title: Novel functional analysis of MET exon 14 skipping alteration in driving cancer invasion and metastatic dissemination

city: Bronx

first: Feng

last: Wang

address: 1300 Morris Park Ave

institute: albert einstein college of medicine

summary: MET exon 14 skipping alteration (MET∆14Ex) is an actionable oncogenic driver that occurs in 2-4% of non-small cell lung cancer (NSCLC) cases. However, the precise role of MET∆14Ex in tumor progression in NSCLC is poorly understood. We here demonstrate that MET∆14Ex expression increases receptor kinase activity and downstream signaling by impairing receptor internalization and endocytic degradation, which significantly boosts tumor cell scattering and invasion as well as metastasis. To explore the key mechanisms in regulation of these phenotypes, RNA sequencing (RNA-seq) studies were conducted on HGF-treated MET∆14Ex and MET cell models in an effort to identify the global change of transcriptome signature and key functional pathways involved in MET∆14Ex-medieated tumorigenesis. Both Ingenuity pathway analysis (IPA) and gene set enrichment analysis (GSEA) revealed an induction of a tight cluster of functional pathways associated with cell movement in HGF-treated MET∆14Ex models (vs MET) in a time-dependent manner.

overall_design: In order to gain insights into the key molecular pathways involved in the biological effects of METD14Ex, an RNA-seq study was conducted on MET and METD14Ex cells treated with HGF for 0, 6 and 24h. Then, both Ingenuity pathway analysis (IPA) and gene set enrichment analysis (GSEA) were conducted to identify the global change of transcriptome signature and key functional pathways involved in MET∆14Ex-medieated tumorigenesis.

first: Wang

last: Feng

first: Liu

last: Yang

first: Cheng

last: Haiying

first: Halmos

last: Balazs


title: IL-37 negatively regulates IL-33 expression in human keratinocytes

status: Public on Dec 31 2021

city: Fukuoka

first: Gaku

last: Tsuji

address: Maidashi

country: Japan

institute: Kyushu University

summary: Interleukin (IL)-37 suppresses systemic and local inflammation. It is expressed in the epidermis, the external layer of the skin, and is decreased in inflammatory skin diseases including atopic dermatitis (AD) and psoriasis. Therefore, an agent applied topically on the skin that can increase IL-37 could be promising for treating AD and psoriasis; however, the mechanism regulating IL-37 remains largely unknown. Given that IL-37 expression is induced in differentiated keratinocytes, a major component of the epidermis, and that activation of aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor, promotes keratinocyte differentiation, we hypothesized that AHR might be involved in the IL-37 expression in human keratinocytes. We analyzed normal epidermal human keratinocytes (NHEKs) treated with tapinarof and Galactomyces fermentation filtrate (GFF), which are potent AHR modulators. We found that tapinarof and GFF upregulated IL-37 in NHEKs, which was canceled by the knockdown of AHR using siRNA transfection, indicating that AHR mediates IL-37 expression in NHEKs. Furthermore, we found that the knockdown of IL-37 resulted in the upregulation of  IL-33, an alarmin cytokine with crucial roles in the pathogenesis of AD and psoriasis. These findings suggest that IL-37 negatively regulates IL-33 expression in NHEKs. Finally, we examined whether tapinarof and GFF treatment modulates IL-33 expression in NHEKs. Such treatment inhibited IL-33 expression, which was partially reversed by the knockdown of either AHR or IL-37. Taken together, our findings provide the first evidence that tapinarof and GFF could have potential to prevent IL-33-overexpressing disorders such as AD and psoriasis via the AHR/IL-37 axis.

overall_design: Human keratinocytes transfected either siRNA control or siRNA against IL-37 were analyzed (N=3).

first: Akiko

last: Hashimoto-Hachiya

first: Tomoyo

last: Matsuda-Taniguchi

first: Ayako

last: Takai-Yumine

first: Masaki

last: Takemura

first: Xianghong

last: Yan

first: Masutaka

last: Furue

first: Takeshi

last: Nakahara


title: Small RNA sequencing of extra-cellular RNAs from arsenite-stressed HeLa cells and mouse embryonic fibroblasts

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: Stress-induced tRNA fragmentation is an evolutionarily conserved molecular phenomenon. A variety of the resulting tRNA-derived small RNAs (tsRNAs) have been associated with a multitude of cellular processes including cell survival during adverse environmental conditions. However, application of experimental stressors under laboratory conditions often differs from stress encountered naturally. This raises important questions about the extent of experimental bias when studying stress biology including tRNA fragmentation, especially in cell culture. Here, we have revisited one of the most often used experimental paradigms for modeling oxidative stress and tRNA fragmentation, the exposure of cultured cells to sodium arsenite. These experiments revealed that transient exposure to sodium arsenite concentrations that caused robust tRNA fragmentation resulted in extensive cell death during the stress recovery. Importantly, released material from dying cells contained also tsRNA species, which were sufficiently stable against nuclease digestion.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In order to determine the identity of RNAs that were sufficiently stable for 24 hours after being released by dying cells that had been transiently exposed to sodium arsenite (0.75 mM for one hour), cell culture medium was collected after 24 hours recovery, all RNAs were extracted and sequenced.

first: Matthias

middle: R

last: Schaefer


title: Acute Transcriptomic Response After Mouse Spinal Cord Injury

city: San Francisco

first: Jonathan

last: Pan

state: CA

address: 1001 Potrero Ave, Bldg 5, Room 3C38

department: Anesthesia and Perioperative Care

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: In order to characterize genomic response and identify molecular marker for acute neural injury, we performed RNA-sequencing 4 hours after spinal cord injury. We found a group of genes with significant differential expression (DEG) after Benjamini-Hochberg FDR multiple corrections. These DEGs mainly include early response genes, neuroinflammation, and cell injury and death. Notely, activating transcription factor 3 (ATF3) is one of the most significantly upregulated genes by 9.9 folds and is a well-recognized molecular marker for DRG sensory neuron injury in peripheral nerve injury model.

overall_design: Unilateral C5 (cervical) contusion injury or laminectomy only was performed in wildtype mice (n=3 in each group). Spinal cord tissue was collected 4 hours after SCI and stored at -80 degrees. Total cellular RNA was prepared using TRIzol and RNA miniprep kit (Qiagen). RNA sequencing was performed using 1ug total RNA. Sequencing type: single-end 50bp by Illumina HiSeq 4000, Lexogen Quantseq Forward library kit with STAR_2.7.2b aligner. mm10, Ensembl mouse GRCm38.96 Alignment Genome was used.

first: Wei

last: Sun

first: Joshua

last: Rudolph

first: Walter

last: Eckalbar

first: Zhonghui

last: Guan


title: Next Generation Sequencing Facilitates Quantitative Analysis of brown adipose tissues (iBATs) from D3BKO female mice and their respective wild type control mice

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

institute: Georgia State University

summary: our RNA-seq analysis revealed an up-regulation of thermogenic program in brown fat of the female Dnmt3b knockout mice.

overall_design: Brown adipose tissue mRNA profiles of WT and D3bKO mice

first: Hang

last: Shi


title: Early cardiac ageing: Phenotypic and transcriptional transitions in young to middle-aged mice

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

summary:
While much research has focussed on advanced stages (and mechanisms) of ageing, this fundamental process may commence at a relatively early age, impacting organ function and resilience throughout the adult lifespan. In male C57BL/6 mice, multiple phenotypic and transcriptional features of cardiovascular ageing were evident from 16 weeks of age, well in advance of 'middle age'.
Phenotypic changes include declining cardiac and coronary reserves and resistance to ischaemic insult. Gene changes support early constitutive stress together with a plateau in transcriptome responsiveness to ischaemia, and declining induction of cardioprotective and quality control pathways vs. increasing induction of genes promoting signalling dysfunction, hypertrophy and cell death. These findings support cardiac ageing from early adulthood. Molecular changes reflect declining adaptive capacity/quality control, consistent with evolutionary theories of biological ageing.

overall_design: Total RNA obtained from isolated left ventricular myocardium of aged male mice (8wk, 16wk, 32wk, 48wk), tissue collected pre- and post-ischemia (n=6/group)

middle: J

first: John

middle: P

last: Headrick

first: Melissa

middle: E

last: Reichelt


title: Whole genome bisulfite sequencing of muscle, liver, brain tissues in cattle

city: Beijing

first: Shengli

last: Zhang

address: 2rd, Yuanmingyuan West Road

department: Colledge of Animal Science and Techonology

country: China

institute: China Agricultural University

type: Methylation profiling by high throughput sequencing

summary: In this study, we generated whole genome bisulfite sequencing data 3 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues.

overall_design: Genomic DNA for each tissue was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA). The quality of DNA samples was evaluated using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) including degradation, and potential RNA contamination, and purity (OD260/OD280), and concentration using a spectrophotometer (NanoDrop Technologies, Rockland, DE) to meet the requirements for library construction. The qualified genomic DNA from somatic tissues and sperm were used to construct a library. The library different lanes of a HiSeq X Ten (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads by Novogene (Novogene, Beijing, China).

first: Shuli

last: Liu

first: Siqian

last: Chen


title: Multi-Dimensional Epigenetic Analysis Reveals Transcription as a Primary Driver of Radiation Induced Double Strand Break Recognition

city: Chicago

first: Julian

last: Lutze

state: IL

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DNA Double Strand Breaks (DSBs) are a deleterious product of genotoxic agents or radiotherapy. Despite the inherent chromatin localization of DSBs, the literature has largely ignored the effect of local chromatin or histone post translational modifications (PTMs) on DSB induction or recognition especially in a therapy-relevant setting. Analysis of epigenetic linkages to the DNA Damage Response are challenging owing to the random nature of exogenous DSB induction. Here, we directly measure stochastic DNA damage induced by ionizing radiation (IR) and infer relationships between basal epigenetic states and cellular ability to detect DSBs. Contrary to the expected uniform localization of DSBs and γH2AX, we show that DSB recognition is separate from DSB induction and that both processes are dependent on the local chromatin milieu. In general, actively transcribed regions contain more γH2AX than heterochromatic regions suggesting a link between transcription and the DDR. In contrast to previous studies, we suggest that transcription proximal to DNA damage is necessary for early DSB detection and suggest a requirement for transcription mediated repair in genome maintenance. Finally, we reveal a dual effect of the repressive mark H3K27me3 on the DNA damage response. While basal H3K27me3 attenuates γH2AX deposition, transcribed regions recruit H3K27me3 following DSB induction possibly as an obligate step in DSB recognition. We uncover epigenetic determinants of DSB recognition and suggest new mechanisms by which the epigenome direct DNA repair. Our findings suggest new targets for radio-adjuvant therapy and reframe the current stochastic model of radiotherapy induced damage.

