title: Increased expression of LOC100506314 in T cells from patients with vitiligo and contributed to the pathogenesis of vitiligo

city: Chia-Yi

first: Hui

middle: Chun

last: Yu

address: No. 2, Min-Sheng Rd, Dalin Town

department: Medical research

institute: Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

summary: The aim of this study was to investigate the differential expression of long non-coding RNAs (lncRNAs) in T cells from patients with vitiligo and their roles in the pathogenesis of vitiligo. The expression profiles of the RNA transcripts in T cells from three patients with vitiligo and three controls were conducted using microarray analysis. These aberrantly-expressed genes were further validated using T cells from 41 patients with vitiligo and 28 controls. The biologic function of the specific lncRNAs was investigated using transfection, RNA pull-down assay plus proteomic approach and Western blotting. As the results, the expression levels of 134 genes, were significantly increased, whereas the expression levels 142 genes were significantly decreased in T cells from patients with vitiligo compared with the controls. After selection and validation, the expression levels of 11 genes increased and two genes decreased in T cells from patients with vitiligo. We confirmed that LOC100506314 could interact with the signal transducer and activator of transcription 3 (STAT3) and macrophage migration inhibitory factor (MIF). The transfection of LOC100506314 could suppress STAT3, AKT, and ERK phosphorylation and nuclear protein levels of p65. Finally, overexpressed LOC100506314 decreased the T cell expression of IL-6 and IL-17.  In conclusion, among the lncRNAs, we found that the expression levels of LOC100506314 were increased in T cells from patients with vitiligo. LOC100506314 could bind to STAT3 and MIF and suppress the expression of IL-6 and IL-17 through the inhibition of the STAT3, AKT, ERK, and NF-κB pathway. Increased the expression of LOC100506314 in T cells could be a potential therapeutic strategy for vitiligo.

overall_design: The T cells isolation from three Vitilogo patinets PBMC and three heathly controls PBMC

first: Hui-Chun

first: Ming-Chi

last: Lu


title: OT-I T cell activation in Lrrc8af/f and Lrrc8af/f Cd4-Cre;OT-I mice

status: Public on Sep 26 2023

city: WuHan

first: TeDing

last: Chang

state: HuBei

address: No.1095, Jiefang Avenue, Qiaokou

country: China

institute: HuaZhong University of science and technology

type: Expression profiling by high throughput sequencing

summary: Splenocytes were separated from Lrrc8af/f and Lrrc8af/f Cd4-Cre;OT-I mice. The splenocytes were stimulated with indicated peptides (unstime/ SIINFEKL-10pM(NL)/ SIINFEKL-1000pM(NH)/ SIIGFEKL-1000nM(G4)) for 6 hours. The OT-I CD8+ T cells were labeled with Va2-PE/CD8-A700 and sorted for the sequencing.

overall_design: OT-I CD8+ T cells stimulated with different peptides (unstim. /NH/NL/G4) were subjected to bulk RNA-Seq.

first: Yuman

last: Wang

first: Zaiqiao

last: Sun

first: Jieming

last: Ping

first: Jianlong

last: Tang

first: Boxiao

last: He

first: Teding

first: Qian

last: Zhou

first: Shijie

last: Yuan

first: Zhaohui

first: Xin

last: Li

first: Yan

first: Ran

first: Ximiao

first: Zheng

last: Liu

first: Lei

last: Yin

first: Ning

last: Wu


title: Effect of unmethylated deoxycytidyl-deoxyguanosine (CpG) oligodeoxynucleotide (ODN) and the oxidative phosphorylation inhibitor IM156 on gene expression of mouse splenic B cells

city: Seoul

first: Lucy Eunju

last: Lee

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Division of Rheumatology, Department of Internal Medicine

country: South Korea

institute: Yonsei University College of Medicine

summary: Current treatment strategies for autoimmune diseases may not sufficiently control aberrant metabolism in B-cells. To address this concern, we investigated a biguanide derivative, IM156, as a potential regulator for B-cell metabolism in vitro and in vivo on overactive B-cells stimulated by the pro-inflammatory receptor TLR-9 agonist CpG oligodeoxynucleotide, a mimic of viral/bacterial DNA. Using RNA sequencing, we analyzed the B-cell transcriptome expression, identifying the major molecular pathways affected by IM156 in vivo. We also evaluated the anti-inflammatory effects of IM156 in lupus-prone NZB/W F1 mice. CD19+B-cells exhibited higher mitochondrial mass and mitochondrial membrane potential compared to T-cells and were more susceptible to IM156-mediated oxidative phosphorylation inhibition. In vivo, IM156 inhibited mitochondrial oxidative phosphorylation, cell cycle progression, plasmablast differentiation, and activation marker levels in CpG oligodeoxynucleotide-stimulated mouse spleen B-cells. Interestingly, IM156 treatment significantly increased overall survival, reduced glomerulonephritis and inhibited B-cell activation in the NZB/W F1 mice. Thus, our data indicated that IM156 suppressed the mitochondrial membrane potentials of activated B-cells in mice, contributing to the mitigation of lupus activity. Hence, IM156 may represent a therapeutic alternative for autoimmune disease mediated by B-cell hyperactivity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the splenic B cells of lupus-prone mice treated with CpG-ODN, IM156, or both

first: Joo

middle: S

last: Shim

first: Eun

middle: J

last: Kim

first: Lucy

first: Joon

middle: Y

first: Yuri

last: Cho

first: Hanna

first: Jieun

first: Sung

middle: H

last: Jang

first: Jimin

last: Son

first: Jae-Ho

last: Cheong

first: Aekyong

first: Beom

last: Lim

first: San-Jun

last: Ha

first: Jason

last: Song


title: Cell-Intrinsic and -Extrinsic Effects of SARS-CoV-2 RNA on Pathogenesis: Single Cell Meta-Analysis

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

country: USA

institute: Tulane University

summary: We used single cell RNA sequencing (scRNA-seq) to investigate the SARS-CoV-2 RNA dissemination.

overall_design: K18-hACE2 48 hours COVID post-infection mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Shamima

last: Khatun

first: T

last: Parks Remcho

first: Xuebin

last: Qin

middle: K


title: Single-Cell Multiomics Reveals Distinct Cell States at the Top of the Human Hematopoietic Hierarchy

status: Public on Sep 27 2023

city: Lund

first: Göran

last: Karlsson

state: Scania

address: Kilinkgatan 26 BMC B12

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide DNA methylation profiling of cell-free DNA in nipple aspirate fluid for breast cancer

city: Houston

first: Minsun

last: Jeon

address: 2121 W Holcombe Blvd

institute: Texas A&M Institute of Biosciences & Technology

type: Methylation profiling by high throughput sequencing

summary: Nipple aspriate fluid (NAF) were obtained from 7 women including 3 breast cancer patients. Cell-free DNA (cfDNA) were isolated and bisulfite sequencing using Illumina HiSeq X Ten platform.

overall_design: cfDNA libraries of normal and breast cancer NAF samples were constructed and sequenced for genome-wide DNA methylation profiling.

first: Ke

last: Zhang


title: Impact of  shear stress of cytotrophoblast stem cell derived from naïve PSC

city: Kyoto

first: ASAKO

last: INOHAYA

address: Shogoin, Sakyoku

department: Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: In order to investigate the effects of shear stress on trophoblasts in the intervillous space, we cultured the cytotrophoblast stem cells derived from naïve PSC (nCT) under shear stress.

overall_design: Analyzing transcriptonal profile of nCT, nCT cultured with ST medium under static condition (static) or shear stress (flow).

first: YOSHITSUGU

last: CHIGUSA


title: Transcriptomic analysis of Pseudomonas aeruginosa under the treatment of bismuth subsalicylate(BSS), eravacycline or the combination

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: To get the different expression genes under the treatment.

overall_design: 8 samples, 2 biological replicates for each studied condition

first: Yushan

last: Xia

first: Oscar

middle: P

last: Kuipers


title: Effect of Ichthyophthirius multifiliis on gene expression after treatment with magnolol in vivo

city: Yangling

first: shenye

last: qu

address: LiTai road Yangling, shaanxi

institute: Northwest A&F university

summary:
To investigate the antiparasitic mechanism of magnolol, we performed RNA-seq analysis to probe the significantly regulated genes after treatemnt by magnolol.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 13 independent parasite samples collected form various treatment goups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for I. multifiliis without and with magnolol treatment (Control:C1-C4,Treatemnt:T1-T3, T4-T6, T7-T9).

first: Qu

last: Shenye

first: Ling

last: Fei


title: R-loops act as a master regulatory switch modulating transcription of cold-responsive genes in rice

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

summary: Cold is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in plants. R-loops can function in a series of biological processes, including normal development and stress responses, in plants. However, how R-loops function in cold responses is still largely unknown in plants, especially in cold sensitive rice. Herein, we conducted DRIP-seq in combination with other newly generated omics data (RNA-seq, DNase-seq, ChIP-seq and MNase-seq) in rice with or without cold treatment. We found that cold treatment caused R-loop dynamics across the genome, indicating that R-loops are cold sensitive non-B DNA structures. Moreover, cold biased R-loops had high GC content and novel motifs the binding of distinct TFs as compared to CK biased R-loops, indicative of occurrence of differential biological implications of R-loop dynamics in response to cold stress. More importantly, we for the first time to provide evidence showing that, in addition to the direct involvement of R-loops in the regulation of cold-responsive gene transcription, R-loops can indirectly modulate transcription of subsets of cold-responsive genes through R-loop overlapping TF-centered or cis-regulatory element related regulatory networks and lncRNAs in rice. Thus, our study for the first time provides evidence showing functions of R-loop dynamics in rice cold responses. It also provides some potential R-loop loci for genetic and epigenetic manipulation towards breeding of enhanced cold tolerance rice varieties.

overall_design: we conducted DRIP-seq in combination with other newly generated omics data (RNA-seq, DNase-seq, ChIP-seq) in rice with or without cold treatment.

first: Wenli


title: RNA expression in human placental tissue with Hemoglobin Bart's  Hydrops Fetalis Syndrome

city: Nanning

first: Lingjie

last: Deng

address: a. Department of Prenatal Diagnosis and Genetic Diseases, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Road, Nanning, Guangxi, China

type: Non-coding RNA profiling by high throughput sequencing


title: MRNAs and non-coding RNAs expression in human placental tissue with Hemoglobin Bart's  Hydrops Fetalis Syndrome

institute: The First Affiliated Hospital of Guangxi Medical University

summary: Hemoglobin Bart’s hydrops fetalis syndrome (BHFS) is the most severe form of α-thalassemia. Histological alternations can be observed in placenta, but placental transcriptome profile and circular RNAs have not been study in this disease. The aim of this study was to define the placental transcriptional changes and find relevant circular RNAs in BHFS. We performed high-throughput RNA sequencing to detect placental samples from fetuses affected by BHFS (n=5) and normal fetuses (NF, n=5). Our results showed 152 differentially expressed genes (DEGs), 112 circRNAs, and 45 microRNAs that were differentially expressed. DEGs were found to be involved in Gene Ontology terms related to gas transport, cell adhesion, oxidative stress, organ development, hemopoiesis, etc. Our study characterized the placental transcriptome of BHFS.

