title: Disulfiram inhibits neutrophil extracellular trap formation and protects rodents during acute lung injury and SARS-CoV-2 infection

city: New

first: Sean

last: Houghton

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Assess the ability of disulfiram to inhibit NET formation and improve disease outcome in a Syrian hamster model of COVID-19. RNA sequencing was performed Golden Syrian hamster lung inoculated with SARS-CoV-2 in PBS or PBS only and treated with disulfiram or vehicle control sesame oil with dexamethasone.

overall_design: RNA sequencing of Mock infected or SARS-CoV-2 treated hamsters treated either with sesame oil vehicle or disulfiam

first: Robert

last: Schwartz

first: Mikala

last: Egelbad


title: Knockdown of the nucleoside diphosphate linked moiety X-type motif Nudt19 increases fatty acid oxidation and ATP production in murine liver cells

status: Public on Apr 11 2022

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

summary: Changes in intracellular CoA levels are known to contribute to the development of non-alcoholic fatty liver disease (NAFLD) in type 2 diabetes (T2D). The underlying genetic basis for the development and progression of these complex disorders, however, is still poorly understood. Due to their diverse susceptibility towards metabolic diseases, mouse inbred strains have been proven to serve as powerful tools in the identification of novel genetic factors that are fundamental in the pathophysiology of diabetes and NAFLD. Transcriptome analysis revealed the nucleoside diphosphate linked moiety X type motif Nudt19 as novel candidate gene responsible for NAFLD and T2D development. Knockdown (KD) of Nudt19 increased both mitochondrial and glycolytic ATP production rates in Hepa 1-6 cells. The enforced utilization of glutamine or fatty acids as energy substrate reduced uncoupled respiration in NT cells. This reduction was prevented upon knockdown of Nudt19. Furthermore, incubation with palmitate or oleate increased mitochondrial ATP production and uncoupled respiration in Nudt19 KD cells, but not in NT cells. The enhanced fatty acid oxidation in Nudt19 KD cells was accompanied by an increased abundance of Pdk4. This study describes for the first time Nudt19 as regulator of hepatic lipid metabolism and potential mediator of NAFLD and T2D development.

overall_design: We used microarrays to enable the detection of candidate genes.

first: Sarah

last: Goerigk

first: Christan

last: Binsch

first: Alexandra

last: Chadt

first: Hadi

last: Al-Hasani


title: The lncRNAs, circRNAs and mRNAs involved in gefitinib-resistance of PC9 cells

city: Shijiazhuang

first: Yunlong

last: Jia

state: Hebei

address: Tianshan Road

department: Department of Tumor Immunotherapy

country: China

institute: Fourth Hospital of Hebei Medical University

summary: In this study, we established an gefitinib resistant lung adenocarcinoma cell line (i.e. PC9/GR) from lung adenocarcinoma PC9 cell line which was sensitive to gefitinib. Then microarray was performed to elucidate the lncRNAs, cirRNAs and mRNAs involved in gefitinib resistance.

overall_design: gefitinib resistant PC9/GR cells with three replications; gefitinib-sensitive PC9 cells with three replications

first: Jiali

last: Wang

first: Lihua

last: Liu


title: Single-cell based elucidation of molecularly distinct GBM states and drug sensitivity

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

country: USA

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: Glioblastoma heterogeneity and plasticity remain controversial, with proposed subtypes representing the average of highly heterogeneous admixtures of independent transcriptional states.  Single-cell, protein-activity-based analysis identified four novel, molecularly distinct subtypes that successfully harmonize across multiple GBM datasets, including previously published bulk and single-cell profiles and single cell profiles from seven orthotopic PDX models, representative of prior subtype diversity. From these studies, GBM emerges as the plastic equilibrium of single tumor cells coexisting in two mutually-exclusive developmental states, with additional stratification provided by their proliferative potential. Consistent with these findings, all previously proposed subtypes could be recapitulated by mixtures of single cells representing these newly identified states. Most critically, drug sensitivity was predicted and experimentally confirmed as highly state-dependent, both in single-cell assays from patient-derived explants and in PDX models treated with clinically relevant drugs, suggesting that successful therapeutic strategies will likely require combinations of multiple drugs targeting these distinct tumor states.

overall_design: Single-cell RNA-sequencing of control and drug-treated slice cultures of human glioma surgical specimens.

first: Wenting

last: Zhao

first: Eleonora

last: Spinazzi

first: Athanassios

last: Dovas

first: Tamara

last: Marie

first: Pavan

last: Upadhyayula

first: Jeff

last: Bruce

last: Canoll


title: Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

city: Egham

first: Alessandra

last: Devoto

address: Egham Hill

country: United Kingdom

institute: Royal Holloway University of London

summary:
To analyze the extent of the overlap between MeJA-induced transcripts and MeJA- induced histone acetylation, the expression profiles of WT untreated (WT), WT+MeJA, axe1-5 untreated and axe1-5+MeJA samples were analysed using the catalog microarray (Agilent design ID:21169).
Whole A. thaliana seedlings of axe1-5 mutant and DR5 wild-type lines (Murfett et al 2001) were grown in vitro for 12 days on 1% Murashige and Skoog (MS) medium (Duchefa) supplemented with 1% sucrose, 0.8% phytoagar (Duchefa) and buffered to pH 5.8. Stratification of seeds was performed for 3 days at 4°C in the dark. Seeds were then grown with plates approximately 20° to vertical under 16h light/8h dark cycles for 12 days at 22°C and a light intensity of 100-120 µmol m-2s-1. Twelve-day-old in vitro grown whole seedlings were transferred to 50 µM MeJA or mock plates and sampled after 3 hours for  microarray analysis. Expression profiles were analyzed using the catalog microarray (Agilent design ID:21169).

overall_design: Total 8 samples were analyzed.

first: Stacey

last: Vincent

first: Jong-Myong

last: Kim

first: Imma

last: Pérez-Salamó

first: Taiko

middle: K

last: To

first: Chieko

last: Torii

first: Junko

last: Ishida

first: Maho

last: Tanaka

first: Takaho

last: Endo

first: Prajwal

last: Bhat

first: Paul

last: Devlin

first: Motoaki

last: Seki


title: Transcriptome Analaysis of humanized lungs in COVID-19 [Bulk_RNAseq]

status: Public on Apr 10 2022

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

summary: Mice with a human immune system (humanized mice), generated by transplantation of human hematopoietic stem and progenitor cells (HSPCs), serve as invaluable tools to study the development and function of the human immune system in vivo. MISTRG6 mouse model, engineered by a human/mouse homolog gene-replacement strategy, provides physiological factors for essentially all classes of human HSPCs to develop in mice. MISTRG6 (acronym for genes replaced) mice encode humanized M-CSF (enabling monocytes and  tissue macrophage development), GM-CSF/IL-3 (to provide lung alveolar macrophages), SIRPa (establish macrophage tolerance to human cells), ThPO (hematopoiesis and platelets), and IL-6 (better engraftment allowing study of adult human patients and improved antigen-specific antibody responses as well as human IL-6 per se), in a Rag2/Gamma common chain deleted background. By adapting recombinant adeno-associated virus (AAV)-driven gene therapy to deliver hACE2 to the lungs, which allows infection with SARS-CoV-2 of MISTRG6 mice engrafted with HPSCs, we created a humanized mouse model of COVID-19 that recapitulates the distribution and function of the human innate and adaptive immune system and is amenable to the mechanistic study of COVID-19 and its myriad of complications. We evaluated the lung transcriptional landscape and response to therapeutics in this model. First, we assessed the impact of anti-IFNAR2 and Remdesivir combined therapy and control dexamethasone therapy on the immunological transcriptome of SARS-CoV-2 infected MISTRG6-hACE2 mice by focusing on differentially regulated human genes in whole lung tissue. We treated infected MISTRG6-hACE2 mice with Remdesivir, anti-IFNAR2 antibody or a combination of the two starting 7dpi, to sequentially target viral replication and the IFN-dependent cascade downstream of infection. As a control, we also treated mice with dexamethasone, one of the few treatments that significantly reduced hospitalization and mortality in the clinic. Next, we compared the single cell transcriptomes of human immune cells from infected mice late in disease (28dpi) with their uninfected counterparts to gain a deeper understanding of transcriptional changes at the cellular level. Finally, we focused our efforts on deeper characterization of monocyte/macrophage clusters at early (4dpi) or late (14 and 28dpi) infection.

overall_design: We successfully delivered AAV-hACE2 to lung tissues of immune-reconstituted MISTRG6 mice (MISTRG6-hACE2) that have been engrafted with human HSPCs. MISTRG6-hACE2 mice were then infected with SARS-CoV-2.  Mice were treated with therapeutics starting at 7dpi. For whole tissue transcriptional analysis in response to therapeutics: whole lungs, collected at 14dpi and 28dpi, were homogenized. RNA was RNA was extracted with the RNeasy mini kit (Qiagen) per the manufacturer’s protocol.For single cell transcriptional analysis: lungs from infected mice were collected and digested at 37°C for 20 min using digestion cocktail containing 1 mg/ml collagenase D (Sigma) and 30 µg/ml DNase I (Sigma-Aldrich) in RPMI. Single cell suspensions from digested lungs were stained with antibodies against human CD45 and mouse CD45. Human immune cells were sorted (humanCD45+mouseCD45-DAPI-) and stained with TotalSeq (TotalSeq™-B0251 anti-human Hashtag 1 Antibody: GTCAACTCTTTAGCG; TotalSeq™-B0252 anti-human Hashtag 2 Antibody: TGATGGCCTATTGGG) antibodies (Biolegend) prior to processing for droplet based scRNA-seq. Duplicates from each condition/time point were pooled in equal numbers to ensure 10000 cells were encapsulated into droplets using 10X Chromium GEM technology. Libraries were prepared in house using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics). scRNA-seq libraries were sequenced using Nova-Seq. Raw sequencing reads were processed with Cell Ranger 3.1.0 using a human-mouse combined reference to generate a gene cell count matrix.

first: Esen

last: Sefik

first: Richard

last: Flavell


title: Direct-induced human retinal ganglion cells mimic fetal RGCs and are neuroprotective after transplant in vivo

city: Palo Alto

first: Ziming

last: Luo

state: CA

address: 1651 Pagemill Rd.

