title: Transcriptome profiling of the intramuscular fat content in Longissimus dorsi between Angus and Chinese Simmental cattle

status: Public on Apr 30 2022

city: Lanzhou

first: Ya

last: zheng

address: No. 1, Yingmen Village, Anning District

country: China

institute: Gansu Agricultural University

type: Expression profiling by high throughput sequencing

summary: The intramuscular fat (IMF) content of different beef cattle breeds varies greatly, which plays an important role in taste and nutritional value. However, the molecular mechanism of fat metabolism and deposition in beef cattle is still not very clear. In this study, the meat quality traits of Angus cattle and Chinese Simmental cattle were compared, the transcriptome of the longissimus dorsi muscle (LD) between Angus cattle and Chinese Simmental cattle was then analyzed to identify key genes related to fat metabolism and adipogenesis by high-throughput RNA-seq technology. In the current study conducted a comprehensive analysis on the transcriptome of the longissimus dorsi muscle (LD) of Angus and Simmental cattle, and identified differentially expressed genes related to lipid metabolism，which may have a great impact on on the formation of IMF.

overall_design: RNAseq profiles of  Angus and  Chinese Simmental longissimus dorsi (LD)

last: Zheng

first: Qunli

last: Yu

first: Ling

last: Han

first: Yongfang

last: Gao

first: Yayuan

last: Yang


title: Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome

city: New Delhi

first: Manoj

middle: K.

last: Sharma

state: Delhi

department: School of Biotechnology

country: India

institute: Jawaharlal Nehru University

summary: We report transcriptome profiling from three developing stages of  middle internode in  sweet sorghum. Sequencing of 6 libraries (two replicates from each stage) each stage yielded  approximately 80 million reads.

overall_design: Examination of 3 different stages of middle internode  development in sweet Sorghum variety SSV84

first: Neeraj

last: Kumar

first: Vinay

last: Singh

first: Anuj

last: Dwivedi

middle: K

first: Rita


title: Impaired efferocytosis enables apoptotic osteoblasts to escape osteoimmune surveillance during aging (miRNA)

city: Nanjing

first: Rongyao

last: Xu

address: 140 Hanzhong Road, Nanjing, Jiangsu Province 210029, China.

institute: Nanjing medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: Macrophages efferocytosis of apoptotic osteoblasts (apoOBs) is a key osteoimmune process for bone homeostasis that is highly regulated in osteoimmune surveillance. However, apoOBs accumulate in aged bone marrow, where they might mount proinflammatory responses and progressive bone loss. Why apoOBs were not cleared during aging remains unknown. Here, we show that apoOBs upregulate immune checkpoint molecule CD47 with age to evade macrophages clearance. Using osteoblast- and myeloid-specific gene knockout mice, we identify histone deacetylase SIRT6 as an essential regulator of the CD47–SIRPα checkpoint. Further, apoOBs that require SIRT6-mediated chemotaxis signals can recruit macrophages by releasing apoptotic extracellular vesicles. Therapeutically, we develop two targeting delivery strategies to enhance SIRT6 activity, showing increased apoOBs clearance and delayed age-related bone loss. Collectively, our data revealed a previously unknown linkage between immune surveillance and bone homeostasis and targeting the mechanism of SIRT6-regulated apoOBs clearance could be a promising therapeutic strategy for age-related bone diseases.

overall_design: Comparative gene expression profiling analysis of miRNA-seq data in extracellular vesicles  from apoptotic osteoblasts (apoEVs)  from SIRT6f/f and Prx1cre;SIRT6f/f mice


title: Comparative RNA-seq based transcriptome profiling of waterlogging response in cucumber hypocotyls

status: Public on Apr 29 2022

city: Yangzhou

first: chen

last: xiang

address: 48 wenhui eastroad, Yangzhou, Jiangsu , China

institute: Yangzhou University

summary: Purpose: To gain a better understanding of the molecular mechanisms that enable de novo AR primordia emergence upon waterlogging, the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, Zaoer-N (waterlogging tolerant) and Pepino (waterlogging sensitive), which differed in their abilities to form AR were compared. Conclusion: This research broadens our understanding of the mechanism underlying waterlogging-triggered ARs emergence, and provides valuable information for the breeding of cucumber with enhanced waterlogging tolerance.

overall_design: expressed genes of 6 different hours  after waterlogging

first: Xuewen


title: Transcriptome changes in 11 organs after endogenous melatonin reduction

status: Public on Apr 28 2022

city: Changchun

first: Boqi

last: Zhang

state: Jilin

address: 5333 Xian Road

institute: Jilin University

summary: We knocked out the Aanat gene of mice by CRISPR CAS technology, and performed RNA-seq on brain, heart, liver, kidney, lung, skin, stomach, spleen, testis, skeletal muscle, and EWAT of 10-week-old wild-type(WT) and Aanat knockout(Aanat-/-) mice. Through the analysis of differentially expressed genes, we found the genes related to disease and tissue development. Finally, these differential genes were verified by qRT-PCR

overall_design: 11 organs mRNA profiles of 10-week-old wild type (WT) and Aanat-/- mice

first: Chunjin

last: Li

first: Xu

last: Zhou


title: Detection of gene expression level of Yersinia pestis vaccine strain EV76 at 21 and 37 degrees Celsius

city: Dali

first: Lihua

address: No. 5, Wenhua Road, Xiaguan Town, Dali Prefecture, Yunnan Province

institute: Yunnan Institute for Endemic Disease Control and Prevention

summary: In order to study the gene expression differences of ev76 in the environment and the appropriate growth temperature of flea (21 ℃) and mouse body temperature (37 ℃), we cultured ev76 at 21 ℃ and 37 ℃ respectively, collected bacterial precipitation and sequenced the transcriptome

overall_design: The experiment was divided into 21 ℃ group and 37 ℃ group. Each group was set with three parallel controls: A, B and C


title: Hypothalamic transcriptome in pure (Iberian x Iberian) and crossbred (Iberian x Large White) pigs at 2 months old

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

summary: The hypothalamus is implicated in controlling feeding and adiposity, besides many other physiological functions, and thus can be of great importance in explaining productive differences between lean and fatty pig breeds. The present study aimed to evaluate the hypothalamic transcriptome of pure Iberian (IBxIB) and Large White x Iberian crossbreds (IBxLW) at 60 days-old, produced in a single maternal environment. Results showed the implication of gender and genotype in the hypothalamic transcriptome, with 51 differentially expressed genes (DEGs) between genotypes and 10 DEGs between genders. Fourteen genotype by sex interactions were found, due to a higher genotype effect on transcriptome found in males. In fact, just 31 DEGs were identified when using only females but 158 using only males. A higher expression of genes related to mitochondrial activity in IBxIB male animals (ND3, ND4, ND5, UQCRC2 and ATP6) was found, which was related to a higher oxidative phosphorylation and greater reactive oxygen species and nitric oxide production. IBxLW male animals showed higher expression of SIRT3 regulator, also related to mitochondrial function. When females were analysed, no such differences were found, since only some differences in genes related to the tricitric acid cycle were observed. Thus, the results indicate a significant effect and interaction of the breed and the sex on the hypothalamic transcriptome at this early age.

overall_design: In total, 20 hypothalamus samples were analyzed, 5 coming from males and 5 coming from females within each genotype.

first: Ana

last: de las heras Molina


title: A novel single TCR gamma chain fused with antibody-based binding domain facilitates T cell cytotoxicity for potent anti-tumor response without forming TCR-CD3 complex

status: Public on Apr 27 2022

city: San Diego

first: Zhao

last: Chen

state: California

address: 4955 Directors Pl

country: USA

institute: Sorrento Therapeutics Inc.

summary: To test the hypothesis that the activation and regulatory signaling in γ-TCRγ-T cells could be dissimilar from the conventional TCR-T, we stimulated anti-PD-L1 δ-TCRγδ- and γ-TCRγ-T cells engineered from three different donors, and then compared the genome-wide transcriptome profiles by RNA sequencing (RNA-Seq).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  γ-TCRγ-T cells (gamma9 group) and δ-TCRγδ-T cells (g9d2 group) after antigen stimulation

first: Chen

last: Zhao

first: Yuan

last: Xiaomei

last: Runqiang


title: Dissecting genetic components associated with eye disease using integrative genomic analysis [Capture HiC]

city: San Francisco

first: Kirsty

last: Jamieson

address: 400 Parnassus Ave

institute: University of California

summary: GWAS studies have revealed thousands of variants strongly associated with AMD, yet connecting these variants to their cognate genes has not been explored. In this study we fine-mapped AMD risk loci and examined long-range cis chromatin interactions at essential genes of RPE function and disease-associated variants in iPSC-induced retinal pigmented epithelium (RPE) and primary RPE.

overall_design: Capture HiC from iPSCs (2 replicates), iPSC-induced RPE (2 replicates).

first: Yin

last: Shen


title: Real-time quantitative PCR analysis of microRNAs in serum

first: Ankita

last: Ray

address: Safdarjung hospital campus

institute: ICMR-National Institute of Pathology

summary: Human serum samples were collected from patients with history of three or more recurrent spontaneous abortion and non- pregnant women with two or more successful deliveries. Chlamydia trachomatis infection was detected in the samples collected from the patients and real time PCR was perform to study the expression of microRNA genes in these patients.

overall_design: qPCR gene expression profiling of microRNAs 101-3p, 133a, 146b-5p, 320b, 24, 559 genes in serum samples

first: Sangita

last: Rastogi


title: High throughput sequencing of MARC145, A549, HEK293, and HRT18 cells infected with Shaan virus

city: Cheongju

first: Jiyeong

last: Noh

address: Chungdae-ro 1

country: South Korea

institute: Chungbuk National University

summary:
Purpose: The goals of this study are to monitor the evolution pattern of Shaan virus in depending host cells by viral transcriptome sequencing analysis of MARC145, A549, HEK293, and HRT18 cells infected with Shaan virus.
Methods: The original isolate of Shaan virus (B16-40, Genbank accession no. MG230624.1) was passaged in MARC-145 cells. Low-passaged virus was obtained from the virus 4 times serially passaged in MARC-145 cells. The shaan virus which was 44 times serially passaged in MARC-145 cells was used for high-passaged virus.  The prepared low- (p4) and high passaged shaan virus (p44) in MARC-145 cells were inoculated in triplicate to different host cells, HEK-293, A549, and HRT18 cell lines at M.O.I of 0.5 for 2 hours. The infected cells were incubated with the maintenance medium for each cell line for 24hrs. The infected cell pellets were resuspended to 250µl with fresh medium, to extract RNA for the high-throughput sequencing. The RNA samples were sequenced with illumine TruSeq Strand Total RNA LT kit and illumine NovaSeq6000 plaform form Macrogen, Inc (Seoul, Korea) for high throughput sequencing. The raw reads were trimmed with BBDuk and mapped the isolate Bat-ParaV/B16-40 (Genebank accession number. MG230624.1) with Bowtie 2 using Geneious program 2021.2.2. Transcript expression level in cells infected with shaan virus were calculated based on annotation on a reference shaan virus.
Result: The total reads counts were between 50,285,454 and 76,298,278. The reference mapping of the trimmed reads with a reference genome (Genbank accession no. MG230624.1) showed different coverage values. The mapped reads were normalized and expressed as Transcript per Million (TPM) value. There were no noticeable differences of TPM values of each gene between the cells infected with low- and high-passaged shaan virus. However, the nucleocapsid (N) and matrix (M) gene-associated transcripts were shown to be differently measured among the host cells.
Conclusion: In this regard, we tried to investigate certain selected mutation patterns by host switching using shaan virus isolate in MARC-145 cells. Therefore, this study provided potential evidence for host-specific selective mutation patterns by cell types as well as host of cells for shaan virus evolution.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: Monitor of mutation pattern of Shaan virus transcript depending on host cells by high throghput sequencing analysis

first: Seong

middle: S

last: Jang

first: Min

middle: C

last: Kim

first: Hyun

middle: A

last: Lim

first: Hye


title: miRNA analysis after three months on GH treatment and contribute to explain the growth response after 12 months.

