title: Gene expression response of wolf epidermal keratinocytes to PolyI:C and canine distemper virus

city: Durham

first: Rachel

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

institute: Duke University

summary: The goal of the study was to test whether CBD103 genotype of North American gray wolves impacts the gene expression response to polyI:C or to live canine distemper virus. We established 24 primary cultures of epidermal keratinocytes from skin punches of North American gray wolves, and also generated an immortalized keratinocyte line and a CRISPR/Cas9 edited cell line. We evaluated the gene expression response of cells to either 24 hours challenge with 1 ug/ml polyI:C or to five days challenge with live canine distemper virus (100 TCID50/ml). Every challenged cell culture had a paired null control sample (plated and collected at same time points).

overall_design: mRNA profiles of epidermal keratinocytes from 24 North American gray wolves (Canis lupus), representing 14 and 10 wolves with the Kyy and KyB CBD103 genotypes, respectively. We tested for an effect of CBD103 genotype on the gene expression response to polyI:C (N = 48 samples), to canine distemper virus (N = 12), and to polyI:C after cell immortalization (N = 8).

first: Wayne

last: Robert


title: Expression data of circRNAs from the fetal rats with anorectal malformations

status: Public on May 06 2021

city: Shenyang

first: Yu Zuo

last: Bai

state: Liaoning Province

address: No. 36 Sanhao Street

country: China

institute: Shengjing Hospital of China Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Anorectal malformations (ARMs) are among the most common congenital terminal digestive tract malformations. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play roles in the development of the digestive system; however, their contributions to the pathogenesis of ARMs are not well-established. Many dysregulated circRNAs as the primary factor could play an important role in the development of anorectum. We used high-throughput sequencing to reveal the regulatory mechanism of gene expression underlying the development of anorectal malformations. These results provide original insight into the roles of circRNAs in ARMs and provide a valuable resource for further analyses of molecular mechanisms and signaling networks.

overall_design: We explored the mechanism underlying ethylenethiourea (ETU)-induced ARMs by profiling circRNA expression via RNA-seq. Nine pregnant rats were gavage-fed a single dose of 125 mg/kg 1% ETU (ARM group) on gestational day 10 (GD10), and another 9 pregnant rats received a similar dose of saline (normal group) as a control. Embryos were obtained by cesarean section on the key time-points of anorectal development (GD14, GD15, and GD16). Hindgut samples isolated from the fetuses were evaluated by high-throughput sequencing.

first: Si

middle: Y

last: Li

first: Chen

last: Wang

first: Yun

middle: X

last: Xiao

first: Xiao

middle: B

last: Tang

first: Zheng

middle: W

last: Yuan

first: Yu

middle: Z


title: Transcriptome Analysis Revealed Ameliorative Effects of Bacillus Based Probiotic on Immunity and Metabolism under an Experimentally Induced Eimeria tenella Infection in Chicken

city: Nanning

first: Fareed Uddin

last: Memon

state: Guangxi

address: Department of Clinical Veterinary Medicine, Collage of Animal Sciences and Technology, Guangxi University, Nanning, P.R. China.

department: Clinical Veterinary Medicine

institute: Guangxi University

type: Expression profiling by high throughput sequencing

summary: In order to explore the potential therapeutic mechanisms of Bacillus subtilis (B. subtilis) probiotic under Eimeria tenella (E. tenella) infection, we performed Transcriptome analysis. A total of 63 Chinese native yellow chickens were purchased from a commercial hatchery and reared in 9 coccidia-free cages with free access to feed and water for up to 28 days. Upon arrival, all chicks were weighed and randomly divided into one of three experimental groups with 21 birds in each group. The three groups consisted of negative control untreated non-challenged group (NC), positive control untreated challenged group (PC) and B. subtilis-fed challenged group (BS + ET). Challenged and non-challenged groups were housed in two different rooms for avoiding the transmission of disease. Temperature (32 to 34 °C for 1st week and then decreased by 2 °C per week), humidity (60 to 80%) and light (23 h L:1D) of both rooms were maintained during the entire period of experiment. On day 21 of age, the chickens in group PC and BS + ET were challenged with 6 × 10^4 E. tenella sporulated oocysts, whereas the chickens in group NC were gavaged with normal saline to provide same management stress. On day 28 of age (day 7 post-infection), 3 individual chickens per group were euthanized humanely by direct heart puncture and caecum tissue samples of all groups were collected for analyzing the whole transcriptional responses to the exposure of probiotic under an induced E. tenella infection in chickens. Totally, 1902 DEGs were up-regulated and 1589 DEGs were down-regulated in the positive control group versus negative control group. 341 up-regulated and 124 down-regulated DEGs were found in the comparison of BS + ET group versus NC Group, while 784 up-regulated and 493 down-regulated DEGs were found in BS + ET versus PC group.

overall_design: Includes 9 samples: 3 from NC group, 3 from PC group and 3 from BS + ET group.

first: Fareed

middle: U

first: Yunqiao

last: Yang

first: Imdad

last: Leghari

first: Hongbin

last: Si


title: Characterization of the chromatin accessibility profile of Plagl1+/-pat retina

status: Public on May 05 2021

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

country: Canada

institute: University of Lethbridge

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Retinal damage triggers reactive gliosis in Müller glia across vertebrate species, but only in regenerative animals, such as teleost fish, do Müller glia initiate repair; proliferating and undergoing neurogenesis to replace lost cells. We found that Plagl1, a maternally imprinted gene, is dynamically regulated in reactive Müller glia post-insult, with transcript levels transiently increasing before stably declining. To study Plagl1 retinal function, we examined Plagl1+/-pat null mutants postnatally, revealing defects in retinal architecture, visual signal processing and a reactive gliotic phenotype. Plagl1+/-pat Müller glia proliferate ectopically and give rise to inner retinal neurons and photoreceptors. Transcriptomic and ATAC-seq profiles revealed similarities between Plagl1+/-pat retinas and neurodegenerative and injury models, including an upregulation of pro-gliogenic and pro-proliferative pathways, such as Notch, not observed in wild-type retinas Plagl1 is thus an essential component of the transcriptional regulatory networks that retain mammalian Müller glia in quiescence.

overall_design: ATAC-seq of post-natal (P)7 Plagl1 Knock-out (3 biological samples) and wild-type (3 biological samples) retinas

first: Yacine

last: Touahri

first: Igor

last: Kovalchuk

first: Carol

last: Schuurmans


title: Paired transcriptomic and proteomic analysis implicates IL-1β in the pathogenesis of papulopustular rosacea explants [RNA-seq]

city: Guangzhou

first: Jin

last: Xu

state: Guandong

address: No. 135 Xingang Xilu

department: School of Life Sciences

institute: Sun Yat-Sen University

summary:
The goal of this study is to utilize human papulopustular rosacea biopsy explants to integrate both differentially expressed genes and differently expressed proteins in paired non-lesional and lesional papulopustular rosacea tissues.
Methods:  mRNA profiles from non-lesional and lesional papulopustular rosacea human skins were generated by deep sequencing, in duplicate using Illumina system. Proteomic profiles were also investigated using both the MSD and the OLINK proteomic platforms.
Conclusions: Our study suggests that MAPK and TNF signaling pathways are the most significantly upregulated pathways in lesional papulopustular rosacea human skins, highlighting IL-1β as a potential central mediator.

overall_design: mRNA profiles of non-lesional human skins (with or without IL-1β treatment) and lesional papulopustular rosacea human skins (without treatment) were generated by deep sequencing, in duplicates.


title: MicroRNA-200c/141 confines ERα  activity and expression pattern by targeting Ccnd1

city: Shanghai

first: Ting

last: Wu

address: 320 Yue-Yang Road

institute: Institute of Biochemistry and Cell Biology, Chinese Acadamy of Sciences

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

overall_design: Refer to individual Series


title: Decreased Peptidoglycan Synthesis Induces the RSI Invasion Switch in Agrobacterium tumefaciens

city: Columbia

first: Jacob

middle: Matthew

last: Bouchier

state: Missouri

address: 105 Tucker Hall

department: Division of Biological Sciences

country: USA

institute: University of Missouri

summary: We report that depletion of PBP1a in Agrobacterium tumefaciens induces transcriptional changes remarkably similar to the RSI invasion switch. Using RNA-seq with NextSeq 500 sequencing, we identified genes that are differentially expressed during depletion of PBP1a after 6 hours and after 16 hours. Depletion of PBP1a after 6 hours results in upregulation in genes associated with Type VI Secretion and succinoglycan production and downregulation of genes associated with flagellar motility and chemotaxis. After 16 hours, additional differentially expressed genes were identified, including those encoding ABC transporters.

overall_design: Examination of transcriptional changes associated with PBP1a depletion after 6 hours and after 16 hours. 20 samples were examined: 4 replicates of each WT, WT + IPTG, PBP1a + IPTG, PBP1a 6 hour, and PBP1a 16 hour.

first: Michelle

middle: A

last: Williams

middle: M

first: Pamela

middle: J

last: Brown


title: Receptor-mediated mitophagy regulates EPO production and protects against renal anemia

status: Public on May 07 2021

city: TianJin

first: Changlu

state: TianJin

address: 288 Nanjing Rd, Heping

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

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

summary: Erythropoietin (EPO) drives erythropoiesis and is secreted mainly by the kidney upon hypoxic or anemic stress. The paucity of EPO production in renal EPO-producing cells (REPs) causes renal anemia, one of the most common complications of chronic nephropathies. Although mitochondrial dysfunction is commonly observed in several renal and hematopoietic disorders, the mechanism by which mitochondrial quality control impacts renal anemia remains elusive. In this study, we showed that FUNDC1, a mitophagy receptor, plays a critical role in EPO-driven erythropoiesis induced by stresses. Mechanistically, EPO production is impaired in REPs in Fundc1-/- mice upon stresses, and the impairment is caused by the accumulation of damaged mitochondria, which consequently leads to the elevation of the reactive oxygen species (ROS) level and triggers inflammatory responses by up-regulating proinflammatory cytokines. These inflammatory factors promote the myofibroblastic transformation of REPs, resulting in the reduction of EPO production. We therefore provide a link between aberrant mitophagy and deficient EPO generation in renal anemia. Our results also suggest that the mitochondrial quality control safeguards REPs under stresses, which may serve as a potential therapeutic strategy for the treatment of renal anemia.

overall_design: Here, we performed RNA-seq of R2 erythrocytes from Fundc1 deficient mouses and WT to further study the molecular changed between KO and WT.

first: Guangfeng

last: Geng

first: Jinhua

last: Liu

first: Quan

last: Chen

first: Yushan

last: Zhu

first: Lihong

last: Shi


title: Epigenetic Plasticity Enables CNS-Trafficking of EBV-infected B Lymphocytes

