title: CUT&RUN of TAF4b and H3K4me3 in E16.5 prospermatogonia

status: Public on Oct 04 2023

city: Providence

first: Megan

last: Gura

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

summary: Taf4b-deficient male mice are initially sub-fertile and become infertile due to a depletion of the spermatogonial stem cell (SSC) reserve. During embryonic time points, significantly reduced numbers of germ cells have been observed in the Taf4b-deficient male gonad and previous research has shown that Taf4b mRNA expression peaks at E15.5. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates cell cycle and SSC gene programs. However, the direct targets of TAF4b have not been thoroughly explored. Therefore, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in E16.5 mouse prospermatogonia.

overall_design: E16.5 prospermatogonia were obtained through fluorescence-activated cell sorting (FACS) from Oct4-EGFP embryonic mice

first: M

last: Bartholomew

first: K

last: Abt

first: S

last: Relovska

last: Seymour

first: R

last: Freiman


title: Prospermatogonia transcriptome changes in Taf4b-deficient male mice

country: USA

type: Expression profiling by high throughput sequencing

summary: Taf4b-deficient male mice are initially sub-fertile and become infertile due to a depletion of the spermatogonial stem cell (SSC) reserve. During embryonic time points, significantly reduced numbers of germ cells have been observed in the Taf4b-deficient male gonad and previous research has shown that Taf4b mRNA expression peaks at E15.5. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates cell cycle and SSC gene programs. We performed RNA-seq to examine gene expression changes in E14.5 and E16.5 male Taf4b-wildtype, Taf4b-heterozygous, and Taf4b-deficient germ cells

overall_design: E14.5 and E16.5 prospermatogonia were obtained through fluorescence-activated cell sorting (FACS) from Taf4b-wildtype, Taf4b-heterozygous, and Taf4b-deficient male germ cells

middle: A

middle: M

middle: N


status: Public on Oct 05 2023

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

summary:
Rosiglitazone-targeted transcriptional networks as gene expression signature of physiological and pathological mineralization – a top-down approach to identify novel targets for bone and vascular health
Clinical studies have recently revealed detrimental skeletal and vascular effects of the insulin sensitizer rosiglitazone. At the cellular level, we have shown earlier that rosiglitazone accelerates osteoblast differentiation from human mesenchymal stem cells (hMSC) at the expense of increased oxidative stress and apoptosis. In calcifying human vascular cells, rosiglitazone stimulates pathological mineralization, an effect that was diminished by the antioxidant resveratrol. In order to elucidate the transcriptional networks underlying the rosiglitazone-enhanced mineralization phenotype, we performed genome-wide transcriptional profiling of osteogenic hMSCs treated with rosiglitazone for short-term periods of 1 up to 48h during the first two days of culture time, a phase that we show is sufficient to mediate the stimulatory effect of rosiglitazone on mineralization. Microarray-based mRNA expression analysis revealed 190 probes that were differently expressed in at least one condition compared to vehicle-treated control. This rosiglitazone gene signature contained confirmed primary PPAR targets and was also endogenously regulated during osteogenic differentiation from hMSCs and osteoblast-like differentiation of vascular smooth muscle cells (VSMCs) into calcifying vascular cells (CVCs). Further comparative analysis revealed rosiglitazone targets that were commonly enriched in osteoblasts and CVCs or specifically enriched in either osteoblasts or CVCs. Finally, we compared the expression patterns of CVC-specific genes with patient expression data from carotid plaque versus intact adjacent tissue, and identified five rosiglitazone targets that were differentially regulated in CVCs and carotid plaque but not osteoblasts when compared to their respective non-mineralizing counterparts. These targets, i.e PDK4, SDC4, SPRY4, TCF4, and DACT1 may specifically control extracellular matrix mineralization in vascular cells and hence provide interesting candidates for further investigations to improve vascular health.

overall_design: Total RNA obtained from osteogenic hMSCs, 2 days after induction of differentiation and treatment with rosiglitazone for 1, 3, 6, 24 or 48 h backwards from time-point of harvest compared to 1 h of vehicle control treatment.

first: Claudia

last: Bruedigam

first: Johannes

middle: P

last: van Leeuwen


title: Expansion of Plasma MicroRNAs over the First Month Following Human Stroke

city: Washington

first: Matthew

last: Edwardson

state: DC

address: 4000 Reservoir Rd NW, Building D, Room 207

department: Neurology

institute: Georgetown University

summary: Few have characterized miRNA expression during the transition from injury to neural repair and secondary neurodegeneration following stroke in humans.  We compared expression of 754 miRNAs from plasma samples collected 5, 15, and 30 days post-ischemic stroke from a discovery cohort (n=55) and 15-days post-ischemic stroke from a validation cohort (n=48) to healthy control samples (n=55 and 48 respectively) matched for age, sex, race and cardiovascular comorbidities using qRT-PCR.  Eight miRNAs remained significantly altered across all time points in both cohorts including many described in acute stroke.  The number of significantly dysregulated miRNAs more than doubled from post-stroke day 5 (19 miRNAs) to days 15 (50 miRNAs) and 30 (57 miRNAs).  Twelve brain-enriched miRNAs were significantly altered at one or more time points (decreased expression, stroke versus controls: miR-107; increased expression: miR-99-5p, miR-127-3p, miR-128-3p, miR-181a-3p, miR-181a-5p, miR-382-5p, miR-433-3p, miR-491-5p, miR-495-3p, miR-874-3p, and miR-941).  Many brain-enriched miRNAs were associated with apoptosis over the first month post-stroke whereas other miRNAs suggested a transition to synapse regulation and neuronal protection by day 30.  These findings suggest that a program of decreased cellular proliferation may last at least 30 days post-stroke, and points to specific miRNAs that could contribute to neural repair in humans.

