title: Multiple genetic programs contribute to CD4 T cell memory differentiation and longevity by maintaining T cell quiescence

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

summary: While memory T-cells (Tmem) represent a hallmark of adaptive immunity, and despite extensive characterization of CD8+ Tmem, little is known about regulation of CD4+ Tmem cell survival. In this study, we analyzed antigen-specific CD4+T cell memory populations in mice and human to characterize their unique genetic and surface phenotypes. First, using microarray technology, we studied dynamic gene expression of antigen specific CD4+ T cells during infection, memory differentiation, and survival up to nearly a year. In murine CD4+T cells, we observed reduced expression of genes that induce cell proliferation and increased expression of anti-apoptotic and pro-survival genes. Importantly, these genetic programs revealed multiple transmembrane markers enriched in the murine CD4+ Tmem population. We verified the ability of these markers to denote CD4+ Tmem populations using influenza vaccination, and observed enrichment of these surface markers in antigen-specific cells.  Finally, we tested the ability of these markers to denote human memory CD4+ T cells. We found that their expression exclusively co-localized with existing human memory marker CD45R0, and that sorting of cells positive for these markers recovered more responding antigen-specific CD4+T cells than the general CD4+T cell population. In sum, this study presents unique gene signatures of long-lived murine CD4+ Tmem cells along with new surface markers some of which were validated in human. The new information can improve our assessment of CD4 memory T cells can be incorporated for novel therapeutics and vaccine design.

overall_design: The study intended to examine the distinct genetic programs utilized by antigen-specific CD4+T cells differentiating into long-lived memory cells.   Using Agilent microarray technology, we monitored gene expression in mouse CD4+ T cells  undergoing various stages of differentiation post-immunization at times 0 and 9 days, 5 weeks, 6- and 10.5 months.  The gene expression of CD4+ T cells of naive female DO11.10 mice was profiled as a control reference.

first: Scheherazade

last: Sadegh-Nasseri

first: Nianbin

last: Song


title: Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis and retinoic acid

status: Public on Dec 22 2020

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

type: Expression profiling by high throughput sequencing

summary: Vertebrate axial skeletal patterning is controlled by coordinated collinear expression of Hox genes and axial level-dependent activity of Hox protein combinations. Transcription factors of the Meis family act as cofactors of Hox proteins and profusely bind to Hox complex DNA, however their roles in mammalian axial patterning have not been established. Similarly, retinoic acid (RA) is known to regulate axial skeletal element identity through the transcriptional activity of its receptors, however whether this role is related to Meis/Hox regulation or functions in axial patterning remains unknown.  Here we study the role of Meis factors in axial skeleton formation and its relationship to the RA pathway by characterizing Meis1, Meis2 and Raldh2 mutant mice. We report that Meis and Raldh2 regulate each other in a positive feedback regulatory loop that controls axial skeletal identity. Meis elimination produces homeotic transformations similar to those found in Raldh2 and anterior-Hox mutants and disrupts the expression of Hox target genes without changing the transcriptional profiles of Hox complexes. We propose that Meis regulates vertebrate axial skeleton patterning by exclusively affecting Hox protein function, and that alterations in RA levels can produce homeotic transformations without altering Hox transcription through regulating Meis expression.

overall_design: Transcriptomic analysis comparing control embryos to embryos mutant for Meis1 and Meis2 conditionally deleted using Delta1Cre.  The aim was to identify Meis target genes involved in anterior-posterior skeletal patterning.  To discriminate between early patterning effects and alterations during the somite differentiation phase, we separately analyzed the posterior axial bud together with the 10-12 newly formed somites and the rest of the embryonic axis, excluding the anterior regions devoid of somites.

first: Alejandra

middle: C

last: López-Delgado

first: Miguel

last: Torres


title: Cockayne syndrome proteins CSA and CSB maintain mitochondrial homeostasis through NAD+ signaling [HumanHT-12 V4.0]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

summary: Cockayne syndrome (CS) is a rare premature aging disease, which in the majority of cases is caused by mutations of the genes encoding the CSA or CSB proteins. CS patients display cachectic dwarfism and severe neurological manifestations and die by 12 years of age on average. The CS proteins are involved in transcription and DNA repair, including a specialized form of DNA repair called transcription-coupled nucleotide excision repair (TC-NER). However, there is also evidence for mitochondrial dysfunction in CS, likely contributing to the severe premature aging phenotype of this disease. Our cross-species transciptomic analysis in CS postmortem brain tissue, CS mouse and C. elegans models showed that mitochondrial dysfunction is indeed a common feature in CS. Interestingly, the restoration of mitochondrial dysfunction through NAD+ supplementation significantly improved lifespan and healthspan in the C. elegans models of CS, highlighting mitochondrial dysfunction as a major driver of the aging features of CS. We proceeded to perform molecular studies on cerebellar samples obtained from CS patients. We found that these patients exhibited molecular signatures of dysfunctional mitochondrial dynamics that can be corrected with NAD+ supplementation in primary cells with depleted CSA or CSB. Our study provides support for the interconnection between two major aging theories, DNA damage and mitochondrial dysfunction. Together these two agents contribute to an accelerated aging program that can be averted by NAD+ supplementation.

overall_design: Postmortem samples of Cockayne syndrome (CS, N = 7) and control (WT, N=5) cerebellum was obtained  from the NIH NeuroBioBank’s Brain and Tissue repository at the University of Maryland, Baltimore.

first: Mustafa

middle: N

last: Okur

first: Evandro

middle: F

last: Fang

first: Elayne

middle: M

last: Fivenson

first: Vinod

last: Tivari

first: Jesse

middle: S

last: Kerr

first: Deborah

middle: L

last: Croteau

first: Hilde

last: Nilsen

first: Vilhelm

middle: A

last: Bohr


title: β-NGF promotes cartilage to bone conversion, accelerating endochondral fracture repair

city: San Francisco

first: Robert

last: Blelloch

state: California

address: 35 Medical Center Way

department: Dept. of Urology

institute: UC, San Francisco

summary: During endochondral fracture repair, a myriad of biochemical and phenotypic changes occur at the chondro-osseuous junction that regulate cartilage to bone conversion. Osteogenic and angiogenic factors have long been studied for accelerating fracture repair. In our concise study, we focused on the neurotrophic factor nerve growth factor (NGF) and its receptor tropomyosin receptor kinase A (TRKA) as understudied therapeutic targets for accelerating endochondral fracture repair. We first characterized endogenous expression of NGF and TRKA during endochondral repair of tibial fractures. We then analyzed gene expression data from β-NGF stimulated hypertrophic cartilage and observed a promotion in endochondral ossification associated markers. Additional gene ontology analyses revealed promotion of genes associated with Wnt activation, PDGF binding, and integrin binding. Subsequent histological analyses of in vivo samples confirmed Wnt activation following local β-NGF injections via reporter mice. Finally, we tested the therapeutic efficacy of local β-NGF injections in mice, which resulted in a decrease of cartilage and increase of bone volume. Moreover, the newly formed bone contained higher trabecular number, connective density, and bone mineral density. Collectively, we demonstrate the ability for β-NGF to promote endochondral fracture repair in a murine model and uncover mechanisms that will serve to further understand the molecular switches that occur during endochondral ossification.

overall_design: We extracted and prepared 6 total samples from fractures of 6 different mice. Fractures callus-derived hypertrophic cartilage from each mouse were minced, pooled, then split into a control and treatment group. In a total of 3 control/treatment groups, 3 samples were treated with recombinant human β-NGF and 3 samples were not treated.

first: Kevin

middle: O

last: Rivera

first: Fabrizio

last: Russo

first: Ryan

last: Boileau

middle: E

last: Tomlinson

first: Theodore

last: Miclau

first: Ralph

last: Marcucio

first: Tejal

last: Desai

first: Chelsea

last: Bahney


title: RNA-seq data of porcine satellite cells at 24h and 36h of differentiation

city: Wuhan

first: Jingxuan

last: Li

state: Hubei

address: Shizishan Street NO.1

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education

country: China

institute: Huazhong Agricultural University

summary: We isolated and cultured porcine skeletal muscle satellite cells (PSCs).  PSCs were induced to differentiate. At 24h and 36h of differentiation, the PSCs were collected for RNA-seq. Each group had three biological replicates.

overall_design: Transcriptome sequencing of porcine satellite cells at 24h and 48h of differentiation

first: Changchun


title: Low dose bisphenol A gene signature and endometrial cancer

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: We found rats exposed to 250ug/kg/day BPA (BPA250) showed abnormal transition in estrous cycle at postnatal (PND) 90 whereas 25ug/kg/day BPA (BPA25) and BPA250 in 1-year-old rats showed prolonged estrus phase, suggesting that BPA25 and BPA250 may act like high dose EE2 (EE2-05) in disrupting normal estrous cycling. To dissect the underlying molecular mechanism, we performed RNA-sequencing on 1-year-old samples and found that both BPA25 and BPA250 groups shared similar gene signature. Pathway analysis suggested that 710 unique genes from both groups were associated with estradiol and also linked to female cancer as suggested by disease prediction analysis.

overall_design: Five BPA exposed groups (2.5, 25,250,2500,25000ug/kg body weight); two EE2 exposed group (EE(0.5) and EE(0.05); One vehicle control group; n=4 per group;

first: Yuet-Kin

last: Leung

first: Jacek

last: Biesiada

first: Govindarajah

last: Vinothini

first: Jun

last: Ying

first: Ady

last: Kendler

first: Shuk-Mei

last: Ho


title: Cholangiopathy and biliary fibrosis in Cyp2c70-deficient mice are fully reversed by ursodeoxycholic acid

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary:
Background and Aims - Bile acids (BAs) aid intestinal fat absorption and exert systemic actions by receptor-mediated signaling. BA receptors have been identified as drug targets for human diseases, but differences in BA metabolism between humans and mice hamper translation of pre-clinical outcomes. Cyp2c70-ablation in mice prevents synthesis of mouse/rat-specific muricholic acids (MCAs), but potential (patho)physiological consequences of their absence are unknown. We therefore assessed age- and gender-dependent effects of Cyp2c70-deficiency in mice.

Methods - BA-related parameters, hepatic and intestinal gene expression patterns, liver morphology and intestinal barrier function were assessed in male and female Cyp2c70-/- mice and WT controls at different ages. Effects of ursodeoxycholic acid (UDCA) treatment were evaluated in young adult female mice.