department: Ophthalmology

institute: Stanford University

summary: Since retinal ganglion cells (RGCs) do not regenerate after injury, RGC replacement therapy could provide an approach to vision restoration in glaucoma and other optic neuropathies. Here we developed a rapid protocol for direct induction of RGC (iRGC) differentiation from human iPSCs and ESCs in less than two weeks, by overexpression of NGN2 in RGC survival-promoting medium supplemented with a Notch inhibitor. Neuronal morphology and neurite growth were observed within one week of induction. Immunostaining and qRT-PCR for characteristic RGC-specific genes confirmed identity. Calcium imaging was used to evaluate iRGCs’ electrophysiologic maturation, and demonstrated GABA-induced excitatory calcium influx characteristic of immature RGCs. Using single cell-RNA sequencing (scRNA-seq) we further delineated iRGCs’ differentiation and compared iRGC transcriptomic profiles to fetal human and retinal organoid-derived RGCs. Unbiased clustering showed high similarities of transcriptomic profiles among iRGCs, early-stage fetal human RGCs and early-stage retinal organoid-derived RGCs. However, for some markers, including BRN3a, BRN3b and NEFL, iRGCs demonstrated expression patterns more similar to fetal RGCs than to retinal organoid RGCs. After intravitreal injection into rodent eyes, transplanted iRGCs survived and migrated into host retinas where they were detected one week and one month after transplant. Prior optic nerve trauma to the recipient host did not significantly enhance or detract from iRGC integration, but iRGCs protected host RGCs from neurodegeneration.  Taken together, these data demonstrate rapid iRGC generation in vitro into an immature cell with high similarity to human fetal RGCs and capacity for retinal integration after transplant, including after optic nerve injury. The simplicity of this system may benefit translational studies on human RGCs.

overall_design: Induce RGC-like cells from human induced pluripotent stem cells by overexpression of NGN2

first: Kun-Che

last: Chang

first: Jeffrey

middle: L

last: Goldberg


title: Single-cell RNA sequencing of LPA induction in Normal Human Epidermal Keratinocytes (NHEKs)

status: Public on Apr 12 2022

city: Kyoto

first: Ratklao

last: Siriwach

address: Sakyo-ku, Shogoin Kawahara-cho

department: Department of Drug Discovery Medicine

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: We hypothesized that stimulation of keratinoctye with LPA induced differentiation of heterogenecity subpoppulation among keratinocytes. We employed the single-cell  RNA-seq to identify keratinocyte subpoppulation induced by LPA.

overall_design: 10μM Oleoyl-L-α-lysophosphatidic acid  induced gene expression in NHEKs were measured at 72h compared to vehicle control. Single cells were obtained using Fluidigm C1 platform for RNA sequencing.

first: Anh

middle: Q

last: Ngo

first: Dean

last: Thumkeo


title: Endothelial-immune crosstalk contributes to vascular injury in non-alcoholic fatty liver disease

city: Singapore

first: Christine

last: Cheung

address: Nanyang Dr

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary: Cardiovascular complications are major causes of death in non-alcoholic fatty liver disease (NAFLD) but the underlying endothelial pathophysiology remains understudied. Here, we cultivated blood outgrowth endothelial cells (BOECs) from NAFLD patients and healthy controls. Our transcriptomic analysis revealed that NAFLD BOECs were activated with chemokine hallmarks, in particular, enhanced CXCL12 was confirmed in arterial tissues of mouse NAFLD models. Immunoprofiling by single-cell analysis further uncovered T cell intensification and potentially T-helper type 1 inflammatory reactions in NAFLD. In evaluating CXCL12-CXCR4 axis in chemotaxis, CXCR4 antagonist (AMD3100) substantially modulated the migration of CD4+ T cells, natural killer cells and monocytes towards NAFLD BOECs, which was not observed in healthy control coculture. We found that NAFLD and healthy BOECs might preferentially recruit distinct subsets of immune cells, as a result of unique chemokine ligand-receptor interactions. Finally, we enumerated two folds more circulating endothelial cells, a biomarker of vascular injury, in NAFLD patients than healthy subjects. Our work provides insights for modulation of endothelial-immune crosstalk as an avenue for mitigating endothelial dysfunction in NAFLD.

overall_design: BOECs were derived from healthy or NAFLD subjects (n = 3 each) and RNA-seq was performed in triplicate each.

first: Chun-Yi

last: Ng


title: Crotamiton derivative JM03 extends lifespan and improves oxidative and hypertonic stress resistance in Caenorhabditis elegans via inhibiting OSM-9

city: shanghai

first: song

last: zhouzhi

address: Lingyun Road, Xuhui District

institute: East China University of Science and Technology

summary: While screening our in-house 1,072 marketed drugs for their ability to extend the lifespan using Caenorhabditis elegans (C. elegans) as an animal model, crotamiton (N-ethyl-o-crotonotoluidide) showed anti-aging activity and was selected for further structural optimization. After replacing the ortho-methyl of crotamiton with ortho-fluoro, crotamiton derivative JM03 was obtained and showed better activity in terms of lifespan-extension and stress resistance than crotamiton. It was further explored that JM03 extended the lifespan of C. elegans through osmotic avoidance abnormal-9 (OSM-9). Besides, JM03 improves the ability of nematode to resist oxidative stress and hypertonic stress through OSM-9, but not osm-9/capsaicin receptor related-2 (OCR-2). Then the inhibition of OSM-9 by JM03 reduces the aggregation of Q35 in C. elegans via upregulating the genes associated with proteostasis. SKN-1 signaling was also found to be activated after JM03 treatment, which might contribute to proteostasis, stress resistance and lifespan extension. In summary, this study explored a new small molecule derived from crotamiton, which has efficient anti-oxidative, anti-hypertonic and anti-aging effects, and could further lead to promising application prospects.

overall_design: Examination of JM03-treated and control group in C. elegans and osm-9 mutants by RNA-seq, in triplicate

first: Bao

last: Keting

first: Liu

last: Wenwen

first: Hu

last: Zelan

first: Li

last: Jian


title: Regenerating axolotl retinas regrow diverse cell types with modulation by Notch signaling and reconnect to the brain

city: Boston

first: James

middle: R

last: Monaghan

state: MA

address: 360 Huntington Ave.

department: Biology

institute: Northeastern University

summary: We examined uninjured and regenerating axolotl salamander retinas, including their transcriptional profile. We report that at 27 days after a retinectomy (early-mid regeneration), regenerating axolotl retinas exhibit downregulation of genes associated with neuronal networks but upregulation of genes associated with angiogenesis and the extracellular matrix. We also report differential expression of two Notch pathway effector genes, Hes1 and Hes5.

overall_design: RNA profiles of uninjured and regenerating (27 dpi) axolotl salamander retinas

first: Rebecca

last: Carrier

first: Anastasia

last: Yandulskaya

first: Melissa

last: Miller


title: RNA microarray-based comparision of innate immune phenotypes between human macrophages stimulated with two BCG strains

city: Ciudad de México

first: Antonia

middle: Isabel

last: Castillo-Rodal

state: Ciudad de México

address: Av. Universidad 3000, Circuito Exterior S/N, Facultad de Medicina, Alcaldía Coyoacán,

department: Microbiología y Parasitología

country: Mexico

institute: Universidad Nacional Autónoma de México

summary:
Currently, the only available vaccine against tuberculosis is Mycobacterium bovis Bacille Calmette-Guérin (BCG). Pulmonary tuberculosis protection provided by the vaccine varies depending on the strain, the patient’s age, and the evaluated population. Although the adaptive immune responses induced by different BCG strains have been widely studied, little conclusive data is available regarding innate immune responses, especially in macrophages. Here, we aimed to characterize the innate immune responses of human THP-1-derived macrophages at the transcriptional level following a challenge with either the BCG Mexico or Phipps strains.
After a brief in vitro characterization of the bacterial strains and the innate immune responses, including nitric oxide production and cytokine profiles, we analyzed the mRNA expression patterns and performed pathway enrichment analysis using RNA microarrays. Our results showed that multiple biological processes were enriched, especially those associated with innate inflammatory and antimicrobial responses, including tumor necrosis factor (TNF)-α, type I interferon (IFN), and IFN-. These findings indicated the pro-inflammatory stimulation of macrophages induced by both BCG strains, at the cytokine level and in terms of gene expression. Our results demonstrated that both strains activated the innate immune response, with better modulation induced by BCG Phipps.

overall_design: The total RNA of 9 cultures of macrophage derived from THP-1, 3 biological replicates of macrophages infected with BCG Mexico, 3 biological replicas of macrophages infected with BCG Phipps and 3 biological replicas of macrophages derived from THP-1 non infected as a negative control group.

first: Gabriela

last: Molina-Olvera

first: Claudia

middle: I

last: Rivas-Ortiz

first: Alejandro

last: Schcolnik-Cabrera

first: Yolanda

last: López-Vidal


title: Deletion of Bak1 alleviates microglial necroptosis and neuroinflammation after experimental subarachnoid hemorrhage

city: Luzhou

first: Qiu

last: Xiancheng

address: No.25 of Taiping Street

institute: Southwest medical college

summary: Microglial necroptosis exacerbates neurodegenerative diseases, central nervous system injury and demonstrates a pro-inflammatory process, but its contribution to subarachnoid hemorrhage (SAH) is poorly characterized. BCL-2 homologous antagonist-killer protein (Bak1), a critical regulatory molecule of endogenous apoptosis, can be involved in the pathological process of necroptosis by regulating mitochondrial permeability. In this study, we revealed microglia undergo necroptosis after subarachnoid hemorrhage in vivo and vitro. We found that Bak1 was elevated at 24h after SAH. Knocked-down of Bak1 by adeno-associated virus attenuates microglial necroptosis, alleviates neuroinflammation, and improves neurological function after SAH. To further explore the corresponding mechanisms, oxyhemoglobin induces necroptosis in BV2 microglia, increasing Bak1 expression and mediating pro-inflammatory phenotype transformation, exacerbating oxidative stress and neuroinflammation. Abrogating BV2 Bak1 reduces necroptosis by downregulating the expression of phosphorylated pseudokinase mixed lineage kinase domain-like protein (p-MLKL), then downregulates pro-inflammatory phenotype gene expression. RNA-Seq shows that disrupting BV2 Bak1 downregulates multiple immune and inflammatory pathways and ameliorates cell injury by elevating Thrombospondin 1 (THBS1) expression. In summary, we identified a critical regulatory role for Bak1 in microglial necroptosis and neuroinflammation after SAH. Bak1 is expected to be a new therapeutic target, and it provides a new idea for the treatment strategy of SAH.

overall_design: NC-BV2 and Bak1-KD BV2 mouse microgial cells were treated with 10mM oxyhemoglobin for 0, 12 or 24 hours and harvested to produce RNA samples

first: Xiancheng

last: Qiu

first: Qianke

last: Tao

first: Lihan

last: Zhang


title: Genomic analysis of kidneys from male and female F1 Fischer F344 rats following dietary ochratoxin A exposure in utero and throughout development.

city: Ottawa

first: Lauren

middle: E

last: Carter

state: ON

address: 251 SIR FREDERICK BANTING

country: Canada

institute: Health Canada

summary: A toxicogenomic approach was used to assess the sex-specific transcriptomic changes in kidney tissue of rats from a one generation reproductive toxicity study. Transcriptomic data from both F0 and F1, male and female rats were assessed.

overall_design: Compare and contrast transcriptomic data from male and female F0 and F1 Fischer F344 rats between OTA doses, sexes, and generations.

