title: Transcriptomic evaluation of pediatric localized scleroderma skin with histological and clinical correlation

city: Pittsburgh

first: Kathryn

last: Torok

state: Pennsylvania

address: 530 45th St, Rangos 9161 Bay1

department: Peds Rheumatology

institute: University of Pittsburgh

summary: In this study, we explored enhanced results of RNA transcriptomic expression between pediatric localized scleroderma skin tissue and healthy control skin. Additional histological and clinical comparison of LS patient features with DEGs supports an inflammatory and fibroproliferative grouping demonstrated in unsupervised clustering of the transcriptomic data.

overall_design: Comparision between localized scleroderma and healthy controls in bulk sequencing of the skin with histological clinical data

first: Christina

last: Schutt

first: Emily

last: Mirizio

first: Claudia

last: Salgado

first: Miguel

last: Reyes-Mugica

first: Xinjun

last: Wang

first: Wei

last: Chen

first: Lorelei

last: Grunwaldt

first: Kaila

middle: L

last: Schollaert


title: Histone H3K27me3 demethylase act as a regulator of stemness in hypoxic cancer cells that are detached from extracellular matrix

status: Public on Jun 11 2021

city: Jeddah

first: Mohammed Razeeth

middle: Shait

last: Mohammed

state: Makkah

address: Department of biochemistry, faculty of science, King Abdulaziz University

department: Department of biochemistry

country: Saudi Arabia

institute: KIng Abdulaziz UNiversity

type: Expression profiling by high throughput sequencing

summary: Metastasis of cancer cells requires detachment from Extra Cellular Matrix (ECM) to seed cancer cells in a distant organ. Hypoxia is prevalent in this matrix detached cancer cells. Studies have established hypoxia as a chromatin modifier, as it transcriptionally controls expression of various histone demethylases (KDMs); therefore, we hypothesized that the presence of hypoxia could modulate the expression of KDMs in matrix detached cancer cells. Our study showed that in matrix detached cancer cells, both hypoxia and one of the hypoxia regulated H3K27me3 histone demethylase, namely KDM6B, was increased. Simultaneously, we found increased expression of stemness-associated genes, namely SOX-2, SOX-9, and CD44, in hypoxic matrix detached cancer cells. We discovered that KDM6B occupies the promoter region of both SOX-2 and CD44 to regulate their expression epigenetically. Targeting KDM6B reduces its occupancy, thereby expressing the stemness-related genes in matrix detached cancer cells. Further, we noticed increased occupancy of HIF1α promoter by KDM6B, suggesting its regulatory role in maintaining hypoxia in matrix detached cancer cells. This observation was further strengthened as we found a significant positive association between KDM6B and HIF1α in various cancer types. Overall, we found that matrix detachment modulates epigenome by inducing KDM6B activity to regulate the expression of stemness-related genes and hypoxia primarily through HIF1α in matrix detached conditions. KDM6B can be developed as a therapeutic target to eliminate matrix detached cancer cells bound for metastatic events

overall_design: Examination whole transcriptome between ECM attached and ECM detached

first: Mohammmed

middle: R

last: Shait Mohammed

first: Mohammad

middle: I

last: Khan

first: Hani

last: Choudhry

first: Mazin

middle: A

last: Zam Zami


title: Regulating stem cell-related genes induces the plastic differentiation of cancer stem cells to treat cancer [in vivo]

status: Public on Jun 13 2021

city: Beijing

first: Jingying

last: Zhang

address: No. 38·, Xueyuan Road Haidian District

department: School of Pharmaceutical Sciences

country: China

institute: Peking University

summary: Relapse of cancer is associated with multi-directional differentiation, and unrestricted proliferative replication potential of cancer stem cells. Herein, we propose the plastic differentiation strategy for irreversible differentiation of cancer stem cells. Whole gene expression analysis revealed that salinomycin induced the cancer stem cells into normal cells, dormant cells, and mature cancer cells. Besides, the results indicated that the gatekeeper was related to the inhibition of PKC α signaling pathway. The differentiated normal or dormant cells were incorporated into normal tissue, while the rest were killed by chemotherapy. Our findings would offer the evidence for plastic differentiation of cancer stem cells, and propose an invert strategy for cancer therapy.

overall_design: 4 samples

first: Qian

last: Luo

first: Jiarui

last: Xu

first: Jing

last: Bai

first: Limin

last: Mu

first: Yan

last: Yan

first: Jialun

last: Duan

first: Yinuo

last: Cui

first: Zhanbo

last: Su

first: Ying

last: Xie

first: Wanliang

last: Lu


title: Comparison of retinal gene expression among Chx10-cre;Tsc f/f, Chx10-cre;Tsc+/+ and 24-month-old C57BL/6 mice

status: Public on Jun 12 2021

city: Shanghai

first: Yu-Qing

last: Rao

address: Kongjiang Road No.1665

department: Department of ophthalmology

institute: Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine

summary: Retina aging is the main cause of vision decline in elderly population and it is also an important risk factor for the development of degenerative and angiogenic retinal diseases. Therefore it is important to explore the mechanisms which drive retina aging. In this study, we found that retina from old-aged mice had increased mTORC1 activity. Whole transcriptome microarray expression profiling of the retina tissue among among Wild Type Control, Chx10-specific Tsc1 knockout and natural aging mice showed that the most significantly enriched Gene Ontology terms were substantially in common in knockout and aging mice compared to Control mice. we further demonstrated that the activation of mTORC1 in Chx10-expressing cells led to accelerated retina aging and degeneration, with significant functional decline measured by electroretinogram, ganglion cell senescence, microglial cell activation and the accumulation of oxidative stress and inflammatory responses. Inhibition of microglial cells by minocycline partially prevented photoreceptor cell loss and restored the electroretinogram responses. The results demonstrated that mTORC1 activation accelerated retina aging, suggested that microglial cell contributed significantly to overall retinal degeneration.

overall_design: Retinal mRNA profiles of 5-month-old Chx10-cre;Tsc1f/f mice, age-matched Wild Type Control mice and 24-month-old C57BL/6 mice were generated by transcriptome microarray. Three independent experiments were performed for knockout and Control group, and 2 for C57-old group in the study

first: Yu-Tong

last: Zhou

first: Wen-Chuan

first: Jia-Kai

last: Li

first: Bao-Jie


title: Impaired antigen-specific memory B cell and plasma cell responses including lack of specific IgG upon SARS-CoV-2 BNT162b2 vaccination among Kidney Transplant and Dialysis patients

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: Single cell transcriptome, cell-surface proterin, TCR and BCR sequencing of FACS-sorted activated T and B cells of the peripheral blood of patients vaccinated against COVID19 after kidney transplant transplantation

overall_design: Sequencing of RNA, TCR and BCR was performed from FACS-sorted activated T cells (CD38+ HLA-DR+), memory B cells (CD38low CD27+) and plasmabolasts (CD38high CD27high) from the peripheral blood of four patients vaccinated against COVID19 after kidney transplantation, using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit

first: Eva

last: Schrezenmeier

first: Marta

last: Ferreira-Gomes

first: Gabriela

middle: M

last: Guerra

first: Katrin

last: Lehmann

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi


title: Four-and-a-half LIM domain protein 2 (FHL2) deficiency protects mice from diet-induced obesity and high FHL2 expression correlates with obesity in man.

status: Public on Jun 14 2021

city: Amsterdam

first: Carlie

last: de Vries

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam University Medical Center

summary: Four-and-a-Half-LIM-domain-protein 2 (FHL2) modulates multiple signal transduction pathways but has not been implicated in obesity or energy metabolism. In man, FHL2 expression increases with age and high FHL2 expression is associated with increased body weight in human and mice, leading us to hypothesize that FHL2 is a determinant of diet-induced obesity. Accordingly, loss of FHL2 protects mice from high-fat diet-induced weight gain. This is associated with enhanced energy expenditure in FHL2-/- mice. In an attempt to discover the origin of the increased energy expenditure in FHL2-/- mice, we performed transcriptome analysis (RNA-seq) on the heart, since FHL2 is highly expressed in this organ and gonadal white adipose tissue in WT and FHL2-/- mice.

overall_design: Gene expression profiling by RNA-seq was performed in heart and gonadal white adipose tissue (gWAT) from WT and FHL2-/- mice after 8 weeks of high fat diet.

first: Maria

middle: P

last: Clemente-Olivo

first: Jayron

middle: J

last: Habibe

first: Aldo

last: Jongejan


title: Differential usage of Zeb2 enhancer distinguishes adult and embryonic hematopoiesis

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

country: USA

institute: Stanford 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: Human STAT3 variants underlie autosomal dominant hyper-IgE syndrome by negative dominance

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: Here we describe patients with an autosomal recessive form of HIES due to loss-of-function mutations of a previously uncharacterized gene, ZNF341.

overall_design: Examination of gene expression in EBV-B cells from healthy and ZNF341 patients stimulated with IL-21, IL-6, IL-23, IL-10, and IFNa

first: Joëlle

last: Khourieh

first: Geetha

first: Danielle

middle: T

last: Avery

first: Alain

last: Lefèvre-Utile

first: Marie-Olivia

last: Chandesris

first: Aziz

last: Belkadi

first: Maya

last: Chrabieh

first: Hanan

last: Alwaseem

first: Virginie

last: Grandin

first: Françoise

last: Sarrot-Reynauld

first: Agathe

last: Sénéchal

first: Olivier

last: Lortholary

first: Xiao-Fei

last: Kong

first: Stéphanie

last: Boisson-Dupuis

first: Capucine

last: Picard

first: Anne

last: Puel

first: Vivien

last: Béziat

first: Qian

last: Zhang

first: Laurent

last: Abel

first: Henrik

last: Molina

first: Nico

last: Marr

first: Stuart

middle: G

last: Tangye

first: Jean-Laurent

last: Casanova

first: Bertrand

last: Boisson


title: Double knock-in pig models with elements of binary Tet-on and phiC31 intergrase systems for controllable and switchable gene expression

status: Public on Jun 10 2021

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

summary: In summary, we have for the first time generated a Dox inducible and switchable tdTomato pig strain with dual knock-in at Hipp11 and Rosa26 locus. This pig model provide a versatile tool model to produce stable transgenic pigs with inducible overexpressing any gene of interest by using the technology of phiC31 integrase-mediated cassette exchange. Based on this approach, an inducible hKRASG12D-expressing pig model line was established and tumor formation was induced after Dox administration. We expect that the inducible tool pig model would greatly facilitate the production of controllable transgenic pigs, and broaden the applications of transgenic pigs in biomedicine and agriculture fields.