overall_design: Includes 55 longitudinal samples collected 5, 15, and 30 days post-stroke from a discovery cohort and 55 matched controls as well as 48 samples from a validation cohort collected 15 days post-stroke and 48 matched controls.  Note that some of the controls are overlapping between the discovery and validation cohorts and not all of the stroke and control samples are used in the analysis due to wrong time post-stroke or poorly matched control, etc.


title: Microglial cannabinoid receptor type 1 mediates social memory deficits  produced by adolescent THC exposure and 16p11.2 duplication

status: Public on Oct 03 2023

city: Baltimore

first: ATSUSHI

last: KAMIYA

state: MD

address: 600 North Wolfe St, Meyer 3-162A

department: Psychiatry

institute: Johns Hopkins University

summary: Adolescent cannabis use increases the risk for cognitive impairments and psychiatric disorders. Cannabinoid receptor type 1 (Cnr1) is expressed not only in neurons and astrocytes, but also in microglia, which shape synaptic connections during adolescence. Nonetheless, until now, the role of microglia in mediating the adverse cognitive effects of delta-9-tetrahydrocannabinol (THC), the principal psychoactive constituent of cannabis, has been unexplored. Here, we report that adolescent THC exposure produces microglial apoptosis in the medial prefrontal cortex (mPFC), which was exacerbated in the mouse model of 16p11.2 duplication, a representative copy number variation (CNV) risk factor for psychiatric disorders. These effects are mediated by microglial Cnr1, leading to reduction in the excitability of mPFC pyramidal-tract neurons and deficits in social memory in adulthood. Our findings highlight the importance of microglial Cnr1 to produce the adverse effect of cannabis exposure in genetically vulnerable individuals.

overall_design:
We performed RNA sequencing (RNA-seq)-based analyses to determine transcriptome changes in the microglia produced by adolescent THC treatment and 16p11dup.
We isolated CD11b+/CD45+/P2ry12+ microglia from the mPFC at P51 using fluorescence-activated cell sorting (FACS). FACS-isolated microglia were subjected to RNA-seq analysis using the Smart-seq2 protocol that is applicable for a limited number of FACS-collected cells with full-length coverage.

first: Atsushi

last: Kamiya

first: Yuto

last: Hasegawa

first: Gianluca

last: Ursini


title: A2AR-eGFP reporter mouse enables elucidation of A2AR expression dynamics during anti-tumor immune responses

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Understanding of the mechanism by which A2AR is regulated has been limited by difficulty in identifying the cell types that express A2AR due to a lack of robust antibodies for these receptors. To overcome this we developed an A2AR-eGFP reporter mouse and assessed the expression of A2AR during ongoing anti-tumor immune responses.

overall_design: A2AR eGFP reporter mice were injected with 5 x 10^5 AT-3 ova tumors subcutaneously and where indicated treated at days 14 and 18 post tumor inoculation with anti-PD-L1. At day 21 post tumor inoculation CD8+ GFP+ or GFP- tumor-infiltrating lymphocytes were flow sorted and analyzed by 3’RNA-Sequencing.

first: Kirsten

last: Todd

first: Paul

last: Beavis

last: Sek


title: Effect of silencing of p53 on gene expression in MDA-MB 231 TNBC cell line in medium with 100% and medium with 25% of amino acids. [aa]

status: Public on Oct 06 2023

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
Mutant p53 can acquires oncogenic properties supporting tumor growth, metastases and chemoresistance, by reprogramming cancer cell transcriptome, proteome and metabolome. To investigate what is the gene expression network regulated by mutant p53 in condition of limited amino acids availability, we silenced mutant p53 expression in MDA-MB-231 Triple Negative Breast Cancer (TNBC) cell line, grown in medium with 100% and medium with 25% of amino acids.
We performed gene expression profiling analysis using data obtained from RNA-seq of MDA-MB 231.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB 231 cells,  grown in medium with 100% and medium with 25% of amino acids and transfected with Control or p53 siRNAs, each in duplicate.

first: Camilla

last: Tombari

first: Alessandro

last: Zannini

first: Giannino

last: Del Sal


title: COMPREHENSIVE IMMUNE PROFILING OF BLUETONGUE VIRUS INFECTION IN SHEEP REVEALS ACUTE IMMUNOSUPPRESSIVE EFFECTS ON T CELL RESPONSES

status: Public on Oct 10 2023

city: Madrid

first: Isabel

last: García-García

state: Madrid

address: Calle José Antonio Novais, 12

department: Genética, Fisiología y Microbiología

country: Spain

institute: Universidad Complutense de Madrid (UCM)