first: Steven

last: Bugiel

first: Andrée

last: Nunnikhoven

first: Adrian

middle: J

last: Verster

first: Genevieve

middle: S

last: Bondy

first: Ivan

middle: H

last: Curran


title: A methanolic extract of Zanthoxylum bungeanum modulates secondary metabolism regulator genes in Aspergillus flavus and shuts down aflatoxin production

city: Turku

first: Anssi

last: Malinen

address: Tykistökatu 6

department: Life technologies

country: Finland

institute: University of Turku

summary:
Purpose: Aflatoxin B1 is the most toxic and carcinogenic compound in nature produced by Aspergillus fungi. In our study, we applied RNA-seq to compare the transcriptomic profiles of Aspergillus flavus strains in the presence and absence of medicinal plant Zanthoxylum bungeanum.
Methods: mRNA profiles of Aspergillus flavus supplemented with 250 µg/ml of methanolic extract fraction (treated samples) or DMSO (control samples) were generated in triplicate, by an Illumina platform using paired-end 150 bp sequencing strategy. Clean paired-end reads were mapped to the reference genome of A. flavus NRRL3357. Gene expression quantification was calculated by FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced). The differentially expressed genes (DGEs) between the control and test samples were analyzed using the DESeq2 R package.
Results: RNA-seq produced 24.5–32.1 million clean paired-end reads (150 bp read length) per sample and most of them (83–91%) were uniquely mapped to the reference genome of A. flavus NRRL3357. Eighty-two percent of genes displayed FPKM value ≥1 and were thus classified as expressed genes. Ninety-six percent of the expressed genes were expressed both in the control and test groups whereas 2.3% and 1.8% of the genes were expressed only in the control or test group, respectively. With the combination of FPKM fold change ≥2 and adjusted p-value <0.05, we found in total 950 DEG’s. Among them, 515 genes were downregulated and 435 genes were upregulated. We used FungiFun software to analyze the functions of the DEGs based on FunCat pathways and categories. About half of the DEG’s had a relevant annotation in the FunCat database, and 60–70% of the annotated DEG’s were found to be enriched in specific functional pathways.
Conclusions: we showed that simple organic extracts from Z. bungeanum inhibit both the growth and aflatoxin production by Aspergillus flavus. The repression of AF pathway is mediated by global regulators instead of pathway specific regulators AflR or AflS. Consistently, the expression of Velvet complex, a prominent regulator of fungal secondary metabolism and development, was substantially reduced. Natural compound extracts from Z. bungeanum have potential to facilitate the development of safe and economical control strategies that shutdown aflatoxin production in aflatoxigenic Aspergillus species.

overall_design: overall six samples were analysed, 3 controls and 3 test samples

first: Asmaa

last: Abbas

first: Colin

middle: W

last: Wright

first: Nagwa

last: El-Sawi

first: Tapani

last: Yli-Mattila

middle: M


title: Analysis of chromatin accessibility upon NODAL/Activin signalling reveal mechanisms of SMAD2-regulated transcription

city: London

first: Caroline

last: Hill

address: 1 Midland Road

department: Developmental Signalling

institute: Francis Crick Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this experiment patterns of chromatin accessibility  were compared in P19  mouse embryonic teratoma cells treated with either the Nodal/Activin singalling inhibitor SB-431542, or with Activin for 1hr (acute signalling) and 8 hr (prolonged signalling), or left untreated (chronic signalling)

overall_design: in this study we performed ATAC-seq in P19 mouse embryonic teratoma cells in four different signaling states: inhibited (SB-431542 treated); acute (1 hr Activin-treated); prolonged (8 hr Activin-treated) and untreated (chronic signalling). Experments were done in biological duplicates.

first: Davide

last: Coda

first: Harshil

last: Patel


title: The Effects of Nitric Oxide on Choroidal Gene Expression

status: Public on Apr 09 2022

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: We determined the effect of nitric oxide on chick choroids using the NO donor PAPA-NONOate

overall_design: Choroids from 15 day-old normal chick eyes were harvested and treated with PAPA-NONOate and total RNA was isolated for RNA-seq

first: Jody

last: Summers

first: Elizabeth

last: Martinez

first: Diana

last: Soriano

first: Makenzie

last: Merkley

first: Ken


title: Karrikin Receptor KARRIKIN INSENSITIVE2 Positively Regulates Heat Stress Tolerance in Arabidopsis thaliana

city: El Sokhna

first: MOSTAFA

middle: ABDELWAHED

last: Abdelrahman

state: SUZE

address: Suze

country: Egypt

institute: GALALA UNNIVERSITY

summary: In this study, we investigated the potential role of the karrikin receptor KARRIKIN INSENSITIVE2 (KAI2) in the response of Arabidopsis seedlings to high temperature stress.

overall_design: We performed phenotypic, physiological and transcriptome analyses of Arabidopsis kai2 mutant and wild-type (WT) plants under control (kai2_C and WT_C, respectively), and 6h and 24h heat stress conditions (kai2_H6, kai2_H24, WT_H6, WT_H24, respectively) to understand the basis for KAI2-regulated heat stress tolerance.

first: Mostafa

first: Son

last: Tran


title: Altered gene expression in the small intestine of Mfge8 null and Cd36 null mice

city: san francisco

first: Kamran

last: Atabai

state: California

address: 555 Mission bay Blvd

institute: UCSf

summary: We aimed to investigate the role of Mfge8 and Cd36 in intestinal lipid metabolism. We looked at the effect of the genetic deletion of Mfge8 and Cd36 in the small intestine by 3' Tag RNA sequencing.

overall_design: We obtained primary enterocytes from WT and Mfge8 null mice, isolated RNA and performed 3'Tag RNA sequencing. We also isolated small intestinal RNA from WT and Cd36 null mice and then performed 3'Tag RNA sequencing.

first: Ritwik

last: Datta

first: Carlos

last: Valenzuela


title: Corynoline protects Ang II-induced hypertensive heart failure by increasing PPARα and inhibiting NF-κB pathway

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

summary: Heart failure is a fairly common outcome of hypertension. Recent studies have highlighted the key role of the non-hemodynamic activity of angiotensin II (Ang II) in hypertensive heart failure via inducing cardiac inflammation. Drugs that disrupt Ang II-induced cardiac inflammation may have clinical utility in the treatment of hypertensive heart failure. A naturally occurring compound, corynoline, exhibit anti-inflammatory activities in other systems. C57BL/6 mice were injected with Ang II via a micro-osmotic pump for four weeks to develop hypertensive heart failure. The mice were treated with corynoline by gavage for two weeks. RNA-sequencing analysis was performed to explore the potential mechanism of corynoline. We found that corynoline could inhibit inflammation, myocardial fibrosis, and hypertrophy to prevent heart dysfunction, without the alteration of blood pressure. RNA-sequencing analysis indicates that the PPARα pathway is involved Ang II-induced cardiac fibrosis and cardiac remodeling. Corynoline reversed Ang II-induced PPARα inhibition both in vitro and in vivo. We further found that corynoline increases the interaction between PPARα and P65 to inhibit the NF-κB pro-inflammatory pathway in H9c2 cells. Our studies show that corynoline relieves Ang II-induced hypertensive heart failure by increasing the interaction between PPARα and P65 to inhibit the NF-κB pathway.

overall_design: we performed RNA sequencing analysis on the heart tissues of three control group mices and three Ang II-induced mices.

first: Mengyang

last: Wang

first: Guang

last: Liang


title: Glucocorticoid recptor knockdown in primary amnion epithelial cells treated with MPA and TNFa

city: Durham

first: Sarah

middle: Jean

last: Cunningham

state: NC

address: 101 Science Dr, IGSP Box 3382

institute: Duke University

summary: To analyze the effect of glucocorticoids on primary amnion epthelial cells, we harvested tissue samples from 10 healthy ceseaean section patients. We knocked down the glucocorticoid receptor with an siRNA or used a control siRNA. We treated samples with medroxyprogesterone acetate. Half the cells we subjected to a TNFa challenge

overall_design: Primary amnion epithelial cells were transfected with a glucocorticoid receptor knockdown or control siRNA and then 72 hours later treated with 10-6M MPA for 6 hours . A subset of cells were them treated with a TNFa challenge for 24 hours.

first: Terrence

last: Allen

first: Tim

last: Reddy

first: Alejandro

last: Barrera


title: Heart-on-a-chip model of SARS-CoV-2 infection and treatment with induced pluripotent stem cell derived extracellular vesicles

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Abstract: Although COVID-19–associated heart dysfunction has identified in individuals with SARS-CoV-2 infection, complex and multifaceted pathophysiology in patients complicates the investigation of pathogenesis related to clinical manifestations and mechanisms of cardiac dysfunction after viral invasion. This study comprehensively investigated pathogenesis regarding SARS-CoV-2 infection via tissue model established from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and cardiomyopathy model induced by angiotensin II. We recapitulated cytopathic features of SARS-CoV-2-induced cardiac damage and monitored the course of cardiac complications after infection, which is critically important to develop therapeutics. We found that SARS-CoV-2 infection of hiPSC-CMs models progressively impaired contractile function and calcium handling and led to cell death. Therapeutics potential towards myocardial injury was further developed in our tissue model. We evaluated cardioprotective effects of extracellular vesicles (EVs) derived from hiPSC source on the infected tissues, indicating that EVs alleviated the impairment of contractile force and cardiac cell death following SARS-CoV-2 infection. We showed that enriched microRNA in hiPSC-EVs can modulate cardiac-specific processes. These findings suggested that cardiac manifestations examined from tissues models provided insights into cardiac injury induced by SARS-CoV-2 infection, and model systems allow the investigation of mechanisms driving cardiac dysfunction and iPSC-EVs served as a promising therapy to rescue cardiac damage from infection.

overall_design: Gene expression profiles of engineered human cardiomyocytes untreated (Control) and treated with SARS-Cov-2 (MOI5), iPSC-derived extracellular vescicles (MOI5-EV), and/or angiotensin II (Ang II)

first: Qinghua

last: Wu

first: Naimeh

last: Rafatian

first: Karl

middle: T

last: Wagner

first: Jacob

last: Blamer

last: Smith

first: Sargol

last: Okhovatian

first: Praful

last: Aggarwal

first: Erika

middle: Y

first: Arinjay

last: Banerjee

first: Yimu

last: Zhao

first: Rick

middle: X

last: Lu

first: Louis

middle: P

last: Esquivel

first: Chen

last: Li

first: Uros

last: Kuzmanov

first: Serena

last: Mandla

first: Benjamin

middle: F

last: Lai

first: Anthony

last: Gramolini

first: Teoder

last: Veres

first: Gordana

last: Vunjak-Novakovic

first: Boyang

last: Zhang

first: Karen

last: Mossman

first: Milica

last: Radisic


title: Multiplexed, Sequential Secretion Analysis of the Same Single Cells Reveals Distinct Effector Response Dynamics Dependent on the Initial Basal State

city: New Haven

first: Zhuo

last: Chen

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

summary: The effector response of immune cells is a highly dynamic process. To explore time course of human macrophage response to toll-like receptor 4 (TLR4) ligand, human U937 cell line-derived macrophages were stimulated with lipopolysaccharide (LPS) and single-cell RNA-Sequencing were conducted at 0, 2, 4 and 6 hours after the initial treatment. The data demonstrated the existence of two major activation states at the transcriptional level, which were enriched for translation versus inflammatory programs, respectively. These results show a cell-intrinsic heterogeneous response in a phenotypically homogeneous cell population, providing dynamic information to better understand how immune cells react to pathogenic challenges over time and how they together constitute a population response.