overall_design: 18 samples for RNA-seq, including  tumor tissues at nose, mouth, and scrotum from induced DIK pig (DIK-nose-1, 2, 3; DIK-mouth-1, 2, 3; DIK-scrotum-1, 2, 3) and normal nose, mouth, and scrotum tissues of wild-type pig (WT-nose-1, 2, 3; WT-mouth-1, 2, 3; WT-scrotum-1, 2, 3)

first: Qin

last: Jin

first: Xiaoyu

last: Yang

first: Xiaoyi

last: Liu

first: Zhenpeng

last: Zhuang

first: Yanhui

last: Liang

first: Hui

last: Shi

first: Jiayuan

last: Huang

first: Han

last: Wu

first: Yu

last: Zhao

first: Zhen

last: Ouyang

first: Quanjun

first: Zhaoming

first: Fangbing

last: Chen

first: Weikai

last: Ge

first: Jingke

last: Xie

last: Li

first: Chengdan

last: Lai

first: Xiaozhu

first: Jiaowei

last: Wang

first: Meng

last: Lian

first: Lei

first: Longquan

last: Quan

first: Yinghua

last: Ye

first: Kepin

first: Liangxue


title: Time-lapse SLAM-seq for nuclear RNA

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Xist RNA, which directs the process of X chromosome inactivation in mammals, localizes in cis over the chromosome from which it is transcribed, recruiting chromatin modifiers to silence underlying genes.  To analyze cis-limited Xist RNA localization we have developed time-resolved super-resolution imaging of individual Xist RNA molecules in single cells. Using this approach, we quantify fundamental parameters underpinning Xist RNA dynamics, demonstrating a feedback mechanism linking Xist RNA synthesis and degradation, and an unusual coupling behavior that physically links temporally separated Xist RNA molecules. Additionally, we show that the protein SPEN, a key factor for Xist-mediated gene-silencing, has a separable function in Xist RNA localization, stability and in coupling behavior. Our results provide important insights towards understanding the unique and unusual behavior of Xist RNA.

overall_design: SLAM-seq was used to assay Xist RNA's half-life. Initially, the cells expressing Xist were exposed to 4sU-containing medium for 4 hours, followed by 4sU washout and change back to normal medium. After 0min, 30min, 60min, 90min,120min, and 150min, harvest the cells, and extracts the nuclei becuase Xist RNAs were located in nuclei, to enrich the Xist signal. T2C signature were counted for each treated sample, and accordingly calculated the half-life for different RNA.

first: L

last: Rodermund

first: H

last: Coker

first: G

first: N

last: Brockdorff


title: Single cell RNA sequencing detects persistent cell type- and methylmercury exposure paradigm-specific effects in human cortical neurodevelopmental model

city: WEST LAFAYETTE

first: Shaojun

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

summary: The developing human brain is uniquely vulnerable to methylmercury (MeHg) intoxication. Given the limited experimental access to MeHg-intoxicated human fetal brain, neither the threshold levels for neurotoxic effects nor the mechanisms underlying neurodevelopmental MeHg toxicity are clear. The observed persistent and latent effects in human and animal exposures and the relatively nonspecific neurodevelopmental changes suggest that MeHg impacts fundamental neurodevelopmental processes. Human cortical development is characterized by the sequential emergence of different neural stem cells, precursors, intermediate progenitors and postmitotic neurons, a sequence that can be replicated in human-induced pluripotent stem cell (hiPSC)-derived differentiating neuronal cultures. As the developing human cortex has been shown to be particularly vulnerable to fetal MeHg exposure, we assessed here by means of single cell RNA sequencing (scRNAseq) MeHg’s effects on different stages of differentiation and cell types present in early cortical cultures differentiated from hiPSC cells. Cortical cultures differentiating from hiPSC were exposed to toxicologically relevant MeHg (0.1 and 1.0 µM) continuously for 6 days at two different time points (days 4-10; and/or days 14-20) of early cortical differentiation under conditions below the cytotoxic threshold. Previous analysis at days 21-23 revealed subtle changes in cortical differentiation markers and cellular energetics, but no effect on glutathione levels, a biomarker of acute MeHg toxicity. Therefore, here we assessed the possibility of persistent effects on neurodevelopment at day 38 of differentiation (18 or 28 days after cessation of MeHg exposure). At this time, we observed subtle but significant changes in the population size of different cell types and the fractions of cells present in the different phases of the cell cycle. The observed MeHg-induced changes were developmental-stage and MeHg paradigm-specific. We further assessed overall differential gene expression, quantifying the number of genes showing significantly up- or down-regulated expression and identifying the genes affected at least partially identified biological processes affected. Importantly, the MeHg-induced changes in gene expression were also developmental-stage and MeHg-exposure paradigm specific. Thus, our studies demonstrate for the first time in a human model that MeHg exposure induces persistent changes in gene expression well after cessation of exposure, these changes are cell type- and developmental stage-specific, and this outcome is highly dependent on the concentration and timing of MeHg exposure. We conclude hiPSC-derived developing neuronal cultures provide an excellent human model to study persistent neurodevelopmental toxicity of MeHg in the developing human cortex.

overall_design: Exposures to 1 µM and 0.1 µM MeHg (Alfa Aesar, Ward Hill, MA; #33553) were performed continuously either only early during differentiation on days 4-10 (E exposure) or early and later, on days 4-10 and days 14-20 (E+L exposure) of differentiation.  Thus, the four exposure paradigms are referred to as E 0.1 µM, E 1 µM, E+L 0.1 µM, and E+L 1 µM.

first: Aaron

middle: B

last: Bowman

first: Jyothi

last: Thimmapuram

first: Michael

last: Aschner

first: Lisa

last: Prince

first: M

middle: D

last: Neely


title: Integrated analysis of transcriptome and proteome of the human cornea and aqueous humor reveal novel biomarkers for corneal endothelial cell dysfunction

city: Giheung-gu, Yongin-si, Gyeonggi-do 16995

first: Yong Woo

last: Ji

address: 363, Dongbaekjukjeon-daero

country: South Korea

institute: Department of Ophthalmology, Yonsei University College of Medicine, Yongin Severance Hospital

summary: Previous studies have reported that elevated protein levels in the aqueous humor (AH) are associated with corneal endothelial cell dysfunction (CECD), but the detailed underlying mechanism as well as specific biomarkers for CECD remain elusive.   In the present study, we aimed to identify protein markers in AH directly associated with changes in Corneal endothelial cells (CECs), as AH can be easily obtained for analysis. We carried out an in-depth proteomic analysis of patient-derived AH   as well as transcriptomic analysis of CECs from the same patients with bullous keratopathy (BK) resulting from CECD. We first determined differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) from CECs and AH in   CECD, respectively. By combining transcriptomic and proteomic analyses, 13 shared upregulated markers were observed between DEGs and DEPs. Through data integration with individual analysis via data-independent acquisition, three upregulated   transcripts and proteins were identified, namely metallopeptidase inhibitor 1 (TIMP1), Fc fragment of IgG binding protein (FCGBP), and angiopoietin-related protein 7 (ANGPTL7). Furthermore, we confirmed AH biomarkers for CECD using individual   proteome verification and immunoassay validation. Conclusively, our findings may provide valuable insights into the disease process and identify biofluid markers for the assessment of CEC function during BK development.

overall_design: human corneal endothelium mRNA profiles of Normal and CECD were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000.

first: Chae-Eun

last: Moon

first: Jae

middle: H

last: Jung


title: mRNA-seq of PTC-028 treated fusion-positive rhabdomyosarcoma cells

city: Atlanta

first: Karmella

last: Haynes

state: GA

address: 1760 Haygood Dr NE

department: Wallace H. Coulter Department of Biomedical Engineering

institute: Emory University

summary:
Purpose: This study aims to identify novel targets in the rare pediatric cancer, fusion-positive rhabdomyosarcoma (FP-RMS), and examine differences/similarities in FP-RMS tumor responses to BMI1 (B lymphoma Mo-MLV insert region 1 homolog) inhibition.
Methods: FP-RMS cell lines Rh28 and Rh30 were treated with DMSO (vehicle) or PTC-028, a BMI1 inhibitor, and RNA was collected after 24 or 48 hr in triplicate. RNA-seq was performed, and gene expression data were analyzed through Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses. Data from OncoPPi and the STRING database were also utilized in this study.
Results: Both Rh28 and Rh30 had some overlapping pathways affected by PTC-028, notably downregulation of cell cycle progression, the DNA damage response, and cholesterol biosynthesis. Rh30+PTC-028 had more genes containing TEAD-motifs downregulated compared to Rh28+PTC-028. Rh28 and Rh30 also had differing changes in expression in kinases of LATS1/2, EPHA2, and PDGFRA.
Conclusion: Overall, these results bring new insights into pathways influenced by BMI1 expression and contrasting intertumor drug responses in FP-RMS.

overall_design: Fusion-positive rhabdomyosarcoma cell lines (Rh28 and Rh30) were treated with either DMSO (24 hr) or PTC-028 (24 hr or 48 hr).  Total RNA was extracted from DMSO and PTC-028 treated cells. Cells were analyzed by RNA-seq in triplicate.

first: Cara

middle: E

last: Shields

first: Robert

middle: W

last: Schnepp


title: Signalling networks constructed by integrative analysis of multi-omics in peripheral blood mononuclear cells in systemic lupus erythematous patients

city: shenzhen

first: Donge

last: Tang

state: Guangdong

address: NO.1017 Dongmen North, Shenzhen People’s Hospital, Shenzhen, Guangdong

institute: shenzhen people's hospital

type: Methylation profiling by high throughput sequencing

summary: Omics technologies and biomolecules included genomics (DNA), whole transcriptomics (miRNAs, lncRNAs, circRNAs and mRNAs), proteomics (proteins) were used for collecting high throughput data from peripheral blood mononuclear cells (PBMCs) of subjects in our study. The joint analysis method of multi-omics was taken advantage of in our studies for uncovering some SLE disease-related molecular regulatory networks. For WGBS study, PBMCs of blood samples from the people recruited by our study were collected and used for whole-genome bisulphite sequencing (WGBS). There were 10322 genes presenting differential methylation levels in PBMCs of SLE patients (6305 hypermethylation genes and 4017 hypomethylation genes).

overall_design: Examination of PBMCs from healthy control and SLE patients by multi-omics technologies.

first: Wencong

last: Song

first: Fengping

last: Zheng

first: Shaoying

last: Huang

first: Wanxia

last: Cai

first: Haiyan

last: Yu

first: Jingquan

last: He

first: Xiaoping

last: Hong

first: Weier

last: Dai

first: Lianghong

last: Yin

first: Dongzhou

last: Liu

first: Yong


title: Gene expression data from human breast cancer MCF-7 cells and its 4-hydroxytamoxifen-resistant derivative OHTR cells treated with an siRNA targeting TRIM47

city: Tokyo

first: Kotaro

last: Azuma

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

summary: To evaluate the effect of TRIM47 on NF-κB signaling in breast cancer cells, expression of TRIM47 was knocked down in MCF-7 cells and its 4-hydroxytamoxifen (OHT)-resistant derivative OHTR cells by small interfering RNA (siRNA). Microarray analysis was performed to analyze gene expression profiles of these cells.