city: Bologna

first: Gloria

last: Ravegnini

state: BO

address: via irnerio 48

department: PHARMACY AND BIOTECHNOLOGY

country: Italy

institute: UNIVERSITY OF BOLOGNA

summary: Context: There is growing evidence on the role of epigenetic regulation of growth, and miRNAs potentially play a role. Objective: To identify changes in circulating miRNAs following GH treatment in subjects with isolated idiopathic GH deficiency (IIGHD) after the first 3 months on treatment, and verify whether these early changes can predict growth response. Methods: The expression profiles of 384 miRNAs were analyzed in serum in 10 prepubertal patients with IIGHD (5 M,5 F) at two time points before starting GH treatment (t-3, t0), and at 3 months on treatment (t+3). MiRNAs with a fold change (FC) >±1.5 at t+3 were considered as differentially expressed. In silico analysis of target genes and pathways led to a validation step on 8 miRNAs in 25 patients. Clinical and biochemical parameters were collected at baseline, 6 and 12 months. Simple linear regression analysis and multiple stepwise linear regression models were used to explain the  growth response.  Results: 16 miRNAs were up-regulated and 2 down-regulated at t+3 months. MiR-199a-5p (p=0.020), miR-335-5p (p=0.001), and miR-494-3p (p=0.026) were confirmed to be up-regulated at t+3.  Changes were independent of peak GH values at testing, and levels stabilized after 12 months. The predicted growth response at 12 months was considerably improved compared with models using the common clinical and biochemical parameters. Conclusion: miR-199a-5p, miR-335-5p, and miR-494-3p changed after 3 months on GH treatment and likely reflected both the degree of GH deficiency and the sensitivity to treatment. Furthermore, they were of considerable importance to predict growth response.

overall_design: qPCR miRNA expression profiling. Total RNA from serum of 10 IIGHD patients was extracted at 2 time points before starting GH treatment (t-3; t0) and after 3 months on treatment.

first: Cecilia

last: Catellani

first: Maria

middle: E

last: Street


title: Effect of STAT3 deletion on gene expression in HepG2 cell line

city: Wuhan

first: Deng

middle: wen

last: sheng

address: Qing ling street

department: School of Life Sciences and Health

institute: Wuhan University of Science and Technology

summary: Gene expression differential display

overall_design: To investigate the effect of STAT3 knockdown on other genes, we constructed control and STAT3 knockdown HepG2 cell lines by shRNA.We then performed gene expression profiling analysis using data obtained  from RNA-seq of CtrlshRNA and STAT3shRNA.

last: Wensheng

first: Zhang

last: Cheng


title: Bulk transcriptomic profiling of pluripotent stem cell-derived alveolar type 2 cells (iAT2s) cultured in spheres and at air-liquid interface and human HTII-280-sorted AT2s from a pediatric and adult donor lungs cultured in spheres

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

summary: We performed bulk transcriptomic profiling of pluripotent stem cell-derived alveolar type 2 cells (iAT2s) and HTII-280-sorted human AT2s cultured with CK+DCI media. We used previously described distal lung directed differentiation protocol to generate alveolar type 2 cells (iAT2s). We used the SPC2-ST-B2 (“SPC2”) line containing a SFTPC-tdTomato knock in reporter. iAT2s were cultured in 3D spheres and at air-liquid interface. Human AT2s were HTII-280-sorted from a pediatric donor lung (13 months old) and an adult, nonsmoker human lung (32 years old) and cultured as spheres in the presence of MRC5s. After deconvolution, we find that iAT2s cultured in ALI correlate more closely to primary cultured AT2s than do iAT2s cultured in 3D spheres on the basis of lung epithelial gene expression.

first: Kristy

last: Abo

first: Carlos

last: Villacorta-Martin

first: Andrew

last: Wilson


title: Expression data from cholangiocarcinoma cell lines and regorafenib treatment.

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary:
We demonstrate that regorafenib treatment suppresses multiple canonical pathways and transcriptions factors
We used microarrays to analyze the potential mechanism by which regorafenib regulates gene expression.

overall_design: HuccT1 and KKU-100 cell lines with or without regorafenib treatment for RNA extraction and hybridization on Affymetrix microarrays.

first: Yu-Chan

last: Chang


title: A partially sex-reversed giant kelp sheds light into the mechanisms of sexual differentiation in UV sexual system

city: ROSCOFF

first: Olivier

last: GODFROY

address: Place Georges Teissier CS90074

department: Station Biologique de Roscoff

country: France

institute: CNRS

summary: In UV sexual systems, sex is determined during the haploid phase of the life cycle and males have a V chromosome whereas females have a U chromosome. Previous work in the model Ectocarpus revealed that the V chromosome has a dominant role in male sex determination and the female developmental program being a ‘default’ program, triggered in the absence of the male master sex determination gene(s). Here, we describe the identification of a genetically male giant kelp strain presenting phenotypic features typical of a female, despite lacking the U-specific region. The conversion to the female developmental program is however incomplete, because gametes of this feminised male are unable to produce the sperm-attracting pheromone lamoxiren. We identify the transcriptomic pathways underlying the male and female specific developmental programs and show that the phenotypic feminisation of the variant strain is associated with both feminisation and de-masculinisation of gene expression patterns. Importantly, the feminisation phenotype was associated with the dramatic downregulation of two V-specific genes including a candidate sex-determining gene on the V-specific region. Our results reveal the transcriptional changes associated with sexual differentiation in a UV system with extensive sexual dimorphism, disentangling the role of sex-linked genes and autosomal gene expression in the initiation of the male and female developmental programs. Overall, the data presented here imply that the U-specific region in the giant kelp is not required to initiate the female developmental program, but is critical to produce fully functional eggs, arguing against the idea that female is the ‘default’ sex in this species.

overall_design: RNAseq analyses of 3 gametophytic strains (2 replicats per strains)

last: Godfroy

first: Susana

middle: M

last: Coelho


title: The gene expression of aged HDF cells.

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

institute: Ajou University School of Medicine

summary: Analysis of the gene expression of young, mid old and old cells

overall_design: HDF cells were cultured for replicated senescence then cells were harvested according to the young, mid old and old time point. The harvesting cells were extracted RNA and analysis RNA sequencing.

first: Younghwa

last: Kim

first: Tae

middle: J


title: Characteristic of the transcriptomics in the early subcortical vascular cognitive impairment [miRNA-Seq]

first: Shuwen

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

summary: Two cohorts with cerebrovascular disease are included in the present study, i.e., SCD group and VCI group. Participants in SVD group has the normal cognitive function and others in VCI group show the worse cognitive function. The whole-blood is collected from each participant, and RNA sequencing is conducted in whole-blood samples. Characteristic of circRNA, lncRNA, miRNA and mRNA are identified in the present blood samples.

overall_design:
Total samples are twenty. Ten independent samples are included in two groups, respectively.
VCI-A003 VCI-A013 VCI-A021 VCI-A023 VCI-A025 VCI-A032 VCI-A034 VCI-A041 VCI-A044 VCI-A065
SCD-A005 SCD-A008 SCD-A012 SCD-A020 SCD-A022 SCD-A029 SCD-A031 SCD-A038 SCD-A040 SCD-A067


title: Single-cell sequencing analysis of the db/db mouse hippocampus reveals cell-type-specific insights into the pathobiology of diabetes-associated cognitive dysfunction

first: renjun

last: lv

address: 222 Tianshui South Road, Chengguan District

institute: lanzhou university

summary: Diabetes-associated cognitive decline (DCD) is one of the complications of diabetes, which is characterized by a series of neurophysiological and pathological abnormalities. However, the exact pathogenesis of DCD is still unknown. Single-cell RNA sequencing (scRNA-seq) could discover unusual subpopulations, explore functional heterogeneity and identify signaling pathways and potential markers. The aim of this research was to provide deeper opinion into molecular and cellular changes underlying DCD, identify different cellular types of the diabetic mice hippocampus at single-cell level, and elucidate the factors mediating the pathogenesis of DCD. To elucidate cell specific gene expression changes in the hippocampus of diabetic encephalopathy, single-cell RNA sequencing of hippocampus from db/m and db/db mice was carried out. Subclustering analysis was performed to further describe microglial cell subpopulations. Interestingly using immunohistochemistry, these findings were confirmed at the protein level. Single cell analysis yielded transcriptome data for 14621 hippocampal cells and defined 11 different cell types. Analysis of differentially expressed genes in the microglia compartments indicated that infection- and immune system process- associated terms, oxidative stress and inflammation play vital roles in the progression of DCD. Compared with db/m mouse, experiments at the protein level supported the activation of microglia, increased expression of inflammatory factors and oxidative stress damage in the hippocampus of db/db mouse. In addition, a major finding of our research was the subpopulation of microglia that express genes related to pro-inflammatory disease-associated microglia (DAM). Our research reveals pathological alterations of inflammation and oxidative stress mediated hippocampal damage in the db/db mice, and may provide potential diagnostic biomarkers and therapeutic interventions for DCD.

overall_design: Examination of two samples from the hippocampus of db/db and db/m mice, respectively.

first: Qingqing

last: Yin

first: Shizhan

last: Ma

first: Renjun

last: Lv

first: Wenkai

last: Bi


title: Impact of SLC-0111 (U-104) on HUH6 hepatoblastoma cell transcriptome in normoxic and hypoxic conditions

city: Helsinki

first: Katja

last: Eloranta

address: Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

summary: Carbonic anhydrase 9 (CAIX) is a transmembrane metalloenzyme whose main function is to maintain the acid-base balance of the cell and hypoxic condition induces its expression. Solid tumors often exhibit regions with low oxygen content in areas where the blood supply is insufficient. CAIX is overexpressed in multiple solid tumors, including hepatoblastoma, the most frequent childhood liver malignancy. SLC-0111 is a commercially available CAIX inhibitor that is currently passed Phase I clinical trial on solid tumors. In this study we assessed the impact of SLC-0111 on transcriptomic changes of HUH6 hepatoblastoma cell line cells in both normoxic and hypoxic condition.