overall_design: Examination of Double Strand Break recognition by gamma-H2AX profiling in two different cell types by CUT&RUN sequencing


title: IFNg Regulates NAD+ Metabolism in Human Monocytes

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: IFNg is an essential and pleiotropic activator of monocytes, but little is known about the changes in cellular metabolism required for IFNg-induced activation. We sought to characterize and elucidate the mechanisms by which IFNg reprograms monocyte metabolism to support its immunologic activities. Monocytes from healthy controls and patients with gain-of-function mutations in STAT1 (STAT1 GOF), or loss-of-function mutations in mitochondrial complex I (Leigh syndrome) and NADPH oxidase (chronic granulomatous disease, CGD) were metabolically phenotyped. We found that IFNg increased oxygen consumption rates (OCR), indicative of reactive oxygen species generation by both mitochondria and NADPH oxidase. Transcriptional profiling of human monocyte derived macrophages revealed that this oxidative phenotype was driven by an IFNg-induced reprogramming of NAD+ metabolism, which is dependent on nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ salvage to generate NADH and NADPH for oxidation by mitochondrial complex I and NADPH oxidase, respectively. Monocytes from patients with STAT1 GOF demonstrated higher than normal OCR, while monocytes from Leigh syndrome and CGD patients demonstrated reduced OCR. Chemical inhibition of NAMPT completely abrogated the IFNg-induced oxygen consumption, comparable to levels observed in CGD patients. These data identify an IFNg-induced, NAMPT-dependent, NAD+ salvage pathway that is critical for IFNg activation of human monocytes.

overall_design: Transcriptome profiling by mRNA sequencing from CD14+ human monocytes that were differentiated with M-CSF, and then stimulated without or with IFNg treatment for 24h.

first: Katelyn

last: McCann

first: Steve

last: Christensen

first: Peter

last: McGuire

first: Ian

middle: A

last: Myles

first: Christa

middle: S

last: Zerbe

first: Gauthaman

last: Sukumar

first: Clifton

middle: L

last: Dalgard

first: Warren

last: Leonard

first: Beth

last: McCormick

first: Steven

middle: M

last: Holland


title: Differential expression of myocardial microRNAs is implicated in dexmedetomidine induced cardioprotection in rats

city: Kunming

first: Jinqiao

last: Qian

address: #295 Xichang Road

department: Anesthesiology

institute: the First Affiliated Hospital of Kunming Medical University

summary: Using the highly sensitive miRNA array, we screened 83 microRNAs abundant in the myocardium and we explored the functions of these miRNAs by Gene Ontology and Kyoto Encyclopedia of Genes annotation. The enrichment results indicated that these miRNAs mainly participated in the phosphatidylinositol signaling system, PI3K-Akt, and MAPK. Furthermore, the TTC staining  results showed that dexmedetomidine preconditioning attenuates myocardial ischemia-reperfusion injury by desregulation of several miRNAs and their potential target genes, which will give new insights into disclosing the mechanism of dexmedetomidine-induced cardioprotection.

overall_design: In this study, three samples from each group (control, C; ischemia-reperfusion, IR; dexmedetomidine preconditioning, DP) were used to acquire the miRNA expression profiling and the function of the abudant miRNAs in the myocrdium were analyzed by bioinformatic methods. Left ventricle infarct sizes were determine by the TTC staining. Finally, dysregulated miRNAs and their potential target genes were predicted to uncover mechanisms of dexmedetomidine-induced cardioprotection.


title: High-throughput transcriptomics reveals mechanisms of nanopesticides – nanoformulation vs conventional pesticides and active ingredient – a case study with Enchytraeus crypticus

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

country: Portugal

institute: CESAM & University of Aveiro

summary: Nanoformulations are developed to offer controlled release of active ingredients (a.i.) and thus aim to keep functionality while having a smaller environmental footprint. However, the toxic effects of nanoformulations, particularly to non-target organisms, is poorly known, and even more so at the mechanistic level. The aim of the present study was to investigate the mechanisms of toxicity of atrazine when delivered as a nanoformulation of atrazine (nano_ATZ), a commercial atrazine-based formulation (Gesaprim), and the pure a.i. (ATZ). The high-throughput gene expression microarray (4 x 44K) was used to assess transcriptomics in Enchytraeus crypticus (a non-target species). Organisms were exposed, in soil, to equitoxic reproduction effect concentrations (EC10 and EC50) for 3 and 7 days. Results showed activation of both general and well-known mechanisms of detoxification (e.g. cytochrome P450 and GST) for all the atrazine forms, and it also showed effects on energy metabolism pathways. Common to all, was also the effect on arachidonic acid metabolism, which was linked to reproductive effects. Uniquely activated by nano_ATZ were changes in the processes cell death and immune system response, which was associated to increased cellular ROS generation. Further, effects of nano_ATZ on transcripts linked to secretion, translocation and vesicle trafficking, suggested that differentiated - nano-specific - uptake and/or cellular transport was taking place. In summary, this study on the transcriptomics of a nanoformulation, the first so far, suggested differentiated mechanisms of toxicity among the nanoformulation, the a.i. and the conventional pesticides, shedding light onto the issues of sustainability and safer-by-design for the agrochemical industry.

overall_design: Gene expression profile of Enchytraeus crypticus was analysed after 3 and 7 days of exposure to atrazine based pesticides: nanoformulation of atrazine (nano_ATZ), a commercial atrazine-based formulation (Gesaprim), and the pure a.i. (ATZ), in two different concentrations that reduce reproduction in 10 and 50% (EC10 and EC50). The exposure was performed in LUFA 2.2 soil. Three biological replicates per test treatment and controls (control: un-spiked soil for nano_ATZ and Gesaprim; and control-acetone for ATZ treatments) were used.

middle: I

first: Estefânia

middle: V

last: Campos

first: Leonardo

middle: F

last: Fraceto

first: Renato

last: Grillo

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: Exercise Mitigates Skeletal Muscle Epigenetic Aging

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary: Exercise late in life mitigates skeletal muscle epigenetic aging, providing evidence that physical activity is a "fountain of youth".

overall_design: TA muscle from 5 young sedentary mice, 5 24 month old sedentary mice, and 5 aged mice exercise trained from 22-24 months were analyzed for DNA methylation via RRBS and DNAge.

first: Murach

last: Kevin


title: DNA damage-induced phosphorylation of CtIP at a conserved ATM/ATR site promotes lymphomagenesis in NHEJ/p53-double deficient mice

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

institute: Columbia University

summary: Human lymphoid malignancies are often characterized by oncogenic translocations involving the antigen receptor gene loci. CtIP is a DNA end-resection factor that has been widely implicated in alternative end-joining (A-EJ) mediated chromosomal translocations in reporters. The ATM and ATR kinases phosphorylate CtIP at T859 (T855 in mouse) and other sites to promote DNA end-resection. Using two classical non-homologous end-joining (cNHEJ) and Tp53-double deficient mouse models, we identified a role of CtIP T855 phosphorylation in the neonatal development of Xrcc4-/-Tp53-/- mice and the IgH-Myc translocation driven lymphomagenesis in DNA-PKcs-/-Tp53-/- mice. Mechanistically, we found that CtIP T855 phosphorylation is important for the progression of DNA end-resection, while dispensable for hairpin opening and inter-sister DNA break ligation. Moreover, we found that CtIP-T855 phosphorylation supports the proliferation of Myc-driven lymphoma cells by promoting the transition from ATM-mediated to ATR-mediated G2/M cell cycle checkpoint. Correspondingly, the CtIP-T855A mutation delays splenomegaly in l-Myc mice. Collectively, our findings suggest that DNA damage-induced CtIP phosphorylation has a checkpoint function during lymphomagenesis independent of its role in A-EJ-mediated chromosomal translocation

overall_design:
In this study, we examine how CtIP-mediated end resection contributes to A-EJ-mediated chromosomal translocations and lymphomagenesis by characterizing cNHEJ/Tp53-double deficient mice with or without the CtIP-T855A mutation. Specifically, we found that the CtIP-T855A mutation causes neonatal lethality in Xrcc4-/-Tp53-/- mice without apparent lymphomas or hematopoietic failure. Instead, the CtIP-T855A mutation exacerbate the G2/M arrest of Xrcc4-/-Tp53-/- olfactory neurons. In contrast, CtIPT855A/T855AKu70-/- mice are viable although small. Moreover, the CtIP-T855A mutation delays lymphomagenesis and alters the tumor spectrum of DNA-PKcs-/-Tp53-/- mice. High-throughput genome-wide translocation sequencing (HTGTS) of RAG- and endonuclease-initiated DSBs shows that CtIP T855 phosphorylation is not required for hairpin opening or the initiation of end-resection, but instead promotes extensive end-resection. Furthermore, CtIPT855A/T855A cells show defects in G2/M checkpoints maintenance, suggesting a role for T855 phosphorylation in lymphomagenesis beyond translocation. Correspondingly, the Ctip-T855A mutation also attenuates splenomegaly in the λ-Myc transgenic model.
CJ and PPoI refer to the types of breaks or junctions that each sample was analyzed for. More specifically, CJ stands for "coding joins" which means that those samples specifically looked at the Coding Join junctions that formed during V(D)J recombination. Samples annotated with "PPoI" were analyzed for junctions formed at PPoI-endonuclease recognition cutting sites after the genome was exposed to the PPoI-endonuclease through retroviral infection and subsequent nuclear localization

first: Xiaobin

last: Wang

first: Zhengping

last: Shao

first: Brian

last: Lee

first: Yunyue


title: ChIP-seq and RNA-seq profiling of mice hippocampus before and after Arid1a conditional knockout.