overall_design: MCF-7 and OHTR cells were treated with a specific siRNA targeting TRIM47 and a control siRNA without specific targets. Total RNA was extracted from the cells for gene profiling 48 h after transfection of siRNA. RNA integrity number (RIN) was measured by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). It was confirmed that RINs of all RNAs were above 9. RNAs extracted from biological triplicates treated with the same siRNA were combined, and subjected to the microarray analysis using Clariom S Array, Human (Affymetrix/Thermo Fisher Scientific, Walthan, MA, USA).


title: Exocyst protein subnetworks integrate Hippo and mTOR signaling to promote virus detection and cancer

city: San Francisco

first: Aubhishek

last: Zaman

state: CALIFORNIA

address: 600 16th St. Genentech hall N216.R, The Bivona laboratory

institute: UCSF

summary: We report the transcriptomic landscape of HeLa cells in reponse to immune stimulus. We use this data to identify the genes that are commonly upregulated in response to the immunogenic stimuli. The data represent RNAseq reads/abundance for the genes listed in the processed data.

overall_design: Transcriptomic abundance in HeLa cells reponse to polyI:C and Sendai virus stimuli compared to untreated cells using RNAseq technology


title: Identification of clinical trait–related small RNA biomarkers with weighted gene co-expression network analysis for personalized medicine in endocervical adenocarcinoma

city: ShangHai

first: Jacky

last: Shi

address: Handan Road.220

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Endocervical adenocarcinoma (EAC) is an uncommon aggressive type of endocervical adenocarcinoma that is not associated with human papillomavirus (HPV). At present, molecular research on EAC mainly focuses on the genome and mRNA transcriptome, the investigation of small RNAs in EAC has not been fully described. Here, we systematically explored small RNAs in 14 different subtypes of EAC using small RNA sequencing. miRNAs and tRNA-derived RNAs (tDRs) accounted for the majority of mapped reads the total number of miRNAs and tDRs maintained a relative balance. To explore the correlations between small RNAs and EAC with different clinical characteristics, we performed the weighted gene co-expression network analysis (WGCNA) and screened for hub small RNAs. From the key modules, we identified 9 small RNAs that were significantly related to clinical characteristics in EAC patients. Gene Ontology and pathway analyses revealed that these molecules could have roles in the pathogenesis of EAC. Our work provides new insight into EAC pathogenesis, and identify small RNAs as candidate biomarkers for diagnosis and prognosis of EAC.

overall_design: Examination of samll RNA in endocervical adenocarcinoma.

first: Keqin

last: Hua

first: Junjun

last: Qiu

first: Zhiwen

first: Xinyu

last: Qu

first: Chenyan

last: Guo


title: Cell cycle dysregulation with overexpression of KIF2C/MCAK is a critical event in nasopharyngeal carcinoma

city: Chongqing

first: Chuntao

last: Tao

state: State...

address: China

institute: Chongqing Medical University

summary:
Purpose: Nasopharyngeal carcinoma (NPC) is a common malignant carcinoma of the head and neck, and the biological mechanisms underlying the pathogenesis of NPC remain not fully understood.Thus, more studies are needed to identify novel critical molecular events and key hub genes to develop novel diagnostic and therapeutic strategies for the management and treatment of NPC.
Methods: In the present study, we systematically analyzed four independent NPC transcriptomic da-tasets and focused on identifying the critical molecular networks and novel key hub genes implicated in NPC. We found totally 170 common overlapping differentially expressed genes (DEGs) in the four NPC datasets. GO and KEGG pathway analysis revealed that cell cycle dysregulation is a critical event in NPC. Protein-protein interaction (PPI) network analysis identified a 15 hub-gene core network with overexpressed kinesin family member 2C (KIF2C) as a central regulator.
Results: Loss-of-function study demonstrated that knockdown of KIF2C significantly inhibited cell growth and cell motility, and delayed cell cycle progression, accompanied with dramatic mitotic defects in spindle formation in NPC cells. RNA-seq analysis revealed that KIF2C knockdown led to deregulation of various downstream genes. KIF2C could also regulate the AKT/mTOR pathways, and enhance paclitaxel sensitivity in NPC cells.
Conclusions: Taken together, our results suggest that cell cycle dysregulation is a critical event during NPC pathogenesis and KIF2C is a novel key mitotic hub gene with therapeutic potential in NPC.

overall_design: mRNA profiles of NCsh and KIF2Csh in HNE-1 cells

first: Xiaofeng

last: Zuo

first: Peixin

last: Meng


title: Downregulation of let-7 by electrical acupuncture increases protein synthesis in mice

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Our previous study found that acupuncture with low frequency electrical stimulation (Acu/LFES) prevents muscle atrophy by attenuation of protein degradation in mice.  The current study examines the impact of Acu/LFES on protein synthesis.  C57/BL6 mice received Acu/LFES treatment on hindlimb for 30 minutes once.  Acupuncture points were selected by WHO Standard Acupuncture Nomenclature and electric stimulation applied using an SDZ-II Electronic acupuncture instrument.  Muscle protein synthesis was measured by the surface-sensing of translation (SUnSET) assay.  Exosomes were isolated using serial centrifugation and concentration and size of the collected exosomes were measured using a NanoSight instrument.  The mature microRNA library in serum exosomes was validated using a High Sensitivity DNA chip.  Protein synthesis was enhanced in the both hindlimb and forelimb muscles.  Blocking exosome secretion with GW4869 decreased the Acu/LFES-induced increases in protein synthesis.  MicroRNA-deep sequencing demonstrated that four members of the Let-7 miRNA family were significantly decreased in serum exosomes.  Real time qPCR further verified Acu/LFES-mediated decreases of let-7c-5p in serum exosomes and skeletal muscles.  In cultured C2C12 myotubes, inhibition of let-7c not only increased protein synthesis, but also enhanced protein abundance of Igf1, Igf1 receptor.  Using a luciferase reporter assay, we demonstrated that let-7 directly inhibits Igf1.  Conclusion: Acu/LFES on hindlimb decreases let-7-5p leading to upregulation of the Igf1 signaling and increasing protein synthesis in skeletal muscles. This provides a new understanding of how the electrical acupuncture treatment can positively influence muscle health.

overall_design: Three C57/BL6 mice received Acu/LFES treatment on hindlimb for 30 minutes once.  Acupuncture points were selected by WHO Standard Acupuncture Nomenclature and electric stimulation applied using an SDZ-II Electronic acupuncture instrument.  Three control mice had acupuncture needles inserted in close proximity to the ACU/LFES insertion position, needles were connected to the LFES device, but electrical stimulation was not applied. Muscle protein synthesis was measured by the surface-sensing of translation (SUnSET) assay.  Exosomes were isolated using serial centrifugation and concentration and size of the collected exosomes were measured using a NanoSight instrument.  The mature microRNA library in serum exosomes was validated using a High Sensitivity DNA chip.

first: Ying

last: Huang

first: Manshu

first: Akihiro

last: Kuma

first: Janet

last: Klein

first: Hui

last: Cai

first: Xiaonan

last: Wang


title: IRF8-dependent control of pDC terminal differentiation and MYC repression

city: St. Louis

first: David

middle: Alexander

last: Anderson III

state: Missouri

address: 660. S Euclid Ave., Campus Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: A switch from MYC expression in bone marrow progenitors to MYCL expression in terminal dendrtitic cell (DC) subsets occurs during DC development. The present study identifies the precise stage during DC development when this switch occurs, and identifies a role for IRF8 in control of this switch. IRF8 is found to be required for both MYC repression and MYCL induction during DC specification in vivo.

overall_design: Splenic pDCs were isolated from WT and IRF8-deficient mice for expression microarray analysis.

last: Anderson

first: Kenneth

last: Murphy


title: Specific Interaction of DDX6 with an RNA Hairpin in the 3?-UTR of the Dengue Genome Mediates G1 Phase Arrest

city: Nakhon Pathom

first: Opas

last: Choksupmanee

address: 25/25 Phuttamonthon 4 Rd., Salaya, Phuttamonthon

country: Thailand

institute: Institute of Molecular Biosciences, Mahidol University

summary: The extent to which viral genomic RNAs interact with host factors and contribute to host response and disease pathogenesis is not well known. Here, we report that the human RNA helicase DDX6 specifically binds to the viral most conserved RNA hairpin in the A3 element in the dengue 3´-UTR, with nanomolar affinities. DDX6 CLIP confirmed the interaction in HuH-7 cells infected by dengue virus serotype 2. This interaction requires three conserved residues, Lys307, Lys367, and Arg369, as well as the unstructured extension in the C-terminal domain of DDX6. Interestingly, alanine substitution of these three basic residues resulted in RNA-independent ATPase activity, suggesting a mechanism by which RNA-binding and ATPase activities are coupled in DEAD-box helicases. Furthermore, we applied a cross-omics gene enrichment approach to suggest that DDX6 is functionally related to cell cycle regulation and viral pathogenicity. Indeed, infected cells exhibited cell cycle arrest in G1 phase and a decrease in the early S phase. Exogeneous expression of intact DDX6, but not A3-binding-deficient mutants, alleviated these effects by rescue of the DNA pre-initiation complex expression. Disruption of the DDX6-binding site was found in dengue and Zika live-attenuated vaccine strains. Our results suggested that dengue virus has evolved an RNA aptamer against DDX6 to alter host cell states, and defined DDX6 as a new regulator of G1/S transition.

overall_design: Next generation sequencing of DENV-2 (16681) infected and uninfected HuH-7 cells in the presence/absence of exogeneous DDX6 expression, in duplicate, using BGISEQ-500RS

first: Krittanai

last: Trisakulwattana


title: TGF-b-dependent Lymphoid Tissue Residency of Stem-like T cells Limits the Response to Tumor Vaccine

city: San Antonio

first: Nu

last: Zhang

state: TX

address: 7703 Floyd Curl Drive

institute: University of Texas Health Science Center at San Antonio

summary: We report the transcriptional profiles of tumor-specific CD8+ T cells isolated from tumor draining lymph nodes (TDLN) and tumor following tumor vaccination in C57BL/6 mice. In addition, we included wild type (WT) and TGF-b receptor conditional knockout (Tgfbr2-/-) CD8+ T cells.

overall_design: WT and Tgfbr2-/- Pmel-1 TCR transgenic T cells were adoptively transferred into recipient mice followed by B16 tumor subcutaneous inoculation. Around 14 days later, all recipient mice were immunized with Pmel-1 cognate peptide plus poly I:C. Together with tumor vaccination, all mice received FTY720 treatment to limit cell migration. Donor Pmel-1 T cells were FACS sorted 4 days after vaccination and subjected to RNA-seq analysis.