summary: Bluetongue virus (BTV), the prototypical Orbivirus that belongs to the Sedoreoviridae family, is transmitted by the bite of infected Culicoides midges and affects domestic and wild ruminants producing great economic losses. The infection induces an IFN response, followed by an adaptive immune response that plays a critical role in disease clearance. BTV can nonetheless impair IFN and humoral responses. The main goal of this study was to gain a more detailed understanding of BTV pathogenesis and its effects on immune cell populations. To this end, we combined flow cytometry and transcriptomic analyses of several immune cells at different times post-infection (pi). Four sheep were infected with BTV serotype 8 and blood samples collected at days 0, 3, 7 and 15pi to isolate peripheral blood mononuclear cells. Transcriptomic analysis of B-cell marker+, CD4+, CD8+, and CD14+ sorted cells showed that the maximum number of differentially expressed genes occurred at day 7pi, which coincided with the peak of infection. KEGG pathway enrichment analysis in B-cell marker+, CD4+, and CD14+ cells indicated that genes belonging to virus sensing and immune response initiation pathways were enriched and day 3 and 7 pi. Transcriptomic analysis also showed that T cell exhaustion pathway was enriched in CD4+ cells at day 7pi, while CD8+ cells showed downregulated immune response initiation pathways at this timepoint. When T cell functionality was assessed, ELISpot assays, intracellular cytokine staining, and proliferation assays demonstrated that BTV produced an acute inhibition of CD4+ and CD8+ T cell activation at the peak of replication. Furthermore, this coincided with PD-L1 upregulation on the surface of CD4+ and CD8+ T cells as well as monocytes. Taken together, these data indicate that BTV exploits the PD1/PD-L1 immune checkpoint to impair T cell responses. These findings identify several mechanisms in the interaction between host and BTV, which could help develop better tools to combat the disease.

overall_design: Four sheep were infected with BTV serotype 8 and blood samples collected at days 0, 3, 7 and 15pi to isolate peripheral blood mononuclear cells. Then, RNA was extracted and sequenced and transcriptomic analysis of B-cell marker+, CD4+, CD8+, and CD14+ sorted cells were carried out.

first: Andrés

last: Louloudes-Lázaro

first: José

last: Rojas

first: Daniel

last: Rodríguez-Martín

first: Esther

last: Morel

first: Verónica

last: Martín

first: Noemí

last: Sevilla


title: Ferroptosis inhibition by oleic acid mitigates iron-overload-induced injury

status: Public on Oct 02 2023

city: W 120 St

first: Brent

middle: R

last: Stockwell

state: New york

department: Biology

institute: Columbia University

summary: Iron overload, characterized by accumulation of iron in tissues, induces a multiorgan toxicity whose mechanisms are not fully understood. Using cultured cell lines, Caenorhabditis elegans, and mice, we found that ferroptosis occurs in the context of iron-overload-mediated damage. Exogenous oleic acid protected against iron-overload-toxicity in cell culture and Caenorhabditis elegans by suppressing ferroptosis. In mice, oleic acid protected against FAC-induced liver lipid peroxidation and damage. Oleic acid changed the cellular lipid composition, characterized by decreased levels of polyunsaturated fatty acyl phospholipids and decreased levels of ether-linked phospholipids. The protective effect of oleic acid in cells was attenuated by GW6471 (a PPAR-𝛂 antagonist), as well as in Caenorhabditis elegans lacking the nuclear hormone receptor NHR-49 (a PPAR-𝛂 functional homologue). These results highlight ferroptosis as a driver of iron-overload-mediated damage, which is inhibited by oleic acid. This monounsaturated fatty acid represents a potential therapeutic approach to mitigating organ damage in iron overload individuals.

overall_design: To investigate the effect of oleic acid supplementation on ferric ammonium citrate (FAC induced) ferroptosis, we cultured HEK293 cells under 4 conditions: vehicle, oleic acid supplemented, FAC (ferroptosis induction), and oleic acid supplemented + FAC; triplicate samples for each condition. We then performed differential gene expression analysis across all 4 conditions to assess for transcriptomic changes.

first: Josiane

last: Mann

first: Eduard

last: Reznik

first: Melania

last: Santer

first: Mark

last: Fongheiser

first: Nailah

last: Smith

first: Tal

last: Hirschhorn

first: Fereshteh

last: Zandkarimi

first: Rajesh

middle: K

last: Soni

first: Alcir

middle: L

last: Dafre

first: Antonio

last: Miranda-Vizuete

first: Marcelo

last: Farina


title: Extracellular pyridine nucleotides mediate systemic acquired resistance in Arabidopsis thaliana

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Systemic acquired resistance (SAR) is a long-lasting broad-spectrum plant defense mechanism that is induced by mobile signals generated in the primarily infected leaves. Although multiple mobile SAR signals have been proposed, how these signals are perceived in the systemic leaves is unknown. Here, we show that extracellular nicotinamide adenine dinucleotide (phosphate) (eNAD(P)) accumulates in the systemic leaves and that both eNAD(P) and its receptor, the lectin receptor kinase (LecRK), LecRK-VI.2, are required in the systemic leaves for the establishment of SAR. Moreover, the mobile signal N-hydroxypipecolic acid (NHP) induces de novo NAD(P) leakage in the systemic leaves through the respiratory burst oxidase homolog RBOHF-produced reactive oxygen species (ROS). Importantly, NHP-induced systemic immunity depends on ROS, eNAD(P), and the eNAD(P) receptor complex LecRK-VI.2/ BAK1, indicating that NHP triggers SAR through the ROS-eNAD(P)-LecRK-VI.2/BAK1 signaling pathway. Our results uncovered a long-sought-after mechanism underlying the perception of mobile SAR signals in the systemic leaves

overall_design: To investigate how extracellular pyridine nucleotides mediate systemic acquired resistance in Arabidopsis thaliana by infiltrating the lower leaves with MgCL2 or Pseudomonas syrigae pv. Maculicola

first: Qi

last: Li

first: Mingxi

last: Zhou

first: Shweta

last: Chhajed

first: Fahong

last: Yu

first: Sixue

last: Chen

first: Yanping

last: Zhang

first: Zhonglin

last: Mou


title: Dual targeted extracellular vesicles regulating oncogenic genes in pancreatic cancer [Mouse Array]