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute


title: Chromatin remodeler Arid1a regulates subplate neuron identity and wiring of cortical connectivity

city: Ann Arbor

first: Kenneth

last: Kwan

state: MI

address: 109 Zina Pitcher Pl

department: MBNI & Human Genetics

institute: University of Michigan

summary: Loss-of-function mutations in chromatin remodeler gene ARID1A are a cause of Coffin-Siris syndrome, a developmental disorder characterized by dysgenesis of corpus callosum. Here, we characterize Arid1a function during cortical development and find unexpectedly selective roles for Arid1a in subplate neurons. Subplate neurons (SPNs), strategically positioned at the interface of cortical grey and white matter, orchestrate multiple developmental processes indispensable for neural circuit wiring. We find that pan-cortical deletion of Arid1a leads to extensive mistargeting of intracortical axons and agenesis of corpus callosum. Sparse Arid1a deletion, however, does not autonomously misroute callosal axons, implicating non-cell autonomous Arid1a functions in axon guidance. Supporting this possibility, the ascending axons of thalamocortical neurons, which are not autonomously affected by cortical Arid1a deletion, are also disrupted in their pathfinding into cortex and innervation of whisker barrels. Coincident with these miswiring phenotypes, which are reminiscent of subplate ablation, we unbiasedly find a selective loss of SPN gene expression following Arid1a deletion. In addition, multiple characteristics of SPNs crucial to their wiring functions, including subplate organization, subplate-thalamocortical axon co-fasciculation (“handshake”), and extracellular matrix, are severely disrupted. To empirically test Arid1a sufficiency in subplate, we generate a cortical plate deletion of Arid1a that spares SPNs. In this model, subplate Arid1a expression is sufficient for subplate-thalamocortical axon co-fasciculation and extracellular matrix assembly. Consistent with these wiring functions, subplate Arid1a sufficiently enables normal callosum formation, thalamocortical axon targeting, and whisker barrel development. Thus, Arid1a is a multifunctional regulator of subplate-dependent guidance mechanisms essential to cortical circuit wiring.

overall_design: We analyzed a total of 12 samples of rRNA-depleted RNA from E15.5 mouse cortex using UMI RNA-seq. Libraries were generated using Click-seq. 6 samples were controls and 6 samples were Emx1-Cre Arid1a conditional mutants.

first: Daniel

last: Doyle

first: Mandy

last: Lam

first: Yaman

last: Qalieh

first: Adel

first: Alice

last: Sorel

first: Owen

middle: H

last: Funk


title: Transcriptome profile of Human Mesenchymal Stem Cells with Reduced Senescence and Increased Trilineage Differentiation Ability upon Drug Treatment

city: Harbin

first: Yue

last: CHEN

state: Heilongjiang

address: 92 Xidazhi St, Nangang

institute: Harbin Institute of Technology, China

summary: Human Mesenchymal stem cells (hMSCs) are multi-potential cells which are widely used in cell therapy. However, the frequently emerged senescence and decrease of differentiation capabilities limited the broad applications of MSC. In this study, hMSCs were treated by rapamycin, oltipraz, metformin, and vitamin C for the indicated time and the cells were subjected to senescence evaluation and trilineage differentiation. Transcriptomics dataset of hMSCs after drugs treatment was analyzed to interpret biological pathways responsible for the anti-senescence effects. Although four drugs exhibited significant activities in promoting MSC osteogenic differentiation, metformin is the optimal drug to promote trilineage differentiation. GO terms illustrated that the anti-aging effects of drugs were mainly associated with cellular senescence, mitotic and meiosis process. The method established and discussed in this study can be used to study different biological phenotypes upon drug intervention in MSC which will extend the clinical application of hMSCs.

overall_design: mRNA profiles of the hMSCs which were treated by rapamycin, oltipraz, metformin, vitamin C and control for the indicated time


title: Oncogene-induced maladaptive activation of Trained Immunity in the pathogenesis of human inflammatory myeloid neoplasm [ECD]

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: Trained immunity (TI) is a pro-inflammatory program induced in monocyte/macrophages upon sensing of specific pathogens and characterized by immunometabolic and epigenetic changes enhancing cytokine production. Maladaptive activation of TI (i.e., in the absence of infection) might result in detrimental inflammation and disease development; however, the exact role and extent of inappropriate activation of TI in the pathogenesis of human diseases is undetermined.

overall_design: We reveal oncogene-induced, maladaptive induction of TI in the pathogenesis of a human inflammatory myeloid neoplasm (Erdheim-Chester disease, ECD, characterized by the BRAFV600E oncogenic mutation in monocyte/macrophages and excess cytokine production).

first: Giulio

last: Cavalli


title: Pharmacological inhibition of WIP1 sensitizes acute myeloid leukemia cells to MDM2 inhibitor Nutlin-3a

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

summary: The wild-type p53-inducible protein phosphatase WIP1, encoded by the PPM1D gene, is a negative regulator of p53 and is involved in cell cycle control and DNA damage stress-response. In acute myeloid leukemia (AML), the restoration of p53 activity through MDM2 inhibition proved efficacy in a number of combination strategies. We investigated the therapeutic potential of its inhibition through the selective WIP1 inhibitor (WIP1i) GSK2830371, in association with the MDM2 inhibitor Nutlin-3a (Nut-3a) in a panel of AML cell lines and performed gene expression analysis of single agent and combined treatments. A p53-related signature was significantly upregulated in the TP53-wildtype MV-4-11 AML cell line. Moreover, drug-specific transcriptional changes likely contribute to the synergistic combination effect.

overall_design: TP53-wildtype MV-4-11 and TP53-mutated NOMO-1 cells treated with Nutlin-3a or GSK2830371, or the drug combination (or vehicle) for 16h were used for RNA extraction and hybridization on microarrays.

first: Maria

middle: C

last: Fontana

first: Martina

last: Pazzaglia

first: Giovanni

last: Martinelli


title: Epigenetic Plasticity Enables CNS-Trafficking of EBV-infected B Lymphocytes [RNA-Seq]

summary: Subpopulations of B-lymphocytes traffic to different sites and organs to provide diverse and tissue-specific functions. Here, we provide evidence that epigenetic differences confer a neuroinvasive phenotype.  An EBV+ B cell lymphoma cell line (M14) with low frequency trafficking to the CNS was neuroadapted to generate a highly neuroinvasive B-cell population (MUN14).  MUN14 B cells efficiently infiltrated the CNS within one week and produced neurological pathologies. We compared the gene expression profiles of viral and cellular genes using RNA-Seq and identified one viral (EBNA1) and several cellular gene candidates, including secreted phosphoprotein 1/osteopontin (SPP1/OPN), neuron navigator 3 (NAV3), CXCR4, and germinal center-associated signaling and motility protein (GCSAM)) that were selectively upregulated in  MUN14. ATAC-Seq and ChIP-qPCR revealed that these gene expression changes correlated with epigenetic changes at gene regulatory elements. The neuroinvasive phenotype could be attenuated with a neutralizing antibody to OPN, confirming the functional role of this protein in trafficking EBV+ B cells to the CNS.  These studies indicate that B-cell trafficking to the CNS can be acquired by epigenetic adaptations and provide a new model to study B-cell neuroinvasion associated CNS lymphoma and autoimmune disease of the CNS, including multiple sclerosis (MS).cell infection to investigate the underlying mechanisms that control EBV-induced B-cell immortalization. ATAC-seq revealed that over a third of accessible chromatin is altered with the most perturbed sites overlapping Ets-family, including PU.1 and RUNX1 transcription factors.  EBV nuclear antigens (EBNAs) clustered with different gene categories and RNA-seq identified the transcriptional response of these gene.  Focusing on EBNA1 revealed a selection of gene targets involved in nucleotide metabolism.  Metabolomics indicated that adenosine and purine metabolism are significantly altered by EBV immortalization, and we validated that adenosine deaminase (ADA) is a direct and critical target of EBNA1 and the EBV-directed immortalization process. These findings reveal that purine metabolism and ADA inhibitors may be a useful therapeutic for EBV-driven lymphoid cancers

overall_design: ATAC-seq and RNA-seq in EBV+ B cell lymphoma cell line (M14) with low frequency trafficking to the CNS and highly neuroinvasive B-cell population (MUN14)

first: Paul

last: Lieberman

first: Samantha

last: Soldan


title: CDK8/19 small molecule inhibition promotes naïve features in human and mouse pluripotent stem cells II

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Pluripotent stem cells (PSCs) can transition between cell states in vitro, closely reflecting developmental changes in the early embryo. PSCs can be stabilized in their naive state by blocking extracellular differentiation stimuli, particularly FGF5 MEK signaling. Here, we report that multiple features of the naive state in human and mouse PSCs can be recapitulated without affecting FGF-MEK-signaling.  Mechanistically, chemical inhibition of CDK8 and CDK19 kinases (CDK8/19i) removes their ability to repress the Mediator complex at enhancers. Thus CDK8/19i increases Mediator-driven recruitment of RNA Pol II to promoters and enhancers.  This efficiently stabilizes the naive transcriptional program, and confers resistance to enhancer perturbation by BRD4 inhibition. Moreover, naive pluripotency during embryonic development coincides with reduction in CDK8/19.  We conclude that global hyperactivation of enhancers drives naive pluripotency, and this can be captured in-vitro by inhibiting extracellular FGF-MEK-signaling, or downstream, by CDK8/19i. These principles may apply to other contexts of cellular plasticity.

overall_design: Five human pluripotent stem cell lines (PSCs) were cultured in two conditions ("Primed" vs "CDK8/19i") for long-term/10passages, and then transcriptomic differences between the two groups were assessed by RNAseq.  Culture conditions were either standard primed conditions ("Primed" = mTeSR media with FGF2 and TGFb1, feeder-free, on matrigel), or including additional media supplementation with recombinant human LIF (20 ng/ml) and CDK8/19-small molecule inhibitor at 0,4 mM (= "CDK8/19i" or "8i").  The five cell lines were H1, D2#2, D2#4, CB5 and WIBR3.