first: Guo

last: Li

first: Liwen

first: Chaoyu

last: Ma


title: A chemical and synthetic biology approach to control plant membrane receptor kinase signaling

city: seoul

first: Sara

last: Kim

address: 서울 성북구 안암동5가 1-2 고려대학교 안암캠퍼스 하나과학관 505호

department: Life sciences and biotechnology

institute: Korea university

summary: Plants have a large family of membrane receptor kinases (RKs) which sense extracellular signals to control plant growth, development, immunity, and stress response. The largest group of RKs contains an extracellular leucine-rich repeat (LRR) domain with over 200 members in Arabidopsis. However, the functional understanding of most of the LRR-RKs has been hampered by their genetic redundancy and the subtle phenotypes of RK overexpression. Here we show that the rapamycin-mediated heterodimerization of chimeric cytosolic kinase domains from receptor/co-receptor pairs in the plasma membrane can activate their downstream cellular signaling pathway, inducing the specific biological responses, including brassinosteroid, plant immunity, stomatal development, and lateral root development. This chemically controlled synthetic biology approach will be useful to investigate biological functions of LRR-RKs and their signaling pathways.

overall_design: Arabidopsis seedlings were grown on medium containing 2 μM PPZ with 100 nM brassinolide or 100 nM rapamycin in the dark for 5 days before harvesting for total RNA extraction.

first: Eunkyoo

last: Oh


title: RNA-SEQ OF 24H TIME COURSE OF MOUSE FIBROBLASTS ENTRAINED WITH DIFFERENT CYCLIC METABOLIC  ENTRAINMENTS

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: In our daily routine we are continually exposed to feeding ang fasting cycles, and it is important to take into consideration the overall coherence between metabolism and circadian rhythms. The loss of such a coherence, translating in a misalignment, may contribute to the weakening or desynchronization of oscillators.   In this study we asked whether the synchronization between the feeding-fasting cycles and the cell-autonomous clock affects the entire transcriptome of mouse fibroblasts in vitro. We found that in the metabolic entrainment proposed in this work and based on sustained 3 days of feeding and fasting cycles (HL, LH, HH), RNA-sequencing data from this work show a significant number of oscillating genes (N=500) belong to the transcriptome in all the dietary regimes. This result could be the consequence of the cyclical nature of the metabolic perturbations implemented in our study.    Moreover, our investigation has also shown that the fasting phase is important to have a phase polarization of the transcriptome, that is completely missing in the HH condition where the cells were always kept in high level of nutrients. It is worth mentioning that the misalignment leads to a polarized expression of ECM protein which is a typical mechanism of stimulated fibroblasts that is frequently associated with fibrosis. It was observed that this polarization involves different pools of genes and as consequence is enriched for different metabolic functions. All these findings confirm that regulation of metabolism by the circadian clock and its components is reciprocal, attesting that metabolism and circadian clocks are tightly interlocked: clocks drive metabolic processes, and various metabolic parameters affect clocks, producing complex feedback relationships.

overall_design: Comparison of the different effects of metabolic oscillations  on the transcrioptome entrainment

first: Onelia

last: Gagliano

first: Camilla

last: Luni

first: Yan

first: Francesco

last: Panariello

first: Davide

last: Cacchiarelli

first: Joseph

middle: S

last: Takahashi

first: Nicola

last: Elvassore


title: Evaluation of immune pathways in the conjunctiva of Sjogren Syndrome keratoconjunctivitis sicca

city: Houston

first: Cintia

middle: S.

last: de Paiva

address: 6565 Fannin Street NC505G

department: Ophthalmology

institute: Baylor College of Medicine

summary: After signing the informed consent, female SS patients (n = 7) and age-and-sex-matched healthy controls (n = 19) completed a series of oral, ocular surface exams. Symptom severity scores were evaluated using validated questionnaires (OSDI and SANDE). All patients fulfilled the ACR/EULAR criteria for SS and the criteria for KCS. Tear meniscus height was measured by optical coherence tomography. Fluorescein and lissamine green dye staining evaluated tear-break-up time (TBUT), corneal and conjunctival disease, respectively. Impression cytology of the temporal bulbar conjunctiva was performed using the Eyeprim™ device. The cells collected were then lysed, total RNA was isolated and subjected to gene expression analysis using the human nCounter® Nanostring Immunology Panel.

overall_design: The RNA from the conjunctiva of female SS patients (n = 7) and age-and-sex-matched healthy controls (n = 19) was assayed using the Immunology Pannel 2 from NanoString.

first: Stephen

middle: C

last: Pflugfelder

first: Claudia

last: Trujillo-Vargas

first: Laura

last: Schaeffer

first: Zhiyuan

last: Yu

first: Robert

last: Britton


title: Specific Interaction of DDX6 with an RNA Hairpin in the 3´-UTR of the Dengue Genome Mediates G1 Phase Arrest

first: Opas

last: Choksupmanee

overall_design: Next generation sequencing of DDX6 CLIP-seq of DENV-2 (16681) infected and uninfected HuH-7 cells, in triplicate, using Illumina HiSeq4000

first: Worapol

last: Tangkijthavorn

first: Kenneth

last: Hodge

first: Veerakorn

last: Narkthong

first: Worawich

last: Phornsiricharoenphant

first: Sarun

last: Tulakarnwong

first: Chumpol

last: Ngamphiw

first: Sissades

last: Tongsima

first: Sarin

last: Chimnaronk

first: Krittanai

last: Trisakulwattana


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in Wild Type or BMI1-KO Macrophages (MΦs) and Multiple Myeloma-Associated Macrophages (MM-MΦs)

city: Chengdu

first: Jingcao

last: Huang

state: Sichuan

address: No.88, South Keyuan Road

department: Department of Hematology

institute: West China Hospital, Sichuan University

summary: Multiple myeloma (MM) is an aggressive malignancy characterized by terminally differentiated plasma cells accumulation in the bone marrow (BM). MM BM exhibits elevated MΦs (macrophages) numbers relative to healthy BM. Here, we found that BMI1 modulates the pro-myeloma functions of MM-MΦs. We generated MΦs and MM-MΦs in vitro from wild type and BMI1-KO mice bone marrow. Total RNA was extracted using TRI reagent (MRC, Cat No.TR 118,USA) from flow sorted CD11b+ F4/80+ cells from murine BM-derived MΦs and MM-MΦs. Libraries were prepared using the VAHTSTM total RNA-seq library prep Kit for IIumina (Vazyme, Cat No. NR603, China). RNA-seq was performed by GENEWIZ (Suzhou, China) on an Illumina Hiseq platform.

overall_design: Examination of mRNA profiles in wild type (WT) or BMI1-KO MΦs and MM-MΦs

first: Danfeng

last: Zhang

first: Fangfang

last: Wang

first: Yuhuan

last: Zheng


title: Evolution of the quorum sensing regulon in cooperating populations of Pseudomonas aeruginosa

status: Public on Jun 09 2021

city: Seattle

first: Nicole

last: Smalley

state: Washington

address: 1705 NE Pacific St Health Sci Bldg  K-359

department: Pulmonary, Critical Care and Sleep Medicine

institute: University of Washington

summary: We used the AHL-degrading enzyme AiiA-lactonase to interrogate the evolution of the LasR-dependent QS regulon of P. aeruginosa in conditions where QS is required to obtain carbon and energy, and show that populations of P. aeruginosa adaptively reduced the size of their QS regulon over ~1000 generations.

overall_design: Using a metatranscriptomic approach, we compared the QS-activated regulons of two PAO1-derived populations from early and late timepoints of a 160-day CAM evolution experiment using three treatment regimes: LB-grown cultures were prepared as  (i) “plus AiiA lactonase” with added AiiA in 250 ul protein buffer (100 ug/ml final AiiA concentration), (ii) “natural AHL accumulation” with 250 ul of protein purification buffer, and (iii) “plus AHLs” with added 2 uM 3OC12-HSL and 10 uM C4-HSL plus 250 ul of protein purification buffer.  Two biological replicates were prepared for each sample condition.

first: Amy

middle: L

last: Schaefer

first: Kyle

last: Asfahl

first: Crystal

last: Perez

first: E

last: Greenber

first: Ajai

last: Dandekar


title: Integrative mRNA-miRNA interaction analysis associated with the immune response of rainbow trout Oncorhynchus mykiss to infectious hematopoietic necrosis virus infection

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

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

overall_design: Refer to individual Series


title: Differentially expressed transcriptomes of NADases mutant in Arabidopsis

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: The purpose of this experiment is to find differentially expressed genes in Arabidopsis NADases mutant in daytime and night time. This result indicated that PARPs regulate the expression of only a few genes. However, we found profound effects of reduced sirtuin 1 expression on gene expression during the day but not at night,

overall_design: Arabidopsis Col-0, parp1-2, parp2-1, parp3-1, parp1-2x2-1x3-1, srt1-4 hete, srt2-1 and srt1-4 hete x srt2-1 mutant seedlings were grown for two weeks in the conditions of ZT6 and ZT18, representing the day and night samples.

first: Jun

last: Kim

first: Laura

last: Bell

first: Xiao

first: Rinuckshi

last: Wimalasekera

first: Krystyna

middle: A

last: Kelly

first: Matthew

last: Hannah

first: Alex

middle: R

last: Webb


title: The expression profile in EA.hy926 cells after exposure to hypoxic conditions was evaluated by RNA-sequencing.

city: chengdu

first: Guodan

last: Zeng

state: sichuan

address: Keyuan Road 4, Gaopeng Street

department: West China Hospital

institute: 四川大学

summary: Hypoxia is an imbalance between oxygen supply and demand that occurs in embryonic development, as well as in pathological situations such as cancer, ischemic heart disease, and wound healing. To cope with decreased oxygen concentrations, a series of biological processes that endothelial cells participate in such as angiogenesis, are transcriptionally activated. In this work, we performed RNA-sequencing to profile activated genes in EA.hy926 cells after 8 hours of hypoxia, to reveal the changes of gene expression profile in endothelial cells under hypoxia.

overall_design: RNA-sequencing analysis was performed to identify genes whose expression in EA.hy926 cells changed significantly after 8 h of hypoxia.

first: Zeng

last: Guodan

first: Wang

last: Tao


title: Next Generation Sequencing of endothelial cells (HUVECs) after treatment by conditioned media obtained from gastric cancer anoikis resistant(GCAR) cells in the presence or absence of neutralizing antibody against PDGFB

city: nanjing

first: zhi

last: yang

state: jiangsu

address: 101 Longmian Avenue

institute: nanjing medical university

summary: To identify the dominant signaling events downstream of GCAR-derived PDGFB in HUVECs，we performed RNA sequencing (RNA-seq) in HUVECs treated by conditioned media obtained from  GCAR cells in the presence or absence of neutralizing antibody against PDGFB. The RNA-seq data shows that GCAR cells derived PDGFB may promote angiogenesis through MAPK/ERK signaling pathway.