overall_design: Examination of 4 time points (0, 2, 4 and 6 hours) upon LPS activation in human U937-derived macrophages

first: Rong

last: Fan


title: Effective therapy of AML with RUNX1 mutation by co-treatment with inhibitors of protein translation and BCL2 [RNA-seq]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Majority of RUNX1 mutations in AML are missense or deletion-truncation and behave as loss-of-function mutations. Following standard therapy, AML patients expressing mtRUNX1 exhibit inferior clinical outcome than those without mutant RUNX1. Studies presented here demonstrate that as compared to AML cells lacking mtRUNX1, their isogenic counterparts harboring mtRUNX1 display impaired ribosomal biogenesis and differentiation, as well as exhibit reduced levels of wild-type RUNX1, PU.1 and c-Myc. Compared to AML cells with only wild-type RUNX1, AML cells expressing mtRUNX1 were also more sensitive to the protein translation inhibitor homoharringtonine (omacetaxine) and BCL2 inhibitor venetoclax. HHT treatment repressed enhancers and their BRD4 occupancy, as well as reduced levels of c-Myc, c-Myb, MCL1 and Bcl-xL. Consistent with this, co-treatment with omacetaxine and venetoclax or BET inhibitor induced synergistic in vitro lethality in AML expressing mtRUNX1. Compared to each agent alone, co-treatment with omacetaxine and venetoclax or BET inhibitor also displayed improved in vivo anti-AML efficacy, associated with improved survival of immune depleted mice engrafted with AML cells harboring mtRUNX1. These findings highlight superior efficacy of omacetaxine-based combination therapies for AML harboring mtRUNX1.

overall_design: 14 samples; replicates are included and controls are provided for each data set

first: Christopher

last: Mill

first: Kapil

middle: N

last: Bhalla


title: Effective therapy of AML with RUNX1 mutation by co-treatment with inhibitors of protein translation and BCL2 [ChIP-seq]

overall_design: 8 samples


title: Effective therapy of AML with RUNX1 mutation by co-treatment with inhibitors of protein translation and BCL2 [scRNA-seq]

overall_design: 2 samples


title: Effective therapy of AML with RUNX1 mutation by co-treatment with inhibitors of protein translation and BCL2

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

overall_design: Refer to individual Series


title: Identification of a multipotent lung progenitor for lung regeneration

summary: We recently showed that a suspension of mouse or human fetal or adult lung cells infused intravenously following appropriate conditioning of recipient mice leads to marked lung chimerism within alveolar and bronchiolar lineages, in distinct 'patches'. A large proportion of these donor-derived 'patches' contain both epithelial and endothelial cells. We show here, using R26R-Confetti mice as donors, that these multi-lineage patches are derived from a single lung progenitor. Fluorescence activated cell sorting of adult mouse lung cells revealed that the putative patch-forming progenitors co-express the endothelial marker CD31 (PECAM-1) and the epithelial marker CD326 (EPCAM). Transgenic Cre/lox mice expressing GFP under different promoters support this duality by demonstrating expression of additional epithelial and endothelial markers in this double-positive lung subpopulation. These findings could pave the way not only for effective lung regeneration but also for better understanding of lung vasculature and airways development and maintenance in health and disease.

overall_design: Long term chimerism in recipient lungs after transplantation of td-tomato labeled cells:  In our previous studies we followed by immuno-histology (IH) lung chimerism up to 4 months. We have now performed 6-8 months follow up of chimerism using and combining results of  immunohistology with single cell RNA transcriptome analysis , showing donor derived epithelial (ciliated cells, club cells, AT1 and AT2 cells,) and endothelial clusters (lymphatics, endothelial progenitors, as well as the newly described gCap -“general”, and aCap -“aerocytes” capillary cells). The resulting clusters were defined based on marker genes and gene set analysis results, using publicaly available LGEA (Lung Gene Expression Analysis) Web Portal. For definition of each cluster we used well definied hallmark gene sets. We conducted single cell transcriptome analysis of the chimeric lung, using FACS purified donor- and recepient-derived lung cells.  Three chimeric lungs were first verified to exhibit significant chimerism by fluorescent microscopy, pooled, enzymatically dissociated and FACS separated after gating on CD45-, single, live cells into donor and recipient compartments based on Td-Tomato expression.

first: Yair

last: Reisner

first: Chava

last: Rosen


title: PPARdelta signaling activation improves metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes

city: New York

first: Nadeera

middle: Madhavi

last: Wickramasinghe

address: 3227 Broadway

institute: Columbia University

summary: Pluripotent stem cell-derived cardiomyocytes (PSC-CMs) provide an unprecedented opportunity to study human heart development and disease. A major caveat however is that they remain functionally and structurally immature in culture, limiting their potential for disease modeling and regenerative approaches. Here we address the question of how different metabolic pathways can be modulated in order to induce efficient cardiac maturation of hPSC-CMs. We show that PPAR signaling acts in an isoform-specific manner to balance the glycolysis and fatty acid oxidation (FAO) pathways. PPARd activation or inhibition results in efficient respective up- or down-regulation of the gene regulatory networks underlying FAO in hPSC-CMs. PPARd induction further increases mitochondrial and peroxisome content, enhances mitochondrial cristae formation and augments FAO flux. Lastly PPARd activation results in enhanced myofibril organization and increased numbers of bi-nucleated hPSC-CMs. Transient lactate exposure, commonly used in hPSC-CM purification protocols, induces an independent program of cardiac maturation, but when combined with PPARd activation equally results in a metabolic switch to FAO. In summary, we identify multiple axes of metabolic modifications of hPSC-CMs including a role for PPARdelta signaling in inducing the metabolic switch to FAO in hPSC-CMs. Our findings provide new opportunities to generate and use metabolically mature hPSC-CMs including for disease modeling and regenerative therapy.

overall_design: 36 total samples were analyzed, consisting of 6 treatment conditions with 3 biological replicates each. Control samples are included (Sample 1, 7, 13)

first: David

last: Sachs

last: Gonzalez

first: Bhavana

last: Shewale

first: Priyanka

last: Dhanan-Krishnan

first: Denis

last: Torre

first: Elizabeth

last: LaMarca

last: Raimo

first: Rafael

last: Dariolli

first: Madhavika

last: Serasinghe

first: Joshua

last: Mayourian

first: Robert

last: Sebra

first: Kristin

last: Beaumont

first: Srinivas

last: Iyengar

first: Deborah

last: French

first: Arne

last: Hansen

first: Thomas

last: Eschenhagen

first: Jerry

last: Chipuk

first: Eric

middle: A

last: Sobie

first: Adam

last: Jacobs

first: Scharam

last: Akbarian

first: Harry

last: Ischiropoulos

first: Avi

last: Ma'ayan

first: Sander

last: Houten

first: Kevin

last: Costa

first: Nicole

middle: C

last: Dubois


title: Effect of LPS treatment on gene expression in the murine adrenal cortex

status: Public on Apr 08 2022

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

summary: The aim was to investigate LPS-induced chages in cell metabolic pathways in the adrenal cortex. Bulk RNASeq was performed in microdissected adrenal cortices, followed by gene expression profiling analysis.

overall_design: Mice were treated for 6 hours with 1 mg/kg LPS or PBS (n=3 mice per group), the adrenal cortex was isolated by laser microdissection, total RNA was isolated and bulk RNASeq was performed.

first: Ivona

last: Mateska

middle: V

first: Anupam

last: Sinha


title: Vanished MDM2 amplification in a poorly differentiated sarcoma with amplified TERT-TRIO fusion gene: a targeted effect of radiotherapy?

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

summary: The identification of genetic alterations in sarcoma may give precious clues for the diagnosis. The detection of MDM2 amplification has an important impact since it may orientate towards a dedifferentiated liposarcoma (DDLPS) or more rarely towards an intimal sarcoma. Here we describe a poorly differentiated sarcoma initially diagnosed as a DDLPS, mainly on the basis of FISH analysis that detected MDM2 amplification. The patient was treated by adjuvant radiotherapy and, when the tumor recurred a few years later, MDM2 amplification was not observed anymore. We report the clinical, immunohistological, genomic and molecular description of the primary tumors and his recurrences.

overall_design: Genetic alterations in sarcoma

first: Samantha

last: Goffinet

first: Ilaria

last: Di Mauro

first: Berengere

last: Dadone-Montaudie

first: Jerome

last: Doyen

first: Florence

last: Pedeutour


title: Single nuclear RNASeq Analysis of Anaplastic and Favourable Histology Hu_Wilms Tumor

city: MEMPHIS

first: Andrew

middle: Jackson

last: Murphy

state: TN

address: 262 DANNY THOMAS PLACE, MS 133 DEPARTMENT OF SURGERY

department: Surgery

institute: St. Jude Children's Research Hospital

summary: Wilms tumor is the most common pediatric kidney cancer. The best predictor of clinical outcome for Wilms tumor patients is how their tumor looks under the microscope (histology). Usually, the resistant/anaplastic component of the tumor makes up only a fraction of the total number of cells in the cancer. A critical barrier to understanding therapeutic resistance in this disease is that studies performed to sequence the resistant component is diluted by the other components of the tumor.Therefore, the current proposal aims to using single-nuclear-RNA sequencing to isolate the gene expression patterns of individual cell types in Wilms tumor and to focus on the anaplastic/resistant cells.

overall_design: Patient frozen tumor was analyzed using single cell nuclear RNASeq.  The single cell nucleus was isolated and  Single nuclear RNAseq was performed using 10X genomics -Single cell gene expression kit V3.

first: Sivaraman

last: Natarajan

first: John

last: Easton

first: Xiang

last: Chen


title: Control of aortic root formation by SOX17 links aortic valve defects to coronary artery anomalies

city: Bronx

first: Deyou

last: Zheng

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Located at the junction of left ventricle and ascending aorta, aortic root is a central cardiovascular structure consisting of aortic valve and coronary ostium that are essential for systemic and coronary circulation, respectively. Malformations of aortic valve and coronary ostium are common birth defects and may occur together in human patients, leading to complex complications including aortic valve stenosis, myocardial ischemia, heart failure and sudden cardiac death. Despite of their physiological and clinical significances, the developmental and molecular mechanisms by which coordinate the formation of aortic valve and coronary ostium remain poorly understood. Here we report that SOX17 (SRY-box 17) is an essential transcription factor required for the maturation of aortic root, as well as the patterning of aortic valve and coronary ostium. We show in mouse that deletion of Sox17 in the aortic root endothelium results in defective aortic valve with underdeveloped non-coronary leaflet (NCL) or bicuspid aortic valve (BAV) without NCL. The valve defects are accompanied by misplaced left coronary ostium that reduces coronary blood flow, leading to myocardial hypoxia and death of embryos. Mechanistically, deletion of Sox17 decreases the expression of Pdgfb (Platelet derived growth factor, B polypeptide) in the aortic root endothelium and the PDGF growth signaling in the NCL mesenchyme and aortic root smooth muscle, both of which are derived from the second heart field (SHF) cardiomyocyte precursors. Furthermore, the deletion upregulates the expression of Ctgf (Connective tissue growth factor) and the extracellular matrix (ECM) genes, whereas downregulates the vascular smooth muscle genes, in the forming aortic root. Together, these findings support a developmental disease mechanism in which delayed growth and maturation of aortic root, due to lack of SOX17-PDGF/CTGF signaling, contributes to BAV and CAAs, two common congenital cardiovascular defects.