first: Manuel

last: Serrano

first: Raquel

last: Bernad


title: Levels and Characteristics of mRNAs in Dormant Spores of Firmicute Species

city: Farmington

first: Peter

last: Setlow

state: CT

address: 263 Farmington Ave

department: Molecular Biology and Biophysics

institute: UConn Health

summary: Spores of Bacillales and Clostridiales species contain 100s of different mRNAs, and their major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate.  In new work, RNA was isolated from spores of five Bacillales and one Clostridioides species and relative spore mRNA levels were determined by RNA-seq.  Determination of RNA levels in single spores allowed calculation of RNA nt/spore, and assuming mRNA is 3% of spore RNA allowed calculation that only ~6% of spore mRNAs were present at ≥ 1/spore. Bacillus subtilis, Bacillus atrophaeus and Clostridioides difficile spores had 49, 42 and 51 mRNAs at >1/spore, respectively. Numbers of mRNAs at ≥1/spore were ~10 to 50% higher in Geobacillus stearothermophilus and Bacillus thuringiensis Al Hakam spores, respectively, and ~ 4-fold higher in Bacillus megaterium spores. Notably, in all species: i) many of the 60 most abundant spore mRNAs were transcribed by RNA polymerase with forespore-specific s factors; ii) some to many of the most abundant spore mRNAs encoded  orthologs of those encoded by abundant B. subtilis spore mRNAs and proteins present in dormant spores ; and iii) some spore mRNAs were likely transcribed in the mother cell compartment of the sporulating cell.  Indeed , analysis of the coverage of RNA-seq reads on mRNAs from all six species suggested that abundant spore mRNAs were at least somewhat fragmented. This observation was confirmed by RT-qPCR analysis of three abundant mRNAs each from B. subtilis and C. difficile spores.  These data add to a growing body of evidence indicating that the great majority of mRNAs in spores of Firmicutes are degradation and function as a ribonucleotide depot for new RNA synthesis when spores germinate.

sample_organism: Geobacillus stearothermophilus ATCC 12980

overall_design: RNA from spores of 5 different Bacillales and 1 Clostridiales were isolated and submitted for next generation sequencing via illumina HiSeq.

first: Melissa

last: Caimano

first: Wendy

last: Mok


title: HP1γ/CBX3 Promotes Lung Adenocarcinoma by Activating Rho GTPases Signaling Pathway

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We performed CBX3 knockdown in lung adenocarcinoma cells along with RNA sequencing. The expression profiling showed Rho GTPases signaling as a potential CBX3 target and the conclusions were also verified in clinical samples.

overall_design: RNA sequencing in A549 cell lines with si-Control or si-CBX3

first: H

first: X

last: Jin


title: Galectin-9 suppresses tumor growth of colon cancer in vitro and in vivo

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.


title: Oncogene-induced maladaptive activation of Trained Immunity in the pathogenesis of human inflammatory myeloid neoplasm [BRAF]

first: Ivan

last: Merelli

first: Giulio


title: Oncogene-induced maladaptive activation of Trained Immunity in the pathogenesis of human inflammatory myeloid neoplasm


title: MicroRNA-200c/141 confines ERα  activity and expression pattern by targeting Ccnd1 [bulk RNA-seq]

first: Ting

last: Wu

summary: ERα is one of the most important transcription factors and therapeutic targets in breast cancer. The patterns of ERα expression in normal breast tissue and cancerous lesions are strikingly different. What drives the change of ERα pattern during lesions formation remains unclear. Here, we describe a novel regulatory mechanism through which miR-200c/141 regulates the level as well as the distribution of ERα in the mammary gland. miR-200c/141 is specifically expressed in luminal cells. Luminal-deletion of miR-200c/141 (miR-cKO) leads to a drastic expansion of ERα+ cell proportion. Single cell RNAseq reveals that miR-cKO generates aberrant luminal subpopulations with increased proliferative and anti-apoptotic features. In vivo lineage tracing of ER- luminal cells demonstrates that miR-200c/141 deletion can convert ER- cells into ER+ cells, which contribute partly to the increase of ERα+ luminal cells. Mechanistic study identifies  Ccnd1  as a novel target of miR-200c/141 .  Upon miR-200c/141deletion, elevated  Ccnd1  level corroborates ERα transcriptional activation, leads to enhanced ERα signaling activity, consequently increased transcription of ERα coding gene  Esr1  through self-activation at promoter E1. Our findings reveal a new miR-200c/141-Ccnd1-ERα axis, and provide new molecular insights into how miR-200c/141-Ccnd1 enforces the lineage barrier between ER- and ER+ luminal cells, and what drives the change of ERα expression pattern.

overall_design: Examination of gene expression changes in mouse mammary luminal cells after knockout of miR-200c/141.


title: Galectin-9 suppresses tumor growth of colon cancer in vitro and in vivo [in vitro CW]

summary: We examined the ability of Gal-9 to inhibit cell proliferation via apoptosis, and the effects of Gal-9 on cell cycle-related molecules in various human colon and colorectal cancer cell lines. In addition, Gal-9-mediated changes of activated tyrosine kinase receptors and angiogenic molecules were assessed using protein array chips in colon and colorectal cancer cells. Moreover, miRNA array analysis was performed to examine Gal-9-induced miRNA expression profiles. We also elucidated if Gal-9 inhibited tumor growth murine in vivo model.

overall_design: Effect of galectin-9 was examined using colon cancer cell lines and xenograft animal model.

first: Asahiro

last: Morishita

first: Hisakazu

last: Iwama


title: Epigenetic Plasticity Enables CNS-Trafficking of EBV-infected B Lymphocytes [ATAC-Seq]

first: Priyankara

last: Wickramasinghe

first: Paul


title: MicroRNA-200c/141 confines ERα  activity and expression pattern by targeting Ccnd1 [single-cell RNA-seq]

overall_design: Examination of gene expression changes in mammary cells after knockout of miR-200c/141.


title: TDP-43 prevents endogenous RNAs from triggering a lethal RIG-I-dependent interferon response

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: RIG-I-like receptors (RLRs) are involved in the discrimination of self vs non-self via the recognition of dsRNA. Emerging evidence suggests that immunostimulatory dsRNAs are ubiquitously expressed yet they are disrupted or sequestered by cellular RNA binding proteins (RBPs). TDP-43 is an RBP associated with multiple neurological disorders and is essential for cell viability. Here, we demonstrate that TDP-43 regulates the accumulation of immunostimulatory dsRNA. The immunostimulatory RNA was identified as RNA Polymerase III transcripts, including 7SL and Alu retrotransposons, and we demonstrate that the RNA binding activity of TDP-43 is required to prevent immune stimulation. The dsRNAs activate a RIG-I-dependent interferon response which promotes necroptosis. Genetic inactivation of the RLR-pathway rescues the interferon-mediated cell-death associated with loss of TDP-43. Collectively, our study describes a role for TDP-43 in preventing the accumulation of endogenous immunostimulatory dsRNAs and uncovers an intricate relationship between the control of cellular gene expression and IFN-mediated cell-death.

overall_design: Profiling the gene expression after TDP-43 knockdown in SH-SY5Y cells.

first: William

last: Dunker

first: Xiang

last: Ye

first: John

last: Karijolich


title: Expression data from ferulic acid treated C. elegans

city: Changchun

first: hui

last: li

address: qianjinstreet

institute: jilin university

summary: Gene expression in N2 worms treated with 500 μM  or 0 μM ferulic acid, at days 5.  Effects of ferulic acid in C. elegans gene expression is studied, as our results indicate a lifespan extension effect produced by this molecule.  RNA-seq were used to detail the global programme of gene expression underlying the lifespan extension and identified distinct classes of up/down-regulated genes in animals treated with ferulic acid.

overall_design: L4 C. elegans  treated with ferulic acid  for 5 days were selected for RNA extraction and  RNA-seq

first: Hui

last: Li

first: Xiaoxuan

first: Fanwei

last: Meng

first: Liping

last: Wang


title: Galectin-9 suppresses tumor growth of colon cancer in vitro and in vivo [in vivo CW 90]

first: Satoshi


title: An Adipocyte-like Signature in Ovarian Cancer Minimal Residual Disease Identifies Metabolic Vulnerabilities of Tumor Initiating Cells

city: Oxford

first: Zhiyuan

last: Hu

address: John Radcliffe Hospital/Headley Way

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Recurrence and metastasis are the main causes of death for cancer patients. Relapse can also occur when complete response is achieved, due to the Minimal Residual Disease (MRD) cells that survive treatment. Here we show that the knowledge gap in solid tumors MRD biology can be reduced studying ovarian cancer and we provide the first molecular characterization of MRD. Transcriptomics analysis of 120 tumor biopsies from 17 patients with different response to treatment revealed that the MRD cells have a very specific adipocyte-like signature. These cells also upregulate fatty acid oxidation (FAO), displaying a vulnerability that can be targeted therapeutically. These findings identify FAO as an attractive target to eradicate MRD in ovarian cancer and make a compelling case for the use of FAO inhibitors in neo-adjuvant settings.

overall_design: RNA-Seq of pre- and post-chemotherapy high-grade serous ovarian tumours

first: Mara

last: Artibani

first: Kenta

last: Masuda

first: Ahmed

last: Ahmed


title: miRNA expression profiles of MDA-MB-231 TNBC cells with defected RARalpha serine-77 phosphorylation

city: Hangzhou

first: Huajun

last: Zhao

address: 548 Binwen Road

institute: Zhejiang Chinese Medical University

summary: microRNAs have been shown to be involved in the pathogenesis of TNBC as important regulators of cell proliferation and apoptosis. However, whether the activation of retinoic acid receptor alpha (RARα), a transcription factor, is involved in mediating transcriptional regulation of microRNAs remains elusive. Here, we investigated the differentially expressed miRNAs in triple negative breast cancer cell line MDA-MB-231 overexpressing a phosphorylation-defective mutant RARαS77A, which mimicked activated RARα, in comparison to non-transfected control cells.

overall_design: MDA-MB-231 cells were transfected with lentiviral RARαS77A, a total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Non-transfected cells were used as controls, experiments were performed in triplicates.

first: Siyue

last: Lou

first: Hang

last: Gao

first: Huanwu

last: Hong

first: Zhihui

last: Zhu


title: YTHDF2 inhibits gastric cancer cell growth by regulating FOXC2 signaling pathway

city: Qingdao

first: Yu

last: Cao

address: 308 Ningxia Road

institute: Qingdao University

summary: we found that YTHDF2 has lower expression in GC tissues and GC cells, and promotes the growth, migration and invasion of GC cells. In addition, the analysis of clinical data found that the expression level of YTHDF2 was closely related to the stage of GC and the survival of patients with GC. RNA-seq showed that overexpression of YTHDF2 significantly reduced protein expression in the FOXC2 (Forkhead box protein C2, FOXC2) signaling pathway.

overall_design: The gene expression of Vector and MGC-803 cell lines overexpressing YTHDF2 were detected by RNA sequencing.

first: Xudong

last: Shen

first: Kui


title: Galectin-9 suppresses tumor growth of colon cancer in vitro and in vivo [in vivo Caco-2 90]

last: Kondo

overall_design: In the study, effect of galectin-9 was examined using colon cancer cell lines and xenograft animal model.