city: Seattle

first: Inyoul

last: Lee

state: WA

address: 401 Terry Ave. North

institute: Institute for Systems Biology

summary: Pancreatic ductal adenocarcinoma (PDAC) tumours carry multiple gene mutations and respond poorly to treatments. There is currently an unmet need for drug carriers that can deliver multiple gene cargoes to high solid tumour burden like PDAC. Here, we report a dual-targeted extracellular vesicle (EV) carrying high loads of RNA that effectively suppresses large PDAC tumours in mice. The EV surface contains a CD64 protein that has a tissue targeting peptide and a humanized monoclonal antibody. Cells sequentially transfected with plasmid DNAs encoding for the RNA and protein of interest by Transwell®-based asymmetric cell electroporation released abundant targeted EVs with high RNA loading. Together with a low dose chemotherapy drug, Gemcitabine, dual-targeted EVs effectively suppressed large orthotopic PANC-1 and patient derived xenograft tumours in mice and extended animal survival. This work presents a clinically accessible and scalable way to produce abundant EVs for delivering multiple gene cargoes to large solid tumours.

first: Kai

last: Wang

first: Shannon

last: Fallen

first: L

first: Nick

last: Chiang


title: Dual targeted extracellular vesicles regulating oncogenic genes in pancreatic cancer [Human Array]

summary: Pancreatic ductal adenocarcinoma (PDAC) tumors carry multiple gene mutations and respond poorly to treatments. There is currently an unmet need for drug carriers that can deliver multiple gene cargoes to high solid tumor burden like PDAC. Here, we report a dual-targeted extracellular vesicle (EV) carrying high loads of RNA that effectively suppresses large PDAC tumors in mice. The EV surface contains a CD64 protein that has a tissue targeting peptide and a humanized monoclonal antibody. Cells sequentially transfected with plasmid DNAs encoding for the RNA and protein of interest by Transwell®-based asymmetric cell electroporation released abundant targeted EVs with high RNA loading. Together with a low dose chemotherapy drug, Gemcitabine, dual-targeted EVs effectively suppressed large orthotopic PANC-1 and patient derived xenograft tumors in mice and extended animal survival. This work presents a clinically accessible and scalable way to produce abundant EVs for delivering multiple gene cargoes to large solid tumors.


title: Salicylic acid treatment and overexpression of a novel polyamine transporter gene for astaxanthin production in Phaffia rhodozyma

status: Public on Oct 16 2023

city: Hangzhou

first: Guoliang

last: Bao

address: No. 182 Tianmushan Road

country: China

institute: Hangzhou medical college

summary: Phaffia rhodozyma is an ideal microbial astaxanthin resource. However, the low productivity of astaxanthin in this yeast obstructs the process of industrial production. Although P. rhodozyma is isolated from plant material and the phytohormone has proved to be an effective stimulator for microbial production, the effects and mechanisms of phytohormones on astaxanthin synthesis in P. rhodozyma have been rarely reported. In this study, a concentration of down to 0.5 mg/L exogenous salicylic acid (SA) could promote biomass, astaxanthin content and yield by 20.8%, 95.8% and 135.3% in P. rhodozyma, respectively. Further transcriptomic analysis showed that SA could discriminate well the transcriptomic profile of P. rhodozyma cells. The differently expressed genes (DEGs) in P. rhodozyma cells between the SA-treatment and the SA-free groups were identified, and involved in astaxanthin and its competitive metabolite synthesis, material supply, biomolecules metabolism and transportation, anti-stress and signal transductions at a global-cell level. A regulation mechanism of astaxanthin synthesis induced by SA, including perception and transduction of the SA signal, expression regulations of the downstream genes by transcription factors, and cellular stress response to the SA, is put forward in this study. The polyamine transporter gene (PT), as an up-regulated DEG, was overexpressed in the P. rhodozyma to obtain the transformant Prh-PT-006. It was found that biomass, astaxanthin content and yield of the Prh-PT-006 under 0.5 mg/L SA treatment could reach 6.6 g/L, 0.35 mg/g DCW and 2.3 mg/L, 24.5%, 143.1% and 199.0% higher than the wild strain at the SA-free condition, respectively. The result will provide the engineering targets for constructing strains with high-yield of astaxanthin, and help to accelerate the industrialization process of microbial astaxanthin.

overall_design: Two groups of Phaffia rhodozyma cells with and without salicylic acid treatment. Each group has 3 repeats.

first: Jianping

last: Jia

first: Feifei

first: Yifei

last: Luan

first: Siru

last: Liu

first: Zhitao


title: Effect of TP53 missense mutation R172H on the single cell gene expression of pre-neoplastic mouse mammary gland

first: Silvio

last: Bicciato

summary: Mutations in the TP53 gene are the most common genetic alterations in breast cancer. To investigate at a single cell level what is the gene expression network that is regulated by mutant p53 at a non-tumoral stage, we employed a pre-neoplastic mouse model harboring the germline hotspot missense mutation R172H. We thus performed scRNAseq of cells derived from the normal mammary glands of mice harboring wt or mutant p53.

overall_design: Single cell-RNA seq of cells isolated from the normal mammary glands of one p53+/+ mouse (p53WT)and one p53R172H/R172H Ki mouse (p53MUT)

first: Camilla

last: Tombari

first: Alessandro

last: Zannini

first: Giannino

last: Del Sal


title: Single Nuclei RNA Sequencing of the Gastrocnemius Muscle Reveals Unique Transcriptomic Signatures of Peripheral Artery Disease

city: Gainesville

first: Terence

middle: E.

last: Ryan

state: Florida

address: 1864 Stadium Rd

department: Applied Physiology and Kinesiology

institute: University of Florida

summary: This study examines the transcriptional profile at the single-nuclei resolution human gastrocnemius skeletal muscle from 20 patients with Peripheral artery disease (PAD) and 12 non-PAD controls. In all libraries, muscle specimens were pooled prior to nuclei isolations were performed.