first: Yebin

last: Lu

first: Dongmei

last: Yang

first: Fang

first: Heyun

last: Ruan

first: Changqiang

last: wei

first: Ketong

last: Lai

first: Lihong

last: Pang


title: Transcriptomic landscape of geriatric SC after CPEB4 virus infection

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: We infected the geriatric SCs with CPEB4 containing adenovirus. Afterwards, we harvested total RNA for sequencing.

overall_design: Two biological replicates of GFP virus infection compared with two sets of CPEB4 infected geriatric SCs. BGI DNBSEQ-G400 Sequencer. PE100 sequencing set

last: CHEUNG

first: Wenshu

last: ZENG


title: Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells

status: Public on Sep 25 2023

city: Philadelphia

first: Naveen

last: Jain

state: PA

address: Room 415, 415 Currie Boulevard

institute: University of Pennsylvania

summary: Pluripotency can be induced in somatic cells by the expression of the four “Yamanaka” factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually only a rare subset of cells admit reprogramming, and the molecular characteristics of this subset remain unknown. Here, we apply retrospective clone tracing to identify and characterize the individual human fibroblast cells that are primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis led to increased reprogramming efficiency, identifying it as a barrier to reprogramming. Changing the frequency of reprogramming by inhibiting the activity of LSD1 led to an enlarging of the pool of cells that were primed for reprogramming. Our results show that even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for hiF-T cells with CRISPR knockdown of individual genes. Biological replicates are included and indicated.

first: Yogesh

last: Goyal

first: Margaret

middle: C

last: Dunagin

first: Christopher

last: Cote

first: Ian

middle: A

last: Mellis

first: Benjamin

last: Emert

first: Connie

middle: L

last: Jiang

last: Dardani

first: Sam

last: Reffsin

first: Arjun

last: Raj


title: Abnormal lactate metabolism is linked to albuminuria and kidney injury in diabetic nephropathy

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

summary: Diabetic nephropathy (DN) is a leading cause of end-stage kidney disease worldwide. Susceptibility to DN is inherited but genetic determinants of DN have not been precisely defined. We have previously described a mouse model combining genetic type 1 diabetes (Akita) with a renin transgene (ReninTg) that exhibits characteristic features of human DN including albuminuria, glomerulosclerosis, and genetic predisposition for kidney disease. We performed single-cell sequencing (10x Chromium) of glomerular cell suspensions obtained from the wildtype (WT) and Akita- ReninTg (AR) mice at 10 weeks of age before overt pathological abnormalities are present in kdiney.

overall_design: Kidneys from Akita-Renin trangenic and wildtype mice were collected and processed according to 10X Genomics Chromium protocol for single-cell RNAseq.

first: Kengo

last: Azushima

first: Thomas

middle: M

last: Coffman


title: The transcriptomic profile of peripheral blood nuclear cells in dogs with atopic dermatitis before and after 6 months allergen-specific immunotherapy.

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

summary:
The aim of the study was to identify genes which are differentially expressed in the blood of dogs with canine atopic dermatitis (AD) before and after 6 months of allergen-specific immunotherapy (ASIT)  in comparison to healthy control dogs. Diagnosis of AD was based on compatible history and clinical signs determined using Willemse and Prélaud diagnostic criteria, completed by Favrot criteria as follows: pruritus sine material, indoor lifestyle  and  the exclusion of other causes of pruritus ongoing for at least one year. Clinical diagnosis of atopic dermatitis was confirmed by serological allergy testing (IDEXX allergic panel test) and intradermal skin testing (Artuvetrin test set, Netherlands). In order to avoid the role of food antigens as a cause of the skin condition elimination diet was used for 6–8 weeks.
No anti-inflammatory drugs were given for at least 3 weeks prior examination with serological test,  intradermal test and blood collection. All dogs, which were classified to the investigated group had positive reactions in serological allergy testing and intradermal skin testing.
Subsequently, subcutaneous allergen-specific immunotherapy was applied. Allergen extracts were prepared on the basis of the results of intradermal tests by the Artuvetrin company and were administered subcutaneously in increasing concentrations during 6 months according to the manufacturer's recommendations. Aside from gene regulation, this experiment also examined the participation of individual lymphocyte subpopulations (like: B, T, Th, Tc, Treg)  and the level of interleukins in the blood of AD dogs before and after therapy.

overall_design: Twenty  two two-color microarrays were performed,  one microarray for each patient was used (8 samples from healthy dogs, 7  samples from AD dogs before therapy and 7 samples from the same dogs after 6 months allergen-specific immunotherapy). cRNA of  healthy  dogs and dogs with  AD was hybridized to Agilent two color microarrays with a common reference. The common reference comprised a pool of equal amounts of RNA from 13 healthy dogs which did not take part in the experiment.

first: Kourou

last: Dembele

first: Małgorzata

last: Gajewska


title: several colorectal cancer patient derived tumor organoid RNAseq data

city: China Tianjin

first: Liu

last: Jinming

address: Nankai University Biological Station, Nankai District

department: School of Life Sciences

institute: Nankai University

summary: Acquired drug resistance is a major challenge for cancer therapy and the leading cause of cancer mortality. However, the mechanisms of drug resistance are diverse and the strategy to specifically target drug resistant cancer cells remains an unmet clinical issue. We establisheda32 colorectal cancer (CRC) PDO biobank and induced acquired drug resistance by repeated low-level exposures of chemo-agents. Chemosensitivity profiling and transcriptomic analysis studies34 revealed that chemo-resistant PDOs exhibited elevated expression of LGR4 and activationof the35 Wnt signaling pathway. Further, we performed antibody screening against LGR4 and selecteda36 monoclonal antibody (LGR4-mAb) that potently inhibited the LGR4/Wnt signaling. In drug resistant PDOs and xenograft models, treatment with LGR4-mAb significantly sensitizeddrug- 38 induced ferroptosis. Mechanistically, LGR4 dependent Wnt signaling transcriptionally up-regulated SLC7A11, a key inhibitor of ferroptosis, to confer acquired drug resistance. Targeting40 Wnt signaling by LGR4-mAb and by other modulators augments ferroptosis when co-administrated with chemotherapeutic agents. Finally, LGR4-mAb therapy was effective against other cancers that express high levels of LGR4. Collectively, our results demonstrate a new strategy to selectively activate ferroptosis and provide a new opportunity to fight refractoryand44 recurrent cancers.

overall_design: The IC50 of chemotherapy drugs 5-Fu and Cisplatin were detected by detecting tumor organoid from different patients, and the gene expression differences were compared in different groups.


title: Combined gene therapy for angiogenesis and muscle growth modifies several cell types and enhances hypertrophy and body composition

city: Jyväskylä

first: Riikka

last: Kivelä

address: Rautpohjankatu 8

country: Finland

institute: University of Jyväskylä

summary: Blood capillary vessels are important for muscle growth and function. The aim of this study was to combine gene therapy with Pro-MSTN (myostatin propeptide) and VEGF-B (Vascular Endothelial Growth factor B) to induce skeletal muscle hypertrophy and angiogenesis simultaneously in mouse skeletal muscles. Previously, effects of VEGF-B and MSTN blocking have been studied at the whole muscle level, but in the present study, with single-cell RNA sequencing (scRNASeq), we give also insights into cell-type specific actions.

overall_design: Mice TA (m. tibialis anterior) muscles were injected i.m. with rAAVs (CTRL, Pro-MSTN and VEGF-B) alone or in combination. Muscle mononuclear cells were isolated and analyzed by using 10x Genomics scRNASeq.

first: Aino

last: Männistö

first: Alfredo

last: Ortega-Alonso


title: Organellar Remodelling of Lipids Determines the Epigenetic Reprogramming and Maternal-to-Zygotic Transition in Early Development

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

institute: The First Affiliated Hospital of Zhengzhou University

summary: Metabolic reprogramming of glucose and amino acids has been documented to affect early development. Here, we show that peroxisome-mediated β-oxidation is involved in lipids reprogramming to achieve H3K4me3 erasure and then zygotic genome activation (ZGA) in early embryo development. The metabolic patterns of fatty acids (FAs), triglyceride (TG) and phospholipid (PL) are reprogrammed during the oocyte-to-embryo transition. Very long-chain fatty acids (VLCFAs), arachidonic acid (ARA), phosphatidylethanolamine (PE), lysophosphatidylethanolamine (Lyso-PE), lysophosphatidylcholine (Lyso-PC), and methyl donors are stored in oocytes, and after fertilization, they are converted into phosphatidylcholine (PC) at the 2-cell stage. Mitochondrial β-oxidation prevails in oocytes, while peroxisomal β-oxidation plays a critical role in shortening the VLCFA to form TG and synthesize PC and balancing the ratio of saturated and unsaturated FAs, which consumes the methyl donors as conducive to H3K4me3 erasure at the 2-cell stage. Inhibiting the peroxisome-mediated β-oxidation disrupts lipids metabolism remodellingH3K4me3 erasure and subsequent ZGA, leading to embryo arrest at the 2-cell stage. Oocytes from obese mice show I a relatively low level of VLCFAs, defective peroxisomal β-oxidation, and incomplete H3K4me3 erasure and ZGA. Microinjection of two saturated fatty acids, palmitic and myristic acids, rescues 2-cell arrest caused by peroxisome-mediated β-oxidation inhibition and obesity, and overexpressing Pemt to consume the methyl donors has the same rescue effect. These results elucidate a novel link among the peroxisomal-β-oxidation-mediated lipid metabolism reprogramming, H3K4me3 modification and ZGA during oocyte-embryo transition, and may provide a unique approach to improve reproduction in obese women.

overall_design: Control embryos at 2-cell stages and siAcox1 embryos at 2-cell embryos for three replicates are performed RNA sequencing.

first: Linli

first: Guohui

last: Zhangxiao

first: Xie

last: Feng

first: Shiming

last: Luo

first: Qingyuan

last: Sun

first: Xianghong

last: Ou


title: RNA-seq analysis identifies the effect of PM2.5 on human nasal epithelial cells cultured under air-liquid interface (ALI) conditions until differentiated.