overall_design: we performed RNA-seq analysis of E12.5 wild type (WT) and Sox17eKO outflow tract (OFT) to identify Sox17 targets. Each group included two biological replicates, by pooling from 10 hearts' OFT for each replicate

first: Pengfei

last: Lu

first: Ping

last: Wang

first: Yidong

first: Bingruo

last: Wu

first: Yukiko

last: Sugi

first: Jonathan

last: Butcher

first: Jack

last: Lenz

first: Bin

last: Zhou


title: Carbon-monoxide Induced PERK Regulated Autophagy Reprograms Anti-Tumor  T Cells with Robust Immunometabolic Phenotype

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

summary: Mitochondria and Endoplasmic reticulum (ER) share structural and functional networks and  activates well-orchestrated signaling processes to shape a cell’s fate and function. While  persistent ER stress (ERS) response leads to mitochondrial collapse, moderate ERS condition  promotes mitochondrial function. Strategies to boost anti-tumor T cell function by targeting ERMitochondria  crosstalk have not been exploited yet. Thus, we used carbon monoxide (CO), a  short-lived gaseous molecule, to test if engaging moderate ERS conditions can improve T cells  mitochondrial function and anti-tumor function. Using melanoma antigen specific T cells, we  identify that CO induced transient activation of ERS sensor ‘protein kinase R-like endoplasmic  reticulum kinase (PERK)’ dramatically increase anti-tumor T cell function. Furthermore, COinduced  PERK activation temporarily halts protein translation and induces protective autophagy  (that includes mitophagy). To get further insight, we used LC3-GFP to differentiate between the  cells that prepare themselves to undergo active autophagy (LC3-GFPpos) and those that fail to  enter into the process (LC3-GFPneg). We found that LC3-GFPpos T cells show robust anti-tumor  potential whereas, LC3-GFPneg cells show T regulatory-like phenotype, harbor dysfunctional  mitochondria, and accumulate abnormal metabolite content. These anomalous ratios of  metabolites render the cells with a hypermethylated state and distinct epigenetic profile limiting  their anti-tumor activity. Overall, the study highlights that ERS activated autophagy pathways  modify mitochondrial function and epigenetically reprogram the T cells towards a superior antitumor  phenotype to achieve robust tumor control.

overall_design:
Examination of mRNA profiles in T cells using RNA-seq.
Examination of chromatin accessibility in T cells using ATAC-seq.

first: Paramita

last: Chakraborty

first: Rasesh

last: Parikh

first: Shikhar

last: Mehrotra


title: Nuclear lamina binds the EBV genome during latency and regulates viral gene expression [Hi-C]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Approximately 90% of the world population is infected with EBV and carries the virus in a silent, asymptomatic state for life. In immunocompromised individuals, EBV infection can cause B-cell transformation and malignancies. One approach to control EBV infectivity is by changing the expression of viral genes. We are interested in how epigenetics contributes to regulating the gene expression patterns adopted by EBV during latency. The host’s hijacking is a well know strategy adopted by viruses to modify the epigenome, the transcriptome and the proteome of the host with the aim to survive and remain silent in the host. We observed that in B cells, EBV infection mimics antigen-mediated activation, resulting in the induction of specific proteins named Lamin A/C. Lamins have multiple and central roles: they provide nuclear physical support, anchor the heterochromatin to the nuclear periphery and seem to play a role in several nuclear functions requiring the chromatin structure rearrangement. The interaction with lamins has already been studied in the context of EBV lytic reactivation, but their role in the control of the EBV latency states and as epigenetic regulators of different EBV genes expression profiles has not been investigated. The binding of the Lamin AC to important regulatory regions of EBV genome was assessed through ChIP-Seq, and gene expression (RNA-Seq) profiles were evaluated in wild type and Lamin AC KO cell lines. Differences in protein and RNA expressions in B cells activated by using both EBV and a simulation of the immune response were analyzed. Our data suggest two main conclusions: lamins might contribute to the epigenetic control of EBV genes expression during latency changing the interaction of the host structural proteins with key regulatory regions in the viral genome and a possible mechanism with who EBV modifies the nucleus and hijacks cellular mechanisms.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: HiC experiment in LAMIN A/C WT and KO cells. The analysis was focused on the EBV genome only.

first: Lisa

last: Caruso

first: Italo

last: Tempera


title: Induction of defense responses and protection of almond plants against Xylella fastidiosa by endotherapy with a bifunctional peptide

city: Girona

first: Luis

middle: Alejandro

last: Moll Dos Santos

state: Catalonia

address: Pic de Peguera 15, Edifici Jaume Casademont

department: Department of Chemical and Agricultural Engineering and Agrifood Technology

country: Spain

institute: University of Girona

summary: Xylella fastidiosa is a plant pathogenic bacterium that has been introduced in the European Union (EU), causing significant yield losses in economically important Mediterranean crops. Almond leaf scorch (ALS) is currently one of the most relevant diseases observed in Spain, and no cure has been found to be effective for this disease.  In previous reports, the peptide BP178 has shown a strong bactericidal activity in vitro against X. fastidiosa and to other plant pathogens, and to trigger defense responses in tomato plants. In the present work, BP178 was applied by endotherapy to almond plants cv. Avijor using preventive and curative strategies. The capacity of BP178 to reduce the population levels of X. fastidiosa and to decrease disease symptoms, and its persistence over time were demonstrated under greenhouse conditions. The most effective treatment consisted of a combination of preventive and curative applications and the peptide was detected in the stem up to 60 days post-treatment. Priming plants with BP178 induced defense responses mainly through the salicylic acid pathway, but also overexpressed some genes of the jasmonic acid and ethylene pathways. It is concluded that the bifunctional peptide is a promising candidate to be further developed to manage ALS caused by X. fastidiosa.

overall_design: The transcriptome of Prunus dulcis cv Avijor plants treated by a combination of spray and endotherapy applications of the peptide BP178 were compared to non-treated ones 24h post-treatment. Four biological replicates were used. Each biological replicate consisted of 5 plants.

first: L

last: Moll

first: A

last: Baro

last: Montesinos

first: E

last: Badosa

last: Bonaterra


title: Open chromatin and single-cell sequencing analysis reveals the contribution of Wnt4-lineage cells and the importance of chromatin regulators in renal tubular and interstitial differentiation

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Although Wnt4 is an early marker of nephron differentiation, how Wnt4-lineage cells differentiate into the renal interstitium and other cells types is unclear. Cell fate, proliferation, migration, and differentiation are controlled by precise spatiotemporal gene expression programs that are coordinately regulated by cell-cycle, lineage-specific transcription and chromatin regulatory factors. However, little is known about the roles of epigenetic/chromatin regulators in renal tubular and interstitial differentiation and diseases. We deleted the chromatin regulator Brg1 in Wnt4-expressing cells and FACS-purified Wnt4-lineage cells of wild-type and Brg1-deficient kidneys. We then carried out assay for transposase-accessible chromatin sequencing (ATAC-seq) to determine how Brg1-deficiency alters chromatin accessibility. We further performed single-cell RNA sequencing (scRNA-seq) to define the population and the effects of Brg1-deficiency in the differentiation of Wnt4-lineage cells. Our ATAC-seq analysis shows that Brg1-deficiency alters accessibility at thousands of active enhancers harboring motifs for an array of transcription factors. Unbiased scRNA-seq analyses identify 35 clusters of Wnt4-descendant cells and uncover novel cell types and genes that have so far not been linked to Wnt4-lineage cells. Brg1-deficiency leads to increased endothelial, stromal, and smooth-muscle cells and decreased nephron tubular cells. In Brg1-deficient kidneys, the expression of Pttg1 and proliferation are increased in Wnt4-expressing precursors, which cannot transition to a characteristic tubular state and appear to undergo fibrosis. Our results provide crucial insight into chromatin remodeling events and Wnt4-lineage cell-associated gene expression dynamics, highlighting the importance of chromatin regulators in controlling the differentiation of these cells and the expression of disease-associated genes.

overall_design: ATAC-seq of FACS-purified Wnt4-lineage cells of control and Brg1-deficient  kidneys at E18.5

first: Jinshu

last: Xu

first: Xianxiao

last: Zhang

first: Pin-Xian


title: Transcriptional effects of bipolar disorder drugs on NT2-N cells

city: Highton

first: Trang

last: Truong

state: Victoria

address: 75 Pigdons Rd, Waurn Ponds VIC 3216, Waurn Ponds Campus

department: Department of Health

country: Australia

institute: Deakin University

summary: Human neuronal-like cells (NT2-N) were treated with either lamotrigine (50 µM), lithium (2.5 mM), quetiapine (50 µM), valproate (0.5 mM) or vehicle control for 24 hours. Genome wide mRNA expression was quantified by RNA-sequencing. Results offer insights on the mechanism(s) of action of bipolar disorder drugs at the transcriptional level.