overall_design: Nuclei were isolated from gastrocnemius skeletal muscle from 20 patients with Peripheral artery disease (PAD) and 12 non-PAD controls.

first: Caroline

middle: G

last: Pass

middle: E


title: GM-CSF-activated STAT5A but not STAT5B regulates macrophage functions and inflammation in atherosclerosis

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

institute: Maastricht University

summary: Inhibition of STAT5 was recently reported to reduce mouse atherosclerosis. However, the regulatory role of STAT5 isoforms STAT5A and STAT5B in human disease and more specifically in macrophages remains unknown. Here, we demonstrate reciprocal expression regulation of STAT5A and B in human atherosclerotic lesions. The former was highly upregulated in ruptured over stable plaque and correlated with macrophage presence, a finding that was corroborated by the high chromosomal accessibility of STAT5A but not B gene in plaque macrophages. Phosphorylated STAT5 correlated with macrophages confirming its activation status. As macrophage STAT5 is activated by GM-CSF, we studied the effects of its silencing in GM-CSF differentiated human macrophages. STAT5A knockdown blunted NF-kB pathway, phagocytosis, cholesterol metabolism, and apoptosis terms. These changes at transcriptional level could be confirmed at functional level, with significant increases in apoptosis and phagocytosis and decreases in lipid uptake and IL-6, IL8, and TNFa cytokine secretion after STAT5A knockdown. Finally, inhibition of general and isoform A specific STAT5 inhibitor significantly reduced the secretion of TNFa, IL-8 and IL-10 in ex vivo tissue slices of advanced human atherosclerotic plaques. In summary, we identify STAT5A as important determinant of macrophage functions and inflammation in the context of atherosclerosis and show its promise as therapeutic target for human atherosclerotic plaque inflammation.

overall_design: Gene expression profiling using RNA-Seq. Human monocytes differentiated into macrophages with GM-CSF for 7 days and subsequent treatment with siRNA for 24h and an additional 24h resting period.

first: Jan

last: Nagenborg

first: Adele

last: Ruder

first: Barend

last: Mees

first: Lieve

last: Temmerman

first: Marjo

last: Donner

first: Pieter

last: Goossens

first: Erik

last: Biessen


title: PAP-gamma associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we have identified additional subunits of PAXT, including many orthologs of MTREC found in S. pombe. In particular, we show that polyA polymerase gamma was associated with PAXT. Genome-wide mapping of the binding sites of ZFC3H1, RBM26 and PAPgamma, showed that PAXT is recruited to the TSS of hundreds of genes. Loss of ZFC3H1 abolished recruitment of PAXT subunits including PAPgamma to TSSs and concomitantly increased the abundance of PROMPTs at the same sites. Moreover, PAPgamma polyadenylated PROMPTs and modulated their stability. Our results thus provide key insights into the direct targeting and degradation of PROMPT ncRNAs by PAXT, at their genomic sites and depending on polyadenylation of RNAs.

overall_design:
We used the technology of ChIP-seq to quantify occupancy of PAXT subunits, ZFC3H1, RBM26 and a newly identified subunit, PAPgamma, as well as RNA polymerase II in control cells. Localization of PAXT subunits  was also identified by ChIP-seq in cells expressing shRNAs targeting ZFC3F1 or a non-targeting control.
We used the RNA-seq technology to quantify RNA expression changes upon loss of PAP-Gamma using siRNA.

first: Xavier

last: Contreras

first: David

last: Depierre

first: Charbel

last: Akkawi

first: Olivier

last: Cuvier


title: Lactylation of METTL16 promotes cuproptosis via m6A-modification on FDX1 mRNA in gastric cancer

city: Shanghai

first: Yuan

last: Zhang

address: 650 Xinsongjiang Road

department: Department of Gastrointestinal Surgery

institute: Shanghai General Hospital

summary: To investigate the targets of METTL16-induced m6A modification, we established AGS lines in which METTL16 has been knocked down by shRNA.

overall_design: Comparative gene expression profiling analysis and m6A modification analysis of MeRIP-seq data for AGS control cells (shNC) and its KD derivatives (shMETTL16).

first: Lianhui

last: Sun

first: Boyu

last: Yang

first: Sijun


title: Dual targeted extracellular vesicles regulating oncogenic genes in pancreatic cancer

status: Public on Oct 01 2023

first: Inyoul

last: Lee

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: LncRNA DCRT protects against dilated cardiomyopathy via binding to PTBP1

status: Public on Sep 30 2023

city: WUHAN

first: heng

middle: zhi

last: du

address: 1095 Jiefang Dadao, Wuhan City, Hubei Province, China

institute: Wuhan Tongji Hospital


title: Spatial Transcriptomics Reveal Basal Sex Differences in Supraoptic Nucleus Gene Expression of Adult Rats Related to Cell Signaling and Ribosomal Pathways

city: Fort Worth

first: J.

