that went on to develop BPD (n = 6) or not (nonBPD, n = 17)  was applied to Illumina HumanHT-12 arrays, we identify differentially expressed genes associated with BPD.

overall_design: Cord blood mRNA from preterm neonates that went on to develop BPD (n = 6) or not (nonBPD, n = 17)  was applied to Illumina humanHT-12 arrays. We identify differentially expressed genes associated with BPD.


title: AOS10-FMT could rescure the adverse effects of STZ on the liver

city: Qingdao

first: Yong

last: Zhao

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of STZ on the liver, and found that the AOS could rescure the side-effect of STZ in many factors,such as lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged liver induced by STZ

first: Yana

last: Hao


title: mRNA expression quantitative Analysis of Kasumi-1 treated with I13 compared with control

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are toevaluate the mRNA expressions of genes in Kasumi-1 cell lines treated with I13

overall_design: There are 6 samples for Kasumi-1 cell line ( control and I13-treated).


title: cDC1 retain a niche for precursor exhausted T cells during chronic viral infection

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: Tumors and chronic infections result in sustained antigen exposure, which promotes impaired functional responsiveness in T cells referred to as exhaustion. Checkpoint immunotherapy can induce the reinvigoration of cellular immunity by activating a recently identified precursor of exhausted T (TPEX) cell population. This activation requires cellular interactions between TPEX cells and professional antigen-presenting cells, likely conventional dendritic cells (cDC). Currently, it is unknown where cDC - TPEX cell interactions take place and which cDC subsets are involved. To address these questions, we first mapped the differentiation trajectory of TPEX cell subsets via transitory cellular states towards terminally exhausted T (TEX) cells, identified transcriptionally distinct subpopulations and defined their localization in the spleen during chronic viral infection. We found that cDC were required for TPEX cell proliferation, differentiation and viral control during PD-L1 treatment. In particular cDC1, a specialized subset of dendritic cells, colocalized with TPEX cells and regulated their maintenance by promoting the functionality of stromal cells that support TPEX cell survival. Additionally, during PD-L1 treatment, the splenic cDC1 network was significantly reorganized at the marginal zone, a site of TPEX cell differentiation. As a consequence, viral control during checkpoint immunotherapy and cellular integrity of the marginal zone depended on the presence of cDC1. Since cDC2 were sufficient to drive initial TPEX cell proliferation and TEX cell generation but not viral control, our data suggest a new concept in which cDC1 decelerate the speed of differentiation of TPEX cells via transitory cellular states and thereby generate a therapeutic window for effective immunotherapy. Together, our findings reveal how the dynamic spatial organization of the DC network supports cellular niches that guide the maintenance and differentiation of TPEX cells and opens new avenues to optimize checkpoint immunotherapy.

overall_design: B/6 Mice were infected with 2x10^6 IU LCMV clone13 after 2 times CD4 T cell depletion (d2 and d0) with 300µg GK1.5 antibody. At the chronic infection phase (> d30), splenocytes were isolated and CD8+, PD-1+, Tim-3 low cells were sorted using FACS AriaIII. Treated mice were injected i.p. 200µg aPD-L1 antibody (clone 10F.9G2) 24h before sacrificing the mice. Cells were pooled form 4 mice per group.

first: Konrad

last: Knöpper

first: Panagiota

last: Arampatzi

first: Antoine

middle: E

first: Wolfgang

last: Kastenmüller


title: Vasoactive intestinal peptide expressing pDC effects on T cells

city: Atlanta

first: Jingru

last: Zhu

address: 1365 E Clifton Rd NE Building C

department: Hematology/Oncology

institute: Winship Cancer Institute

summary: B10.BR mice were lethally irradiated and infused with 5000 FACS-sorted HSCs and 1000000 T cells from C57B/6J donors with 50000 FACS-purified wild-type pDCs or VIP-KO pDCs. On day 8 and day 15 after the bone marrow transplant, donor T cells were isolated and the RNA expression were detected.

overall_design: 24 samples are analysed, including 4 replicates in each group and 2 groups as control.

first: Sruthi

last: Ravindranathan


title: AOS10-FMT could rescure the adverse effects induced by STZ on the Spleen

summary: We report the side-effects of STZ on the spleen, and foud that the AOS10-FMT could rescure the side-effect of STZ in many factors,such as inflammation

overall_design: Exploration of the FMT effects on the damaged spleen induced by STZ

first: Yanan


title: BCG therapy downregulates HLA-I on malignant cells to subvert antitumor immune responses in bladder cancer [NanoString_IMM]

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Patients with high-risk non-muscle-invasive bladder cancer (NMIBC) frequently relapse after standard intravesical BCG therapy and may have a dismal outcome. Resistance mechanisms to such immunotherapy remain misunderstood. Here, using cancer cell lines, freshly resected human bladder tumors and cohorts of bladder cancer patients pre- and post-BCG therapy, we demonstrate two distinct patterns of immune subversion upon BCG relapse. In the first pattern, intracellular BCG infection of cancer cells induced a post-transcriptional downregulation of HLA-I membrane expression via an inhibition of the autophagy flux. Patients with HLA-I deficient cancer cells post-BCG therapy displayed a myeloid immunosuppressive tumor microenvironment with epithelial-to-mesenchymal transition (EMT) characteristics and dismal outcomes. Conversely, patients with HLA-I proficient cancer cells post-BCG therapy presented with CD8+ T cell tumor infiltrates, upregulation of inflammatory cytokines and inhibitory immune checkpoint molecules. Those patients had a very favorable outcome. We surmise that HLA-I expression in bladder cancers at relapse post-BCG does not result from immunoediting but rather from an immune subversion process directly induced by BCG on cancer cells, which predicts dismal prognosis. Cancer cells HLA-I scoring by immunohistochemistry (IHC) staining can be easily implemented by pathologists in routine practice to stratify future urothelial cancer patient treatment strategies.

overall_design: NanoString Pan-Cancer Immune Panel on paired T1 human bladder tumors pre-BCG therapy and ≥T2 bladder tumors post-BCG therapy.

first: Mathieu

last: Rouanne

first: Julien

last: Adam

first: Camelia

last: Radulescu

first: Tuan

first: Aurélien

last: Marabelle


title: LncRNA LYPLAL1-DT screening from type 2 diabetes with macrovascular complication contributes protective effects on human umbilical vein endothelial cells via regulating the miR-204-5p/SIRT1 axis.

first: yihan

last: liu

address: No.10 Xitoutiao, Youanmen, Fengtai District

institute: Capital Medical University

summary: Long noncoding RNAs (lncRNAs) are involved in diabetes related diseases. However, the role of lncRNAs in the pathogenesis of type 2 diabetes with macrovascular complication (DMC) has seldomly been recognized. This study screened lncRNA profiles of leukocytes from DMC patients and explored protective role of lncRNA LYPLAL1-DT in endothelial cells (EC) under high glucose (HG) and inflammatory conditions (IS). Between DMC and healthy controls, 477 differential expression lncRNAs (DE-lncRNAs) were identified. The enrichment and pathway analysis showed that most of the DE-lncRNAs belonged to inflammatory, metabolic, and vascular diseases. A total of 12 lncRNAs was validated as significant DE-lncRNAs in expanding cohorts. Furthermore, these DE-lncRNAs were shown to be significantly related to hypoxia, HG, and IS in EC, especially lncRNA LYPLAL1-DT. LYPLAL1-DT overexpression results in the promotion of the proliferation, and migration of EC, as well as an elevation of autophagy. Overexpressed LYPLAL1-DT reduces the adhesion of monocytes to EC, boosts anti-inflammation, and suppresses inflammatory molecules secreted in the medium. Mechanistically, LYPLAL1-DT acts as competing endogenous RNA (ceRNA) by downregulating miR-204-5p, therefore enhancing SIRT1 and protecting EC autophagy function; thus, alleviating apoptosis. Finally, exosome sequencing revealed LYPLAL1-DT expression was 4 times lower in DMC cells than in healthy samples. In general, we identified LYPLAL1-DT having protective effects on EC as ceRNA mediated through the miR-204-5p/SIRT1 pathway. Therefore, it inhibits the autophagy of EC as well as modulating systemic inflammation. This approach could be regarded as a new potential therapeutic target in DMC.