first: Asahiro

last: Morishita

first: Hisakazu

last: Iwama


title: Galectin-9 suppresses tumor growth of colon cancer in vitro and in vivo [in vivo CW 30]


title: Identification and characterization of C4 dicarboxylic acid transporters in Pichia kudriavzevii CY902 strain

city: Tianjin

first: Feiyu

last: Fan

state: Tianjin

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

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

summary: RNA-seq libraries were constructed for three samples, including (I) ΔURA3 strain grown in SD medium containing 2% w/v glucose(pH=5.0);(II)ΔURA3 strain grown in SD medium containing  2%w/v glucose and 2% w/v succinic acid(pH=5.0);(III)ΔURA3 strain grown in SD medium containing  2% w/v succinic acid(pH=5.0). For preparation of RNA samples, ΔURA3 cells grown overnight were inoculated into 50 ml liquid Synthetic Dextrose (SD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 24 hours to the logarithmic growth phase (OD600= 2-3). The cells were collected by centrifugation at 6000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 50 mL SD medium containing carbon sources of different combinations of glucose and succinic acid .The pH of the culture sample is adjusted to 5.0 with NaOH. After flask culturing at 30°C and 250 rpm for an additional three hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction.  Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end RNA-seq libraries were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s Hiseq X Ten platform (Illumina, San Diego, USA). Each sample contains two biological replicates.

overall_design: mRNA profiles of  ΔURA3 strain grown in SD medium containing carbon sources of different combinations of glucose and succinic acid were generated by deep sequencing, using Illumina’s Hiseq X Ten platform

first: Yongyan

last: Xi

first: Tao

last: Zhan

first: Hongtao

last: Xu

first: Jing

last: Chen

first: Changhao

last: Bi

first: Xueli

last: Zhang


title: Single-cell Atlas Reveals Fatty Acid Metabolites Regulate the Functional Heterogeneity of Mesenchymal Stem Cells

city: Guangzhou

first: Jiayi

last: Xie

state: Guangdong

address: North Campus, Sun Yat-sen University

institute: Sun Yat-sen University

summary: Here, using scRNA-seq on bone marrow MSCs, we identified pre-MSCs and lineage-committed MSC clusters, and revealed their potential regulatory mechanisms in MSC lineage commitment. Our data indicated a novel potential role of MSCs responding to fatty acid treatment, which could be applied to in vitro culture.

overall_design: Single-cell RNA-seq on bone marrow MSCs

first: Meng

last: Zhao

first: Qi


title: Galectin-9 suppresses tumor growth of colon cancer in vitro and in vivo [in vitro Caco2]

first: Satoshi


title: Host-informed molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

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

overall_design: Refer to individual Series


title: Host-informed molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine [RNA-seq]

summary: We analyzed the transcriptomes of K. phaffii strains secreting the VP8-P[6] serotype of the rotavirus antigen, and compared against null strains as well as strains secreting the VP8-P[4] or VP8-P[8] serotype in order to diagnose bottlenecks limiting robust secretion of P[6].

overall_design: Multiple replicates and clones of K. phaffii strains expressing either VP8-P[4], VP8-P[6], or VP8-P[8] as well as null (non-expressing) strains were analyzed for RNA expression. All strains were sampled following biomass accumulation in glycerol-containing medium for 24 hr following by induction of protein expression by growth in methanol-containing medium for an additional 24 hr.

first: Joseph

middle: R

last: Brady

first: Charlie

first: J

last: Love


title: Galectin-9 suppresses tumor growth of colon cancer in vitro and in vivo [in vivo Caco-2 30]

first: Asahiro


title: Transcriptomic comparison of WT and yebEFG mutant of Salmonella enterica ATCC 14028 strains grown in LB and in the presence of sublethal concentration of nalidixic acid

city: Sevilla

first: Ángela

last: Mérida-Floriano

state: Sevilla

address: Avda. Reina Mercedes 6

department: Genetics

institute: Universidad de Sevilla

summary: RNA-sequencing of two Salmonella enterica strains (WT, ∆yebEFG) in standard laboratory conditions (LB to ESP), and in SOS-response inducing conditions (LB+nalidixic acid)

overall_design: For ATCC 14028 WT, three biological replicates in ESP and in the presence of 8.5ug/ml of nalidixic acid; for ATCC 14028 ∆yebEFG, three biological replicates in ESP and in the presence of 8.5ug/ml of nalidixic acid

first: Angela

last: Merida-Floriano

first: Rocio

last: Canals

first: Will

middle: P

last: Rowe

first: Jay

last: Hinton

first: Josep

last: Casadesus


title: Expression data of PRDM1α or empty vector-transduced NK92 or KHYG1 cell lines

city: İzmir

first: Can

last: Küçük

address: Dokuz Eylül University Health Campus, Mithatpaşa Avenue. No: 58/5

department: İzmir Biomedicine and Genome Center

country: Turkey

institute: Dokuz Eylül University

summary:
CD25 (IL2RA) is a subunit of IL2 receptor complex, which determines the sensitivity of the receptor to IL2. Here, we investigated whether PRDM1, a transcriptional repressor implicated as a tumor suppressor in NK cell malignancies, directly represses CD25 (IL2RA).  Using ChIP-seq, we identified a direct binding site of PRDM1 within 1st intron of CD25 (IL2RA) in activated primary human NK cells.
We used DNA microarrays on two PRDM1α transduced NK cell lines (i.e. NK92 and KHYG1) to address whether PRDM1 transcriptionally represses CD25.

overall_design: Exponentially growing NK92 and KHYG1 cell lines were transduced with PRDM1α-PMIG or empty PMIG retroviral constructs. GFP+ cells were sorted with FACS 48h post-transduction. Total RNA was purified from sorted cells and subjected to DNA microarray.

first: John

last: Chan


title: Microarray analysis of U87 Glioblastoma Multiforme cell line exposed to proton irradiation during acute hypoxia.

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

summary: Glioblastoma multiforme (GBM), is the most malignant and common tumor among glial neoplasms. It is characterized by a peak of incidence between 45 and 70 years and a patient median survival time of 14.6 months. In addition, GBM undergoes malignant progression under hypoxic conditions that contributes to strong radioresistance and chemoresistance; alters the metabolism of the tumor cells; generates a strong genome instability, increases the angiogenesis, vasculogenesis, and contributes to the formation of the Cancer Stem Cells (CSCs) and the infamous Circulating Tumor Cells (CTCs) involved in metastasis formation. Moreover, GBMs have a poor prognosis due to treatment (such as surgical resection, conventional RT and chemotherapy) plan failures. In this sense, since standard GBM treatments are not effective, new promising strategies such as Proton Therapy (PT), are under investigation because supported by encouraging results. Considering these assumptions, the main aim of this study was to analyze GBM response to PT innovative treatment during induced acute hypoxia, by using a whole gene expression analysis. Thus, in this work we have reported in a descriptive way, the most statistically and biologically relevant pathways deregulated in U87 GBM cell line, according to specific PT plans during hypoxia condition, and in addition, some interesting biomarker networks were following discussed.

overall_design: Proton-induced gene expression changes in U87 GBM cell line after 2 and 10 Gy of proton doses during acute hypoxia, were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays. Samples were named as follow: U87 Hypoxia 2Gy and U87 Hypoxia 10Gy.


title: Convolutional neural network modelling: advancing identification of true mRNA cleavage sites

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavages by small RNAs. Here we developed an extension module based on a deep learning convolutional neural network (CNN) in a machine learning environment to discriminate false from true cleavage sites applied on datasets from potato (Solanum tuberosum, St) and the oomycete pathogen Phytophthora infestans (Pi). The core of the CNN module is a stochastic gradient descent optimizer with cyclical learning rate (CLR) which together with Bayesian optimization scored a validation accuracy of 100%. To verify the recognition of cleavage sites we applied the module on Arabidopsis thaliana microRNA cleavages. Our module managed to recognize all cleavages, confirming the reliability of the module. When applying this new model to evaluate our data, 7.3% of all cleavage windows represented true cleavages distributed as 214 sites in P. infestans and 444 sites in potato. The sRNA landscape of the potato-P. infestans interaction is complex with uneven sRNA production and cleavage regions. In total, 222 endogenous Pi-sRNAs, 565 endogenous St-sRNAs, 91 trans-acting Pi-sRNAs and 14 trans-acting St-sRNAs were discovered from our datasets. Groups of self-regulatory sRNAs, and sRNAs generated from effector sequences like RXLR and Crinklers suggest dual effector functions. In the potato genome, resistance genes were most targeted mainly as self-regulation but also as results of a trans-action event. Our new analytic model is freely accessible for anyone working on complex biological systems.

sample_organism:
Solanum tuberosum
Phytophthora infestans

overall_design: 9 small RNA samples sequenced from Co-IP.  3 replicates for each of the following: StAgo1-GFP H2O, StAgo1-GFP 11388, StAgo1-GFP 88069. 4 small RNA libraries  were sequenced.   2 replicates from each of the following: Potato leaves (cv. Sarpo Mira) inoculated with H20 or 88069. 10 degradome libraries were sequenced. 2 replicates from each of the following: Mycelia of P. infestans strains 88069 or PiAgo1-GFP. Leaf samples of Potato (cv. Bintje) inoculated with H2O. Infected leaf samples with P. infestans strains 88069 or PiAgo1-GFP.

last: Hodén

first: Xinyi

last: Hu

first: German

last: Martinez-Arias

first: Christina

last: Dixelius


title: RNA-seq of Escherichia coli MG1655 and SR under fluctuating ammonia availability (limitation-depletion)

city: Stuttgart

first: Julia

last: Zieringer

department: Biochemical Engineering

country: Germany

institute: University of Stuttgart

summary: In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs which result in production yield losses. This study is focused on transcriptional changes due to fluctuating ammonia supply, while sampling a continuously running two-compartment bioreactor system comprising a stirred tank reactor (STR) and a plug flow reactor (PFR). A previously created mutant E.coli SR was used to limit the reaction to environmntal influences via knock-out of stringent response. E. coli WT revealed highly diverging short-term transcriptional responses in ammonia fluctuation compared E. coli SR.

overall_design: Experimental design consists of a stirred tank (STR) connected to a plug-flow reactor (PFR). The feeding point was placed in the STR creating a starvation zone in the PFR, which allowed to resolve different timescales of cellular response. The chemostat was operated at a dilution rate of D = 0.2 h-1 and ammonium was chosen as the limiting nutrient. The steady state prior to the PFR connection was used as reference state (S0: t = 0 h). Periodic passage from the STR through the PFR then creates a repeated short nitrogen starvation stimulus. The short-term response of cells to the PFR stimulus was monitored by sampling from five ports along the PFR (P1- P5) at distinct residence times and the long-term response of cells investigated from samples taken from the STR after 5 min and 28 h. The experiment was conducted twice.

first: Martin

last: Ziegler

first: Ralf

last: Takors


title: LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct


title: LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [LoopSeq]

summary: In this study, we used a barcoding-based synthetic long read (SLR) isoform sequencing approach (LoopSeq) to generate sequencing reads sufficiently long and accurate to identify isoforms using standard short read Illumina sequencers.