middle: Thomas

last: Cunningham

state: TX

address: 3500 Camp Bowie Blvd

department: Physiology & Anatomy

institute: UNT Health Science Center

summary: Our study used spatially-resolved transcriptomics to visualize gene expression profiles in the supraoptic nucles of adult male (n=4) and female (n=4) Sprague-Dawley rats using Visium Spatial Gene Expression (10x Genomics).  Briefly, 10 μm coronal sections (~4x4 mm) containing the SON were collected from each rat and processed using Visium slides and recommended protocols. Data were analyzed using 10x Genomics’ Space Ranger and Loupe Browser applications and other bioinformatic tools. Two unique differential expression (DE) analysis methods, Loupe Browser and DESeq2, were used. Loupe Browser DE analysis of the SON identified 116 significant differentially expressed genes (DEGs) common to both sexes (e.g., Avp and Oxt), 31 significant DEGs unique to the males, and 73 significant DEGs unique to the females. DESeq2 analysis revealed 183 significant DEGs between the two groups. Gene Ontology (GO) enrichment and pathway analyses using significant genes identified via Loupe Browser revealed GO terms and pathways related to 1) neurohypophyseal hormone activity, regulation of peptide hormone secretion, and regulation of ion transport for the significant genes common to both males and females, 2) Gi signaling/G-protein mediated events for the significant genes unique to males, and 3) potassium ion transport/voltage-gated potassium channels for the significant genes unique to females, as some examples. GO/pathway analyses using significant genes identified via DESeq2 comparing female vs. male groups revealed GO terms/pathways related to ribosomal structure/function. Ingenuity Pathway Analysis (IPA) identified additional sex differences in canonical pathways (e.g., ‘Mitochondrial Dysfunction’, ‘Oxidative Phosphorylation’) and upstream regulators (e.g., CSF3, NFKB complex, TNF, GRIN3A).

overall_design: Ten micron fresh frozen coronal brain sections were collected from adult male (n=4, 3-4 months, 450-600g) and female (n=4, 3-4 months, 250-400g) Sprague-Dawley rats (Charles River Laboratories, Inc., Wilmington, MA, USA). One section containing the supraoptic nucleus was used from each rat. Samples were prepared using the Visium Spatial Gene Expression pipeline. For each sample, corresponding raw FASTQ files and brightfield images were processed using 10x Genomics’ Space Ranger (version 1.3.0) software. The reference genome used for these analyses was Rattus norvegicus (genome assembly mRatBN7.2), which is available from the National Library of Medicine (https://www.ncbi.nlm.nih.gov/assembly/GCF_015227675.2/). Visium data were visualized and analyzed using Loupe Browser (version 6.0.0, 10x Genomics). One supraoptic nucleus was identified in each section for subsequent analyses.

first: D

middle: H

last: Nguyen

first: V

last: Duque

first: N

last: Phillips

first: A

last: Souza Mecawi

first: J

middle: T


title: NULISA: a novel proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing

status: Public on Sep 29 2023

city: Fremont

first: Xiao-Jun

last: Ma

state: California

address: 47071 Bayside Pkwy

institute: Alamar Biosciences

summary: The blood proteome holds great promise for precision medicine but poses daunting challenges due to the low abundance of the majority of plasma proteins and the vast dynamic range across the proteome. We report the development and validation of a novel proteomic analysis technology – NUcleic acid Linked Immuno-Sandwich Assay (NULISA™) – that incorporates a dual capture and release mechanism to suppress the assay background to the minimum, thus drastically improving the signal-to-noise ratio. NULISA improves the sensitivity of the proximity ligation assay by over 10,000-fold to the attomolar level, which is enabled by antibody-conjugated DNA sequences that mediate the purification of immunocomplexes and contain target-and sample-specific barcodes for next-generation sequencing-based, highly multiplexed analysis. To demonstrate its performance and utility, we developed a 200-plex NULISA targeting 124 cytokines and chemokines and 80 other immune response-related proteins that demonstrated superior sensitivity for detecting low-abundance proteins and high concordance with other immunoassays. The ultra-high sensitivity enabled the detection of previously difficult-to-detect but biologically important, low-abundance biomarkers in patients with autoimmune diseases and COVID-19. Fully automated NULISA uniquely addresses longstanding challenges in the proteomic analysis of liquid biopsy samples and makes broad and in-depth proteomic analysis accessible to the general research community and future diagnostic applications.

overall_design:
Comparative protein expression profiling analysis in plasma using NULISAseq and Olink Explore technologies.
Submitter declares that the raw data cannot be provided because the files include proprietary barcodes and ligation sequences.

first: Wei

last: Feng

first: Joanne

last: Beer

first: Ishara

middle: S

last: Ariyapala

first: Kasun

last: Buddika

first: Dwight

last: Kuo


title: Physical activity regulates the immune response to breast cancer by a hematopoietic stem cell-autonomous mechanism

city: WORCESTER

first: Lyne

last: Khair

state: MA

address: 368 PLANTATION STREET

department: SURGERY

institute: UMASS MEDICAL SCHOOL

summary: To investigate the role of physical activity in the regulation of tumor incidence, we performed differential gene expression analysis on tumors from sedentary  (SED) and phsyically active (PA) mice at an early (week12) and late (week18) stage of tumor development. We also performed differential gene expression analysis on hematopoietic stem cells (HSCs) from SED and PA mice, as well as from SED mice transplanted with PA HSCs.

overall_design: Comparative gene expression analysis of RNA-seq data of tumors and hematopoietic from sedentary and phsyically active mice


title: SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: Regulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection. To characterize host RNA-binding proteins involved in this process, we biochemically identified proteins bound to genomic and subgenomic SARS-CoV-2 RNAs. We find that the host protein SND1 specifically binds to the 5'-end of negative-sense viral RNA and is required for SARS-CoV-2 RNA synthesis. SND1-depleted cells form smaller replication organelles and display diminished virus growth kinetics. We discover that NSP9, a viral RNA-binding protein and direct SND1 interaction partner, is covalently linked to the 5'-ends of positive and negative-sense RNAs produced during infection. These linkages occur at replication-transcription initiation sites, consistent with NSP9 priming viral RNA synthesis. Mechanistically, SND1 remodels NSP9 occupancy and alters the covalent linkage of NSP9 to initiating nucleotides in viral RNA. Our findings implicate NSP9 in the initiation of SARS-CoV-2 RNA synthesis and unravel an unsuspected role of a cellular protein in orchestrating viral RNA production.