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

summary: To gain a deeper insight into roles of Arid1a in mice hippocampus development, we performed ChIP-seq and RNA-seq to analyze the genome-wide changes of histone marks and transcriptome changes before and after Arid1a deletion in hippocampus of the E16.5 and P21 mouse using Cre-lox system.

overall_design: Total RNA was extracted from WT and Arid1a-cKO hippocampus and generated by deep sequencing, in two or three biological replicates, using BGISEQ-500. ChIP-seq was sequenced withput biological replicates on BGISEQ-500 platform .

first: Shang-Kun

last: Dai


title: Fingerprints of Hepatocellular Carcinoma-Infiltrated  γδT Cells Revealed by Single-Cell Sequencing

city: Guangzhou

first: Yifang

last: Gao

address: NO.58 zhongshan 2nd road, YueXiu district

institute: sun yat-sen University

summary: We report the application of single cell RNA sequencing for profiling the fingerprints of γδT cells of hepatocellular carcinoma compared with healthy donors. By comparing the transcriptome and TCR clonality of γδT cells from 3 HCC patients and expanded γδT cells from 3 healthy donors, we found that expanded γδ T cells derived from different donors shared great transcriptomic similarity and we found higher enrichments of major γδ TCRs in expanded γδ T cells compared to infiltrated but not peripheral ones in HCC. Analysis of differentiation trajectory demonstrated a branched structure in expanded γδ T cells, implying functional and differentiation stage diversity, and γδ T cells from HCC patients are localized to the far end of the trajectory. Furthermore, GVSA analyses made on metabolic pathways demonstrated strong enrichments in major metabolic pathways such as OXPHOS, glycolysis, and fatty acid metabolism in expanded γδ T cells versus peripheral ones of HCC. The comparison indicated higher cytotoxicity score of expanded γδ T cells compared to infiltrated or peripheral ones of HCC. The successful application of allogeneic γδ T cells immunotherapy in late-stage liver cancer patients was supported by our current scRNA transcriptomic analyses, which suggested strong anti-tumor functional complementation by the ex-vivo expanded γδ T cells.

overall_design: We report the application of single cell RNA sequencing for profiling the fingerprints of γδT cells of hepatocellular carcinoma compared with healthy donors. Transcriptomic and TCR clonality analysis were both applied. The results showed that expanded γδ T cells derived from different donors shared great transcriptomic similarity and higher enrichments of major γδ TCRs in expanded γδ T cells. Analysis of differentiation trajectory demonstrated a branched structure in expanded γδ T cells, implying functional and differentiation stage diversity, and γδ T cells from HCC patients are localized to the far end of the trajectory. Furthermore, GVSA analyses made on metabolic pathways demonstrated strong enrichments in major metabolic pathways such as OXPHOS, glycolysis, and fatty acid metabolism in expanded γδ T cells versus peripheral ones of HCC. The comparison indicated higher cytotoxicity score of expanded γδ T cells compared to infiltrated or peripheral ones of HCC.

first: Wenjing

last: He

first: Yi

last: Hu

first: Dan

last: Chen

first: Dongmei

last: Ye

first: Qiang

last: Zhao

first: Yijia

last: Li

first: Li

last: Lin

first: Xiaomin

last: Shi

first: Xiaoshun

first: Ligong

last: Lu

first: Zhinan

last: Yin

first: Yangzhe

last: Wu


title: Next Generation Sequencing Facilitates Qunatitative Analysis of MondoA+/+Foxp3Cre and MondoAfl/flFoxp3Cre Treg cells Transcriptomes

city: Shanghai

first: Ying

address: 280 S. Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: RNA-seq of Treg cells derived from MondoA+/+Foxp3Cre and MondoAfl/flFoxp3Cre mice.

overall_design: Total RNA of nTregs, anti-CD3/CD28 antibody-stimulated nTregs and iTregs from MondoA+/+Foxp3Cre and MondoAfl/flFoxp3Cre mice were isolated and  RNA-seq experiments were performed subsequently. mRNA profiles were further analyzed and compared according to standard protocols.

first: Xuemei

last: Tong


title: Expression data from vtiligo skin

city: Goyang-si

first: Ai-Young

state: Gyeonggi-do

address: Ilsandong-gu Siksa-dong Dongguk-ro 27

department: Dermatology

country: South Korea

institute: Dongguk University School of Medicine

summary:
Vitiligo is a skin disorder due to loss of melanocytes. There are depigmented lesions mixed with normally-pigmented non-lesions. Gene expression profiles have been different between lesional skin and non-lesional skin. Primary cilia have been involved in various cellular functions including cell survival.
We used microarrays to detail the programme of gene expression underlying melanocyte survival in vitiligo and identified distinct cilia-related genes involved in melanocyte apoptosis.

overall_design: Lesional and non-lesional skin specimen sets were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain up- or down-regulated gene profiles in lesional skin compared to those in non-lesional skin specimens.  To that end, we biopsed lesional and non-lesional skin specimens from the same patient.

first: Aiyoung


title: Fully human umbilical cord-derived organoid for acute liver failure

last: Xiao

address: No. 253, Industrial Avenue, Haizhu District

institute: Southern Medical University

summary: We report a fully human UC-derived organoid system that integrates ECM hydrogel, MSCs and reprogrammed hepatocytes, achieving the treatment of acute hepatic failure in case of extreme failure.To  explore the mechanism of our organoid  in hepatic failure, we performed single cell RNA sequencing of transplanted organoids  as well as the original organoid prior to transplantation, we have demonstrated that MSCs were primarily responsible for inhibiting the secretion of inflammatory-inducing cytokines and promoting the secretion of inflammation-inhibiting cytokines by recruiting immune cells migrating into organoid to triggering immune response.

overall_design: single-cell RNA-seq  of transplanted organoids (including both human MSCs and rat cells) on day 3 and 10, as well as the original organoid (only human MSCs) prior to transplantation.

first: Xiao

last: Yi

first: Feng


title: Distinct hippocampal expression profiles in obese type 2 diabetes db/db mice after DMDD treatment

city: Nanning

first: Lihui

last: Wang

address: No. 22 Shuangyong Road

institute: Guangxi Medical University

summary: 2-Dodecyl-6-Methoxycyclohexa-2, 5 -Diene-1,4-Dione (DMDD) was purified from the roots of Averrhoa carambola L. Previous research demonstrated that DMDD is a small molecular compound with significant therapeutic potential for diabetes. However, the efficacy of DMDD to ameliorate diabetic cognitive impairment in type 2 diabetes mice has not been reported. In present study, we detected gene expression profiles in the hippocampi of diabetic db/db mice after DMDD treatment. 9-week-old male db/db mice were treated with DMDD (50 mg/kg) for 28 days followed by Y maze and novel object recognition test for behavioral evaluation. Our results showed that DMDD attenuated the spatial working memory and object recognition memory impairment in db/db mice. Using mouse lncRNA array analysis, 11 lncRNAs and 4 mRNAs with significant differential expression were identified after DMDD treatment. Among these, Hif3a expression was significantly increased in the hippocampi of diabetic db/db mice compared with db/m control mice and then decreased after DMDD treatment. Besides, DMDD treatment reduced tau protein expression, the formation of a-synuclein oligomers and high glucose-induced apoptosis in the hippocampi of db/db mice and high glucose-treated HT22 cells. DMDD protected neural cells from apoptosis by repression of Hif3a. These data suggest that DMDD can alleviate cognitive impairment by regulating apoptosis through the pro-apoptotic protein Hif3a. In conclusion, our study suggests that DMDD has great potential to be a new preventive and therapeutic compound for diabetic cognitive impairment.

overall_design: Microarray analysis was performed on the hippocampal tissues of 3 db/db_vehicle and 3 db/db_DMDD mice.

first: Jinjin

last: Cao

first: Qianqian

last: Xu

first: Chunlin

last: Zou


title: Insights into the modes of action of tritium on the early-life stages of zebrafish, Danio rerio, using transcriptomic and proteomic analyses

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

summary: In the environment, populations are exposed to different kinds of ionizing radiations. Little is known about their modes of actions on non-human species, and whether or not they are similar for alpha, beta and gamma radiations, considered as the reference. In this context, tritium effects (beta emitter) under the form of tritiated water (HTO) were investigated in zebrafish, a common model in toxicology and ecotoxicology with fully sequenced genome. Experiments were conducted on early life stages, considered to be highly sensitive to pollutants, by exposing eggs to 0.4 mGy/h of HTO until 10 days post fertilization. Tritium internalization was quantified and effects were investigated using a combined approach of transcriptomic and proteomic analyses. Results highlighted similarities in the biological pathways affected by HTO by both techniques, such as defense response, muscle integrity and contraction, and potential visual alterations. These results correlated well with previous data obtained on earlier developmental stages (1 and 4 dpf). Interestingly, HTO effects were partly overlapping those obtained after gamma irradiation, underlying potential common modes of action. This study therefore brought a body of evidence on the molecular effects of HTO on zebrafish larvae. Further studies could investigate if the effects persist in adult organisms.

overall_design: RNAseq analysis of 7 and 10 days post-fertilization zebrafish larvae exposed to 0,4 mGy/h of tritiated water (HTO). Experiment was conducted with 3 biological replicates for both control and contaminated larvae for both stages.

first: Caroline

last: Arcanjo

first: Olivier

last: Armant

first: Béatrice

last: Gagnaire


title: Single-cell  Sequencing  Analysis of Head and Neck Squamous Cell Carcinoma

city: Tianjin

first: xuan

last: zhou

address: West huanhu road

institute: Tianjin Medical University Cancer Institute and Hospital

summary: To better understand tumor microenvironment and tumor heterogeneity in head and neck squamous cell carcinoma, we profiled primary tumors from two treatment naive patients by single-cell sequencing.

overall_design: Primary tumors from two treatment naive patients, and fresh HNSCC tissues were dissociated with the Gentle MACS Dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Next, single cells were counted using automated cell counter and adjusted to the concentration of 1000 cells/μL and we retained single-cell transcriptomes for 13,903 cells after initial quality controls. Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Cells were lysed, and the RNAs were reverse-transcribed into cDNAs. Libraries were generated from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Finally, the cDNA libraries were sequenced using the nova 6000 Sequencing System (Illumina). The SRA Study accession is SRP293588 and the BioProject accession is PRJNA679702.

first: Xuan

last: Zhou


title: Cell cycle-dependent chromatin and transcriptional changes

first: Kristian

last: Helin

address: 430 East 67 street

institute: MSKCC

summary: The cellular and nuclear states are constantly changing and closely linked to DNA replication and cell division, defining cell cycle phases. Pharmacological inhibition is a widely used strategy to enrich for specific phases to study them in isolation. However, it is important to understand how synchronization influences chromatin openness and gene expression compared to unperturbed cell cycle states.  Here, we use an integrated approach to obtain G1, S and G2/M phases from mouse embryonic stem cells (mESC) and to profile their chromatin accessibility and marks as well as steady and nascent transcripts levels. We demonstrate that synchronization with thymidine and nocodazole leads to dramatic changes in chromatin compaction and gene expression, which only partially resemble bona fide cell cycle-dependent differences. Blocking with CDK1 inhibitor results in efficient synchronization and evokes moderate changes in chromatin accessibility, resembling G2/M phase. Correlative analysis suggests that cell cycle-specific variations in chromatin openness in unperturbed mESCs are mediated by CDK1 substrates and CTCF. This integrated strategy can be applied to most cultured cell lines under any conditions and holds the potential to further our understanding of cell cycle-dependent susceptibility to external cues and chromatin regulation.

overall_design: Examination of chromatin accessibility and transcription in sorted cell cycle phases

first: Daria

last: Shlyueva


title: Golden Pompano (Trachinotus blochii) improves tolerance to acute hypoxic stress by changing the mode of glucose and lipid metabolism

city: Haikou

first: JunLong

last: Sun

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

summary: Due to the increase in stocking density, eutrophication of water quality, and high-temperature conditions aggravate the possibility of hypoxia, and inevitably lead to hypoxic stress, affecting the development of its aquaculture industry. We simulated severe hypoxia stress conditions and constructed two different hypoxia tolerance groups. We used next-generation sequencing to analyze the mRNA expression profiles of the brain and liver under hypoxia to clarify the main pathways and metabolic pathways involved in hypoxia, to systematically reveal the reasons for the differences in hypoxia tolerance among different groups.

overall_design: We used RNA sequencing to detect the liver and brain mRNA transcriptomes of the golden pomfret the hypoxia intolerance group (Intol) and hypoxia tolerance group (Tol), and compared them (3 vs 3).

first: Junlong

first: Tian

last: Jiang

first: Jian

last: Luo


title: Innate immune sensing of influenza virus through IFI16 promote pyroptosis.