overall_design: Loop transcriptome sequencing on 8 colon cancer samples. ID 1, 2 and 3 are for patient ID. N, T and M are for benign colon tissue adjacent to cancer samples, tumor samples and metastasis samples.

first: Silvia

first: Indira

last: Wu

first: Yan-Ping

last: Yu

first: Michael

last: Balamotis

first: Baoguo

last: Ren

first: Tuval

last: Yehezkel

first: Jian-Hua

last: Luo


title: LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [RNA-seq]

overall_design: Amplicon RNA-sequencing targeting on gene FAM104A and PABPC1 across 6 colon cancer samples. ID 1, 2 and 3 are for patient ID. T and M are for tumor and metastasis samples. GRM and PHU are for two enzymes.


title: mRNA Expression Changes in Organotin-Driven NLRP3 Inflammasome Activation in Murine Bone Marrow Derived Macrophages

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Trimethyltin (TMT) and triethyltin (TET) are two tri-organotin compounds, a group of substances reported to affect mitochondria function. These compounds were also found to activate the NLRP3 inflammasome, an inflammatory cascade that occurs in myeloid cells when primed with a Toll-like receptor ligand (i.e. LPS) followed by activation by an exogenous or endogenous danger signal.  The inflammasome is a very tightly regulated mechanism, with several miRNAs playing an important role. To determine differential miRNA changes between TMT and TET induced inflammasome activation, miRNA expression profiles were evaluated in LPS-primed murine bone marrow derived macrophages (BMDMs) exposed to TMT or TET as compared to saline. mRNA expression arrays were also performed and analyzed to identify miRNA target genes in order to elucidate the key mechanism(s) by which TMT and TET activate the NLRP3 inflammasome pathway.  These studies will help us understand the inflammasome regulation in macrophages by organotin.

overall_design: Murine bone marrow derived macrophages were exposed to LPS (33ng/ml) as a priming agent for 3 hours followed by either TMT OH (1.25 microMolar), TET (10 microMolar), or saline to induce NLRP3 inflammasome activation.  Comparisons were performed between each organotin and saline.  Three biological replicates for each group were set up.

first: G

last: Harry

first: Gabrielle

last: Childers

first: Stella

last: Sieber

first: Jian

middle: L


title: mRNA Expression and microRNA Expression Changes in Organotin-Driven NLRP3 Inflammasome Activation in Murine Bone Marrow Derived Macrophages

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

platform_organism:
Mus musculus
synthetic construct


title: The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis

city: Philadelphia

first: Sylvia

middle: N

last: Michki

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

summary: In this work, Michki et. al. isolate neurons and neural progenitors from the developing Drosophila brain. Through a combination of in silico and in situ techniques, they map out the expression dynamics of a variety of molecular factors that may play a role in specifying terminal neural fates at the RNA level, and provide tools to enable similar analyses to be performed in other systems.

overall_design: R9D11-Gal4 genetic driver was used with a UAS:hH2B-2xmNG reporter to label type-II neural lineages in third instar larval brains. 20 brains were dissected, dissociated, and sorted on a Sony MA900 FACS machine. 10,000 cells were sequenced in a single lane of a 10Xchromium chip using their v3 chemistry. Cells were sequenced on an Illumina NovaSeq/HiSeq4000 with 400M reads allocated to this library. 6092 cells were identified with a mean read count of 97,604 reads/cell when aligned to the BDGP6(2014-07) Drosophila genome assembly from ENSEMBL using STAR. Downstream filtering and analysis were performed using scanpy.

first: Nigel

middle: S

first: Ye

first: Kayvon

last: Sanjasaz

first: Yimeng

last: Zhao

first: Fred

last: Shen

first: Logan

last: Walker

first: Wenjia

last: Cao

first: Cheng-Yu

last: Lee

first: Dawen

last: Cai


title: Transcriptome comparison between emergent and historical emm4 group A Streptococcus strains from North America

city: Houston

first: Anthony

last: Flores

state: TX

address: 6431 Fannin St., MSB 3.130

institute: UTHSC/McGovern Medical School

summary: Clonal emergence is a major driver for changes in bacterial disease epidemiology.  Recently, it has been proposed that episodic emergence of novel, hypervirulent clones of group A Streptococcus (GAS) results from horizontal gene transfer (HGT) and recombination events leading to increased expression of the cytotoxins Nga (NADase) and SLO (streptolysin O).  We previously described a gene fusion event involving the gene encoding the GAS M protein (emm) and an adjacent M-like protein (enn) in the emm4 GAS population, a GAS emm type that lacks the hyaluronic acid capsule.  Using whole genome sequencing of a temporally and geographically diverse set of 1,127 isolates, we discovered that the North American emm4 GAS population has undergone clonal replacement with emergent GAS strains completely replacing historical isolates by 2017.  Emergent emm4 GAS strains were defined by a handful of small genetic variations, including the emm-enn gene fusion, and showed a marked in vitro growth defect compared to historical strains. In contrast to other previously described GAS clonal emergence events, emergent emm4 GAS lacked significant HGT events and showed no significant increase in transcript levels of nga/slo toxin gene via RNA sequencing and quantitative real-time PCR analysis relative to historic strains.  Despite the in vitro growth differences, emergent emm4 GAS strains demonstrated hypervirulence in mouse and ex vivo growth in human blood compared to historical strains.  Thus, these data detail the emergence and dissemination of a hypervirulent acapsular GAS clone defined by small genetic variation thereby defining a novel model for GAS strain replacement.

overall_design: Comparison  of transcriptomes between emm4 group A Streptococcus subpopulations

first: Sruti

last: DebRoy

first: Misu

last: Sanson

first: Chioma

last: Odo

first: Samuel

last: Shelburne


title: Messenger RNA Biomarkers of Bovine Respiratory Syncytial Virus Infection in whole blood of dairy calves

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

summary: Bovine Respiratory Syncytial Virus (BRSV) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in respiratory tissues. If these changes are observed in tissues which are accessible in live animals, such as whole blood, they may be used as biomarkers of the disease. Therefore, the objective of the current study was to elucidate the whole blood transcriptomic response to an experimental challenge with BRSV, in dairy calves. Holstein-Friesian calves were either inoculated with virus (103.5 TCID50/ml x 15 ml) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). Clinical signs were scored daily and whole blood was collected in Tempus RNA tubes immediately prior to euthanasia, at day 7 post-challenge. RNA was extracted from blood and sequenced (150 bp paired-end). Sequence reads were aligned to the UMD3.1 bovine reference genome and differential gene expression analysis was performed using EdgeR. An MDS plot displayed an obvious separation between BRSV challenged and control calves based on whole blood gene expression changes, despite an observed mild clinical manifestation of the disease. There were 281 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. The top enriched KEGG pathways and gene ontology terms were associated with viral infection and included “Influenza A”, “defense response to virus”, “regulation of viral life cycle” and “innate immune response”. Highly DE genes involved in these pathways are may be beneficial for the diagnosis of subclinical BRD from blood samples.

overall_design: Examination of a single tissue type (whole blood) in two different treatment groups, BRSV challenged calves (n=12) and control calves (n=6)

first: Bernadette

last: Earley

first: Matthew

last: McCabe

first: JaeWoo

last: Kim

first: Jeremy

middle: F

last: Taylor

first: Ken

last: Lemon

first: Catherine

last: Duffy

first: Michael

last: McMenamy

first: S

last: Cosby

first: Sinead

last: Waters


title: Chromatin accessibility governs the differential response of cancer and T-cells to arginine starvation (ATAC-seq)

status: Public on May 10 2021

first: Thomas

last: Milne

address: John Radcliffe Hospital, Headington

summary: Depleting the microenvironment of important nutrients such as arginine is a key strategy for immune evasion by cancer cells. Many tumors overexpress arginase but it is unclear how these cancers, but not T-cells, tolerate arginine depletion. Here, we show that tumor cells synthesize arginine from citrulline by upregulating argininosuccinate synthetase 1 (ASS1). Under arginine starvation, ASS1 transcription is induced by ATF4 and CEBPbeta binding to a previously uncharacterized enhancer within ASS1. T-cells cannot induce ASS1, despite the presence of active ATF4 and CEBPbeta, as the gene is repressed. Arginine starvation drives global chromatin compaction and repressive histone methylation which disrupts ATF4/CEBPbeta binding and target gene transcription. We find that T-cell activation is impaired in arginine-depleted conditions, with significant metabolic perturbation linked to incomplete chromatin remodeling and misregulation of key genes. Our results highlight a T-cell behavior mediated by nutritional stress, exploited by cancer cells to enable pathological immune evasion.

overall_design: ATAC-seq (33 samples)

first: Nicholas

middle: T

last: Crump

first: Andreas

middle: V

last: Hadjinicolaou

first: I-Jun

last: Lau

first: Laura

last: Godfrey

first: Vincenzo

last: Cerundolo


title: New Roles of Transcriptional and Translational Regulation in Early Stages of Cotton Fiber Development

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: The fibers of cotton (Gossypium spp.) are a key agronomic resource. These fibers are made up of individual epidermal cells on the surface of the cotton seed which undergo a dramatic developmental shift, elongating into cells that are up to several centimeters long. Efforts to understand the causes of this shift has been hampered by the difficulty of isolating fiber cells from epidermal cells at the earliest stages of development. To address this issue, we characterized mRNA populations of early fiber and epidermal cells using laser capture microdissection (LCM) to isolate cell types with a high degree of specificity, and using RNA-seq, we were able to reveal key differences in the developmental programs between fibers and underlying epidermal cell layer. We were able to characterize cell type differences and temporal changes that occur in the earliest stages of fiber initiation and development at 0 and 2 Day Post Anthesis (DPA). We found differences in the expression of genes responsible for hormone activity, numerous transcription factor families, ribosomal activity, and cell cycle regulation, which leads the hypothesis that developmental changes leading to the arrest of the cell cycle in epidermal cells induces ribosome biosynthesis, leading to fiber cell initiation. Using chemical inhibitors of ribosome biosynthesis, Rbin-1, and cell cycle progression, Roscovitine, we were able to significantly affect the amount of fibers produced in cultured ovules, validating predictions made from our expression data. These results shed light on the early changes in gene activity controlling fiber development in cotton.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: Examination of transcripts (mRNA) in cotton epidermal and fiber cells (ovule) at 0 and 2 DPA in TM-1 (G.hirsutum), 3-79 (G.barbadense), and fiberless mutant MD17

first: Atsumi

last: Ando

first: Ryan

last: Kirkbride

first: Z


title: The cytoplasmic SYNCRIP mRNA interactome of mammalian neurons

city: Marburg

first: Sharof

last: Khudayberdiev

department: Institute for Physiological Chemistry, Biochemical-Pharmacological Center Marburg

institute: Philipps-University of Marburg,

summary: SYNCRIP, a member of the cellular heterogeneous nuclear ribonucleoprotein (hnRNP) family of RNA binding proteins, regulates various aspects of neuronal development and plasticity. Although SYNCRIP has been identified as a component of cytoplasmic RNA granules in dendrites of mammalian neurons, only little is known about the specific SYNCRIP target mRNAs that mediate its effect on neuronal morphogenesis and function. Here, we present a comprehensive characterization of the cytoplasmic SYNCRIP mRNA interactome using iCLIP in primary rat cortical neurons. We identify hundreds of bona fide SYNCRIP target mRNAs, many of which encode for proteins involved in neurogenesis, neuronal migration and neurite outgrowth. From our analysis, the stabilization of mRNAs encoding for components of the microtubule network, such as doublecortin (Dcx), emerges as a novel mechanism of SYNCRIP function in addition to the previously reported control of actin dynamics. Furthermore, we found that SYNCRIP interacts with miRISC and synergizes with pro-neural miRNAs, such as miR-9. Based on our findings, we propose a model whereby SYNCRIP promotes early neuronal differentiation by a two-tier mechanism involving the stabilization of pro-neural mRNAs by direct 3’UTR interaction and the repression of anti-neural mRNAs in a complex with neuronal miRISC. Together, our findings provide a rationale for future studies investigating the function of SYNCRIP in mammalian brain development and disease.

overall_design: SYNCRIP iCLIP in primary rat cortical neurons (DIV6) was performed. As a control, species and isotype matching IgG was used. Experiment was performed in three biological replicates and sequenced on Illumina HiSeq2000 platform

last: Soutschek

first: Irina

last: Ammann

first: Anika

last: Heinze

first: Marco

middle: B

last: Rust

first: Stefan

last: Baumeister

first: Gerhard

last: Schratt


title: Host-informed molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine [Ribo-seq]

first: Charles

last: Whittaker

summary: We analyzed total RNA and ribosome footprints collected from a K. phaffii strain secreting the VP8-P[6] serotype of the rotavirus antigen and compared against a strain secreting the VP8-P[4] serotype for reference.

overall_design: K. phaffii strains expressing either VP8-P[4] or VP8-P[6] were analyzed for total mRNA expression and ribosome protected mRNA quantification. All strains were sampled following biomass accumulation in glycerol-containing medium for 24 hr followed by induction of protein expression by growth in methanol-containing medium for an additional 16 hr.

first: Joseph

last: Brady

first: Charlie

middle: A

first: J

last: Love


title: Enhancer profiling of glioblastoma uncovers core oncogenic dependency and therapeutic opportunity [RNA-seq]

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Here, by mapping H3K27ac deposition, we analyze the active regulatory landscapes across primary GBM biopsies, normal brain tissues, and cell line counterparts. Analysis of differentially regulated enhancers, especially super-enhancers between GBM and normal brain tissues, as well as among GBM samples with matched RNA-sequencing data, uncovered unrecognized layers of oncogenic core transcriptional dependency and inter-tumor heterogeneity. Moreover, we demonstrate the functional relevance of leading candidates of super-enhancer-driven transcriptional factors, long non-coding RNAs, and druggable targets in GBM. Through profiling of transcriptional enhancers, our integrative study provides clinically relevant insights into GBM molecular classification, pathogenesis, and therapeutic innovations.

overall_design: ChIP-seq and RNA-seq were performed on GBM samples

first: Liang

last: Xu

first: Ye

first: H

last: Koeffler


title: Effects of aging and exercise on peripheral blood mononuclear cell gene expression

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

institute: University of Colorado Boulder

summary: Aging is associated with altered gene expression and dysregulation of non-coding RNAs, including repetitive element transcripts. The purpose of this study was to characterize age- and exercise-related differences in gene and repetitive element expression in humans using RNA-seq.

overall_design: Total (ribo-depleted) RNA isolated and purified from flash-frozen human peripheral blood mononuclear cells of young, older and older habitually exercising adults.


title: LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [Loop QC]

first: Shuchang

last: Liu

state: PA

overall_design: Loop transcriptome sequencing on ERCC synthetic RNA (ThermoFisher Scientific) for quality control.

first: Silvia

first: Indira

last: Wu

first: Yan-Ping

last: Yu

first: Michael

last: Balamotis

first: Baoguo

last: Ren

first: Tuval

last: Yehezkel

first: Jian-Hua

last: Luo


title: Methylation profiles of microglandular adenosis

city: Hannover

first: Helge

last: Stark

address: Carl-Neuberg-Straße 1

department: Institute of Pathology

institute: Medical School Hannover

type: Methylation profiling by genome tiling array

summary: MGA lesions were highly similar with respect to histomorphology and immunophenotype, but showed variable DNA CNAs and mutational characteristics. Defining molecular alterations of MGA may not have been fully captured by CN profiling and mutational analyses. In an explorative, hypothesis generating approach, we examined genome-wide DNA methylation patterns in MGA in comparison to normal mammary glands, HR-positve breast cancer and triple-negative breast cancer.

overall_design: DNA methylation patterns were studied in a cohort of MGA, normal mammary glands, HR-positive and triple negative

first: Martin

last: Radner

first: Matthias

last: Christgen

first: Hans

last: Kreipe


title: EGFR/FOXO3a/BIM signalling pathway determines chemosensitivity of BMP4-differentiated glioma stem cells to temozolomide

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

summary: Accumulating evidence suggests that glioma stem cells (GSCs), rare cells characterised by pluripotency and self-renewal, are responsible for glioblastoma (GBM) propagation, recurrence and resistance to therapy. Differentiation with bone morphogenic proteins (BMPs) is considered to be a promising approach to eliminate GSCs and sensitise glioma to chemotherapeutics. Epidermal growth factor receptor (EGFR) gene alterations are detected in more than a half of GBMs, however, the role of EGFR in chemoresistance of glioma stem cells remain elusive. Here, we investigated whether EGFR signalling affects BMP4-induced differentiation of GSCs and their response to an alkylating drug temozolomide (TMZ). We show that BMP4 triggers Smad signalling cascade in glioma stem cells independently of the EGFR level. BMP4 down-regulated levels of pluripotency markers (SOX2 and OLIG2) with the concomitant induction of astrocytic (GFAP) and neuronal (b-Tubulin III) markers. However, significant differences in chemotherapy outcomes were observed in glioma stem cells with different EGFR levels. BMP4-induced differentiation did not enhance sensitivity to TMZ in EGFRlow GSCs, in contrast to EGFRhigh GSCs, which were undergoing apoptosis. We identified differences in cell cycle regulation by analyses of cell cycle phase distribution and cell-cycle-related proteins. In cells with lower EGFR expression BMP4 triggered the G1 cell cycle arrest, not detected in EGFRhigh cells. RNA-seq profiles further highlighted transcriptomic alternations and distinct processes characterizing EGFR-dependent responses in course of BMP4-induced differentiation. We identified AKT/FOXO3a axis controlling of BIM (the pro-apoptotic BCL-2 family protein) as operating only in EGFRhigh BMP4-differentiated and TMZ-treated cells.

overall_design: Examination of BMP4-triggered differentiation of glioma stem cells with regard to EGFR signaling

first: Iwona

last: Ciechomska

first: Bartlomiej

last: Gielniewski

first: Bartosz

last: Wojtas

first: Bozena

last: Kaminska


title: Muscle transcriptomic profiling of chronological aging and metabolic syndrome in men

city: Saint Genes Champanelle

first: Daniel

last: Bechet

address: Theix

department: UNH

country: France

institute: INRA

summary:
Skeletal muscle aging is characterized by a progressive decline in muscle mass and function, which is referred to as sarcopenia. Aging is also a primary risk factor for metabolic syndrome (SX), which is a cluster of risk factors for cardiovascular diseases and type 2 diabetes. However, the molecular mechanisms implicated in sarcopenia and changes in muscle proteome associated with SX in elderly men remain unclear.
In this dataset, we include the expression data obtained from vastus lateralis muscle biopsies of young and old men with or without metabolic syndrome. These data are used to identify 479 genes that are differentially expressed with aging, 328 being associated with aging alone and 117 with metabolic syndrome.

overall_design: 30 Total samples were analyzed. Data were processed using GeneSpring GX 14.9 13 (Agilent) and analyzed by oneway ANOVA followed by pairwise comparisons using Tukey HSD post Hoc test. Benjamini-Hochberg multiple testing correction were performed to identify differentially expressed entities with a significance threshold set at P < 0.05. We generated the following pairwise comparisons using : young (YO) vs. healthy old (EL), EL vs. old with metabolic syndrome (SX), YO vs. SX.

first: Marine

last: Gueugneau

first: Cecile

last: Coudy-Gandilhon


title: microRNA Expression Changes in Organotin-Driven NLRP3 Inflammasome Activation in Murine Bone Marrow Derived Macrophages

first: Jian-Liang

last: Li

summary: Trimethyltin (TMT) and triethyltin (TET) are two tri-organotin compounds, a group of substances reported to affect mitochondria function. These compounds were also found to activate the NLRP3 inflammasome, an inflammatory cascade that occurs in myeloid cells when primed with a Toll-like receptor ligand (i.e. LPS) followed by activation by an exogenous or endogenous danger signal. The inflammasome is a very tightly regulated mechanism, with several miRNAs playing an important role. To determine differential miRNA changes between TMT and TET induced inflammasome activation, miRNA expression profiles were evaluated in LPS-primed murine bone marrow derived macrophages (BMDMs) exposed to TMT or TET as compared to saline. mRNA expression arrays were also performed and analyzed to identify miRNA target genes in order to elucidate the key mechanism(s) by which TMT and TET activate the NLRP3 inflammasome pathway.  These studies will help us understand the inflammasome regulation in macrophages by organotin.

first: G

last: Harry

first: Gabrielle

last: Childers

first: Stella

last: Sieber

first: Jian


title: Enhancer profiling of glioblastoma uncovers core oncogenic dependency and therapeutic opportunity

first: Tuan Zea

last: Tan

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

overall_design: Refer to individual Series


title: Identification of  RNF4 dependent gene signature in melanoma tumors

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

summary: Among hallmarks of cancer is impaired proteostasis, that is characterized by increased oncoprotein stability. Here we demonstrate that RNF4, a ubiquitin ligase implicated in the stabilization  of short-lived oncoproteins, is important for melanoma tumorigenesis. High levels of RNF4 in melanoma patient-derived specimens coincide with poor prognosis. Accordingly, RNF4, is essential for the growth and migration and survival of melanoma cells, both in culture and in xenograft models. RNA-seq analyses of RNF4-expressing tumors identified a gene signature related to melanoma growth and migration. Among the upstream regulators of RNF4-dependent gene signature are c-Myc and HIF1a which exhibit elevated protein levels that also coincided with stabilization of the translation initiation regulator p-eIF2a. Correspondingly, the effects of RNF4 on melanomagenesis are p-eIF2a-dependent, thus highlighting an unexpected regulatory axis in melanoma via RNF4-and ubiquitin-dependent protein stabilization

overall_design: we injected human A375 cells with stable expression of either GFP or Doxycycline (Dox)-inducible WT or catalytic inactive RING mutant RNF4C159A (termed RNF4RM) into immunocompromised nude mice. RNF4 expression was induced 3 days post injection by the addition of Dox to drinking water. Dox-induced expression of RNF4, but not of RNF4RM, accelerated tumor growth compared with GFP-expressing tumors (control) Therefore, to determine changes in gene signature upon RNF4 expression we performed RNA-seq analysis of the above xenograft-derived tumors . Each two similar tumors were pooled to extract RNA, thus 3 samples containing six tumors were analyzed from each group

first: Emily

last: Avitan-Hersh


title: Enhancer profiling of glioblastoma uncovers core oncogenic dependency and therapeutic opportunity [ChIP-seq]

first: Liang

last: Xu

first: Ye

last: Chen

first: H

last: Koeffler


title: An examination of the transcriptional control of energetic efficiency in cattle divergent for RFI

city: Meath

first: Clare

last: Mckenna

address: Dunsaney

department: Animal Bioscience

summary: The selection of cattle with high feed efficiency is of paramount importance with regard to reducing feed costs in the beef industry. Global gene expression patterns in metabolically important tissues can be used to identify genes that are potentially involved in regulating feed efficiency. We identified 5 genes (p<0.001;FDR <0.1) to be differentially expressed in skeletal skeletal muscle between high and low residual feed intake heifers with all 5 transcripts being upregulated in the low residual feed intake phenotype. Among these differentially expressed genes, all transcripts were related to oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (p<0.001;FDR <0.1) were differentially expressed in hepatic tissue tissue between high and low residual feed intake bulls with 8 transcripts being upregulated and 3 being downregulated in the low residual feed intake phenotype.  These differentially expressed genes were related to oxidative response, protein mediation and cell signalling. Pathway analysis on the RNAseq data indicates a relationship between oxidative phosphorylation and residual feed intake in skeletal muscle and aldosterone signalling and NRF2 mediated oxidative stress in hepatic tissue.

overall_design: Residual feed intake was calculated in heifers (n= 20) and bulls (n=20) under ad libitum feeding conditions which were subsequently ranked, within gender, as high (n=5) or low (n=5) residual feed intake. RNA sequencing was performed on liver and skeletal skeletal muscle biopsies from high and low residual feed intake animals in order to identify differentially expressed genes that may be associated with this trait.

first: David

last: Kenny

first: Richard

middle: K

last: Porter

first: Sinead

last: Waters

first: Paul

last: Cormican


title: Genomic profiling of anaplastic meningioma identifies recurrent genetic alterations with relevance to lower-grade meningioma

status: Public on May 04 2021

city: Bethesda

first: Patrick

middle: J.

last: Cimino

state: MD

address: 10 Center Dr

department: NINDS

institute: National Institutes of Health

summary: Genomic profiling of anaplastic meningioma can inform prognostic gene level alterations in lower-grade meningiomas, potentially reflecting evolution of anaplastic meningioma from lowergrade precursor tumours. Larger scale studies in paired primary and recurrent meningiomas are warranted to unravel the evolutionary path to anaplastic meningiomas and prognostic genomic alterations in detail

overall_design: Eight cases of anaplastic meningioma with snap frozen tissue underwent RNA sequencing, with approval for the use of human subject material from the Institutional Review Board for the University of Washington

first: P

middle: J

first: R

last: Yoda

first: H-G

last: Wirsching

first: J

middle: I

last: Warrick

first: M

middle: O

last: Dorschner

last: Ferreira


title: Pt-ttpy, a G-quadruplex binding platinum complex, induces telomere dysfunction and G-rich regions DNA damage

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: Pt-ttpy (tolyl terpyridin-Pt complex) covalently binds to G-quadruplex (G4) structures in vitro and to telomeres in cellulo via its Pt moiety. Here, we identified its targets in the human genome, in comparison to Pt-tpy, its derivative without G4 affinity, and cisplatin. Pt-ttpy, but not Pt-tpy, induces the release of the shelterin protein TRF2 from telomeres concomitantly to the formation of DNA damage foci at telomeres but also at other chromosomal locations. -H2AX chromatin immunoprecipitation (ChIP-seq) after treatment with Pt-ttpy or cisplatin revealed accumulation in G- and A-rich tandemly repeated sequences, but not particularly in potential G4 forming sequences. Collectively, Pt-ttpy presents dual targeting efficiency on DNA, by inducing telomere dysfunction and genomic DNA damage at specific loci.

overall_design: Genome binding/occupancy profiling by high throughput sequencing

first: Samar

last: Ali

first: Emilia

last: Puig Lombardi

first: Deepanjan

last: Ghosh

first: Tao

last: Jia

first: Géraldine

last: Vitry

first: Lina

last: Saker

first: Joel

last: Poupon

first: Marie-Paule

last: Teulade-Fichou

first: Alain

last: Nicolas

first: Arturo

last: Londono-Vallejo

first: Sophie

last: Bombard


title: RNA-Seq of Col-0, dek3-2, dek4-2, and dek3-2 dek4-2 (dd-2) 7-day-old seedlings in Arabidopsis

first: Wei

last: Zong

state: Texas

institute: University of Texas at Austin

summary:
Evolutionarily conserved DEK domain-containing proteins have been implicated in multiple chromatin-related processes, mRNA splicing, and transcriptional regulation in eukaryotes.
Here, we show that two DEK proteins, DEK3 and DEK4, redundantly control the floral transition in Arabidopsis. DEK3 and DEK4 directly associate with chromatin of related flowering repressors, FLOWERING LOCUS C (FLC), and its two homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, to promote their expression.
The binding of DEK3 and DEK4 to histone octamer in vivo affects histone modifications at FLC, MAF4 and MAF5 loci. In addition, DEK3 and DEK4 interact with RNA polymerase II and promote the association of RNA polymerase II with FLC, MAF4 and MAF5 chromatin to promote their expression.
Our results show that DEK3 and DEK4 directly interact with chromatin to facilitate the transcription of key flowering repressors and thus prevent precocious flowering in Arabidopsis.

overall_design:
7-day-old seedlings of Col-0, dek3-2, dek4-2, and dd-2 were examined with RNA-Seq to identify differentially expressed genes caused by DEK3 and DEK4 mutation in Arabidopsis.
8 samples from Col-0, dek3-2, dek4-2, and dd-2 7-day-old seedlings grown under long day condition with two biological replicates.

first: Sibum

last: Sung


title: Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: We applied time-course transcriptomics and genetics to identify sigma factors, metabolic processes and adhesins that drive biofilm formation. These analyses revealed that extracellular pyruvate induces biofilm formation in the presence of DOC. In the absence of DOC, pyruvate supplementation was sufficient to induce biofilm formation in a process that was dependent on pyruvate transport by the membrane protein CstA.

overall_design: Total RNA was extracted from 3 independent biological replicates of 630 C. difficile strains at 3 conditions with 120µM, 240µM and without Deoxycholate at 9h, 14h, 24h and 48h (36 samples).

first: Yannick

last: Tremblay

first: Marc

last: Monot


title: Real-time quantitative PCR analysis of Chromatin-associated snoRNA in human NB4 cells using Arraystar_384  platform

city: Guangzhou

first: Wen-Tao

last: Wang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

summary: 10 million cells were used for each sample. The cells were pre-treated with or without Doxorubicin (2µM for 4h) before collection and washed with ice-cold 1 × PBS. The nuclei pellet was further fractionated into nucleoplasmic fraction (supernatant) and chromatin pellet by using MWS buffer. All the buffers above were supplemented with protease inhibitor cocktail (Thermo Fisher Scientific) and Ribonuclease Inhibitors (Promega). The RNA precipitation solution (RPS) buffer was added into the cytoplasmic fraction and nucleoplasmic fraction immediately and each fraction was stored at -20°C for at least 1h. The two fractions were centrifuged and the resulting pellets were washed with 75% ethanol. All the pellets from the chromatin fraction, nucleoplasmic fraction and cytoplasmic fraction were added with 1mL TRIzol (Invitrogen) to extract RNA. The RNA pellet in TRIzol was fully dissolved by adding EDTA to the final concentration of 5mM and heat it to 65°C. The resulting RNAs from each fraction were subjected to DNase I (Sigma-Aldrich) treatment followed by phenol/chloroform extraction to remove any contaminant DNA. The RNA pellets of each fraction were then dissolved in equal volumes of RNase-free water and used for snoRNA qRT-PCR analyses.

overall_design: qPCR snoRNA expression profiling.  NB4 cells were used and treated separately as indicated in the summary. Equal amount total RNA was used to analyze the gene expression.

first: Yue-Qin

last: Chen

first: Cai

last: Han

first: Lin-Yu

last: Sun


title: The embryonic ontogeny of the gonadal somatic cells in mice and monkeys [10x]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: In the early fetal stage, the gonads are bipotent and only later become the ovary or testis, depending on the genetic sex. Despite many studies examining how sex determination occurs from biopotential gonads, the spatial and temporal organization of bipotential gonads and their progenitors is poorly understood. Here, using lineage tracing in mice, we find that the gonads originate from a T+ primitive streak through WT1+ posterior intermediate mesoderm and appear to share origins anteriorly with the adrenal glands and posteriorly with the metanephric mesenchyme. Comparative single cell transcriptomic analyses in mouse and cynomolgus monkey embryos reveals the convergence of the lineage trajectory and genetic programs accompanying the specification of biopotential gonadal progenitor cells. This process involves sustained expression of epithelial genes and upregulation of mesenchymal genes, thereby conferring a unique epithelial/mesenchymal hybrid state. Our study provides key resources for understanding early gonadogenesis in mice and primates.

overall_design: Single cell transcriptome analysis of cynomolgus monkey embryo  using 10x chromium Single Cell Gene expression system.