overall_design: mRNA profiles of HUVECs after treatment by conditioned media obtained from  gastric cancer anoikis resistant(GCAR) cells in the presence or absence of neutralizing antibody against PDGFB

first: Du

last: Shangce

first: Yang

last: Zhi


title: Dengue and Zika RNA-RNA interactomes reveal virus permissive and restrictive factors in human cells.

city: SINGAPORE

first: Yu

last: Zhang

address: 60 Biopolis Street, Genome, #07,

country: Singapore

institute: GIS, A*STAR

summary: Identifying host factors is key to understanding RNA virus pathogenicity. Besides proteins, RNAs can interact with virus genomes to impact replication. Here, we used proximity ligation sequencing to identify virus-host RNA interactions for four strains of Zika virus (ZIKV) and one strain of dengue virus (DENV-1) in human cells. We found hundreds of coding and non-coding RNAs that bind to DENV and ZIKV viruses. Host RNAs tend to bind to single-stranded regions along the virus genomes and the binding is primarily driven by hybridization energetics. We observed that virus interacting host RNAs tend to be downregulated upon virus infection and identified a conserved set of virus responders that binds to most DENV and ZIKV. Knockdown of several short non-coding RNAs, including miR19a-3p, SCARNA2 and 7SK RNA resulted in a decrease in virus growth, suggesting that they act as virus permissive factors. In addition, the 3’UTR of DYNLT1 mRNA acts as a virus restrictive factor by binding to the conserved dumbbell region on DENV and ZIKV 3’UTR to decrease virus replication. This study demonstrates that host RNAs in themselves can impact virus growth in permissive and restrictive ways, expanding our understanding of host factors and RNA-based gene regulation during virus pathogenesis.

overall_design: RNA-seq was done on zika infected and non-infected hNPCs at 0hr, 2hr, 16hr and 24hr

first: XinNi

last: Lim

first: Xuping

last: Xie

first: Anna

last: Sundstrom

first: KiatYee

last: Tan

first: Jing

last: Zou

first: Amanda

last: Makha Bifani

first: KuoChieh

last: Liao

first: HuiXian

last: Poh

first: JiaJia

last: Chen

first: WyChing

last: Ng

first: SuYing

first: EngEong

last: Ooi

first: October

middle: M

last: Sessions

first: Yvonne

last: Tay

first: Pei-Yong

last: Shi

first: Roland

last: Huber

first: Yue

last: Wan


title: Validation of molecularly-defined olfactory bulb projection neurons targeting anterior or posterior brain areas

city: London

first: Andreas

last: Schaefer

address: 1 Midland Road

institute: The Francis Crick Institute

summary:
To validate different projection targets of already molecularly-defined olfactory bulb projection neurons we used viral targeting specifically into anterior or posterior cortical areas, Fluorescence Activated Nuclei Sorting (FANS) to enrich for olfactory bulb projection neurons, and single-nuclei RNA sequencing (sn-RNA seq)
To isolate GFP-labelled nuclei, 1 individual replicate of AON or PCx-injected mice was used. Ipsilateral and controlateral sides were minced separately and placed into two different tubes. The minced tissue was gently homogenized in Nuclei PURE Lysis Buffer and 10% Triton X-100 using an ice-cold dounce and pestle, and filtered two times through a 40 μm cell strainer on ice. After centrifuging at 500 rpm for 5 min at 4 °C, the supernatant was aspirated and gently resuspended in 500 μl of cold buffer (1x of cold Hanks' Balanced Salt Solution HBSS, 1% nuclease-free BSA, RNasin Plus and 1/2000 DRAQ5).
Our study identifies molecularly distinct subtypes of mitral cells projecting to anterior or posterior olfactory cortices.

overall_design: we used AAV viral targeting and Fluorescence Activated Nuclei Sorting (FANS) to enrich for olfactory bulb projection neurons, and single-nuclei RNA sequencing (10x Genomics)

first: Sara

last: Zeppilli

first: Robin

last: Attey

first: Tobias

last: Ackels

first: Kimberly

last: Ritola

first: Stefan

last: Boeing

first: Alexander

last: Fleischmann

first: Nell

last: Klimpert

first: Anton

last: Crombach


title: Molecular Signatures of Idiopathic Pulmonary Fibrosis

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

type: Methylation profiling by genome tiling array


title: Next Generation Sequencing Facilitates Quantitative Analysis of Different Transcriptomes betwwen AA, AG, GG pDCs

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

summary:
Purpose: NCF1 gene single nucleotide polymorphism (SNP) rs201802880 (G to A change) promotes the activation of plasmacytoid dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation.
Methods: Mouse plasmacytoid dendritic cells isolated from GG, AG or AA allele mice, were stimulated with R848 for 12 hours. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Results: Genes in the TLR7-IRF7 pathway were augmented by NCF1 SNP. As a result, the production of type I IFNs increased in AA pDCs.

overall_design: MRNA profiles of R848 stimulated pDCs with different alleles were generated by deep sequencing, in triplicate, using illumina HiSeq ⅹ10 system


title: A signature protein of Mycobacterium tuberculosis (Rv000) modulates the transcriptome of Mycobacterium smegmatis.

city: New Delhi

first: Nasreen

middle: Zafar

last: Ehtesham

state: Delhi

address: Safdarjung Hospital campus

country: India

institute: National Institute of Pathology

summary: The world’s second deadliest disease tuberculosis is caused by the organism Mycobacterium tuberculosis. Mtb has 4173 genes (Mycobrowser) and some of these genes are essential for its survival. There are many uncharacterized genes in Mtb which play an important role in its survival strategies to combat the immune system of the host. In order to identify vital genes required for its survival were characterized by in silico approach. Based on computational analysis, we have identified 2 proteins which are only present in Mtb complex and named as Signature Protein 1 & 2. The Signature protein 2 (Rv000) has DNA methyltransferase activity and also protects the DNA from DNase-I digestion. Knock in of this gene in Mycobacterium smegmatis modulates its transcriptome and thereby enhances the survival. RNA seq analysis of M. smegmatis showed that more than 3000 genes were up regulated at the transcriptional level. These results suggested that the gene encoding signature protein 2 (Rv000) is acting as a global transcriptional regulators. These genes encode proteins that belong to different categories of biological and molecular function i.e. transcriptional regulators, regulatory proteins, conserved hypothetical proteins, transporter proteins (ABC transporters, antiporter, sugar transporter and Major facilitator superfamily genes) and TonB dependent receptors (required for iron scavenging) were upregulated. The proteins encoded by these genes may be targeted for drug development against Mtb..

overall_design: 2 Wild Mycobacterium smegmatis, 2 recombinant mycobacterium smegmatis grown under normal conditions

first: Manjunath

last: Pichipalli

middle: Z


title: RNA-seq of human small airawy epithelial cells in patients with COPD and Never-smoker

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

summary: Chronic obstructive pulmonary disease (COPD) is a progressive disease that obstructs the airflow from the lungs, and tobacco smoking is the major cause of COPD. Here, we applied single-cell RNA sequencing to analyze COPD pathogenesis in COPD patients, non-COPD smokers and never-smokers and investigated the disease progression at single-cell resolution. By single-cell transcriptome analysis, we identified a novel subpopulation of Alveolar Type 2 epithelial cells that emerged in smokers, such as COPD patients, and specifically expressed a series of chemokines and PD-L1. Since the number of cells in the basal cell clusters increased in only the COPD lungs but not in the non-COPD smoker or never-smoker lungs, we also tried to clarify the difference in phenotype between COPD and other basal cells with single-cell RNA-seq. However, due to the small number of cells in each, no clear difference could be found. To further investigate the functional properties of basal cells in COPD, we isolated small airway epithelial cells from surgical samples of COPD or never-smoker lungs and expanded the cells in vitro.Total RNA was extracted from early passaged cells , and bulk RNA-seq was performed to characterize these cells in detail. Finally, we found that the COPD basal cells retained the inflammatory response and basal/stem-related signals, even after a few passages in culture, and it might cause basal cell expansion in vivo.

overall_design: Human small airway epithelial cell(HSAEC) were isolated from surgical samples of 3 COPD and 3 never-smoker lungs and expanded the cells in vitro. Morphologically, small airway epithelial cells from COPD and never-smokers were similar, and the expression patterns of basal cell markers such as Krt5 and p63 were similar. Total RNA was extracted from early passaged cells (less than passage 3), and bulk RNA-seq was performed to characterize these cells in detail.

first: Naoaki

last: Watanabe

first: Jun

last: Nakayama


title: Differential gene expression analysis between adherent U87MG cells and U87MG cell-derived glioma stem-like cells (P4E8 cells).

city: Okayama

first: Masato

last: Maruyama

address: 1-1-1, Tsushima-naka, Kita-ku

institute: Okayama University

summary: We established tumorspheres from human glioblastoma U87MG cells by single cell-derived tumorsphere formation.  Among these tumorspheres, P4E8 clone showed cancer stem cell like properties such as self-renewal capacity, expression of cancer stem cell markers, resistance to anti-cancer agents and in vivo tumorigenicity.  To find novel therapeutic target molecules, we performed differential gene expression analysis between U87MG and P4E8 cells.

overall_design: RNA samples harvested from three separate dishes of U87MG cells and P4E8 cells were used for microarray analysis.


title: Cytomegalovirus subverts macrophage identity

status: Public on Jun 15 2021

city: Freiburg

first: Sebastian

last: Baasch

address: Breisacher Str.