overall_design: gene expression profiling analysis of RNA-seq data for 6 patients diagnosed with DMC(type 2 diabetes with macrovascular complication) and 6 health controls

first: Xiaoyan

first: Yihan

last: Liu

first: Xiao


title: PARP1 binds and regulates expression of extracellular matrix genes in renal tubular epithelial cells [RNA-Seq]

first: Jing

last: Ke

summary: PARP1 (Poly adenosine diphosphate ribose polymerase 1) is a ribozyme activated by a broken single-stranded DNA. Recent studies implicate PARP1 not only binds DNA but also be an RNA-binding protein. PARP1 participate in the regulation of renal ischemia-reperfusion injury through binding RNAs, but the mechanism is not clear. Reduced levels of PARP1 led to a significant decrease in cell proliferation and necrosis in the renal ischemia-reperfusion injury cells. In this study, RNA‑seq analysis of the transcriptomes of HK-2 cells with PARP1 knockdown, revealed that genes related extracellular matrix organization and immune response were under global transcriptional regulation.

overall_design: transcrptional analysis of PARP1 knockdown and control in HK-2 cells

first: Xiongfei

last: Wu


title: Morphogenetic and transcriptomic signature of syncytialization from human trophoblast stem cells

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We reveal that STB which differentiated from hTSCs could recapitulate morphogenetic events that physiologically occur during human embryo implantation. STB could also recapitulate the genetic signature of trophoblast differentiation during implantation. It will provide a reliable model to investigate the syncytialization of trophoblast during implantation. Our discovery was potentially valuable in advancing not only our current understanding of implant progression but also paying the way to investigate recurrent implantation failure.

overall_design: Human trophoblast stem cells (hTSCs) were derived from human embryos and induced for the differentiation of extravillous trophoblast cells (EVT) and syncytiotrophoblast (STB). STB was cultured in Matrigel to mimic the morphogenesis of primary syncytialization in human embryos during implantation. To evaluate the similarity between syncytialization from hTSCs and syncytialization in human embryos, three-dimensional culture and immunofluorescence staining of STB, single-cell RNA sequencing, and culturing human embryos to the post-implantation stage were performed.

first: Yiming

last: Wang

first: Hongmei


title: Identification of distinct miRNAs associated with SARS-CoV-2 infection

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

institute: First Affiliated Hospital of Xi 'an Jiaotong University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) have been shown to play important roles in the pathogenesis of viral infections, but little is known about the miRNA alternations associated with SARS-CoV-2 infection. Here, we performed high throughout sequencing to detect miRNAs in the plasma samples collected from 61 healthy controls, 16 asymptomatic individuals and 100 symptomatic COVID-19 patients. In total, we identified 2,336 known miRNAs and 361 novel miRNAs, including 75 differentially expressed miRNAs with p value<0.05 between various groups. We also found a number of miRNAs that were associated with various clinical presentations and viral persistence of COVID-19, such as hsa-miR-370-3p, hsa-miR-146a-3p, hsa-miR-885-5p, hsa-miR-214-3p and hsa-miR-10b-5p. Further analysis of the target genes, gene ontology and KEGG pathways revealed a panel of miRNAs that were linked to immune responses, viral infections, inflammation and apoptosis. Our findings may help understand the contribution of miRNAs to the pathogenesis of COVID-19 and identify potential biomarkers and molecular targets for the diagnosis and treatment of SARS-CoV-2 infection.

overall_design: 233 peripheral blood samples included 165 samples derived from 116 COVID-19 patients at different times, 2 suspected samples and 66 samples derived from 61 healthy controls.

first: Chengsheng

last: Zhang


title: Response of aspen cell cultures fed piperonylic acid to methyl jasmonate.

first: Chung-Jui

last: Tsai

summary:
To better understand the role of phenylpropanoid pathway perturbation in plant metabolism, Populus tremuloides cell cultures previously established from leaf mesophyll tissue were fed with piperonylic acid (PIP) alone, or in combination with methyl jasmonate (MJ_PIP) approximately 5 days after transfer to fresh medium.  Methyl jasmonate is an elicitor that activates a suite of defense responses including phenylpropanoid metabolism, while PIP acts as an inhibitor of cinnamate-4-hydroxylase (C4H).  Sample tissues were contemporary with those used to generate Series GSE16773.
Samples were harvested 48 hrs after initiation of the experiment.  Total RNA was extracted and gene expression measured using Affymetrix poplar genome microarrays.

overall_design: Populus tremuloides cells suspended in liquid culture were fed with piperonylic acid dissolved in DMSO (PIP) either alone or in combination with methyl jasmonate in DMSO (MJ).  Two replicates of total RNA were utilized for microarray analysis from a total of six or seen replicates produced per treatment condition.

first: Raja

last: Payyavula

first: Lei

last: Du

first: Scott

last: Harding


title: PTBP1 promotes hematopoietic stem cell maintenance and red blood cell development by ensuring sufficient availability of ribosomal constituents

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

summary: Ribosomopathies constitute a range of disorders associated with defective protein synthesis mainly affecting hematopoietic stem cells (HSCs) and erythroid development. Here we demonstrate that deletion of Polypyrimidine Tract Binding Protein 1 (PTBP1) in the hematopoietic compartment led to the development of a ribosomopathy-like condition. Specifically, loss of PTBP1 was associated with decreases in HSC self-renewal, erythroid differentiation and protein synthesis. Consistent with its function as a splicing regulator, PTBP1 deficiency led to splicing defects in hundreds of genes, and we demonstrate that the up-regulation of a specific isoform of CDC42 could partly mimic the protein synthesis defect associated with loss of PTBP1. Furthermore, PTBP1 deficiency was associated with a marked defect in ribosome biogenesis and a selective reduction in the translation of mRNAs encoding ribosomal proteins. Collectively, this work identifies PTBP1 as a key integrator of ribosomal functions and highlights the broad functional repertoire of RNA binding proteins.

overall_design: RNA-seq transcriptomic analysis of FACS sorted bone marrow progenitors; HSC (Lin-, Sca-1+, c-kit+, CD150+, CD48-) preMegEs and pre-CFU-Es from Ptbp1 fl/fl (wt) and Ptbp1 -/-  (KO) mice. Three biological replicates per genotype and population were sequenced.

first: Matilda

last: Rehn

first: Anne

last: Wenzel

first: Ying

last: Ge

first: Nicolas

last: Rapin

first: Johan

last: Jendholm


title: Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype (ATAC-Seq)

city: Oxford

first: Mohsin

last: Badat

address: Headley Way

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

summary: Analyses of mutations within the a-globin cluster which downregulate a-globin expression and cause a-thalassaemia provide the basis for genetic counselling and pre-natal diagnosis of this common form of anemia. Understanding the mechanisms by which such mutations cause a-thalassemia has established many of the principles by which mammalian genes are regulated and how this goes awry in human genetic disease. ATAC-Seq and NG Capture-C data from an individual (NSE) with a unique a-globin genotype involving a deletion of the main alpha-globin enhancer on one allele and the --/SEA mutation on the other help to address how the human a-globin cluster is normally regulated.

overall_design: To identify new regulatory elements as marked by chromatin accessibility, which might explain the mild phenotype, ATAC-seq was carried out at day 13 of erythroid differentiation from CD34+ cells isolated from the patient’s peripheral blood. Sequencing was carried out on two culture samples grown in parallel from the patient in identical culture conditions, with 3 technical replicates within each overall duplicate.

first: James

last: Davies

first: Douglas

middle: R

last: Higgs


title: Effect of extremely low frequency weak magnetic fields

city: Nagoya

first: Mikako

last: Ito

address: 65 Tsurumai, Showa-ku

institute: Nagoya University Graduate School of Medicine

summary: We used AML12 cells exposured with pulsed extremely low frequency weak magnetic fields for 4 msec at increasing frequency of 1, 2, 3, 4, 5, 6, 7, and 8 Hz for 1 sec each. The 1-to-8 Hz pulses over 8 sec were repeated indefinitely. Peak magnetic intensity was 100 mG.  AML12 cells were incubated for 1 h under extremely low frequency weak magnetic fields.

overall_design: AML12 mRNA profile, 4 samples as cultured under extremely low frequency weak magnetic fields, 4 samples as control,

first: Kinji

last: Ohno

first: Takuro

last: Toda

first: Jun-ichi

last: Takeda


title: Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype

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

overall_design: Refer to individual Series


title: An elemental diet protects mouse salivary glands from 5-fluorouracil-induced atrophy.