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

summary: We report that IFI16, which was previously identified as a cytosolic DNA sensor, is essential for the activation of programmed cell death pathways in IAV infected cells. We have identified IFI16 as an innate immune sensor of the influenza A virus. We find that IFI16 recognizes viral genomic RNA upon infection. The activation of IFI16, in turn, triggers the production of type I, III interferons, and also other pro-inflammatory cytokines via the STING-TBK1 and Pro-caspase-1 signalling axis, thereby promoting cell death (apoptosis and pyroptosis in IAV infected cells).

overall_design: To investigate the effects of IFI16 on cell death during influenza infecction, A549 cells were transfected with either scrambled shRNA (shSCR) or IFI16 specific shRNA (shIFI), cells were

first: Akhilesh

first: Shalabh

last: Mishra


title: Comparison of the Transcriptomic Signatures in Pediatric and Adult CML

city: Stanford

first: Minyoung

last: Youn

address: 269 Campus Drive, CCSR 1210

department: Pediatrics

institute: Stanford University

summary:
The goals of this study are to test whether the differences in clinical presentation of pediatric CML are due to unique molecular characteristics that differ from adult CML.
Methods: CD34+ hematopoietic stem/progenitor cells mRNA profiles of pediatric normal/CML and adult normal/CML were generated by deep sequencing as reverse paired-end (75 bp) runs on the HiSeq 4000 sequencer. Raw fastq files were trimmed with Trimmomatic/0.36 and reads were aligned to the mm10 reference genome with STAR/2.5.1b aligner. Gene level counts were determined with STAR –quantMode option using gene annotations from GENCODE (vM13). QC assessments such as unique alignment counts, unique/multiple ratio or exon/intron ratio was derived with ngsutilsj-0.3-2180ca6 using the bam-stats option. Differential gene expression and all other pathway analysis are conducted with R/3.4.3. Samples were imported, normalized with trimmed mean of Mvalues (TMM) from the EdgeR/3.20.9 package and further transformed with VOOM from the Limma/3.34.9 package, resulting in a log2 normalized count matrix. A linear model using the Limma/3.34.9 package was then used to obtain p-values, adjusted pvalues and log-fold changes (LogFC). qRT–PCR validation was performed using TaqMan assays.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study demonstrates that unique molecular characteristics of pediatric CML, such as dysregulated Rho pathway, which may contribute to the clinical differences at presentation between adult and pediatric patients.

overall_design: CD34+ hematopoietic stem/progenitor cells mRNA profiles of pediatric CML, pediatric normal, adult CML, and adult normal samples.

first: Hee-Don

last: Chae

first: Alex

middle: G

last: Lee


title: Expression data from stroke patients brain samples

city: Barcelona

first: Laura

last: Ramiro

state: Barcelona

address: Passeig De La Vall D'hebrón 119-129, Edificio Mediterránea, Laboratorio 120

country: Spain

institute: Vall d'Hebron Institute of Research

summary:
Stroke is still a major cause of death and disability worldwide. A better comprehension of stroke pathophysiology is fundamental to reduce its dramatic outcome.
Our aim was to identify and verify gene expression changes that occur in the human brain after ischemia.

overall_design: Six ischemic stroke patients who died during hospitalization in the Vall d’Hebron Hospital (Barcelona, Spain) were included. Tissue collection was done under the supervision of an experienced neuropathologist. Brain pieces from the infarct core (IC) and the healthy contralateral (CL) areas were gathered within the first hours after death, snap-frozen in liquid nitrogen and stored at -80ºC. Total RNA was isolated from frozen brain samples using the Fatty Tissue RNA Purification kit (Norgen Biotek Corp., Canada), following manufacturer’s instructions. DNase treatment was performed in solution with the DNA-free DNA removal kit (Ambion, ThermoFisher). All RNAs were kept at -80ºC.  The integrity of the isolated RNA was determined using the Bioanalyzer 2100 platform (Agilent, UK), with an average integrity number of 6.4 ± 1.5.

first: Teresa

last: García-Berrocoso

first: Joan

last: Montaner


title: Transcriptome-based screening of ion channels and transporters in a migratory chondroprogenitor cell line isolated from late-stage osteoarthritic cartilage

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

summary:
Chondrogenic progenitor cells (CPCs) may be used as an alternative source of cells with potentially superior chondrogenic potential compared to mesenchymal stem cells (MSCs), and could be exploited for future regenerative therapies targeting articular cartilage in degenerative diseases such as osteoarthritis.
We studied the profiles of those ion channel and transporter families that may be relevant to chondroprogenitor cell physiology using Affymetrix microarrays.

overall_design: Total RNA was isolated from CPC and MSC cell cultures grown in monolayers in 75 cm2 cell culture flasks. Whole-genome transcriptome analysis was conducted by hybridising three biological samples of total RNA per cell type to Affymetrix Human Gene 2.1 ST Arrays Strips. Gene expression data were analysed using Partek Genomics Suite 6.6 software.

first: Csaba

last: Matta

first: Marcos

middle: C

last: Uribe

first: Sean

last: May


title: Comparative transcriptomic analysis of in the hindbrain of olive flounder (Paralichthys olivaceus) with distinct personality and oxygen metabolism

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

summary: In previous studies, we employed multiple behavior assays, including propensity to feed, simulated trawl capture and escape response, to prove the presence of bold and shy personality in olive flounder. However, the molecular mechanism of the different personality has not been elucidated. In the present study, the transcriptomic profiles of the hindbrain from flounder with distinct personalities were compared. A total of 144 differently expressed genes were identified, including 74 up-regulated and 70 downregulated genes. Genes involved in hypoxia stress were detected in SP flounder, accompanied by down-regulation of ribosomal RNA synthesis. In addition, genes related to calcium signaling pathway, including endothelin, b-Fos, c-Fos and c-Jun were up-regulated in SP flounder. Furthermore, personality-related genes, including UI, CCK, c-Fos showed a significantly higher level in SP flounder compared with BP flounder. GO enrichment analysis indicated that the GO categories “the tight junction pathway” and “lipid transport or localization pathway” are enriched in SP flounder, suggesting that the central nervous system homeostasis would be compromised. Finally, a simple and scalable DNA methylation profiling allows for methylation analysis for different genes. The results found that part of gene expression is negatively related to methylation of promoter. Altogether, identification of the related genes in flounder with different personalities will shed new light to improve critical industry issues related to stress and increase aquaculture production of flounder.

overall_design: Olive flounder (101.06 ± 6.39 g, mean ± SD) were obtained in central experimental station of Chinese academy of fisheries sciences (Hebei, China), and preserved in aquarium facilities in aerated 500 L tanks under a 12:12 light: dark cycle at 18 °C at Shanghai Ocean University. Fish were fed to satiation twice daily (8:00 and 18:00) with commercial fish pellets. Bold personality (BP) and shy personality (SP) flounder were selected according to methods previous reported (Rupia et al, 2016b).  Fish were humanly killed by anesthesia with 0.1% 2-phenoxyethanol, and the blood was collected from the caudal 114 vein with the heparinized syringess. The blood was diluted and the red blood cell (RBC) was count on a microscope. The concentration of haemoglobin in blood was measured using a commercial assay kit (Nanjing Jiancheng Bioengineering Institute, Nanjing, China). Hindbrain tissues were collected and stored in liquid nitrogen for further analysis.  Total RNA was extracted from each sample using Trizol Reagent according to the manufacturer’s protocol, and was treated with DNaseI to eliminate potential genomic DNA contamination. The concentration and integrity were were determined by spectrophotometry (NanoDrop ND-1000 system, Thermo Fisher Scientific, DE, USA)) and gel electrophoresis. Equal amounts of RNA from the hindbrain were obtained from six individuals. The Illumina TruSeq mRNA Stranded Sample Preparation kit was used in constructing the Illumina sequencing libraries according to previous methods (Zhang et al., 2017). The libraries were then sequenced on Illumina HiSeq 2000 using a 100-bp paired-end sequencing module.

first: Huafeng

last: Zou

first: Mengmeng

last: Shi

first: Weiqun

last: Lu


title: Expression profiles and their potential roles of tRNA-derived small RNAs in hippocampus of nicotine dependence rat

city: Changsha

first: Jiali

last: Shao

state: Hunan

address: 281 Tongzipo Road, Changsha, Hunan, China

department: Department of Anesthesiology

institute: The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

summary: The mechanism of nicotine dependence and nicotine related pain remains unclear. tRNAs, a major source of small noncoding RNAs (ncRNA), are the immediate areas of research focus, which have an important role in many pathophysiological processes. However, the role of tRNAs on nicotine dependence and related pain hasn’t been explored yet. In this study, our results indicated that the expression profiles of tRNAs have changed in nicotine treated rats as compared with normal rats, and among those, some differentially expressed tRNAs might be novel targets for nicotine dependence or nicotine related pain.

overall_design: The expression profiles of tRNAs sequences were conducted using RNA extracted from the hippocampus of nicotine and saline treat rats.

first: Jinfeng

last: Yang

first: Yanxia

last: Fei

first: Chen

last: Su


title: Lactic Acid as an Epigenetic Metabolite in Glioblastoma

city: NY

first: Markus

last: Siegelin

address: 630 west 168th street

department: Pathology & Cell Biology

institute: Columbia University

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

overall_design: Refer to individual Series


title: Bacillus subtilis BJ3-2 transcriptome sequencing

city: Guiyang

first: Yongjun

last: Wu

state: Guizhou

address: JiaXiu South Road

department: College of Life Sciences

institute: Guizhou University

summary: Soybeans fermented by Bacillus subtilis BJ3-2 exhibits strong ammonia taste in medium temperature below 37℃ and prominent soy sauce-like aroma moderate temperatures above 45℃. The transcriptome sequencing of Bacillus subtilis BJ3-2 (incubating at 37°C and 45°C) has been completed, screening of differentially expressed genes (DEGs) through data analysis, and analyzing their metabolic pathways, laying a foundation for exploring the regulatory mechanism of soy sauce-like aroma formation.