overall_design: Transcription profiles of NT2-N cells after 24-hour treatments with one of the four bipolar disorder drugs or their respective vehicle

first: Chiara

last: Bortolasci

first: Briana

last: Spolding

first: Bruna

last: Panizzutti

first: Srisaiyini

last: Kidnapillai

first: Zoe

last: Liu

first: Mark

last: Richardson

first: Laura

last: Gray

first: Craig

last: Smith

first: Olivia

last: Dean

first: Jee

middle: H

last: Kim

first: Michael

last: Berk

first: Ken

last: Walder


title: Genomic profiling identifies genes and pathways dysregulated by HEY1-NCOA2 fusion and shed a light on mesenchymal chondrosarcoma tumorigenesis [RNA-seq]

city: Memphis

first: Wojciech

last: Rosikiewicz

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

summary: Mesenchymal chondrosarcoma is a rare and often aggressive cancer that accounts for 2-10% of all chondrosarcomas. Genetically, this tumor is characterized by the recurrent HEY1-NCOA2 fusion. However, the oncogenic function of HEY1-NCOA2 fusion in mesenchymal chondrosarcoma remains to be elucidated. We stably transduced HEK293 as well as iPSC-derived mesenchymal stem cells (MSCs) with inducible- expression HEY1, NCOA2 and HEY1-NCOA2 construct, respectively. Using the stably transduced cell lines, we investigated the intracellular localization of HEY1-NCOA2 fusion protein and performed genome-wide chromatin Immunoprecipitation sequencing (ChIP-seq) and expression profiling (RNA-seq) to identify HEY1-NCOA2-dependent transcriptional regulation. In this study, HEY1-NCOA2 fusion protein was found to be localized to the nucleus, like wild-type HEY1; and extreme similarity in genome-wide DNA-binding pattern between HEY1-NCOA2 and wild-type HEY1 was observed. By gene expression profiling, HEY1-NCOA2-expression (MSC-HN+), HEY1-expression (MSC-HEY1+) and NCOA2-expression (MSC-NCOA2+) iPSC-MSCs can be robustly separated, and the combined differential gene expression (DGE) analysis and Gene Set Enrichment Analysis (GSEA) revealed that genes downregulated by HEY1 were positively enriched in MSC-HN+ versus control.  Functional classification of HEY1-NCOA2 upregulated genes according to KEGG networks highlighted various pathways related to promoting cell proliferation in cancer, such as cell cycle pathway, Hedgehog and WNT signaling as well as PI3K-Akt signaling pathways. Indeed, MSC-HN+ cells displayed significantly accelerated proliferation and a significant increase in cell cycle transit when compared with control cells. In 3D spheroidal growth model, we also observed both accelerated cell proliferation and distinct morphological features of the MSC-HN+ cells in contrast to the control cells. Our data provide functional evidence that HEY1-NCOA2 fusion protein preferentially binds to DNA regions that are originally occupied by the wild-type HEY1 transcription factor, and the expression of some HEY1 target genes as well as their related pathways, that are normally repressed by HEY1, are activated in the presence of HEY1-NCOA2 fusion protein.

overall_design: Identify targets of HEY1-NCOA2 fusion protein in MSC cells, and comare it with targets of HEY1.

first: Wenqing

last: Qi

first: Zhaohong

last: Yin

first: Beisi

first: Lu

last: Wang


title: Genomic profiling identifies genes and pathways dysregulated by HEY1-NCOA2 fusion and shed a light on mesenchymal chondrosarcoma tumorigenesis [ChIP-seq]

last: Xu


title: Transcriptomic effects of medical treatment on gene expression of  growth hormone secreting pituitary neruoendocrine tumour biology

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

summary: Pituitary neuroendocrine tumours (PitNET) are rare neoplasms of the pituitary gland that can overproduce pituitary hormones or cause headaches and visual impairment due to mass effect. Growth hormone overproducing somatotroph PitNETs cause acromegaly leading to wide range of connective tissue, metabolic and oncologic disorders. The medical treamment of acromegaly is somatostin analogues (SSA) in specific cases combined with dopamine agnoists (DA), but almost half of patients excert SSA resistence and potential causes of this is unknown.  The aim of this study was to characterize transcriptomic patterns of somatotroph PitNETs specifically assessing impact of SSA treatment effects. We investigated gene expession on several levels and functional models of GH PitNETs - tumour tissue of patients with and without SSA preoperative treamtment, tumour derived pituisphere model and classically used GH3 cell line treated with SSA.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: We investigated gene expession on several levels and functional models of growth hormone secreting PitNETs - tumour tissue of patients with and without somatostin analogues' preoperative treamtment, tumour derived pituisphere model and classically used GH3 cell line treated with somatostin analogues.

first: Rihards

last: Saksis

first: Olesja

last: Rogoza

first: Helvijs

last: Niedra

first: Kaspars

last: Megnis

first: Ilona

last: Mandrika

first: Inga

last: Balcere

first: Liva

last: Steina

first: Janis

last: Stukens

first: Austra

last: Breiksa

first: Jurijs

last: Nazarovs

first: Jelizaveta

last: Sokolovska

first: Ilze

last: Konrade

first: Vita

last: Rovite


title: RNA-seq analysis of cilia knockout human pluripotent stem cells vs. isogenic controls

city: Seattle

first: Benjamin

last: Freedman

state: WA

address: 850 Republican St

department: Medicine/Nephrology

institute: University of Washington

summary: Cilia are antenna-like organelles present on diverse cell types. To assess cilia functions, we generated human pluripotent stem cells incapable of forming cilia, and analyzed their transcriptomes, compared to isogenic control cell lines.

overall_design: Multiple clones of KIF3A and KIF3B knockout cells were analyzed, alongside isogenic controls.

middle: S


title: Transcriptome analysis of BNRF1 depletion in P3HR1-Z/R-HT cells

city: BOSTON

first: Stephanie

middle: Pei Tung

last: Yiu

state: Massachusetts(MA)

address: 181 Longwood Ave

department: Virology

institute: Harvard University

summary: EBV tegument protein, BNRF1, was found to inhibit a common host restriction factor, the SMC5/6 complex, during primary infection and viral lytic replication. RNAseq was used to identify host and viral transcriptome changes in BNRF1 knock-out P3HR1-Z/R-HTI cells, to get insights into other viral processes that is inhibited by the SMC5/6 complex.

overall_design: BNRF1-KO P3HR1-Z/R-HT cells were subjected to lytic induction by 4-HT and sodium butyrate, which were further used for RNAseq analysis. The P3HR1Z/R-HT cells expressing control sgRNA was used as the control.

middle: E

last: Gewurz


title: Transcriptomic analysis of xdrA difficient Staphylococcus aureus

city: Tampa

first: Lindsey

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

summary: The success of Staphylococcus aureus as a pathogen results from the production of a wealth of virulence determinants that aid in immune evasion, host cell invasion and dissemination of infection. Given the niche specific roles of these factors in infection, their production is controlled by a complex network of regulatory factors. In a continued effort to understand this network, the present study is aimed at characterizing the role of the transcriptional regulator XdrA and its effects on S. aureus gene expression. Using an unbiased global analysis, we find that XdrA has a broad impact on gene expression, influencing the transcription of several important virulence determinants, and factors involved in gene regulation. When assessing the role of XdrA in virulence, we find that an xdrA mutant has an increased ability to survive in whole human blood, mediated in part by increased survival within neutrophils, and an upregulation in expression of several factors involved in immune evasion, including sbi, fnbpA and efb. Furthermore, the increased survival within neutrophils appears to result from an upregulation in expression of sodM, recA, and sae, all of which assist bacterial cells in combating the effects of oxidative stress. In addition to these changes, we find that the xdrA mutant has a decreased abundance of cytolytic toxins, likely resulting from changes in agr and sae activity. We suggest that the broad impact of XdrA on the expression of genes involved in immune evasion, DNA damage, and oxidative stress tolerance, collectively result in a survival advantage allowing for the increased ability to causes disease in vivo, when xdrA is disrupted. In sum, our findings shed new light on the role of XdrA and its seemingly novel influence on S. aureus survival during infection.

overall_design: S. aureus RNA was extracted to compare global gene expression of two samples: HOU wildtype and HOU xdrA transposon mutant. HOU wildtype serves as the parental control strain. Each sample was generated by pooling three independent biological replicate RNA preps.

first: Brooke

middle: R

last: Tomlinson


title: SLFN11 is widely expressed in pediatric sarcoma and induces variable sensitization to 1 replicative stress caused by DNA damaging agents

first: Geoffrey

last: Neale

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Schlafen family member 11 (SLFN11) increases sensitivity to replicative stress and has been proposed as a biomarker to predict sensitivity to DNA damaging agents (DDA). However, the role of SLFN11 in pediatric cancer has not been well explored. In this study, we found that protein expression strongly correlated with response to the PARP inhibitor talazoparib and the topoisomerase I inhibitor irinotecan in sarcoma cell lines, with SLFN11 knockout resulting in significant loss of sensitivity in vitro and in vivo. However, in contrast to its activity in adult tumors, high SLFN11 expression did not correlate with favorable outcome in a retrospective study of children with sarcoma. Our work suggests that the potential of SLFN11 to act as a biomarker may be limited to certain tumor backgrounds or contexts, and that impaired apoptotic response may be one targetable mechanism of resistance to DDA-induced replicative stress

overall_design: We used microarrays to compare gene profiles expressed in the parental ES8 Ewings sarcoma cell line against profiles expressed in a derivative ES8 cell line (ES8-1F2)created by knockout of the human SLFN11 gene using CRISPR/Cas9. The parental ES8 cells and derivative ES8-SLFN-ko cells were treated with 0 Gy or 2 Gy irradiation, then RNA harvested at 4h or 24 h post-treatment.

first: Jessica

last: Gartrell

first: Marcia

last: Mellado-Largarde

first: Anang

last: Shelat


title: Myxoid liposarcoma tumor gene expression by array analysis

city: Gothenburg

first: Pierre

last: Åman

address: Medicinaregatan 1G

department: Institute of Biomedicine, University of Gothenburg

country: Sweden

institute: Sahlgrenska Center for Cancer Research

summary: Gene expression analysis of myxoid liposarcoma (MLS) tumors from five different patients

overall_design: Five MLS tumors (of which two belong to the more aggressive subgroup MLS round-cell type, MLSRC) with fibrosarcoma cell line HT1080 as reference

first: P

first: M

last: Lindén


title: Single-Cell Analysis of The Transcription Factor Controlled Early T Cell Differentiation Dynamics and Trajectory Topology

city: Pasadena

first: Wen

last: Zhou

address: 1200 E California Blvd, Mail Code 250-86

department: BBE

institute: California Institute of Technology

summary: The single cell expression profiles of mouse bone marrow derived early T cells with perturbations

overall_design: Examination of single-cell gene expression profile of bone-marrow derived early pro-T cells. Experiment was performed using droplet-based 3′ end RNA expression profiling using Chromium Single Cell 3′ Reagent Kits v3 according to manufacturer’s protocol (10x Genomics), with the different biological replicates tagged with Totalseq-A hashtags (Biolegend).  The cDNA library was sequenced on Illumina Novaseq or HisSeq4000 for 400-500 million reads, and tag library and gRNA library (if applicable) on HiSeq4000 for 20 million reads, both in pair-end mode following manufacturer's instructions.

first: Fan

last: Gao

first: Ellen

last: Rothenberg


title: bulk and single-cell RNA-seq on bone marrow derived early T cells

summary: The single cell and bulk expression profiles of early pro T-cell progenitors generated from purified mouse bone marrow, cultured on different stromal cell systems

overall_design: Examination of expression profiles of thymic DN1-DN2 population with bulk RNAseq and single cell RNAseq. 10X V2: Droplet-based 3′ end massively parallel single-cell RNA sequencing droplets were prepared using Chromium Single Cell 3′ Reagent Kits v2 according to manufacturer’s protocol (10x Genomics).  Bulk: Bulk RNAseq from FACS sorted early T cell populations were performed. RNAeasy MicroKit (Qiagen) were used to purify the total RNA according to manufacturer’s recommendations. Purified RNA samples were constructed into sequencing library using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) from ~1 μg of total RNA following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50-51 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.