overall_design: HUH6 cells were treated with CAIX/XII inhibitor SLC-0111 (U-104) under normoxic or hypoxic conditions for 48 h. Cells were lysed and RNA was extracted. RNA sequencing was utilized to define transcriptomic changes caused by SLC-0111 treament in normoxia and hypoxia. In each group, four technical replicates were sequenced.

first: Marjut

last: Pihlajoki


title: RNASeq to investigate SOX2 and SOX9 function in human fetal lung tip progenitor cells

city: Cambridge

first: Dawei

last: Sun

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: In order to understand transcription factor SOX2 and SOX9 function, we have knocked down SOX2 and SOX9 in human fetal lung tip progenitor organoids using an inducible CRISPRi system. We discovered that SOX2 knockdown didn't appear to influence organoid cell survival and led to minimal gene expression changes at transcriptome level. By contrast, SOX9 knockdown led to organoid cell self-renewal defects and we have detected hundreds of genes differentially expressed after SOX9 knockdown.

overall_design: We used 2 independent organoid parental lines infected with inducible CRISPRi system. 2 different non-targeting control (NT) gRNAs, which do not bind to anywhere of the genome, 2 different gRNAs targeting for SOX2 knockdown, and 2 different gRNAs targeting for SOX9 knockdown were used to control non-specific effect from organoid lines, lentiviral infection and different gRNAs.

first: Walfred

middle: W

last: Tang

first: Emma

middle: L

last: Rawlins


title: RNA-sequencing in skeletal muscle from a mouse model of laparotomy with pre-operative running wheel exercise

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: This study aimed to characterize the effects of pre-operative volitional running wheel exercise on post-operative physical function and skeletal muscle gene expression in 24-month-old C57BL/6N mice following laparotomy. Soleus muscles collected on post-operative day 5 (POD 5) were used for this study.

overall_design: 12 soleus muscle samples from 24-month-old C57BL/6N male mice were analyzed by RNA-sequencing. Muscles were collected from the laparotomy groups and age matched control groups 5 days post laparotomy surgery. 6 samples (3 replicates for control and 3 replicates for laparotomy) were analyzed for two groups of 24-month-old mice designated as 24-month-old low functioning (LF) and 24-month-old high functioning (HF) groups based on the animal’s performance on the accelerating rotarod. The expression levels for the laparotomy groups were compared to the control groups.

first: Fred

last: Ko

first: Samantha

last: Asche-Godin


title: Copy number variations of Ph+ ALL, Ph+ MPAL and Ph+ AML

city: Suzhou

first: Wenzhi

last: Cai

address: 296 Shizi Street

institute: The First Affiliated Hospital of Soochow University

type: Genome variation profiling by genome tiling array

summary:
We aim to compare the genomic discrepancies across de novo Ph+ ALL, Ph+ MPAL and Ph+ AML, three diseases characterized by the occurrence of BCR-ABL1 transcripts but showing varied immunophenotypes. The data we are now submitting is the genomic copy number variants of these three groups. The following is the abstract with associated manuscript.
The chromosome abnormality of Philadelphia (Ph) is typically seen in de novo acute lymphoblastic leukemia (ALL). It has also been identified in mixed phenotype acute leukemia (MPAL) and acute myeloid leukemia (AML) in the revisions to World Health Organization classification of myeloid neoplasms and actue leukemia. The discrepancies between these patients and potential mechanisms underlying differentiation fate of the leukemia cells remain poorly defined. We evaluated the clinical, genomic and transcriptomic features of Ph+ ALL, Ph+ MPAL and Ph+ AML by taking advantage of high-density genomic analysis, including next-generation sequencing array comparative genomic hybridization and gene expression profiling for transcriptomic analysis. Our results showed that the three cohorts demonstrated diversified clinical features. Ph+ ALL had the best response to induction therapy, with a complete remission (CR) rate of 93.5 and molecular response of 43.5%. Ph+ MPAL had a 90.0% CR rate but only 5.9% of molecular response. The CR rate of Ph+ AML was only 68.8%. Ph+ ALL was characterized by loss and mutations of B-cell development gene IKZF1 and PAX5, and frequent histone H3K36 trimethyltransferase SETD2 mutations. SETD2 mutations were detected in 11.3% of Ph+ ALL patients and predicted higher relapse rate. Ph+ MPAL and Ph+ AML featured high frequency of RUNX1 mutations. Further studies showed RUNX1-R177X mutation inhibited 32D cell differentiation induced by G-Csf, and cooperated with BCR-ABL1 to lead to myeloid differentiation arrest of human cord blood CD34+ cells. It is therefore presumed that these additional mutations work in synergy with BCR-ABL1 fusion gene to facilitate the development of Ph-positive acute leukemia in different immunophenotypic classifications.

overall_design:
Biological replicates of mononuclear cells from patients at diagnosis with Ph+ ALL (37 patients), Ph+ MPAL (7) and Ph+ AML (6)

Please note that processed data (log2[test/control] ratios) is provided in multiple Series supplementary files as indicated in the corresponding sample description field.

first: Suning

last: Chen


title: Genomic Profiling of MYC in 797 cells containing BRD4-NUT with JQ1 treatment

first: Mitzi

middle: I

last: Kuroda

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital/Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The oncogene cMYC (HGNC ID: HGNC:7553) is a critical genomic target of the BRD4-NUT (B4N) protein that defines many of the NUTM1-rearrangement cancer subtypes.  B4N interacts with the EP300 lysine acetyltransferase (KAT) to create hyperacetylated “megadomains” that activate downstream genes such as MYC. However, it is less well understood how mis-regulation of MYC in turn affects its protein interactions and target genes.  The goals of this study are to define the protein and genomic interactions of MYC in NUT carcinoma, and to test whether those change in response to B4N inactivation.  We used CRISPR-Cas9 mediated knock-in of a BioTAP affinity tag to analyze MYC protein expressed from its normal chromosomal context.  This allowed us to adapt a crosslinking purification method termed BioTAP-XL to preserve MYC integrity and chromatin association for genomic and mass spectrometry-based proteomic analyses.  We found that MYC interacts primarily with NuA4 KAT subunits and that the interactions were maintained despite a decrease in MYC levels after JQ1 treatment. We propose that future analysis of MYC transcriptional regulation in NUT carcinoma, and likely other cancers, should prioritize how MYC recruits KAT complexes to modify the chromatin of its many gene targets.

overall_design: Chromatin immunoprecipitation of MYC-BioTAP in 797 cells containing the BRD4-NUT fusion protein treated with DMSO or JQ1

first: Barry

last: Zee

first: Artyom

last: Alekseyenki

first: Anne

last: Smolko


title: GATA-3 is a proto-oncogene in T-cell lymphoproliferative neoplasms [RNA-seq]

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

summary: In order to identify GATA-3 target genes in T-cell lymphoproliferative neoplasms, we performed GATA-3 ChIP-seq on 3 cutaneous T-cell lymphoma (CTCL) and 4 T-cell acute lymphoblastic leukemia (T-ALL). We have also established cell lines in which GATA-3 was knocked down by shRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 7 cell lines and its KD derivatives.

first: Xiangrong

last: Geng

first: Ryan

last: Wilcox


title: Characteristic of the transcriptomics in the early subcortical vascular cognitive impairment [RNA-Seq]

city: Nanjing

first: Shuwen

last: Cheng


title: The gene expression of co-cultured mid old cells

first: Tea jun

last: Park

summary: Investigation of the rejuvenation effect to mid old cell, we co-cultured mid old cell with young cell or mid old cells. After 30days we harvest cells and extrect RNA then anlaysis the gene expression.

overall_design: The mid old cells co-cultured with young cell or mid old cell.

first: Younghwa

last: Kim

first: Tae


title: Transcriptome analysis of Scramble control and Cdk14-sh mouse mammary basal cells

city: wuhan

first: Mengna

last: Zhang

state: State...

address: Donghu Road, No. 115, Wuchang District

institute: wuhan university

summary: Wnt/β-catenin signaling pathway has become a key signaling pathway regulating mammary organogenesis and oncogenesis. However, the therapeutic methods by targeting Wnt pathway against breast cancer has been limited. To address this challenge, we investigated the function of cyclin-dependent kinase 14 (CDK14), a member of Wnt signaling pathway, in mammary development and breast cancer progression. We showed that CDK14 was expressed in the mammary basal layer and elevated in triple negative breast cancer (TNBC). CDK14 knockdown reduces colony formation ability and regeneration capacity of mammary basal cells, and significantly inhibits murine MMTV-Wnt-1 basal-like mammary tumor progression. Excitingly, knockdown of CDK14 or pharmacological inhibition of CDK14 by FMF-04-159-2 significantly inhibited the progression and metastasis of human TNBC. Mechanistically, CDK14 inhibition inhibits mammary regeneration and TNBC progression by attenuating Wnt/β-catenin signaling. Together, we demonstrated that CDK14 regulates mammary regeneration and breast tumorigenesis, and is a promising therapeutic target for TNBC.

overall_design: Examination the different mRNA level in Scramble control and CDK14-sh MDA-MB-231 cells

first: Cheguo

first: Lingxian


title: Transcriptomic analysis of fumarate compounds identifies unique effects of isosorbide di-(methyl fumarate) on NRF2, NF-kappaB and IRF1 pathway genes

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

summary: Dimethyl fumarate (DMF) has emerged as first-line therapy for relapsing-remitting multiple scle-rosis (RRMS). This treatment, however, has been limited by adverse effects, which has prompted development of novel derivatives with improved tolerability. We compared effects of fumarates on gene expression in astrocytes. Our analysis included diroximel fumarate (DRF) and its metabolite monomethyl fumarate (MMF), along with a novel compound isosorbide di-(methyl fumarate) (IDMF). Treatment with IDMF resulted in the largest number of differentially expressed genes. The effects of DRF and MMF were consistent with NRF2 activation and NF-kappaB inhibition, respectively. IDMF responses, however, were concordant with both NRF2 activation and NF-kappaB inhibition, and we confirmed IDMF-mediated NF-kappaB inhibition using a reporter assay. IDMF also down-regulated IRF1 expression and IDMF-decreased gene promoters were enriched with IRF1 recognition se-quences. Genes altered by each fumarate overlapped significantly with those near loci from MS genetic association studies, but IDMF had the strongest overall effect on MS-associated genes. These results show that next-generation fumarates such as DRF and IDMF have effects differing from those of the MMF metabolite. Our findings support a model in which IDMF attenuates oxidative stress via NRF2 activation, with suppression of NF-kappaB and IRF1 contributing to mitigation of in-flammation and pyroptosis.

overall_design: We treated human fetal astrocytes with sterile distilled water (CTL), MMF (2.5 µM), DRF (2.5 µM) or IDMF (2.5 µM) for 24 hours (n = 3 per treatment) and evaluated gene expression using Clariom S microarray assays.

first: Krzysztof

last: Bojanowski

first: Ratan

last: Chaudhuri


title: Characteristic of the transcriptomics in the early subcortical vascular cognitive impairment

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

overall_design: Refer to individual Series


title: Effect of overexpression of yeast Ppz1 protein phosphatase on gene remodeling in response to changes in carbon source

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

summary: Our previous results (Calafi et al 2020; PMID: 32339526) demonstrated a defect in cell proliferation when PPZ1 was overexpressed under the control of a tetO-based promoter that was, up to some extent, dependent of the availability of glucose. To further investigate this phenomenon, we have determined the transcriptional response triggered by the shift form high to low glucose, or to galactose, in normal cells and in cells overexpressing PPZ1 from the tetO7–driven multicopy pCM190 plasmid. Our data suggest that, under these circumstances, overexpression of Ppz1 interferes with the proper activation of a set of genes mainly involved in carbon metabolism, thus impairing the normal transcriptional adaptation to conditions in which glucose becomes limiting.

overall_design: Two different types of BY4741-based yeast cells were used: 1) cells containing the empty pCM190 plasmid and 2) cells carrying the same pCM190 plasmid with the PPZ1 coding region under control of the doxycycline-repressed tetO7 promoter.     Both types of cells were shifted to medium containing 2% glucose, 0.25% glucose or 2% galactose, and grown for 1h before sample collection.

first: Antonio

last: Casamayor

first: María

last: López-Malo

first: Joaquin

last: Ariño


title: Capped nascent RNA sequencing reveals novel therapy-responsive enhancers in prostate cancer

city: Ithaca

first: Haiyuan

last: Yu

address: 335 Weill Hall

department: Department of Computational Biology

institute: Cornell University

summary: Mounting evidence suggests that enhancer RNA (eRNA) transcription start sites (TSSs) provide higher sensitivity and specificity for enhancer identification than histone modifications and chromatin accessibility. The extent to which changes in eRNA transcription correspond to changes in enhancer activity, however, remains unclear. Here, we used precision run-on and capped RNA sequencing (PRO-cap) to assess changes in enhancer activity in response to treatment with the androgen receptor signaling inhibitor, enzalutamide. We identified 6,189 high-confidence candidate enhancers in the human prostate cancer cell line, LNCaP, 853 of which demonstrated significant changes in activity in response to drug treatment. Notably, we found that 67% and 54% of drug-responsive enhancers did not show similar changes in activity in previous studies that utilized ChIP-seq and ATAC-seq, respectively. More strikingly, 79% of regions with increased eRNA transcription showed no other biochemical alterations, implying that PRO-cap can capture a set of precise changes in enhancer activity that classical approaches lack the sensitivity to detect. We performed in vivo functional validations of candidate enhancers and found that CRISPRi targeting of PRO-cap-specific drug-responsive enhancers impaired ENZ regulation of downstream target genes, suggesting that changes in eRNA TSSs mark true biological changes in enhancer activity with high sensitivity. Our study highlights the utility of using PRO-cap as a complementary approach to canonical biochemical methods for detecting precise changes in enhancer activity, in particular for better understanding disease progression and responses to treatment.

overall_design: We used precision run-on and capped RNA sequencing (PRO-cap) to assess changes in enhancer activity in response to treatment with the androgen receptor signaling inhibitor, enzalutamide in the human prostate cancer cell line, LNCaP.

first: Kellie

last: Cotter

first: Sagar

last: Shah

first: Mauricio

last: Paramo

first: Shaoke

last: Lou

first: Li

last: Yao

first: Philip

middle: D

last: Rubin

first: You

last: Chen

first: Mark

last: Gerstein


title: Epigenome analysis of formalin-fixed paraffin-embedded (FFPE) meningioma samples

city: New York

first: Department of Pathology

last: NYU Langone Health

state: NY

address: 240 East 38th Street

department: Department of Pathology

institute: NYU Langone Health Ambulatory Care Center

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of formalin-fixed paraffin-embedded (FFPE) meningioma samples. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 methylation sites across the genome at single-nucleotide resolution.

overall_design: Bisulphite converted DNA from the 64 samples were hybridised to the Illumina Infinium MethylationEPIC Human Methylation Beadchip v1.0.

first: Cai

last: Chunyu

first: Snuderl

last: Matija


title: Potential and functional prediction of six Circular RNAs as diagnostic markers for colorectal cancer

city: Yinchuan

first: Yuan

middle: li

last: Liu

state: Ningxia

address: Guangdong Medical University, 1 Xincheng Avenue, Songshan Lake Science and Technology Industrial Park, Dongguan City, Guangdong Province

institute: Clinical Laboratory and Diagnosis Center of Ningxia Hui Autonomous Region People's Hospital

summary: In order to search for circRNA differentially expressed in colorectal cancer tissues and adjacent normal tissues, the cancer tissues and adjacent normal tissues of 3 patients with colorectal cancer(TNM:ⅡB) were selected for circRNA microarray detection. Differentially expressed circRNAs were screened.Then qRT-PCR was used to verify.

overall_design: Three patients with CRC were selected for circRNA Microarray analysis, and Arraystar Human circRNA Array V2 was used for analysis. Sample markers and chip hybridization were Based on Agilent One-color Microarray-based Gene Expression Analysis experimental scheme (Agilent Technology).

first: Liyuan


title: NAD+ Modulates the Proliferation and Differentiation of Adult Neural Stem/Progenitor Cells via Akt Signaling Pathway

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

summary: Collectively, our findings provide some insights into the roles and mechanisms in which NAD+ regulates aNSPCs and neuronal development.

overall_design: In the present study, we studied the roles of nicotinamide adenine dinucleotide hydrate (NAD+) in regulating aNSPCs.

first: Xiaoli

last: Huang

first: Xuekun

last: Li


title: Environmental Induced Epigenetic Transgenerational Inheritance of Pathology: Systems Epigenetics in Disease Etiology and Generational Toxicology

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Several epigenome-wide association studies (EWAS) have been shown to identify epigenetic alterations (i.e., epimutations) associated with diseases. The sperm epimutations potentially involved in the transgenerational inheritance of specific pathologies have been identified. Transgenerational sperm epimutations associated with kidney, prostate, puberty, testis, obesity, and multiple pathologies have been identified for a variety of environmental toxicants including dioxin, plastics, pesticides, glyphosate, methoxychlor, atrazine, and jet fuel. The transgenerational sperm epimutations for exposure and disease-specific epimutations have been identified in these EWAS studies. The current study used the information from these previous toxicant-induced epigenetic transgenerational inheritance EWAS rat studies and adds a comparable control group, rats that have not been exposed to any particular toxicant. Two additional control groups were collected and are presented here.

overall_design: From embryonic day E8 to E14 the F0 generation gestating females were administered daily intraperitoneal injections of dimethyl sulfoxide (DMSO) (vehicle control) with an equal volume of sesame oil (Sigma) to prevent irritation at the injection site. The offspring F1, F2 and F3 generations were all aged to 70-90 days of age and bred within the generation and within the control lineage. The F3 generation is the first without a direct exposure to the vehicle control and is thus comparable to the transgenerational generation in the exposure lineages. All the animals were aged to 1 year and euthanized for pathology and sperm collected for epigenetic analyses. No sibling or cousin breeding was used to prevent any inbreeding artifacts in the control lineage. An MeDIP-seq approach was used to identify DMRs associated with specific transgenerational diseases.

first: Daniel

last: Beck

first: Eric

last: Nilsson

first: Millissia

middle: B

last: Maamar


title: AC-265347 inhibits neuroblastoma tumor growth by induction of differentiation without causing hypocalcemia

city: Esplugues de Llobregat

first: Soledad

last: Gómez-González

address: Santa Rosa, 39-57, 4a planta

department: Oncology

institute: Hospital Sant Joan de Déu

summary: Neuroblastoma is the most common extracranial solid childhood tumor with clinical manifestations ranging from benign tumors that spontaneously regress to highly aggressive metastatic disease. Unfortunately, there is no therapy known to be curative for high-risk neuroblastoma. The calcium-sensing receptor (CaSR) is a G protein-coupled receptor that senses plasmatic fluctuation in the extracellular concentration of calcium and plays a key role in maintaining calcium homeostasis. We have previously reported that this receptor exhibits tumor suppressor properties in neuroblastoma. The activation of CaSR with cinacalcet, a positive allosteric modulator of CaSR, reduces neuroblastoma tumor-growth by promoting differentiation, ER stress and apoptosis. However, these promising results came with an associated side effect, since cinacalcet exposure resulted in hypocalcemia. Based on the biased signaling shown by calcimimetics, we aimed to identify a new drug that might exert tumor-growth inhibition similar to cinacalcet without affecting plasma calcium levels. We identified a structurally different calcimimetic AC-265347 as a promising therapeutic agent for neuroblastoma, since it reduced tumor-growth by induction of differentiation, without affecting plasma calcium levels. Microarrays analysis suggested biased allosteric modulation of the CaSR signaling by both calcimimetics towards distinct intracellular pathways since no upregulation of genes involved in calcium signaling and ER stress were observed in PDX models exposed to AC-265347. Moreover, the most significant upregulated biological pathways promoted by AC-265347 were linked to RHO GTPases signaling. AC-265347 also up-regulated cancer testis antigens (CTAs), thus providing new opportunities for CTA-based immunotherapies. Taken together, this study helps to shed light about the importance of the biased allosteric modulation when targeting GPCRs in cancer. More importantly, the capacity of AC-265347 to promote differentiation of malignant neuroblastoma cells provides new opportunities, alone or in combination with other drugs, to control minimal residual disease and to prevent relapse in patients affected with neuroblastoma.

overall_design: Total RNA was extracted from 8 tumor xenografts exposed to CIN, AC-265347 or their vehicle.

last: Gomez-Gonzalez

first: Silvia

last: Mateo-Lozano

first: Cinzia

last: Lavarino


title: Rec8 cohesin-mediated loop-axis chromatin architecture is required for meiotic recombination

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

summary: During meiotic prophase, cohesin-dependent axial structures are formed in the synaptonemal complex (SC). However, functional correlation between these structure formation and cohesion remains elusive. Here we examined formation of the cohesin-dependent axial structure in fission yeast, which forms atypical SCs composed of linear elements (LinEs) resembling the lateral elements of SC but lacking the central elements, and found that Rec8 cohesin is crucial for the formation of the loop-axis structure within the atypical SC. Furthermore, the Rec8-mediated loop-axis structure is formed in the absence of LinEs, and provides a structural platform for aligning homologous chromosomes. We also succeeded to identify a rec8 mutant that lost the ability of assembling the loop-axis structure without losing cohesion. Remarkably, this mutant showed defects in LinE assembly, resulting in great reduction of meiotic recombination. Collectively, our results demonstrate an essential role of the Rec8-dependent loop-axis structure in LinE assembly, facilitating meiotic recombination.

overall_design: Hi-C experiment during meiosis of fission yeast

first: Takeshi

last: Sakuno

first: Sanki

last: Tashiro

first: Osamu

last: Iwasaki

first: Da-Qiao

last: Ding

first: Tokuko

last: Haraguchi

first: Ken-ichi

last: Noma

first: Yasushi

last: Hiraoka


title: Gene profile of human medullary thyroid cancer

city: Milan

first: Emanuela

last: Minna

state: Select...

address: via Amadeo 42

institute: Istituto Nazionale dei Tumori

summary: We report gene expression profiling in a series of 17 human medullary thyroid cancer (MTC) tissues, including 8 primary tumors and 9 patient paired neck nodes metastases, in comparison with 3 non-neoplastic thyroid tissues. For the same series we have previously reported miRNA expression profiles (GSE97070 series).

overall_design: Eight sporadic MTC patients were selected for the gene microarray analysis. A total of 17 MTCs (8 P = primary tumor and 9 M = nodal metastasis) and 3 non-neoplastic thyroids (N) were obtained from formalin-fixed paraffin-embedded (FFPE) surgical specimens. The primary tumors and the matched nodal metastases were obtained from the initial surgery or from a subsequent lymphadenectomy. Referring to the matched primary tumor, 6 of the nodal metastases were synchronous and 3 were metachronous (one patient had both metastasis types included in the array). Non-neoplastic thyroid samples were obtained from patients with pathologies other than thyroid cancer. For each specimen haematoxylin and eosin-stained sections and calcitonin-stained sections were evaluated by an experienced pathologist to confirm the histological diagnosis and to select areas in which tumor cells represented at least the 80% of the total cells. MTC samples correnspond with those reported in GSE97070 miRNA series, as well as 2 of the 3 non-neoplastic thyroids (N_a and N_g). The other non-neoplastic thyroid sample (N_c) was not available for gene profiling and replaced by a new control sample (N_b).

first: Paola

last: Romeo

first: Maria

middle: G

last: Borrello

first: Loris

last: De Cecco

first: Matteo

last: Dugo


title: Transcriptomics of THP-1 macrophages treated with or without IL-26 for 24h

city: Shanghai

first: zhihua

last: Ran

address: 160 pujian road

department: Division of Gastroenterology and Hepatology

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

summary: Purpose: The aim of this study was to obtain a comprehensive transcriptomic analysis of IL-26-exposed macrophages.  Methods: THP-1 derived macrophage were generated by incubating THP-1 cells with PMA (50 ng/ml) for 24h.Then THP-1 macrophages were treated with IL-26 for 24h, which were collected and applied to RNA-sequencing. The constructed sequencing library was sequenced using an Illumina Novaseq 6000 system. The expression of transcripts was calculated as fragments per kilobase of exon model per million mapped reads (FPKM).  Results: In total, we identified 1303 differentially expressed protein-coding genes between untreated and IL-26-treated macrophages, including 667 up-regulated and 636 down-regulated genes.

overall_design: THP-1 macrophages treated without (Control; n=3) or with IL-26 (0.28 μM,Treatment; n=3)

first: Dongjuan

last: Song

first: Lijie

last: Lai

first: Juntao

last: Lu

first: Jinlu

last: Tong

first: Zhihua


title: Differential Expression Profiles of tRNA-derived Small RNAs in Muscle-Invasive Bladder Cancer in Chinese Population

city: Beijing

first: Chuan

last: Qin

address: No.95,yong an road.

department: Department of Urology

institute: Beijing Friendship Hospital, Capital Medical University

summary: The goals of this study are to screen differential expression profiles of tRNA-Derived small RNAs (tsRNAs) in muscle-invasive bladder cancer (MIBC) in Chinese population using next-generation sequencing and qRT-PCR.As a result, in MIBC tissues, 406 tsRNAs were differentially expressed between in MIBC tissues. Of them, 91 tsRNAs were significantly differentially expressed (fold change>1.5; P<0.05): 65 tsRNAs were significantly up-regulated whereas 26 were significantly down-regulated in MIBC.Taken together,this study explored, for the first time, the significant alteration of tsRNA expression profiles in MIBC  in Chinese population and offered deep insights into many possible treatment targets of MIBC by regulating tsRNAs.

overall_design: This sequencing study includes tissue samples from 4 MIBC patients, all of whom had undergone surgery for MIBC at the department of urology in Beijing Friendship Hospital affiliated to Capital Medical University (Beijing, China) in 2021. This study was approved by the ethics committee of the Beijing Friendship Hospital affiliated to Capital Medical University and conducted according to 1975 Declaration of Helsinki ethical standards, as revised in 2008. MIBC specimens (T group) and adjacent control mucosal tissues (N group) with a distance of 3 cm from the tumor) were collected during the surgery and immediately stored in liquid nitrogen to prevent RNA degradation. In total, 4 pairs of tissues (tumor and paracancer) were used for tsRNA sequencingAll patients who participated provided written informed consents.The expression profiles of tsRNAs were generated by deep sequencing, using NextSeq 500/550 V2 kit (#FC-404-2005, Illumina).

first: Ye

last: Tian


title: MITF deficiency accelerates GNAQ-driven uveal melanoma

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Cutaneous melanoma (CM) and uveal melanoma (UM) both originate from the melanocytic lineage but are primarily driven by distinct oncogenic drivers, BRAF/NRAS or GNAQ/GNA11 respectively. The melanocytic master transcriptional regulator, MITF, is essential for both CM development and maintenance, but its role in UM is largely unexplored. Here, we use zebrafish models to dissect the key UM oncogenic signaling events, and establish the role of MITF in UM tumors. Using a melanocytic lineage expression system, we showed that patient-derived mutations of GNAQ (GNAQQ209L) or its upstream CYSLTR2 receptor (CYSLTR2L129Q) both drive UM when combined with a cooperating mutation, tp53M214K/M214K. The tumor-initiating potential of the major GNAQ/11 effector pathways, YAP and PLCβ-ERK, was also investigated in this system, and thus showed that while activated YAP (YAPAA) induced UM with high potency, the patient-derived PLC4 mutation (PLCB4D630Y) very rarely yielded UM tumors in the tp53M214K/M214K context. Remarkably, mitfa deficiency was profoundly UM promoting, dramatically accelerating the onset and progression of tumors induced by Tg(GNAQQ209L);tp53M214K/M214K or Tg(CYSLTR2L129Q);tp53M214K/M214K. Moreover, mitfa loss was sufficient to cooperate with GNAQQ209L to drive tp53-wildtype UM development, and allowed Tg(PLCB4D630Y);tp53M214K/M214K melanocyte lineage cells to readily form tumors. Notably, all of the mitfa-/- UM tumors, including those arising in Tg(mitfa:PLCB4D630Y);tp53M214K/M214K;mitfa-/- fish, displayed nuclear YAP while lacking hyperactive ERK indicative of PLCβ signaling. Collectively, these data show that YAP signaling is the major mediator of UM, and that MITF acts as bona fide tumor suppressor in UM, in direct opposition to its essential role in CM.

overall_design: Comparison of zebrarfish uveal melanomal tumors from 5 genotypes/anatomical locations: Tg(mitfa:GNAQ_Q209L), tp53-/-, mitfa-/- (n=10); Tg(mitfa:GNAQ_Q209L), mitfa-/- (n=10); Tg(mitfa:GNAQ_Q209L), tp53-/-, eye (n=8); Tg(mitfa:GNAQ_Q209L), tp53-/-, skin (n=9); Tg(mitfa:BRAF_V600E), tp53-/- (n=9);

first: Hannah

last: Hagen

first: Grace

last: Phelps

first: Adam

last: Amsterdam

first: Jacqueline

last: Lees


title: Purine synthesis inhibitor L-Alanosine impairs mitochondrial function and stemness of brain tumor initiating cells

city: Durham

first: Simranjit

middle: X.

last: Singh

state: NC

address: 203 Research Drive, MSRB1 Room 143

institute: Duke University

summary: Glioblastoma (GBM) is a lethal brain cancer exhibiting high levels of drug resistance, a feature partially imparted by tumor cell stemness. Recent work shows that homozygous MTAP deletion, a genetic alteration occurring in about half of all GBMs, promotes stemness in GBM cells. Exploiting MTAP loss-conferred deficiency in purine salvage, we demonstrate that purine synthesis blockade via treatment with L-Alanosine (ALA), an inhibitor of de novo purine synthesis, attenuates stemness and mitochondrial function of MTAP-deficient GBM cells. Here, we use RNA-Seq with ALA-treated patient-derived GBM cells to investigate the transcriptomic impact of long-term ALA treatment.

overall_design: mRNA-seq analysis of L-Alanosine-treated patient-derived GBM cells

middle: X

first: Yiping

last: He


title: Alteration of ileal lncRNAs after bariatric surgery is associated with regulation of lipid and amino acid metabolism

first: Yongjun

last: Liang

address: 2800 Gongwei Road

department: Center for Medical Research and Innovation

institute: Shanghai Pudong Hospital

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

summary: Metabolic and bariatric surgery (MBS) can generate a drastic shift of coding and non-coding RNAs expression pattern, which triggers organ function remodeling and may induce type 2 diabetes (T2D) remission. Our previous studies demonstrated that the altered expression profiles of duodenal and jejunal long noncoding RNAs (lncRNAs) after the duodenal-jejunal bypass (DJB), an investigational procedure and research tool of MBS, can improve glycemic control by modulating entero-pancreatic axis and gut-brain axis, respectively. As an indiscerptible part of intestine, the ileal lncRNAs expression signatures after DJB and the critical pathways associated with postoperative correction of impaired metabolism need to be investigated

overall_design: A cohort of male C57BL/6 mice were received from Shanghai Slyke Laboratory Animal Corporation (Shanghai, China). After one-week acclimatization, mice started to undergo high fat diet. At the end of 12 weeks HFD, 8 animals with typical diabetic phenotypes were selected and randomized into DJB or Sham groups based upon the procedure received.

first: Peng

last: Zhang


title: Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe Universität Frankfurt am Main


title: Histone deacetylase inhibitors impair glioblastoma cell motility and proliferation

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
Despite being subjected to high dose chemo and radiotherapy, glioblastoma (GBM) patients still encounter almost inevitable relapse due to the capability of tumor cells to disseminate and invade normal brain tissues. Moreover, the presence of a Cancer Stem Cell (CSC) subpopulation, already demonstrated to better resist and evade treatments, further frustrate potential therapeutic approaches. In this context, we previously demonstrated that GBM is characterized by a tightly regulated balance between the β-catenin cofactors TCF1 and TCF4, with high levels of TCF4 responsible for sustaining CSC in these tumors, thus supporting their aggressive features. Since Histone Deacetylase Inhibitors (HDI) have been reported to strongly reduce TCF4 levels in colon cancer cells, we hypothesized they could exert a similar therapeutic action also in GBM. Here, we treated primary GBM cultures with Trichostatin-A and Vorinostat, demonstrating their ability to strongly suppress the Wnt dependent pathways, thus promoting CSC differentiation, and concomitantly impairing GBM cell viability and proliferation. More interestingly, analysis of their molecular effects suggested a prominent HDI action against GBM cell motility/migration, that we demonstrated to be dependent on the inhibition of the RhoA-GTPase and interferon intracellular cascades. Our results suggest HDI as potential therapeutic agents in GBM through their action on multiple cancer hallmarks.
Glioblastoma (GBM) is considered the deadliest brain tumor, with patients displaying a high incidence of relapse and a 3-year survival of only 3-5%. For these reasons, investigation of the molecular basis of the disease could provide novel targets for therapy and improve patient prognosis. Based on our previous data demonstrating that high levels of the transcription factor TCF4 (TCF7L2) sustain the aggressiveness and the stem cell features of these tumors, in this study we tested the ability of the histone deacetylase inhibitors (HDI) Trichostatin-A and Vorinostat to suppress TCF4 levels. We demonstrated that HDI treatment impairs proliferation and viability of GBM cells. Moreover, molecular analysis of HDI effects disclosed their ability to counteract tumor cell motility by affecting the RhoA-GTPase and the interferon pathways, supporting their further characterization as potential anti-GBM agents

overall_design: Gene expression was measured using Affymetrix platform in primary GBM cells trated with HDAC inhibitors (Trichostatin-A and Vorinostat)

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

summary: The aim of the project was to investigate the effect of nuclear receptor activation, particularly of the vitamin D receptor, on chromatin structure, and associated functional changes in the transcriptional response of THP-1 cells.

overall_design: HiC was performed on THP-1 cells, with either control (24 h vehicle) or 24 h 100 nM 1,25(OH)2D3 treatment.

first: Sabine

last: Seuter

first: Ralf

last: Brandes


title: The effect of chondrocytes cocultured with bone marrow stem cells (BMSCs)

city: Nanjing

first: Ziyang

last: Zheng

address: Longmian Avenue NO.101

institute: The first affiliated hospital of nanjing medaical university

summary: To investigate the altered gene expression levels in chondrocytes cocultured with BMSCs. Each group had a biological repeat (n=3). Results provide insight into the effect of chondrocytes cocultured with bone marrow stem cells

overall_design: Three groups of chondrocytes cocultured with bone marrow stem cells (coculture group) versus three groups of chondrocytes cultured alone (control group).

first: Qiang

last: Zuo

first: Kai

last: Shen


title: Intellectual disability associated with craniofacial dysmorphism due to POLR3B mutation and defect in spliceosomal machinery

city: Tehran

first: kolsoum

last: InanlooRahatloo

address: velenjak

country: Iran

institute: University of social welfare and rehabilitation sciences

summary: Intellectual disability (ID) is a clinically important disease and a most prevalent neurodevelopmental disorder. The etiology and pathogenesis of ID are poorly recognized.   Exome sequencing revealed a homozygous missense mutation in the POLR3B gene in a consanguineous family with three Intellectual disability with craniofacal anomalies patients. POLR3B gene encoding the second largest subunit of RNA polymerase III. To explore how genetic variants alter cell expression in ID patients, RNA sequencing on blood samples was performed and to obtain insights into the biological pathways influenced by POLR3B mutation, we applied our RNA-Seq data to several gene ontology programs such as ToppGene, Enrichr, KEGG. We detected a significant decrease expression of several spliceosomal RNAs, ribosomal proteins and transcription factors in our ID patients. We hypothesize that POLR3B mutation dysregulates the expression of some important transcription factors, ribosomal and spliceosomal genes and impairments in protein synthesis and splicing mediated in part by transcription factors such as FOXC2, GATA1, .. contribute to impaired neuronal function and concurrence of intellectual disability and craniofacial anomalies in our patients. Our study highlights the emerging role of spliceosome and ribosomal proteins in intellectual disability.

overall_design: comparison of expression profile between intellectual disability patients and controls

first: Kolsoum

first: Mostafa

last: Saghi


title: Loss of talin in cardiac fibroblasts results in augmented ventricular cardiomyocyte hypertrophy in response to pressure overload

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

summary: To look at the affect of talins in cardiac fibroblasts (CF), we subjected Tln2-null and Tln2-null; Tln1-specific CF knockout mice to AngII stimulation for 8 weeks to induce pressure overload injury. We found that Tln2-null; Tln1-specific CF knockout mice had increaed cardiomyocyte hypertrophy and systolic blood pressure, with not change in intersitial fibrosis.

overall_design: Left Ventricle tissue was collected from Tln2-null and Tln2-null; Tln1-specific CF knockout hearts of mice treated with AngII for 8 weeks. Eeach group consisted of 8 mice (4 males and 4 females).

first: Natalie

last: Noll

first: W

last: Merryman


title: Phenotype of Mrps5-associated polymorphisms is intimately linked to mitoribosomal misreading

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Recently, we have identified a point mutation V338Y in mammalian nuclear-encoded mitochondrial protein MrpS5 that confers error-prone mitochondrial protein synthesis. In-vivo, mutation V338Y was associated with a distinct phenotype including impaired mitochondrial function, enhanced susceptibility to noise-induced hearing damage, anxiety-related behavioral alterations, and age-associated metabolic changes in muscle. To challenge the link between V338Y-mediated misreading and in-vivo phenotype, we introduced mutation G315R into the MRPS5 gene; MRPS5 G315R is homologous to the established bacterial ram mutation uS5 G104R. In contrast to the phylogenetically closely related bacterial translation, the corresponding MRPS5 G315R mutation did not affect the accuracy of mitochondrial protein synthesis. In addition, in the absence of mitochondrial misreading, homozygous mutant MRPS5G315R/G315R mice did not show phenotype distinct from wild-type animals.

overall_design: Transcriptomic profile of total RNA extracted from HEK cells stably transfected with MRPS5 WT or mutant

first: Erik

middle: C

last: Böttger

first: Dimitri

last: Shcherbakov

first: Rashid

last: Akbergenov


title: Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

first: Timothy

last: Warwick

summary: The aim of the project was to investigate the effect of nuclear receptor activation, particularly of the vitamin D receptor, on CTCF-defined 3D chromatin structure, and associated functional changes in the transcriptional response of THP-1 cells.

overall_design: CTCF HiChIP of three biological replicates of either 1,25D or control treated THP-1 cells.


title: Smarcb1 is indispensable for the nervous system development and its loss results in a deregulation of esBAF binding [RNA-seq]

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: Using RNA-seq technology, we aimed to provide insight into the consequences of the knockdown of Smarcb1, an essential esBAF subunit, for the gene expression of murine embryonic stem cells. We were able to show that knockdown cells show both, an upregulation and a downregulation, of a high number of genes. Further, many of these genes are connected to central cellular processes like cell organization or cell adhesion as well as to critical developmental processes like nervous system development.

overall_design: mRNA profiles of Smarcb1 wildtype and Smarcb1 knockdown murine ESC

first: Kornelius

last: Kerl

first: Amelie

last: Alfert


title: Smarcb1 is indispensable for the nervous system development and its loss results in a deregulation of esBAF binding [ChIP-seq]

summary: Using ChIP-seq technology, we aimed to provide insight into the consequences of the knockdown of Smarcb1, an essential esBAF subunit, for the binding of the esBAF complex (Smarca4), the PRC2 complex (Ezh2) as well as for histone marks H3K27me3, H3K27ac and H3K4me3. We show that Smarcb1 knockdown results in the change of BAF complex binding in both directions: decreased binding (potentially by loss of function) as well as increased binding (potentially by retargeting). Furthermore, we see that binding changes especially occur in regions important for basic cellular functions (adhesion, cell organization, metabolism) as well as regions crucial for development (especially nervous system development). In addition, we depicted binding changes in enhancer regions in which a decrease of BAF binding was much more prominent than in gene regions.

overall_design: Genome-wide binding of Smarca4, Ezh2, H3K27me3, H3K27ac and H3K4me3 in Smarcb1 wildtype and Smarcb1 knockdown mESC


title: Smarcb1 is indispensable for the nervous system development and its loss results in a deregulation of esBAF binding.

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

overall_design: Refer to individual Series


title: RNA-seq Analysis of the target genes of ALV-miR-p19-01 in DF-1 cells

city: Guangzhou

first: Yiming

last: Yan

address: Wushan Road

institute: South China Agricultural University

summary: In order to found the target genes of ALV-miR-p19-01 which encoded by ALV-J, we used RNA-pull down and RNA-seq. The resulted showed there were 917 potential target genes of ALV-miRNA-p19-01 had been identified

overall_design: The labeling RNA incubated with  cell lysate to form RNA protein complex, and then separated the complex to obtain mRNA. The mRNA were identified by RNA-seq.


title: miRNA expression profiling of intestinal epithelial cells from a spontaneous mice model of ulcerative colitis

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

summary: Increased intestinal permeability is associated to the onset of inflammatory bowel disease (IBD) since the exposition to luminal content causes an immunological response that promotes intestinal inflammation. Several studies have been shown that microRNAs (miRNAs) are involved in IBD pathogenesis. Here, we aimed to functionally characterize the role of miRNAs in the regulation of intestinal permeability. miRNA profile of intestinal epithelial cells (IECs) isolated by colon of a UC mice model were identified using microarray. To predict the target genes of modulated miRNAs, we performed a bioinformatic analysis. To validate biologically miRNA targets, we performed transient transfection experiments in HT-29, Caco2 and T84 cell lines. To assess their role in barrier function, trans-epithelial electrical resistance and dextran flux assays were used. To investigate the in vivo effect of miR-195-5p, we employed a DSS-induced colitis model in mice. We identified 18 deregulated miRNAs in IECs from UC mice model and control mice. Among them, down-regulated miR-195-5p targeted CLDN2 and are involved in altered intestinal permeability. CLDN2 expression levels were increased in UC mice models and negatively correlated with the miR-195-5p expression. We demonstrated that the gain-of-function of miR-195-5p in colonic epithelial cell lines decreased the CLDN2 levels. We in vitro confirmed that miR-195-5p was able to control the intestinal barrier integrity. We also in vivo demonstrated that miR-195-5p attenuated the colonic inflammatory response in DSS-induced colitis and reduced the colonic permeability. All together our data support a previously unreported role of miR-195-5p in intestinal permeability and provide a potential pharmacological target for new therapeutic approaches in IBD.

overall_design: miRNA profiling of intestinal epithelial cells isolated from 4 wild-type mice and 4 Winnie mice (ulcerative colitis mice model).

first: Viviana

last: Scalavino

first: Emanuele

last: Piccinno

first: Gianluigi

last: Giannelli

first: Raffaele

last: Armentano


title: Anticancer Agent P-Bi-Tat Links The Thyroid Hormone Receptor On Integrin Αvβ3 To Cancer Cell Metabolism/Atp Generation [Suit2-P-biTAT]

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Microarray analysis was carried out on human SUIT2 cells exposed to P-bi-TAT (10-6 M tetrac equivalent) for 24 h. P-bi-TAT significantly downregulated electron transport chain genes ATP5A1 (ATP synthase A1), ATP51, ATP5G2, COX6B1 (cytochrome c oxidase subunit 6B1), NDUFA8 (NADH dehydrogenase [ubiquinone] FA8), NDUFV2 and other NDUF genes, SLC25A6 (solute carrier group 2), UCP2 ([mitochondrial] uncoupling protein 2) and COX5A. The NDUF and ATP genes are also relevant to control of oxidative phosphorylation and transcription. Six additional NDUF genes linked to oxidative phosphorylation were affected. Conclusions. P-bi-TAT caused downregulation of expression of a panel of genes involved in electron transport, oxidative phosphorylation, and cytoplasmic ribosomal protein generation in GBM cells. A key component of the anticancer activity of P-bi-TAT relates to disordering of ATP generation mechanisms in tumor cells.

overall_design: Studied the anticancer functions of P-bi-TAT in SUIT cells in terms of modulation of transcription by the drug of genes essential to cancer cell mitochondrial function. Compared with triplicate SUT2 cells with SUIT2 cells treated with P-bi-TAT (30 µM) for 24 h.

first: Gennadi

last: Glinsky

first: Thangirala

last: Sudha

first: Godugu

last: Kavitha

first: Shaker

middle: A

last: Mousa

first: Paul

last: Davis


title: Facile Diversification of Interleukin-2 Pharmacology with Surrogate Agonists

city: Stanford

first: Michelle

last: Yen

state: CA

address: 279 Campus Dr. West, Beckman Center, room B-173

department: Molecular and Cellular Physiology

institute: Stanford University

summary: Cytokines, such as interleukin-2, initiate signaling by dimerizing their receptors into orientations and proximities that induce intracellular signaling. We wished to explore a new pharmacological strategy for cytokine discovery based on variation of receptor dimer geometries using surrogate ligands, since natural cytokines are structurally limited as engineering scaffolds. Here, we report a structurally agonistic approach based on a modular, ‘plug and play’ class of ligands, that is amenable to high-throughout screening. We isolated nanobodies (Nb) and scFvs against human IL-2Rβ and γc, and generated a 40-member combinatorial matrix of tandem single-chain bispecific (IL-2Rβ:γc) molecules. We identified 28 surrogate IL-2 ligands exhibiting a wide range of agonist strengths and biased signaling properties, including cell-type bias for NK expansion and cytotoxity relative to T cells. Crystal structures of select Nb:receptor complexes validated that alternative receptor dimer geometries underly the functional diversification. This “cytokine med-chem” approach is generalizable to many dimeric cell surface receptor systems.

overall_design: RNA-seq analysis of human CD8+ T cells that were stimulated with native cytokines (IL-2, IL-15, IL-7), IL-2 surrogate agonists, or unstimulated for 24 hr.


title: Targeting the tumor mutanome for personalized vaccination in lung cancer

city: Southampton

first: JAYA

last: THOMAS

address: MP824 Somers Building, Southampton General Hospital, Tremona Road,

department: Cancer Science

institute: University of Southampton

summary: Cancer is characterized by an accumulation of somatic mutations, of which a significant subset can generate cancer-specific neoepitopes that are recognized by autologous T cells. Neoepitopes are emerging as important targets for cancer immunotherapy, including personalized cancer vaccination strategies. We used whole-exome and RNA sequencing analysis to identify potential neoantigens for a patient with non-small cell lung cancer. Sequencing revealed a low tumor mutational burden: 2,219 sequence variants were identified from the primary tumor, of which 23 were expressed in the transcriptome, involving 18 gene products. We assessed autologous T-cell reactivity to the candidate neoantigens using a long peptide approach and could demonstrate spontaneous T-cell responses to 5/18 (28%) mutated gene variants. Further, analysis of the TCR repertoire of neoantigen-specific CD4+ and CD8+ T cells revealed TCR clonotypes that were expanded in both blood and tumor tissue. In parallel, the 18 gene variants were incorporated into a Modified Vaccinia Ankara-based vaccine, which was evaluated in the transgenic HLA-A*02-restricted HHD mouse model. Following vaccination, de novo T-cell responses were generated to 4/18 (22%) mutated gene variants, of which 2 were also observed in the autologous setting; we determined the MHC restriction of the T-cell responses and used in silico prediction tools to determine the likely neoepitopes. Our study demonstrates the feasibility of efficiently identifying tumor-specific neoantigens that can be targeted by vaccination in tumors with a low mutational burden, and promises successful clinical application, with trials currently underway.

overall_design: The immune profile of the patient of interest's primary lung tumor (TP01; Fase461) and parasternal metastasis (TP02; Fase548) was contextualized using whole tumor RNA-seq data from a cohort of 18 lung tumor samples (submitted here);  plus 47 consecutively collected HNSCC tumor samples that have previously reported (data available in GEO accession number GSE72536)

first: Katy

last: McCann

first: Adrian

last: von Witzleben

first: Jaya

last: Thomas

first: Chuan

last: Wang

first: Oliver

last: Wood

first: Divya

last: Singh

first: Kaidre

last: Bendjama

first: Nathalie

last: Silvestre

first: Finn

last: Nielsen

first: Gareth

first: Tilman

last: Sanchez-Elsner

first: Jason

last: Greenbaum

first: Stephen

last: Schoenberger

first: Bjoern

last: Peters

first: Pandurangan

last: Vijayanand

first: Natalia

last: Savelyeva

first: Christian

middle: H

last: Ottensmeier


title: miRNA profiling in DVT patients and control subjects

city: Jinan

first: Chu

last: Chu

address: 18877 Jingshi Road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary:
Microarray and quantitative real-time PCR (qRT-PCR) results showed that the Caspase-1 expression was increased while miR-513c-5p level was decreased substantially in DVT patients, and there was significant negative correlation between miR-513c-5p and Caspase-1. Knockdown of miR-513c-5p could aggravate DVT formation by enhancing Caspase-1-mediated pyroptosis, while overexpression of miR-513c-5p could alleviate DVT formation via inhibiting Caspase-1 expression.
we identified pyroptosis of PBMCs with elevated expression of Caspase-1 in DVT patients. miRNA microarray analysis revealed miR-513c-5p as the most significantly down-regulated miRNA in DVT and the receiver operating characteristic (ROC) analysis showed that miR-513c-5p level could sensitively discriminate DVT from healthy controls.

overall_design: Total RNA was extracted from PBMCs using TRIzol (Invitrogen, Carlsbad, CA, USA). The genome-wide analysis of miRNA expression in DVT patients (n= 6) and control subjects (n= 6) were performed using Human miRNA, Release 21.0 (8*60K, Design ID:070156).

first: Bin

first: Wen

last: Liu

first: Xia

last: Li


title: Tumor microenvironment and transcriptional analysis of CD45+ leukocytes isolated from syngeneic MC38 tumors from mice fed ketogenic diet or control diet

city: Lexington

first: Qingding

address: 760 Press Ave

institute: University of Kentucky

summary: Tumor microenvironment (TME) has a dynamic composition that affects targeted therapies for colorectal cancer (CRC). Cancer associated fibroblasts (CAFs) direct and induce infiltration of immunosuppressive cells through secreted cytokines such as CXCL12. Here, we show that decreased ketogenesis is a signature of CRCs and that an increase in ketogenesis, using a ketogenic diet (KD), decreases CXCL12 in CAFs, tumors, serum, livers, and lungs. Increase in ketogenesis results in the decreased expression of KLF5, which binds to the CXCL12 promoter and induces CXCL12 expression. KD decreases intratumoral accumulation of M2 macrophages and myeloid-derived suppressor cells (MDSCs), increases infiltration of NK and cytotoxic T cells and enhances the anticancer effects of PD-1 blockade in murine-derived CRCs. Moreover, an increase in ketogenesis inhibits CRC migration, invasion, and metastasis in vitro and in vivo. Importantly, our studies demonstrate that downregulation of de novo ketogenesis in the TME is a critical step in CRC progression.

overall_design: Single-cell transcriptional analysis of CD45+ leukocytes isolated 14 days post-implantation from subcutaneous MC38 tumors in C57BL6/J mice fed control or ketogenic diet. Each sample contains CD45+ cells combined from 5 mice.


title: Transcriptomic differences in murine AML bone marrow samples with different Gab2 genotypes

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Internal tandem duplications (ITD) of FLT3 predict poor prognosis in acute myeloid leukemia (AML) and often co-exist with inactivating DNMT3A mutations. In a genetically modified mouse model harboring these genetic aberrations, we analyzed the role of the adaptor protein Gab2 in this disease. We observed Gab2 to be essential for the development of Flt3-ITD driven AML in vivo, which was corroborated by RNA sequencing data of whole murine bone marrow with different Gab2 genotypes

overall_design: Whole bone marrow was isolated from AML mice (Mx1-Cre; Dnmt3a+/-; Flt3ITD/ITD) with different Gab2 genotypes. Three of these donor mice were Gab2 WT, three Gab2 KO and two mice were Gab2 HET. After RNA isolation, samples were sequenced on an Illumina HiSeq4000.

first: Melanie

last: Boerries

first: Corinna

last: Spohr

last: Brummer


title: Toxicological Transcriptome of Human Airway Constructs After Exposure to Indoor Air Particulate Matter: In Search of Relevant Pathways of Moisture Damage -Associated Health Effects