Results – Cyp2c70-/- mice were completely devoid of MCAs and showed high abundances of chenodeoxycholic and lithocholic acids. BA pool size was unaffected in young-adult male but reduced by 40% in female Cyp2c70-/- mice. Interestingly, plasma BAs and transaminases were highest in Cyp2c70-/- mice at weaning and spontaneously decreased with age. Although bile flow and biliary BA secretion were unchanged in young-adult Cyp2c70-/- mice, indicating absence of cholestasis, plasma BA and transaminase levels were still elevated. These young-adult Cyp2c70-/- mice displayed cholangiocyte proliferation, mild portal fibrosis, altered microbiome composition and increased gut permeability. Only the female Cyp2c70-/- mice developed bridging fibrosis with age (7-8 months). UDCA treatment normalized hepatic and intestinal functions and fully restored liver morphology in female Cyp2c70-/- mice.

Conclusion – Cyp2c70-/- mice show transient neonatal cholestasis and develop cholangiopathic features which progress to bridging fibrosis in female mice only. These consequences of Cyp2c70-deficiency are fully restored by treatment with UDCA.

overall_design: Total RNA optained from liver 22 samples where compaired in 4 different groups ( WT , WT+UDCA , CYP2C70KO , CYP2C70KO+UDCA) , each group  consisting of  n=5,6 biological replicates

first: J

last: De Boer

first: H

middle: D

last: de Vries

first: A

last: Palmiotti

first: R

first: N

last: Mulder

first: M

middle: V

last: Hovingh

last: Koehorst

last: Kloosterhuis

first: V

middle: W

last: Bloks

first: B

last: van de Sluis

first: F

last: Kuipers

middle: T

last: Haas

last: Staels

first: D

last: Dombrowicz

last: Hoogerland

last: Doestzada

last: Fu

last: Westerterp

last: Wolters

last: La Rose


title: Cockayne syndrome proteins CSA and CSB maintain mitochondrial homeostasis through NAD+ signaling [Agilent-020186 array]

first: Supriyo

last: De

overall_design: N2 (Ctr), CSA and CSB mutant lines (csa1, csb1, and csa,csb1) worms (N=4 per condition) were exposed to 500 µM of the NAD+ precursor Nicotinamide riboside (NR) a from the L4 stage and whole body tissue was collected for microarray analysis at adult day 7.

first: Mustafa

last: Okur

first: Evandro

last: Fang

first: Elayne

last: Fivenson

first: Vinod

last: Tivari

first: Jesse

last: Kerr

first: Deborah

last: Croteau

first: Hilde

last: Nilsen

first: Vilhelm

last: Bohr


title: Platelets facilitate primary progressive tuberculosis by restricting the oxidative burst in phagocytes

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: Tuberculosis (TB) remains the leading cause of death by a single infectious agent worldwide. Despite decades of active research, host factors which underly susceptibility to Mycobacterium tuberculosis (Mtb), the etiologic agent of TB, are still ill defined. We investigated the role of platelets (PLTs) during primary TB in mice as these cells were recently assigned multiple immunological functions. PLTs were present at the site of infection, formed aggregates with different myeloid subsets during experimental TB and such aggregates were detected also in TB patients. PLTs were detrimental during the early phase of infection and this effect was uncoupled from their canonical activation. PLTs left lung cell dynamics and patterns of anti-mycobacterial T-cell responses unchanged. PLTs hampered cell autonomous defense by restricting production of reactive oxygen species (ROS) in lung residing myeloid cells. Thus, PLTs orchestrate immunity in TB by modulating innate immune responsiveness during primary lung infection and may be amenable to new interventions for this deadly disease.

overall_design: Design include 8 control samples and 8 samples collected 36h after PLT depletion antibody or isotype control injection on d14 p.i. In total 16 samples collected from M. musculus (strain: 129S2) BALs. There was no replicats.

first: Anca

last: Dorhoi

first: Joanna

last: Żyła

first: Lisa

last: Scheuermann


title: Cockayne syndrome proteins CSA and CSB maintain mitochondrial homeostasis through NAD+ signaling

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

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design: Refer to individual Series


title: MicroRNA  expression in Alcoholic Chronic Pancreatitis

city: Kalyani

first: Bishnupriya

last: Chhatriya

state: West Bengal

address: PO NSS

country: India

institute: National Institute of Biomedical Genomics

summary:
Microarray was used to find out the differentially expressed miRNAs in Alcoholic Chronic Pancreatitis as compared to healthy control.
Resulting miRNAs could be further used to understand the disease as well as could act as secretory biomarker.

overall_design: Total 8 samples were used, 4 Chronic Pancreatitis(CP) and 4 healthy control samples were used

first: Srikanta

last: Goswami


title: Next Generation Sequencing Transcriptomes Analysis of Irradiated mouse submandibular glands with or without transient activation of Hedgehog signaling

city: College Station

first: Fei

last: Liu

address: 206 Olsen Blvd

institute: Texas A&M University Health Science Center

summary:
Purpose: To compare transcriptomes of nontreated (NT), Irradiated (IR and IR+GFP) and Hedgehog-activated (IR+Gli1 and IR+Shh) mouse submandibular glands (SMGs)
Methods: SMG mRNA profiles of male adult NT mice or mice 7 days after local IR were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by HTseq. qRT–PCR validation was performed using SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) and identified 20,743 transcripts in the SMGs with TopHat workflow.  Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: Our study represents the first detailed analysis of SMG transcriptomes after IR with or without transient activation of Hedgehog (Hh) signaling, with biologic replicates, generated by RNA-seq technology. Our results show that IR impaired macrophages and related innate immune responses in SMGs, whereas transient Hh activation recovered them.


title: H3K9me3 ChIP-seq in MLL-rearranged leukemic stem cells and hematopoietic stem cells

city: Tianjin

first: Yajing

last: Chu

address: Nanjing Road 288

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology, Chinese Academy of Medical Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acute myeloid leukemia (AML) with rearrangement of the mixed-lineage leukemia (MLL) gene are the most aggressive hematopoietic malignancies. Previous studies demonstrated the distribution of several epigenetic modifications including H3K9me3, H3K79me2, H3K36me3, H3K4me3 and H3K27me3, in MLL-AF9 transformed murine cells. Here, we examined the H3K9me3 distribution in c-Kit+ cells (enriched with stem/progenitor cells) from both MLL-AF9 transformed murine cells in parallel with control wild-type cells, and found an overall lower distribution of H3K9me3 in leukemia stem cells than normal hematopoietic stem/progenitor cells.

overall_design: c-Kit+ cells were isolated with CD117 beads from bone marrow of wild-type and moribund leukemic mice (MLL-AF9 and MLL-NRIP3 fusion transformed murine c-Kit+ cells). c-Kit+ cells were then cross-linked, sonicated and incubated with H3K9me3 antibody. ChIPed DNA were purified with classic phenol chloroform extraction protocol. H3K9m3 ChIPed DNA profiles of these c-Kit+ cells were generated by DNA sequencing using Illumina Hiseq2500.

first: Chu

last: Yajing


title: Gene expression profile of WT and PD-1 -/- CD8+ T cells from murine skin (ear)

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Gene expression changes were computed between naïve, WT and PD-1 -/- T Cells. WT or PD-1 -/- OT-1+ CD8+ donor T cells were sorted from the ear skin of recipient mice at day 14 after VACV-OVA skin scarification. Naïve CD8+ OT-1 T cells were isolated from lymph node and spleen of naive mice by negative selection on MACS beads

overall_design: 1X10^5 WT CD8+ OT-1 T cells were mixed with 1x10^5 PD-1 -/- CD8+ OT-1 T cells and were co-adoptively transferred to WT recipients one day before VACV-OVA infection. Recipient mice were vaccinated by VACV-OVA skin scarification on each ear with 1x10^6 and on the base of the tail with 2x10^6 viral p.f.u. At day 14, WT or PD-1-/- donor CD8+ T cells were isolated from ear skin, sorted into Trizol medium and sequenced. Naive CD8+ OT-1 T cells were isolated from lymph node and spleen of naive mice by negative selection on MACS beads, stored in Trizol medium and sequenced.

first: Niroshana

last: Anandasabapathy

first: K

last: Devi

first: Abhinav

last: Jaiswal

first: Olivier

last: Elemento


title: Expression data and H3K27me3 occupancy profiling by high throughput sequencing from control and SETD2 knockout organoids cells.

city: Shanghai

first: Huairui

last: Yuan

address: 320 Yueyang Road

department: Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

summary: To understand the molecular basis how Setd2 loss enhances metastatic traits of PCa, we carried out RNA-seq and H3k27me3 Chip-seq using mice-derived prostatic organoid cells from 3-month-old PtenPC+/− and PtenPC+/−;Setd2PC−/− mice.To further validate Setd2 loss accelerated prostate tumorigenesis is dependent on EZH2 upregulation,we conduct high throughput sequencing of organoid cells derived from PtenPC+/− and PtenPC+/−;Setd2PC−/−  mice with Ezh2 knockout.To understand the molecular basis whether the tumor suppressive function of Setd2 is depends on its methylation of EZH2 at k735, we also carried out RNA-seq using mice-derived prostatic organoid cells from 2-month-old PtenPC-/- and PtenPC-/-;Ezh2K735R mice.We integrated all the RNA-seq and chip-seq data generated from organoid cells.

overall_design: The prostatic organoid cells were isolated from 3-month-old PtenPC+/- and PtenPC+/-; Setd2PC-/- mice with or without Ezh2 knockout according to previously reported protocol (Drost et al., 2016). Total RNA was extracted from mouse organoids using TRIzol reagent and then subjected to PE150 Hiseq. Each sample contained pooled RNA from 3 biological replicates and was mixed with equal mass of RNA to minimize variation across samples. Similar approaches were used to generate organoid cells from 2-month-old PtenPC-/- and  PtenPC-/−;Ezh2K735R mice. Each group has two replications.The chromatin from prostatic organoid cells with or without SETD2 deletion was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K27me3 (Active Motif).

first: Jun

last: Qin


title: Global analysis of kidney gene expression by RNA-Seq of aged CTRP1-deficient mice

first: Guang

middle: William

last: Wong

state: MD

address: 855 N Wolfe Street

department: School of Medicine

institute: The Johns Hopkins University

summary: Aging affects multi-organ systems. What local and systemic factors influence renal structure and function in aging are not well understood. We and others have shown that the secretory protein, C1q/TNF-related protein 1 (CTRP1), regulates systemic metabolism and cardiovascular function. Whether CTRP1 has a role in kidney function is unknown. We provide evidence here that CTRP1 modulates renal physiology in an age- and sex-dependent manner. In addition to adipose tissue, CTRP1 is also expressed in kidney glomeruli, with podocyte being a major cell source. In mice lacking CTRP1, we observed significant increase in kidney weight and glomeruli hypertrophy in aged (~1 year) male, but not female or younger mice. Although glomerular filtration rate, plasma renin and aldosterone levels, and renal response to water restriction are not different between genotypes, aged CTRP1-deficient male mice have elevated blood pressure. Echocardiogram and pulse wave velocity measurements indicate normal heart function and vascular stiffness in CTRP1 knockout animals. Increased blood pressure is not due to greater salt retention. Paradoxically, CTRP1-deficient mice have elevated urinary sodium and potassium excretion, resulting, in part, from reduced expression of genes involved in renal sodium and potassium reabsorption. Despite renal hypertrophy, gene expression related to inflammation, fibrosis, and oxidative stress are significantly lower in CTRP1-deficient mice.  RNA sequencing and pathway analyses reveal additional alterations and enrichments of genes in metabolic processes in the kidney of CTRP1-null animals. These results highlight novel contributions of CTRP1 to aging-associated changes in renal structure and function

overall_design: Kidney RNA sequenceing and bioinformatics analyses were performed on age-matched 49 week-old wildtype (WT) and CTRP1-/- mice, with 4 biological replicates for each genotype.