title: Selective activation and expansion of regulatory T cells using lipid encapsulated mRNA encoding a long-acting IL-2 mutein

status: Public on Apr 07 2022

city: Cambridge

first: Chiaowen

middle: Joyce

last: Hsiao

state: MA

address: 200 Technology square

institute: Moderna Therapeutics

summary: Interleukin-2 (IL-2) is critical for regulatory T cell (Treg) function and homeostasis. At low doses, IL-2 can suppress immune pathologies by expanding Tregs that constitutively express the high affinity IL-2Rα subunit. However, even low doses IL-2, signaling through the IL2-Rβ/γ complex, may lead to the activation of proinflammatory, non-Treg T cells, so improving specificity toward Tregs may be desirable.  Here we used messenger RNAs (mRNA) to encode a half-life-extended human IL-2 mutein (HSA-IL2m) with mutations promoting reliance on IL-2Rα.  Our data show that IL-2 mutein subcutaneous delivery in lipid-encapsulated mRNA nanoparticles selectively activates and expands Tregs in mice and non-human primates, as well as reduces disease severity in mouse models of acute graft versus host disease and experimental autoimmune encephalomyelitis. Single cell RNA sequencing of murine splenic CD4+ T cells identifies multiple Treg states with distinct response dynamics following IL-2 mutein treatment. Our results thus demonstrate the potential of mRNA-encoded HSA-IL2m immunotherapy to treat autoimmune diseases.

overall_design: Spleens were collected from C57BL/6 female mice dosed with HSA-IL2wt or HSA-IL2m at 0.05mpk at 2 days and 4 days post injection (n = 3 mice each condition and timepoints) and from untreated mice for baseline comparison (n = 2). Each spleen was homogenized by mechanical disruption and CD4 T cells were isolated using a negative selection magnetic enrichment kit (StemCell). CD4 T cells collected from each treatment condition were pooled across individual mice, resulting in five single-cell suspensions. For each sample, the purity exceeded 98% purity and viability exceeded 99%. Each sample was diluted to a 1 million cells per mL.      Library preparation. 10x Genomics 3’ Library and Gel Bead Kit (Chromium Next GEM v3.1 516 1000128, 1000157, 1000213) and Single Cell Chip G kit (Chromium Next GEM 1000127) were used to prepare libraries using the 10x Genomics Chromium Controller according to the manufacture’s guidelines (CG00052 Rev D). Two chips were used with a target 10,000 cells collected in each lane. The five pooled samples were each split into technical replicates and distributed to the two chips as follows: The untreated pooled sample was split into four technical replicates with two replicates distributed to each chip. For the treated conditions, each pooled sample was split into three technical replicates, with one replicate from Day 2 and two replicates from Day 4 on Chip 1, and two replicates from Day 2 and one replicate from day 4 on Chip 2.

first: Seymour

last: de Picciotto

first: Nicholas

last: DeVita

first: Christopher

last: Honan

first: Sze-Wah

last: Tse

first: Mychael

last: Nguyen

first: Joseph

middle: D

last: Ferrari

first: Wei

last: Zheng

first: Brian

middle: T

last: Wipke

first: Eric

last: Huang


title: Single-cell transcriptomic characterization primary  HNSCC tumors

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: Despite aggressive multi-modal treatment, advanced head and neck squamous cell carcinoma (HNSCC) patients are at high risk of recurrence. Matched pairs (n=38) of primary/recurrent tumors were subjected to whole exome and RNA sequencing. Mutational landscapes and genomic copy number alterations indicated diverging clonal origins in a subset of cases. Transcriptional subtyping (classical/CL, basal/BA, inflamed-mesenchymal/IMS) in primary and recurrent HNSCC (n=112) revealed more frequent CL and IMS in primary tumors with low recurrence rates and a prevalence of BA in recurrent tumors associated with p-EMT and early recurrence. 44% of matched cases underwent a subtype change from primary to recurrent tumors, preferably from IMS to BA or CL. In recurrences, HYPOXIA, P-EMT and RADIATION RESISTANCE signatures were up- and TUMOR INFLAMMATION down-regulated compared to index tumors. A therapy-induced selection of transcriptional subtypes demonstrates the importance of molecular characterization of recurrences for second-line therapy decisions to enable optimally tailored treatments.

overall_design: three primary HNSCC tumor samples.

first: Claus

last: Belka


title: Transcriptomic characterization of paired primary and recurrent HNSCC tumors

overall_design: 34 paired primary and recurrent HNSCC tumor samples.


title: Comparison of oligodendrocyte mRNAs in normal and differentiated conditions in culture

city: Seoul

first: Macrogen

last: Inc.

address: 12F, World Meridian Venture Center #254 Beotkkot-ro, Geumcheon-gu

country: South Korea

institute: Macrogen Inc.

summary: Oligodendrocyte mRNAs in control and differentiated conditions are compared.

overall_design: Oligodendrocyte mRNAs in control and differentiated conditions are isolated and compared.

first: Yuki

last: Miyamoto

first: Junji

last: Yamauchi


title: mRNA profiling in pooled human umbilical vein endothelial cells stimulated with Coronavirus Disease 2019 (COVID-19) patient plasma

city: Toronto

first: Dakota

last: Gustafson

address: 101 College Street, 3-309

institute: University Health Network

summary: The purpose of this study was to identify mRNAs that were dysregulated after exposure to COVID-19 patient plasma and thus possibly contribute to vascular inflammation. Therefore, we conducted a multi-center, retrospective longitudinal cohort study enrolling 142 patients with laboratory-confirmed SARS-CoV-2 infection who presented to two Canadian hospitals from May 2020 – December 2020 along with a cohort of 27 SARS-CoV-2 patients with mild upper respiratory tract symptoms and 69 SARS-CoV-2-negative patients from the ICU. Blood was biobanked from SARS-CoV-2 positive patients in the emergency department (mild), ward (moderate) or intensive care unit (severe). Assessment of gene regulatory networks, gene set enrichment analysis, and in vitro permeability follow-up suggested functional reductions in junctional protein expression. Following this, confirmed critical reductions in VE-cadherin and ZO-1 which may drive pathology in moderate and severe cases of COVID-19.

overall_design:
RNA was extracted from pooled human umbilical vein endothelial cells (pHUVECs) that have either been left unstimulated (PBS-/- control) or have been stimulated with 20% (v/v) plasma from either: (1) SARS-CoV-2 negative patients with mild upper respiratory tract symptoms, (2) patients with mild COVID-19, (3) patients with moderate COVID-19, or (4) patients with severe COVID-19. Sample Groups:

(1) n=5 unstimulated
(2) n=5 SARS-CoV-2 negative patients (mild respiratory tract symptoms)
(3) n=5 patients with mild COVID-19
(4) n=5 patients with moderate COVID-19
(5) n=5  patients with severe COVID-19

Samples were co-incubated for six hours prior to the isolation of RNA using a Qiagen RNeasy Plus Micro Kit (Cat#: 74004) only after washing twice with ice-cold Dulbecco's Phosphate Buffered Saline (PBS) without magnesium and calcium. RNA quantities and quality were assessed using the Agilent 2100 Bioanalyzer with all samples passing a quality control threshold (RIN ≥ 7.0) to proceed to library preparations and RNA-seq. A total amount of 20 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 minutes followed by five minutes at 95 °C before PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. The resulting PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Sequencing was carried out on an Illumina NovaSeq® 6000 (Illumina, San Diego, California, United States), using paired end 2×150 bp chemistry at a depth of 20 million reads per sample.

first: Jason

last: Fish

first: Kathryn

last: Howe

first: Michael

last: Wilson

first: Huayun

last: Hou

first: Michelle

last: Ngai


title: Transcriptome profiling of NUP133 mutant podocytes

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

institute: University Medical Center Freiburg

summary: We generated NUP133 mutant podocytes to model human hereditary SRNS in vitro. A subtype of SRNS is caused by monogenetic mutations of the nuclear pore complex including NUP133. Human immortalized podocytes were genome edited applying the CRISPR/Cas9 technique to create NUP133 KO cells (“KO-1”). cDNA of NUP133-WT or  causative variants NUP133 c.2922T>G (“Mutation-1”) or NUP133 c.3335-11T>A (“Mutation-2”) were stable expressed into this KO background by lentiviral transduction. Transcriptome profiling (RNA-Sequencing) and differential gene expression analysis was performed in triplicate for each cell line. NUP133 mutant podocytes showed no overt transcriptional changes compared to NUP133-WT cells.

overall_design: mRNA analysis of NUP133-WT, NUP133-Mutant-1, NUP133-Mutant-2 immortalized human podocyte cell lines (3 replicates respectively)

first: Christoph

last: Schell


title: Expression data from mice

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

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

summary:
Mice are sensitive to chemical substance and often used as an in vivo model for environmental toxicology research.
We used microarrays to detail the global program of gene expression underlying cellularisation and identified distinct classes of up-regulated genes after treated with chemical substance.

platform_organism:
Mus musculus
synthetic construct

overall_design: Mice were selected at early development stages for RNA extraction and hybridization on Affymetrix microarrays. We tested the expression data of mice treated with PM2.5 and/or melatonin.

first: Junchao

last: Duan

first: Zhiwei

last: Sun


title: RNAseq to compare chemokine expression profiles in  KP line vs total KP lung tumors tissues

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: To investigate the chemokines expressed by the KP cancer line and to compare it to chemokines expressed in lung tissues upon inoculation of KP tumor cells

overall_design: RNA extraction of the KP cells line were prepared in triplicates. Lung tissues were pooled from 3 mice injected with KP cells in 3 independent experiments .

first: Federica

last: Benvenuti

first: Francesca

last: Simoncello

first: Roberto

last: Amadio

first: Giulia

last: Canarutto


title: Whole transcriptome miRNA profiling of Coronavirus Disease 2019 (COVID-19) patient plasma.

type: Non-coding RNA profiling by high throughput sequencing

summary: The purpose of this study was to identify miRNAs that were dysregulated after the onset of COVID-19 and thus potentially be used for risk stratification (i.e., mortality). Therefore, we conducted a multi-center, retrospective longitudinal cohort study enrolling 142 patients with laboratory-confirmed SARS-CoV-2 infection who presented to two Canadian hospitals from May 2020 – December 2020 along with a cohort of 27 SARS-CoV-2 patients with mild upper respiratory tract symptoms and 69 SARS-CoV-2-negative patients from the ICU. Blood was biobanked from SARS-CoV-2 positive patients in the emergency department (mild), ward (moderate) or intensive care unit (severe). Assessment of miRNA expression and co-regulatory network generation revealed significant transcriptome dyregulation in pateints with severe COVID-19 that was largely different from SARS-CoV-2 negative patients in the ICU.

overall_design:
Platelet reduced plasma from either: (1) SARS-CoV-2 negative patients with mild upper respiratory tract symptoms, (2) patients with mild COVID-19, (3) patients with moderate COVID-19, (4) patients with severe COVID-19, and (5) SARS-CoV-2 negative patients from the ICU with upper respiratory tract illnesses was taken from a -80 freezer and thawed on ice.