first: Jie

last: Zhong

first: Zhongjie


title: Expression data from LAM-associated fibroblasts and normal human lung fibroblasts co-cultured with TSC2-/- 621-101 cells

summary:
Patients with Lymphangioleiomyomatosis (LAM) develop nodules of cells within the lung parenchyma. These lesions contain both TSC2-/- LAM cells, and wild type fibroblasts. We investigated the effect of TSC2-/- cells on the transcriptional profile of both normal fibroblasts and fibroblasts isolated from LAM patient tissue (LAFs) using Affymetrix Gene Chip arrays, to identify upregulated pathways which could contribute to LAM pathology.
We used Affymetrix microarrays to detail the changes in the global profile of gene expression in fibroblasts following co-culture with 621-101 cells, and identified upregulation of several chemokines, indicating that the fibroblasts had adopted an inflammatory phenotype.

overall_design: LAFs derived from three donors (LAMFB1, 2, 3) and normal humal lung fibroblasts (NHLFs) derived from three donors (NORMFB1, 2, 3)  at matched passages, were used for this analysis. NHLFs and LAFs were cultured for 96 hours +/- 621-101 cells in a non-contact Boyden chamber co-culture system, in serum free DMEM-F12 medium with 10nM β-oestradiol at 37˚C and 5% CO2. Fibroblasts were harvested, RNA extracted and microarray hybridisation performed.

first: Arundhati

last: Dongre

first: Simon

last: Johnson


title: Lactic Acid as an Epigenetic Metabolite in Glioblastoma [ATAC-Seq]

summary: We investigate the role of lactic acid in GBM cells as an epigenetic metabolite in the regulation of pro-survival gene expression

overall_design: KNS42 cells were growth for 24h in different media conditions with or without L-lactic acid for 24h. Thereafter, cells were harvested and subject to ATAC-seq kit protocol. DNA was subsequently processed for ATACseq.

first: Torrini

last: Consuelo

first: Siegelin

last: Markus


title: RB-N phosphorylation promotes BRD4-mediated GPCR signaling hyperactivation and BET inhibitor resistance

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: The combination of CREB inhibitor and JQ1 could overcome the resistance to BET inhibitors in RB loss prostate cancer. Our study firstly showed that ADRB2-CREB pathway was activated after RB loss and considered as the potential target for the prostate cancer therapy

overall_design: To find the candidate genes which are regulated by RB, endogenous RB in PC-3 cells were knocked down by shRNA and cells were collected for RNA-seq after puromycin selection.

first: Haojie

last: Huang

first: Donglin

last: Ding

first: Liguo

last: Wang

first: zhenqing

last: Ye


title: PIF transposases are recurrently domesticated as ovary and nervous system regulatory proteins in Drosophila

city: Arlington

first: Diwash

last: Jangam

state: TX

address: 701 S. Nedderman Drive

institute: University of Texas at Arlington

summary: Proteins encoded by transposable elements (TEs) play a vital role in their proliferation in host genomes. In recent years, an increasing number of studies have shown that TE proteins have contributed to the emergence of novel host proteins. In Drosophila, there are several proteins derived from the PIF/Harbinger transposase superfamily called Drosophila PIF Like Genes (DPLGs). Here, we investigated the function of four DPLGs (DPLG1-4) in D. melanogaster that are highly conserved and present across Drosophila but are deeply diverged from each other, and likely originated through independent domestication of the transposase from distinct PIF-like TE families. We have analyzed transcript localization of DPLG 1-4, tagged DPLG3 and DPLG4 and studied their protein localization and, produced null alleles for DPLG1 and DPLG4. RNA in situ hybridization reveals that DPLG1-4 have strikingly similar pattern of transcript localization in the gonads, and in the nervous system during embryogenesis, suggesting their domestication for related functions. DPLGs show co-expression enrichment with transcription factors in ovaries and during embryogenesis supporting that they may be domesticated as regulatory proteins in flies. DPLG3 and DPLG4 tagged proteins localize with DNA in the nucleus of the ovaries consistent with this hypothesis. Loss of DPLG1 or DPLG4 results in viability and/or fertility effects, while loss of both DPLG1 and DPLG4 resulted in no effect in viability or fertility suggesting genetic interaction between these two genes. Further, loss of DPLG4 showed increased survival in flies, and increased fertility in older females indicating its involvement in the process of ageing. Transcriptional analyses in the ovaries showed that the loss of either DPLG1 or DPLG4 protein leads to modest changes in transcription of a large and significantly overlapping set of genes, and also affects transposable elements activity. The observed functional overlap of independently domesticated transposases from the same TE family and genetic interaction between them suggests a stepping stone model in which domestication of a PIF/Harbinger transposase might promote the domestication of related transposases for gonad and nervous system regulatory functions.

overall_design: Comparison of transcripts from ovaries of DPLG1 and DPLG4 mutants flies with control flies. All samples consisted of three biological replicates.

first: Fatema

middle: B

last: Ruma

first: Varsha

last: Bhargava

first: Dragomira

middle: N

last: Markova

first: Suzanne

last: Howell

first: Michael

last: Buszczak

first: Cédric

last: Feschotte

first: Esther

last: Betrán


title: Expression profiling suggests loss of surface integrity and failure of regenerative repair as major driving forces for COPD progression

city: Vienna

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

institute: AIT

summary: Chronic Obstructive Pulmonary Disease poses a major risk for public health, yet remarkably little is known about its detailed pathophysiology. Definition of COPD as non-reversible pulmonary obstruction may thus reveal more about the spatial orientation of the disease than about its mechanisms. We conducted a controlled observational study allowing for simultaneous assessment of clinical and biological development in COPD. 16 healthy controls and 104 subjects with chronic bronchitis, with or without pulmonary obstruction at baseline, were investigated using both extent and change of bronchial obstruction as main scoring criteria for the analysis of gene expression in lung tissue. We identified 410 genes significantly associated with progression of COPD. 110 of these genes demonstrated a distinctive expression pattern, their functional annotations indicating a participation in the regulation of cellular coherence, membrane integrity, growth and differentiation as well as inflammation and fibroproliferative repair.   The regulatory pattern indicates a sequentially unfolding pathology that centers on a two-step failure of surface integrity commencing with a loss of epithelial coherence as early as chronic bronchitis. Decline of regenerative repair starting in GOLD stage I then activates degradation of ECM hyaluronan causing structural failure of the bronchial wall only to be resolved by scar formation.

overall_design: 205 transbronchia biopsies from 88 patients (COPD GOLD stages I - IV, healthy controls, patients with chronic bronchitis); up to 3 longitudinal samples per patient.

first: Rolf

last: Ziesche


title: MicroRNA profiles in leaves of Sorghum exposed to drought or heat or their combination

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: MicroRNAs (miRNAs) are part of gene regulatory networks that direct all most all biological processes in plants including their growth and development, as well as adaptation to biotic and abiotic stresses. Sorghum is largely grown for its grain production, but recently it also emerged a major feedstock for biofuel production. Interestingly, Sorghum is relatively drought tolerant crop and largely grown in semi-arid tropical and sub-tropical regions where the drought or high temperature or their combination co-occur in the field. Although miRNA profiles have been reported in Sorghum leaves exposed to drought, but thus far miRNAs in heat- or drought and heat-exposed conditions have not been reported. In this study, we report miRNA profiles in Sorghum leaves exposed to drought or heat or their combination. The bioinformatic analysis of small RNA libraries revealed the expression of approximately 30 conserved miRNA families represented by 81 individual miRNAs as well as 11 novel miRNA families in Sorghum leaves. Of these, 26 miRNAs were found to be differentially regulated in response to one or more of the stress treatments. Overall, the number of miRNAs regulated by heat was more than the drought. Furthermore, miRNA profiles revealed more similarities between heat and the combination of drought and heat stresses. We also have analyzed degradome profiles in control and drought-exposed plants to identify potential targets for the miRNAs. This study provides a frame work for better understanding of miRNA-guided gene regulations that vary between individual drought or heat or combination of drought and heat treatments.

first: Ramanjulu

last: Sunkar


title: PABP stabilizes select mRNAs populations in human cells

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: Gene expression is tightly regulated at the levels of both mRNA translation and stability. The poly(A) binding protein (PABP) plays a role in regulating these processes by binding the mRNA 3´ poly(A) tail and interfacing with both the translation initiation and mRNA deadenylation machineries.  Here we directly investigate the impact of PABP on the translation and stability of endogenous mRNAs in human cell lines.  Remarkably, our transcriptome-wide analysis does not generally detect changes to mRNA translation in PABP-depleted cells. In contrast, rapidly depleting PABP alters transcriptome abundance and stability, albeit non-uniformly.  Transcripts with long half-lives and short 3’UTRs are preferentially depleted in PABP-depleted cells.  PABP depletion induces cell death; however, disrupting the mRNA decapping and 5’-3’ decay machinery can partially suppress this lethality. Finally, we show that disrupting the LSM1-7 complex prevents the premature decay of mRNAs that are destabilized in PABP-depleted cells.  Taken together, these findings suggest that PABP plays an important role in preventing the untimely decay of select mRNA populations in human cells.

overall_design: 3 biological replicates of PABPC1DHFR HeLa cells  cultured in the presence or absence of TMP.

first: Shan

last: Chen


title: The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine


title: The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential [ChIP-Seq]

summary: Lysine 27 to methionine mutation (H3K27M) of the H3F3A gene, which encodes the variant histone H3.3, is found in the majority of Diffuse Intrinsic Pontine Gliomas (DIPGs). DIPGs are the most aggressive form of pediatric gliomas and have a median survival of <1 year from diagnosis. As H3K27M mutation is necessary but not sufficient to cause DIPGs, it is accompanied by several other mutations in tumors. However, the mechanisms by which H3K27M increases vulnerability to DIPG tumorigenesis, while expected to involve altered epigenetic regulation is unclear. Thus, in this work we built pairs of isogenic human embryonic stem cell lines with versus without this mutation, in the absence of other DIPG contributory mutations, to investigate mechanisms by which H3K27M mutation could affect cellular proliferation and differentiation and how these were related to alterations in the transcriptome, H3K27me3, and the DNA methylome. We found that H3K27M increased stem cell proliferation and interfered with differentiation, resulting in loss of most H3K27me3 and resulting in anomalous onset of expression of developmental genes during multilineage or directed differentiation. This work suggests mechanisms by which H3K27M mutation influences stem cell properties, contributing to DIPG tumorigenesis.