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

institute: University of Eastern Finland

summary: Background - Multiple health effects are associated with moisture damage in buildings. Studies explaining these associations and cell-level mechanisms behind the observed health effects are urgently called for.  Objectives - Alongside general toxicological markers, we focused on characterizing gene expression in human airway epithelium after exposure to indoor air particulate matter (PM) sampled from houses with and without moisture damage.  Methods - We performed detailed technical building inspections in 25 residential houses and categorized them based on the detection of moisture damages and the probability of occupant exposure. PM sampling was complemented by microbiological and volatile organic compound assessment. We exposed airway constructs to three doses (1:16, 1:8, 1:4) of PM from moisture-damaged (index) and non-moisture-damaged (reference) houses. The RNA of exposed constructs was sequenced targeting toxicology -related genes. We did groupwise comparisons between index and reference houses and pairwise comparisons in matched index/reference houses. We analyzed general toxicological markers and imaged the constructs with electron microscopy.  Results - In pairwise comparison, several genes were differentially expressed. Genes related to multiple toxicological pathways were highlighted, while none of the genes was consistently expressed in all the comparisons. In groupwise comparison, CYP1A1 was statistically significantly over-expressed in index houses at all doses (dose 1:16 log2FC = 0.007, padj = 0.03; dose 1:8 log2FC = 0.077, padj = 0.018; dose 1:4 log2FC = 0.270, padj = 0.002) and NFKB1 at the highest dose 1:4 (log2FC = 0.124, padj = 0.029). General toxicological markers did not separate the index/reference houses.  Discussion - The exposure to PM from index houses activates toxicology -related genes in airway constructs. While differential expression was not consistent among all the index/reference pairs, possibly due to compositional differences of bioactive particles, our study highlights CYP1A1 and NFKB1 as potential targets in moisture damage -associated cellular responses.

overall_design: Human airway constructs (differentiated from normal human bronchial epithelial [NHBE] cells) were exposed to three doses (1:16, 1:8, 1:4) of indoor air particulate matter from moisture-damaged (index) and non-moisture-damaged (reference) houses in synthetic lung lining fluid, and RNA-sequenced in 3-4 replicates, targeting toxicology -related genes.

first: Kati

last: Huttunen

first: Maria-Elisa

last: Nordberg


title: Global gene expression analysis of CD10+/CD19+ pre B lymphoblasts from bone marrow and peripheral blood of B-ALL patients

city: TLALNEPANTLA

first: LAURA

last: CASTAÑEDA-PARTIDA

state: ESTADO DE MÉXICO

address: AV. DE LOS BARRIOS 1

department: BIOLOGY

country: Mexico

institute: FES IZTACALA, UNAM

summary:
Acute lymphoblastic leukemia (ALL) is the most frequent childhood cancer. Mexico City has one of the highest incidences in the world, with pediatric patients showing a poor response to conventional therapy, low survival rates and high relapse rates.
We performed a global gene expression profile of pre B lymphoblasts from bone marrow (BM) and peripheral blood (PB) samples from B-ALL patients to find the upregulated and downregulated genes in both cell populations in the context of this childhood cancer.

overall_design: We implemented a flourescence activated cell sorting (FACS) protocol to isolate CD10+/CD19+ precursor B (pre-B) lymphoblasts from four bone marrow (BM) and nine peripheral blood (PB) samples of B-ALL patients for RNA extraction and hybridization on Affymetrix microarrays  We sought to prevent contamination with other mononuclear or non-leukemic cells and have high purity RNA. This would allow to obtain more accurate data on the gene expression from both pre-B lymphoblasts populations in mexican pediatric patients.

first: Laura

last: Castañeda-Partida

first: Rodolfo

last: Ocadiz-Delgado

first: Enrique

last: García-Villa

first: José

last: Peñaloza-González

first: Martha

middle: M

last: Velázquez-Aviña

last: Torres-Nava

first: Jorge

last: Martín-Trejo

first: Karina

last: Solís-Labastida

first: Francisco

last: Guerra-Castillo

first: Vilma

last: Bekker-Méndez

first: Víctor

last: Rosales-García

first: Dámaris

last: Romero-Rodríguez

first: Raúl

last: Mojica-Espinoza

last: Sánchez-López

first: Alfonso

last: Mendez-Tenorio

first: Crystel

last: Ramírez-Calzada

first: Elízabeth

last: Álvarez-Ríos

first: Juan

last: Mejía-Aranguré

first: Patricio

last: Gariglio


title: High-throughput sequencing of primary proximal tubule cells from male and female C57BL/6 Diet1+/+ and Diet1–/– mice

city: Los Angeles

first: Karen

last: Reue

address: 695 Charles E Young Dr South

institute: University of California, Los Angeles

summary: RNA sequencing was performed on primary proximal tubule cells from 1 month old male and female mice with or wtihout the Diet1 gene

overall_design: Primary proximal tubule cells were passaged once and then submitted for RNA sequencing

first: Jessica

last: Ong


title: Effect of Crenigacestat treatment in xenograft model of  HUCCT1 intrahepatic cholangiocarcinoma

first: Grazia

last: Serino

summary:
Intrahepatic Cholangiocarcinoma (iCCA) is a difficult type of cancer to diagnose, extremely aggressive and resistant to therapeutic options with an increased incidence and mortality over time. The overexpression of Notch pathway is implicated in iCCA to create an ecosystem that drives the tumor aggressiveness. Specifically, Notch1 is overexpressed in iCCA tissue of patients, playing an important role on tumor growth. Our purpose was to investigate the effectiveness of Crenigacestat in in vivo experiments, using Hucct1 injected in CD1 mice to generate an iCCA xenograft mouse model. In the present study, in order to explore modulated factors and genes by treatment we performed a transcriptomic analysis validated by Western Blotting and qRT-PCR on iCCA tumor masses of xenograft mice. Our results indicate that the treatment significantly inhibited Notch1 and HES1 genes and proteins triggering a strong immune response. Nevertheless, moderate fibrosis was shown in this model which may have hindered response to therapy to promote tumor progression.
We used microarray technology to understand the molecular mechanisms affected by Crenigacestat in HUCCT1 xenograft model of intraepatic cholangiocarcinoma.

overall_design: Expression profiling of HUCCT1 xenograft mice model of intrahepatic cholangiocarcinoma after and before Crenigacestat treatment.

first: Serena

last: Mancarella

first: Gianluigi

last: Giannelli


title: The Caspase-Activated DNAse drives chromosomal instability and cancer metastasis

first: Elham

last: Bavafaye Haghighi

address: Breisacherstr. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

institute: University Hospital of Freiburg

summary: Chromosome-segregation errors in cancer cells are linked to chromosomal instability, the appearance of micronuclei and subsequent intracellular signaling events that drive cancer metastasis. The cause of these aberrations is not well-defined but a link to DNA-damage has been established. The Caspase-Activated DNAse (CAD) has been discovered for its role in the degradation of DNA in apoptotic cells but can also be activated in the absence of cell death. We here show that spontaneous CAD-activity drives chromosome missegregation, micronuclei generation, invasive growth and metastasis in human cancer cells. Genomic deletion of CAD reduced chromosome missegregation in mouse intestinal organoids as well as in tumor cells. CAD-deficient human cancer cells showed reduced migration, invasion and anchorage-independent growth in vitro as well as reduced metastatic potential in zebrafish and in mice. CAD-deficient cells displayed a substantially altered gene-expression profile, which overlapped with the profile of cells deficient in the Stimulator of Interferon Genes (STING). Multiple cancer signaling pathways were found to be regulated by CAD. A CAD-associated gene expression signature strongly predicted poor survival in cancer patients. These results identify CAD as a regulator of a signaling programme that determines cancer progression and prognosis.

overall_design: Total RNA was isolated from ctrl, CAD deficient, STING deficient, or zVAD treated Hela 229 and MDA-MB-231 cell lines. 4 riplicates were used for "Sequencing"

first: A

last: Haimovici

first: C

last: Höfer

first: MT

last: Badr

first: E

first: M

last: Börries

first: P

last: Bronsert

first: I

last: Glavynskyi

first: D

last: Fanfone

first: G

last: Ichim

first: T

last: Brummer

last: Spohr

first: R

last: Öllinger

first: KP

last: Janssen

last: Rad

last: Häcker


title: Epilepsy progression mediates cumulative DNA methylation changes in inflammatory genes.

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

summary: DNA methylation profiling of hippocampus and anterior temporal neocortex from MTLE-HS patients subjected to resective epileptic surgery and cadaveric non-epileptic controls. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in brain homogenates.

overall_design: Bisulphite converted DNA from the 33 samples were hybridised to theIllumina Infinium MethylationEPIC Beadchip.

first: Ricardo

last: Martins-Ferreira

first: Bárbara

last: Leal

first: Chaves

last: João

first: Tianlu

last: Li

first: Laura

last: Ciudad

first: Rui

last: Rangel

first: Agostinho

last: Santos

first: António

last: Martins da Silva

first: Paulo

middle: P

last: Costa


title: Differential expression of circRNAs discriminates between different maturational stages of human intrathymic thymocytes.

city: Madrid

first: Pilar

last: López Nieva

address: Nicolas Cabrera 1

institute: Centro de Biología Molecular Severo Ochoa

summary: Circular RNAs (circRNAs) are stable single stranded RNA molecules which form a covalently closed continuous loop. They are involved in multiple biological processes,  functioning mainly through interactions with microRNAs and proteins or by the expression of specific peptides. Preliminary data exist on circRNA expression in different peripheral blood cell populations. Deregulation of circRNAs has been shown to be key in the development of T-cell acute lymphoblastic leukemia (T-ALL). However, a detailed analysis on circRNAs expression in intrathymic thymocyte populations was still missing and might be key to understanding thymus development as well as tumours arising in the lymphoblastic line. The aim of this study was to investigate whether circRNAs are differentially expressed in thymocytes at different maturational stages during the intrathymic differentiation process.

overall_design: Differential circRNA expression analysis in thymocytes at different stages of intrathymic differentiation

first: Jose

last: Fernandez-Piqueras

last: Lopez Nieva

first: Pablo

last: Fernandez Navarro

first: María

last: Ángeles Cobos-Fernández

first: Iria

last: González Vasconcellos

first: Javier

first: Raúl

last: Sánchez Pérez

first: Ángel

last: Aroca


title: A developmentally programmed splicing failure attenuates the DNA damage response during mammalian zygotic genome activation

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

institute: UCL

summary: The transition from maternal to embryonic transcriptional control is a crucial step in embryogenesis. However, how alternative splicing is regulated during this process and how it contributes to early development is unknown. Using transcriptomic data from pre-implantation stages of human, mouse and cow, we show that the stage of zygotic genome activation (ZGA) exhibits the highest levels of exon skipping diversity reported for any cell or tissue type. Interestingly, much of this exon skipping is temporary, leads to disruptive non-canonical isoforms, and occurs in genes enriched for DNA damage response in the three species. We identified two core spliceosomal components, Snrpb and Snrpd2, as regulators of these patterns. These genes have low maternal expression at the time of ZGA and increase sharply thereafter. Consistently, microinjection of Snrpb/d2 mRNA into mouse zygotes reduces the levels of temporary exon skipping at ZGA, and leads to an increase in etoposide-induced DNA damage response. Altogether, our results suggest that mammalian embryos undergo an evolutionarily conserved and developmentally programmed specific splicing failure at the time of genome activation that attenuates cellular responses to DNA damage at these early stages.

overall_design: SNRPB/D2 OE vs control in 1-2cell mouse embryos

first: Barbara

last: Pernaute

first: Manuel

last: Irimia