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

summary: In cancer patients, an elemental diet (ED) reduces adverse effects of chemotherapy, including oral mucositis. However, the detailed mechanism(s) of the healing effects of an ED remains unclear. In this study, the protective effects of the ED, Elental®, were examined against 5-fluorouracil (5-FU)-induced oral mucositis and salivary gland atrophy in mice. Mucositis was induced in female ICR mice by injection of 5-FU. The mice were orally administered Elental® (ED group) or saline (control group). After treatment, whole transcriptome analysis and network analysis were conducted to understand the mechanism(s) of action of Elental® against oral mucositis. Whole transcriptome analysis and Ingenuity Pathways Analysis (IPA) data suggested that Elental® contributed to the recovery of mitochondrial function in 5-FU-damaged salivary glands.

overall_design: Salivary glands mRNA profiles of  5FU-treated mice with or without ED.

first: Koji

last: Harada

first: Tarannum

last: Ferdous

first: Rieko

last: Fujiwara

first: Kenji

last: Watanabe

first: Katsuaki

last: Mishima


title: Coordinated Cross-Talk Between the Myc and Mlx Networks in Liver Regeneration and Neoplasia

city: pittsburgh

first: Huabo

last: Wang

state: Pennsylvania

address: 4401 Penn Avenue

department: Pediatrics

institute: Children hospital of pittsburgh

summary: The Myc bHLH-ZIP transcription factor is deregulated by most cancers. As a heterodimer with the bHLH-ZIP protein Max, Myc regulates target genes that contribute to metabolism and proliferation. This “Myc Network” cross-talks with the “Mlx Network” comprised of the Myc-like bHLH-ZIP proteins MondoA and ChREBP and the Max-like bHLH-ZIP protein Mlx. This “Extended Myc Network” regulates genes with both common and distinct functions. We have generated hepatocytes lacking Mlx (mlxKO) or Mlx+Myc (double KO or DKO) and quantified their abilities to replace dying hepatocytes in a murine model of Type I tyosinemia. We find that this function deteriorates as the Extended Myc Network is progressively dismantled. Genes dysregulated in mlxKO and DKO hepatocytes include those involved in translation and mitochondrial function. The Myc and Mlx Networks thus cross-talk with the latter playing a disproportionate role. mycKO and mlxKO mice also develop age-dependent non-alcoholic fatty liver disease and mlxKO and DKO mice develop extensive hepatic adenomatosis not observed in wild-type, mycKO, chrebpKO or mycKOxchrebpKO mice. In addition to demonstrating cooperation between the Myc and Mlx Networks, this study reveals the latter to be more important in maintaining metabolic and translational homeostasis, while concurrently serving as a suppressor of benign tumorigenesis.

overall_design: RNA purification from four to six representative livers of each group was performed using Qiagen RNAeasy columns (Qiagen, Inc., Valencia, CA) followed by DNase digestion. Sample integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).  All samples had RIN values of 8.5-10 prior to any further processing.  Sequencing was performed on a NovaSeq 600 Instrument (Illumina, Inc., San Diego, CA) by Novagene, Inc. (Sacramento, CA).

first: Edward

middle: V

last: Prochownik


title: RNA-seq analysis of 22Rv1 cells with PRMT5, MEP50, pICln knockdown

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201. S. University St, HANS 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: PRMT5 is a methyltransferase that catalyzes symmetric dimethylation of arginine residues in histones (H4R3, H3R8, H3R2, and H2AR3) to regulate transcription of target genes. While PRMT5 is generally considered an epigenetic repressor, recent evidence from our lab and others demonstrate that PRMT5 also functions as an epigenetic activator. Although in vitro biochemical studies suggest that the PRMT5 interacting proteins methylosome protein 50 (MEP50) and methylosome subunit pICln enhance PRMT5 enzymatic activity, how these interacting proteins cooperate with PRMT5 to regulate gene transcription in vivo remains to be elucidated. Here we perform RNA-seq analysis of prostate cancer cells 22Rv1 with knockdown of PRMT5, MEP50, and pICln, in order to elucidate how these proteins control transcriptome.

overall_design: 22Rv1 cells with or without doxycyline-induced shRNA-mediated knockdown of PRMT5, MEP50, and pICln

first: Elena

last: Beketova

first: Sheng

last: Liu

first: Shuyi

last: Fang

first: Jun

last: Wan


title: BCG therapy downregulates HLA-I on malignant cells to subvert antitumor immune responses in bladder cancer [NanoString IO360]

first: Tuan Zea

last: Tan

overall_design: NanoString IO-360 panel post-BCG therapy on human bladder cancer cell lines.

first: Mathieu

last: Rouanne

first: Julien

last: Adam

first: Camelia

last: Radulescu

first: Tuan

first: Aurélien

last: Marabelle


title: CPEB4-mediated translational regulation of LPS response in BMDMs

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: Here we show that the RNA-binding protein CPEB4 sustains the expression of anti-inflammatory factors in LPS-stimulated BMDMs, by binding to the corresponding mRNAs and promoting their stabilization. in macrophages.

overall_design: RNA-immunoprecipitation sequencing of CPEB4-associated mRNAs in Wild type and CPEB4-KO BMDMs

first: Clara

last: Suñer

first: Raul

last: Mendez


title: A molecular circuit that creates the phloem pattern

city: Toyonaka

first: Tatsuo

last: Kakimoto

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

institute: Osaka University

summary: The vascular system of plants consists of xylem, phloem and procambium in a specific pattern. The phloem consists of sieve elements, the apparatus for bulk flow of photo-assimilates, and companion cells, which mediate transport of photo-assimilates between the sieve elements and surrounding cells and support the biological activities of the sieve element cells. The regulatory mechanisms of vascular development are being uncovered. Here we show that PHLOEM EARLY DOFs (PEARs) and related genes (collectively phloem-Dofs) not only regulate the number of procambium cell files, but also positively regulate phloem differentiation. Overexpression of phloem-Dofs induced cells that expressed either sieve element or companion cell marker genes, which are mutually exclusive. Conversely, disruption of phloem-Dofs caused loss of phloem. Phloem-Dofs induce CLAVATA3/EMBRYO SURROUNDING REGION-RELATED25 (CLE25) and CLE26 peptides, which in turn inhibit expression of phloem-Dofs and phloem formation, forming a negative feedback loop. Disruption of multiple genes for either phloem-expressed CLEs, BARELY ANY MERISTEM (BAM)-class receptors, or their coreceptors, CLAVATA3 INSENSITIVE RECEPTOR KINASEs (CIKs), caused excess formation of phloem cell files. We further show that phloem-Dofs are under positive self and mutual regulation. These positive and negative feedback loops create the proper phloem pattern.

overall_design: Dof genes expressed preferentially expressed in the phloem were overexpressed by using estrogen-inducible expression vector, ER8. Arabidopsis lines produced after transformation with ER8Dof1.1, ER8Dof2.2, and ER8PEAR were treated with or without estriol for 16 hours, and RNA samples were prepared from roots, and subjected to a microarray experiments.

first: Miki

last: Zaizen

first: Yukiko

last: Sugisawa


title: A small molecule BAG1 inhibitor as therapeutic agent for androgen receptor positive prostate cancer

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

summary: BAG1 is a family of polypeptides with a conserved C-terminal BAG domain that functions as a nucleotide exchange factor for the molecular chaperone HSP70. BAG1 proteins also bind to diverse cellular proteins and control several signaling processes including proteostasis, apoptosis and transcription. The largest BAG1 isoform (BAG1L) controls the activity of the androgen receptor and is upregulated in prostate cancer. Here, we show that BAG1L binds to the AR N-terminal domain (NTD) and regulates AR dynamics and the expression of AR target genes. We further show that disruption of the BAG1L-AR NTD action by targeting the BAG domain with a small molecule, 2-(4-fluorophenyl)-5-(trifluoromethyl)-1,3-benzothiazole (A4B17), downregulates AR target gene expression and blocks proliferation of AR-positive prostate cancer cells. A4B17 also inhibits tumor development in mouse xenograft models under castration conditions. A4B17 is therefore a BAG1 inhibitor with unique properties to inhibit prostate cancer growth.