first: Kotaro

last: Sasaki

first: Akiko

last: Oguchi

first: Keren

last: Cheng

first: Yasuhiro

last: Murakawa

first: Ikuhiro

last: Okamoto

first: Hiroshi

last: Ohta

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Takuya

last: Yamamoto

first: Yasunari

last: Seita

first: Mitinori

last: Saitou


title: Bulk RNA-sequencing of CD49fHigh and CD49fLow populations from hESCs-derived HSPCs and Hemogenic Endothelium

city: Shanghai

first: Aining

last: Xu

address: 197 Rui Jin Er Road

institute: State Key Laboratory Of Medical Genomics, Rui-jin Hospital

summary: CD49f has been used to define human hematopoietic stem cells (HSCs). Tracing the origin of CD49f+ HSCs shall enhance our understanding of the regulatory mechanisms and improve in vitro generation of HSCs. Here, we employed the hematopoietic differentiation system from human pluripotent stem cells and performed a computational trajectory analysis of the cells throughout this process based on integrated calculating the levels of 10 HSC markers. We observed two clades of cell populations in the trajectory tree, one of which represents the phenotypic CD49fHigh HSCs, and the other diverges only by low CD49f level. Live cell imaging revealed that CD49f expression is persistent during endothelial-to-hematopoietic transition, suggesting that the phenotypic CD49fHigh HSCs are pre-defined in hemogenic endothelial cells (HECs), while the concurrently emerged CD49fLow cells represent HSC-independent progenitors. Colony forming assays showed that the CD49fHigh cells have multilineage potential, whereas the CD49fLow cells lack lymphoid potential but show a strong erythroid preference. The aim of the experiment was to compare newly defined CD49fHigh and CD49fLow populations from hESCs-derived HSPCs and Hemogenic Endothelium.

overall_design: CD49fHigh and CD49fLow cells were sorted from hESCs-derived HSPCs (CD43+CD34+CD38-CD45RA-CD90+) at day 8, and also CD49fHigh and CD49fLow cells were sorted from hESCs-derived hemogenic endothelium (CD34+CD31+CD43-) at day 6

first: Ai-ning

first: Yu-ting

last: Dai

first: Dan

last: Liu

first: Jinyan

last: Huang

first: Xiao-Jian


title: Investigation of alteration in gene expression during oxidative stress in ∆wee1S. pombe cells

city: Kolkata

first: Geetanjali

last: Sundaram

address: 35 Ballugunje circular road

department: Biochemistry

country: India

institute: University of Calcutta

summary: Treating wild-type S. pombe cells and ∆wee1 mutant with 20mM H2O2, we observed that aberrant Cdc2 activity, as in case of ∆wee1 cells can lead to major changes in the Spc1 dependent global transcriptional response to oxidative stress.

overall_design: Differential gene expression studies were carried out using Next Generation Sequencing , following 20mM H2O2 treatment in a Wee1 ldeletion mutant w.r.t untreated cells. Two biological replciates per condition and genotype.

first: A

last: Ghosal

first: S

last: Datta

first: G


title: Transcriptome analysis by RNA sequencing of human trisomy 21 and normal control blood cells

city: Bologna

first: Allison

last: Piovesan

address: Via Belmeloro 8

department: Department of Experimental, Diagnostic and Specialty Medicine

institute: University of Bologna

summary: The aim of this study is to analyse trisomy 21 (T21) transcriptome. We generated RNA sequencing (RNA-Seq) paired-end data from ribosomal RNA-depleted total RNA isolated from blood cell samples of four T21 and four normal control individuals.

overall_design: 4 individuals with T21 and 4 normal control individuals.

first: Francesca

last: Antonaros

first: Rossella

last: Zenatelli

first: Giulia

last: Guerri

first: Matteo

last: Bertelli

first: Chiara

last: Locatelli

first: Beatrice

last: Vione

last: Catapano

first: Alice

last: Gori

first: Lorenza

last: Vitale

first: Maria

middle: C

last: Pelleri

first: Giuseppe

last: Ramacieri

first: Guido

last: Cocchi

first: Pierluigi

last: Strippoli

last: Caracausi


title: Nasopharyngeal carcinoma and paracancerous tissue

first: Yiqun

last: Yu

address: 83 Fengyang Road, Xuhui

department: Otolaryngology

institute: Eye, Ear, Nose and Throat Hospital, Fudan University

summary: We reported RNA-seq data for three nasopharyngeal carcinoma tissues and three counterparting paracancerous tissues.

overall_design: Transcript landscape of nasopharyngeal carcinoma and paracancerous tissues

first: Wenwen

last: Ren


title: Triple-negative breast cancer cell line MDA-MB-231 +/- CD43 knockdown

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: The triple-negative breast cancer cell line MDA-MB-231 with high CD43 expression was stably transfected with a vector expressing a non-functional shRNA or 4 of these same vectors each expressing a different shRNA targeting human CD43 mRNA. The transcriptomes of these two daughter lines were then compared by differential microarray analysis.

overall_design: Differential microarray analysis of the triple-negative breast cancer cell line MDA-MB-232 +/- CD43 knockdown.

first: Carl

last: Shelley

first: Sylvie

last: Galiègue-Zouitina


title: Effects of IL-4 and IL-6 on gene expression in macrophages

city: Philadelphia

first: Yi

last: Fan

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

summary: Mouse bone marrow-derived macrophages were treated with IL-4 or IL-6. RNA was isolated and analyzed by RNAseq. The effects of IL-4 and IL-6 on gene expression was determined.

overall_design: Bone marrow cells were isolated from three C57BL/6 mice and treated with 10 ng/ml MCSF for 3 days, followed by treatment with 10 ng/ml MCSF plus 10 ng/ml IL-4 or 100 ng/ml IL-6 for 4 days. RNA was analyzed by RNAseq.

first: Yang

first: Zhang

last: Duo

first: Fan

last: Yi


title: Single-cell RNA sequencing of CCNB1+, polyploid, and diploid human iPSC-derived cardiomyocytes

city: Farmington

first: Travis

last: Hinson

state: Connecticut

address: 10 Discovery Dr

institute: JAX-GM

summary: We characterize transcriptional determinants and consequences of human cardiomyocyte polypolidization and CCNB1 insufficiency

overall_design: CCNB1-eGFP reporter cardiomyocytes were FACS sorted to isolate single cells representing 2n, 4n, and GFP+ populations, followed by droplet-based single-cell RNA sequencing

first: Anthony

middle: M

last: Pettinato

first: John


title: CRISPR screen analysis of human cardiomyocyte polyploidization and CCNB1 expression

summary: We characterize genetic determinants of human cardiomyocyte polypolidization and CCNB1 insufficiency using pooled CRISPR screen methods

overall_design: CCNB1-GFP iPSCs were transduced with lentiviral Cas9 and libraries of sgRNA to generate pools of single-gene knockout cells, which were differentiated into cardiomyocytes, FACS sorted by ploidy and GFP status, and sequenced to assess gRNA representation


title: The embryonic ontogeny of the gonadal somatic cells in mice and monkeys [sc3seq]

first: Yukihiro

last: Yabuta

sample_organism:
Macaca fascicularis
Mus musculus

platform_organism:
Macaca fascicularis
Mus musculus

overall_design: Single cell transcriptome analysis of mouse and cynomolgus monkey embryo  using SC3-seq technology.

first: Kotaro

last: Sasaki

first: Akiko

last: Oguchi

first: Keren

last: Cheng

first: Yasuhiro

last: Murakawa

first: Ikuhiro

last: Okamoto

first: Hiroshi

last: Ohta

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Takuya

last: Yamamoto

first: Yasunari

last: Seita

first: Mitinori

last: Saitou


title: PolyA RNA sequencing of HEL human erythroleukemia cell line under LSD1 inhibition

city: Kumamoto

first: Kensaku

last: Kohrogi

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Department of Medical Cell Biology

institute: Kumamoto University

summary: To understand the role of LSD1 in transcriptional regulation, RNA-seq analyses of LSD1-inhibited HEL cells were carried out. Cells were collected after the introduction of lentiviral LSD1 shRNA or the treatment with a specific LSD1 inhibitor, S2101. We found that LSD1 inhibition led to decreased expression of genes involved in various metabolic pathways.

overall_design: LSD1 inhibition was done with LSD1-KD and specific LSD1 inhibitor S2101.

first: Shinjiro

last: Hino

first: Mitsuyoshi

last: Nakao


title: Expression data from primary human bronchial epithelial basal cells from smokers non-COPD and COPD in Air-Liquid Interface (ALI) culture at the on-set of differentiation in absence or presence of TGFb

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
Bronchial epithelial basal cells in Air-Liquid interface culture differentiate and reconstitute a bronchial epithelium in 3-4 weeks following a tightly controlled genetic programme where specific sets of genes are up or down-regulated.
We used microarrays to detail the global programme of gene expression at the on-set of differentiation in absence or presence of TGFb and identified up- and down-regulated genes during this process.

overall_design: Bronchial epithelial basal cells from smokers non-COPD and COPD, either undifferentiated or differentiated for 6 days, were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Chams-Eddine

last: Ben Brahim

first: Charlotte

last: Courageux

first: Ariane

last: Jolly

first: Pascale

last: Leroy


title: The embryonic ontogeny of the gonadal somatic cells in mice and monkeys

first: Yukihiro

last: Yabuta

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

overall_design: Refer to individual Series


title: Six months of gender affirming hormone treatment modifies the methylome in the transgender population

status: Public on May 03 2021

city: A Coruña

first: Rosa

last: Fernandez

state: None / N/A

address: Campus Elviña

department: Psychology

institute: University of A Coruña

summary: The main objective was to carry out a prospective global CpG (cytosine-phosphate-guanine) methylation analysis before vs. after six months of gender affirming hormone treatment (GAHT), in a transgender population vs. a cisgender population.

overall_design: A global CpG methylation analysis was performed on 16 transgender people before vs. after GAHT and compared to 16 cisgender people, using the Illumina© Infinium Human Methylation 850k BeadChip. Global methylation was analyzed with the Partek® Genomics® Suite program (false discovery rate correction FDR p < 0.05; fold change ≥ ±2) by a 3-way ANOVA test comparing populations by group, assigned sex at birth and GAHT. We added six contrast interactions: trans men (before vs. after), trans women (before vs. after), cis men vs. trans women (before and after), and cis women vs. trans men (before and after).

first: Karla

last: Ramírez

last: Fernández

first: Sarah

last: Collet

first: Meltem

last: Kiyar

first: Enrique

last: Delgado-Zayas

first: Tibbert

last: Van Den Eynde

first: Esther

last: Gómez-Gil

first: Guy

last: T'Sjoen

first: Antonio

last: Guillamon

first: Sven

last: Mueller

first: Eduardo

last: Pásaro


title: Epstein-Barr Virus facilitates KLF14 expression by regulating the cooperative binding of E2F-Rb-HDAC in latent infection

city: Shenzhen

first: Yonggang

last: Pei

state: GD

address: 1088 Xueyuan Avenue

department: School of Public Health and Emergency Management

institute: Southern University of Science and Technology

overall_design: Examination of E2F6, E2F1, Rb, HDAC1, and HDAC2 binding features in EBV-transformed LCL1 cells.

first: Hem

last: Jha

first: Erle

last: Robertson