overall_design: The H3F3a-K28M-Puro clonal cell lines (mutant clone 1 and clone 9)  were generated from H1 embryonic stem cell (H1ESC) line (obtained from WiCell) by the Genome Engineering and iPSC Center (GEiC), Washington University in St. Louis. These lines were used for derivation of neural progenitor cells, as described below, and comparisons of gene expression in the wild type versus mutant hESCs and neural progenitor cells were performed. MeDIP was performed on four biological replicates of WT and H3K27M mutant undifferentiated H1 hESCs and their 5-day differentiated neural EB derivatives cultured in parallel to those used for RNA-sequencing.

first: Santhi

last: Pondugula

first: Najla

last: Kfoury

first: Ramachandran

last: Prakasam

first: Scot

last: Matkovich

first: Hiroko

last: Yano

first: Albert

last: Kim

first: Josh

last: Rubin


title: Gene expression data from spleen, cervical spinal cord, and thalamic regions of ME7-inoculated mouse

city: Anyang

first: Yeong-Gon

last: Choi

state: Kyeonggi-do

address: Kwanpyeongro 170 beongil 15, Dongan-gu

department: Ilsong Institute of Life Science

institute: Hallym University

summary:
An essential and remarkable process of the biochemical and physiological features in prion diseases is the conversion of a host-encoded prion protein (PrPC) into a misfolded isoform (PrPSc). The conversion of PrPC and the replication of prions, in cases of peripheral infection, occur following the uptake and subsequent spread of prions to brain via spinal cord.
We investigated the changes of gene expression profiles in the spleen, cervical spinal cord and thalamus following intraperitoneal inoculation of ME7 scrapie prion and the inter-tissue alterations of the differentially expressed genes through Venn diagram to find genes which are commonly influenced by ME7 scrapie prion spread in the three tissues.

overall_design: C57BL/6 mice were divided into two experimental groups; C: Control,  ME7: intraperitoneally ME7-inoculated. At the terminal stage (270 ± 8 days after the clinical signs are evident) of ME7 scrapie prion disease total RNA was isolated from three tissue regions of two experimental group (2 experimental group × 3 tissue samples of each experimental group × 2 mice  = total 12 samples).


title: Loss of ARNT Impair Adaptability of Muscular Exercise in Aged Mice

city: Boston

first: Yuteng

last: Zhang

state: MA

address: 20 Shattuck St

department: Surgery

institute: Brigham and Women's Hospital

summary: The adaptation of regimented exercise in skeletal muscle including muscular hypertrophy and enhanced strength decline significantly with aging. Transcriptome analysis following RNA sequencing reveals extensive activation of hypoxia-related genes in young exercised mice versus the sedentary, but absent in aged exercised mice. Particularly, less expression of aryl hydrocarbon receptor translocator (ARNT) was observed in response to exercise in aged mice. Young mice underwent skeletal muscle-specific knockout of ARNT (ARNT mKO) obtain deficient benefit from exercise resembling the aged mice. The deletion of ARNT associated with decreased expression of Notch1 intracellular domain(N1ICD) impair muscle hypertrophy and regeneration. Administration of ML228, a systematic agonist of ARNT, rescued skeletal muscle adaptabilities in old mice, which was suppressed by administrating N1ICD inhibitor(DAPT). These results suggest that the loss of skeletal muscle ARNT is partially responsible for diminished response to exercise in aging and activation of hypoxia signaling holds promise for rescuing the adaptability in aged muscle.

overall_design: Quadriceps femoris mRNA profile of young and old mice subjected to 8 weeks of treadmill running exercise regimen or sedentary activity

first: Indranil

last: Sinha


title: Degradome profiles in leaves of Sorghum exposed to drought or heat or their combination

overall_design: degradome sequencing profiles in Sorghum leaves exposed to drought or heat or their combination


title: The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential [RNA-Seq]

overall_design: The H3F3a-K28M-Puro clonal cell lines (mutant clone 1 and clone 9)  were generated from H1 embryonic stem cell (H1ESC) line (obtained from WiCell) by the Genome Engineering and iPSC Center (GEiC), Washington University in St. Louis. These lines were used for derivation of neural progenitor cells, as described below, and comparisons of gene expression in the wild type versus mutant hESCs and neural progenitor cells were performed by RNA-seq analysis.


title: Epigenetic reprogramming in adaptive drug resistance to BRAF inhibitor therapy

first: Steven

last: Offer

address: 200 First Street Southwest

summary: The development of drug resistance is a major limiting factor to the efficacy of BRAF inhibitor therapy for melanoma. The goal of this study was to identify and characterize pathways that contribute to adaptive drug resistance to BRAF inhibitors.

overall_design: Venurafenib resistant cells were derived and profiled. Cells harboring specific genetic changes were also generated and profiled to identify and characterize relevant mechanisms.

first: Zhiquan

last: Wang


title: The validation case study of read-across based on IATA for hepatotoxicity of Naphthalene and its structurally similar analogs

city: Tochigi

first: shota

last: Nakagawa

address: 2606, Akabane, Ichikai-Machi, Haga-Gun

institute: Kao Corporation

summary: Comparing biological similarity with in vitro test is expected to improve the reliability of read-across for systemic toxicity without animal test. However, because of few case studies, it was hindered to use of this concept for regulatory context. Thus, we compared biological similarity with in vitro test for structurally similar chemicals to demonstrate its validity for grouping chemicals and extract key considerations in read-across. In this study, we selected the hepatotoxicity of Naphthalene and its structurally similar analogs which have 90-day repeated dose toxicity data including 2,7-Naphthalenediol, 1,5-Naphthalenediol, and 1-Naphthol. To elucidate the potential mechanisms and compared them, we conducted in vitro microarray analysis with rat primary hepatocytes

overall_design: We conducted microarray analysis with Wister rat primary hepatocytes exposed by 2,7-Naphthalenediol, 1,5-Naphthalenediol, 1-Naphthol, and Naphthalene. After 24 h pre-culture, the cells were exposed to each chemical at 30 µM for 24 h. Three independent experiments were performed at each condition.

first: Shota


title: Establishment of primitive endoderm stem cell lines in mice

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN


title: Single cell RNA-seq for brain cerebral cortex transcriptome

city: Uppsala

first: Ying

last: Sun

state: Uppsala

address: Dag Hammarskjölds väg 20

department: Department of Immunology, Genetics and Pathology

institute: Uppsala University

summary: By analyzing brain cerebral cortex transcriptome, we provide the gene expression profile from diverse cell types from brain.

overall_design: We profiled the brain cerebral cortices from three pooled mice using droplet based 10X method (10x Genomics Chromium).

first: Ahmed

last: Osman

first: Klas

last: Blomgren


title: The Ontogeny and Vulnerabilities of Lapatinib Drug Tolerant Persisters [Parental (P) vs. Drug-Tolerant Persister (DTP)]

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

summary: Despite significant advances in HER2-targeted therapies, therapeutic resistance in HER2-positive (HER2+) breast cancer remains a significant clinical problem, especially in the metastatic setting. “Drug tolerant persisters” (DTPs), a sub-population of cancer cells that survive via reversible, non-genetic mechanisms, are implicated in resistance to tyrosine kinase inhibitors (TKIs) in several cancer models, but DTPs for HER2-targeted TKIs (e.g., lapatinib, neratinib, tucatinib) have not been characterized extensively. Here, we report that HER2+ER+ and HER2+ER- breast cancer lines give rise to distinct types of “lapatinib-DTPs,” characterized by different transcriptional programs and sensitivity to lapatinib/anti-estradiol combination. Lapatinib-DTPs from HER2+/ER+ cells rewire the PI3K/AKT/mTORC1 pathway via transcriptional induction of SGK3 to enable AKT-independent mTORC1 activation and survival. Lentiviral barcoding experiments, combined with single cell RNA-sequencing, suggest that HER2+ cells stochastically cycle through a cell state (“pre-DTP”) capable of transition to DTPs. Collectively, our results provide insight into DTP ontogeny and therapeutic vulnerabilities.

overall_design: mRNA profiles of Parental (P) vs. Drug-Tolerant Persister (DTP) BT474, EFM192A, HCC1419 and SKBR3 breast cancer cells

first: Chang

last: Anderson

first: Sayad

last: Azin

first: Neel

last: Benjamin


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [Patient scATAC-seq]

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Master regulators, such as the hematopoietic transcription factor (TF) GATA1, play an essential role in orchestrating lineage commitment and differentiation1. However, the precise mechanisms by which such TFs regulate transcription through interactions with specific cis-regulatory elements remain incompletely understood2,3. Here, we characterize a distinct form of congenital hemolytic anemia caused by missense mutations in an intrinsically disordered region of GATA1, with a poorly understood role in transcriptional regulation. Through integrative functional approaches, we demonstrate that these mutations perturb GATA1 transcriptional activity by partially impairing nuclear localization and selectively altering precise chromatin occupancy by GATA1. These alterations in chromatin occupancy and concordant accessibility changes alter faithful gene expression, with failure to both effectively silence and activate select genes necessary for effective red cell production. We demonstrate how disease-causing mutations can reveal regulatory mechanisms that enable the faithful genomic targeting of master TFs during cellular differentiation.

overall_design: In vitro cultured human bone marrow mononuclear cells from a patient carrying the GATA1 p.R307C mutation and healthy controls cells were sorted and forwarded to 10x scATAC-seq

first: Leif

last: Ludwig


title: The Ontogeny and Vulnerabilities of Lapatinib Drug Tolerant Persisters

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

overall_design: Refer to individual Series


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [Patient Cut&Run]

overall_design: In vitro cultured human bone marrow mononuclear cells from a patient carrying the GATA1 p.R307C mutation and healthy controls cells were sorted and forwarded to GATA1 CUT&RUN.


title: The Ontogeny and Vulnerabilities of Lapatinib Drug Tolerant Persisters [NPY1R]

overall_design: mRNA profiles of NPY1R high vs. low BT474 breast cancer cells

first: Anderson

last: Chang

first: Azin

last: Sayad

first: Benjamin

last: Neel


title: Hemoglobin induced changes in the transcriptome of normal subjects

city: New Delhi

first: Rahul

last: Pal

state: Delhi

address: Aruna Asaf Ali Marg

institute: National Institute of Immunology

summary: The expression of genes peripheral blood mononuclear cells from normal subjects exposed to hemoglobin.

overall_design: Differential expression of inflammatory genes in normal subects upon hemoglobin stimulation.