overall_design: LAPC-4 cells were treated with vehicle, A4B17 and enzalutamide

last: Gourain

first: Valeria

last: Solozobova

first: Nane

last: Kuznik

first: Andrew

last: Cato


title: Epigenome-wide association study of bronchopulmonary dysplasia in preterm infants

city: Research Triangle Park

first: Xuting

last: Wang

address: 111 TW Alexander Dr

institute: NIEHS/NIH


title: Sex-Specific Differences in MicroRNA Expression during Human Fetal Lung Development

city: Aurora

first: Sunita

last: Sharma

address: 13199 East Montview Blvd

department: Medicine-Pulmonary Sciences & Critical Care

institute: University of Colorado Hospital

summary: Our study demonstrates differential expression of numerous autosomal miRNAs between the male and female developing human lung. Additionally, the expression of some miRNAs are modified by age across the pseudoglandular stage in a sex-specific way.  Some of these differences in miRNA expression may impact susceptibility to pulmonary disease later in life. Our results suggest that sex-specific miRNA expression during human lung development may be a potential mechanism to explain sex-specific differences in lung development and may impact subsequent disease susceptibility

overall_design: Identifing sex differences in miRNA expression profiles of human fetal lung tissue after controling for smoke exposure, age, and technicial effects.

first: Nancy

last: Lin

first: Cuining

last: Liu

first: Ivana

last: Yang

first: Lisa

last: Maier

first: Dawn

last: DeMeo

first: Shuyu

last: Ye

first: Margaret

middle: H

last: Cruse

first: Vong

last: Smith

first: Carrie

last: Vyhlidal

first: Katerina

last: Kechris

first: Cheyret

last: Wood


title: Marking the difference in acutely responding human CD8 T cells

city: Epalinges

first: Silvia Asuncion

last: Fuertes Marraco

address: Chemin des Boveresses 155

department: Department of Oncology

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois (CHUV) - University of Lausanne

summary: The CD8 T cell response features functions that are fundamental for long-lasting immune protection, including antigen-specific cytolysis and memory. Accordingly, a range of differentiation subsets have been described with diverse functionalities and corresponding profiles of expression of markers. In both mouse and human systems, a major distinction has been “memory” versus “effector” terms. On the one hand, these terms may relate to temporality within the immune response : “effector” indicates the acute phase, “memory” refers to the post-contraction, resting phase. On the other hand, the terms also assign prototypic differentiation phenotypes that may be found at the same time-point : memory or effector subsets, based on characteristic markers. In this study, we analyse the human CD8 T cell response to YF-17D vaccination as the best-known model of acute immune response in humans. We study 21 characteristic markers conventionally used in mice and in humans to analyse and describe differentiation, activation, cycling, and so-called effector functions such as cytokine production and degranulation. We find clearly distinct ‘acute traits’ at the peak of the response that are shared amongst all non-naïve antigen-specific subsets, including in memory phenotype cells. These acute traits were low BCL-2 and high Ki67, CD38, HLA- DR, as well as increased Granzyme B and Perforin, which have been previously attributed only to effector cells at the peak of the response. Altogether, we evidenced ‘acute traits’ independent of differentiation phenotypes, supporting the semantic and marker distinction between “effector” and “acute” terms in the human CD8 T cell response.

overall_design: Single cell ATAC sequencing of CD8 T cells derived  from peripheral blood samples and sorted into different subsets: naïve, SCM or effector. Naive are polyclonal; SCM and effector either polyclonal or A2/LLW-specific. Three donors were sampled 14 days after YF-17D vaccination, i.e. at the peak of the acute phase of immune response.  Three donors were sampled several years  after YF-17D vaccination, i.e. in the long-term phase.

first: Silvia

first: Daniel

last: Alpern

last: Speiser


title: A comprehensive transcriptome portrait of colorectal cancer derived organoid at single cell levels (Single cell RNA-seq)

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

summary: Due to the highly heterogeneous nature of tumor, it is very challenging to study the molecular mechanisms of tumorigenesis. Recently, in vitro derived 3D organoid culture system were developed and may serve as a good model for studing the cancer molecular mechanisms in vitro, which allows long-term expansion of human colorectal colon cancer. To fully evaluate the organoid culture system, we perform a single cell RNA-seq survey of 4,792 single cells of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer to investigate their gene expression signatures. We also apply whole-exon sequencing, whole genome sequencing and Sanger sequencing to characterize their genomic features accordingly. We found that tumor-derived organoid in vitro in general faithfully maintained the gene expression signatures, gene regulatory network, tumor-microenvironment cross-talk, as well as mutations such as copy number variants and point mutations of tumor cells in vivo. However adjacent normal tissue-derived organoid, despite remaining normal in genomic levels, changed their gene expression profiles drastically and acquired tumor-like gene expression signatures.

overall_design: Single cell transcriptome profiles of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer were generated by next generation sequencing using illumina 4000.

first: Wendong

first: Yunuo

last: Mao


title: Revisiting the Role of Notch in Nephron Segmentation Confirms A Role for Proximal Fate Selection During Mouse and Human Nephrogenesis

status: Public on May 04 2022

city: CINCINNATI

first: Praneet

last: Chaturvedi

state: OH

address: 240 Albert Sabin Way

department: Developmental Biology

institute: Cincinnati Children's

summary: Notch signaling promotes maturation of nephron epithelia, but its proposed contribution to nephron segmentation into proximal and distal domains has been called into doubt. We leveraged single cell and bulk RNA-seq, quantitative immunofluorescent lineage/fate tracing, and genetically modified human iPSC to revisit this question in developing mouse kidneys and human kidney organoids. We confirmed that Notch signaling is needed for maturation of all nephron lineages, and thus mature lineage markers fail to detect a fate bias. By contrast, early markers identified a distal fate bias in cells lacking Notch2, and a concomitant increase in early proximal and podocyte fates in cells expressing hyperactive Notch1 was observed. Orthogonal support for a conserved role for Notch signaling in the distal/proximal axis segmentation is provided by the demonstration that Nicastrin-deficient hiPSCs-derived organoids differentiate into TFA2B+ distal tubule and CDH1 connecting segment progenitors, but not into HNF4A+ or LTL+ proximal progenitors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from kidneys isolated from experimental animals expressing activated Notch1 in nephron progenitors, and control litter mates without Cre.

first: Kathryn

last: Duvall

first: Lauren

last: Crist

first: Alison

middle: J

last: Perl

first: Naomi

last: Pode Shakked

first: Raphael

last: Kopan


title: Icaritin inhibits PLK1 to activate DNA damage response in NK/T cell lymphoma and increases sensitivity to GELOX regime

city: Shanghai

first: Songmei

last: Wang

address: 131 Rd Dong'an, Xuhui District

institute: Fudan University

summary: NK/T cell lymphoma (NKTCL) is a highly aggressive subtype of non-Hodgkin lymphoma. GELOX (gemcitabine, oxaliplatin, and L-asparaginase) is one of the first-line chemotherapy regimens of NKTCL. Yet, the prognosis of NKTCL is poor. Icaritin (ICT) is an herb-derived monomer from icariin with antitumor effects. We found that icaritin induced proliferation inhibition and apoptosis of NKTCL both in vitro and in vivo. Moreover, icaritin inhibited the dissemination of NKTCL in vivo. RNA sequencing (RNA-seq) revealed the polo-like kinase 1 (PLK1) gene and DNA damage response (DDR) as the targets of icaritin. Mechanistically, icaritin inhibited PLK1 to promote checkpoint kinase 2 (Chk2) homodimerization and its T387 phosphorylation, which further activated p53, leading to the activation of the DDR pathway. Moreover, inhibiting PLK1 increased Forkhead box O3a (FOXO3a) nuclear localization, the latter of which activated Ataxia-telangiectasia mutated (ATM), an early sensor of DNA damage. Then ATM phosphorylated Chk2 T68 and initiated Chk2 activation. Remarkably, combined treatment of icaritin and GELOX achieved better antitumor efficacy than single treatment in vivo. In summary, our results proved the efficacy of icaritin treating NKTCL, and provided insights into its antitumor molecular mechanism, and revealed the application value of icaritin in facilitating clinical NKTCL treatment.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 3 NKTCL cell lines treated with icaritin

first: Canjing

last: Zhang

first: Huiwen

last: Xu

first: Xuanyi


title: Hypoxia Induces Lung Inflammation and Immunity by ILC2 through Stimulating Adrenomedullin from Epithelial Cells

city: San Diego

first: Ashu

last: Sethi

address: 9420 Athena Circle

department: Health Sciences

institute: La Jolla Institute for Immunology

summary: Hypoxia contributes to airway inflammation and remodeling in several lung diseases; however, exactly how hypoxic pulmonary epithelium regulates allergic inflammation remains to be fully characterized. Here we report that conditional deletion of the E3 ubiquitin ligase VHL in lung epithelial cells resulted in exacerbated type 2 responses accompanied by selective increase of group 2 innate lymphoid cells (ILC2s) at steady state and following inflammation or helminth infection. Ablation of expression of the hypoxia-inducible factor 2 (HIF2a significantly reversed VHL-mediated ILC2 activation. VHL deficiency in lung epithelial cells caused the increased expression of the peptide hormone adrenomedullin (ADM), and our data suggest HIF2a controls Adm expression.  ADM directly promoted ILC2 activation both in vitro and in vivo. Our findings indicate that the hypoxic response mediated by the VHL-HIF2a axis is critical for control of pulmonary type 2 responses by increasing ADM expression in lung epithelia causing ILC2 activation.

overall_design: Lung bronchiolar epithelial mRNA profiles of WT and VHL conditional knockout mice

first: Jihye

last: Han

first: Qingqing

last: Wan

first: Goo-Young

last: Seo

first: Kenneth

last: Kim

first: Sarah

last: el Baghdady

first: Jee

last: Lee

first: Mitchell

last: Kronenberg

first: Yun-Cai

last: Liu


title: BRB-seq analysis of PFOS-induced thyroid hormone system disrupted rats reveal organ-specific effects

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

summary: Perfluorooctanesulfonic acid (PFOS) is a persistent anthropogenic chemical that can affect the thyroid hormone system in humans. In experimental animals, PFOS exposure decreases thyroxine (T4) and triiodothyronine (T3) levels, without a compensatory upregulation of thyroid stimulating hormone (TSH). In adults, THs are regulated by the hypothalamus-pituitary-thyroid (HPT) axis, but also organs such as the liver and potentially the gut microbiota. PFOS and other xenobiotics can therefore potentially disrupt the TH system through various entry points of disruption. To start addressing this issue, we performed a PFOS exposure study to identify effects in multiple organs and pathways simultaneously.

overall_design: Hypothalamus, pituitary, thyroid, and liver transcriptional profiles of adult male rats exposed for 7 days to either vancomycin, PFOS or a combination vancomycin + PFOS (from PD56-62) were generated by BRB-sequencing.

first: Frederic

first: Nichlas

last: Davidsen

first: Indusha

last: Kugathas

first: Terje

last: Svingen


title: Effect of TWEAK or TGF-α on gene expression of primary human keratinocytes (PHKs)

city: Xi'an

first: Yale

state: China (+86)

address: No.157, Xiwu Road, Xincheng District

department: Dermatology

institute: Xi'an Jiaotong University

summary:
To investigate the transcriptome of TWEAK or TGF-α in the regulation of human primary keratinocytes
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 replicates at two different time points

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary human keratinocytes

first: Sijia


title: Dissecting the molecular control of immune cell accumulation in the inflamed joint

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

institute: University of Glasgow

summary: Mechanisms governing entry and exit of immune cells into, and out of, inflamed joints, remain poorly understood. We sought herein to identify the key molecular pathways regulating such migration. Using murine models of inflammation in conjunction with mice expressing a photoconvertible fluorescent protein we characterized the migration of cells from joints to draining lymph nodes (LN) and performed RNA-seq analysis on isolated cells, identifying genes associated with migration and retention. We further refined the gene list to those specific for joint inflammation. RNA-seq data revealed pathways and genes previously highlighted as characteristic of Rheumatoid arthritis (RA) in patient studies, validating the methodology. Focusing on pathways associated with cell migration, adhesion and movement, we identified genes involved in the retention of immune cells in the inflamed joint, namely JAM-A, and identified a role for such molecules in T cell differentiation in vivo. Thus, using a combination of novel cell tracking approaches and murine models of inflammatory arthritis we have identified genes, pathways and anatomically specific tissue signatures regulating cell migration in a variety of inflamed sites. This unique skin and joint specific dataset will be an invaluable resource for the identification of novel therapeutic targets for arthritis and other inflammatory disorders.

overall_design: Bulk RNA-seq of non-migrated and migrated CD45+ leukocytes from inflammed ear and joint.

first: Hannah

last: Scales


title: A comprehensive transcriptome portrait of colorectal cancer derived organoid at single cell levels

first: Rui

last: WANG

overall_design: Single cell transcriptome profiles of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer were generated by next generation sequencing using illumina 4000 (GSE120065). For each sample, we also extracted the genomic DNA for whole genome sequencing and whole exon sequencing by using illumina 4000 (EGA database with accession number EGAS00001003229). Tumor cells highly expressed PPAR signaling pathway target gene SCD, so we cultured tumor-derived organoid with PPAR inhibitor FH535 or DMSO for 5 days. Then, RNA were extracted for bulk RNA sequencing by using illumina 4000 (GSE121454).


title: Spontaneous cholemia in C57BL/6 mice predisposes to liver cancer in NASH

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: C57BL/6 mice are the most widely used inbred strain for metabolic and interventional studies. It is commonly known that high-caloric diet feeding induces a heterogeneous phenotype in C57BL/6 mice similar to humans with the majority developing obesity and metabolic dysfunction whilst others remaining lean and metabolically healthy. Nevertheless, the underlying mechanism(s) for this remains unknown. Here, we show that a subset (5-25%) of all C57BL/6 mice develop spontaneous cholemia with elevated total serum bile acids and increased liver damage at early time points upon high-caloric diet feeding. Although cholemic mice are resistant to obesity and metabolic dysfunction, they develop accelerated liver damage and liver fibrosis, which ultimately predisposes them to early liver cancer compared to non-cholemic mice fed a Western-diet or choline-deficient high-fat diet. Hitherto, these mice have been overlooked, which may have led to inconsistent or perplexing findings. Therefore, C57BL/6 mice included in metabolic and cancer studies relating to the liver are strongly recommended to be screened and excluded for cholemia.

overall_design: Transcriptomics data from whole liver homogenates of H-TBA (high total bile acids) and L-TBA (low tital bile acids) mice fed a Western diet for 30 weeks.

first: D

last: Withers

first: M

last: Heikenwalder


title: Brown adipose TRX2 deficiency activates mtDNA-NLRP3 to impair thermogenesis and protect against diet-induced insulin resistance

city: Guangzhou

first: Yanrui

last: Huang

address: 58 Zhongshan Er Lu

institute: Sun Yet-sen University

summary:
Brown adipose tissue (BAT), a crucial heat-generating organ, regulate whole-body energy metabolism by mediating thermogenesis. BAT inflammation is implicated in the pathogenesis of mitochondrial dysfunction and impaired thermogenesis. However, the link between BAT inflammation and systematic metabolism remains unclear. Herein, we sought whether BAT inflammation regulates systematic metabolism and thermogenesis.
By using mice with BAT deficiency of thioredoxin-2 (TRX2), a protein that scavenges mitochondrial reactive oxygen species (ROS), we evaluated the impact of BAT inflammation on metabolism and thermogenesis and its underlying mechanism. Our results describe that BAT-specific TRX2 ablation improves systematic metabolic performance via enhancing lipid uptake, which protects mice from diet-induced obesity, hypertriglyceridemia, and insulin resistance. TRX2 deficiency impairs adaptive thermogenesis by suppressing fatty acid oxidation. Mechanistically, loss of TRX2 induces excessive mitochondrial ROS, mitochondrial integrity disruption, and cytosolic release of mitochondrial DNA, which in turn activate aberrant innate immune responses in BAT, including the cGAS-STING and the NLRP3 inflammasome pathways. We identify NLRP3 as a key converging point, as its inhibition reverses both the thermogenesis defect and the metabolic benefits seen under nutrient overload in BAT-specific Trx2-deficient mice. In conclusion, we identify TRX2 as a critical hub integrating oxidative stress, inflammation, and lipid metabolism in BAT; uncovering an adaptive mechanism underlying the link between BAT inflammation and systematic metabolism.

overall_design: The mRNA profiles of interscapular brown adipose tissues (iBAT) from 16-week-old control (Ctrl) and ob/ob(OB) mice

first: Wang

last: Min


title: A single intranasal dose of human parainfluenza virus type 3-vectored vaccine induces effective antibody and tissue-resident T cell response in the lungs and protects hamsters against SARS-CoV-2

city: Galveston

first: Alexander

last: Bukreyev

state: Texas

address: 301 University Boulevard

institute: University of Texas Medical Branch at Galveston

summary: Respiratory tract vaccination has an advantage of needle-free delivery and induction of mucosal immune response in the portal of SARS-CoV-2 entry. We utilized human parainfluenza virus type 3 vector to generate constructs expressing the full spike (S) protein of SARS-CoV-2, its S1 subunit, or the receptor-binding domain, and tested them in hamsters as single-dose intranasal vaccines. The construct bearing full-length S induced high titers of neutralizing antibodies specific to S protein domains critical to the protein functions. Robust tissue-resident T cell responses in the lungs were also induced, which represent an additional barrier to infection and should be less sensitive than the antibody responses to mutations present in SARS-CoV-2 variants. Following SARS-CoV-2 challenge, animals were protected from the disease and detectable viral replication. Vaccination prevented induction of gene pathways associated with inflammation. These results indicate advantages of respiratory vaccination against COVID-19 and inform the design of mucosal SARS-CoV-2 vaccines.

overall_design: 5 replicates each of vaccinated and unvaccinated hamsters were infected with SARS-CoV-2, followed by RNA extraction from lung tissue 3 days post-infection. 4 unvaccinated and uninfected hamsters were used as naïve controls.

first: Philipp

last: Ilinykh

first: Sivakumar

last: Periasamy

first: Kai

first: Natalia

last: Kuzmina

first: Palaniappan

last: Ramanathan

first: Michelle

middle: N

last: Meyer

first: Chad

last: Mire

first: Ivan

last: Kuzmin

first: Preeti

last: Bharaj

first: Jessica

last: Endsley

first: Maria

last: Chikina

first: Stuart

last: Sealfon

first: Steven

middle: G

last: Widen

first: Mark


title: Small extracellular vesicles induce resistance to anti-GD2 immunotherapy unveiling tipifarnib as an adjunct to neuroblastoma immunotherapy

city: Hershey

first: Hong-Gang

last: Wang

state: PA

address: 500 University Drive, H085, Rm C7833B

institute: Penn State College of Medicine

summary: We utilize the syngeneic 9464D-GD2 mouse model to investigate the role of neuroblastoma-derived small extracellular vesicles (sEVs) in developing resistance to the anti-GD2 monoclonal antibody dinutuximab. RNA-sequencing and flow cytometry analysis of whole tumors revealed that neuroblastoma-derived sEVs modulate immune cell tumor infiltration upon dinutuximab treatment to create an immunosuppressive tumor microenvironment that contains more tumor-associated macrophages (TAMs) and fewer tumor-infiltrating NK cells. Importantly, tipifarnib, a farnesyltransferase inhibitor that inhibits sEV secretion, drastically enhanced the efficacy of dinutuximab and reversed the immunosuppressive effects of neuroblastoma-derived sEVs.

overall_design: We performed RNA-seq after isolated subcutaneous tumors from female mice receiving 5 treatments of dinutuximab or dinutuximab plus sEVs derived from 9464D-GD2 cells. Each treatment group contains two biological replicates.

first: Xiaoming

last: Liu


title: A comprehensive transcriptome portrait of colorectal cancer derived organoid at single cell levels (Bulk RNA-seq)

first: Rui

last: WANG

summary: Due to the highly heterogeneous nature of tumor, it is very challenging to study the molecular mechanisms of tumorigenesis. Recently, in vitro derived 3D organoid culture system were developed and may serves as a good model for studing the cancer molecular mechanisms in vitro, which allows long-term expansion of human colorectal colon cancer.To fully evaluate the organoid culture system, we perform a single cell RNA-seq survey of 4,792 single cells of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer to investigate their gene expression signatures. We also apply whole-exon sequencing, whole genome sequencing and Sanger sequencing to characterize their genomic features accordingly. We found that tumor-derived organoid in vitro in general faithfully maintained the gene expression signatures, gene regulatory network, tumor-microenvironment cross-talk, as well as mutations such as copy number variants and point mutations of tumor cells in vivo. However adjacent normal tissue-derived organoid, despite remaining normal in genomic levels, changed their gene expression profiles drastically and acquired tumor-like gene expression signatures.

overall_design: Tumor-derived organoids were cultured with PPAR inhibitor FH535 or DMSO control for 5 days (3 replicates each). Then, RNA were extracted for bulk RNA sequencing by using illumina 4000.

first: Wendong

first: Yunuo

last: Mao


title: Genome-wide DNA methylation profiling reveals candidate biomarkers and probable molecular mechanism in metabolic syndrome [array]

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: The goals of this study are to investigate the molecular mechanism and biomarker by DNA methylation profiles in patients with metabolic syndrome compared to normal.

overall_design: In this study, we performed Infinium MethylationEPIC BeadChIP and RNA-seq with same patients to explore a molecular targets for the prediction of metabolic syndrome. A total of 20 participants, including 11 patietns with metabolic syndrome and 9 normal were enrolled in our study.

first: Hee

last: Jin

first: Siwoo

last: Lee


title: Genome-wide DNA methylation proifling reveals candidate biomarkers and probable molecular mechanisms in metabolic syndrome [RNA-seq]


title: Genome-wide DNA methylation proifling reveals candidate biomarkers and probable molecular mechanisms in metabolic syndrome

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

overall_design: Refer to individual Series


title: Genome-wide gene expression profile of mouse proliferating / differentiating cerebellar granular progenitor cells (CGNPs)

city: Houston

first: Shinji

last: Maegawa

address: 7777 Knight Road

institute: University of Texas, MD Anderson Cancer Center

summary: To study the gene expression changes during neuronal differentiation of mouse cerebellar granular progenitor cells (CGNPs), we generated neurospheres (proliferating CGNPs) and differentiated the cells (differentiating CGNPs). Then we performed RNA-Seq analysis.

overall_design: mRNA profiles of mouse CGNPs (proliferation condition and differentiation condition).

first: Lei

last: Guo

first: Jyothishmathi

last: Swaminathan

first: Lin

last: Xu

first: Vidya

last: Gopalakrishnan


title: Photo-isolation chemistry for high-resolution and deep spatial transcriptome with tissue sections

city: Kyoto

first: Shinya

last: Oki

address: 53 Kawahara-cho, Shogoin

institute: Kyoto University

summary: We established a high-depth spatial transcriptomics technology, photo-isolation chemistry (PIC; Honda, et al., Nat Commun, 2021), which is able to isolate gene expression profiles only from photo-irradiated region out of whole tissues. In the original protocol, only the fresh-frozen sections were available, but we have now optimized it applicable to formalin-fixed frozen and formalin-fixed paraffin sections. Here, we provide an updated protocol of PIC.

overall_design: We performed PIC analysis to isolate expression profiles of hippocampal regions [CA1, CA2 and dentate gyrus (DG)] from fresh frozen, formalin-fixed frozen and formalin-fixed paraffin sections of mouse brain.

first: Mizuki

last: Honda

first: Ryuichi

last: Kimura

first: Akihito

last: Harada

first: Kazumitsu

last: Maehara

first: Kaori

last: Tanaka

first: Yasuyuki

last: Ohkawa


title: RNA Sequencing of BV2 cells stimulated by sTREM-1

city: Nanjing

first: Li

last: Lu

address: The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University

institute: Nanjing university

summary:
Purpose:  The goals of this study are to compare the transcriptome of  BV2 cells stimulated with or without sTREM-1, explore its effect on the phenotype and function of BV2 cells, and explore potential signaling pathways.
Methods: BV2 cells were incubated with or without sTREM-1 recombinant protein (1ug/mL) for 6 h, then the mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx.
Results: Sequencing libraries were generated using the NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) and sequenced on an Illumina platform. Paired-end reads were then generated and evaluated for quality control. Clean raw data with high quality were aligned to the reference genome using Spliced Transcripts Alignment to a Reference (STAR) software. For quantification, FeatureCouts was used to count the read numbers mapped of each gene, 17047 transcripts were identified. Differential expression analysis between two groups was performed using the Edge R package. Genes with an adjusted RNAs with P < 0.05 and |log2FC | > 1 were identified as differentially expressed. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to sTREM-1 function. Gene ontologies (GO) Analyses were conducted to assess biological processes, molecular functions, and cellular components.
Conclusions: Our study represents the detailed analysis of BV2 cells transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that BV2 cells are activated after sTREM-1 recombinant protein stimulation, and the phagocytic function is enhanced.

overall_design: Stimulate BV2 cells with sTREM-1 in vitro, and explore mRNA profiles through RNA-Seq.

first: Xuan

last: Liu

first: Juanhua

last: Fu

first: Jun

last: Liang

first: Yayi

last: Hou

first: Huan

last: Dou


title: RNA-seq from MFN2;Stra8-Cre cKO vs WT spermatocytes in mice

city: Shenzhen

first: Chenxi

last: Guo

state: Guangdong

address: No.1 Haiyuan 1st Rd, Futian

department: Reproductive Medicine Center

institute: The University of Hong Kong-Shenzhen Hospital

summary: The Mfn2 gene was conditionally knock-out from male mice germ cells using Stra8-Cre mice. The spermatocytes were collected from PD 24 and PD 52 male mice, and were further isolated as pachytene cells (P) and leptotene/zygotene cells (L/Z). The transcriptome between MFN2 WT and MFN2 cKO spermatocytes were analyzed via RNA-seq in P and L/Z populations at different ages, PD 24 amd PD 52, respectively.

overall_design: Spermatocytes mRNA profile of MFN2 WT and MFN2 CKO(Mfn2 loxp/loxp; Stra8-Cre) at PD 24 and PD 52

first: Jingkai

last: Gu

first: Yuan

last: Xiao


title: Expression profiling of CD4+and CD8+ T cells in peripheral blood (PB) of AML patients who were treated with induction chemotherapy plus pomalidomide

city: Baltimore

first: Hanna

last: Knaus

state: Maryland

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins

summary: Transcriptional profiles of highly purified (≥ 98%) PB CD4+ or CD8+  T cells at early lymphocyte recovery (ELR) from newly diagnosed AML patients, who were treated with standard induction chemotherapy plus pomalidomide were compared to age-matched AML controls, who received standard induction chemotherapy only.

overall_design: AML patients treated with induction chemotherapy + Pomalidomide (CP) vs. AML patients treated with induction chemotherapy only (C)

first: Leo

last: Luznik


title: Endothelial Phospholipase C gamma2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy

city: Pittsburgh

first: Chandan

last: Sen

address: 450 Technology Drive

department: Surgery

institute: University of Pittsburgh

summary:
The single cell transcriptional profile from three diabetic and five non-diabetic human skin samples was analyzed

The spatial transcriptomics of 1 non-diabetic and 1 diabetic human skin were analyzed

overall_design:
Single-cell suspensions were generated from the unwounded human skin. Briefly, the tissue was chopped into small pieces and subjected to enzymatic dissociation using whole skin dissociation kit (cat. no. 130-101-540) in MACS C Tubes (cat. no. 130-093-237) (Miltenyi Biotec Inc., San Diego, CA). The samples were incubated in a water bath at 37Â°C for approximately 3 hours. After incubation, the samples were diluted by adding 0.5 mL of cold cell culture medium in order to stop the enzymatic reaction. The C Tubes were then tightly closed and attached upside down onto the sleeve of the gentleMACSâ„¢ Octo dissociator and UW human skin dissociation program was performed. The cell suspension was subjected to a pre-Separation Filter, 70 Âµm, placed on a 15 mL tube in order to remove the debris. RBC were lysed using 10X RBC lysis buffer (cat. no. 420301, BioLegend, San Diego, CA). The resulting cell suspension was utilized for single cell RNA sequencing using the 10x Genomics platform using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1(10x Genomics, Inc.) and sequenced on an Illumina NovaSeq 6000 (Illumina, Inc).

20µm thick section was taken on visium spatial gene expression slide followed by permeabilization for 12 mins. cDNA libraries were synthesized using Visium spatial gene expression reagent kit as per manufacture?s recommendations (PN-100186, 100190; 10x Genomics) and sequenced using NovaSeq 6000 (Illumina, Inc). Generated reads were pre-processed using the standard Space Ranger (https://support.10xgenomics.com/spatial-gene-expression/software) pipeline to align the raw sequencing reads onto hg38 genome and obtained the respective h5-format and spatial image files for UW human skin. Resulting pre-processed files were loaded in Seurat for further downstream data processing and analysis.

first: Kanhaiya

last: Singh

first: Yashika

last: Rustagi

first: Rajneesh

last: Srivastava

first: Ahmed

middle: S

last: Abouhashem


title: Master transcription factors of plant immunity are targeted by a Ralstonia solanacearum effector

city: Wuhan

first: mengling

last: Huang

state: Hubei

address: shizisan

department: College of Plant Science and Technology

institute: Huazhong Agricultural Universityhuazong

summary: We found the Type III effector protein RipAB could suppress multiple plant immune responses and is important for the virulence of bacterial wilt pathogen Ralstonia solanacearum.

overall_design: RNA-seq analysis was performed with 10-day-old seedlings of WT, OERipAB transgenic Arabidopsis plants ( hereinafter referred to OERipAB ) with or without 500 μM INA treatment for 1 h. Three independent repeats were performed for RNA-seq analysis.

first: Peipei

last: Qi

first: Mengling

first: Xuehan

last: Hu

first: Ying

last: Zhang

last: Wang

first: Pengyue

last: Li

first: Shiyun

last: Chen

first: Sen

last: Cao

first: Wanting

last: Zhu

first: Jiatao

last: Xie

first: Yanping

first: Jiasen

last: Cheng

first: Daohong

last: Jiang

first: Xiao

last: Yu

first: Bo


title: Single-cell RNA sequencing reveals transcriptional signatures and immune cell responses in Patients with acute kidney injury

city: CHANG SHA

first: YONG

last: ZHONG

address: XIANGYA ROAD

institute: XIANGYA HOSPITAL

summary: It has been widely recognized that Acute kidney injury (AKI)represents a multifactorial, heterogeneous syndrome, or a spectrum of diseases. AKI is associated with prolonged hospitalization and high mortality, and it predisposes individuals to chronic kidney disease. To date, no effective AKI treatments have been established. This study used single-cell RNA sequencing (scRNA-seq) to explore novel molecular mechanisms and gene targets for AKI. We identifies a distinct cell-specific gene expression profile, pathogenic signaling pathways and potential cell-cell communications in the pathogenesis of AKI. These findings will provide a promising novel landscape for mechanisms and treatment of AKI.

overall_design: We analyzed kidney samples from 2 patients with AKI and 2 healthy control subjects using single-cell RNA sequencing. We then identified distinct cell clusters through unsupervised clustering analysis of kidney specimens. Identification of the differentially expressed genes (DEGs) and enrichment analysis in different  cells as well as the interaction between cells were also performed. In addition, the differences of gene expression and enrichment pathway in patients with different levels of proteinuria were analyzed.

first: Rong

last: Tang

first: Wei

last: Lin

first: Yong

last: Zhong

first: Xiangcheng

last: Xiao


title: Single-cell transcriptomic analysis reveals the landscapes of key metabolic tissues in lactating dairy cows

city: Hangzhou

first: Jiajin

last: Wu

state: Zhejiang

address: Yuhangtang road

institute: Zhejiang University

summary: The complicated biological process of how dairy cows convert indigestible nutrients for humans into nutritious milk is orchestrated by various tissues. Here, we deciphered the single-cell landscapes of 10 bovine tissue types covering 88,013 cells. We characterized the metabolic features of epithelial cell subtypes that exert unique functions to the tissues of residence. We also identified the cell subtypes that are essential for the transport of certain nutrients. Th17 cells were specifically enriched in the rumen, reticulum, and omasum tissues and predominantly interacted with the epithelial cell subtypes with high potential uptake capacities of short-chain fatty acids through IL-17 signaling. The comparison between IL17RAhighIL17RChigh cells and other cell types explained the important role of Th17 cells in regulating the epithelial cellular transcriptional response to nutrients transport in these three tissues. The findings enhance our understanding of ruminants biology and open new avenues for an improved animal production in dairy cows.

overall_design: Single-cell RNA sequencing for 88,013 cells from 9 tissues types of dairy cow.

first: Senlin

first: Fengfei

last: Gu

first: Huizeng

last: Sun


title: Single-cell RNA Sequencing Reveals Transcriptional Signatures and Cell-cell crosstalk in Patients with Hypertensive Nephropathy

summary: Hypertensive nephropathy (HTN) is one of the leading causes of end-stage renal disease, yet the precise mechanisms and cell-specific gene expression changes are still unknown. This study used single-cell RNA sequencing (scRNA-seq) to explore novel molecular mechanisms and gene targets for HTN.Our data identifies a distinct cell-specific gene expression profile, pathogenic signaling pathways and potential cell-cell communications in the pathogenesis of HTN. These findings will provide a promising novel landscape for mechanisms and treatment of HTN.

overall_design: We analyzed kidney samples from 2 patients with HTN and 2 healthy control subjects using single-cell RNA sequencing. We then identified distinct cell clusters through unsupervised clustering analysis of kidney specimens. Identification of the differentially expressed genes (DEGs) and enrichment analysis in different  cells as well as the interaction between cells were also performed. In addition, the differences of gene expression and enrichment pathway in patients with different levels of proteinuria were analyzed.


title: Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype (NG Capture C)

city: Oxford

first: Mohsin

last: Badat

address: Headley Way

institute: MRC Weatherall Institute of Molecular Medicine

summary: Analyses of mutations within the a-globin cluster which downregulate a-globin expression and cause a-thalassaemia provide the basis for genetic counselling and pre-natal diagnosis of this common form of anemia. Understanding the mechanisms by which such mutations cause a-thalassemia has established many of the principles by which mammalian genes are regulated and how this goes awry in human genetic disease. ATAC-Seq and NG Capture-C data from an individual (NSE) with a unique a-globin genotype involving a deletion of the main alpha-globin enhancer on one allele and the --/SEA mutation on the other help to address how the human a-globin cluster is normally regulated.

overall_design: To identify which regulatory elements were interacting with the alpha-globin promoters on the functional allele we performed high resolution chromatin conformation capture (3C) using NG CaptureC (Davies 2016). NG CaptureC was performed on primary human cells in triplicate on Day 13 of erythroid differentiation from CD34+ cells isolated from peripheral blood. Capture was performed with biotinylated oligonucleotides targeting sequences adjacent to DpnII sites.

first: James

last: Davies

first: Douglas

last: Higgs


title: Supplementation of specific collagen peptides following high-load resistance exercise upregulates gene expression in pathways involved in skeletal muscle signal transduction

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Previous evidence suggests that resistance training in combination with specific collagen peptides (CP) improves adaptive responses of the muscular apparatus. Although beneficial effects have been repeatedly demonstrated, the underlying mechanisms are not well understood. Therefore, the primary objective of the present randomized trial was to elucidate differences in gene expression pathways related to myofibrillar protein synthesis following acute high-load resistance exercise with and without CP intake.  Recreationally active male participants (n=30) were equally randomized to high-load (80% one-repetition maximum) leg extension exercise in combination with 15g CP or placebo (PLA) supplementation. Muscle biopsies from the vastus lateralis muscle were obtained at baseline as well as 1h, 4h and 24h post exercise to investigate gene expression using next generation sequencing analysis.   Several important anabolic pathways including PI3K-Akt and MAPK pathways were significantly upregulated at 1h and 4h post-exercise (p<0.05). Significant between-group differences for both pathways were identified at the 4h time point. Gene expression related to the mTOR pathway demonstrated a higher visual increase in the CP group compared to PLA with no statistically significant group differences.  The current findings revealed a significantly higher upregulation of key anabolic pathways (PI3K-Akt, MAPK) in human skeletal muscle in response to acute resistance training combined with intake of 15 g collagen peptides compared to placebo. Further investigations are needed to examine potential long-term effects on anabolic pathways on the protein level.

overall_design: A randomized, controlled, double-blinded design was implemented to investigate the effects of collagen peptides (CP) ingestion combined with acute resistance exercise on skeletal muscle anabolic gene expression.   One week before the acute exercise trial, participants visited the laboratory and underwent a preliminary screening, which included a survey of the complete medical history and a general medical examination to ensure compliance with the study-specific inclusion criteria. After the assessment of eligibility, participants were randomly allocated into two groups either supplemented with CP or placebo. A random number generator was used for allocation sequence generation. All outcome assessors, statistical analysis group, as well as trainers and participants were blinded to group assignments.

first: Christoph

last: Centner

first: Daniel

last: König


title: Comprehensive transcriptome profiling of BET inhibitor-treated HepG2 cell line

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

institute: Hanyang Univ.

summary: We comprehensively analyzed the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) underlying the antitumor functions of BET inhibitors of human HCC cells using RNA sequencing (RNA-Seq).   The pan-BET inhibitor ABBV-075 and BD2 specific inhibitor ABBV-744 attenuates the IFNγ-induced inflammatory response. In addition, BD2 inhibitors were predominantly effective in inflammatory response.

overall_design: The gene expression profile was performed with control DMSO-treated HepG2 (Con), ABBV-075-treated HepG2 (ABBV-075 50 nM), ABBV-744-treated HepG2 (ABBV-744 50 nM), ABBV-744-treated HepG2 (ABBV-744 500 nM), IFNγ-treated HepG2 (IFNγ),  IFNγ+ABBV-075-treated HepG2 (IFNγ+ABBV-075 50nM), IFNγ+ABBV-744-treated HepG2 (IFNγ+ABBV-744 50nM), IFNγ+ABBV-744-treated HepG2 (IFNγ+ABBV-744 500nM) . Samples were generated by deep sequencing, in triplicate, using Illumina 2500.

first: Young


title: Genome wide RNA expression profile of endometrial stromal cells stimulated by cAMP, and cAMP under PGC-1a-knockdown

city: Ube

first: Haruka

last: Takagi

institute: yamaguchi university

summary: To know the role of PGC-1a in the change of mRNA expression during desidualization, we compared the mRNA expression profiles between cAMP-stimulation and cAMP-stimulation under PGC-1a-knockdown.

overall_design: ESCs were transfected with control or PGC-1a siRNA and then treated with or without cAMP for 4 days. The mRNA-seq libraries were generated. After the quality of the library was validated using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), the samples were subjected to sequencing with a next-generation sequencer (Genome Analyzer GAIIx, Illumina, San Diego, CA). Gene expression values were calculated as “reads per kilobase of exon unit per million mapped reads” (RPKM).

first: N

last: Sugino

first: I

last: Tamura


title: Roles of SIRT1 in  Hematopoietic Stem Cell Aging

city: Duarte

first: WenYong

last: Chen

address: 1500 East Duarte Road

department: Cancer Biology

institute: City of Hope

summary: The purpose of this study was to determine gene expression changes in hematopoietic stem cells (HSCs) in young and old BALB/c mice, and the impact of Sirt1 gene knockout on HSC aging.

overall_design: Hematopoietic Stem Cells (HSCs) were purified by Lin-  side population sorting from old wild type (WT), old SIRT1 Knockout (KO), as well as Young wild-type (YWT) BALB/c mice

first: Zhiqiang

last: Wang

last: CHen