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: In this study, we performed high-throughput sequencing to evaluate the gene expression profiles of  human nasal epithelial cells (HNECs) cultured under air-liquid interface (ALI) conditions until differentiated and then stimulated with PM2.5 (100 μg/ml) for 24 hours.

overall_design: Comparison of mRNA expression profiles between PM2.5 exposed HNECs and control cells.

first: Weitian

last: Zhang


title: MiRNAs expression in human placental tissue with Hemoglobin Bart's Hydrops Fetalis Syndrome

first: Lingjie

last: Deng

overall_design: We performed high-throughput RNA sequencing to detect placental samples from fetuses affected by BHFS (n=5) and normal fetuses (NF, n=5).

first: Yebin

last: Lu

first: Dongmei

first: Fang

first: Heyun

last: Ruan

first: Changqiang

last: wei

first: Ketong

last: Lai

first: Lihong

last: Pang


title: Astrocyte growth during morphogenesis is driven by the Tre1/S1pr1 phospholipid-binding G protein-coupled receptor

city: Portland

first: Taylor

middle: Reagan

last: Jay

email: taylor.jay@case.edu, jayta@ohsu.edu

state: OR

address: 3181 Sam Jackson Park Rd.

department: Vollum Institute

institute: Oregon Health & Science University

summary: TRAPseq was performed on Drosophila melanogaster astrocytes at different stages of development to assess the changes in gene translation that occur in astrocytes at these different stages.

overall_design: Ribosomes were tagged in astrocytes using flies which expressed elaV-Gal80 and alrm-Gal4, UAS-EGFP-L10a. Ribsosomes were pulled down using GFP antibodies and the associated transcripts were isolated. Each sample contains 200 pooled fly heads; males and females were both used. Samples were isolated from flies at 4 timepoints: 48-72hr after puparium formation (P), 1-3 days post-eclosion (13), 10-12 days post-eclosion (1012) and 50-60 days post-eclosion (5060).

middle: R

first: Jiakun

last: Chen

first: Marc

last: Freeman


title: Expression of vesicular miRNAs from plasma of Brazilian breast cancer patients

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

summary: in this study, we aimed to determine the vesicular miRNA profile between five cohorts of BC patients according to main molecular subtypes. These samples were classified according to their age at diagnosis in two groups: Young (diagnosed before 40 years old) and Elderly (diagnosed after 40 years old). We isolated vesicular miRNA from the plasma of these patients and then assessed their miRNA levels using a high-throughput and high-resolution technique based on digital barcode hybridization.

overall_design: We collected plasma samples of breast cancer patients diagnosed at Hospital das Clinicas, Medicine School (Universidade de São Paulo). Using 200 uL of this plasma, we isolated extracellular vesicles (EVs) using the qEV original size-exclusion chromatography (SEC) columns. Then, we treated EVs with proteinase K and RNAse before isolating vesicular miRNA by following the instructions of the miRNeasy Serum/plasma kit (cat. 217184, Qiagen). Next, we quantified the vesicular miRNA by spectrophotometry and used 40 or 120 µL of each sample to concentrate up to 4 µL using the Eppendorf® 5301 concentrator for 20 or 35 minutes at 45 °C following the manufacturer’s recommendations. After concentration, 0.5 µL of each sample was loaded into the NanoDrop™ 8000 Spectrophotometer (ThermoFisher) to verify the miRNA mass. Then, ~65 ng of vesicular miRNA were hybridized for 16.5 hours with molecular barcoding for 827 experimentally validated human miRNAs (from miRBase v21) using the nCounter Master Mix (NanoString® Technologies, cat. NAA-AKIT-012). Subsequently, miRNAv3 NanoString® cartridges (NanoString® Technologies, cat. CSO-MIR3-12) were loaded with the mix per sample, sealed, and transferred to a nCounter® Digital Analyzer device (NanoString® Technologies) for data collection. miRNA expression data were analyzed in the nSolver™ Data Analysis v.4.0 software (NanoString® Tech.) with the default protocol by the manufacturer. For vesicular miRNA, we normalize the expression of human miRNAs by the geometric mean of all negative (negative normalization) and positive (positive normalization) probes. Then, we used the top 15 more stable regions to normalize the content set data. Data were exported in comma-separated value (*.csv) format for further analysis.

first: Alexis

middle: G

first: Luciana

last: Andrade

first: Roger

last: Chammas


title: Expression of vesicular miRNAs from plasma of Brazilian breast cancer patients diagnosed before 40 years old

summary: in this study, we aimed to determine the vesicular miRNA profile between four cohorts of BC patients according to main molecular subtypes. These samples were classified according to their age at diagnosis in two groups: Young (diagnosed before 40 years old) and Elderly (diagnosed after 40 years old). We isolated vesicular miRNA from the plasma of these patients and then assessed their miRNA levels using a high-throughput and high-resolution technique based on digital barcode hybridization.

overall_design: We collected plasma samples of breast cancer patients diagnosed at Hospital das Clinicas, Medicine School (Universidade de São Paulo). Using 1mL of this plasma, we isolated extracellular vesicles (EVs) using the qEV original size-exclusion chromatography (SEC) columns. Then, we treated EVs with proteinase K and RNAse before isolating vesicular miRNA by following the instructions of the miRNeasy Serum/plasma kit (cat. 217184, Qiagen). Next, we quantified the vesicular miRNA by spectrophotometry and used 20 µL of each sample were concentrated up to 4 µL using the Eppendorf® 5301 concentrator for 20 minutes at 45 °C following the manufacturer’s recommendations. After concentration, 0.5 µL of each sample was loaded into the NanoDrop™ 8000 Spectrophotometer (ThermoFisher) to verify the miRNA mass. Then, all vesicular miRNA were hybridized for 16.5 hours with molecular barcoding for 827 experimentally validated human miRNAs (from miRBase v21) using the nCounter Master Mix (NanoString® Technologies, cat. NAA-AKIT-012). Subsequently, miRNAv3 NanoString® cartridges (NanoString® Technologies, cat. CSO-MIR3-12) were loaded with the mix per sample, sealed, and transferred to an nCounter® Digital Analyzer device (NanoString® Technologies) for data collection. miRNA expression data were analyzed in the nSolver™ Data Analysis v.4.0 software (NanoString® Tech.) with the default protocol by the manufacturer. For  vesicular miRNA, we normalize the expression of human miRNAs by the geometric mean of all negative (negative normalization) and positive (positive normalization) probes. Then, we used the top 15 more stable regions to normalize the content set data. Data were exported in comma-separated value (*.csv) format for further analysis.


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [RNA-seq]

city: New York

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

institute: NYU Langone Health

summary: Cancer progression is associated with genetic and epigenetic aberrations that affect chromatin 3D organization in the nucleus. Changes in loop extrusion or phase separation alter the relationships between enhancer and promoter elements, defining novel gene expression programs that are selected to promote growth and survival. Here, we provide an integrative approach based on chromatin conformation, accessibility and transcription, further validated by CRISPR interference screenings in order to identify chromatin topologies relevant to different subtypes of T-cell leukemia, namely T-ALL and ETP-ALL. By focusing on highly interconnected elements, we characterized 3D hubs as headquarters of leukemia progression and identity, demonstrating that oncogenes and disease markers are regulated by multiple cis-regulatory regions.

overall_design: Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed. To enrich for blast representation, samples were sorted based on clinical immune-phenotype, for CD2 and/or CD7 surface expression

last: Rodriguez-Hernaez

first: Francesco

last: Boccalatte

first: Giovanni

last: Gambi

first: Bettina

last: Nadorp

first: Ioannis

last: Aifantis

first: Aristotelis

last: Tsirigos


title: Glucocorticoid receptor signaling in adipose tissue II

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Comparison of differences in gene expression in white and brown adipose tissues in the presence and absence of glucocorticoid receptor expression.

overall_design: RNA from white adipose tissue in wild-type mice (x 4 biological reps), RNA from brown adipose tissue in wild-type mice (x 4 biological reps), RNA from white adipose tissue in Adipose-tissue specific GR Knockout mice (x 4 biological reps), and RNA from brown adipose tissue in Adipose-tissue specific GR Knockout mice (x 4 biological reps)

first: Diana

last: Cruz-Topete

first: John

last: Cidlowski


title: Glucocorticoid receptor signaling in adipose tissue

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

overall_design: Refer to individual Series


title: Expression of cell-free miRNAs from plasma of Brazilian breast cancer patients

summary: in this study, we aimed to determine the cell-free miRNA (cf-miRNA) profile between five cohorts of BC patients according to main molecular subtypes. These samples were classified according to their age at diagnosis in two groups: Young (diagnosed before 40 years old) and Elderly (diagnosed after 40 years old). We isolated total miRNA from the plasma of these patients and then assessed their miRNA levels using a high-throughput and high-resolution technique based on digital barcode hybridization.

overall_design: We collected plasma samples of breast cancer patients diagnosed at Hospital das Clinicas, Medicine School (Universidade de São Paulo). Using 200 uL of this plasma, we isolated cell-free miRNA (cf-miRNA) following the instructions of the miRNeasy Serum/plasma kit (cat. 217184, Qiagen). Then, we quantified the cf-miRNA by spectrophotometry and used 40 or 120 µL of each sample were concentrated up to 4 µL using the Eppendorf® 5301 concentrator for 20 or 35 minutes at 45 °C following the manufacturer’s recommendations. After concentration, 0.5 µL of each sample was loaded into the NanoDrop™ 8000 Spectrophotometer (ThermoFisher) to verify the miRNA mass. Then, ~25 ng of cf-miRNA were hybridized for 16.5 hours with molecular barcoding for 827 experimentally validated human miRNAs (from miRBase v21) using the nCounter Master Mix (NanoString® Technologies, cat. NAA-AKIT-012). Subsequently, miRNAv3 NanoString® cartridges (NanoString® Technologies, cat. CSO-MIR3-12) were loaded with the mix per sample, sealed, and transferred to an nCounter® Digital Analyzer device (NanoString® Technologies) for data collection. miRNA expression data were analyzed in the nSolver™ Data Analysis v.4.0 software (NanoString® Tech.) with the default protocol by the manufacturer. For cf-miRNA, we normalize the expression of human miRNAs by the geometric mean of all negative (negative normalization) and positive (positive normalization) probes. Then, we used the top 15 more stable regions (up to 15% of the coefficient of variation) to normalize the content set data. Data were exported in comma-separated value (*.csv) format for further analysis.

last: Carrasco

middle: N


title: Gene expression panel analysis of CD11c+ cells from WT and RELMα KO lung homogenate at day 30 post infection with Nippostrongylus brasiliensis.

city: Riverside

first: Meera

last: Nair

state: CA

address: 243 SOM Research 3401 Watkins Drive

institute: UC Riverside

summary: WT or KO mice were subctaneously injected with 500 L3 larvae or saline and euthanized after 7 days. The lungs were excised and digested to generate a single cells suspension, from whichCD11c+ cells were bead-enriched for gene expression analysis. Cell lysates were used directly with the hybridization probes using the manufacterers protocol (Nanostring).

overall_design: We used the nanostring Mouse Myeloid Innate Immunity Panel to analyze 754 genes associated with innaute immunity.

first: Jiang

last: Li


title: Gene expression panel analysis of CC10 Cre- and CC10 Cre+ RELMα flox/flox lung homogenate at day 30 post infection with Nippostrongylus brasiliensis.

summary: Mice were administered 100μL of 20mg/mL tamoxifen every other day for 5 doses, and recovered for 1 week before being  subctaneously injected with 500 L3 larvae or saline. Mice were euthanized after 30 days. The lungs were excised and digested to generate a single cells suspension, from which total RNA was extracted from 1 million cells for gene expression analysis.