department: Institute for Immunodeficiency; Center for Chronic Immunodeficiency

institute: University Medical Center


title: Genome-wide effect   of STING-mediated activation in T cells

last: Poltorak

state: MA

address: 150 Harrison avenue, J529

institute: tufts

summary: Using wild type mice and mice deficient forSTING , we compared genome-wide expressionof RNA in  response to STING activation with DMXAA

overall_design: To look for the role of STING-mediated pathway in activation of T cells, we activated naïve T cells with DMXAA, a synthetic agonist of STING, together with activation of TCR. To define a STING-specific effect, STING-deficient animals were used as a control. We isolated naïve T cells from peripheral lymph nodes, negatively selected them using magnetic beads coated with antibodies, and activated cells for 4 hours in specified conditions. Next, we isolated RNA and made library using TruSeq kit (Illumina) for the library construction.One replica of each sample is provided

first: Bridget

last: Larkin


title: Single-cell RNA-seq reveals cellular heterogeneity of activated pDCs stimulated by R848

summary:
Purpose: PDCs will differentiated into different subclusters upon single stimulation. The goals of this study are to identify the heterogeneity of activated pDCs stimulated by R848.
Methods: Human primary plasmacytoid dendritic cells were stimulated with R848 for 16 hours. Then, after FACS sorting, about 12000 pDCs were counted and the viability was confirmed to be >90%. Single-cell suspensions were loaded on a 10x Genomics Chromium single-cell 3’ v2 chip to prepare the libraries according to the manufacturer’s protocol. The library quality was checked by Agilent 2100 Bioanalyzer and Qubit fluorometric quantitation. Samples were sequenced on an Illumina NovaSeq 6000 with a sequencing depth of at least 50000 reads per cell.
The raw fastq data were processed with CellRanger (v2.1.1) by using GRCh38 annotation (v1.2.0) (Zheng, G.X., et al.Nat Commun 2017;8,14049.). Output from CellRanger was loaded into R and used Seurat (v3.1.1) for further analysis (Stuart, T., et al. Cell 2019;177,1888-1902 e1821.). Cells with fewer than 1000 or more than 4500 expressed genes, and a high percentage of mitochondrial genes (>5%) were removed. We also used cell selection as Peter Karchenko-the Pagoda way to define outliers. Among them, 6010 cells passed the filtering. After normalizing and scaling, we used ‘Find Variable Features’ to identify 1000 highly variable genes. Then we used 992 highly variable genes (removing mitochondrial and ribosomal genes) for PCA. Upon ‘Elbow plot’, we selected the first 20 PC for clustering and UMAP visualization with default parameters. For clustering, we selected resolution parameter=0.2 which produced 4 clusters. To obtain cluster-specific gene signatures, we identified differential expression analysis of each cluster with default parameters. IFN scores based on IFN gene sets were calculated for each cell as the average of scaled expression of these genes and corrected by subtracting the average of a large set of similar genes, as proposed by Tirosh et al (Tirosh, I., et al. Science 2016;352,189-196.).
Results: 4 subcluster of pDCs were obtained.Group 0 express chemokines, group 1 express Gzmb, group 2 express type I interferons, and group 3 express Id2 and IL-23A.

overall_design: Single cell analysis of pDC subclusters by using 10×Genomics technology.

first: Chao

last: Yao

first: Jianyang

last: Ma

last: Shen


title: The effect of aging on the transcriptional profile of female mice exposed to x-ray radiation

city: New York

first: Constantinos

last: Broustas

state: NY

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

summary:
Background: In the event of an improvised nuclear device or radiological dirty bomb detonation large numbers of people will be exposed to radiation that would require a timely and accurate biodosimetry to identify the highly exposed individuals who would require medical treatment from those who have received low or no radiation (the “worried well”). Gene expression signatures in response to radiation have been derived from mice and human peripheral blood and the impact of a number of variables, such as dose, time, genotype, and gender, on gene expression has been analyzed. However, the impact of aging on radiation gene profiling has not been taken into consideration.
Results: Global gene expression was measured in the blood of young (2 mo) and old (24 mo) female C57BL/6J mice 1 day after they were exposed to 4 Gy x-rays or they were sham irradiated (control) using the Agilent Mouse Whole Genome microarrays. Ingenuity Pathway Analysis revealed that “Integrin signaling” was the most overrepresented canonical pathway in both young (p = 1.69E-10) and old (p = 2.93E-10) female mice exposed to x-ray irradiation. In contrast, immune-related processes, such as “Communication between Innate and Adaptive Immune Cells” (p = 2.33E-11), were overrepresented in young but not old irradiated mice. On the other hand, “Molecular Mechanisms of Cancer” processes were significant only in irradiated old mice (p = 5.78E-07). Finally, a number of phagocytosis pathways, involved in apoptotic cell elimination and tissue homeostasis preservation, were enriched in irradiated young, but not old, mice.
Conclusions: We show that age is a variable that has the potential to fundamentally alter the transcriptomic profile of irradiated female mouse blood. A number of biological processes, including phagocytosis, are differentially represented in young and old mice exposed to x-ray radiation. Our results highlight the significance of age as a variable that can have profound biological effects that will affect medical management and treatment decisions in case of a radiological emergency.

overall_design: Radiation induced gene expression in  blood from young (2 month) and old (24 months) female mice was measured 24 h after 4 Gy of x-rays. Five independent experiments were performed at each age.

middle: G


title: Molecular Signatures of Idiopathic Pulmonary Fibrosis [RNA-seq]

summary: Genome-wide DNA methylation of IPF and normal lung tissue samples

overall_design:
500 ng total RNA was used to prepare libraries with the TruSeq stranded mRNA library prep kit. rRNA-depleted libraries were prepared from 1 ug total RNA with the Epidemiology Ribo-Zero Gold rRNA Removal Kit. Libraries were sequenced at 80M reads on the Illumina NovaSeq 6000.
***The submitter indicated that Raw RNA-Seq files cannot be deposited in a publicly accessible database due to patient confidentiality***

first: Iain

last: Konigsberg

middle: V


title: Single-cell transcriptomic analysis reveals hepatic stellate cell activation roadmap and myofibroblast origin during liver fibrosis

city: Amsterdam

first: Wu

address: B7, Plesmanlaan 121 1066CX Amsterdam

institute: Netherlands Cancer Institute

summary:
Purpose: analyze the transcriptomic differences in liver of CCL4 and BDL mouse model
Methods: Fresh isolated HSC suspensions of CCL4 and BDL were loaded on the 10x Genomics Chromium Single Cell Platform using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3
Results: We revealed the HSC activation roadmap and portal fibroblasts are major contributor to myofbroblast in BDL model.

first: Hao

last: He

first: Junhao

last: Hu


title: Molecular Signatures of Idiopathic Pulmonary Fibrosis [methylation array]

first: Ivana

last: Yang

overall_design: Bisulfite converted DNA from 37 samples were hybridised to the Illumina Infinium  Human MethylationEPIC (850k) Beadchip


title: Neonatal nephron loss during active nephrogenesis results in altered expression of renal developmental genes and markers of kidney injury

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary: Preterm neonates are at high risk for nephron loss under adverse clinical conditions (e.g., cardiocirculatory decompensation, nephrotoxic drugs). Importantly, the onset of renal damage potentially collides with the proceeding nephrogenesis of prematurity prior 36 weeks of gestation. Recent animal studies suggest that early nephron loss within this vulnerable phase is associated with more severe glomerular and tubulointerstitial alterations later in life, irrespective of the occurrence of arterial hypertension. It is known that nephrogenic pathways are reactivated after acute kidney injury supporting renal repair and regeneration. In this study we hypothesized that nephron loss during nephrogenesis leads to an alteration of the kidney developmental program which in turn impairs homeostasis and repair and thus aggravates kidney injury later in life. Preterm infants prior to 36 weeks of gestation show an active nephrogenesis after birth.  In rats, nephrogenesis is still active until day 10 of life. Mimicking the human situation of acute nephron loss in preterm neonates with ongoing nephrogenesis, rats were uninephrectomized at day 1 of life (UNXd1). A second group of animals was uninephrectomized at day 14 of life (UNXd14), which resembles a nephron loss after terminated nephrogenesis. Age-matched control groups were sham operated. Three days after uninephrectomy the animals were sacrificed. Transcriptional renal changes were analyzed by RNAseqencing, followed by in silico functional pathway analysis. In UNXd1 animals 1182 genes were differentially regulated compared to the respective control group. The functional groups “renal development” and “kidney injury” were among the most differentially regulated groups and revealed distinctive alterations in UNXd1 animals. Reduced expression levels of candidate genes concerning renal development (Bmp7, Gdnf, Pdgf-B, Wt1) and kidney injury (nephrin, podocin, Tgf-β1) were detected in the kidney of UNXd1 animals. The downregulation of Bmp7 and Gdnf expression in the remaining kidney of UNXd1 animals persisted until day 28 of life. In UNXd14 rats Six2 was upregulated and Pax22 downregulated compared to controls. We conclude that neonatal nephron loss during active nephrogenesis affects renal development and induces persistently reduced expression levels of genes which in turn might hinder tissue repair after kidney injury later in life.

overall_design: Analysis of renal gene expression in an animal of neonatal uninephrectomy elucidating the effects of early nephron loss under postnatally ongoing nephrogenesis.

first: Carlos

last: Menendez-Castro

first: Arif

middle: B

last: Ekici

first: Philipp

last: Kirchner

first: Christian

last: Büttner

first: Roman

last: Raming


title: Integrative mRNA-miRNA interaction analysis associated with the immune response of rainbow trout Oncorhynchus mykiss to infectious hematopoietic necrosis virus infection [miRNA-seq]

first: Pan

last: Cai

summary: Infectious hematopoietic necrosis virus (IHNV) can cause widespread death of rainbow trout (Oncorhynchus mykiss), understanding the molecular mechanisms that occur in the rainbow trout in response to IHNV infection will be useful to decrease IHN-related morbidity and mortality in trout aquaculture. However, the molecular mechanisms of rainbow trout in response to IHNV are very limited. This study performed analysis of mRNAs and miRNAs based on RNA-seq technology on the intestine of rainbow trout infected with IHNV and control. There were 80 differentially expressed miRNAs that regulated 3355 target mRNAs, which overlapped with differentially expressed mRNAs obtained from RNA-seq. The expression patterns of DEGs and miRNAs differentially expressed were validated by qRT-PCR. GO enrichment and KEGG pathway analyses of the potential target genes of the DE miRNAs, revealed DEGs were mainly enriched in immune-related pathways such as Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and IL-17 signaling pathway. These findings improve our understanding of the molecular mechanisms of IHNV infection. The study analyzed the immune regulatory target gene pairs and signal pathways of rainbow trout intestine against IHNV infection at the transcriptional level, and provided basic data for the study of rainbow trout against IHNV immune regulatory.

overall_design: In this study, the target gene pairs and signaling pathways of immune regulation against IHNV infection in rainbow trout intestinal tract were analyzed at the transcriptional level.

first: Jinqiang

last: Huang

first: Lu

last: Zhao


title: MSC-induced lncRNA expression changes in breast cancer cells

city: Boston

first: Antoine

middle: Elias

last: Karnoub

address: 3 Blackfan Circle

department: Pathology

institute: Beth Israel Deaconess Medical Center and Harvard Medical School

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

summary:
The development of triple-negative breast cancers (TNBCs) – a subset of tumors with particularly aggressive pathogenesis – is critically regulated by certain tumor-microenvironment-associated cells called mesenchymal stem/stromal cells (MSCs), which we and others have shown promote TNBC progression by activating a multitude of signaling nodes that propagate malignant traits in neighboring cancer cells. Characterization of these signaling cascades will better our understanding of TNBC biology, and stands to bring about novel therapeutics that can eliminate the morbidity and mortality associated with advanced disease. Here, we particularly focused on an emerging family of non-coding RNAs – called long non-coding RNAs or lncRNAs – and utilized a MSC-supported TNBC progression model to identify specific lncRNAs of functional relevance to TNBC pathogenesis.
We used Affymetrix arrays to identify the gene expression changes that breast cancer cells (in this case, MDA-MB-231 cells) exhibit as they interact with admixed human MSCs

overall_design: Green fluorescent protein (GFP) -labeled MDA-MB-231 cells were admixed with human MSCs (at 1:3 ratio of cancer cells to MSCs) and cultured in complete media consisting of DMEM, 10%FBS, and Pen/Strep.  After 3 days, cultures were trypsinized, filtered through 70 micometer mesh, suspended, and FACS-sorted to recover GFP-positive cells. GFP-MDA-MB-231 cells cultured alone and treated identically to the co-cultured counterparts were used as controls.