first: Susana

last: Rodriguez

first: Hannah

last: Little

first: Blythe

last: Shepard

first: Stefanie

middle: Y

last: Tan

first: Andrew

last: Wolfe

first: Muhammad

middle: U

last: Cheema

first: Saneedp

last: Jandu

first: Owen

last: Woodward

first: C

last: Talbot Jr

first: Dan

last: Berkowitz

first: Jennifer

last: Pluznick

first: G


title: Epigenetic rewiring towards mesenchymal-epithelial transformation in ovarian cancer-associated mesenchymal stem cells drives metastasis

city: Houston

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

institute: The University of Texas MD Anderson Cancer Center

summary: Ovarian cancer develops early intra-peritoneal metastasis establishing a pro-tumorigenic  tumor microenvironment (TME) through reprogramming normal mesenchymal stem cells into carcinoma-associated mesenchymal stem cells (CA-MSCs). CA-MSCs are the stromal stem cell of the TME, supporting cancer growth, increasing desmoplasia, angiogenesis and chemotherapy resistance. We demonstrate epigenetic rewiring drives CA-MSC formation via enhancer-enriched DNA hypermethylation, altered chromatin accessibility and differential histone modifications inducing a partial mesenchymal to epithelial transition (MET) increasing tumor cell adhesion. Direct CA-MSC:tumor cell interactions, confirmed in patient ascites, facilitate ovarian cancer metastasis through co-migration. WT1, a developmental mediator of MET, and EZH2, mediate CA-MSC epigenetic reprogramming. WT1 overexpression induces CA-MSC conversion while WT1 knock-down, in combination with EZH2 inhibition, blocks CA-MSC formation. EZH2 inhibition subsequently decreases intra-abdominal metastasis.

overall_design: 13 cancer-associated mesenchymal stem cell, and 19 normal mesenchymal stem cell samples are profiled.

first: Shen

last: Hui

first: Coffman

last: Lan


title: hnRNPDL extensively regulates transcription and alternative splicing

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: RNA binding proteins (RBPs) are key players of genome regulation. Here we report the transcriptome study of HnRNP D-Like protein, which belongs to the hnRNP family. We used RNA-seq to analyze the global transcript level and alternative splicing on hnRNPDL shRNA-treated cells and control. Sh-hnRNPDL extensively increased in the expression of genes involved in female pregnancy, cell apoptosis, cell proliferation and cell migration. HnRNPDL regulated alternative splicing of hundreds of genes enriched in transcription regulation and signalling pathways including NOD-like receptor signaling, Notch signaling, and TNF signaling. This study provides the first transcriptome-wide analysis of hnRNPDL regulation of gene expression, which adds to the understanding of critical hnRNPDL functions.

overall_design: mRNA profiles of shRNPDL knockdown HeLa cells and control were generated by deep sequencing, in replicates, using Illumina Illumina HiSeq 4000.

first: Ruth

middle: Z

last: Li

first: Yi

last: Zhang


title: RNA profiling of Suv39h1 overexpressed MLL-AF9 induced acute myeloid leukemia (AML) cells

first: Yajing

last: Chu

summary: Acute myeloid leukemias (AMLs) with rearrangement of the mixed-lineage leukemia (MLL) gene are the most aggressive hematopoietic malignancies. By analyzing the clinical data, we found the expression of SUV39H1 was significantly decreased in AML patients and MLL-AF9 (MA9) induced AML mice, in comparison with controls. Remarkably, when overexpress Suv39h1 in MA9 AML mice, the survival of AML mice was significantly prolonged.To examined the mechanism mediated by Suv39h1 overexpression (SUV-OE), we performed the RNAseq profiling of SUV-OE MA9 AML cells and control cells.

overall_design: c-Kit+ cells were isolated from Suv39h1 overexpessed MA9 and corresponding control AML mice bone marrow. mRNA profiles of these c-Kit+ cells were generated by RNA sequencing.

first: Chu

last: Yajing


title: Chorioamnion after choriodecidual Group B Streptococcal infection

city: Seattle

first: James

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Choriodecidual infection is associated with preterm premature rupture of membranes (pPROM) and preterm birth. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression and may be involved in the pathway leading to chorioamnion weakening following infection. The study objective was to determine if a miRNA profile in the chorioamnion is associated with Group B Streptococcal infection and membrane weakening.

overall_design: Ten chronically catheterized pregnant monkeys (Macaca nemestrina) at 118-125 days gestation (term=172 days) received one of two experimental treatments: 1) choriodecidual and intra-amniotic saline infusions (n=5), or 2) GBS choriodecidual inoculation (n=5).

first: Theodor

middle: K

last: Bammler

first: Richard

middle: P

last: Beyer

first: Jeroen

last: Vanderhoeven

first: Michael

middle: G

last: Gravett

first: Kristina

last: Adams-Waldorf

first: Lakshmi

last: Rajagopa

first: Craig

last: Bierle

first: Samantha

last: Weed

first: Erica

last: Boldenow

first: Ed

last: Parker

first: William

last: Carter

first: Denny

last: Liggitt

first: Brian

last: Johnson


title: Lung tumorigenic model employing human pluripotent stem cell-derived lung organoids that conditionally overexpress HER2

status: Public on Dec 21 2020

city: okayama

first: Takeshi

last: Takarada

state: okayama

address: 2-5-1 Shikata-cho

department: Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

country: Japan

institute: Okayama university

summary: Compare the gene expression profiles of parental (1383D2) or iHER2-iPSC derived lung organoids

overall_design: RNA samples extracted from lung organoids derived from parental or iHER2-iPSC

first: Daisuke

last: Yamada

first: Masahiro

last: Nakamura


title: Gene expression profiling study by RNA-seq to identify gene signature resposed to chemo-radiotherapy in colorectal cancers.

status: Public on Dec 25 2020

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The objective of this study is to assess gene expression changes and identify gene sets associated with chemo-radiotherapy (CRT) in colorectal cancer (CRC) patients. We performed RNA-seq based transcriptome profiling using primary tumor samples obtained from 22 CRC patients. By a number of statistical tests, a total of 575 genes were statistically significant, indicating a gene set profoundly responded to chemo-radiotherapy in CRC. To select the genes showing strong gene expression intensities and critically validate the differences between treatment-responded and non-responded patients, we applied more rigorous cut-off for gene selection, revealing a total of 8 final gene candidates. These genes were applied to the downstream experimental assays.

overall_design: RNA-seq data of 22 CRC samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).

first: Jeong-Hwan

first: Seon-Young

first: Jin-Cheon


title: Gene expression changes induced by over-expression of miR-181b-5p in db/db mouse

city: Saitama

first: Hiroki

last: Ishii

address: 1-847 Amanuma-cho, Omiya-ku

department: First Department of Integrated Medicine

institute: Jichi Medical University Saitama Medical Center

summary: The microRNAs (miRNAs) that can influence diabetic kidney disease (DKD) have not been fully characterized. The aim of this study was to identify the miRNAs that affect DKD and could be used as specific biomarkers or therapeutic agents. First, kidneys from two DKD mouse models were screened for differences in miRNA expression from control mice. We found that miRNA-125b-5p and miRNA-181-5p were specifically differentially expressed in the kidneys of DKD mice. Next, we administered miRNA-181b-5p-mimic to DKD mice, which reduced the albuminuria and abnormal mesangial expansion. Pathway analysis revealed that overexpression of miRNA-181-5p significantly altered the expression of 51 genes in the kidneys of DKD mice. Furthermore, the serum level of miRNA-125b-5p was significantly higher and that of miRNA-181-5p was lower in patients with DKD than in patients with other kidney diseases. These results suggest that miRNA-125b-5p and miRNA-181b-5p may represent novel diagnostic biomarkers and that miRNA-181b-5p may represent a therapeutic target for DKD.

overall_design: Gene microarray analysis was performed on kidney tissue from each group: normal mice (n=2), untreated db/db mice (n=2), db/db mice administered miRNA-181b-5p-mimic-PEI-NPs (n=2), and db/db mice administered control-miRNA-PEI-NPs (n=2).


title: Investigating PCR bias in TnSeq

city: Little Rock

first: Stephanie

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

summary: As transposon sequencing (TnSeq) assays have become prolific in the microbiology field, it is of interest to scrutinize their potential drawbacks. TnSeq results are determined by counting transposon insertions following the PCR-based enrichment and subsequent deep sequencing of transposon insertions. Here we explore the possibility that PCR amplification of transposon insertions in a TnSeq library skews the results by introducing bias into the detection and/or enumeration of insertions. We compared the detection and frequency of mapped insertions when altering the number of PCR cycles in the enrichment step. In addition, we devised and validated a novel, PCR-free TnSeq method where the insertions are enriched via CRISPR/Cas9-targeted transposon cleavage and subsequent Oxford Nanopore sequencing. These PCR-based and PCR-free experiments demonstrate that, overall, PCR amplification does not significantly bias the results of the TnSeq assay insofar as insertions in the majority of genes represented in our library were similarly detected regardless of PCR cycle number and whether or not PCR amplification was employed. However, the detection of a small subset of genes which had been previously described as essential is indeed sensitive to the number of PCR cycles. We conclude that PCR-based enrichment of transposon insertions in a TnSeq assay is reliable but researchers interested in profiling essential genes should carefully weigh the number of amplification cycles employed in their library preparation protocols. In addition, we present a PCR-free TnSeq alternative that is comparable to traditional PCR-based methods although the latter remain superior owing to their accessibility and high sequencing depth.

overall_design: Twenty-two samples were sequenced. 18 of the samples were sequenced using Illumina HiSeq, the remaining 3 samples were sequenced using Oxford Nanopore Technologies (ONT). The 18 Illumina-sequenced samples comprise three groups, each with a unique transposon-genomic junction enrichment method. Each of the three groups includes two types of samples: 3 biological replicates of the TnSeq library grown to exponential phase; 3 biological replicates of the same libraries grown to stationay phase. 3 samples were subjected to amplification-free transposon-genomic junction enrichment and subsequent sequencing using MinION ONT- these are experimental replicates of one TnSeq library grown to stationary phase. One sample (labeled TnSeq_WGS) was sequenced on MinION ONT without enrichment of the transposon.

first: Duah

last: Alkam

first: Piroon

last: Jenjaroenpun


title: Expression of miRNAs in the kidneys of AKITA mouse

overall_design: The expression of miRNAs in kidneys of AKITA mice were measured in four samples compared to age-matched control mice.


title: Expression of miRNAs in the kidneys of db/db mouse

overall_design: The expression of miRNAs in kidneys of db/db mice were measured in four samples compared to age-matched control mice.


title: An orphan LuxR homolog of Bradyrhizobium japonicum is important for oxidative stress tolerance and competitiveness during soybean nodulation

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

summary: Expression data from B. japonicum wild-type and Dblr1880 (6498) strains under free-living and symbiotic conditions

overall_design: B. japonicum transcriptome was determined under free-living and symbiotic conditions including mutant analysis (blr1880 deletion mutant)

first: A

last: Kessler

last: Lindemann

first: M

last: Koch

first: H

last: Hennecke

first: G

last: Pessi


title: Expression Signatures of diabetic mouse and miR-181b-5p overexpression in db/db mouse

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

overall_design: Refer to individual Series


title: Targeting Interleukin-2-Inducible T-cell Kinase (ITK) differentiates GVL and GVHD in allo-HSCT

city: Syracuse

first: Adam

middle: Tully

last: Waickman

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

summary: Allogeneic hematopoietic stem cell transplantation is a potentially curative procedure for many malignant diseases. Donor T cells  prevent  disease recurrence via graft-versus-leukemia (GVL) effect. Donor T cells also contribute  to graft-versus-host disease (GVHD), a debilitating and potentially fatal complication.  Novel treatment strategies are needed which allow preservation of GVL effects without causing GVHD. Using murine models, we show that targeting IL-2-inducible T cell kinase (ITK) in donor T cells reduces GVHD while preserving  GVL effects.  Both CD8+ and CD4+ donor T cells from Itk-/- mice produce less inflammatory cytokines and show decrease migration to GVHD target organs such as the liver and small intestine, while maintaining GVL efficacy against primary B-cell acute lymphoblastic leukemia (B-ALL). Itk-/- T cells exhibit reduced expression of IRF4 and decreased JAK/STAT signaling activity, but upregulating expression of Eomesodermin (Eomes) and preserve cytotoxicity, necessary for GVL effect.  Transcriptome analysis indicates that ITK signaling controls chemokine receptor expression during alloactivation, which in turn affects the ability of donor T cells to migrate to GVHD target organs. Our data suggest that inhibiting ITK could be a therapeutic strategy to reduce GVHD while preserving the beneficial GVL effects following allo-HSCT treatment.

overall_design: ITK KO pre-and post transfer and Wildtype pre-and post transfer

first: Mobin

last: Karimi

first: Mahinbanu

last: Mammadli


title: Intravenous injection of oncolytic virus M1 awakes antitumor T cells and overcomes resistance to checkpoint blockade

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

summary: Gene set enrichment analysis (GSEA) revealed that upon M1 treatment, apoptotic and inflammation associated genes were largely upregulated, suggesting that M1 killed tumor cells and triggered inflammatory response. The GSEA also revealed that DNA repair pathway was down-regulated in M1 treated tumors, which is consistent with our previous finding that M1 induces DNA damage and then leads to tumor cells apoptosis. Additionally, gene sets marked the release of immune-boosting cytokines such as interferon (IFN)-α, IFN-γand tumor necrosis factor (TNF)-α were deployed in M1 treated tumors, providing potential pro-inflammatory signals to generate antitumor immunity. All the results above demonstrate that M1 induces ICD and shapes TME to an inflammatory state.

overall_design: C57BL/6J mice were implanted subcutaneously in the right flank with B16F10 cells at day 0 and treated intravenously with PBS (n=4) or C6V1(M1) (n=4) (1x107 pfu) daily on day 6-10. Tumors were harvested on day 12, total RNA was extracted and then performed RNA-sequencing.

first: Yang

last: Liu

first: X

last: CLiu


title: Multi-omic data integration allows baseline immune signatures to predict hepatitis B vaccine response in a small cohort

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

type: Methylation profiling by genome tiling array

summary: Vaccination remains one of the most effective means of reducing the burden of infectious diseases globally. Climate change is projected to lead to an increase in the burden of vector- and water-borne, as well as zoonotic infectious diseases including COVID-19. Improving our understanding of the molecular basis for effective vaccine response is of paramount importance if we are to ensure the success of future vaccine development efforts. We applied cutting edge multi-omics approaches to characterize temporal molecular responses following vaccination with hepatitis B virus (HBV) vaccine. Data were integrated across cellular, epigenomic, transcriptomic, proteomic, and fecal microbiome profiles, and correlated to final hepatitis B antibody titres. Using both a molecular-interaction network integration method (NetworkAnalyst) and a data-driven integration approach (DIABLO), we overcame the p>>>n problem (predictors much greater than observations) and uncovered baseline molecular patterns and pathways associated with more effective vaccine responses to HBV. Correlations were identified with signalling pathways such as JAK-STAT and interleukin signalling, Toll-Like Receptor Cascades, interferon signalling and Th17 cell differentiation. This study provides further evidence that baseline cellular and molecular characteristics of an individual’s immune system influence vaccine responses, and highlights the utility of integrating information across many parallel molecular datasets.

overall_design: A total of 75 samples (15 participants, each samples at five time points) representing both pre- and post-vaccination blood draws.

first: Casey

last: Shannon

first: Travis

middle: M

last: Blimkie

first: Rym

last: Ben-Othman

first: Nicole

last: Gladish

first: Nelly

last: Amenyogbe

first: Sibyl

last: Drissler

first: Rachel

last: Edgar

first: Queenie

last: Chan

first: Leonard

middle: J

last: Foster

middle: S

first: William

last: Mohn

first: Ryan

middle: R

last: Brinkman

first: Kim-Anh

last: Cao

first: Richard

middle: H

last: Scheuermann

first: Scott

last: Tebbutt

first: Robert

last: Hancock

first: Wayne

middle: C

last: Koff

first: Tobias

last: Kollmann

first: Manish

last: Sadarangani

first: Amy

last: Lee


title: Transcriptional heterogeneity between primary adult grey and white matter astrocytes underlie differences in modulation of in vitro myelination

city: Groningen

first: Marissa

last: Dubbelaar

address: Antonius Deusinglaan 1

department: Biomedical Sciences of Cells & Systems

institute: University Medical Center Groningen

summary:
Background: Multiple sclerosis (MS) is an inflammation-mediated demyelinating disease of the central nervous system, which eventually results in secondary axonal degeneration due to remyelination failure. Successful remyelination is orchestrated by astrocytes (ASTRs) and requires sequential activation, recruitment, and maturation of oligodendrocyte progenitor cells (OPCs). In both MS and experimental models, remyelination is more robust in grey matter (GM) than white matter (WM) that is likely related to local differences between GM and WM lesions. Here, we investigated whether adult gmASTRs and wmASTRs differently modulate myelination.
Methods: Differences in modulation of myelination between adult gmASTRs and wmASTRs were examined using in vitro myelinating cultures that rely on a feeding layer of ASTRs. Transcriptional profiling and weighted gene co-expression network analysis were used to analyze differentially expressed genes and gene networks. Potential differential modulation of OPC proliferation and maturation by adult gmASTRs and wmASTRs, in response to Toll-like receptor (TLR) 3 and TLR4 agonists, were assessed.
Results: Our data reveal that adult wmASTRs are less supportive to in vitro myelination than gmASTRs. WmASTRs more abundantly express reactive ASTR genes and genes of a neurotoxic subtype of ASTRs, while gmASTRs have more neuro-reparative transcripts. A gene network module, containing cholesterol biosynthesis enzyme genes that positively correlated with gmASTRs, and a network module, containing extracellular matrix-related genes that positively correlated with wmASTRs, are identified. Adult wmASTRs and gmASTRs responding to TLR3 agonist Poly(I:C) differently modulate OPC behavior, while LPS treatment of both gmASTRs and wmASTRs results in a prominent decrease in myelin membrane formation.
Conclusions: Primary adult gmASTRs and wmASTRs are heterogeneous at the transcriptional level, differed in their support of in vitro myelination, and their pre-existing phenotype determined TLR3 agonist responses. These findings point to a role of ASTR heterogeneity in regional differences in remyelination efficiency between GM and WM lesions.

overall_design: Identification of the gene expression differences between astrocytes from grey and white matter regions

first: W

last: Baron

first: B

last: Eggen


title: Evolution of the Epigenetic Landscape in Childhood B Acute Lymphoblastic Leukemia and Role in Drug Resistance [eRRBS]

first: Shella

last: Saint Fleur-Lominy

address: 550 First Avenue, Smilow Building 1207

department: Medicine

institute: NYU Langone Health

type: Methylation profiling by high throughput sequencing

summary: B cell acute lymphoblastic leukemia (ALL) is the most common malignancy in children and while highly curable, it remains a leading cause of cancer-related mortality. The outgrowth of tumor subclones carrying mutations in genes responsible for resistance to therapy has led to a Darwinian model of clonal selection. Previous work has indicated that alterations in the epigenome might contribute to clonal selection yet the extent to which the chromatin state is altered under the selective pressures of therapy is unknown. To address this, we performed chromatin immunoprecipitation, gene expression analysis, and enhanced reduced representation bisulfite sequencing on a cohort of paired diagnosis/relapse samples from individual patients who all but one relapsed within 36 months of initial diagnosis. Collectively, our data show that the chromatin state at diagnosis varies widely among patients. While the majority of peaks remained stable between diagnosis and relapse, a significant fraction were either lost or newly gained with some patients showing few differences and others showing massive changes of the epigenetic state. Evolution of the epigenome are associated with pathways previously linked to therapy resistance as well as novel candidate pathways through alterations in pyrimidine biosynthesis and downregulation of polycomb repressive complex 2 targets. We also discovered three novel, relapse-specific super-enhancers shared by a majority of patients including one associated with S100A8, the top upregulated gene seen at relapse in childhood B-ALL. Our results support the role of the epigenome in driving clonal evolution and uncover new candidate pathways associated with relapse.

overall_design: Primary pediatric B ALL diagnosis/relapse paired samples were used to study the evolution of the epigenome. For Cohort 2 (17 pairs, 3 relapse only), eRRBS was performed  to determine the DNA methylation statues at CpGs at diagnosis and relapse.

first: Nikki

middle: A

last: Evensen

first: Teena

last: Bhatla

first: Gunjan

last: Sethia

first: Sonali

last: Narang

first: Jun

last: Choi

first: Xiaotu

last: Ma

last: Yang

first: Stephen

last: Kelly

first: Elizabeth

last: Raetz

last: Harvey

first: Cheryl

last: Willman

first: Mignon

middle: L

last: Loh

last: Hunger

first: Patrick

last: Brown

first: Kylie

last: Getz

first: Cem

last: Meydan

first: Christopher

middle: E

last: Mason

first: Aristotelis

last: Tsirigos

last: Carroll


title: Evolution of the Epigenetic Landscape in Childhood B Acute Lymphoblastic Leukemia and Role in Drug Resistance [RNA-seq]

last: Saint Fleur-Lominy

overall_design: Primary pediatric B ALL diagnosis/relapse paired samples were used to study the evolution of the epigenome. For Cohort 2, RNA was extracted from 10 pairs using Qiagen RNeasy kit and RNAseq was run to determine relative expression levels.

last: Evensen

last: Bhatla

last: Sethia

first: Richard

first: William


title: Evolution of the Epigenetic Landscape in Childhood B Acute Lymphoblastic Leukemia and Role in Drug Resistance [ChIP-seq]

first: Shella

overall_design: Primary pediatric B ALL diagnosis/relapse paired samples were used to study the evolution of the epigenome. Two cohorts were used, the first had 14 paired patients for which traditional ChIPseq was performed for H3K4me3, H3K27ac, H3K27me3, H3K9ac,  H3K9me3, and an IgG control without replicas. For the second cohort 19 paired samples were analyzed using ChIPseq for H3K27ac, H3K27me3, H3k9ac, and an IgG control.

first: Nikki

last: Narang

last: Choi

last: Ma

last: Yang


title: Differentially expressed long non-coding RNAs and mRNAs in plasma of clear cell renal cell carcinoma patients based on microarray and bioinformatic analysis

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

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

summary: Objective: The diagnostic roles of long non-coding RNAs (lncRNAs) in clear cell renal cell carcinoma (ccRCC) are still not well defined. We aimed to identify differentially expressed lncRNAs and mRNAs in plasma of ccRCC patients and health controls systematically. Methods: Expression profile of lncRNAs and mRNAs in plasma from ccRCC patients and healthy controls was analyzed by microarray assay. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway based approaches were used to investigate biological functions and signaling pathways affected by the differentially expressed mRNAs. SOCS2-AS1 was selected for validation using Real-Time PCR. The differentially expressed genes were further compared with E-MTAB-1830 datasets by Venn and NetworkAnalyst website. The expression level and overall survival (OS) of differentially expressed mRNAs were analyzed in GEPIA and ULCAN website. Results: Compared with healthy controls, a total of 3,664 differentially expressed lncRNAs were revealed by heatmap and volcano-plot, including up-regulation in 1,511 and down-regulation in 2,153 (fold change ≥ 2 and P < 0.05), respectively. And differential expression was noticed in 2,268 mRNAs, including up-regulation in 932 mRNAs and down-regulation in 1,336 mRNAs, respectively (fold change ≥ 2 and P < 0.05). Pathways analysis based on deregulated mRNAs were mainly involved in melanogenesis and Hippo signaling pathway (P < 0.05). The expression of SOCS2-AS1 was down in ccRCC plasma and tissues, as well as in cell lines, which was the same as the results of lncRNA microarray. Compared with the E-MTAB-1830 gene expression profiles, we identified 18 lncRNAs, and 87 mRNAs were differently expressed in both plasma and neoplastic tissues of ccRCC. Ten mRNAs (EPB41L4B, CCND1, GGT1, CGNL1, CYSLTR1, PLAUR, UGT3A1, PROM2, MUC12, and PCK1) were correlated with the overall survival (OS) rate in ccRCC patients based on the GEPIA and ULCAN website.Conclusions: We first reported differentially expressed lncRNAs in ccRCC patient and healthy control systemically. Combined with the published dataset, we identified several differentially expressed lncRNAs and mRNAs which might to be diagnostic or prognostic markers. The biological functions of those lncRNAs and mRNAs should be further validated. Taken together, this study provided the basis for future treatment of ccRCC and novel insights into cancer biology.

overall_design: Five cases of ccRCC patients and 5 healthy controls were enrolled in this study. Whole blood was collected from each participant in EDTA tubes as an anticoagulant followed by centrifugation at 1,000 g for 10 min at 4°C. Plasma was then transferred to sterile polypropylene tubes on ice and centrifuged again at 10,000g for 10 min at 4°C to remove cell debris.

first: Bing

last: Zhang

first: Hong

last: Ji

first: Wei

last: Chu

first: Jingjing

last: Wang

first: Li

first: Jing

last: Zheng


title: Evolution of the Epigenetic Landscape in Childhood B Acute Lymphoblastic Leukemia and Role in Drug Resistance

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


title: Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media

city: Burnaby

first: Amy

middle: H.

last: Lee

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

summary: Pseudomonas aeruginosa causes severe multi-drug resistant infections that often lead to bacteremia and sepsis. Physiologically relevant conditions can increase the susceptibility of pathogens to antibiotics, such as azithromycin (AZM). When compared to minimal inhibitory concentrations (MIC) in lab media, AZM had a 16-fold lower MIC in tissue culture medium with 5% MHB, and a 64-fold lower MIC in this tissue culture medium with 20% human serum. AZM also demonstrated increased synergy in combination with synthetic host defence peptides DJK-5 and IDR-1018 under host-like conditions and in a murine abscess model. To mechanistically study the altered effects of AZM under physiologically relevant conditions, global transcriptional analysis was performed on P. aeruginosa with and without effective concentrations of AZM. This revealed that the arn operon, mediating arabinosaminylation of lipopolysaccharides, and related regulatory systems, were downregulated in host-like media when compared to MHB. Inactivation of genes within the arn operon led to increased susceptibility of P. aeruginosa to AZM and great increases in synergy between AZM and other antimicrobial agents, indicating that dysregulation of the arn operon might explain increased AZM uptake and synergy in host-like media. Furthermore, genes involved in central  and energy metabolism, and ribosome biogenesis were dysregulated more in physiologically relevant conditions treated with AZM, likely due to general changes in cell physiology as a result of the increased effectiveness of AZM in these conditions. These data suggest that, in addition to the arn operon, there are multiple factors in host-like environments that are responsible for observed changes in susceptibility.

overall_design: RNA-Seq of P. aeruginosa grown in MHB, RPMI+5% MHB, or RPMI+5% MHB+20% human serum with or without AZM treatment

first: Corrie

last: Belanger

first: Daniel

last: Pletzer

first: Reza

last: Falsafi

first: Robert

last: Hancock


title: Human iNSC-derived brain organoid model of lysosomal storage disorder in Niemann-Pick disease type C

city: Seoul

first: SeungEun

address: 1 Gwanak-Ro, Gwanak-gu

department: Veterinary

institute: Seoul National University

summary: Recent studies on developing three-dimensional (3D) brain organoids from stem cells have allowed the generation of in vitro models of neural disease and have enabled the screening of drugs because these organoids mimic the complexity of neural tissue. Niemann-Pick disease, type C (NPC) is a neurodegenerative lysosomal storage disorder caused by mutations in the NPC1 protein. The pathological features underlying NPC are characterized by the abnormal accumulation of cholesterol in acidic compartments, including late endosomes and lysosomes. Due to the inaccessibility of brain tissues from human NPC patients, we developed NPC brain organoids with induced neural stem cells from NPC patient-derived fibroblasts. NPC organoids exhibit significantly reduced size and proliferative ability, which are accompanied by accumulation of cholesterol, impairment in neuronal differentiation and autophagic flux and dysfunction of lysosomes; therefore, NPC organoids can recapitulate the main phenotypes of NPC patients. Furthermore, these pathological phenotypes observed in NPC organoids were reversed by treatment with valproic acid, which is known to be an effective treatment for several neurodegenerative diseases. Our data present patient-specific phenotypes in 3D organoid-based models of NPC and highlight the application of this model to drug screening in vitro.

overall_design: All brain organoids grown for 4weeks were analyzed: Wild type, NPC brain oragnoids and NPC brain organoids after VPA treatment. Three samples at week 4, each consisting of 5-7 pooled organoids, for both  and corrected. Whole transcriptome from each organoids were performed as single-end 75 sequencing using NextSeq 500  (Illumina, Inc., USA).


summary: Vaccination remains one of the most effective means of reducing the burden of infectious diseases globally. Climate change is projected to lead to an increase in the burden of vector- and water-borne, as well as zoonotic infectious diseases including COVID-19. Improving our understanding of the molecular basis for effective vaccine response is of paramount importance if we are to ensure the success of future vaccine development efforts. We applied cutting edge multi-omics approaches to characterize temporal molecular responses following vaccination with hepatitis B virus (HBV) vaccine. Data were integrated across cellular, epigenomic, transcriptomic, proteomic, and fecal microbiome profiles, and correlated to final hepatitis B antibody titres. Using both a molecular-interaction network integration method (NetworkAnalyst) and a data-driven integration approach (DIABLO), we overcame the p>>>n problem and uncovered baseline molecular patterns and pathways associated with more effective vaccine responses to HBV. Correlations were identified with signalling pathways such as JAK-STAT and interleukin signalling, Toll-Like Receptor Cascades, interferon signalling and Th17 cell differentiation. This study provides further evidence that baseline cellular and molecular characteristics of an individual’s immune system influence vaccine responses, and highlights the utility of integrating information across many parallel molecular datasets.

overall_design: A total of 75 samples (15 participants, each sampled at five time points) representing both pre- and post-vaccination blood draws.

first: Casey

last: Shannon

first: Travis

last: Blimkie

first: Rym

last: Ben-Othman

first: Nicole

last: Gladish

first: Nelly

last: Amenyogbe

first: Sibyl

last: Drissler

first: Rachel

middle: D

last: Edgar

first: Queenie

last: Chan

first: Mel

last: Krajden

first: Leonard

last: Foster

first: Michael

last: Kobor

middle: W

last: Mohn

first: Ryan

last: Brinkman

first: Kim-Anh

last: Le Cao

first: Richard

last: Scheuermann

first: Scott

last: Tebbutt

first: Wayne

last: Koff

first: Tobias

last: Kollmann

first: Manish

last: Sadarangani


title: The transcriptome profile in skeletal muscle of young male mice and aging male mice fed with or without eicosapentaenoic acid (EPA)

city: Tokyo

first: Hiroki

last: Yamazaki

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Biochemistry

institute: Keio University School of Medicine

summary: Age-related sarcopenia is associated with a variety of changes in skeletal muscle. These changes are interrelated with each other and associated with systemic metabolism, the details of which, however, are largely unknown. Eicosapentaenoic acid (EPA) is a promising nutrient against sarcopenia and has multifaceted effects on systemic metabolism. Although several human studies have suggested that EPA supplementation protects against sarcopenia, the causal relationship of EPA supplementation and an increase of muscle strength has poor evidence in vivo. We demonstrated that aging skeletal muscle in male mice shows lower grip strength and fiber type changes, both of which can be inhibited by EPA supplementation irrespective of muscle mass alteration. We hypothesized that the aging process in skeletal muscle can be intervened by the administration of EPA, via transcriptomic changes in skeletal muscle. This analysis revealed fast-to-slow fiber type transition in aging muscle, which was partially inhibited by EPA.

overall_design: Seventy-five-week-old male mice were randomly assigned to groups fed with EPA-deprived control diet (EPA-) or EPA-enriched diet with 1wt% EPA (EPA+) for 12 weeks. Twenty-four-week-old male mice were also analyzed (Young). Pooled RNA samples extracted from Gas+Pl muscle were used (Young, n = 3; EPA-, n = 6; EPA+, n = 6).

first: Mayu

last: Nishimura

first: Masaaki

last: Uehara

first: Akiko

last: Kuribara-Souta

first: Motohisa

last: Yamamoto

first: Noritada

last: Yoshikawa

first: Ken-ichirou

last: Morohashi

first: Hirotoshi

last: Tanaka


title: Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: Purpose   Immune reactions following corneal transplantation are the most common cause of transplant failure. However, the underlying mechanisms of corneal graft rejection are not yet fully understood but increasing evidence points to a crucial role of the innate immune system in this context. Using a human in vitro model, we aimed to assess the response of human macrophages to stimulation with human corneal tissue and whether corneal endothelial cells (CEC) have immune-modulating properties.  Methods   Human monocytes were isolated from peripheral blood mononuclear cells (PBMC) and differentiated into monocyte-derived macrophages (MDM). A standardized protocol was used for disintegration of human corneas into fragments of defined sizes. MDMs were stimulated using processed corneal material with or without CEC. Lipopolysaccharide (LPS) or interferon-gamma (IFNγ) served as controls. RNA sequencing was applied to analyze the impact of differential stimulation of MDMs on their transcriptional profile.  Results  The transcriptional profile of MDMs was significantly modulated by the type of stimulus used for MDM activation as well as by the individual donor. LPS- or IFNγ-stimulation resulted in distinct transcriptional alterations compared to unstimulated MDMs including an upregulation of various cytokines such as CXCL9 and CCL3, 4, 5 and 19. Corneal tissue induced the differential expression of 45 genes when compared to unstimulated MDMs, with several metallothioneins (MTs) among the upregulated factors (MT1A, MT1E, MT1F, MT1G, MT1H, MT1L, MT1M, MT1X, MT2A). This effect was independent of the presence or absence of CEC.  Conclusions   The MDM in vitro model proved to be a robust tool to study the effects of LPS, IFNγ and corneal tissue homogenates on the transcriptional activity of MDM. Human macrophages showed a distinct upregulation of various MTs when challenged with human corneal allogen with or without corneal endothelium, which might have an immune-modulatory effect. As a general observation, it appears that in MDM-based studies a significant donor-dependent effect on the transcriptional profile of MDMs needs to be considered and adjusted before downstream analysis.

overall_design: MACE RNA sequencing of 25 human MDM-samples (5 each stimulated with LPS, IFNg, corneal tissue with endothelium, corneal tissue without endothelium and 5 unstimulated MDM samples).

first: Julian

last: Wolf

first: Xinyu

last: Zhuang

first: Antonia

last: Hildebrand

first: Stefaniya

last: Boneva

first: Paola

middle: K

last: Betancor

first: Jiaqi

last: Fan

first: Daniel

last: Böhringer

first: Philip

last: Maier

first: Thomas

last: Reinhard

first: Günther

last: Schlunck

first: Thabo

last: Lapp


title: Increased expression of myelin-associated genes in frontal cortex of SNCA overexpressing rats and Parkinson’s disease patients

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

summary: Parkinson’s disease is an age-dependent neurodegenerative disorder. Besides characteristic motor symptoms, patients suffer from cognitive impairments linked to pathology in cortical areas. Due to obvious challenges in tracing molecular perturbations underlying alterations in human brain over time, we took advantage of a well-characterized rat model. Using RNA sequencing, we profiled the frontocortical transcriptome of post-mortem patient samples and aligned expression changes with perturbation patterns obtained in the model at 5 and 12 months of age reflecting a presymptomatic and symptomatic time point. Integrating cell type-specific reference data, we identified a shared expression signature between both species that pointed to oligodendrocyte-specific, myelin-associated genes. Drawing on longitudinal information from the model, their nearly identical upregulation in both species allowed tracing them to two distinctive perturbance modes they originate from. While one mode exhibited age-independent alterations that affected genes like PLP1, the other mode, impacting on genes like MAG, was characterized by interferences of disease gene and adequate adaptations of gene activity along ageing. Our results highlight that even for a small set of functionally linked genes distinct interference mechanisms may underly disease progression that cannot be distinguished by examining the terminal point alone but instead require longitudinal interrogation of the system.

overall_design: Differential gene expression of frontocortical samples was analyzed in samples of 5- and 12-month-old rats. For each time point, 5 wild-type and 5  transgenic rats overexpressing human SNCA were profiled and analyzed.

last: Hentrich


title: RNA-Seq of vocal folds of rabbits exposed to a low relative humidity environment

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

summary: The purpose of this study is to investigate if acute mucosal dehydration as a funcition of low relative humidty environment impacts the vocal folds at the mRNA level. Rabbits were used as animal model to enable a systematic and rigorous assessment of the pathobiology of vocal fold hydration since they can be manipulated in a physiologically realistic manner. We anticipate that the results of this study will help to elucidate the effects of altered mucosal hydration state in response to low ambient humidity on vocal fold epithelium, lamina propria and muscle tissue at the transcriptome level. Together with cellular, structural, and functional techniques that are part of this project, we expect to provide validated scientific recommendations on the adverse effects of mucosal dehydration and the therapeutic benefits of hydration.

overall_design: The transcriptome of vocal folds of rabbits that were exposed to low relative humidity (n=6) were compared to those from rabbits held at a standard ambient humidity (n=6).

first: Taylor

last: Bailey

first: Preeti

last: Sivasankar

first: Abigail

last: Cox

first: Thimmapuram

last: Jyothi

first: Xie

last: Shaojun


title: Transcriptomic profiling of wild type, sigG1 and rsfG mutants of Streptomyces tsukubaensis in liquid culture

city: Porto

first: Marta

middle: V.

last: Mendes

address: Rua Alfredo Allen, 208

country: Portugal

institute: i3S - Instituto de Investigação e Inovação em Saúde

summary: The aim of this work was to compare gene expression of wild type, sigG1 and rsfG mutants, to determine the SigG1-dependent genes in Streptomyces

overall_design: S. tsukubaensis RNA-seq data, generated using na Illumina Hiseq 4000 platform

first: R

last: Oliveira

first: M

middle: V


title: Next Generation Sequencing Facilitates Quantitative Analysis of SiHa cells with or without circCDKN2B-AS1 knockdown

city: Hangzhou

first: Yanan

last: Zhang

state: Zhejiang

address: No. 1 Xueshi Road - Shangcheng

institute: Women’s Hospital, School of Medicine, Zhejiang University

summary: circCDKN2B-AS1 is significantly upregulated circRNA in HPV16 positive cervical cancer tissues comprared with both HPV16 positive and HPV16 negative normal cervical tissues.So we chose it for further study.To explore the mRNA expression profiles  following circCDKN2B-AS1 knockdown, we performed RNA sequencing analysis in SiHa cells with or without circCDKN2B-AS1 knockdown.We performed  RNA sequencing in two pairs of RNA samples  of SiHa cells with or without circCDKN2B-AS1 knockdown.

overall_design: RNA sequencing following circCDKN2B-AS1 knockdown in SiHa cells with or without circCDKN2B-AS1 knockdown,2 cases in each group  were generated by deep sequencing, using Illumina Hiseq 4000


title: Identifying SigG1 binding sites in Streptomyces tsukubaensis

summary: The aim of this work was to determine where SigG1 binds within the S. tsukubaensis chromosome

overall_design: S. tsukubaensis ChIP-seq data, generated using an Illumina Novaseq 6000 platform

first: G

last: Chandra


title: Decoding Human Megakaryocyte Development

city: TianJin

first: Changlu

last: Xu

state: TianJin

address: 288 Nanjing Rd, Heping

department: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Despite our growing understanding of embryonic immune development, rare early megakaryocytes (MKs) remain relatively understudied. Here we used single-cell RNA sequencing of human MKs from embryonic yolk sac (YS) and fetal liver (FL) to characterize the transcriptome, cellular heterogeneity, and developmental trajectories of early megakaryopoiesis. In the YS and FL, we found heterogeneous MK subpopulations with distinct developmental routes and patterns of gene expression that could reflect early functional specialization. Intriguingly, we identified a subpopulation of CD42b+CD14+ MKs in vivo that exhibit high expression of genes associated with immune responses and can also be derived from human embryonic stem cells (hESCs) in vitro. Furthermore, we identified THBS1 as an early marker for MK-biased embryonic endothelial cells. Overall, we provide important insights and invaluable resources for dissection of the molecular and cellular programs underlying early human megakaryopoiesis.

overall_design: Here, we performed droplet-based and mouth pipette picked scRNA-seq of over 50,000 cells to firstly construct a molecular landscape and dissecting the heterogeneity of MK in human embryos.

first: Hongtao

last: Wang

first: Jian

last: He

first: Xiaoyuan

last: Chen

first: Hua

last: Yang

first: Lihong

last: Shi

first: Bing

last: Liu

first: Jiaxi

last: Zhou


title: Gene expression profile of ileum, jejunum and colon

city: Qingdao

first: Shichao

last: Xing

address: No.167, Wutai Mountain Road,

institute: Affiliated Hospital of Qingdao University

summary: The gene expression of ileum, jejunum and colon.

overall_design: Examination of different gene expression.

first: Qiulan

last: lv


title: Transcriptome and Epigenome Characterization of Long Term Trained Immunity in Cotrolled Human Malaria Model

city: Nijmegen

first: Hendrik

middle: G.

last: Stunnenberg

address: Geert Grooteplein 30

institute: Radboud University Nijmegen

overall_design: Refer to individual Series


title: Single-cell RNAseq analysis of pericyte-deficient endothelium

city: Uppsala

first: L.

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: We applied scRNAseq analysis to investigate how the brain mural cell deficiency established in Pdgfb ret/ret mice affects the endothelial cell phenotype.

overall_design: Single endothelial cells from control and pericyte-deficient 3-month-old mouse brains were sorted into 384-well-plates and RNA-sequenced using the SmartSeq2 method

first: Maarja

last: Andaloussi Mäe

first: Michael

last: Vanlandewijck

first: Liqun

first: Christer

last: Betsholtz


title: Next Generation Sequencing Facilitates Quantitative Analysis of Bone Marrow-Derived Macrophage Transcriptomes

first: Yujia

address: Yuhangtang Road No.388

institute: Zhejiang University

summary:
Purpose:The purpose of this study is to detect activated or silenced genes during lncRNA-GMR-deficient  Bone marrow-derived macrophages  and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis.Macrophages RNA profiles were generated by deep sequencing,using Illumina.
Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between lncRNA-GMR-deficient macrophages and the control cells.

overall_design: Bone marrow-derived macrophage  mRNA profiles of wild type (WT) and lncRNA-GMR -/- mice were generated by deep sequencing.

first: Xuetao

last: Cao


title: Transcriptome and Epigenome Characterization of Long Term Trained Immunity in Cotrolled Human Malaria Model [ChIP-seq]

summary: Innate immune memory responses (also termed ‘trained immunity’) have been described in monocytes after BCG vaccination and after stimulation in vitro with microbial and endogenous ligands such as muramyl dipeptide, β-glucan, oxidized LDL, and MSU crystals. Whether clinical infections are also capable of inducing a trained immunity phenotype has not been studied. We evaluated whether Plasmodium falciparum infection can induce innate immune memory by assessing monocyte epigenetic, transcriptional and functional (cytokine production) programs from five volunteers undergoing controlled human malaria infection. During acute infection monocytes produced lower amounts of inflammatory cytokines upon secondary stimulation, but 36 days after malaria infection they produced significantly higher IL-6 and TNF-α in response to various stimuli. Furthermore, transcriptomic and epigenomic data analysis revealed a clear reprogramming of monocytes after malaria infection. Plasmodium challenge induces a long-term deposition of H3K4me3 at the promoter regions of several inflammatory genes of monocytes, these changes remaining stable for several weeks after infection. These findings demonstrate an epigenetic basis of trained immunity in the model of controlled in vivo human malaria infection.

overall_design:
Time Course analysis (Day 0, Day 9, Day 36) of transcription (RNA-seq) and epigenetic (H3K4me3 ChIP-seq) status of human monocytes undergoing controlled malaria infection in order to identify the underlying mechanism of trained immunity.

**Raw data not provided due to patient privacy concerns**

first: Jona

last: Walk

first: Farid

last: Keramati

middle: G

first: Robert

last: Sauerwein


title: Gene expression analysis of miR-214 over-expressing melanoma cells (MA-2)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

summary: Growing evidence shows a strong interplay between post-transcriptional regulation, mediated by miRs and epigenetic regulation. Nevertheless, the number of experimentally validated miRs (called epimiRs) involved in these regulatory circuitries is still very small. Material & methods:We propose a pipeline to prioritize candidate epi-miRs and to identify potential epigenetic interactors of any given miR starting from miR transfection experiment datasets. Results & conclusion: We identified 34 candidate epi-miRs: 19 of them are known epi-miRs, while 15 are new. Moreover, using an in-house generated gene expression dataset, we experimentally proved that a component of the polycomb-repressive complex 2, the histone methyltransferase enhancer of zeste homolog 2 (EZH2), interacts with miR-214, a well-known prometastatic miR in melanoma and breast cancer, highlighting a miR-214-EZH2 regulatory axis potentially relevant in tumor progression.

overall_design: Gene expression profiling was carried out on controls and miR-214 overexpressing cells by using the Whole Human Genome Microarray platform (G4112F, Agilent Technologies). Total RNA was obtained from approximately 106 cells  for each biological replicate. Three biological replicates were analyzed for controls and miR-214 overexpressing cells respectively for a total of  12 microarray experiments.

first: Elisa

last: Penna

first: Francesca

last: Orso

first: Federico

last: Virga

first: Daniela

last: Taverna


title: Transcriptome and Epigenome Characterization of Long Term Trained Immunity in Cotrolled Human Malaria Model [RNA-seq]


title: LINC00266-1-encoded peptide regulates mRNA splicing

city: Guangzhou

first: Guang-Rong

last: Yan

state: Guangdong

address: 63 Duobao Road

institute: Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University

summary: The mRNA transcriptome profiling and splicing profiling mediated by LINC00266-1 and LINC00266-1-encoded peptide were investigated by RNA-seq.

overall_design: The mRNA profiles and mRNA splicing profiles of colon cancer cells HCT-116 (NC), HCT-116 with stably expressing LINC00266-1 ORF for encoding peptide (ORF), and HCT-116 with stably expressing 5'UTR-ORFmut in which start code ATG for encoding peptide was mutated to ATT (MT), were generated by RNA-sequencing (RNA-seq), in triplicate, using Illumina.

first: Song

last: Zhu

first: Jizhong

last: Wang


title: Shared roles for Scl and Lyl1 in murine platelet production and function

city: Clayton

first: Nicholas

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

summary: The Stem Cell Leukemia (Scl or Tal1) protein forms part of a multimeric transcription factor complex required for normal megakaryopoiesis. However, unlike other members of this complex such as Gata1, Fli1 and Runx1, mutations of Scl have not been observed as a cause of inherited thrombocytopenia. We postulated that functional redundancy with its closely related family member, Lymphoblastic Leukemia 1 (Lyl1) might explain this observation. To determine if Lyl1 can substitute for Scl in megakaryopoiesis, we examined the platelet phenotype of mice lacking one or both factors in megakaryocytes. Conditional Scl knockout mice crossed with transgenic mice expressing Cre recombinase under the control of the mouse platelet factor 4 (Pf4) promoter generated megakaryocytes with markedly reduced but not absent Scl. These Pf4SclcKO mice had mild thrombocytopenia and subtle defects in platelet aggregation. However, Pf4SclcKO mice generated on a Lyl1-null background (double knockout, DKO mice) had severe macrothrombocytopenia, abnormal megakaryocyte morphology, defective pro-platelet formation and markedly impaired platelet aggregation. DKO megakaryocytes, but not single knockouts, had reduced expression of Gata1, Fli1, Nfe2 and many other genes that cause inherited thrombocytopenia. These gene expression changes were significantly associated with shared Scl and Lyl1 E-box binding sites that were also enriched for Gata1, Ets and Runx1 motifs. Thus, Scl and Lyl1 share functional roles in platelet production and function by regulating expression of partner proteins including Gata1 and Fli1. We propose that this functional redundancy provides one explanation for the absence of Scl and Lyl1 mutations as a cause of inherited thrombocytopenia.

overall_design: Three-replicate primary megakaryocyte cultures from mice with the following genotypes: wildtype, Scl/Tal1 Knockout, Lyl1 knockout and double Scl/Tal1/Lyl1 knockout were subjected to mRNA Seq analysis.

first: Sung

last: Chiu

first: David

last: Curtis


title: GSTM1 binding RNA RIP-seq

summary: GSTM1 binding RNAs were analyzed by imprinting RNA-sequencing of specific antibody-retrieved complexes from  peritoneal macrophage cells lysis.

overall_design: Examination of GSTM1 binding sites in RNA transcriptome of macrophages


title: Gene expression underlying differential adult brain morphogenesis in honeybee castes

city: Alfenas

first: Angel

middle: Roberto

last: Barchuk

state: Minas Gerais

address: Rua Gabriel Monteiro Silva 700, Campus Unifal

department: Cell and Developmental Biology

country: Brazil

institute: Federal University of Alfenas

summary: Learning and memory-related skills that honeybees use for navigation, foraging and other activities are associated with a central region of the brain, the mushroom bodies, which are relatively more developed in workers than in queens. During larval period, however, the differential feeding offered to prospective queens promotes faster brain development and higher expression of several neurogenic genes (ataxin-2, cryptocephal, dachshund, Eph Receptor, fax, shot, krüppel homolog-1 and tetraspanin 5D). It seems that in some point during pupation there happens a shift in this trend. In fact, queen’s brain experiences net cell death rates while worker’s brain is favored by higher rates of cell proliferation, resulting in caste specific brains. Here we report on transcriptomic results which might represent the molecular underpinnings of the differential brain development between castes. Genome-wide expression analyses using oligonucleotide microarray approach show an opposite pattern to that observed during larval development, with workers’ brain with higher transcription levels of 324 genes (e.g., mesencephalic astrocyte derived neurotrophic factor, minibrain, signal peptide peptidase, and tumbleweed, all associated to neurogenic events or cell death prevention). This suggests that somehow the respective gene products promote differential development of honeybee brain. MANF, for example, a gene superexpressed in workers’ brain, encodes a protein with a domain homologous to SAP Ku70 C-terminal domain. Since this molecule is an inhibitor of apoptotic protein Bax, MANF is a candidate to act as an anti-apoptotic factor during worker brain development (extensive cell death events characterize queens’ pupal brain). Minibrain encodes a protein-kinase involved in regulating cell division during post-embryonic neurogenesis, and is another candidate to participate in the mechanism responsible for the reversing the brain size/body volume rate between queens and workers. Moreover, we assessed by RT-qPCR the transcription profile of the ecdysone receptor (which mediates ecdysteroid action and is probably involved in differential brain cell death/proliferation between castes) variants A and B in three time points during pupal development. Our results suggest the existence of a hormone/receptor threshold above which (hormone excess), in queens, it would be triggered more cell death than proliferation events, which through the differential participation of effector genes, would lead to the morphological differences between adult queens’ and workers’ brain.

overall_design: RNA samples from pools of brains from pharate-adult queens and workers were hybridized in pairs and in dye-swaps (Cy3/Cy5), twice, then, combined in silico.

first: Ana

last: Bomtorin

first: Zilá

middle: P

last: Simões


title: Microarray expression profile of long non-coding RNAs in human lung adenocarcinoma

city: Weifang

first: chonggao

last: Yin

state: Shan dong

address: No.7166,Baotongxi Street

institute: Weifang medical university

summary: To determine the lncRNA expression profile in Lung adenocarcinoma (LAD) with or without lymph node metastasis and matched non-tumor tissues, we uesed lncRNA microArray analysis form Arraystar to examine the expression of lncRNAs in LAD with or without lymph node metastasis and matched non-tumor tissues.