first: Hritika

last: Sharma


title: Gene expression profiling of primary HER2-positive breast cancers treated with neoadjuvant trastuzumab

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Trastuzumab, a humanized monoclonal antibody directed to the HER2 protein, is the standard-of-care treatment for patients with HER2 positive breast cancer, reducing the risk of relapse and death in patients. Nonetheless, some patients do not benefit from this treatment, underscoring the need to identify patients for whom chemotherapy + trastuzumab is adequate versus patients requiring additional drugs. The series comprised 18 incisional biopsies of breast carcinomas derived from patients that received neoadjuvant trastuzumab based therapy.

overall_design: Gene expression profiling was performed using RNA from formalin-fixed paraffin-embedded tissues core biopsies from 18 patients with primary HER2-positive breast cancer before treatment with neoadjuvant chemotherapy and trastuzumab.

first: Tiziana

last: Triulzi


title: Integrated analysis of the transcriptome-wide m6A methylome in gestational diabetes mellitus and healthy control placentas [meRIP-seq]

city: Jinan

first: Jin

last: Wang

state: China

address: No.2,  Jianguo xiaojing road, Jinan City, Shandong Province, PR China

institute: Jinan Maternal and Child Health Care Hospital

summary: N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic mRNA and potential regulatory functions of m6A have been shown by mapping the RNA m6A modification landscape. M6A modification in active gene regulation manifests itself as altered methylation profiles. However, the profiling of m6A modification and its potential role in gestational diabetes mellitus (GDM) has not yet been studied. In this work, placental samples were collected from GDM and control patients. MeRIP-seq was performed to identify differences in m6A methylation. Fragmented mRNAs were incubated for 2 h at 4 °C in the presence of 2 μg m6A antibodies (Synaptic Systems, 202003) in a 500 μl IP reaction system, and some of the fragments were used as input. RNA-seq libraries for m6A antibody-enriched mRNAs and input mRNAs were prepared using the KAPA Stranded mRNA-seq Kit (Illumina, CA, USA). Altered peaks of m6A-modified transcripts were primarily associated with mTOR signaling pathway, Notch signaling pathway, TGF-beta signaling pathway and so on. Our data provide novel information regarding m6A modification alterations in GDM and help our understanding of the pathogenesis of GDM.

overall_design: RNA m6A modification landscape of placental samples of GDM (n=4) and control patients (n=4), were generated by Illumina Hiseq 4000.

first: Hua

last: Jin


title: Integrated analysis of the transcriptome-wide m6A methylome in gestational diabetes mellitus and healthy control placentas


title: Transcriptional response of turkey blood leukocytes challenged with Salmonella enterica serovar Typhimurium UK1

city: Ames

first: Melissa

middle: Susan

last: Monson

state: Iowa

address: 2255 Kildee Hall, 806 Stange Road

department: Animal Science

institute: Iowa State University

summary: Salmonella is one of most common causes of bacterial foodborne disease and consumption of contaminated poultry products, including turkey, is one route of exposure. Minimizing colonization of commercial turkeys with Salmonella could reduce the incidence of Salmonella-associated human foodborne illness. Understanding host responses to these bacteria could lead to potential strategies to minimize colonization and thus food safety risk. In this study, we evaluated bacterial load and blood leukocyte transcriptomic responses of 3-week-old turkeys challenged with the Salmonella enterica serovar Typhimurium (S. Typhimurium) UK1 strain. Turkeys (n = 8/dose) were inoculated with 108 or 1010 colony forming units (CFU) of S. Typhimurium UK1 and fecal shedding and tissue colonization were measured across multiple days post inoculation (dpi). Fecal shedding was 1-2 log10 higher in the 1010 CFU group than the 108 CFU group, but both doses effectively colonized the crop, spleen, ileum, cecum, colon, bursa of Fabricius and cloaca without causing any overt clinical signs in either group of birds. Blood leukocytes were isolated from a subset of the birds (n =3-4/dpi) both pre-infection (0 dpi) and 2 dpi with 1010 CFU and their transcriptomic responses assayed by RNA-sequencing (RNA-seq). After 2 dpi, 647 genes had significant differential expression (DE), including large increases in expression of immune genes such as CCAH221, IL4I1, LYZ, IL13RA2, IL22RA2, and ACOD1. IL1B was predicted as a major regulator of DE in these leukocytes and this DE was predicted to activate cell migration, phagocytosis and proliferation, and to impact the STAT3 and toll-like receptor pathways. These data revealed genes and pathways by which turkey blood leukocytes responded to the pathogen and can provide potential targets for developing intervention strategies or diagnostic assays to mitigate S. Typhimurium in turkeys.

overall_design: RNA-seq of blood leukocytes from 3-week-old turkeys at 0 days-post-inoculation (dpi) and 2 dpi with S. Typhimurium UK1 using the Illumina HiSeq 2500

first: Bradley

last: Bearson

first: Matthew

middle: J

last: Sylte

first: Torey

last: Looft

first: Susan

last: Lamont

first: Shawn


title: Global RNA stability profiling in HEK293T cells under EGF treatment using TimeLapse-seq

city: West Haven

first: Sarah

last: Slavoff

state: CT

address: 300 Heffernan Dr

department: Chemistry

institute: Yale University

summary: We discovered through LC-MS/MS followed by biochemical assays and immunofluorescence that human microprotein NoBody/NBDY can be phosphorylated during EGF signaling transduction, and that this single post-translational modification of the smallest decapping complex component known to date is necessary to the observed disappearance of P-bodies under EGF treatment. RNA stability measurement of a known hDcp2 substrate, RRP41, showed decreased RNA life-time under EGF treatment. We hence wish to investigate the effect of this phospho-NBDY mediated P-body disassembly on global RNA turnover. Here we present a global profile of RNA stability in human HEK293 cells under EGF treatment via TimeLapse-seq. By comparing this dataset to our previous and current work done in DCP2 KO and in NBDY KO cells, respectively, we demonstrate that P-body dissociation observed during EGF signaling does not cause RNA stability change globally except for a few known EGF regulated transcripts.

overall_design: RNA isolated from HEK293T cells treated or untreated with EGF +/- s4U feed was subjected to oxidative-nucleophilic-aromatic-substitution chemistry and sequenced. All sequencing for experimental samples was performed in duplicate per condition assessed, while negative controls were performed as single replicates without s4U treatment.

first: Zhenkun

first: Jeremy

last: Schofield

middle: D

last: Simon


title: Distinct roles of PARP-1 and PARP-2 in c-Myc-driven B cell Lymphoma in mice

city: Barcelona

first: José

last: Yélamos

address: Dr. Aiguader, 88

department: Cancer Research Program

institute: Hospital del Mar Medical Research Institute (IMIM)

summary: To study the implication of PARP-1 deficiency or PARP-2 deficiency in the development of c-Myc overexpression-induced B lymphomas, we have studied by RNAseq the gene expression profile in pre-B cells isolated from bone marrow of mice that overexpress c-Myc in their B lymphocytes (WT) and in those mice with PARP-1 (KO1) or PARP-2 (KO2) deficiency

overall_design: 9 samples: 3 experimental groups with 3 biological replicates each: Wild type, Knock-Out Parp1, Knock-Out Parp2.

first: Jose

last: Yelamos

first: Miguel

last: Galindo

last: Bonnin


title: Lactic Acid as an Epigenetic Metabolite in Glioblastoma [ChIP-Seq]

city: NY

first: Markus

last: Siegelin

state: NY

address: 630 west 168th street

institute: Columbia University

summary: Glioblastoma is the most common primary malignant brain tumor with an unfavorable prognosis and a reprogrammed metabolism. In order to define the role of lactic acid in the context of glioblastoma epigenetic remodeling, pediatric GBM cells, KNS42, were growth for 24h in different media conditions (starvation media -0.5mM Glucose; 0.5mM Glutamate or physiological media -5mM Glucose; 0mM Glutamate) with or without L-lactic acid for 24h. Thereafter, cells were harvested and samples were subjected to ChIP isolation using H3K27ac and H3K9ac antibodies. DNA was subsequently processed for CHIP sequencing to assess epigenetic changes mediated by lactic acid.

overall_design: KNS42 cells were growth for 24h in different media conditions with or without L-lactic acid for 24h. Thereafter, cells were harvested and subjected to CHIP isolation. DNA was subsequently processed for CHIP sequencing.

first: Consuelo

last: Torrini


title: Transcriptional comparison of alveolar macrophages from patients with RA-ILD. IIM-ILD and DI-ILD.

city: Sinjuku-ku

first: Maho

last: Nakazawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Rheumatology, Department of Internal Medicine

institute: Keio University School of Medicine

summary: To examine the differences of AMs by disease.

overall_design: We performed transcriptome analysis of AMs from BALF of the RA-ILD (n = 5), IIM-ILD (n = 6) and DI-ILD groups (n = 5).

first: Tsutomu

last: Takeuchi


title: Heterogeneity in human WT1-specific CD4+ T cell clone

city: Suita

first: Fumihiro

last: Fujiki

address: Yamada-oka, 1-7

institute: Osaka University Graduate School of Medicine

summary: We compared gene expression among central memory (CD62L+CD127+; pop1), effector memory (CD62L-CD127+; pop2), and terminal effector (CD62L-CD127-; pop4) isolated from a single-cell-derived WT1-specific CD4+ T cell clone.

overall_design: A CD4+ T cell clone was expanded by the stimulation with WT1 peptide and IL-2. The expanded cells were rested for O/N in IL-2-free medium and then separated into the 3 fractions on the basis of CD62L and CD127 expression by FACSAria. Gene expression was compared among the three populations in order to identify genes responsible for memory or effector differentiation and their maintenance.


title: Cross-presentation by dendritic cells is limited by non-canonical autophagy.

city: Research Triangle Park

first: Jennifer

last: Martinez

state: NC

address: 111 TW Alexander Dr.

institute: NIEHS

summary: RNA-seq profiling of antigen presentation pathway in bone marrow-derived dendritic cells.

overall_design: FLT3L-derived BMDCs from Rubcn KO or WT mice under various treatment conditions, in triplicate.