overall_design: We used the nanostring Mouse Immunology Panel to analyze 561 genes associated with immunology.

first: Stefanie

last: Sveiven

first: Sang

last: Kim


title: Irisin regulated genes in mouse liver derived AML12 cells

summary: To find genes regulated by irisin in culture media in AML12 cells.

overall_design: Irisin induced gene expression in AML12 cells was measured after 24hr treatment

first: Tatsuya

last: Sueyoshi


title: Gene expression panel analysis of WT and RELMα KO lung homogenate at day 30 post infection with Nippostrongylus brasiliensis.

summary: WT or KO mice were subctaneously injected with 500 L3 larvae or saline and euthanized after 30 days. The lungs were excised and digested to generate a single cells suspension, from which total RNA was extracted from 1 million cells for gene expression analysis.


title: Myeloid and epithelial-derived RELM contribute to tissue repair following lung helminth infection


title: Preclinical quality, safety and efficacy of a human embryonic stem cell-derived product for treatment of people with moderate Parkinson’s Disease (STEM-PD)

city: Lund

first: Malin

last: Parmar

department: Department of Experimental Medical Science, Lund University

institute: Wallenberg Neuroscience Center, MultiPark and Lund Stem Cell Centre

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array
Other


title: Preclinical quality, safety and efficacy of a human embryonic stem cell-derived product for treatment of people with moderate Parkinson’s Disease (STEM-PD) II

summary: Cell replacement therapies for Parkinson’s Disease (PD) based on transplantation of dopaminergic neurons generated from pluripotent stem cell sources are now entering clinical trials. Here, we present the quality, safety and efficacy data supporting a first-in-human clinical trial in PD using an embryonic stem cell product STEM-PD, as well as the design of the trial itself. The cryopreserved STEM-PD product was manufactured under Good Manufacturing Practice (GMP) and fully quality-tested in vitro for regulatory compliance. The product was further tested in an extensive 39-week Good Laboratory Practice (GLP) safety study in immunodeficient rats for toxicity, tumourigenicity and biodistribution, as well as in a 24-week non-GLP efficacy study. These studies showed that the transplanted STEM-PD cells could induce full functional recovery in a pre-clinical rat model of PD, and that the treatment did not give rise to any adverse effects. This cell batch will be used for all participants in the STEM-PD Phase I/IIa clinical trial, where the first of 8 patients with moderate PD have now been transplanted. Furthermore, we observed highly comparable in vivo efficacy results between two different GMP batches of STEM-PD cells, verifying that this product has the potential to be serially manufactured for widespread clinical use.

overall_design: gDNA from STEM-PD DP batch 3 sample  was purified and analysed using the AmpliSeq for Illumina Cancer Hotspot panel v2, which is a targeted sequencing assay for detecting 2,800 COSMIC mutations in 50 cancer and tumour suppressor genes. Libraries were sequenced with an Illumina NextSeq550 instrument. Raw data were pre-processed with the Illumina Local Run Manager and Illumina DNA amplicon analysis module, and further analysed using the Illimuna Variant Studio v3.0. Genetic variants were manually cross-referenced to public databases (dbSNP, ClinVar, COSMIC).

first: Simona

last: Graziano


title: Differential gene expression in Gaddβ KO mice treated with diethylnitrosamine and phenobarbital

summary: To find Gadd45β dependent gene regulation in mouse hepatocellular carcinoma induced by diethylnitorsamine + phenobarbital

overall_design: Phenobarbital treatment-induced gene expression changes in the liver were compared between wild-type and Gadd45b KO mice. 4 mice for each group.


title: Preclinical quality, safety and efficacy of a human embryonic stem cell-derived product for treatment of people with moderate Parkinson’s Disease (STEM-PD) I

overall_design: gDNA from STEM-PD DP batch 1 sample and from the RC17 MCB was purified and analysed using the AmpliSeq for Illumina Cancer Hotspot panel v2, which is a targeted sequencing assay for detecting 2,800 COSMIC mutations in 50 cancer and tumour suppressor genes. Libraries were sequenced with an Illumina MiSeq instrument. Raw data were pre-processed with the Illumina Local Run Manager and Illumina DNA amplicon analysis module, and further analysed using the Illimuna Variant Studio v3.0. Genetic variants were manually cross-referenced to public databases (dbSNP, ClinVar, COSMIC).


title: LncRNAs and genes of sorghum in response to drought stress

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

institute: Shanxi Agricultural University

summary: We analyzed lncRNAs from sorghum leaves under water control treatment using high-throughput sequencing technology and bioinformatic approaches to explore the genome-wide quantity of lncRNAs and their potential function in the regulation of drought responses.

overall_design: There were three levels of drought treatment: normal water supply (CK), mild drought stress (DR1) and severe drought stress (DR2).


title: Preclinical quality, safety and efficacy of a human embryonic stem cell-derived product for treatment of people with moderate Parkinson’s Disease (STEM-PD) III

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Cell replacement therapies for Parkinson’s Disease (PD) based on transplantation of dopaminergic neurons generated from pluripotent stem cell sources are now entering clinical trials.  Here, we present the quality, safety and efficacy data supporting a first-in-human clinical trial in PD using an embryonic stem cell product STEM-PD, as well as the design of the trial itself. The cryopreserved STEM-PD product was manufactured under Good Manufacturing Practice (GMP) and fully quality-tested in vitro for regulatory compliance. The product was further tested in an extensive 39-week Good Laboratory Practice (GLP) safety study in immunodeficient rats for toxicity, tumourigenicity and biodistribution, as well as in a 24-week non-GLP efficacy study. These studies showed that the transplanted STEM-PD cells could induce full functional recovery in a pre-clinical rat model of PD, and that the treatment did not give rise to any adverse effects. This cell batch will be used for all participants in the STEM-PD Phase I/IIa clinical trial, where the first of 8 patients with moderate PD have now been transplanted. Furthermore, we observed highly comparable in vivo efficacy results between two different GMP batches of STEM-PD cells, verifying that this product has the potential to be serially manufactured for widespread clinical use.

overall_design: gDNA from a stem cells (RC17) master cell bank (MCB) and from two different ventral midbrain dopaminergic precursors (STEM-PD) batches (#1 and #3) was purified and analysed using the HumanCytoSNP-12 v2.1. The genetic stability of the MCB and of STEM-PD #1 was tested at thaw and after different passages in culture.

first: Sonja

last: Pikkupeura


title: Talaromyces marneffei suppresses macrophage inflammation by regulating host alternative splicing

first: Wudi

last: Wei

address: 22nd Shuangyong Road

institute: Guangxi Medical University

summary:
To investigate the function of NCOR2-013 in T. marneffei-infected THP-1 macrophages, we established NCOR2-013 overexpression THP-1 macrphages.
We then performed gene expression profiling analysis using data obtained from RNA-seq of T. marneffei-infected NCOR2-013 overexpression THP-1 macrophages and T. marneffei-infected control cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T. marneffei-infected NCOR2-013 overexpression THP-1 macrophages and T. marneffei-infected control cells.

first: Qiang

last: Luo


title: Glucocorticoid receptor signaling in adipose tissue I


title: Small RNAs of sorghum in response to drought stress

summary: We sequenced three small-RNA (sRNA) libraries constructed from leaves of sorghum subjected to three different treatments, well-watered (CK), mild drought (DR1) and severe drought (DR2). These findings will be useful for research on drought resistance and provide insights into the mechanisms of drought adaptation and resistance in sorghum.

overall_design: Three small-RNA (sRNA) libraries were constructed from leaves of sorghum subjected to three different treatments, well-watered (CK), mild drought (DR1) and severe drought (DR2).


title: Transcriptional profiling of dental sensory and proprioceptive trigeminal neurons using single-cell RNA sequencing

first: Junhyong

address: 433 S University Avenue

department: Biology

summary: We used high depth single-cell RNA sequencing (scRNA-seq) combined with retrograde tracing in mice to characterize the molecular composition of five main types of dental primary afferent (DPA) neurons and compared them to the proprioceptive mesencephalic trigeminal nucleus (MTN) neurons.

overall_design: Retrogradely labeled DPA and MTN neurons from the molars of C57BL/6 mice mouse (5-week-old) were harvested and cultured. Neurons were then individually collected with a glass micropipette and analyzed using scRNAseq.

first: Pa

last: Lee

first: Jihoon

first: Heather

last: Rossi

first: Sena

last: Chung

first: Seung

last: Han

first: Seog

middle: B

last: Oh


title: DEK deficiency suppresses mitophagy to protect against house dust mite-induced asthma

status: Public on Sep 24 2023

city: Yanji

first: Guang

middle: hai

last: Yan

address: gongyuan road 977

institute: yanbian university

summary: This study aims to investigate the role and mechanism of DEK in asthmatic airway inflammation and in regulating PTEN-induced putative kinase 1 (PINK1)-Parkin mediated mitophagy, NLRP3 (NOD-like receptor family pyrin domain containing 3) inflammasome activation, and apoptosis. We found that recombinant DEK protein (rmDEK) promoted eosinophils recruitment, mitochondrial fragmentation, and outer membrane 20 (TOM20) and LC3 co-localization representing mitophagosomes  in bronchoalveolar lavage fluid (BALF) in house dust mite (HDM) induced-asthma. rmDEK also reduced co-localization of mitochondrial fusion protein mitofusin1 (MFN1) and mitochondria, and the protein level of manganese superoxide dismutase (MnSOD), enhanced microtubule-associated protein1 light chain 3 (LC3) and voltage-dependent anion channels (VDAC) co-localization which also represent the mitophagosomes  in airway epithelial cells, furthermore, increased dynamin-related protein 1 (DRP1) expression, PINK1-Parkin-mediated mitophagy, NLRP3 inflammasome activation, and apoptosis. In the DEK knockout mice, HDM induced asthmatic airway inflammation, MnSOD, PINK1-Parkin protein level, Parkin mediated mitophagy characterized by LC3 and Parkin co-localization in the airways, ROS generation, NLRP3 inflammation and apoptosis were fully reversed. Similar effects of rmDEK were also observed in the BEAS-2B cells, which were rescued by the autophagy inhibitor 3-MA. Moreover, DEK silencing diminished  the Parkin, LC3, DRP1 translocation to mitochondria; as well as mitochondrial ROS; TOM20 and mitochondrial DNA mediated mitochondrial oxidative damage.  ChIP-sequence analysis showed that DEK was enriched on the AAA domain-containing protein 3A (ATAD3A) promoter and could positively regulate ATAD3A expression. Additionally, ATAD3A was highly expressed in HDM-induced asthma models. Furthermore, ATAD3A interacted with DRP1, and knockdown of ATAD3A could down-regulate DRP1 and mitochondrial oxidative damage. Conclusively, DEK deficiency alleviates airway inflammation in asthma by down-regulating PINK1-Parkin mitophagy, NLRP3 inflammasome activation, and apoptosis. The mechanism may be through the DEK/ATAD3A/DRP1 signaling axis. Our findings may provide new potential therapeutic targets for asthma treatment.