overall_design:
We mapped direct protein-RNA interaction sites of the host protein SND1 in SARS-CoV-2 infected cells using enhanced crosslinking and immunoprecipitation (eCLIP) in combination with RNA-sequencing. Covalent linkages between the non-structural viral protein NSP9 and SARS-CoV-2 RNA were mapped by covalent RNA immunoprecipitation (cRIP), followed by RNA-sequencing.
We used thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) in human cells infected with SARS-CoV-2 at different time points to quantitatively assess the effect of SND1 depletion on the levels of newly synthesized and pre-existing viral RNA.
We identified RNA sequences crosslinked to proteins purified by RNA antisense purification (RAP-MS) for all viral (ALL), genomic (gRNAs), and subgenomic mRNAs (sgmRNA) by following the procedure described in the PROTOCOLS section.

first: Mathias

last: Munschauer


title: Salinity stress-induced phosphorylation of INDETERMINATE-DOMAIN 4 (IDD4) regulates plant growth adaptation in Arabidopsis

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

summary: The objective of the study was to understand the role of IDD4 in transcriptional regulation of genes involved in salt-stress response

overall_design: WT (col-0) and idd4 mutant plants were either mock treated or with 100mM NaCl. For each sample 2 biological replicates were used.

first: Anamika

last: Rawat

first: Ronny

last: Völz

first: Arsheed

last: Sheikh

first: Kiruthiga

last: Mariappan

first: Soon-Kap

last: Kim

first: Naganand

last: Rayapuram

first: Khairiah

last: Alwutayd

first: Louai

last: Alidrissi

first: Moussa

last: Benhamed

first: Ikram

last: Blilou

first: Heribert

last: Hirt


title: Genetically perturbed myelin as a risk factor for neuroinflammation-driven axon degeneration

first: Fabian

last: Imdahl

state: Bavaria

address: Josef-Schneider Str. 2

department: Single-cell-center

institute: helmholtz institute for RNA based infection research

summary: Axon degeneration and neurological dysfunction in myelin diseases is often attributed to loss of myelin. Perturbed myelinating glia can instigate chronic neuroinflammation and contribute to demyelination and axonal damage. We have previously shown in mice that distinct defects in the proteolipid protein 1 gene result in axonal damage which is largely driven by cytotoxic T cells targeting myelinating oligodendrocytes. Here we show in these mutants that persistent ensheathment with perturbed myelin poses a risk for axon degeneration, neuron loss, and behavioral decline. We demonstrate that CD8+ T cell-driven axonal damage is less likely to progress towards degeneration when axons are efficiently demyelinated by activated microglia. Mechanistically, we show that cytotoxic T cell effector molecules induce aberrant cytoskeletal plasticity within myelinating glial processes and constriction of axons at paranodal domains. Our study identifies detrimental axon-glia interactions which promote neurodegeneration and possible therapeutic targets for disorders associated with myelin defects and neuroinflammation.

overall_design: Around 15,000 CD45lowSiglec-H+ and CD45-O1+ single cells were sorted per sample using a FACSAria III (BD Biosciences) before being encapsulated into droplets with the Chromium Controller (10x Genomics) and processed according to the manufacturer’s specifications. Briefly, every transcript captured in all the cells encapsulated with a bead was uniquely barcoded using a combination of a 16-base pair (bp) 10x barcode and a 10-bp unique molecular identifier (UMI). Complementary DNA libraries ready for sequencing on Illumina platforms were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x Genomics) according to the detailed protocol provided by the manufacturer. Libraries were quantified by Qubit 3.0 Fluorometer (Thermo Fisher Scientific) and quality was checked using a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies). Libraries were pooled and sequenced with a NovaSeq 6000 platform (S1 Cartridge; Illumina) in paired-end mode to reach a mean of 44,131 reads per single cell. A total of 13,556, 9,955, and 12,191 cells were captured and a median gene number per cell of 2,268, 2,562, and 2,165 could be retrieved for adult Wt, PLPmut, and PLPtg cells, respectively.

first: Janos

last: Groh

first: Tassnim

last: Abdelwahab

first: Yagita

last: Kattimani

first: Michaela

last: Hörner

first: Silke

last: Loserth

first: Viktoria

last: Gudi

first: Robert

last: Adalbert

first: Antoine-Emmanuel

last: Saliba

first: Michael

last: Coleman

first: Martin

last: Stangel

first: Rudolf

last: Martini


title: Shade-induced RTFL/DVL peptides negatively regulate the shade response by directly interacting with BSKs in Arabidopsis

status: Public on Sep 28 2023

first: Lin

last: Li

address: 2005 Songhu Rd

department: school of life sciences

institute: Fudan university

summary: For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. We report that nonsecreted ROT FOUR LIKE (RTFL)/DEVIL (DVL) peptides negatively regulate the SAS by repressing the activities of BRASSINOSTEROID SIGNALING KINASEs (BSKs) and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in Arabidopsis. To identify RTFL function during SAS, we performed RNA-seq to search for differentially expressed genes (DEGs) by comparing transcript levels between Col-0 and dvl1-1D, bsk36, or pif47 seedlings during white light and shade conditions.

overall_design: 6-day-white-light grown seedlings were treated 6 hr shade before RNA extraction.