first: Yingpei

last: Zhang

first: Payel

last: Sil

first: Sara

last: Grimm


title: Alopecia areata susceptibility variant in MHC region impacts expressions of genes contributing to hair keratinization and is involved in hair loss

city: isehara

first: Akira

last: Oka

address: 143 Shimokasuya

institute: Tokai university

summary:
Background: Alopecia areata (AA) is considered a highly heritable, T-cell-mediated autoimmune disease of the hair follicle. However, no convincing susceptibility gene has yet been pinpointed in the major histocompatibility complex (MHC), a genome region known to be associated with AA as compared to other regions.
Methods: We engineered mice carrying AA risk allele identified by haplotype sequencing for the MHC region using allele-specific genome editing with the CRISPR/Cas9 system. Finally, we performed functional evaluations in the mice and AA patients with and without the risk allele.
Findings: We identified a variant (rs142986308, p.Arg587Trp) in the coiled-coil alpha-helical rod protein 1 (CCHCR1) gene as the only non-synonymous variant in the AA risk haplotype. Furthermore, mice engineered to carry the risk allele displayed a hair loss phenotype. Transcriptomics further identified CCHCR1 as a novel component interacting with hair cortex keratin in hair shafts. Both, these alopecic mice and AA patients with the risk allele displayed morphologically impaired hair and comparable differential expression of hair-related genes, including hair keratin and keratin-associated proteins (KRTAPs).
Interpretation: Our results implicate CCHCR1 with the risk allele in a previously unidentified subtype of AA based on aberrant keratinization in addition to autoimmune events.

overall_design: 10 ng of total RNA from human hair follicle was processed for use on the microarray using the GeneChip WT pico Reagent Kit (Thermo Fisher Scientific) according to the manufacturer's instructions. The resultant single-strand cDNA was fragmented and labeled with biotin, then hybridized to the GeneChip Human Gene 2.0 ST Array. The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G (Thermo Fisher Scientific) according to the manufacturer’s recommendations.

first: Shigaku

last: Ikeda


title: Young Human Plasma Rejuvenates Senescent Vascular Endothelial Cell through Multiple Pathways

city: Wuhan

first: jinhua

last: Yan

address: Jiefang Avenue 1095

institute: Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: A mouse parabiotic model supports the existence of transferable factor(s) in blood that rescue(s) age-related degenerative phenotypes, however, whether it prevents endothelial cell senescence linked to common cardio-cerebral vascular diseases, requires to be inspected. In this study, plasmas donated from 27 young (23.04 ± 4.86 years, young human plasma, YHP) and 26 elderly (55.04 ± 5.42 years, elderly human plasma, EHP) healthy volunteers were used to culture primary human umbilical endothelial cells (HUVEC). When comparing with EHP, we found that the YHP reduced the percentages of SABG-stained cells and prohibited the expressions of senescent markers, including p16, p21, and p53 in HUVEC. Functionally, the YHP decreased the expression of ICAM-1, a marker for endothelial cell activation and increased abilities in tube formation and mobility at late passages that represent an enhanced angiogenic function. Validated by both RNA sequencing and Real-time PCR in HUVECs from all three umbilical cords, nineteen up-regulated and fifteen down-regulated genes were observed in YHP-treated HUVEC compared with group treated with the EHP. Among 34 genes, the expressions of MCM10, DHCR24, WBP1, UNC5B, and CYP26B1 were reversed by the YHP and we showed that these reversed expressions delayed senescence of both HUVEC and human coronary artery endothelial cell (HCAEC) through p16- and/or p21-assocated signaling. The five genes are relevant to maintain or reinstate the ability for proliferation, anti-apoptosis, and endothelial cell related functions, such as angiogenesis and anti-atherosclerosis. Thus, our study suggests that YHP restores biological processes in senescent endothelial cell through multiple pathways.

first: Jin-Hua

first: Xiao-Li

last: Tian


title: RNA expression profiles of mouse vascular smooth muscle cells (VSMCs) transfected with scramble siRNA (scr) and circEsyt2 siRNA (si-circ)

city: Chongqing

first: Xue

last: Gong

address: Changjiang branch Road

institute: Army Medical University

summary: Circular RNAs play an important role in multiple pathological conditions. Recently, we identified a novel circRNA-circEsyt2 from mouse atherosclerosis (AS) model and found its involvement in AS development. To explore the molecular mechanism of circEsyt2, we performed RNA-seq to investigate the regulation of circEsyt2 on mRNA profiles.

overall_design: RNA sequencing of VSMC transfected with scramble siRNA (scr) and circEsyt2 siRNA (si-circ) was performed on the HiSeq platform in the 150 bp pair-end model.

first: Chunyu

last: Zeng


title: circRNA expression profiles of mouse atherosclerotic and normal aortae by RNA-seq.

summary: To explore circRNAs expression profiles of mouse atherosclerotic model, we performed RNA-seq to detect circRNAs with potential functional role in atherosclerosis (AS).

overall_design: CircRNA sequencing was performed on aortic tissues from high-fat diet fed ApoE-/- mice (AS  group) and chow diet fed C57BL/6J and ApoE-/- mice (control) with an Illumina HiSeq 3000 system using the 150bp pair-end model.


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [G1E_ChIPseq]

first: Caleb

last: Lareau

summary: Master regulators, such as the hematopoietic transcription factor GATA1, have numerous roles in lineage commitment and differentiation. While human GATA1 mutations result in several blood diseases, all characterized mutations act relatively early to impair hematopoietic differentiation. Here, we describe a distinct form of hemolytic anemia involving impaired terminal erythropoiesis with a reduced lifespan of circulating red blood cells. We show that this unique blood disorder results from mutations in a poorly characterized and intrinsically disordered C-terminal region of GATA1.

overall_design: Murine G1E cells were transduced with the HMD lentiviral vector encoding HA-tagged human wildtype GATA1 or point mutants p.R307C or p.R307H

first: Leif

last: Ludwig


title: Single-cell RNA-seq reveals neural progenitor subpopulations and divergent astrocyte lineages

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Astrocytes are one of the most abundant cell types in the mammalian central nervous system. Their diversity was widely investigated in the adult brain recently. However, the heterogeneity of astrocyte progenitors in their early developmental stage is still not clear. In this study, we dissected the subpopulations of neural progenitor cells at the neurogenesis and the early gliogenesis stages by single-cell RNA sequencing analysis. Interestingly, we identified two astrocyte progenitor subgroups from the cerebral cortex. The astrocyte subgroups highly express Sparc or Sparcl1, which were reported have contrary functions in astrocytes to regulate synapse formation. Further analysis for subpopulations of neural progenitors from the ventral forebrain also identified two astrocyte progenitor subgroups, showing similar gene expression patterns as in the cortex. Surprisingly, clustering analysis between the subpopulations from the dorsal and the ventral forebrains showed that the astrocyte progenitors expressing Sparc or Sparcl1 were clustered together, irrespective of their derived regions. These results showed an early divergence of astrocyte progenitors and their cross-regional conservation at the start of gliogenesis during brain development.

overall_design: Single-cell RNA-seq of neural progenitor cells during neurogenesis and gliogenesis

first: Jiancheng

last: Liu

first: Qiang

last: Lu


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [G1E_ATACseq]

overall_design: Murine G1E cells were transduced with the HMD lentiviral vector encoding human wildtype GATA1 or point mutants p.R307C or p.R307H


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [Patient_RNAseq]

overall_design: Human bone marrow mononuclear cells from a patient carrying the GATA1 p.R307C mutation were transduced with the HMD lentiviral vector encoding human wildtype GATA1 or point mutants p.R307C or p.R307H


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [Beta-estradiol_RNAseq]

overall_design: Murine G1E-ER4 cells were treated with indicated concentrations of beta-estradiol to induce GATA1 translocation into the nucleus and activate target genes


title: Genetic characerization of early renal changes in diabetes

city: Perth

first: Lois

last: Balmer

state: Western Australia

address: 6 Verdun Street, Nedlands

department: Centre for Medical Research

institute: UWA

summary: Diabetic kidney disease (DKD) appears heritable, suggesting genetic factors influence disease susceptibility. In our study, genes were mapped mediating early renal hypertrophic in response to diabetes. A survey of murine strains (N=15) was conducted to identify variation in kidney hypertrophy following diabetes induction. Mice with greater FVB/N and less C57BL/6 renal hypertrophy were crossed and diabetic F2 generation mice (n=534) were characterised. To confirm loci responsible for the renal hypertrophic response, diabetic congenic mice were generated by backcrossing FVB/N mice that conferred greater or C57BL/6 conferring lower risk into the reciprocal strain mice. Kidney weights of (FVB/N x C57BL/6) F2 diabetic mice were broadly distributed. Quantitative trait locus (QTL) analysis revealed that diabetic mice with kidney weights in the upper quartile shared alleles on chromosomes 6 and 12, with the FVB/N allele on chromosome 6 conferring greater susceptibility. On chromosome 12, C57BL/6 homozygotes were more significantly represented (LOD=3.8) conferring less susceptibility. The diabetic B6.Drc1/2f congenic strain developed kidney damage, while the reciprocal congenic, with FVB.Drc1/2b strain were protected. Microarray analysis identified differentially expressed genes between diabetic C57BL/6 and FVB/N mice. QTL mapping for early renal responses to diabetes identified two loci syntenic with regions identified for human diabetic kidney disease. Providing a new resource to study DKD.

overall_design: Six kidneys were analysed per group and there are four groups. Of the four groups, two are diabetic and two are control. The control mice were saline injected and were urine or blood gluocse tested at the same time as the diabetic mice. All mice were 8 weeks of age and a mix of male and female. All samples were collected at the same time.

middle: A

first: Violet

last: Peeva

first: Kirsty

last: Richardson

first: Grant

last: Morahan


title: Binding of Nucleolin to HBV cccDNA

city: Emeryville

first: Tobias

last: Flecken

address: 5300 Chiron Way

department: Infectious Diseases

institute: Novartis Institutes for Biomedical Research

summary: Covalently closed circular DNA (cccDNA) forms the basis for replication and persistence of hepatitis B virus (HBV) in the chronically infected liver. In this study we sought to identify host factors interacting with the HBV genome. Nucleolin (Ncl) was identified as a potential interactor of HBV cccDNA. This interaction was veriefied using an established ChIPseq protocol. The data show that Ncl binds cccDNA albeit at lower levels than HBcAg. Ncl deposition occurs across the genome without a clear localization and a variable pattern of deposition between experiments. This verifies the interaction of Ncl with HBV-cccDNA.

overall_design: 6 biological replicates of HepG2-hNTCP cell lines were infected with cell culture-derived HBV and used for ChIPseq using antibodies against Ncl, HBcAg, and H3K4me3 as control. Replicates HBV1-3 were processed directly after fixation, HBV4-6 were snap-frozen at -80°C after fixation prior to chromatin isolation. After ChIP, DNA was purified and used for library preparation. Pooled libraries were subject to HBV-specific target enrichment and the product combined with the original library pool. Sequencing was performed using an Illumina MiSeq.

first: Yuchen

last: Xia

first: Peter

last: Skewes-Cox

first: Meghan

last: Holdorf

first: T

last: Liang