Sample Groups:
(1) n=30 SARS-CoV-2 negative patients with mild upper respiratory tract symptoms
(2) n=14 patients with mild COVID-19
(3) n=15 patients with moderate COVID-19
(4) n=45  patients with severe COVID-19
(5) n=31 SARS-CoV-2 negative patients from the ICU with upper respiratory tract symptoms.

A total of 30uL of thawed plasma was co-incubated with 1:1 volumes of HTG Plasma Lysis buffer (pre-warmed to 50 degrees celsius) and 1/10th v/v proteinase K for three hours at 50 degrees celsius with shaking (200rpm).


title: Transcriptome profiling of NUP133 WT and KO podocytes

country: Germany

summary: We generated NUP133 WT and KO podocytes to model human hereditary SRNS in vitro. A subtype of SRNS is caused by monogenetic mutations of the nuclear pore complex including NUP133. Immortalized human podocytes were genome edited applying the CRISPR/Cas9 technique and two independent NUP133 sgRNAs. Two monoclonal cell backgrounds were used to create two matching sets of NUP133 WT and KO cells (WT-1 versus KO-1 and WT-2 versus KO-2).  Transcriptome profiling (RNA-Sequencing) and differential gene expression analysis was performed in duplicate for each cell line. NUP133 KO podocytes exhibit vast transcriptional changes compared to WT cells.

overall_design: mRNA analysis of two NUP133 WT and two NUP133 KO immortalized human podocyte cell lines (2 replicates; 2x WT-1, 2x WT-2, 2x KO-1, 2x KO-2).


title: D-Serine activates glycolysis via mTOR pathway in kidney remodeling and suppresses onset of diabetes

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: D-Serine, a long-term undetected enantiomer of serine1,2, is a novel biomarker that reflects kidney function and disease activity3-5 and has unclear physiological functions. Here we show that D-serine is a physiological molecule that promotes tissue remodeling and suppresses the onset of diabetes. D-serine is quickly and dominantly distributed to the kidney upon injection in mice, suggesting that the kidney is a key target organ. Unilateral nephrectomy in human living kidney donors decreases urinary excretion and thus increases the blood level of D-serine, which in turn promotes the compensatory enlargement of the remnant kidney in mouse model. D-Serine activates cell cycle for tissue remodeling through an mTOR-related pathway, which promotes metabolic reprograming to glycolytic activation. In rodent diabetic model, D-serine promotes glycolysis in the kidney and suppresses the surge of blood glucose levels. D-Serine has physiological activity that influences kidney function and maintains metabolic homeostasis to reduce diabetic propensity.

overall_design: We compared transcriptome of D-serine-treated mice and vehicle-treated mice in triplicates.

first: Atsushi

last: Hesaka

first: Tomonori

last: Kimura


title: RNAseq analysis of DDX21-silenced colorectal cancer cell HCT8

city: Nanjing

first: Peifen

last: Lu

address: Xianlin Street NO.163

country: China

institute: Nanjing University

summary: DEAD-box RNA helicase 21 (DDX21), is a nucleolar protein harboring ATP-dependent double-stranded RNA unwinding activities, essential in rRNA processing and ribosome biogenesis. However, its role in colorectal cancer (CRC) progression remains unclear. In this study, we performed RNAseq in colorectal cancer line HCT8 with or without DDX21 gene silencing, to reveal the role of DDX21 in transcriptional and epigenetic control of CRC cell proliferation.

overall_design: RNA was isolated from HCT8 with or without DDX21 gene silencing HCT8 and subjected to RNAseq

first: Zhao

last: Quan

first: Lu

last: Peifen

first: Yu

last: Zenong


title: Genomic profiling identifies genes and pathways dysregulated by HEY1-NCOA2 fusion and shed a light on mesenchymal chondrosarcoma tumorigenesis

first: Wojciech

last: Rosikiewicz

country: USA

institute: St. Jude Childrens Research Hospital

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

overall_design: Refer to individual Series


title: Amino acid transport represents a druggable process for inhibiting human plasmacytoid dendritic cell activity during autoimmunity

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: IL-3 mediates human plasmacytoid dendritic cell (pDC) survival in vitro, but its mechanism of action is unclear. We show that, through JAK2/STAT5, IL-3 and the related GM-CSF, induce expression of System L amino acid transporters SLC7A5 and SLC3A2. This primes pDC to allow subsequent activation of mTORC1 in response to TLR9 stimulation. Active mTORC1 facilitates increased metabolic activity, type I IFN and TNF production, and the expression of SLC7A11, a subunit of the cystine/glutamate antiporter, xc—. We found that co-expression of SLC7A5, SLC3A2 and SLC7A11 is a major transcriptional signature shared by cytokine-producing pDC in vitro, and pDC at sites of autoimmune kidney damage in systemic lupus erythematosus (SLE).   Targeting the expression or function of these transporters with inhibitors of JAK2 and of xc— synergistically blocked cytokine production by pDC. We propose that such an approach may have value for treating SLE, and other diseases in which pDC are implicated.

overall_design: PBMC from buffy coats from healthy blood donors were isolated by density gradient centrifugation using SepMate tubes and Lymphoprep (both STEMCELL Technologies). pDC were negatively selected from PBMC using the plasmacytoid dendritic cell isolation kit II (Miltenyi Biotec). pDC were cultured with or without ODN for 5h. Single cells were sequenced using the 10x Chromium controller. One sample per treatment was used.

first: Katarzyna

last: Grzes

first: David

last: Sanin

first: Agnieska

last: Kabat

first: Joy

last: Edwards-Hicks

first: Alexandra

last: Hackl

first: Sophie

last: Zahalka

first: Matteo

last: Villa

first: Reinhard

last: Volk

first: Paola

last: Zigrino

first: Mario

last: Fabri

first: Erika

middle: L

last: Pearce

first: Edward


title: Silencing of exercise induced microRNA-501, microRNA-409 leads to aberrant neuronal homeostasis

city: Goettingen

first: Md Rezaul

last: Islam

address: von siebold str. 3a

institute: DZNE

summary: Exercise has been shown to boost cognition in mammals. However, the underlying mechanism remain poorly understood. We hypothesized that circulating microRNAs may correlate to improved cognitive functions, particularly cognitive flexibility after exercise and could be critical for neurons functions. To address this, in our study, healthy human volunteers participated in an exercise paradigm coupled with various cognitive tests performed prior to and after exercise and high quality small RNAome data were generated from total blood collected at two time points (pre- and post-exercise). Advanced comparative computational approaches were employed to select candidate microRNAs and multiple functional experiments were designed to test effect of those candidates on neuronal transcriptome, and neuronal functions. Our analyses revealed a cluster of circulating microRNAs related to improved cognitive flexibility. After rigorous analyses, we selected two candidate microRNAs and inhibition of these microRNAs led to up-regulation of genes, conserved in increased stress responses and downregulation of genes related to synaptic morphology and functions. Functional data revealed that the two microRNAs are indeed critical for maintenance of neuronal functions and morphology. Newly discovered cluster of microRNAs shed light on the mechanism of exercise-improved cognition and the two candidate microRNAs are potential RNA therapeutic target against dementia.

overall_design: Primary hippocampal neurons were treated with anti-miR-409-5p and anti-miR-501-3p at DIV10. After 48 hours, cells were treated with trizol and RNA was isolated and subjected to RNA sequencing.

first: M

first: Andre

last: Fischer


title: TIN2 deficiency leads to ALT-associated phenotypes and differentiation defects in embryonic stem cells

city: Guangzhou

first: Shanshan

last: Yin

state: Guangdong

address: 135 Waihuan Rd. E.

institute: Sun Yat-sen University

summary: Telomere integrity is critical for embryonic development and core telomere-binding proteins such as TIN2 are key to maintaining telomere stability. Here we report that homozygous Tin2S341X resulted in embryonic lethality in mice and reduced expression of Tin2 in the derived mouse embryonic stem cells (mESCs). Homozygous mutant mESCs were able to self-renew and remain undifferentiated but displayed many phenotypes associated with alternative lengthening of telomeres (ALT), including excessively long and heterogeneous telomeres, increased ALT-associated PML bodies, and unstable chromosomal ends. These cells also showed upregulation of Zscan4 expression and elevated targeting of DAXX/ATRX and H3K9me3 marks on telomeres. Furthermore, the mutant mESCs were impeded in their differentiation capacity. Upon differentiation, DAXX/ATRX and PML bodies disassociated from telomeres in these cells, where elevated DNA damage was also apparent. Our results reveal differential responses to telomere dysfunction in mESCs versus differentiated cells and highlight the critical role of TIN2 in embryonic development.

overall_design: RNA-seq from 4 mESC lines including WT-1, WT-2, Tin2 S341X-1, Tin2 S341X-2. Each line has three technical replicates.


title: Transcriptome sequencing lncRNA network construction in cardiac fibrosis and heart failure

status: Public on Apr 06 2022

city: shijiazhuang

first: xitian

last: hu

address: No.9 Fangbei Road, Shijiazhaung City 050000, Hebei Province, China

department: Department of Cardiovasology

institute: Shijiazhuang People’s Hospital

summary:
Background: Cardiac fibrosis (CF) and heart failure (HF) are familiar heart diseases that are harmful to health, and severe CF can lead to HF. In this study, we tried to find their common potential molecular markers, which may help the diagnosis and treatment of CF and HF.
Methods: Firstly, RNA library construction and high-throughput sequencing were performed. In addition, the DESeq2 package in R was used to screen genes with differentially expressed between different samples. Then, take the intersection of the differential mRNA, miRNA and lncRNA obtained for the two diseases. Thirdly, the ConsensusPathDB (CPDB) was used to perform biological functions enrichment for intersection differentially expressed mRNAs (DEmRNAs). Fourthly, construct gene interaction network and screen out key genes. Fifthly, RT-PCR verification was performed. Lastly, GSE104150 and GSE21125 data sets were utilized to validation the expression and diagnostic analysis.
Results: There are 1477 DEmRNAs, 502 differentially expressed lncRNA (DElncRNAs) and 36 differentially expressed miRNA (DEmiRNAs) between CF and healthy control group. There are 607 DEmRNAs, 379 DElncRNAs and 42 DEmiRNAs between HF and healthy control group. CH and FH shared 146 DEmRNAs, 80 DElncRNAs, and 6 DEmiRNAs. Hsa-miR-144-3p, CCNE2, C9orf72, MAP3K20-AS1, LEF1-AS1, AC243772.2, FLJ46284 and AC239798.2 were keys genes in lncRNA-miRNA-mRNA network. In addition, hsa-miR-144-3p and CCNE2 may be considered as potential diagnostic gene biomarkers in CF and HF.

overall_design: blood samples from 3 Cardiac fibrosis patients, 3 heart failure patients and 3 healthy controls patients were used for lncRNA sequencing.


title: Alkaline nucleoplasm facilitates contractile gene expression in the mammalian heart

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford