title: Effect of forkhead box M1 in multiple myeloma

city: Little Rock

first: Yan

last: Cheng

state: Arkansas

address: 4301 W. Markham St.

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

summary: Forkhead Box M1 (FOXM1) is a promising molecular target for high-risk multiple myeloma and relapse and refractory myeloma, but whether FOXM1 is essential in myeloma has not yet been established. To address this knowledge gap, we used Western blotting to measure FOXM1 protein levels in 11 human myeloma cell lines (HMCLs) and then chose the two lines expressing the largest amount of the transcription factor, OPM2 and Delta47, for gene editing using CRISPR-Cas9. In both cases, two independent FOXM1-deficient daughter lines, designated KO-1 and KO-2, were generated. They contained 2 different 10-bp deletions at the target site of their respective guide RNA in case of OPM2 and a 10-bp deletion and 1-bp insertion in case of Delta47. Western analysis confirmed the lack of FOXM1 in all knockout clones. FOXM1-deficient myeloma cells proliferated more slowly than their parental counterparts containing normal levels of FOXM1. Moreover, we added back FOXM1 to FOXM1-KO cells by transfection of a constitutively expressed FOXM1c cDNA gene. The reconstituted OPM2 and Delta47 cells, designated FOXM1 KO-R contained high amounts of FOXM1 protein. Here, we used these cell lines to investigate the role of FOXM1 in regulating the gene expression in multiple myeloma.

overall_design: Three CRISPR-modified synthetic single guide RNAs (gRNAs) were purchased from Synthego to target FOXM1 exon 2. RNA sequences, 5’ to 3’, were as follows: UUG AGA AUC AGU GGC CGA CG, UGA GAA UCA GUG GCC GAC GG and UAA UGA AAA CUA GCC CCC GU. Guide RNA was complexed individually with Cas9 protein (a kind gift from Dr. Miles Pufall, Department of Biochemistry, University of Iowa) to make ribonucleoprotein (RNP). OPM2 and Delta47 cells were electroporated with RNP using a Lonza 4D-Nucleofector in CM-138 mode and individual knock out clones were selected by limited dilution and then verified using Western blotting and Sanger sequencing. For reconstituting of FOXM1, the FOXM1-KO cells were transfected with lentivirus containing a gene expression vector encoding FOXM1c by spininfection and then fractionated based on GFP expression using a cell sorter. Total RNA from those cells were extracted using the RNeasy Plus mini kit from Qiagen and then sent to BGI for RNA sequencing and bioinformatic analysis.

first: Krista

last: Thornton

first: Siegfried

last: Janz


title: The different mRNA expression between cervical cancer tissues and normal cervical tissues

status: Public on Jul 14 2021

city: beijing

first: chunliang

last: Shang

address: 49 North Garden Rd.,Haidian District Beijing ,P.R.China

country: China

institute: peking university third hospital

summary: To investigate the differences in mRNA profiles specially related to metabolism in cervical cancer, 5 primary cervical cancer tissues and 6 normal cervical tissues were collected. The differential expression of metabolism-associated-mRNA was verified using qRT-PCR.

first: Chunliang

first: Jiaming

last: Huang


title: Transcriptome analysis in DNMT3A and 3B mutant female human pluriopotent stem cells.

status: Public on Jul 15 2021

city: Isehara-shi

first: Atsushi

last: Fukuda

country: Japan

institute: Tokai University

type: Expression profiling by high throughput sequencing

summary: We report that the effect of deletion of de novo DNA methyltransferases on transcriptome status in female human ES cell and iPS cell by bulk RNA-sequencing.

overall_design:
Examination of gene expression levels in female human ES cell and iPS cell.

Definitions:
"Eroded" means the cells showing erosion of dosage compensation of X-chromosome inactivation.
"Non-eroded" means that the cells that retain normal X-chromosome inactivation (i.e. the cells does not show erosion of dosage compensation of X-chromosome inactivation).


title: MLL-fusion-mediated activation of FLT3-ITD lesions promotes leukemogenesis

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

country: USA

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: MLL-rearranged (MLL-r) leukemia, a particularly intractable disease, depends on DOT1L-mediated H3K79 methylation. Depletion of this transcriptionally activating mark by DOT1L loss-of-function or high concentrations of highly-specific inhibitor pinometostat (≥1 mM EPZ5676) leads to the downregulation of HOXA9 and MEIS1, and consequent reduction leukemia survival. .  Yet, some MLL-r cell lines are inexplicably susceptible to low-dose pinometostat, below the threshold for downregulating these canonical oncogenic drivers. Here we define alternative pathways disrupted by low-dose pinometostat (10 nM), a concentration that reduces proliferation of the MLL-r MV4;11 cell line without affecting HOXA9 and MEIS1 expression and downregulates a subset of MLL-fusion targets including FLT3, one of the most commonly mutated genes in leukemia. Using quantitative ICeChIP-seq, we observe profound H3K79me2 depletion at downregulated MLL-r targets, with resulting increases in transcriptionally activating H3K4me3 at promoters and reductions in repressive H3K27me3. The presence of co-occurring activating FLT3 mutations, portend greater cytotoxicity to inhibitor treatment. Although downregulation of polycomb components modestly contributes to reductions in proliferation, overexpression of constitutively active STAT5A, a target of FLT3-ITD-signalling, nearly completely rescues proliferation, accounting for the bulk of cytotoxicity from H3K79me2 depletion. We also observe a dependence of FLT3-STAT5A signaling on MLL function, suggesting that the FLT3 locus is exquisitely sensitivity to both H3K79me2 and H3K4me3 depletion and arguing that combinations of DOT1L, MLL1 and FLT3 inhibitors should be explored for treating the ~30% of all leukemias that carry FLT3 mutations.

overall_design: Examination of histone modifications by calibrated ChIP-seq in MV4;11 cells with and without methyltransferase inhibitor

first: William

middle: F

last: Richter

middle: N

first: Alexander

middle: J

last: Ruthenburg


title: Transcriptome Analysis of Kidney Grafts Subjected to Normothermic Ex-Vivo Kidney Perfusion

city: Toronto

first: Markus

last: Selzner

state: Ontario

address: 200 Elizabeth St.,

country: Canada

institute: Toronto General Hospital Research Institute

summary: Normothermic ex-vivo kidney perfusion (NEVKP) has demonstrated superior outcomes for donation-after-cardiovascular death (DCD) grafts compared to static cold storage (SCS). To determine the mechanisms responsible for this, we performed an unbiased genome-wide microarray analysis. Kidneys from 30kg-Yorkshire pigs were subjected to 30min of warm ischemia followed by 8hrs of NEVKP or SCS, or no storage (NS), prior to auto-transplantation. mRNA expression was analyzed on POD3 renal biopsies.

overall_design: Porcine right sided kidneys were subjected to 30minutes warm ischemia, then removed and flushed. For the No Storage group (N=3 animals), the kidneys were immediately re-implanted. In the SCS group (N=3 animals), the kidneys were subjected to 8 hours of static cold storage prior to auto-transplantation. In the NEVKP group (N=3 animals), the kidneys were subjected to 8 hours of Normothermic Ex-Vivo Kidney Perfusion prior to auto-transplantation. In all animals (N=9), the contralateral (left) kidney was removed at the time of auto-transplantation. Kidney biopsies were collected at post-operative day 3 and subjected to expression profiling by microarray. To characterize the gene expression changes, comparisons were made between SCS and NS,  NEVKP and NS respectively, as well as between NEVKP and SCS.

first: Caitriona

last: McEvoy

first: Peter

last: Urbanellis


title: Analysis of the transcriptome response to drought in Larix kaempferi using single-molecule long read isoform sequencing with de novo RNA-seq reads [RNA-Seq]

city: Harbin

first: Jingli

last: Yang

address: Hexing Road 51

institute: Northeast Forestry University

summary: Larix kaempferi is important afforestation species in northeastern China and is one of the most drought-tolerant pine species.Larix kaempferi has a very complex genetic background and a large genome, and study on the molecular mechanisms of drought resistance is still lag behind. Four-month-old of L. kaempferi seedlings grown in the greenhouse into two groups, the drought treatment group was no watering for 14 d (D14), while normally watered seedlings were used as control group (CK). All plants harvested on the same day and at the same time for the upper part of seedling (circa 3 cm from the top), frozen in liquid nitrogen. We designed six samples (CK-1, CK-2, CK-3, D14-1, D14-2, and D14-3) in total for Illumina HiSeq.

overall_design: RNA-seq of the Larix kaempferi seedlings

first: Wenlong

last: Li

first: Chenghao

first: Joobin

last: Lee


title: Identification and functional annotation of circular RNA in young and sexually mature boar testicles

city: HeFei

first: Zhang

last: Fei

address: 130 Changjiang West Road, Shushan Distric

institute: Anhui Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: We identified 34,521 and 31,803 circRNAs in piglet (30 d) and adult (210 d) boar testis by high-throughput sequencing, respectively. Bioinformatics analysis revealed that these circRNAs are widely distributed on autosomes and sex chromosomes. Some of the host genes can generate multiple circRNAs. A total of 2,326 differentially expressed circRNAs (DECs) derived from 1,526 host genes were found in testicular development, of which 1,003 circRNAs were up-regulated in adult boar testes and 1,323 circRNAs were down-regulated. Furthermore, gene ontology (GO) analysis of host genes of DECs revealed that these circRNAs are mainly involved in regulating spermatogenesis, cilia motility, and hormone biosynthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the DECs are markedly enriched to stem cell pluripotency regulation, tight junctions, adhesion junctions, and cAMP signaling pathway. These results indicate that circRNAs are abundantly expressed in boar testes and exhibit dynamic changes during testicular development.

overall_design: Identification  of circRNA expression profiles in young（3 duplicate samples） and sexually mature（3 duplicate samples） Landrace boar testicles.

first: Fei

last: Zhang

first: Zubing

last: Cao

first: Yunhai


title: RNA sequencing analysis of bone-marrow-derived macrophage (BMDMs) stimulated with vehicle or phloretin

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

summary: Analysis of differentially expressed genes in BMDMs treated with vehicle or phloretin and stimulated with or without LPS. The goal of this study was to elucidate the underlying pathway of phloretin-treatment and determine whether phloretin treatment reduces inflammation in BMDMs.

overall_design: BMDMs were isolated from WT C57BL/6JOlaHsd mice (tibial and femoral bone marrow cells from 12-week-old mice). Subsequent differentiated BMDMs treated with vehicle or phloretin and stimulated with or without LPS were lysed using QIAzol.

first: Jeroen

last: Bogie

first: Jerome

last: Hendriks

first: Tess

last: Dierckx


title: Quantitative Analysis of the Transcriptomes of Tyro3- overexpressed and knocked out cell lines

city: Houston

first: Zhou

last: Jiang

state: Texas

address: 6565 MD Anderson Blvd

department: Molecular and Cellular Oncology

institute: MD Anderson Cancer Center

summary: The goals of this study are to compare transcriptome profiling among four different cell lines including parental cells, resistant cells, Tyro3-overexpression cells, and Tyro3 knockout cells.

overall_design: Tyro3 was overexpressed in parental 4T1 cells, and knocked out in 4T1-resistant cells. Gene expression profiling of the cell lines was examined by RNA-seq.

first: Mien-Chie

last: Hung


title: Gene expression profile of Oral cancer cell line treated by olaparib or irradiation.

city: Chiayi County

first: Jie Ting

last: Low

state: Minxiong Township

address: No. 168, Daxue Road, Section 1

country: Taiwan

institute: National Chung Cheng University

summary: Using RNA-Seq, we observed gene expression changes in parent and radioresistant OSCC cells.

overall_design: We used RNA-sequence to compare gene expression profiles of parent OML1 and radioresistant OML1-R OSCC cells in order to select candidate genes responsible for radiation sensitivity.

first: Chih-Chia

last: Yu

first: Michael

middle: Y

last: Chan

first: Hon-Yi

last: Lin

first: Shih-Kai


title: NSD2 interacts with SMARCA2 and regulates expression of oncogenes CCND1 and PRL3 in t(4;14) multiple myeloma

city: Singapore

first: Jing Yuan

last: Chooi

address: 1E Kent Ridge Road

department: Yong Loo Lin School of Medicine

country: Singapore

institute: National University of Singapore

summary: Recurrent chromosomal translocations are central to the pathogenesis of multiple myeloma (MM), with t(4;14) translocation being the second-most common and associated with poor prognosis. The nuclear receptor-binding SET domain 2 (NSD2) is overexpressed as a result of the translocation and has been suggested to be the primary oncogenic factor in t(4;14) MM. However, the detailed oncogenic mechanism of NSD2 in MM is still not completely understood. To address the relevant pathways downstream of NSD2 that contributes to myelomagenesis, SILAC-based mass-spectrometry analysis was used to determine NSD2-interacting proteins. We identified 74 proteins and in silico analysis showed that one of them, SMARCA2, interacts with NSD2. Comparison of SMARCA2 expression across MM cell lines with different translocation statuses showed that SMARCA2 was highly expressed in t(4;14) MM cells but not in non-t(4;14) MM cells. SMARCA2 knockdown in t(4;14) MM cells showed reduced cell growth and capacity to form colonies. We further investigated how NSD2 and SMARCA2 regulate the expressions of key myeloma genes, such as PRL3 and CCND1. This study reveals a spectrum of NSD2-interacting proteins involved in different biological pathways, indicating the importance of NSD2 in t(4;14) MM. The interaction between NSD2 and SMARCA2 in regulating the expression of CCND1 and PRL3 suggests the potential of SMARCA2 as a novel therapeutic target for t(4;14) MM.

overall_design: KMS11 cells were treated with shRNAs for 96 h. Total RNA was extracted by using the Qiagen miRNeasy Mini kit (Germany). Sequencing library was generated with 1 ug of total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s protocol.

first: Jing

first: Wee

last: Chng


title: Gene expression profiles analyzed using integrating RNA sequencing and microarray reveals increased inflammatory

city: Beijing

first: Dai

last: Hui

address: Xue Yuan Road 28, Haidian District

institute: Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University

summary: Pigmented villonodular synovitis (PVNS) is a rare condition that involves benign proliferation of the synovial tissue and is characterized by severe joint destruction and high recurrence even after surgical resection. However, poor understanding of the pathogenesis limitsitseffective therapy.

overall_design: In this study, gene expression profiles of six patients with PVNS and six patients with osteoarthritis (OA) were analyzed using integrating RNA sequencing (RNA-seq) and microarray to investigate the PVNS transcriptome.

first: Hui

last: Dai

first: Xin


title: Transcriptome alteration of cultured SCC23 cells after knockdown of circFAT1

city: Los Angeles

first: Cunyu

last: Wang

state: CA

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

summary: To investigate the function of circFAT1 knock down in SCC23 cells

overall_design: We performed RNA-Seq in SCC23 transfected with shCtrl or shCFAT1.

first: Lingfei

last: Jia


title: Amiloride ameliorates muscle wasting in cancer cachexia through inhibiting tumor-derived exosome release

city: Xiamen

first: Lin

last: Zhou

state: Fujian

address: No.422, Siming South Road

department: School of Chemistry and Chemical Engineering

institute: Xiamen University

summary:
Background: Cancer cachexia (CAC) reduces patient survival and quality of life. Developments of efficient therapeutic strategies are required for the CAC treatments. This long-term process could be shortened by the drug-repositioning approach which exploits old drugs approved for non-cachexia disease. Amiloride, a diuretic drug, is clinically used for treatments of hypertension and edema due to heart failure. Here, we explored the effects of amiloride for ameliorating muscle wasting in murine models of cancer cachexia.
Methods: CT26 and LLC tumor cells were subcutaneously injected into mice to induce cancer cachexia. Amiloride was intraperitoneally injected daily once tumors were formed. Cachexia features of the CT26 and LLC models, respectively, were characterized by phenotypic, histopathologic and biochemical analyses. Plasma exosomes and muscle atrophy-related proteins were quantitatively analyzed. Integrative NMR-based metabolomic and transcriptomic analyses were conducted to identify significantly altered metabolic pathways and distinctly changed metabolism-related biological processes in gastrocnemius.
Results: The CT26 and LLC models displayed prominent cachexia features including decreases in body weight, skeletal muscle, adipose tissue and muscle strength. The amiloride treatment in tumor-bearing mice distinctly alleviated muscle atrophy and relieved cachexia-related features without affecting tumor growth. The CT26 and LLC cachexia mice showed increased particle density of plasma exosomes which were largely derived from tumors. Significantly, the amiloride treatment inhibited tumor-derived exosome release, which did not obviously affect exosome secretion from non-neoplastic tissues or induce observable systemic toxicities in normal healthy mice. Integrative-omics revealed significant metabolic impairments in cachectic gastrocnemius, including promoted muscular catabolism, inhibited muscular protein synthesis, blocked glycolysis and impeded ketone body oxidation. The amiloride treatment evidently improved the metabolic impairments in cachectic gastrocnemius.
Conclusions: Our results demonstrated the efficacy of amiloride in ameliorating cachectic muscle wasting and elucidated the underlying mechanistic rationale for its use as an alternative strategy to improve CAC treatments.

overall_design: Four groups of mice (Nor: normal control mice; CAC: cachexia mice; AM: amiloride-treated mice; KD: mice inoculated with Rab27-knockdown cells) gastrocnemius were analyzed, 4 replicates for each group.

first: Tong

last: Zhang

first: Wei

last: Shao

first: Ruohan

last: Lu

first: Haisheng

last: Liu

first: Bin

first: Shiqin

last: Li

first: Huiqin

last: Zhuo

first: Suheng

first: Qinxi

first: Caihua

last: Huang

first: Donghai


title: High-throughput screening of differentially expressed lncRNAs in peripheral blood plasma between coronary artery disease patients and controls

city: Suzhou

first: Ping

address: 242 Guangji Road，Suzhou ，Jiangsu

institute: The Affiliated Suzhou Hospital of Nanjing Medical University

summary: This study aims to discover unknown LncRNAs associated with Coronary Artery Disease（CAD）in peripheral blood. Three pairs of clinical CAD group and control blood plasma samples were texted in this experiment by high-throughput sequencing methods. Cuffdiff software was used to get the expression profiles of LncRNAs, differentially expressed LncRNAs were identified based on fold change and p-value. Differently expressed genes in peripheral plasma and blood monocytes were verified by Q-PCR in large samples of clinical CAD group and controls. We find three LncRNAs uc003pxg.1, ENST00000565257, ENST00000568324 were up-regulated obviously in peripheral blood mononuclear cells of CAD patients and these outcomes were consistent with the sequencing results. The ideal LncRNAs were detected preliminarily. This founding lays the foundation for further research，and provides theoretical basis of LncRNA using for CAD early clinical screening.

overall_design: Differentially expressed lncRNAs of 6 clinal samples were examinated including 3 clinical CAD and 3 control blood plasma samples.

first: Kangyun

last: Sun


title: Transcriptome Analysis of PBMCs in peripheral blood of patients with RA

city: Chongqing

first: zhuyan

last: jiang

state: Shapingba

address: 30 Gaotanyan Zhengjie, Shapingba District, Chongqing, China

institute: Army Medical University

summary: The aim of this study was to analyze the expression profile of circRNAs in PBMCs in peripheral blood of patients with RA by next-generation sequencing, and to identify potential markers for early diagnosis and prognosis of RA, and to lay a foundation for further study on the mechanism of this molecule in PBMCs.

overall_design: RNA-seq of PBMCs of RA patients and normal controls. Control samples re-used from GSE120663

first: Mengjie

first: Zhuyan

last: Jiang


title: Local and CNS-wide astrocyte intracellular calcium signalling attenuation in vivo with CalExflox mice: experimental and computational exploration

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: In this study, we generated knock-in CalExflox mice (Calcium Extrusion) for Cre-dependent expression of mCherry-hPMCA2w/b to attenuate astrocyte calcium signaling in genetically defined cells in vivo. We crossed CalExflox mice to astrocyte specific Aldh1l1-Cre/ERT2 mice in order to achieve inducible global CNS-wide calicum signaling attenuation. Within six days of induction in the bigenic mice, we observed profoundly altered ambulation in the open field, disrupted motor coordination and gait, and premature lethality, which based on imaging, behavioural, and RNA-seq analyses was likely to be partly due to significant cerebellar defects.

overall_design: CalExflox mice were crossed to astrocyte specific Aldh1l1-Cre/ERT2 mice to generate bigenic mice carrying both alleles (CalExflox; Aldh1l1-Cre/ERT2).  CalExflox mice were used as controls. Both groups of mice received a single dose tamoxifen (75 mg/kg) and the cerebellar and the striata were dissected out 5 days later. The tissues were homogenized in ice-cold lysis buffer and the cerebellar RNA was extracted using a mirVana miRNA isolation kit. RNA samples with RNA integrity number (RIN) greater than 7 were used for multiplexed library preparation with Nugen Ovation RNA-Seq System V2. All samples were multiplexed into a single pool in order to avoid batch effects, and sequencing was performed on Illumina NextSeq 4000 for 2 × 75 yielding at least 45 million reads per sample.

first: Xinzhu

last: Yu

first: Baljit

middle: S

last: Khakh


title: Transcriptome Analysis of PBMCs in peripheral blood of patients with SLE

summary: The aim of this study was to analyze the expression profile of circRNAs in PBMCs in peripheral blood of patients with SLE by next-generation sequencing, and to identify potential markers for early diagnosis and prognosis of SLE, and to lay a foundation for further study on the mechanism of this molecule in PBMCs.

overall_design: RNA-seq of PBMCs of SLE patients and normal controls. Control samples re-used from GSE120663

first: Zhiqiang

last: Tian

first: Qingqing

last: Miao


title: Single cell sequencing of posterior axis development in gallus gallus

city: Boston

first: Charlene

middle: Guillot

last: (Ryan)

state: MA

address: 60 Fenwood Road

department: Pathology

institute: Brigham and Women's hospital

summary: Single cell analysis of 3 developmental stages to study the progenitors of axis formation

overall_design:
Dissection of stage 5, 6 somites and 35 somites
Stage 5 HH files: st51.counts.tsv.gz; st52.counts.tsv.gz; st5_cell_names.txt ;st5_cell_bc_seqs.txt ; st5_gene_names.txt
Stage 6 somites: 6s1.counts.tsv.gz; 6s2.counts.tsv.gz; 6s_cell_names.txt ;6s_cell_bc_seqs.txt ; 6s_gene_names.txt
Stage 35 somites: 35s1.counts.tsv.gz; 35s2.counts.tsv.gz; 35s_cell_names.txt ;35s_cell_bc_seqs.txt ; 35s_gene_names.txt

last: Guillot

first: Olivier

last: Pourquie


title: scRNA-sequencing of in vitro cultured ILC2 from the whole brain tissue of 7 months old 3xTg-AD and Control mice.

city: Albany

first: Ivan Ting Hin

last: Fung

state: NY

address: 47 New Scotland Ave

institute: Albany Medical College

summary: ILC2 are potent producers of IL-5 and IL-13 and Th2 cytokines. We have found that 3xTg-AD mice exhibit diminished ILC2 numbers and functionality in the brain barriers. We have found through scRNA-seq that cultured brain ILC2 from 7 months old 3xTg-AD mice expressed significantly less IL-5 ane Areg but increased Gzma and Gzmb.

overall_design: We used the 10X Genomics platform to prepare scRNA-seq libraries to detail the global programme of different gene expression between cultured ILC2 in the whole brain tissue of 7 months old 3xTg-AD and Control mice.

first: Qi

last: Yang

first: Ivan

last: Ting

first: Hin


title: Serine-Threonine Kinase Receptor-Associated Protein (STRAP) Knockout Decreases the Malignant Phenotype in Neuroblastoma

city: Birmingham

first: Laura

last: Bownes

state: AL

address: 1670 University Blvd, Volker Hall, Volker Hall

institute: UAB

summary:
Purpose: Serine-threonine kinase receptor-associated protein (STRAP) plays an important role in neural development but also in tumor growth. Neuroblastoma, a tumor of neural crest origin, is the most common extracranial malignancy of childhood, and it continues to carry a poor prognosis. The recent discovery of the role of STRAP in another pediatric solid tumor, osteosarcoma, and its known function in neural development, led us to investigate the role of STRAP in neuroblastoma tumorigenesis.
Methods: STRAP protein expression was abrogated in two human neuroblastoma cell lines, SK-N-AS (AS) and SK-N-BE(2). Methods included transient knockdown with siRNA, stable knockdown with shRNA lentiviral transfection, and CRISPR-Cas9 genetic knockout of STRAP. STRAP knockdown and knockout cells were examined for phenotypic alterations in vitro and tumor growth in vivo.
Results: Cell proliferation, viability, motility, and growth were significantly decreased in STRAP knockout compared to wild-type cells. Indicators of stemness, including mRNA abundance of common stem cell markers Oct4, Nanog, and Nestin, the percentage of cells expressing CD133 on their surface, and the ability to form tumorspheres, were significantly decreased in the STRAP KO cells. In vivo, AS STRAP knockout cells formed tumors less readily than wild-type tumor cells.
Conclusion: These novel findings demonstrated that STRAP plays a role in tumorigenesis and maintenance of neuroblastoma stemness.

overall_design: Examine gene expression with serine-threonine kinase receptor-associated protein knockout in neuroblastoma

middle: V

first: Adele

middle: P

last: Williams

first: Elizabeth

middle: A

last: Beierle


title: NATURAL KILLER CELLS ARE PRESERVED BY EARLY ART IN HIV-POSITIVE CHILDREN WITH LOWER RESERVOIR

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary:
Introduction: HIV infection causes pathologic changes in the natural killer (NK) cell compartment that can be only partially restored by antiretroviral therapy (ART). We investigated NK cells phenotype and function in children with perinatally acquired HIV (PHIV) and long term viral control (5years) due to effective ART in a multicentre cross-sectional study (CARMA, EPIICAL consortium). The impact of age at ART start and viral reservoir was also evaluated.
Methods: Peripheral Blood Mononuclear Cells (PBMCs) from 40 PHIV that started ART within two years of life (early treated patients, ET ≤ 6 months; late treated patients, LT > 6 months), with at least five years of HIV-1 suppression (< 40 HIV copies/ml), were collected between November 2017 and August 2018. NK phenotype and function were analysed by flow cytometry and transcriptional profile of PBMCs by RNA-Seq. HIV-1 DNA was measured by real-time PCR. Data were analysed by Spearman correlation plots and multivariable Poisson regression model (adjusted for baseline %CD4 and RNA HIV viral load and for age at ART start as interaction term, either ET or LT) to explore the association between NK cell parameters and HIV reservoir modulated by age at ART start.
Results: A significantly higher frequency of CD56neg NK cells was found in LT compared with ET. We further found in LT a positive correlation of CD56neg NK with HIV-1 DNA. LT also displayed increased expression of the NKG2D and NKp46 activating receptors and perforin compared with ET. Moreover, CD107a+ and IFN-γ+ frequencies in non-stimulated NK were associated with HIV-1 DNA in LT patients. Finally, RNA-Seq analysis showed in LT an upregulation of genes related to NK activating pathways and susceptibility to apoptosis compared with ET.
Conclusions: We show that ET present a preserved NK compartment compared with LT, which is associated with lower HIV-1 reservoir and persist despite long-term viral control due to effective ART.

overall_design: Natural Killer cell subset analysis in a cohort of long term virally suppressed HIV infected children.

first: M

last: Doria

first: S

last: Zicari

first: N

last: Cotugno

last: Domínguez-Rodríguez

first: A

last: Ruggiero

first: G

middle: R

last: Pascucci

last: Tagarro

first: Conejo

last: Rojo

first: E

last: Nastouli

first: K

last: Gärtner

first: B

last: Richardson

first: C

last: Foster

first: SL

last: Rinaldi

first: Rossi

last: De

last: Giaquinto

first: P

last: Rossi

last: Pahwa

last: Palma


title: Comprehensive analysis of the transcriptome-wide m6A methylome in pterygium by MeRIP sequencing

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

type: Methylation profiling by high throughput sequencing

summary: Aim: Pterygium is a common ocular surface disease, which is affected by a variety of factors. Invasion of the cornea can cause severe vision loss. N6-methyladenosine (m6A) is a common post-transcriptional modification of eukaryotic mRNA, which can regulate mRNA splicing, stability, nuclear transport, and translation. To our best knowledge, there is no current research on the mechanism of m6A in pterygium.   Methods: We recruited 24 pterygium patients from Shanghai Yangpu Hospital, and the level of m6A modification was detected using an m6A RNA Methylation Quantification Kit. Expression and location of METTL3, a key m6A methyltransferase, were identified by immunostaining. Then we used m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq), RNA sequencing (RNA-seq) and bioinformatics analyses to compare the differential expression of m6A methylation in pterygium and normal conjunctival tissue.   Results: We identified 2949 dysregulated m6A peaks in pterygium tissue, of which 2145 were significantly upregulated and 804 were significantly downregulated. The altered m6A peak of genes were found to play a key role in the Hippo signaling pathway and endocytosis. Joint analyses of MeRIP-seq and RNA-seq data identified 72 hypermethylated m6A peaks and 15 hypomethylated m6A peaks in mRNA. After analyzing the differentially methylated m6A peaks and synchronously differentially expressed genes, we searched the Gene Expression Omnibus database and identified five genes related to the development of pterygium (DSP, MXRA5, ARHGAP35, TMEM43, and OLFML2A).   Conclusion: Our research shows that m6A modification plays an important role in the development of pterygium and can be used as a potential new target for the treatment of pterygium in the future.

overall_design: mRNA profiles and m6A profiles in pterygium

first: Yaping

last: Jiang

first: Xin

last: Zhang

first: Xiaoyan


title: Next-Generation Sequencing was used to conduct a quantitative analysis of Wild Type (Ctrl) and Stat3 KO (Test) long bone transcriptomes.

first: Prem

middle: Swaroop

last: Yadav

address: 118 Longwood Medical Area

department: HSDM

institute: Harvard University

summary: RNA samples were isolated shaft of the humerus bone of E16.5 embryos. A total of six, three ctrl & three test samples were used. RNASeq analyses were conducted to identify the differentially expressed genes upon Stat3 loss of function during long bone development. Total RNA was isolated from the long bone of E16.5 embryos of the indicated genotypes.

overall_design: Long bone mRNA profiles of E16.5 wild type (Ctrl) and Prrx1Cre; Stat3C/C (Test) embryos were generated by deep sequencing to identify the differentially expressed genes.

first: Yingzi


title: Base editing of general transcription factor Spt15 to enhance yeast stress tolerance

city: Tianjin

first: Qinhong

last: Wang

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: We aimed to explore the application of the Target-AID base editor in genomic in situ protein engineering by generating nonsynonymous mutations. A general transcription factor Spt15 (TATA-box binding protein) gene of Saccharomyces cerevisiae was selected as a target. Based on computational and experimental scanning mutagenesis of the Spt15 gene as well as flask-fermentation screening, three stress-tolerant Spt15 mutant strains (A140G, P169A and R238K) and two stress-sensitive Spt15 mutant strains (S118L and L214V) were obtained. To validate the regulatory mechanisms underlying these different Spt15 mutants, genome-wide transcriptome analysis by RNA sequencing was carried out to quantify global transcription changes in the Spt15 mutant strains compared to the wild type strain at the same culture conditions including the unstressed normal condition as well as hyperosmotic and thermal stress conditions. Results uncover the impacts of the Spt15 point mutations on global transcriptional regulation in response to hyperosmotic and thermal stresses, and provide insight into the applicability of the Target-AID base editor in genomic in situ protein engineering to alter yeast stress tolerance.

overall_design: Six strains including three stress tolerant mutants Spt15-A140G, Spt15-P169A and Spt15-R238K, two stress sensitive mutants Spt15-S118L and Spt15-L214V, as well as the wild type strain BY4741 were subjected to transcriptome analysis using RNA sequencing on Illumina platform using 150-bp paired-end sequencing. Flask fermentation of these six strains were carried out in biological duplicates at hyperosmotic or thermal stress conditions as well as the unstressed normal condition, respectively. We identified differential expressions in comparisons of the SPT15 mutant strains versus the wild type strain BY4741 at each culture condition.

first: Yuping

last: Lin

first: Yanfang

last: Liu

first: Yufeng

last: Guo


title: RNA splicing factors SRRM3 and SRRM4 distinguish molecular phenotypes of castration-resistant neuroendocrine prostate cancer [methylation]

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Neuroendocrine (NE) differentiation in metastatic castration-resistant prostate cancer (mCRPC) usually develops through cellular plasticity. We recently characterized two mCRPC phenotypes with NE features; Androgen receptor (AR)-positive, NE-positive amphicrine prostate cancer (AMPC) and AR-negative small cell or neuroendocrine prostate cancer (SCNPC). Here, we interrogate the RE-1 silencing transcription factor (REST) pathway in mCRPC and demonstrate that SRRM3 has analogous functions to SRRM4 and mediates NE differentiation through alternative splicing of REST. We scrutinize transcriptome datasets across species and tumor types and discover that SRRM3 and SRRM4 expression define molecular phenotypes in AMPC and SCNPC. Notably, we characterize two AMPC phenotypes driven by either REST attenuation or ASCL1 activity and three SCNPC phenotypes with progressive activation of neuronal transcription factor programs. Together, our data provides a biological framework for classifying NE phenotypes in mCRPC that could be useful for future therapeutic development and precision medicine applications.

overall_design: Transcriptome profiling of human prostate tumor cell lines using Illumina TruSeq Library prep sequenced on Illumina NovaSeq and methylation profiling using Illumina Infinium MethylationEPIC BeadChip arrays.

first: Mark

last: Labrecque

first: Lisha

middle: G

last: Brown

middle: M

first: Bryce

last: Lakely

first: Nicholas

last: Brady

first: John

middle: K

last: Lee

first: Holly

last: Nguyen

first: Dapei

last: Li

first: Brian

last: Hanratty

first: Michael

middle: C

last: Haffner

first: David

last: Rickman

first: Lawrence

middle: D

last: True

first: Daniel

middle: W

first: Hung-Ming

last: Lam

first: Joshi

last: Alumkal

first: Eva

last: Corey

first: Peter

last: Nelson

first: Colm

last: Morrissey


title: Genetic alterations associated with multiple primary malignancies

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

summary: Affymetrix OncoScan arrays were used to identify potential driver DNA copy number alterations and somatic mutations that promote the development of multiple primary malignancies in 26 breast cancer patients.

overall_design: Copy number analysis of Affymetrix OncoScan CNV Plus arrays was performed on formalin-fixed paraffin-embedded samples from 26 breast cancer patients (breast cancer and previously diagnosed primary malignancy).

first: Jenny

last: Nyqvist

first: Anikó

last: Kovács

first: Elisabeth

last: Sarenmalm

first: Zakaria

last: Einbeigi

first: Per

last: Karlsson

last: Forssell-Aronsson

first: Khalil

last: Helou

middle: Z


title: RNA splicing factors SRRM3 and SRRM4 distinguish molecular phenotypes of castration-resistant neuroendocrine prostate cancer [RNA-seq]

first: Ilsa

last: Coleman

first: Mark

last: Labrecque

first: Lisha

last: Brown

first: Bryce

last: Lakely

first: Nicholas

middle: J

last: Brady

first: John

last: Lee

first: Holly

last: Nguyen

first: Dapei

last: Li

first: Brian

last: Hanratty

last: Lin


title: RNA splicing factors SRRM3 and SRRM4 distinguish molecular phenotypes of castration-resistant neuroendocrine prostate cancer

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

overall_design: Refer to individual Series


title: IL4 promotes phagocytosis of murine leukemia cells counteracted by CD47 upregulation

city: Lund

first: Pablo

last: Peña-Martínez

address: Klinikgatan 28

department: Clinical Genetics

institute: Lund University

summary: Cytokines are key regulators of tumor immune surveillance by controlling immune cell activity. Here, we investigated whether interleukin 4 (IL4) has antileukemic activity via immune-mediated mechanisms in an in vivo murine model of acute myeloid leukemia driven by the MLL-AF9 fusion gene. Although IL4 strongly inhibited leukemia development in immunocompetent mice, the effect was diminished in immune-deficient recipient mice, demonstrating that the antileukemic effect of IL4 in vivo is dependent on the host immune system. Using flow cytometric analysis and immunohistochemistry, we revealed that the antileukemic effect of IL4 coincided with an expansion of F4/80+ macrophages in the bone marrow and spleen. To elucidate whether this macrophage expansion was responsible of the antileukemic effect, we depleted macrophages in vivo with clodronate liposomes. Macrophage depletion eliminated the antileukemic effect of IL4, showing that macrophages mediated the IL4-induced killing of leukemia cells. In addition, IL4 enhanced murine macrophage-mediated phagocytosis of leukemia cells in vitro. Global transcriptomic analysis of macrophages revealed an enrichment of signatures associated with alternatively activated macrophages and increased phagocytosis upon IL4 stimulation. Notably, IL4 concurrently induced Stat6-dependent upregulation of CD47 on leukemia cells, which suppressed macrophage activity. Consistent with this finding, combining CD47 blockade with IL4 stimulation enhanced macrophage-mediated phagocytosis of leukemia cells. Thus, IL4 has two counteracting roles in regulating phagocytosis in mice; enhancing macrophage-mediated killing of leukemia cells, but also inducing CD47 expression that protects target cells from excessive phagocytosis. Taken together, our data suggests that combined strategies that activate macrophages and block CD47 have therapeutic potential in AML.

overall_design: Macrophages differentiated in vitro for 7 days with CSF1 (20 ng/mL) +/- IL4 (20 ng/mL); and macrophages collected from mice trasnplanted with wild type or IL4-secreting AML cells.

first: Peña-Martínez

last: Pablo


title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages

city: New York

first: Kyung-Hyun

last: Park-Min

email: ParkminK@HSS.EDU, parkmink@gmail.com

address: 535 East 70th Street

institute: Hospital for Special Surgery

summary: MYC activates different metabolic programs in a cell-type and cell-status dependent manner. However, the role of MYC in inflammatory macrophages has not yet been determined. Metabolic and molecular analyses reveal that MYC, but not HIF1, is involved in enhancing early glycolytic flux during inflammatory macrophage polarization. Ablation of MYC decreases lactate production by regulating lactate dehydrogenase (LDH) activity and causes increased inflammatory cytokines by regulating interferon regulatory factor 4 (IRF4) in response to lipopolysaccharide (LPS). Moreover, myeloid-specific deletion of MYC and pharmacological inhibition of MYC/LDH axis enhance inflammation and the bacterial clearance in vivo. These results elucidate the potential role of the MYC/LDH/IRF4 axis in inflammatory macrophages by connecting early glycolysis and inflammatory responses and suggest that modulating early glycolytic flux mediated by the MYC/LDH axis can be utilized to open new avenues for the therapeutic modulation of macrophage polarization to fight against bacterial infection.

overall_design: For the generation BMDMs, bone marrow cells were flushed from femurs and tibias of mice and cultured at 37oC, 5% CO2 in complete α-MEM medium (10% heat-inactivated defined FBS (HyClone Fisher), penicillin-streptomycin (Invitrogen), and L-glutamine (Invitrogen)) with 5% L929 cell supernatant as conditioned medium (CM) as a source of M-CSF (Englen et al., 1995) after lysis of RBCs using ACK lysis buffer (Invitrogen). Then, the non-adherent cell population was recovered the next day and cultured for three additional days. Final concentration of M-CSF in our culture was 23.3 ng/ml. Cells that remained in suspension were removed by aspiration and attached cells were washed twice with PBS, then re-plated and cultured with complete α-MEM medium with 20 ng/ml human M-CSF. Cells were stimulated with LPS (10ng/ml) for 3 hours.


title: LncRNA-42060 Regulates Tamoxifen Sensitivity and Tumor Development via Regulating the miR-204-5p/SOX4 Axis in Canine Mammary Gland Tumor Cells

city: Harbin

first: Xu

last: Enshuang

address: NO.600 Changjiang Road, Xiangfang District

institute: Northeast Agricultural University

summary: Tamoxifen is the drug of choice for endocrine therapy of breast cancer. Its clinical use is limited by the development of drug resistance. There is increasing evidence that long non-coding RNAs (lncRNAs) are associated with tumor drug resistance. Therefore, we established two TAM-resistant cell lines, CHMpTAM and CHMmTAM. The different expression levels of lncRNA and miRNA in CHMmTAM and CHMm were screened by RNA sequencing, and the lncRNA-miRNA interactions were analyzed. LncRNA ENSCAFG42060 (lnc-42060) was found to be significantly upregulated in drug-resistant cells and tumor tissues. Further functional validation revealed that the knockdown of lnc-42060 inhibited proliferation, migration, clone formation, restoration of TAM sensitivity, and reduction of stem cell formation in drug-resistant cells, whereas overexpression of lnc-4206 showed opposite results. Bioinformatics and dual-luciferase reporter gene assays confirmed that lnc-42060 could act as a sponge for miR-204-5p, further regulating SOX4 expression activity and thus influencing tumor cell progression. In conclusion, we screened lncRNAs and miRNAs associated with TAM resistance in canine mammary gland tumor cells for the first time. lnc-42060 served as a novel marker that may be used as an important biomarker for future diagnosis and treatment.

overall_design: three control

first: Enshuang

last: Xu

first: Mengxin

last: Hu

first: Daning

last: Tong

first: Yuying

last: Fan

first: Xiaoli

last: Ren

first: Yun

last: Liu


title: NES_functional_survivin vs NES_mutated_survivin exposed or unexposed to temozolomide (TMZ)

city: Mainz

first: Christian

last: Schwarzenbach

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

country: Germany

institute: University medical center Mainz

summary: Investigation of the impact of survivin subcellular localisation on gene expression upon TMZ in glioblastoma cell clones, ectopically expressing either cytoplasmic or nuclear survivin-GFP. In case of nuclear survivin-GFP, survivin is trapped in the nucleus, because the nuclear export sequence (NES) has been mutated

overall_design: Examination of different survivin subcellular localisation in glioblastoma cells (Grade IV) upon TMZ exposure

first: Maja

middle: T

last: Tomicic

first: Sven

middle: E

last: Bikar

first: Alicia

last: Poplawski


title: The H3K4me1 plays a role in nucleosome depletion at enhancers but does not directly contribute to eRNA synthesis. [RNA-Seq]

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan national university

summary: We found that H3K4me1 contributes to nucleosome depletion at enhancers but was not enhough for eRNA synthesis.

overall_design: Total RNA-seq was performed in control, MLL3/4 SET domain deletion and p300 HAT domain deletion cells.


title: Histone H3K4me1 and H3K27ac play roles in nucleosome depletion and eRNA transcription, respectively, at enhancers


title: miRNA expression profiling of kidney collecting duct from mice lacking Dicer1 in AQP2 expressing cells.

city: Ariano Irpino

first: Fulvio

last: D'Angelo

address: via Camporeale

country: Italy

institute: Biogem

summary: To investigate the role of miRNAs in the principal cell of kidney collecting duct, a Cre-LoxP recombination strategy was used to generate a mouse model lacking the endoribonuclease Dicer in AQP2 expressing cells (DicerAQP2Cre+). To identify miRNAs altered in DicerAQP2Cre+ mice, small RNA-sequencing analysis was performed on inner medulla tissue from 1-month-old DicerAQP2Cre+ mice and controls (n=3+3 mice). Small RNA-sequencing was used as, relative to probe-based microarrays or RT-qPCR plate arrays, this approach allows both the identification of miRNAs when they have been differentially processed and it offers the possibility to identify novel miRNAs.

overall_design: miRNA expression profiles of 1-month-old DicerAQP2Cre+ mice and controls (n=3+3 mice).

first: Francesco

last: Trepiccione

first: Federica

last: Petrillo

first: Michele

last: Ceccarelli


title: Histone H3K4me1 and H3K27ac play roles in nucleosome depletion and eRNA transcription, respectively, at enhancers. [ChIP-Seq]

overall_design: H3K4me1, H3K27ac and H3 ChIP-seq was performed in control, MLL3/4 SET domain deletion and p300 HAT domain deletion cells.


title: Cep135 deficiency promotes cell cycle de-regulation, p53 accumulation and cell deah of neural progenitors

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: Gene expression profiles of Cep135 wildtype and knockout E14.4 and E11.5 mouse embryonic neocortices. Gene expression profiles of in vitro E14.5 cortices-derived primary neurospheres are also included; in vitro samples listed as "12h" or "24h" depending on the duration of the in vitro culture from NPs isolation for incipient neurosphere formation and RNA isolation for RNAseq.

overall_design: E11.5 and E14.5 embryos resulting from matings between cep135 (+/-) mice were sacrificed and dorsal telencephalons dissected out to RNA isolation and RNAseq analysis. In the case of E14.5 telencephalons, E14.5 cortical neural progenitors were also isolated and cultured for 12 and 24h for the formation of incipient neurospheres. RNAseq analysis of these in vitro cultures is also available.

first: José

last: González

last: Graña-Castro

first: Marcos

last: Malumbres


title: ChIP-seq of SMAD1 and β-catenin in mouse osteoblast and endothelial cells

city: Los Angeles

first: Xiuju

last: Wu

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

summary: Vascular endothelium is known to contribute osteoprogenitors to calcification through endothelial-mesenchymal transitions, in which endothial cells gain plasticity and differentiate into osteoblast-like cells. We survey the alteration of SMAD1 and β-catenin using ChIP-seq during the reverse switching of osteoblastic fate to endothelial differentiation.

overall_design: Transcriptional regulation in osteoblast differentiation

first: X

first: J

last: Yao


title: NAMPT-mediated NAD+ salvage is essential for mitochondrial function and swelling, muscle fiber integrity and premature survival

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Skeletal muscle gene expression changed exponential over time in response to NAMPT deletion

overall_design: Gene expression in gastrocnemius muscle of wildtype and skeletal muscle specific Nampt knockout mice at 2, 4, 6, and 8 weeeks of age.

first: Marianna

last: Jensen

last: Altıntaş

first: Astrid

middle: L

last: Basse


title: Differential expression of gut miRNAs in idiopathic Parkinson's disease

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

institute: Ludwig-Maximilians-University Munich

summary: In the present work, we aimed to investigate the expression of microRNAs (miRNAs) in routine colonic biopsies obtained from patients with idiopathic Parkinson's disease (iPD) and to address their value as a diagnostic biomarker for PD and their mechanistic contribution to PD onset and progression.

overall_design: miRNA sequencing of patients with Parkinson's disease (n = 13) and healthy controls (n = 17) was performed. Additionally, miRNA sequencing was performed in biopsies of mucosal and submucosal tissue (n = 3/tissue).

middle: H


title: USP9X-mediated KDM4C deubiquitination promotes lung cancer radioresistance by epigenetically inducing TGFβ2 transcription

city: Wuhan

first: hua

middle: xiao

last: jie

state: Hubei

address: Xinhua Road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: Radioresistance is regarded as the main barrier to effective radiotherapy in lung cancer. However, the underlying mechanisms of radioresistance remain elusive. Here, we show that lysine-specific demethylase 4C (KDM4C) is overexpressed and correlated with poor prognosis in lung cancer patients. We provide evidence that genetical or pharmacological inhibition of KDM4C impairs tumorigenesis and radioresistance in lung cancer in vitro and in vivo. Moreover, we uncover that KDM4C upregulates TGFβ2 expression by directly reducing H3K9me3 level at the TGFβ2 promoter and then activates TGF-β/Smad/ATM signaling to confer radioresistance in lung cancer. Using tandem affinity purification technology, we further identify deubiquitinase USP9X as a critical binding partner which deubiquitinates and stabilizes KDM4C. More importantly, depletion of USP9X impairs TGF-β/Smad signaling and radioresistance by destabilizing KDM4C in lung cancer cells. Thus, our findings demonstrate that USP9X-mediated KDM4C deubiquitination activates TGF-β/Smad signaling to promote radioresistance, suggesting that targeting KDM4C may be a promising radiosensitization strategy in the treatment of lung cancer.

overall_design: Analysis of control and shKDM4C lung cancer cell lines obtained from 3 independent samples each.

first: Xiaohua

last: Jie

first: William

last: Pat Fong

first: Rui

last: Zhou

first: Gang

first: Shuangbing

last: Xu


city: Pohang

first: Ildoo

last: Hwang

state: Kyungbuk

address: 77 Cheongam-Ro, Hyoja-dong, Nam-gu,

department: Department of Life Sciences

institute: POSTECH

summary: Cytokinin (CK) has been known as a cell proliferation activator for a long time in plants; however, its regulatory mechanism in cell division and expansion still remains unclear. Here we revealed that a bHLH transcription factor, CKG (CYTOKININ-RESPONSIVE GROWTH REGULATOR) mediates CK-dependent regulation of cell expansion and cell cycle. Overexpression of CKG increased cell size in a ploidy-independent manner and promoted S-phase entry of cell-cycle especially at early developmental stage, and pleiotropically enhanced organ growth from embryogenesis to reproductive stage, particularly cotyledons. In contrast, ckg loss-of-function mutant exhibited smaller cotyledons. CKG regulates the expression of genes mainly involved in regulation of cell cycle and macromolecule synthesis. We propose that CKG provides a regulatory module of cell cycle and organ growth in CK response.

overall_design: Gene expression in the 7-day-old cotyledons of Col-0 and ckg mutant was measured. Two biological replicates of Col-0 and three biological replicates of ckg line were used.

first: Joonghyuk

last: Park

first: Seungchul

last: Lee

first: Daehee


title: Gene expression profiling by RNA-seq of SW480 and HCT116 cells after TGM2 knockdown

city: Frankfurt am Main

first: Michael

last: Rieger

address: Theodor-Stern-Kai 7

institute: Universitätsklinikum Frankfurt/DKFZ

summary: Molecular characterization of TGM2-knockdown cells reveals p53 as a central mediator of TGM2-signaling

overall_design: Examination of gene expression of SW480 and HCT116 cells by comparing TGM2 knockdown with control cells.

first: Ilaria

last: Lunger

first: Khalil

last: Abou-El-Ardat


title: High-throughput sequencing analyze the differentially expressed miRNA of HUVECs after lncRNA uc003pxg.1 knockdown by siRNA compared with NC group

city: Suzhou

first: Ping

last: Li

address: 242 Guangji Road，Suzhou ，Jiangsu

institute: The Affiliated Suzhou Hospital of Nanjing Medical University

summary: Sequencing of relevant miRNAs was performed in si-uc003pxg.1-transfected HUVECs and control HUVECs. Fourteen upregulated and 5 downregulated miRNAs were selected based on P-values and fold change values. And cell experiments also showed that miR-25-5p was significantly upregulated in HUVECs compared to normal samples following uc003Pxg.1 knockdown. The luciferase activities of the miR-25-5p mimic + uc003pxg.1 wt group were significantly decreased compared with those of the miR-25-5p mimic + uc003pxg.1 mut group, while there was no significant difference in the luciferase activities between the miR-25-5p mimic and NC samples in the mutant group. This result indicated that uc003pxg.1 interacts with miR-25-5p. This study provides a theoretical basis for the study of the molecular mechanism of uc003pxg.1 in HUVECs.

overall_design: Examination the differentially expressed miRNA of HUVECs after lncRNA uc003pxg.1 knockdown by siRNA and NC group

first: Kangyun

last: Sun


title: Gene expression fingerprinting of ameloblasts shows changes in the endocytosis/cytoskeleton interface across stages.

first: Natalie

middle: Christine

last: Kegulian

address: 2250 Alcazar St., CSA 149

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

summary: We used RNA-seq to identify differentially expressed genes across ameloblast stages in rats. We found expression patterns of enamel matrix proteins, ion channels and transporters, and endocytosis regulators such as clathrin to match those found in previous experimental studies on ameloblasts. We hypothesized that ameloblasts change their endocytotic pathways as they progress from stage and stage, and we sought to identify novel patterns in expression of genes at the endocytosis/cytoskeleton interface. We found that maturation ameloblasts preferentially express synaptojanin 1 and intersectin 2 and secretory ameloblasts preferentially express Numb protein and amphiphysin. We also uncovered differential alternative splicing of ECI genes across ameloblast populations. In pointing to endocytotic genes hitherto unexplored in ameloblasts that also regulate cell morphology, this bioinformatics study suggests a mechanism by which cervical loop, secretory, and maturation ameloblasts switch modes of endocytosis in order to express genes that better suit the distinct morphology of each cell stage.

overall_design: cDNA reads reverse-transcribed from mRNA from cervical loop cells, secretory ameloblasts, and maturation ameloblasts dissected from 5 rats were generated by RNA-seq using an Illumina NextSeq 500 sequencer.

first: Kaifeng

last: Yin

first: Sarah

middle: Y

last: Robertson

first: Yi-Bu

last: Chen

last: Paine


title: Sonic Hedgehog signalling to T cells limits induction of chronic murine atopic dermatitis via Gli2-driven immune regulatory function

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

summary: Hedgehog (Hh) proteins are morphogens which regulate embryonic development and adult tissue homeostasis, with distinct outcomes dependent on the strength and duration of their signals.  We show that the Hh signalling pathway modulates the induction and pathology of mouse atopic dermatitis. Sonic hedgehog (Shh) and Hh pathway target genes were upregulated on induction of atopic dermatitis, and the Hh pathway was activated in skin T cells, showing that they respond in vivo to Hh signals secreted from the skin. Shh upregulation reduced skin inflammation in mice, whereas pharmacological Smoothened-inhibition reduced Shh upregulation and exacerbated skin pathology. Hh-signalling to T cells prevented skin inflammation on induction of dermatitis, while inhibition of Hh-mediated transcription in T cells substantially exacerbated the disease. RNA-sequencing analysis of skin CD4+ T cells from mice with chronic atopic dermatitis revealed decreased expression of immune regulatory genes in mice with conditional inhibition of Hh-mediated transcription in T cells, and increased expression of inflammatory and chemokine genes. In contrast, constitutive Hh mediated transcription in T cells led to increased expression of immune regulatory genes in skin CD4+ T cells from mice with chronic atopic dermatitis and protected against inflammation.  Hh-mediated transcription in T cells resulted in increased regulatory T (Treg) cells in the periphery and skin of dermatitis-induced mice, and increased TGF-β expression, supporting their immunoregulatory phenotype, whereas, inhibition of T cell specific Hh-mediated transcription, resulted in impaired Treg function, which permitted progression of skin inflammation.

overall_design: Skin from Wildtype, Gli2ΔN2 and Gli2ΔC2 transgenic mice (n=2) was sorted for CD4+ and CD8+ T cells.  RNA extracted from these cells was sequenced to help understand the transcriptional mechanism that are implicated in dermatitis induction in the presence or absence of Hedgehog signalling pathway.

first: Eleftheria

last: Papaioannou

first: Anisha

last: Solanki

first: Ching-In

last: Lau

first: Diana

last: Yánez

first: Susan

last: Ross

first: Ismael

last: Ranz

first: Masahiro

last: Ono

first: Ryan

middle: F

last: O'Shaugnessy


title: Transcriptomic profiling of blood memory B cell subsets in kidney transplant recipients

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: We compared the transcriptomic profile between patients without donor-specific antibodies (DSA-), patients with donor-specific antibodies without antibody-mediated rejection (DSA+ ABMR-) and patients  with donor-specific antibodies and antibody-mediated rejection (DSA+ ABMR+). We found that patients with DSA+ ABMR+ had a distinct transcriptomic profile compared to DSA- and DSA+ ABMR- patients, characterized by upregulation of genes related to B cell activation and B cell effector functions.

overall_design:
We analysed N=3 resting memory (RM, CD19+ CD38lo CD27+ CD21+), N=3  activated memory (AM, CD19+ CD38lo CD27+ CD21-) and N=3 tissue-like memory B cells (TLM, CD19+ CD38lo CD27- CD21) samples per group of patients (DSA-, DSA+ABMR-, DSA+ ABMR+), without replicates, sequencing was done using the Illumina NextSeq 500 as the platform, and RNA extraction method was Total RNA using the miRNeasy Mini kit

We analysed allograft biopsy samples from N=7 DSA-, N=2 DSA+ABMR-, N=12 DSA+ ABMR+ patients, without replicates, sequencing was done using the Illumina NextSeq as the platform, and RNA extraction method was performed using RNeasy FFPE Kit Qiagen

**RAW DATA NOT PROVIDED DUE TO PATIENT PRIVACY CONCERNS**

first: Kevin

last: Louis

last: Metes

first: Alexander

last: Chang


title: Establishment of a novel mouse model of troglitazone-induced liver injury and analysis of its hepatotoxic mechanism

city: Nagoya

first: Ru

last: JIA

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Drug Safety Sciences

institute: Nagoya University Graduate School of Medicine

summary: Drug-induced liver injury (DILI) is a major problem in drug development and clinical drug therapy. Troglitazone (TGZ), a thiazolidinedione antidiabetic drug for the treatment of type II diabetes mellitus, was found to induce rare idiosyncratic severe liver injury in patients, which led to its withdrawal in 2000. In experimental animals in vivo, however, TGZ has never induced liver injury. In this study, administration of BALB/c female mice with TGZ alone significantly elevated alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels 6 h after the treatment. Co-administration of L-buthionine-(S,R)-sulfoximine (BSO), an inhibitor of glutathione synthesis, unexpectedly restrained the TGZ-dependent increase of ALT and AST. Furthermore, the ratio of oxidative stress marker glutathione/disulfide glutathione was significantly decreased in TGZ-alone- and BSO plus TGZ-administered mice, and increased hepatic mRNA levels of inflammation- and oxidative stress-related factors in liver were observed. Subsequently, microarray studies were performed 6 h after administration and we discovered that the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway was activated in TGZ-induced liver injury. Moreover, the activation of JAK/STAT pathway promoted phosphorylation of STAT3 in TGZ-alone- and BSO plus TGZ-administered mice. Consequently, upregulation of STAT3 activation increased mRNA levels of its downstream genes. In conclusion, the present study is the first time to establish a mouse model of TGZ-induced liver injury with BALB/c mouse for assessing DILI in drug development and the activation of JAK/STAT signaling pathway might be as an important role involved in hepatotoxic mechanisms of TGZ.

overall_design: Liver samples were collected 6 hours after the administration of TGZ or RGZ and vehicle. Total RNA was extracted from these liver samples and equal amount of RNA was pooled from 6 animals in each group.

last: Jia

first: Shingo

last: Oda

first: Koichi

last: Tsuneyama

first: Yuya

last: Urano

first: Tsuyoshi

last: Yokoi


title: Transcriptomic Analysis of Two Homologous Salmonella Serogroup C1-specific Genes (SC0368 and SC0595)

city: Shanghai

first: Xiujuan

last: Zhou

address: 800 Dongchuan RD

institute: Shanghai Jiao Tong University

summary:
Purpose:To reveal the function and relationship of the two homologous Salmonella serogroup C1-specific genes (SC0368 and SC0595 in SC).
Methods: RNA was isolated from late exponential phase bacteria cultures of wild-type and mutants grown in LB medium. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 2500 System. DESeq2 method was used to calculate the differentially expressed genes. qRT–PCR were used to validate RNA-seq result.
Results: The RNA sequencing yielded more than 28 million reads for 12 samples, and 98.83-99.58% of the high-quality reads were mapped to the reference genome sequence, covering more than 4500 genes in the Salmonella genome. According to the DEGseq analysis software, 76, 78, and 217 genes were considered differentially expressed compared to the wild-type (<2-fold changes, FDR< 0.05) in mutant strains △0368, △0595, and △0368△0595, respectively.  RT–qPCR results of 18 selected genes were highly consistent with the RNAseq results.
Conclusions: Combination of biological analyses and RNA-Seq of in-frame deletion mutants, experimental evidence for the possible involvement of SC0368 and SC0595 in regulation of motility, LPS synthesis, growth, virulence, and serotype conversion is provided.

sample_organism: Salmonella enterica subsp. enterica serovar Choleraesuis str. ATCC 10708

overall_design: Three biological repetitions of wild-type, single (Δ0368 and Δ0595) and double (Δ0368Δ0595) mutants. Totally for 12 samples were conducted RNA sequncing. Wild-type was used as control.

first: Bin

last: Liu

first: Xianming

last: Shi


title: Transcriptomic Analysis of the Chorioallantois of Mares with Nocardioform Placentitis

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

summary: Nocardioform placentitis (NP) continues to result in episodic outbreaks of abortion and preterm birth in mares and remains a poorly understood disease. The objective of this study was to characterize the transcriptome of the chorioallantois (CA) of mares with NP. Term CA were collected from mares with gross lesions consistent with NP, and NP was subsequently confirmed in four CA based upon pathology and PCR for Amycolatopsis spp.  CA samples were collected from the margin of the NP lesion (NPL, n=4) and grossly normal region (NPN, n=4). Additionally, CA samples were collected from normal postpartum mares (Control; CRL, n=4).  Transcriptome analysis identified 2,892 DEGs in CRL vs. NPL and 2,450 DEGs in NPN vs. NPL. Functional genomics analysis elucidated that inflammatory signaling, toll-like receptor signaling, inflammasome activation, chemotaxis, and apoptosis pathways dominate NP. The increased leukocytic infiltration in NPL was associated with the upregulation of matrix metalloproteinase (MMP1, MMP3, and MMP8) and apoptosis-related genes, such as caspases (CASP3 and CASP7), which could explain placental separation associated with NP. Also, NP was associated with downregulation of several placenta-regulatory genes (ABCG2, GCM1, EPAS1, and NR3C1), angiogenesis-related genes (VEGFA, FLT1, KDR, and ANGPT2), and glucose transporter coding genes (GLUT1, GLUT10, and GLUT12), as well as upregulation of hypoxia-related genes (HIF1A and EGLN3), which could elucidate placental insufficiency accompanying NP. In conclusion, our findings revealed for the first time, the key regulators and mechanisms underlying placental inflammation, separation, and insufficiency during NP.

overall_design: Chorioallantois (CA) samples were collected from the margin of the NP lesion (NPL, n=4) and grossly normal region (NPN, n=4). Additionally, CA samples were collected from normal postpartum mares (Control; CRL, n=4).  Total RNA was isolated from all CA samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures.  Paired-end reads with 150 nucleotides in length were produced. A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads. The Fastq files were evaluated for read quality using FastQC 0.11.4. Subsequently, Trim Galore 0.4.1 was used for the adapter and read quality trimming (Phred score threshold of 30). Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a, then annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1. Fragments per kilobase per million (FPKM) was used to determine the expression level of genes. Lastly, we used Cuffdiff 2.2.1 to calculate differentially expressed genes (DEGs) between groups. The significance level was set at the FDR-adjusted p-value of the test statistic < 0.05 using the Benjamini-Hochberg correction.

first: Hossam

last: El-Sheikh Ali

first: Shavahn

last: Loux

first: Laura

middle: A

last: Kennedy

first: Kirsten

last: Scoggin

first: Pouya

last: Dini

first: Carleigh

last: Fedorka

first: Ted

last: Kalbfleisch

first: Alejandro

last: Esteller-Vico

first: David

last: Horohov

first: Erdal

last: Erol

first: Craig

middle: N

last: Carter

first: Jacqueline

last: Smith


title: H3K27me3 CHIP-seq of cadmium resistant breast cancer MDA-231 cells

status: Public on Jul 13 2021

city: Aurora

first: Joshua

middle: C

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

overall_design: In this study we compared genome wide H3K27me3 CHIP-seq of cadmium resistant MDA-231 breast cancer cells vs untreated controls. Cells were passaged in the presence of increasing cadmium concentrations to induce heavy metal resistance, generating cadmium resistant cell lines. Parental cells were serially passaged in normal media to generate untreated controls.

first: Philip

last: Tatman

first: Gregory

last: Wright


title: Cut and Run ChIP-seq of SUZ12 and EZH2 in cadmium resistant breast cancer MDA-231 cells

overall_design: In this study we compared genome wide SUZ12 and EZH2 Cut&RUN CHIP-seq of cadmium resistant MDA-231 breast cancer cells vs untreated controls. Cells were passaged in the presence of increasing cadmium concentrations to induce heavy metal resistance, generating cadmium resistant cell lines. Parental cells were serially passaged in normal media to generate untreated controls.


title: Gene expression profiles in BCPAP cells treated with BRAF inhibitors

city: Milano

first: Chiara

last: Gargiuli

address: via Amadeo

department: Dept. of Applied Research and Technological Development

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

summary: We performed gene expression profiling in the human papillary thyroid carcinoma (PTC) derived cell line BCPAP harboring BRAFV600E mutation following the treatment with BRAF selective inhibitors.

overall_design: Gene expression was assessed by microarray analysis in BCPAP cells treated for 48 hours with the BRAF selective inhibitors Dabrafenib (2µM) or Vemurafenib (20µM) or with vehicle DMSO  as control; three technical replicates per condition were analyzed. Gene profiles were established by Affymetrix Clariom™ S assay (Thermo Fisher Scientific).

first: E

last: Bonaldi

last: Minna

first: C

first: M

last: Dugo

first: L

last: De Cecco

middle: G

last: Borrello


title: Engineering skeletal muscle tissues with advanced maturity improves synapse formation with human induced pluripotent stem cell-derived motor neurons

first: Megan

middle: Laura

last: McCain

state: California

address: 1042 Downey Way

department: Biomedical Engineering

summary: To develop effective cures for neuromuscular diseases, human-relevant in vitro models of neuromuscular tissues are critically needed to probe disease mechanisms on the cellular and molecular level. However, previous attempts to co-culture motor neurons and skeletal muscle have resulted in relatively immature neuromuscular junctions (NMJs). In this study, NMJs formed by human induced pluripotent stem cell (hiPSC)-derived motor neurons were improved by optimizing the maturity of the co-cultured muscle tissue. First, muscle tissues were engineered from the C2C12 mouse myoblast cell line, cryopreserved primary human myoblasts, and freshly isolated primary chick myoblasts on micromolded gelatin hydrogels. After three weeks, only chick muscle tissues remained stably adhered to hydrogels and exhibited progressive increases in myogenic index and stress generation, approaching values generated by native muscle tissue. After three weeks of co-culture with hiPSC-derived motor neurons, engineered chick muscle tissues formed NMJs with increasing co-localization of pre- and post-synaptic markers as well as increased frequency and magnitude of synaptic activity, surpassing structural and functional maturity of previous in vitro models. Engineered chick muscle tissues also demonstrated increased expression of genes related to sarcomere maturation and innervation over time, revealing new insights into the molecular pathways that likely contribute to enhanced NMJ formation. These approaches for engineering human-relevant neuromuscular tissues with relatively mature NMJs and interrogating their structure and function have many applications in neuromuscular disease modeling and drug development.

overall_design: mRNA profiles of primary Gallus gallus muscle tissue cultures on gelatin-transglutaminase hydrogels after one (5 replicates) or three (3 replicates) weeks of differentiation. Myogenic cells were derived from E10 chick embryo thighs.

first: Jeffrey

middle: W

last: Santoso


title: Dose- and sex-dependent effects of phlebotomy-induced anemia on inflammation and neurodevelopment in the neonatal mouse hippocampus

city: Minneapolis

first: Tate

last: Gisslen

state: MN

address: 2450 Riverside Avenue, East Building, MB630

institute: University of Minnesota

summary: Phlebotomy-induced anemia (PIA) is universal and highly variable in degree among preterm infants. PIA contributes to the preterm infant’s considerable neurodevelopmental risk. In the mouse, neonatal PIA causes brain tissue hypoxia and iron deficiency accompanied by long-term sex-dependent neurobehavioral abnormalities. The neuroregulatory pathways disrupted by PIA underlying these effects are unknown. This study determined the effects of PIA severity and sex on the hippocampal transcriptome of young mice. ). NGS data from mPIA females showed the least DEGs (0.5% of >22,000 genes) whereas sPIA females had the most (8.6%), indicating a dose-dependent effect. Conversely, mPIA and sPIA males showed similar changes in gene expression (5.3% and 4.7%, respectively), indicating a threshold effect. DEGs were further analyzed using the knowledge-based Ingenuity Pathway Analysis (IPA) to determine altered functional and gene networks. The patterns of gene changes induced by PIA indicate sex-specific and dose-dependent effects with increased pro-inflammation in females and decreased neurodevelopment in males. These changes may underlie the documented reduced recognition memory function in male and abnormal social-cognitive behavior in female adult mice following neonatal PIA. Collectively, these results parallel clinical studies demonstrating sex-specific behavioral outcomes as a function of neonatal anemia management.

overall_design: Neonatal mice were phlebotomized twice daily from P3-P14 at 5.25ul/g to bring hematocrit to 25% for mPIA animals and 18% for sPIA animals.Once threshold was reached,pups were bled once a day at 3.5ul/g up until P14.Non-bled controls only received a non-phlebotomizing prick to the nape.Hippocampus was dissected at P14 and RNA was extracted using the RNAqueous Total RNA isolation kit. RNA from 4 males and 4 females from each group was further processed  for sequencing.

first: Garima

last: Singh

first: Diana

middle: J

last: Wallin

first: Juan

last: Abrahante

first: Phu

middle: V

last: Tran

first: Henry

last: Feldman

first: Michael

middle: K

last: Georgieff


title: Uncovering potential lncRNAs and mRNAs in progression from acute myocardial infarction to myocardial fibrosis to heart failure

city: hebei

first: xitian

last: Hu

address: No.9 Fangbei Road, Shijiazhuang

institute: Shijiazhuang People'sHospital

summary: Background: In spite of modern reperfusion therapies, morbidity and mortality of heart failure (HF) post myocardial infarction (MI) remain elevated. The aim of this study was to identify potential long non-coding RNAs (lncRNAs) and mRNAs in progression from acute myocardial infarction (AMI) to myocardial fibrosis (MF) to HF.   Methods: Firstly, blood samples from 3 AMI patients, 3 MF patients and 3 HF patients were used for RNA sequencing. Secondly, differentially expressed lncRNAs and mRNAs were obtained in MF vs AMI and HF vs MF, followed by functional annotation of common differentially expressed mRNAs between two groups. Thirdly, interaction networks of lncRNA-nearby targeted mRNA and lncRNA-co-expressed mRNA were constructed in MF vs AMI and HF vs MF. Finally, expression validation and diagnostic capability analysis of selected lncRNAs and mRNAs were performed.  Results: Several lncRNA-co-expressed/nearby targeted mRNAs pairs including AC005392.3/AC007278.2-IL18R1, AL356356.1/AL137145.2-PFKFB3 and MKNK1-AS1/LINC01127-IL1R2 were identified. Several signaling pathways including TNF signaling pathway and cytokine-cytokine receptor interaction (involved IL18R1), fructose and mannose metabolism and HIF-1 signaling pathway (involved PFKFB3), hematopoietic cell lineage and fluid shear stress and atherosclerosis (involved IL1R2) and estrogen signaling pathway (involved FKBP5) were screened out. FKBP5, IL1R2, IRAK3, LRG1, RNASE1 and PLAC4 had a potential diagnostic value for HF.

first: X


title: An Engineered IL-15 Cytokine Mutein Fused to an Anti-PD-1 Antibody Improves Intratumoral T Cell Function and Anti-tumor Immunity

city: San Diego

first: Wenjing

last: Yanf

state: CA

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

summary:
The anti-PD-1 antibody-IL-15 cytokine fusion approach was developed to optimally activate intra-tumoral CD8+ T cells.
We engineered a fusion protein of a single, potency-reduced, IL-15 mutein and an anti-PD-1 antibody (αPD1-IL15m). This immunocytokine is designed to deliver PD-1-mediated avidity-driven IL-2/15 receptor stimulation preferentially to PD-1-positive tumor-infiltrating lymphocytes (TILs) while reducing the natural preference of IL-15 for circulating peripheral NK or T cells.

overall_design:
5x10^5 B16-F10 tumor cells were implanted s.c into mice and  tumor resected 11 days post s.c. implantation.
Following resection mice were treated with five different treatments.

last: Yang

first: Yuanming

last: Xu


title: Innate immune response to G-quadruplex binders in cancer cells

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

institute: University of Bologna

summary: G-quadruplex (G4) is non-canonical nucleic acid structure involved in a plethora of fundamental biological processes. In past decades, it has been studied as a promising pharmaceutical target for anticancer therapy. However, no G4-targeting agent has shown significant clinical effects up to date. Pyridostatin (PDS), a well-known G4 binder, can induce double-stranded DNA breaks and genome instability. We have recently shown that Pyridostatin (Pyridostatin) and other G4 binders can trigger micronuclei formation in cancer cells at non-cytotoxic concentrations. As micronuclei can play a crucial role in linking genome instability to innate immunity, we have here wondered whether G4 binders can induce immune gene activation in human MCF-7 breast cancer cells.

overall_design: By using RNA seq technology, we show that non-cytotoxic doses of Pyridostatin (PDS) can activate Interferon beta- and IRF3-dependent genes leading to an innate immune gene response in human cancer cells. In addition, immune gene activation follows the induction of micronuclei formation supporting cytoplasmic DNA as a trigger of immune gene activation.

first: Marco

last: Russo

first: Giulia

last: Miglietta


title: Genetic and Epigenetic Regulation of Skeletal Muscle Ribosome Biogenesis with Exercise

first: Yuan

last: Wen

address: 760 Press Ave

summary: Ribosomes are the macromolecular engines of protein synthesis. Factors mediating ribosome biogenesis in skeletal muscle that facilitate adaptation to exercise are multi-factorial, but may be related to ribosomal DNA (rDNA) dosage and/or epigenetic modifications to rDNA. To investigate these possibilities, we conducted reduced representation bisulfite sequencing (RRBS) on skeletal muscle biopsies from human subjects before and after exercise and to detect differences in methylation patterns during exercise adaptation.

overall_design: Examination of DNA methylation in response to acute resistance exercise. Biopsies were obtaiend at rest, 30 min,and 24h after acute exercse. (n=10, 4 x 7 x 2 exercises); 3 control subjects received biopsies without exercise.

first: Kevin

last: Murach

first: Ferdinand

last: von Walden


title: Regulation of influenza A virus infection by Lnc-PINK1-2:5

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

summary: A549 cells were transduced with a lentivirus expressing lnc-PINK1-2:5 at a MOI of 200 for 48 h. The cells were then infected with PR/8 at a MOI of 0.01 for 48 h. RNA-seq was done on the RNA samples from three vector control and three lnc-PINK1-2:5-overexpressing cells.

overall_design: RNA sequencing analysis of three control and three lnc-PINK1-2:5-overexpressing cells.

first: Chaoqun

last: Huang

first: Lin

last: Liu

first: Samuel

last: Pushparaj


title: Somatic focal copy number gains of noncoding regions of receptor tyrosine kinase genes in epileptogenic neurons

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

type: Methylation profiling by genome tiling array

summary: Epilepsy is a heterogenous group of disorders defined by recurrent seizure activity due to abnormal synchronized activity of neurons. A growing number of epilepsy cases are believed to be caused by genetic factors and copy number variants (CNV) contribute to up to 5% of epilepsy cases. However, CNVs in epilepsy are usually large deletions or duplications involving multiple neurodevelopmental genes. Here we identify focal amplifications of regulatory regions of receptor tyrosine kinase genes as a genetic abnormality in epileptogenic brains. Whole genome DNA methylation profiling identified three main clusters of which one showed strong association with receptor tyrosine kinase genes.  By copy number analysis, we identified focal copy number gains involving EGFR and PDGFRA in brain tissue of patients who underwent seizure focus resection for treatment-resistant epilepsy. The dysplastic neurons showed marked overexpression of pEGFR and pPDGFRA, while glial and endothelial cells were negative. Sequencing and DNA methylation analysis revealed that enhancer regions of EGFR and PDGFRA gene promoter were amplified, while coding regions did not show copy number abnormalities or somatic mutations. Our results identify somatic focal copy number gains of noncoding regulatory regions in the brain as a previously unrecognized genetic driver in epilepsy. Somatic copy number aberrations of regulatory regions represent a mechanism of abnormal activation of receptor tyrosine kinase genes in epilepsy. Upregulated receptor tyrosine kinases provide a potential avenue for therapy in seizure disorders.

overall_design: Dataset of 44 patients with epilepsy due to focal cortical dysplasia analyzed by DNA methylation

first: Matija

last: Snuderl


title: Miz1 Limits Tumor-promoting Function of Hepatocyte NF-κB independently of Its Transcriptional Activity in Chemical Hepatocarcinogenesis

first: Guangyan

last: Zhangyuan

state: Shanghai

address: 197 Ruijin Er Road

department: Department of General Surgery, Pancreatic Disease Center

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: NF-κB has a crucial tumor-suppression role in chemical hepatocarcinogenesis (HCC) by preventing hepatocyte apoptosis-induced compensatory proliferation. However, NF-κB is typically activated in chemical HCC animal models and in ~40% HCC patients, in which its role in tumor progression is largely not known. Here we report that transcription factor Miz1 limits tumor-promoting function of NF-κB independently of its transcriptional activity in chemical HCC. In a murine model, hepatocyte-specific deletion of Miz1 exacerbates HCC progression. Miz1 loss results in a unique sub-group of hepatocytes with upregulated NF-κB activity and pro-inflammatory cytokine production, skewing infiltrating macrophages toward M1-like pro-inflammatory phenotype. Mechanistically, Miz1 sequestrates and prevents IKK-phosphorylation of Metadherin (MTDH), thereby inhibiting NF-κB nuclear translocation and transcription activity. In HCC patient specimens, Miz1 expression is inversely correlated with phosphorylation of RelA and MTDH, and poor prognosis. Thus, Miz1 preventing hepatocytes from promoting infiltrating macrophage M1-like phenotype and inflammation in chemical HCC progression.

overall_design: Analysis of the cells from DEN/CCL4-treated Miz1Δhep and the control Miz1F/F mice

first: Beicheng

last: Sun

first: Anning

last: Lin

first: WenJie

last: Zhang

first: Guang

last: ZhangYuan


title: Functional coordination of BET family proteins

city: Daejeon

first: Seung-Kyoon

last: Kim

address: 99 Daehak-ro, Yuseong-gu,

department: Convergent Bioscience and Informatics

institute: Chungnam National University

summary: Bromodomain and extraterminal proteins (BET) are epigenetic adaptors that play critical roles in gene regulation. This protein family contains two conserved bromodomains which can mediate the interaction with acetylated histone lysine residues and/or other acetylated proteins, and one extraterminal (ET) domain. BET protein inhibition has been recognized as a promising therapeutic strategy for several diseases, including acute myeloid leukaemia, castration resistant prostate cancer, and triple negative breast cancer. BET inhibition by a specific inhibitor JQ1 caused an impairment in various brain functions but the underlying molecular mechanisms are not well understood. Among BET family members, BRD4 has been recognized for its prominent role in epigenetic regulation of gene expression. However, we have found an extensive functional redundancy and coordination among all three major BET family members (BRD2/3/4) during the activity-dependent gene induction in neurons, which is also reflected in learning and memory behavior. Our study further revealed the molecular hierarchy in the coordination of BET family proteins dissecting their distinctive functions during gene induction required for proper brain function and plasticity. Understanding the functional coordination of BET family proteins at the molecular level would be beneficial to the development of more selective interventions for various diseases that are caused by dysregulated epigenetic pathways.

overall_design: mRNA-, nascent RNA-, or ChIP-seq profiles were generated from primary mouse cortical neurons at DIV7, comparing untreated neurons to neurons treated with different stimuli for different length of time or from Fmr1 KO with littermate control in duplicate

first: Xihui

first: Gokhul

last: Kilaru

first: Cheng-Ming

last: Chiang

first: Mingon

last: Kang

first: Kimberly

last: Huber

first: Tae-Kyung


title: Loss of Tsc1 in cerebellar Purkinje cells induces transcriptional and translation changes in FMRP target transcripts

status: Public on Jul 12 2021

city: Boston

first: Kellen

last: Winden

state: MA

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

summary: Tuberous sclerosis complex (TSC) is a genetic disorder that is associated with multiple neurological manifestations. Previously, we demonstrated that Tsc1 loss in cerebellar Purkinje cells (PCs) can cause altered social behavior in mice. Here, we performed detailed transcriptional and translational analyses of Tsc1-deficient PCs to understand the molecular alterations in these cells. We found that target transcripts of the Fragile X Mental Retardation Protein (FMRP) are reduced in mutant PCs with evidence of increased degradation. Surprisingly, we observed unchanged ribosomal binding for many of these genes using Translating Ribosome Affinity Purification (TRAP). Finally, we found that the FMRP target, SHANK2, was reduced in PC synapses, suggesting that compensatory increases in ribosomal binding efficiency may be unable to overcome reduced transcript levels. These data further implicate dysfunction of FMRP and its targets in TSC and suggest that treatments aimed at restoring the function of these pathways may be beneficial.

overall_design: TRAP and bulk RNAseq from cerebellar Purkinje cells from wildtype and mutant Tsc1 animals

first: Jasbir

last: Dalal

first: Mustafa

last: Sahin


title: Gene expression profile unveils different biological effect of serum Vitamin in Hodgkin and Diffuse Large B-Cell Lymphoma

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

institute: Azienda USL- IRCCS di Reggio Emilia

summary: RNA extracted from diagnostic tumor samples of 64 patients affected by HL was analyzed on the nCounter system using the PanCancer Immune Profiling Panel.

overall_design: Gene expression profile were linked to serum Vitamin D level in HL.

first: Alessia

last: Ciarrocchi

first: Stefano

last: Luminari


title: Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (validation cohort)

city: Gainesville

first: Azra

last: Bihorac

state: FL

address: 1600 SW Archer Road

department: Medicine

institute: University of Florida

summary: Sepsis is a time-sensitive condition associated with significant mortality, morbidity, and healthcare costs, especially when the diagnosis is delayed. Clinicians often fail to accurately differentiate between sepsis and a sterile systemic inflammatory response syndrome (SIRS) among patients who incur sterile tissue damage from major surgery. Sepsis is driven by a dysregulated host response to pathogens; SIRS is driven by tissue damage. Transcriptomic profiling of whole blood or of specific cellular components of blood have been utilized for discovering underlying etiological differences between sepsis and uninfected SIRS. Blood-based gene microarrays have demonstrated efficacy in differentiating sepsis from SIRS. Urine is often collected from critically ill patients as standard clinical care, but the diagnostic utility of urine sepsis biomarkers is unknown. In this study we used single-center prospective cohorts of SIRS and sepsis patients, we tested the hypothesis that machine learning feature selection from whole genome transcriptomic urinary RNA signatures can identify gene expression patterns that differentiate between sepsis and sterile SIRS within twelve hours of sepsis onset.

overall_design: Urine was collected from 41 sepsis patients within 12 hours of sepsis onset. Urine was collected from 39 SIRS patients within 4 hours after end of surgery.

first: Sabyasachi

last: Bandyopadhyay

first: Loftus

last: Tyler

first: Tezcan

last: Ozrazgat-Baslanti

first: Ying-Chih

last: Peng

first: Larysa

last: Sautina

first: Maria

last: Lopez

first: Henry

last: Baker

first: Mark

middle: S

last: Segal

first: Parisa

last: Rashidi


title: Next Generation Sequencing Facilitates Quantitative Analysis of Mock/SARS-CoV-2 Infected humanized ACE2 Mice Olfactory Epithelium and Olfactory Bulb Transcriptomes

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

summary: SARS-CoV-2 infection causes a wide spectrum of clinical manifestations in human, and olfactory dysfunction represents as one of the most predictive and common symptoms in COVID-19 patients.  Herein we demonstrate intranasal inoculation of SARS-CoV-2 induces robust viral replication in the olfactory epithelium (OE), not olfactory bulb (OB), resulting in transient olfactory dysfunction in humanized ACE2 mice. To decipher the underlying mechanism of the observed olfactory dysfunction in SARS-CoV-2 infected mice at the molecular level, RNA-Seq analyses of the OE and OB samples from SARS-CoV-2 infected mice were performed in comparison with that from the control animals.

overall_design: To decipher the underlying mechanism of the observed olfactory dysfunction in SARS-CoV-2 infected mice at the molecular level, RNA-Seq analyses of the OE and OB samples from SARS-CoV-2 infected mice (2 and 4 dpi) were performed in comparison with that from the control animals.

first: Cheng-Feng

last: Qin

first: Qing

last: Ye


title: Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation

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

overall_design: Refer to individual Series


title: Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (discovery cohort)

overall_design: Urine was collected from 145 sepsis patients within 12 hours of sepsis onset. Urine was collected from 39 SIRS patients within 4 hours after end of surgery.


title: Niche differentiation of arsenic-transforming microbial groups in rice rhizosphere compartments as impacted by water management and soil-As concentrations

city: Overton

first: Anil

last: Somenahally

state: Texas

department: Texas AgriLife Research

institute: Texas A&M University

summary: Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, porewater and grain samples. Results indicated that intermittent flooding significantly altered As-speciation in the rhizosphere, and reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different metal-transforming functional groups. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial groups. As-transformation was coupled to different biogeochemical cycling processes establishing functional non-redundancy of rice-rhizosphere microbiome in response to both rhizosphere compartmentalization and experimental treatments. This study confirmed diverse As-biotransformation at root-soil interface and provided novel insights on their responses to water management, which can be applied for mitigating As-bioavailability and accumulation in rice grains.

first: Richard

last: Loeppert

first: Jizhong

last: Zhou

first: Terry

last: Gentry


title: Identification of Myotendinous junction (MTJ) related mRNA

city: Copenhagen

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

institute: Bispebjerg Hospital

summary: Myotendinous junction samples from horse superficial digital muscle (SDF) were compared to the neighbouring muscle and tendon tissue to  identify genes with increased expression in myotendinous junction.

overall_design: Samples (MTJ, Muscle and Tendon) from 5 different horses (Equus caballus) were analyzed by RNAseq. Small samples from the SDF muscle with attached tendon were punched out using a 4 mm diameter biopsy puncher. The samples were mounted in for cryosectioning with tendon to one side. By sectioning parallel with the tendon, muscle and tendon specific samples were obtained (approx. 200 micrometer each) as well as a sample containing both muscle, tendon and the myotendinous junction (MTJ). RNA was purified from these 3*5 samples using TriReagent and analyzed using RNA seq.