first: Zhenbo

last: Tu

middle: E


title: Integrative mRNA-miRNA interaction analysis associated with the immune response of rainbow trout Oncorhynchus mykiss to infectious hematopoietic necrosis virus infection [RNA-seq]

institute: Gansu Agricultural University


title: Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states

city: Philadelphia

first: Kamen

middle: P

last: Simeonov

state: PA

address: 3800 Spruce St

institute: University of Pennsylvania

summary: The underpinnings of cancer metastasis remain poorly understood, in part due to a lack of tools for probing their emergence at high resolution. Here we present macsGESTALT, an inducible CRISPR-Cas9-based lineage recorder with highly efficient single-cell capture of both transcriptional and phylogenetic information. Applying macsGESTALT to a mouse model of metastatic pancreatic cancer, we recover ~380,000 CRISPR target sites and reconstruct dissemination of ~28,000 single cells across multiple metastatic sites. We find cells occupy a continuum of epithelial-to-mesenchymal transition (EMT) states. Metastatic potential peaks in rare, late-hybrid EMT states, which are aggressively selected from a predominately epithelial ancestral pool. The gene signatures of these late-hybrid EMT states are predictive of reduced survival in both human pancreatic and lung cancer patients, highlighting their relevance to clinical disease progression. Finally, we observe evidence for in vivo propagation of S100 family gene expression across clonally distinct metastatic subpopulations.

overall_design: Single-cell RNA sequencing of transcriptomes and static plus evolving barcodes to capture lineage information from two mice with metastastic PDAC and from cultured cells


title: BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae (ChIP-Seq)

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

summary: Human BET family members are promising targets in the therapy of cancer and immunoinflammatory diseases, but their mechanism of action and functional redundancies are poorly understood. Yeast BET factors Bdf1/2 were previously proposed to act as anchors for coactivator TFIID. We investigated their genome wide roles in transcription and found that, while they cooperate with TFIID at many genes, their contributions to transcription are often significantly different. Bdf1/2 co-occupy the majority of yeast promoters and affect preinitiation complex formation by participating in recruitment of TFIID, Mediator and basal factors to chromatin. Surprisingly, we discovered that hypersensitivity of genes to Bdf1/2 depletion results from combined defects in initiation of transcription and early elongation. Bdf1/2 are critical components of yeast transcriptional machinery with many functional similarities to human BET proteins, most notably Brd4.

overall_design: Standard ChIP-seq approach including crosslinking, chromatin extraction, DNA fragmentation and immunoprecipitation. All experiments were done in two biological replicates (A and B). Selected samples were treated with either DMSO or 3-indolacetic acid (IAA), which was used to induce degradation of target proteins.

first: Steven

last: Hahn


title: BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae (RNA-Seq)

overall_design: Newly synthesized RNAs were labeled with 4-thioU, purified and analyzed with RNA-seq. Depletion of selected factors was achieved either thorugh targeted degradation (auxin-degron system) or deletion of BDF2 gene. Corresponding control and treatment sample files are labeled DMSO and IAA (3-indolacetic acid), respectively. All experiments were done in two (A,B) or three replicates (A,B,C).


title: Gene expression profiles of senescent biliary epithelial cells induced by serum depletion and GCDC

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
2870 genes and 2789 genes were upregulated in senescent cells induced by seum depletion and GCDC treatment, respectively.
1841 genes were upregulated commonly in both 2 conditions.

overall_design: In the study presented here, biliary epithelial cells treated with serum depletion and GCDC treatment was used to acquire expressions profile of senescenct cells, leading to the successful construction of supervied.

first: Motoko

last: Sasaki

first: Yasunori

last: Sato


title: Spo11 generates gaps through concerted cuts at sites of topological stress

city: Vienna

first: Franz

last: Klein

address: Dr. Bohr-Gasse 9

department: Chromosome Biology

country: Austria

institute: Max Perutz Labs, University of Vienna

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

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus
Saccharomyces kudriavzevii

overall_design: Refer to individual Series


title: Spo11 generates gaps through concerted cuts at sites of topological stress [dDSB]

summary: Meiotic recombination is essential for proper meiotic chromosome segregation and fertility, and is initiated by programmed DNA double-strand breaks (DSBs) introduced by Spo11, a eukaryotic homolog of archaeal topoisomerase VIA. Here we report the discovery of hitherto uncharacterized Spo11-induced lesions, small gaps from 34 bp to several hundred bp, which are generated by coordinated pairs of DSBs (double DSBs or dDSBs). Isolation and genome-wide mapping of the resulting fragments with single base pair precision reveals enrichment at DSB hotspots but also a widely dispersed distribution covering the entire genome. We show that Spo11 prefers to cut at a sequence motif which promotes DNA bending, indicating that bendability of DNA contributes to cleavage site choice. Moreover, fragment lengths display a ~ (10.4n+3) bp periodicity, implying that Spo11 favours cleavage on the same face of underwound DNA. Consistently, dDSB signals overlap and correlate with topoisomerase II binding sites, which points to a role for topological stress and DNA crossings in break formation, and suggests a unified model for DSB and dDSB formation, in which Spo11 traps two DNA strands. Furthermore, gaps resulting from dDSBs, an estimated 20% of all initiation events, can account for full gene conversion events that are independent of both Msh2-dependent heteroduplex repair and MutLγ. Since non-homologous gap repair results in deletions, and ectopically re-integrated dDSB fragments result in insertions, dDSB formation represents a potential source of evolutionary diversity and pathogenic germ-line aberrations.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces kudriavzevii

overall_design: dDSB fragments from specific time points of meiotic yeast cultures were isolated via tagged Spo11 by Protec-Seq and ligated to Illumina adapters for amplification and (single or) paired-end 50 bp or 75 bp sequencing on Illumina platforms. Saccharomyces cerevisiae(S. cer.) cells were mixed with the same batch of Saccharomyces kudriavzevii (S. kud.) cells for downstream quantitative comparison. We are providing 31 immunoprecipitation (IP) and 31 corresponding whole cell extract (WCE) samples from wild-type and various mutant S. cer. strains, as well as one S. kud. sample.

first: Doris

last: Chen

first: Silvia

last: Prieler


title: Spo11 generates gaps through concerted cuts at sites of topological stress [Top2]

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: Chromatin immunoprecipitation (ChIP) of wild-type Saccharomyces cerevisiae (S. cer.) strains with myc-tagged (or untagged) Top2 from meiotic yeast cultures for 0 hrs - 4 hrs (t0 - t4) was performed and deep sequenced with Illumina. S. cer. cells were mixed with Candida glabrata (C. gla.) cells for calibration and downstream quantitative comparison. We are providing 4 immonoprecipitation (IP) and 4 corresponding whole cell extract (WCE) samples.

first: Lingzhi


title: BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae (ChEC-Seq)

overall_design: ChEC-seq method was used to map genome-wide binding of transcription factors following treatment with either DMSO or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins. Experiments were done in two (A,B, three (A,B,C) or six biological replicates (A - F).


title: Identification of competing endogenous RNA (ceRNA) and micro-RNA profiles and regulatory networks in 4-nonylphenol-induced impairment of sertoli cells I

city: xiamen

first: wenjie

last: liu

address: xiangan strict xiamen university

institute: xiamen university

summary: Purpose: To uncover the mechanism of  4-nonylphenol-induced impairment of sertoli cells, we used RNA sequencing technology to compare the  lncRNA expression differences between the control groups and the 4-nonylphenol treated groups. Sertoli cells lncRNA, circRNA, mRNA profiles of the control groups and the 4-nonylphenol  treated groups were generated by deep sequencing, in duplicate. The library quality was determined using a Bioanalyzer 2100 (Agilent). The Illumina hiseq X ten platform was used for lnc RNA sequencing. The quality of RNA-seq reads was examined using FastQC.

overall_design: 4-nonylphenol-treated and control sertoli cells lncRNA, circRNA, mRNA  profiles of 24h were generated by deep sequencing, in duplicate.

first: Wenjie

last: Liu

first: Xiaopeng

last: Hu


title: Identification of competing endogenous RNA (ceRNA) and micro-RNA profiles and regulatory networks in 4-nonylphenol-induced impairment of sertoli cells II

summary: Purpose: To uncover the mechanism of  4-nonylphenol-induced impairment of sertoli cells, we used RNA sequencing technology to compare the  small RNA expression differences between the control groups and the 4-nonylphenol treated groups. Sertoli cells small RNA profiles of the control groups and the 4-nonylphenol  treated groups were generated by deep sequencing, in triplicate. The library quality was determined using a Bioanalyzer 2100 (Agilent). The Illumina BGISEQ platform was used for small RNA sequencing. The quality of RNA-seq reads was examined using FastQC.

overall_design: 4-nonylphenol-treated and control sertoli cells small RNA profiles of 24h were generated by deep sequencing, in triplicate.


title: TNFR2 HnRNPK-YAP Signaling Axis Promotes Primary Liver Cancer Development in Hepatic Progenitor Cells

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

summary: We performed single-cell RNA sequencing (scRNA-seq) analysis using clinical samples of PLC patients. We first generated scRNA-seq profiles of freshly isolated PLC from patients with 10x Genomics. A total of 25,189 single-cell transcriptomes from tumors of two patients were obtained after initial quality controls.

overall_design: We performed scRNA-seq analysis with tumor and adjacent tissue of two PLC patients. Then, we performed t-distributed stochastic neighbor embedding (t-SNE) analysis of all cells, which were grouped mainly according to their cell types as annotated based on known cell lineage-specific marker genes.We further confidently discriminated malignant cells by inferring large-scale chromosomal copy-number variations (CNVs) based on transcriptomes.

first: Lixin

last: Wei


title: A novel and highly effective mitochondrial uncoupling drug (MB1-47) in T-cell acute lymphoblastic leukemia

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy. Despite recent advances in treatments with intensified chemotherapy regimens, relapse rates and associated morbidities remain high. In this context, metabolic dependencies have emerged as a druggable opportunity for the treatment of leukemia. Here, we tested the antileukemic effects of MB1-47, a newly developed mitochondrial uncoupling compound. MB1-47 treatment in T-ALL cells robustly inhibited cell proliferation via both cytostatic and cytotoxic effects as a result of compromised mitochondrial energy and macromolecule depletion, which severely impair nucleotide biosynthesis. Mechanistically, acute treatment with MB1-47 in primary leukemias promoted AMPK activation and downregulation of mTOR signaling, stalling anabolic pathways that support leukemic cell survival. Indeed, MB1-47 treatment in mice harboring murine NOTCH1-induced leukemias or human T-ALL PDXs led to a potent antileukemic effect with 2-fold extension in survival without overlapping toxicities. Overall, our findings demonstrate a critical role for mitochondrial oxidative phosphorylation in T-ALL and uncover MB1-47-driven mitochondrial uncoupling as a novel therapeutic strategy for the treatment of this disease.