overall_design: Lung adenocarcinoma tissues from LAD surgery were distributed into three experimental groups: normal lung tissue group,LAD tissues without lymph node metastasis group,and LAD tissues with lymph node metastasis group, then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar)

first: Zhiyi

last: Yang

first: Hongli

last: Li

first: Zhaoyan

first: Yuling

first: Jie

last: Niu

first: Zhiliang

last: Sun

first: Chonggao


title: Effect of short-term hyperglycemia on primary fetoplacental endothelial cells (fpEC) isolated from human placenta arteries

status: Public on Dec 20 2020

city: Graz

first: Ursula

last: Hiden

address: Auenbruggerplatz 14

department: Obstetrics and Gynecology

country: Austria

institute: Medical University of Graz

summary: In order to investigate the effect of in vitro hyperglycemia on gene expression of fpEC, cells were treated with hypergylcemia (25mM) for 24h.

overall_design: 5 different isolations of primary fpEC (800,000) were split in two gelatin coated 75cm2 culture flasks in EBM medium. After 24h, medium was replaced either by normoglycemic EBM (5.5mM D-glucose) or with EBM containing 25mM D-glucose. After 24h, RNA was isolated using TRI REAGENT. 5µg RNA of all control conditions and 5µg of each hyperglycemic treatment was pooled and the pools used for the microarray experiment.

first: Silvija

last: Cvitic


title: Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic

city: Durham

first: Aashutosh

last: Vihani

state: NC

address: 264 CARL Building

institute: Duke University

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


title: Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic [RNA-Seq of whole olfactory mucosa]

summary: Understanding how genes and experiences work in concert to generate phenotypic variability will provide a better understanding of individuality. Here, we considered this in the context of the main olfactory epithelium, a chemosensory structure with over a thousand distinct cell types, in mice. We identified a subpopulation of at least three types of olfactory sensory neurons, defined by receptor expression, whose abundances were sexually dimorphic. This subpopulation of olfactory sensory neurons was over-represented in sex-separated female mice and responded robustly to the male-specific semiochemicals 2-sec-butyl-4,5-dihydrothiazole and (methylthio)methanethiol. Sex-combined housing led to a robust attenuation of the female over-representation. Testing of Bax-/- mice revealed a Bax-dependence in generating the sexual dimorphism in sex-separated mice. Altogether, our results suggest a profound role of experience and activity in influencing homeostatic mechanisms to generate a robust sexually dimorphic phenotype in the main olfactory epithelium.

overall_design: RNA-Seq of whole olfactory mucosa from sex-separated and sex-combined male and female mice.

first: Hiroaki

last: Matsunami


title: Gene expression profiling in murine mononuclear phagocyte lineage cells

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

summary: To understand the mechanism underlying monocyte and dendritic cell development through the regulation of Irf8 expression by the 56 kb downstream (+56 kb) Irf8 enhancer, we performed transcriptome analysis of bone marrow cells and splenocytes from wild-type, the Irf8 +56 kb enhancer-deficient, and IRF8-deficient mice. Taken together with the epigenetic profiling of mononuclear phagocyte lineage cells in these mice, the Irf8 +56 kb enhancer-mediated high Irf8 expression in hematopoietic progenitor cells promote type 1 classical dendritic cell (cDC1) differentiation, while low Irf8 expression in progenitors led to Ly6C+ monocyte development.

overall_design: RNA from murine hematopoietic stem cells (HSC), multipotent progenitors (MPP), granulocyte-monocyte progenitors (GMP), common dendritic cell progenitors (CDP), common monocyte progenitors (cMoPs), Ly6C+ monocytes (Mo), classical dendritic cells (cDC), and neutrophils (Neu) were isolated from wild-type, the +56 kb Irf8 enhancer-deficient (d+56kb), or IRF8-deficient (IRF8KO) mice was subjected to RNA-seq (biological duplicates for each cell type).

first: Akira

last: Nishiyama

first: Haruka

last: Sasaki

first: Daisuke

last: Kurotaki

first: Koichi

last: Murakami


title: Genome wide profiling of chromatin accessibilities in murine mononuclear phagocyte lineage progenitor cells

summary: To understand the mechanism underlying monocyte and dendritic cell development through the regulation of Irf8 expression by the 56 kb downstream (+56 kb) Irf8 enhancer, we analyzed chromatin accessibility of bone marrow cells from wild-type and Irf8-/- mice. Combined with the epigenetic profiling by H3K27 acetylation ChIP-seq, the +56 kb enhancer opens at LMPP stage, and gets activated at its highest level in mononuclear phagocyte lineage progenitor cells.

overall_design: Purified transposed DNA from murine long-term hematopoietic stem cells (LT-HSC), lymphoid-primed multipotent progenitors (LMPP), monocyte-dendritic cell progenitors (MDP), common dendritic cell progenitors (CDP) in wild-type (WT) mice was subjected to ATAC-seq (biological duplicates for each cell type).


title: Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic [pS6-IP-Seq of whole olfactory mucosa]

overall_design: Phosphorylated S6 ribosomal subunit capture and associated mRNA profiling (pS6-IP-Seq) on whole olfactory mucosa after odorant exposure.


title: An epigenetic mechanism underlying chromosome 17p deletion-driven tumorigenesis

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Chromosome copy number variations are a hallmark of human cancers and among them chromosome 17p loss is the most common one and associated with poor prognosis. Our previous work demonstrates that 17p deletions can promote tumorigenesis more than p53 loss. Herein, with multiple functional genetic strategies, we identify a new 17p tumor suppressor, PHD finger protein 23 (PHF23). PHF23 deficiency impaires B cell differentiation and promotes Myc-driven lymphoma. Mechanistically, PHF23, a H3K4me3 reader, directly binds and represses the deacetylation activity of the SIN3-HDAC complex through its N-terminus, which coordinates two major active histone markers H3K4me3 and H3K27ac for activation of downstream B cell-differentiation genes and tumor suppressors. Further, we show that dysregulation of the PHF23-SIN3-HDAC complex is essential for PHF23 deficiency-induced tumorigenesis and maintenance. Hence, our study reveals a novel epigenetic regulatory mechanism that contributed to the pathology of 17p deleted cancers and suggests novel susceptibility of this miserable disease.

overall_design:
Bulk RNAseq on shPhf23 and shRen(control) in both pre-B cells and lymphoma cells.
Bulk RNAseq on Hdac_inhibitor-treated lymphoma cells.  CHIP-seq on PHF23, HDAC1, H3K4me3 and H3K27ac in Ba/F3 cells.  Drug 264 is Chidamide (Tucidinostat); drug 67 is Entinostat.

first: Mei

last: Chen

first: Xuelan

first: Xiangyu

first: Chong

first: Yu

last: Liu


title: Genome wide profiling of active enhancers and IRF8-binding sites in murine mononuclear phagocyte lineage cells

summary: To understand the mechanism underlying monocyte and dendritic cell development through the regulation of Irf8 expression by the 56 kb downstream (+56 kb) Irf8 enhancer, we performed epigenetic profiling of bone marrow cells and splenocytes from wild-type, the Irf8 +56 kb enhancer-deficient, and IRF8-deficient mice. Taken together with the transcriptome analysis of mononuclear phagocyte lineage cells in these mice, the Irf8 +56 kb enhancer-mediated high Irf8 expression in hematopoietic progenitor cells promote type 1 classical dendritic cell (cDC1) differentiation, while low Irf8 expression in progenitors led to Ly6C+ monocyte development. In addition, IRF8 ChIP-seq of mature cDC1s and monocytes suggested that IRF8 regulates enhancers in cooperation with different transcription factors in each lineage in its expression level.

overall_design: Murine Lin- Sca1+ CD117+ (LSK), lymphoid-primed multipotent progenitors (LMPP), granulocyte-monocyte progenitors (GMP), common dendritic cell progenitors (CDP), common monocyte progenitors (cMoPs), Ly6C+ monocytes (Mo), classical dendritic cells (cDC), and neutrophils (Neu) were isolated from wild-type, the +56 kb Irf8 enhancer-deficient (d+56kb), or IRF8-deficient (IRF8KO) mice, and the immunoprecipitated chromatin from these cells was subjected to ChIP-seq (biological duplicates for each cell type).


title: RNA-seq identifies a distinct response in macrophages stimulated from phagosome with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis

city: Chongqing

first: Fake

state: Chongqing

address: Changjiangzhilu 10 Yuzhong District

department: Clinical Laboratory Medicine

institute: Daping Hospital

summary:
Purpose: The goals of this study are to obtain the NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages, which were stimulated from phagosome with early secreted antigenic target 6-KDa (ESAT6)
Methods: First we fabricated a nanocapsule enclosing ESAT6 (nESAT6) and a nanocapsule enclosing BSA (nBSA) as control. mRNA profiles of THP-1 macrophages treated with nESAT6 were generated by deep sequencing, using Illumina Hiseq3000. The sequence reads that passed quality filters were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0). Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15), and normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package edgeR. qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 23 million sequence reads per sample to the human genome (GRCh38/hg38) and identified 25,343 transcripts.
Conclusions: Our study represents the first detailed analysis of transcriptomes for macrophages response to ESAT6 stimulation in phagosome, generated by RNA-seq technology.

overall_design: NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to early secreted antigenic target 6-KDa (ESAT6) stimulation in phagosome.

first: Ming


title: Genome Engineering for Enhancing Recombinant Protein Expression in E.coli

city: New Delhi

last: Mukherjee

state: Delhi

address: New Mehrauli Road, Munirka

department: School of Biotechnology

institute: Jawaharlal Nehru University (JNU)

summary: Overall aim of this study was to investigate the role of up-regulated genes  in the generation of cellular stress response that is triggered upon induction of recombinant protein synthesis. Up-regulated genes identified previously by transcriptomic analysis,  were knocked out from the host genome  and their impact on cellular health and  expression capabilities was analyzed. Transcriptomic profiling of  the top performing  double knock out (∆(elaA+cysW)  having significantly higher  protein expression levels was compared with the control to demonstrate the ability of this knock-out strain to counter cellular stress.

overall_design: Total RNA obtained was isolated from control (E.coli BW25113), single knock-out strains i.e. ∆elaA & ∆cysW & the combined  double knock-out (∆elaA+∆cysW) . Samples were collected at two time-points i.e. pre-induction(0h) & post-induction(6h). Total  9 samples  were sent to AgriGenome for library preparation & RNA sequencing.

first: Priyanka

last: Jain

first: Ashish

last: Sharma

first: Esha

last: Shukla

first: Madhulika

last: Verma

first: K

middle: J