overall_design: ChIP-Sequence analysis was performed in BEAS-2B cell control group and BEAS-2B cell overexpression group

first: Qiaoyun

last: Bai

first: Ruobai

last: Liu

first: Yilan

last: Song

first: Guanghai


title: DNA methylation pattern in somatotroph pituitary neuroendocrine tumors

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular and Translational Oncology Department

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

summary: Secretion of growth hormone by sporadic somatotroph neuroendocrine pituitary tumors (PitNETs) is the most common cause of acromegaly.Genome-wide DNA methylation was investigated in 48 somatotroph PitNETs with EPIC microarrays. Three subtypes of the tumors were identified. Subtype 1 tumors are densely granulated tumors without GNAS mutation characterized by high expression of NR5A1 (SF-1) and GIPR. The expression of both genes is correlated with specific methylation pattern at gene body and promoter methylation. Subtype 1 has generally lower methylation level at 5’ gene regulatory regions and CpG islands as compared to other tumor clusters. Subtype 2 are densely granulated PiNETs with common GNAS-mutations while Subtype 3 are mainly sparsely granulated tumors. Methylation/expression analysis indicate that the levels of ~50% genes differentially expressed genes between tumor subtypes that are located at in differentially methylated regions are DNA methylation dependent. These DNA methylation-controlled genes include CDKN1B, CCND2, EBF3, CDH4, CDH12 MGMT, STAT5A, PLXND1, PTPRE and MMP16 as wells as genes encoding ion channels and semaphorins.  Results of DNA methylation profiling confirms three molecular subtypes of somatotroph PitNETs that differ in both gene expression and methylation pattern. High expression of NR5A1 and GIPR in subtype 1 tumors is correlated to specific methylation at both genes.

overall_design: The Infinium MethylationEPIC BeadChip Array (Illumina) was used to profile whole-genome DNA methylation of 48 samples.

first: Paulina

last: Kober

first: Julia

last: Rymuza

first: Szymon

last: Baluszek

first: Beata

last: Mossakowska

first: Maria

last: Maksymowicz

first: Aleksandra

last: Nyc

first: Grzegorz

last: Zieliński

first: Jacek

last: Kunicki


title: Native ECM in obesity visceral adipose tissue initiates human adipose stem cell senescence via TGF-beta and mitochondrial signaling

city: Beijing

first: Han

last: Xueya

address: 10 Xitoutiao Street, Fengtai District, Beijing

institute: Capital Medical University

summary:
Background & Aims: Obesity is a complex disease that causes visceral WAT dysfunction and is associated with cardiovascular, chronic inflammatory and other metabolic pathologies.Adipose-derived stem cells (ASCs) are the key cells for adipose tissue homeostasis.However, how obesity may affect the biological functions of hASCs is not clear.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 8 different donors obese group,and 3 different donors lean group

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 8 different donors obese group, and 3 different donors lean group

first: Haiyan

last: Zhang

first: Xueya


title: Effect of depletion of GPR107 on gene expression during high glucose (20 mM) stimulation of human podocytes

city: Hefei

first: Haisheng

last: Zhou

address: 69 Meishan Rd.

institute: Anhui medical university

summary: To investigate the function of GPR107 in the regulation of diabetes, we established HPC cell lines in which target gene has been knocked out.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells with high glucose (20 mM) stimulation for 5 days.


title: An early cortical progenitor-specific mechanism regulates thalamocortical innervation

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: 1, Homi Bhabha Road,, Tata Institute of Fundamental Research,

department: Dept. of Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary: Comparison of the wild-type subplate transcriptome with that of the Emx1Cre11.5;Lhx2lox/lox and NexCre;Lhx2lox/lox subplate and further analysis of differentially expressed genes that were specific to the Emx1Cre11.5;Lhx2lox/lox dataset

overall_design: Microdissected tissue from 2 postnatal day zero (P0) brains was pooled to make one replicate sample. Two samples each of control, Emx1Cre11.5;Lhx2lox/lox and NexCre;Lhx2lox/lox were processed for RNA sequencing after ascertaining that their RIN values were >8. RNA sequencing was performed by Medgenome Technologies, Bangalore. mRNA was isolated from total RNA, cDNA was prepared, and libraries were prepared using the IlluminaTruSeq RNA Sample preparation V2. Libraries were multiplexed and sequenced as 100 base-pairs (bp) pair-end reads using the Illumina HiSEQ2500 platform, at an expected depth of 60M single reads.

first: Suranjana

last: Pal


title: HIF-3α-induced miR-630 expression promotes cancer hallmarks in cervical cancer cells by forming a positive feedback loop [miRNA-seq]

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: Hypoxia has crucial functions in cervical cancer development and metastasis by inducing the level of numerous genes, including microRNA genes. But we know little about how the hypoxia factors and microRNAs orchestrate to regulate hallmarks of cervical cancer cells. Here, we show that hypoxia-induced overexpression HIF-3α increased the expression of dozens of miRNAs, including miR-630. Stable overexpression of miR-630 in HeLa cells promotes cancer hallmarks, including radioresistance, inhibition of apoptosis, increased migration and invasion, and EMT-mediated metastasis. Stable inhibition of miR-630 showed opposite features. Further experiment showed the activation of miR-630 was induced by hypoxia treatment. For the molecular mechanism, we used RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing experiments (ChIP-seq) to investigate the targets of HIF-3α. We showed that hypoxia induces expression of HIF-3α to activate miR-630 expression by directly binding to its promoter. Meanwhile, miR-630 positively regulates HIF-1α expression, but represses HIF-1α. Taken together, our findings implicate a novel hypoxia-induced HIF3a-miR-630 regulatory feedback loop contributing to metastasis and progression of cervical cancer cells, and suggest HIF3a and miR630 might be applied as a potential biomarker and therapeutic target for cervical cancer.

overall_design: We overexpressed HIF-3α and HIF-1α in HeLa cells, with empty vector as control. We then performed micro RNA sequencing (miRNA-seq) in HIF-3α and HIF-1α overexpression cells, as well as control cells. Two biological replicates were obtained for each sample.

first: Junye


title: Differential expression profiles of plasma exosomal microRNAs identify potential biomarkers for rheumatoid arthritis

first: Xiaoke

last: Yang

state: Anhui

address: 218 Jixi Road

department: Department of Rheumatology and Immunology

institute: The First Affiliated Hospital of Anhui Medical University

summary:
Aims: Differential expression profiles of microRNAs (miRNAs) are associated with autoimmune diseases. This study sought to elucidate the plasma exosomal miRNA expression profiles of patients with rheumatoid arthritis (RA) and their potential clinical significance.
Methods: In the screening phase, small RNA sequencing was performed to characterize dysregulated exosome-derived miRNAs in the plasma samples from six RA patients and six healthy controls. In the independent validation phase, the candidate plasma exosomal miRNAs were verified in 40 RA patients and 32 healthy controls using quantitative real-time PCR. The association of miRNA levels with clinical characteristics in RA patients was tested. The value of these miRNAs in diagnosing RA was assessed with the receiver operating characteristic curve.
Results: Totally 177 and 129 miRNAs were upregulated and downregulated, respectively in RA patients versus healthy controls in the screening phase. There were 10 candidate plasma exosomal miRNAs selected for the next identification. Compared with the healthy controls, eight plasma exosomal miRNAs (let-7a-5p, let-7b-5p, let-7d-5p, let-7f-5p, let-7g-5p, let-7i-5p, miR-128-3p, and miR-25-3p) were significantly elevated in RA patients, but miR-144-3p and miR-15a-5p expression exhibited no significant changes. The let-7a-5p and miR-25-3p levels were associated with rheumatoid factor-positive phenotype in RA patients. For the eight miRNAs, the area under the receiver operating characteristic curve (AUC) ranged from 0.641 to 0.843, and their combination had a high diagnostic accuracy for RA (AUC = 0.916).
Conclusions: Our study illustrates that novel exosomal miRNAs in the plasma may represent potential noninvasive biomarkers for RA.

overall_design: Using small RNA sequencing to analyse the differential expression profiles of plasma exosomal microRNAs of RA.

first: Zhixin

last: Wang

first: Mingming

first: ZongWen

last: Shuai


title: Regulation of cellular cholesterol distribution via non-vesicular lipid transport at ER-Golgi contact sites

city: Singapore

first: Yasunori

last: Saheki

state: Singapore

address: 11 Mandalay road

department: Lee Kong Chian School of Medicine

institute: Nangyang Technological University

summary: Abnormal distribution of cellular cholesterol is associated with numerous diseases, including cardiovascular and neurodegenerative diseases. Regulated transport of cholesterol is critical for maintaining its proper distribution in the cell, yet the underlying mechanisms remain unclear. Here, we show that lipid transfer proteins, namely ORP9, OSBP, and GRAMD1s/Asters (GRAMD1a/GRAMD1b/GRAMD1c), control non-vesicular cholesterol transport at points of contact between the ER and the trans-Golgi network (TGN), thereby maintaining cellular cholesterol distribution. ORP9 localizes to the TGN via interaction between its tandem α-helices and ORP10/ORP11. ORP9 extracts PI4P from the TGN to prevent its overaccumulation and suppresses OSBP-mediated PI4P-driven cholesterol transport to the Golgi. By contrast, GRAMD1s transport excess cholesterol from the Golgi to the ER, thereby preventing its build-up. Cells lacking ORP9 exhibit accumulation of cholesterol at the Golgi, which is further enhanced by additional depletion of GRAMD1s with major accumulation in the plasma membrane. This is accompanied by chronic activation of the SREBP-2 signalling pathway. Our findings reveal the importance of regulated lipid transport at ER-Golgi contacts for maintaining cellular cholesterol distribution and homeostasis.

overall_design: To investigate roles of ORP9 and GRAMD1s in the regulation of cholesterol homeostasis, we established HeLa cells lines lacking ORP9 and/or GRAMD1s. We then performed gene expression analysis using the data obtained from RNA-seq from 4 different cell lines.

first: Tomoki

last: Naito

first: Haoning

first: Dylan Hong Zheng

last: Koh

first: Divyanshu

last: Mahajan

first: Lei

last: Lu


title: Oral ingestion of polystyrene nanoplastics causes memory impairment and neuroinflammation by microglial uptake

city: seoul

first: sungguan

last: hong

address: 84, Heukseok-ro, Dongjak-gu, Seoul, 104-407

department: Chemistry

institute: Chung-Ang

summary: Nanoplastics are produced by breakdown of plastics in environmental contamination or commercial use for cosmetics or daily expenses. Emerging evidence indicate that ingested nanoplastics with a size smaller than 100 nm have the potential to reach the brain and induces neurotoxicity. However, the potential toxicity of nanoplastics on brain are limited because of difficulties in synthesize of nanoplastics. In present study, we synthesized the fluorescent polystyrene nanoplastics (PSNPs) and examined the toxicity of PSNPs in brain in vivo and in vitro analyses by comparison to IR-813 fluorophore. Synthesized PSNPs were characterized by fluorescence imaging system, scanning electron microscopy, and Fourier-transform infrared spectroscopy. PSNPs were detected in adult mice brain by oral ingestion. In addition, a series of behavioral analyses showed that oral ingestion of PSNPs induced memory impairments. Among brain cells, PSNPs were predominantly internalized in microglia, and uptake of PSNPs induced microglial activation. In addition, the conditioned medium derived from microglia exposed to PSNPs repressed hippocampal neuronal activity. Furthermore, transcriptome analysis showed that PSNPs changed gene expressions in microglia, elevation of neuroinflammation in contrast to suppression of neurotrophic factors. These results indicated that predominant uptake of PSNPs in microglia induced elevation of neuroninflammatory responses whereas suppression of neurotrophic factors that may contribute to the cognitive impairment.  Our findings indicate the toxic mechanism and potential detrimental effect of nanoplastic in brain and suggest a potential risk of cognitive impairment by exposure to nanoplastics.

overall_design: To delve into the underlying mechanism behind impaired behavior and neuronal activity by PSNPs exposure,  RNA-seq was performed in microglia exposed to IR-813 or PSNPs.

first: Yunn

last: Me Me Paing

first: Yunkyung

last: Eom

first: Gyeong

last: Song

first: Bokyung

last: Kim

first: Myung

last: Choi

first: Sungguan

last: Hong

first: Sung

last: Lee


title: Transcriptome of human myometrial stem cells in the context of uterine fibroids

city: Chicago

first: Qiwei

address: 909 S. Wolcott Ave

department: Surgery

institute: University of Illinois at Chicago

summary: Our study represents a new strategy for identifying drivers and risk factors of uterine fibroids (F) by identifying genes and pathways differentially regulated in  myometrial stem cells (SCs) isolated from myometrium without fibroids (MyoN) and from myometrium adjacent to uterine fibroids (MyoF) using RNA-seq approach. Moreover, we will perform the comparison analysis of the transcriptome between MyoF SCs and fibroid SCs to identify differentially expressed genes.

overall_design: Examine the transcriptome  in human myometrial stem cells (SCs) isolated from myometriums without fibroids (MyoN), myometriums adjacent to fiborids (MyoF), and fibroids (F)

first: Ayman

last: Al-Hendy

first: Mohamed

last: Ali

first: Maria

middle: V

last: Bariani

first: Cheryl

last: Walker

first: Sandra

last: Grimm

first: Cristian

last: Coarfa


title: mRNA sequencing data of pancreatic cancer tumor tissues

status: Public on Sep 23 2023

city: Seoul

first: Woo Young

last: Kwon

address: Yonsei-ro 50

department: Department of Surgery

institute: Severance hospital

summary: We report the gene expression pattern of 125 pancreatic cancer tumor tissues who underwent surgical resectionmouse with IL-15, MCMV-infected mouse without IL-15, and MCMV-infected mouse with IL-15). We found that mouse with MCMV-memory CD8 T cells response to IL-15 and the behaviors of cancer were changed compared to other groups.

overall_design: Explore the gene expression pattern of 125 pancreatic cancer tumor tissues

first: Chang

last: Kang

first: Ho

last: Hwang


title: HIF-3α-induced miR-630 expression promotes cancer hallmarks in cervical cancer cells by forming a positive feedback loop [RNA-seq]

first: dong

last: chen

overall_design: We overexpressed HIF-3α and miR-630 in HeLa cells. Control cells for each treatment were also prepared. We then performed RNA-seq experiment to explore the differentially expressed genes. Two biological replicates were obtained for each sample.

first: Junye

last: Liu


title: HIF-3α-induced miR-630 expression promotes cancer hallmarks in cervical cancer cells by forming a positive feedback loop

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

overall_design: Refer to individual Series


title: RHOF promotes hepatocellular carcinoma metastasis by altering the metabolic status of cancer cells via RAB3D

city: Chengdu

first: Jianling

last: Xia

address: No.32, Section 2, West 1st ring road, Qingyang District, Chengdu

institute: Sichuan Provincial People Hospital

summary:
The mechanism by which tumor cells resist metabolic stress remains unclear, but many oncogenes are known to regulate this process. Accordingly, metabolic stress is closely associated with tumor metastasis. In this study, gene chip technology showed that RHOF, a member of the Rho GTPase family, is an oncogene that is significantly related to hepatocellular carcinoma (HCC) metastasis; however, it has rarely been reported in tumors. This study was aimed to determine the clinicopathological significance and role of RHOF in HCC progression and investigate the associated mechanisms. The results showed that compared to expression in adjacent non-cancerous tissues, RHOF was frequently upregulated in HCC tumor samples and elevated under conditions of glucose deprivation. RHOF expression was associated with TNM stage, T grade, metastasis status, recurrence, and survival in HCC. RHOF also affected cell morphology and promoted migration, invasion, and epithelial–mesenchymal transition (EMT) of HCC cell lines. Analysis of the underlying mechanism showed that RHOF promoted the Warburg effect by upregulating the expression and function of several glycolytic enzymes in HCC cells. This metabolic shift enhanced HCC cell migration and invasion. Specifically, RHOF exerted tumor-promoting effect by directly interacting with AMP-activated protein kinase (AMPK) and increasing the phosphorylation of AMPK. This subsequently affected RAB3D mRNA stability and led to elevated RAB3D expression, thereby amplifying the Warburg effect and malignant biological behaviors of HCC cells. Therefore, RHOF helps tumor cells resist metabolic stress through modulating the Warburg effect and plays a critical role in promoting HCC cell migration, invasion, and EMT, highlighting its important role in remodeling the metastatic microenvironment and regulating tumor metastasis. RHOF shows potential as a new therapeutic target and prognostic biomarker for HCC.
We used microarrays to detail the global programme of gene expression associated with hepatocellular carcinoma metastasis and identified distinct classes of deregulated genes during this process.

overall_design: Tissue samples of metastasis-free hepatocellular carcinoma or hepatocellular carcinoma with extrahepatic metastasis were used for RNA extraction and hybridization on Affymetrix microarrays. We sought to select genes that were associated with the metastasis of hepatocellular carcinoma.


title: The profile of miRNAs secreted into the supernatant during cardiac differentiation and maturation from human induced pluripotent stem cells verified by miRNA array analysis.

status: Public on Sep 22 2023

city: Tokyo

first: Shugo

last: Tohyama

address: 35 Shinanomachi, Shinjuku

institute: Keio University

summary: We performed miRNA array analysis to analyze the miRNAs secreted into the supernatant during the mesoderm/cardiac differentiation and maturation process from human induced pluripotent stem cells  (hiPSCs). Supernatant samples were collected on day -1, day 3, day 5, day 7, day 9, day 21, day 35, and day 51.

overall_design: We conducted mesoderm and cardiac differentiation from hiPSCs(253G4) and cultured over the long term  and supernatant samples were collected on day -1, day 3, day 5, day 7, day 9, day 21, day 35, and day 51 after the initiation of differentiation induction. miRNA was isolated from cell culture supernatant samples and subsequently we performed microarray analysis.

first: Otoya

last: Sekine


title: Transcriptomic effect of high-fat diet and PCN treatment on the skeletal muscle of C57BL/6N mice.

city: Oulu

first: Jukka

last: Hakkola

address: Aapistie 5

department: Research Unit of Biomedicine

institute: University of Oulu

summary: C57BL/7N mice were fed high-fat diet (HFD) and treated with Pregnenolone-16alfa-carbonitrile (PCN), a selective murine PXR agonist, and duodenal effects of the high-fat diet feeding and PCN treatment were studied.

overall_design: n=3/group. Groups: Chow,HFD, HFD Vehicle, HFD PCN

first: Mikko

last: Karpale


title: human induced pluripotent stem cell-derived cardiomyocytes

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


title: LARP7 suppresses endothelial-to-mesenchymal transition by coupling with TRIM28

city: Minhang

first: bing

last: zhang

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: LARP7 plays a pivotal role in regulating endothelial-to-mesenchymal transition(EndMT) and EndMT-associated heart valve formation. LARP7 directly interactes with TRIM28 and cooperatively represses SLUG transcription, which thereby suppresses EndMT of endothelial cells. More importantly, inducible knockout of LARP7 or TRIM28 in the endocardium promotes EndMT in vivo and leads to the valvular hyperplasia.

overall_design: Examination of  the chromatin occupancy of LARP7 and TRIM28 in  Human umbilical endothelial cells

first: Xiaodong

last: Liang

first: Shuo

last: Wu

first: Zilong

last: Geng

first: Li

first: Shasha

last: Zhang

first: Shiyan

last: Wang

first: Yan

first: Yu

last: Huang

first: Bing


title: Changes in gene profiles during the long term culture of human induced pluripotent stem cell-derived cardiomyocytes

summary: To investigate the changes in gene profiles during the long-term culture process of human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes, we conducted microarray analysis on hiPSC(253G4 line)- derived cardiomyocytes at three time points: 20 days, 35 days, and 50 days after the initiation of differentiation induction.

overall_design: hiPSC(253G4 line)- derived cardiomyocytes were cultured in low-glucose medium (MEMα) plus 5% fetal bovine serum (FBS) and samples were collected at three time points: 20 days, 35 days, and 50 days after the initiation of differentiation induction. Subsequently we performed microarray analysis on each samples.


title: Rtf1-dependent transcriptional pausing regulates cardiogenesis

city: Los Angeles

first: Adam

middle: David

last: Langenbacher

address: 615 Charles E Young Dr. S., BSRB 454

department: Molecular, Cell, and Developmental Biology

institute: University of California Los Angeles

summary: During heart development, an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II, as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis, we found that Rtf1 is essential for cardiogenesis and that without Rtf1 activity, cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain, which confers interaction with the pausing/elongation factor Spt5, was required for Rtf1's ability to support cardiac progenitor formation, while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP-seq and found that Pol II signals at the TSS of genes was reduced, suggesting a reduction in transcriptional pausing. Intriguingly, pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.

overall_design: ChIP-seq for RNA Polymerase II on 10-12 somite stage whole zebrafish embryos using Cell Signaling D8L4Y antibody.  Samples include triplicate ChIPs on control, rtf1 morphant, and flavopiridol-treated rtf1 morphant embryos, as well as input chromatin for replicate 1 of each condition.

middle: D

first: Jau-Nian

last: Chen


title: HIF-3α-induced miR-630 expression promotes cancer hallmarks in cervical cancer cells by forming a positive feedback loop [ChIP-seq]

first: dong

overall_design: We used chromatin immunoprecipitation sequencing experiments (ChIP-seq) to investigate the binding targets of HIF-3α. HeLa cells were incubated with HIF3A antibody. Input DNA was treated as control. Two biological replicates were prepared for HIF-3α and Input.

first: Junye


title: Epithelial Gab1 calibrates RIPK3-dependent necroptosis to prevent intestinal inflammation

city: Hangzhou

first: Jiaqi

last: Xu

address: 866 Yuhangtang Road, Hangzhou, Zhejiang, China

institute: Sir Run Run Shaw hospital, Zhejiang University School of Medicine

summary: We report that epithelial-Gab1 deficiency in mice facilitates inflammatory cell infiltration and aggravates colonic inflammation in colitis microenvironment

overall_design: Relative mRNA level in colon tissue obtained from Gab1IEC KO and Gab1fl/fl mice with a 7-day DSS treatment

first: Xue


title: COSMOS: A Platform for real-time morphology-based, label-free cell sorting using deep learning

city: Menlo Park

first: Mahyar

last: Salek

address: 4025 Bohannon Dr.

institute: Deepcell, Inc


title: Inhibition of the Chromatin Remodeling Factor NURF Rescued Sterility by a Clinic Variant of NuRD [RNA-seq]

status: Public on Sep 21 2023

first: Zijie

last: Shen

state: Beijing

address: singhua University, Haidian District

department: School of Life Science

institute: Tsinghua University

summary: The nucleosome remodeling and deacetylase (NuRD) complex is essential for gene expression and cell fate determination, and missense mutations of NuRD caused neurodevelopmental diseases. However, the molecular pathogenesisof clinic NuRD variants is unknown. Here, we introduced a clinic CHD3(L915F) variant into C. elegans homolog LET-418, impairing germline and vulva development and ultimately causing animal sterility. Our ATAC-seq and RNA-seq analyses revealed that this variant generated an abnormal open chromatin structure and disrupted the expression of developmental genes. Through genetic suppressor screens, we uncovered that intragenic mutations, likely renovating NuRD activity, restored animal viability. We also found that intergenic mutations in nucleosome remodeling factor NURF that counteracts NuRD rescued abnormal chromatin structure, gene expression, and animal sterility. We propose that two antagonistic chromatin-remodeling factors coordinate to establish the proper chromatin status and transcriptome and that inhibiting NURF may provide insights for treatment of NuRD mutation-related diseases.

overall_design: We cultured Wild-type and let-418(L781F) C. elegans under 20°C or 26°C. RNA-seq was performed using embryos of each sample


title: Transcriptome analysis of differentially expressed genes by tryptophanyl-tRNA synthetase 1 in human peripheral blood mononuclear cells

city: Incheon

first: Mirim

last: Jin

address: 155, Gaetbeol-ro

institute: Gachon University

summary: Tryptophanyl tRNA synthetase 1 (WARS1) is classically known as an essential housekeeping enzyme that ligates tryptophan to its cognate tRNA for protein synthesis. Interestingly, in the presence of pathogenic infection, WARS1 is immediately released from monocytes into the extracellular space. Secreted WARS1 promotes the innate inflammatory response by activating toll-like receptor (TLR) 2 and TLR4/myeloid differentiation factor-2 (MD-2) signaling. The purpose of this study was to investigate the expression profile of genes associated with the inflammatory response in WARS1-stimulated human peripheral blood mononuclear cells (PBMCs). As a result, WARS1 significantly upregulated the expression of genes associated with TREM1, IL-8, and IL-6 signaling in PBMCs.

overall_design: To investigate gene expression profiling in WARS1-stimulated PBMCs, we isolated and stabilized PBMCs (2 x 10^6 cell/mL)from healthy donor blood and cultured them with WARS1 (50 nM) for 24 h. Total RNA was then quantitated using a Nanodrop spectrophotometer (Thermo Scientific) and quality assessed using the RNA 6000 Nano assay kit (Agilent) and Bioanalyser 2100 (Agilent). NGS sequencing libraries were generated from 1 µg of total RNA using a TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's protocol. The resulting cDNA libraries were then paired-end sequenced (2 × 101 bp) for samples with the Novaseq™ 6000 system (Illumina). The entire operational process of the experiment was performed with the assistance of INSILICOGEN, INC.

first: Yoon

middle: T

last: Kim

first: Sang

last: Lee


title: Genome-wide maps of chromatin accessibility in DN3 thymocytes and splenic naïve CD4 T cells.

city: Shanghai

first: Lin

last: Liangyu

address: 320 Yueyang Road

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

summary: We found that naïve T cells from SCD1-/- mice have an intrinsic preference for regulatory T cells differentiation. Such preference was imprinted to DN3 thymocytes developed in SCD1 deficient thymus and persisted to mature T cells. To investigate the potential epigenetic changes underlying the Treg-bias. We employed ATAC-seq to examine the chromatin accessibility of naïve T cells and DN3 thymocytes from SCD1-/- mice and their littermate controls.

overall_design: We purified spleen-derived naïve CD4 T cells and thymus-derived DN3 cells from both SCD1 knockout mice and their littermate  controls. Harvested cells were subjected to examine chromatin accessibility using ATAC-seq.

first: LIANGYU

last: LIN

first: MINGYUAN

last: HU


title: Phase Ib trial of inhaled iloprost for the prevention of lung cancer with predictive and response biomarker assessment response biomarker assessment

city: Cleveland

first: Jihye

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic


title: The study of ESRRB occupancy in asynchronous and mitotic mESCs.

city: Memphis

first: Xiaolong

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

summary: We performed ChIP-seq for ESRRB and investigated its deposition in asynchronous and mitotic cells.

overall_design: Examination of ESRRB deposition in asynchronous and mitotic mESCs

first: ZHEXIN

last: ZHU

first: XIAOLONG

last: CHEN


title: SARS-CoV-2 pathogenesis mediated by E protein's PBM was prevented by modulators of CFTR function

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: The three human deadly coronaviruses (CoVs) (SARS-CoV, MERS-CoV and SARS-CoV-2) have infected around eight thousand, two thousand six hundred and 262 million people so far (December 2021), causing the death of 10%, 37% and 2% of them, respectively, so their implication in health is very important. These CoVs have proteins with a PBM motif that binds to PDZ cell domains. PDZ domains are found in more than 400 cellular proteins, therefore, viruses with PBM motifs have a high potential to modify cell behavior. It was studied the implication of the E protein PBM motif of various virulent or attenuated human CoVs (hCoVs) in the pathogenesis induced by these viruses. Variants of SARS-CoV, MERS-CoV and SARS-CoV-2 that lack the E protein PBM have been generated by reverse genetics and their pathogenicity has been analyzed in mice. The PBM motifs of these three hCoVs have been shown to be virulence factors and participate in their replication. Furthermore, a collection of SARS-CoV mutants has been constructed in which the E protein PBM domain was replaced by the one derived from virulent or attenuated hCoVs, and their virulence was analyzed. A virulence gradient was observed, depending on whether the E protein PBM domain was derived from an attenuated or virulent hCoV. The gene expression patterns associated with the different PBM motifs in lungs of mice infected with SARS-CoV was analyzed by deep sequencing of the mRNAs expressed in lungs of infected mice, and it was observed that the E protein PBM motif of SARS-CoV and SARS-CoV-2 dysregulates the expression of genes related to ion transport and cell homeostasis. Specifically, a decrease of the mRNA expression of the cystic fibrosis transmembrane conductance regulator (CFTR), which is essential for edema resolution, was observed. The reduction of CFTR mRNA levels was associated with edema accumulation in lungs of mice infected with SARS-CoV and SARS-CoV-2. The effect of compounds that modulate the expression and activity of CFTR on the pathogenesis and replication of SARS-CoV-2 was studied and it was observed that these compounds drastically reduced the production of SARS-CoV-2 in cell culture and protect against SARS-CoV-2 pathogenesis. These results showed the high relevance of the PBM motif in the replication and virulence of CoVs, and have allowed the identification of cellular targets for the selection of antivirals.

overall_design: Comparative gene expression analysis of RNA-seq data for mouse lungs infected with Wild-type or PBM-modifed coronaviruses ("3a", "GGGG", "Mock", "WT", "OC43", "HKU1", "NL63", "MERS") at two different times post infection (2dpi, 4dpi).Three biological replicates per sample.

first: Jose

last: Honrubia

first: Francisco

middle: J

last: Gutiérrez-Álvarez

first: Alejandro

last: Sanz

first: Diego

last: Muñoz

first: Ezequiel

last: González

first: Carlos

last: Castaño-Rodríguez

first: Jorge

last: Ripoll

first: Ana

last: Esteban

first: Raúl

last: Fernández-Delgado

first: Stanley

last: Perlman

first: Paul

last: McCray

first: Luis

last: Enjuanes


title: A Serum- and Feeder-Free System to Generate CD4 and Regulatory T Cells from Human iPSCs

city: Richmond

first: Simona

last: Zompi

state: California

address: 501 Canal Blvd

institute: Sangamo Therapeutics

summary: While feeder-free generation of clinical grade iPSC-derived CD8 T cells has been achieved, differentiation of iPSC-derived CD4sp and regulatory T cells requires mouse stromal cells in an artificial thymic organoid. We developed a serum- and feeder-free differentiation process suitable for large-scale production and used scRNAseq to study the cell identity of the iPSC-derived cells and compared their transcriptional profile to primary human cells.

overall_design: RNA from human iPSC-Tregs, iPSC-CD4sp, primary Tregs, induced Tregs and primary Tconv was extracted following differentiation (iPSC-Tregs and induced Tregs) or isolation and culture (primary Tregs and Tconv). Human primary cells were isolated from leukapheresis.

first: Helen

last: Fong

first: Matthew

last: Mendel

first: John

last: Jascur

first: Laeya

last: Najmi

first: Ken

last: Kim

first: Garrett

last: Lew

first: Swetha

last: Garimalla

first: Suruchi

last: Schock

first: Jing

last: Hu

first: Andres

last: Villegas

first: Anthony

last: Conway

first: Jason

last: Fontenot


title: High-resolution dissection of human cell type-specific enhancers in cis and trans activities

city: Beijing

first: Meng

last: Wang

address: No. 5 Yiheyuan Road

department: School of Life Sciences

institute: Peking University

summary: The spatiotemporal specific gene expression is regulated by cell type-specific regulatory elements including enhancers, silencers and insulators etc. The massively parallel reporter assay (MPRA) methods like STARR-seq facilitate the systematic study of DNA sequence intrinsic enhancer activities in a large scale. However, when applied to human cells, it remains challenging to identify and quantify cell type-specific active enhancers in the genome-wide scale with high-resolution, due to the large size of human genome. In this study, we selected the H3K4me1 associated dinucleosome with the linker DNA sequences as candidate enhancer sequences in two different human cell lines and performed ChIP-STARR-seq to quantify the cell type-specific enhancer activities with high-resolution in a genome-wide scale. Furthermore, we investigated how the activity landscape of enhancer repository would change when transferred from native cells (cis activity) to another cell lines (trans activity). Using ChIP-STARR-seq of the candidate enhancers in native cells and another type of cells, we obtained enhancers cis activity maps and trans activity maps in two different cell lines. The cis and trans activity maps enabled us to identify cell type-specific active enhancers, with enrichment of motifs of differentially expressed TFs. Comparisons between the cis and trans activity maps revealed general consistent regulatory property with different levels of activity in the two cell types, suggesting the sequence intrinsic regulatory properties keep similar in different type of cells. This study provides a new perspective of sequence intrinsic enhancer activities in different types of cells.

overall_design: To investigate the genome-wide cis activity and trans activity in high-resolution, we performed ChIP-STARR-seq in two different human cell lines K562 and A549, by isolating the H3K4me1 associated DNA as candidate enhancers in each cell type, transfected the two sets of candidate enhancer sequences to their native cell type and cross-transfected each set to the other type of cell.

first: Xiaoxu

last: Yang

first: Qixi

last: Wu


title: Stromal-derived NRG1 enables oncogenic KRAS bypass in pancreas cancer

city: Houston

first: Jincheng

last: Han

state: TX

address: 1901 East Rd

department: Cancer Biology

institute: UT Health MD Anderson Cancer Center

summary: Activating KRAS mutations (KRAS*) in pancreatic ductal adenocarcinoma (PDAC) drive anabolic metabolism and support tumor maintenance. KRAS* inhibitors show initial anti-tumor activity followed by recurrence due to cancer cell intrinsic and immune mediated paracrine mechanisms. Here, we explored the potential role of cancer associated fibroblasts (CAFs) in enabling KRAS* bypass and identified CAF-derived NRG1 activation of cancer cell ERBB2/ERBB3 receptor tyrosine kinases as a mechanism by which KRAS* independent growth is supported. Genetic extinction or pharmacological inhibition of KRAS* resulted in upregulation of ERBB2 and ERBB3 expression in human and murine models, which prompted cancer cell utilization of CAF-derived NRG1 as a survival factor. Genetic depletion or pharmacological inhibition of ERBB2/ERBB3 or NRG1 abolished KRAS* bypass and synergized with KRASG12D inhibitor in combination treatments in mouse and human PDAC models. Thus, we found that CAFs can contribute to KRAS* inhibitor therapy resistance via paracrine mechanisms, providing an actionable therapeutic strategy to improve the effectiveness of KRAS* inhibitors in PDAC patients.

overall_design: To investigate the transcriptomic impact of KRAS extinction within PDAC, we established 3 iKPC cell lines and cultured in 3-D Matrigel, treated with or without doxycycline (KrasG12D on or off) treatment and performed gene-expression analysis on the resulting samples.


title: Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants

city: Hannover

first: Philipp

middle: Walter

last: John-Neek

state: Lower Saxony

department: Institute of Experimental Hematology

country: Germany

institute: Medizinische Hochschule Hannover (MHH)

overall_design: Refer to individual Series


title: Transcriptomic effect of high-fat diet and PCN treatment on the duodenum of C57BL/6N mice.

first: Jukka

last: Hakkola

first: Mikko

last: Karpale


title: Transcriptomic effect of high-fat diet and PCN treatment on the livers of of PXR deficient mice

summary: PXR deficient mice were fed high-fat diet (HFD) and treated with PCN, a selective murine PXR agonist, and hepatic effects of the high-fat diet feeding and PCN treatment were studied.


title: Inhibition of the Chromatin Remodeling Factor NURF Rescued Sterility by a Clinic Variant of NuRD

first: Zijie

last: Shen

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


title: Transcriptomic effect of high-fat diet and PCN treatment on the gonadal white adipose tissue of C57BL/6N mice.


title: Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants [bulk]

summary: Safety assessment in retroviral vector-mediated gene therapy remains challenging. In clinical trials for different blood and immune disorders, insertional mutagenesis led to myeloid and lymphoid leukemia. We previously developed the In Vitro Immortalization Assay (IVIM) and Surrogate Assay for Genotoxicity Assessment (SAGA) for pre-clinical genotoxicity prediction of integrating vectors. Murine hematopoietic stem and progenitor cells (mHSPC) transduced with mutagenic vectors acquire a proliferation advantage under limiting dilution (IVIM) and activate stem cell- and cancer-related transcriptional programs (SAGA). However, both assays present an intrinsic myeloid bias due to culture conditions. To detect lymphoid mutants, we differentiated mHSPC to mature T cells and analyzed their phenotype, insertion site pattern, and gene expression changes after transduction with retroviral vectors. Mutagenic vectors induced a block in differentiation at an early progenitor stage (double-negative 2) compared to fully differentiated untransduced mock cultures. Arrested samples harbored high-risk insertions close to Lmo2, frequently observed in clinical trials with severe adverse events. Lymphoid insertional mutants displayed a unique gene expression signature identified by the machine learning algorithm of SAGA. The gene expression-based highly sensitive molecular readout will broaden our understanding of vector-induced oncogenicity and help in pre-clinical prediction of retroviral genotoxicity.

overall_design: Murine lineage negative bone marrow cells were isolated from C57BL/6J mice, transduced with different integrating retroviral vectors and cultured in lymphoid cytokine conditions for up to 54 days. The current study comprises of eight independent experiments. In each experiment, all the different vector types and mock samples (untransduced controls) were tested in triplicates.  At different time points, cells were harvested from the bulk cultures, RNA was isolated and used for microarray analysis. The RNA was hybridized to Agilent ID 084956, which is a custom refined version of the Agilent Whole Mouse Genome Oligo Microarray 4x44k v2 (Design ID 026655, Agilent Techonologies), developed by the Research Core Unit Genomics (RCUG) of Hannover Medical School (GEO accession GPL27545). All non-control probes of design ID 026655 have been printed four times within a region comprising a total of 181560 Features (170 columns x 1068 rows). Four of such regions were placed within one 1M region giving rise to four microarray fields per slide to be hybridized individually (Customer Specified Feature Layout). Data extraction was performed with the ‘FeatureExtraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’.

first: Antonella

last: Bastone

first: Violetta

last: Dziadek

first: Friederike

last: Mansel

first: Jenni

last: Fleischauer

first: Eric

last: Agyeman-Duah

first: Dirk

last: Schaudien

first: Oliver

last: Dittrich-Breiholz

first: Adrian

last: Schwarzer

first: Axel

last: Schambach

first: Michael

last: Rothe


title: Inhibition of the Chromatin Remodeling Factor NURF Rescued Sterility by a Clinic Variant of NuRD [ATAC-seq]

overall_design: We cultured Wild-type and let-418(L781F) C. elegans under 20°C or 26°C. ATAC-seq was performed using embryos of each sample


title: Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants [DN2]

overall_design: Murine lineage negative bone marrow cells were isolated from C57BL/6J mice, transduced with different integrating retroviral vectors and cultured in lymphoid cytokine conditions for up to 54 days. The current study comprises of eight independent experiments. In each experiment, all the different vector types and mock samples (untransduced controls) were tested in triplicates.  On days 25-26, the DN2 population was sorted based on CD44+/CD25+/CD4-/CD8-/CD11b-/Gr-1- marker expression. RNA was isolated from the DN2 cells and used for microarray analysis. The RNA was hybridized to Agilent ID 084956, which is a custom refined version of the Agilent Whole Mouse Genome Oligo Microarray 4x44k v2 (Design ID 026655, Agilent Techonologies), developed by the Research Core Unit Genomics (RCUG) of Hannover Medical School (GEO accession GPL27545). All non-control probes of design ID 026655 have been printed four times within a region comprising a total of 181560 Features (170 columns x 1068 rows). Four of such regions were placed within one 1M region giving rise to four microarray fields per slide to be hybridized individually (Customer Specified Feature Layout). Data extraction was performed with the ‘FeatureExtraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’.


title: 27 Hydroxycholesterol represses G9a expression via Estrogen Receptor alpha in breast cancer

city: Chennai

first: Arumugam

last: Rajavelu

state: Tamil Nadu

address: Adayar

department: Biotechnology

institute: IITM

summary: ChIP-sequencing for the H3K9me2 mark in MCF-7 cells showed that 27-HC treatment reduces the H3K9me2 mark on subset of genes linked to cancer progression, proliferation, and metastasis

overall_design: Global mapping of H3K9me2 mark in MCF-7 cells after treatment with 27-HC

first: Sreeja

last: Sreeharshan

first: Vini

last: Ravindran


title: A novel anti-RdDM element that defends cis-regulatory element against ncRNA-dependent, siRNA-driven, and methylation-imposed transcriptional silencing in plants [ARE ssRNAseq]

city: Kearneysville

first: Zongrang

last: Liu

state: WV

address: 2217 Wiltshire Road

department: Appalachian Fruit Research Station

institute: USDA-ARS

summary: Cis-regulatory elements (CREs) dictate spatiotemporal expression and tissue specificity of proximal genes. However, when in a transgenic state, many of them become highly vulnerable to RNA-Directed DNA Methylation (RdDM) that is often transcriptionally deleterious and biologically detrimental. This transgene-specific RdDM vulnerability suggests the existence of anti-RdDM elements (AREs) to defend CREs against de novo methylation in vivo.  In this work, we identify such an ARE at the Arabidopsis AGAMOUS (AG) locus, which includes a physically separated enhancer and promoter, both of which are highly vulnerable to transgene silencing.  We demonstrate that this ARE effectively represses RdDM activity at its cognate and heterologous CREs via the inhibition of transcription and processing of potent non-coding RNAs (ncRNAs), which act as substrates for the biogenesis of 24-nt small interfering RNAs (siRNAs) that guide RdDM.  Furthermore, we establish that the ARE exploits hypermethylation in a 108-bp internal region (referred to as M1) as a regulatory signal to recruit methyl reader SU(VAR)3-9 homolog 1 (SUVH1), as well as Harbinger transposon-derived protein 2 (HDP2) associated with HDP1, to carry out ARE-imposed transcriptional and post-transcriptional repression, with the former mediating the repression of ncRNA transcription and the latter repressing both ncRNA transcription and processing.  We also show that M1 methylation is indispensable for the repression of methylation in an adjacent, methylation-vulnerable 737-bp region (dubbed M2) to safeguard the ARE’s functional integrity. Taken together, the present study uncovers a novel anti-RdDM element that defends CREs against ncRNA-dependent, siRNA-driven, and methylation-imposed epigenetic interference to safeguard their regulatory integrity.

overall_design: Analyses of ncRNA expression and profile in various Arabidopis lines

first: Huawei

first: Yanjun

last: Li

first: Jia

first: Stacy

last: Singer

first: Dennis

last: Bennet

first: Yazhou

last: Yang

first: Jiang

first: Yi

first: Yingzhen

first: Gan-Yuan

last: Zhong

first: Rick

last: Meyer

first: Wenying

last: Xu

first: Zhen

last: Su

first: Hua

last: Lu

first: Ruhui

first: Kunru

last: Wang

first: Binyu

last: Zhao

first: Yong-Qiang

last: An