overall_design: RNAseq analysis of DND41 cells after treatment with DMSO or MB1-47.

first: Victoria

last: da Silva-Diz

first: Amartya

last: Singh

first: Hossein

last: Khiabanian


title: Transcriptionally regulated energy metabolism drives early erythropoiesis (RRBS)

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Transcription and metabolism both influence cell function yet dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. Through a chemical suppressor screen, we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in bloodless moonshine mutant embryos defective for the transcription elongation factor tif1γ. This rescue depends on the functional link of DHODH to mitochondrial respiration. TIF1γ directly controls coenzyme Q synthesis gene expression. Upon tif1γ loss, coenzyme Q levels are reduced, and a high succinate/α-ketoglutarate ratio leads to increased histone methylation. A coenzyme Q analogue rescues moonshine’s bloodless phenotype. These results demonstrate mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.

overall_design: tif1γ (ENSDART00000020116.9/NM_001002871.2) was knocked down (tif1γ KD) by injecting 1 ng of an ATG-blocking morpholino (Gene Tools, 5’→3’ morpholino sequence ATCTTGGCCTTTGTTGTCCGCCATC) into zebrafish wild-type (TU) embryos at the 1-2 cell stage. As a control (Ctrl KD), 1 ng of a Standard Control oligo (designed by Gene Tools, 5’→3’ morpholino sequence CCTCTTACCTCAGTTACAATTTATA) was injected into zebrafish embryos at the 1-2 cell stage. tif1γ KD and Ctrl KD embryos from each clutch were harvested at 11 hpf, 22 hpf and 48 hpf by snap-freezing them, followed by extraction of genomic DNA and processing for reduced representation bisulfite sequencing (RRBS).

first: Marlies

last: Rossmann

first: Sara

last: Hetzel

first: Raha

last: Weigert

first: Song

last: Yang

first: Alexander

last: Meissner

middle: I


title: Longitudinal single-cell dynamics of mitochondrial mutations in chronic lymphocytic leukemia mirror disease history

first: Livius

last: Penter

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Mitochondrial mutations have the potential to act as natural barcodes that allow the tracking of heterogenous cell populations at the single cell level, but thus far, the dynamics of mitochondrial mutations across time and tissue compartments have not been extensively studied. This dataset was generated using mtscATAC-seq to track mitochondrial mutations in peripheral blood, bone marrow and lymph node from 9 patients with chronic lymphocytic leukemia (CLL) across different clinical scenarios. Our in-depth analysis reveals different patterns of dynamisms in mitochondrial mutations in patients undergoing watchful waiting, chemotherapy with fludarabine, cyclophosphamide and rituximab (FCR), allogeneic stem cell transplantation, ibrutinib treatment or transformation to Richter’s syndrome. We provide evidence that mitochondrial mutations can link CLL subclones with distinct chromatin cell states. Mitochondrial mutations appear to recapitulate disease history in CLL, providing patient-level support of the concept of in vivo natural barcodes as a means for understanding clonal dynamics in cancer.

overall_design: Mononuclear cells from peripheral blood, bone marrow and lymph node were obtained from nine human patients diagnosed with chronic lymphocytic leukemia and sequenced using mtscATAC-seq on the 10x platform

first: L

first: S

middle: H

last: Gohil

first: C

last: Lareau

last: Ludwig

middle: J

last: Wu


title: Integrative analysis of lncRNA and mRNA and profiles in postoperative delirium patients

city: Beijing

first: Jinghua

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

summary: Delirium is a common serious complication that often occurs after major surgery. However, there is little known about the function of long non-coding RNAs (lncRNAs) in postoperative delirium (POD). The goals of this study were to explore the expression profiles and functional networks of lncRNAs and mRNAs in patients of POD.

overall_design: Microarray analysis was performed on the peripheral blood samples to identify differentially expressed (DE) lncRNAs and mRNAs in 4 POD patients and 4 control volunteers. DE lncRNAs and mRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR). Bioinformatic analyses were performed to identify the critical biological functions and signalling pathways involved in POD and to identify the functional networks formed between DE mRNAs and lncRNAs.

first: Yuxiang

last: Song

first: Xiaoyan

last: Wang

first: Aisheng

last: Hou

first: Hao

last: Li

first: Jingsheng

last: Lou

first: Yanhong

last: Liu

first: Jiangbei

last: Cao

first: Weidong

last: Mi


first: Wu

summary:
Purpose:Analyze gene expresson in Riociguat treat fresh isolated mouse HSCs
Methods: 1E6 fresh isolated HSCs are seeded into 6-well and treat with Riociguat with Riociguat or DMSO
Results: Riociguat could rescue HSCs spontaneously activated in vitro

overall_design: 1E6 fresh isolated HSCs are seeded into 6-well and treat with Riociguat or DMSO

last: He

first: Feng

last: Han


title: BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae

first: Rafal

last: Donczew


title: Expression data from tomato fruits silencing gene Asr1

city: Hurlingham

first: Pia

middle: Guadalupe

last: Dominguez

state: Buenos Aires

address: N. REPETTO Y LOS RESEROS S/N

department: IABIMO

country: Argentina

institute: INTA (National Institute of Agriculture Technology)

summary: ASR1 is a transcription factor widely present in plants that is involved in stress responses. In this work, we have silenced ASR1 in tomato fruits using an anti-sense construct and analysed the gene expression in two independent transgenic lines (AS5 and AS17) and in wild-type (WT) fruits.

overall_design: Asr1 was silenced in tomato plants by using an anti-sense construct. Plants were grown in controlled greenhouse conditions (80% relative humidity; 200 mmol PAR s-1m-2; 16 hours of light and 8 hours of darkness). Mature tomato fruits (red ripe stage) from wild-type (WT) and two AS lines (AS5 and AS17) were used for the microarray analyses. Pools of two mature tomato fruit mesocarps from three different plants per line were analysed.

first: Fernando

last: Carrari


title: Heat stress and immune response phenotype affect DNA methylation in blood mononuclear cells from Holstein dairy cows

city: Guelph

first: Alexandra

last: Livernois

state: ON

address: 50 Stone Rd East

department: Pathobiology

country: Canada

institute: University of Guelph

summary: Our goal was to identify epigenetic differences between high and low immune responder cows in response to heat stress. We report genome-wide DNA methylation of blood mononuclear cells (BMCs) isolated from high and low cows, before and after in vitro heat stress. We identified differential methylation of promoter regions associated with a variety of biological processes including immune function, stress response, apoptosis, and cell signalling. The specific differentially methylated promoter regions differed between samples from high and low cows, and results revealed pathways associated with cellular protection during heat stress.

overall_design: Examination of DNA methylation in blood mononuclear cells from bovine

first: Bonnie

last: Mallard

first: Shannon

middle: L

last: Cartwright

first: Angela

last: Canovas


title: The effect of Methionine Restriction using oxidized casein as protein source on the transcriptome of mouse IWAT

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

summary: Ingestion of a diet with a restricted Methionine (MR) content results in robust activation of a set of browning genes in IWAT (inguinal white adipose tissue). So far, data were obtained using a mix of elemental amino acids as the dietary protein source, which was replaced in this experiment with casein. To reduce methionine content, casein was oxidized and methionine was added back to a concentration similar to the diets using  elemental amino acids as protein source. Results show that mice reduce body weight and adiposity on MR containing oxidized casein similar to MR containing elemental amino acids. Similarly, energy expenditure, as well as food and water intake were increased. The RNAseq experiment was conducted to compare the effect of MR using these two protein sources on the IWAT transcriptome.

overall_design: Comparison of the effect of methionine restricted (MR) diet using either elemental amino acids (each 6 samples from Control and MR fed mice) or oxidized casein (each 6 samples from Control and MR fed mice) as protein sources on the hepatic transcriptome. The Control diets contain 0.86% methionine, the MR diets 0.17% methionine.

first: Han

last: Fang

first: Kirsten

last: Stone

first: Jasleen

last: Kaur

first: Richard

last: Carmouche

first: Sara

last: Webb

first: Sujoy

last: Ghosh


title: The effect of Methionine Restriction using oxidized casein as protein source on the transcriptome of mouse livers

summary: Ingestion of a diet with a restricted Methionine (MR) content results in robust activation of hepatic stress pathways regulated by PERK, ATF4, and Nfe2l2. In addition, genes regulating hepatic lipogenesis are downregulated. So far, data were obtained using a mix of elemental amino acids as the dietary protein source, which was replaced in this experiment with casein. To reduce methionine content, casein was oxidized and methionine was added back to a concentration similar to the diets using  elemental amino acids as protein source. Results show that mice reduce body weight and adiposity on MR containing oxidized casein similar to MR containing elemental amino acids. Similarly, energy expenditure, as well as food and water intake were increased. The RNAseq experiment was conducted to compare the effect of MR using these two protein sources on the hepatic transcriptome.


title: Whole genome RNA sequencing of wild type and nath-10(icb99 and icb102) alleles

city: London

first: Michalis

last: Barkoulas

address: Sir Alexander Fleming Building, Imperial College RD

department: Faculty of Natural Sciences

institute: Imperial College London

summary: Using next generation RNA sequencing we aimed to investigate the role of a single point mutation in the nath-10 locus as the causative mutation driving phenotypic variability in the final number of the stem cell like seam cells in epithelium of C. elegans. To this end we performed whole genome RNA sequencing using the illumina Hiseq platform on wildtype and two nath-10 loss of function alleles, nath-10(icb99 and icb102) at the 2nd larval stage of development, around 27 hours post hatching. The sequence reads, generated by BGI (China), that passed quality controls were aligned to the most recent C. elegans (WBcel235) transcriptome using the pseudoalignment tool Kallisto. The generated abundance files were  analysed using an R pipeline for DEseq2.  Results showed that ~3% of the genes in nath-10 loss-of-function mutants had a significant differential change in expression, adjusted p-value <0.1 and fold change ≥1.2. We further found, on calculation of transcript coefficient of variation, global variance in transcript number across replicates was significantly increased in nath-10 loss-of-function alleles compared to wild-type. On further analysis genes that play an essential role in seam cell development were found to be increased in transcript variance upon loss of function, including the key Wnt target gene egl-18. Moreover, when analysed using single molecule fluorescence and transcriptional reporter constructs egl-18 was confirmed to more variable in the loss-of-function allele nath-10(icb102).

overall_design: RNA sequencing profiles of L2 (27hours) wild type and nath-10 loss of function C.elegans

first: Mark

last: Hintze