first: Sha

last: Huang


title: The Hypoxia-regulated Ectonucleotidase CD73 is a Host Determinant of HIV Latency [RNA-seq]

city: Essen

first: Hannah Sabeth

last: Sperber

state: NRW

address: Virchowstr. 171

department: Institute for transaltional HIV Research

institute: Essen University Hospital

summary: Deciphering the mechanisms underlying viral persistence is critical to achieving a cure for HIV infection. Here, we implement a systems approach to discover molecular signatures of HIV latently-infected CD4+ T cells, identifying the immunosuppressive, adenosine-producing ectonucleotidase CD73 as a key surface marker of latent cells. Hypoxic conditioning, reflecting the lymphoid tissue microenvironment, increases the frequency of CD73+ CD4+ T cells and promotes HIV latency. Transcriptomic profiles of CD73+ CD4+ T cells favor viral quiescence, immune evasion, and cell survival. CD73+ CD4+ T cells are capable of harboring a functional HIV reservoir and reinitiating productive infection ex vivo. CD73 or adenosine receptor blockade facilitates latent HIV reactivation in vitro, mechanistically linking adenosine signaling to viral quiescence. Finally, tissue imaging of lymph nodes from HIV-infected individuals on antiretroviral therapy reveals spatial association between CD73 expression and HIV persistence in vivo. Our findings warrant development of HIV cure strategies targeting the hypoxia-CD73-adenosine axis.

overall_design: Relatively little is known about the relevance and function of CD73 in human CD4+ T cells. To address this gap, the transcriptome of blood-derived, primary CD73+ and CD73- CD4+ T cells was characterized by RNA sequencing. To that purpose, CD73-/+ cells were isolated from primary CD4+ T cells by fluorescence-activated cell sorting and analyzed by RNA sequencing.

first: Hannah


title: Dual targeted extracellular vesicles regulating oncogenic genes in pancreatic cancer [sRNAseq]

first: Inyoul

last: Lee

overall_design: Comparative small RNA expression profiling analysis of RNA-seq data for dual-targeted extracellular vesicles carrying high loads of RNA that effectively suppresses large PDAC tumors.

first: Kai

last: Wang

first: Shannon

last: Fallen

first: L

first: Nick

last: Chiang


title: Fanconi Anemia pathway regulation by FANCI in prostate cancer

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary:
Prostate cancer is one of the leading causes of death among men worldwide and thus research on the genetic factors enabling the formation of treatment resistant cancer cells is crucial for improving patient outcomes.Here, we report a cell-line specific dependence on FANCI and related signalling pathways to counteract effects of DNA damaging chemotherapy in prostate cancer. Our results reveal that FANCI depletion results in significant downregulation of Fanconi anemia (FA) pathway members in prostate cancer cells indicating that FANCI is an important regulator of FA pathway. Furthermore, we found that FANCI silencing reduces proliferation in p53-expressing prostate cancer cells. This extends the evidence that inactivation of FANCI may convert cancer cells from a resistant to an eradicable state under the stress of DNA-damaging chemotherapy. Our results also indicate that high expression of FA pathway genes correlates with poorer survival in prostate cancer patients. Moreover, genomic alterations of FA pathway members are prevalent in prostate adenocarcinoma patients; mutation and copy number information for the FA pathway genes in seven patient cohorts (N = 1732 total tumor samples) reveals that 1025 (59.2%) tumor samples have an alteration in at least one of the FA pathway genes, suggesting that genomic alteration of the pathway is a prominent feature in patients with the
disease.

overall_design: Gene expression profiling by RNA-seq from LNCaP and PC3 cells treated with non-targeting siRNA or FANCI targeting siRNA. All sequencing was done with Illumina NovaSeq 6000.

first: Heidi

last: Kaljunen

first: Kirsi

last: Ketola


title: Integrated multi-omics reveals mTOR-LPL-driven dysregulated lipid metabolism induces neuronal hyperexcitability in human microglia of tuberous sclerosis complex

status: Public on Sep 27 2023

city: Atlanta

first: Zhexing

last: Wen

address: 100 Woodruff Circle

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

summary: Tuberous sclerosis complex (TSC) is an autosomal dominant disorder caused by heterozygous pathogenic variants in either TSC1 or TSC2. Emerging evidence suggests a connection between microglia activation and epilepsy as well as cognitive impairment in TSC patients. However, the impact of the causal variants of TSC1/2 genes on human microglia and their contribution to TSC's neurological symptoms remain largely unexplored. In this study, we generated human microglia from induced pluripotent stem cells (iPSCs) from a TSC patient cohort. Through extensive molecular and cellular analysis of TSC microglia, including transcriptomics, proteomics/phosphopreteomics, and lipidomics, we found that heterozygous TSC2 pathogenic variants were sufficient to cause aberrant lipid metabolism marked by increased glycerophosphocholines and fatty acyls. These metabolic changes resulted in enhanced phagocytosis and inflammation. Strikingly, the dysregulated lipid metabolism in TSC microglia is driven by a hyper-activated mTOR-lipoprotein lipase (LPL) pathway. Further, cellular and electrophysiological assessments of neuron/microglia co-cultures revealed that TSC microglia directly affect neuronal development, excitability, and neuronal network activity, which could be largely ameliorated by mTOR/LPL inhibition. Collectively, our research unveiled the molecular and cellular abnormalities in TSC microglia affecting neuronal development and function, and highlighted the mTOR-LPL pathway as a novel potential therapeutic target for the neuropathology of TSC.

overall_design: RNA-seq

first: Weibo

last: Niu

first: Shaojun

last: Yu


title: CRISPR Anchor screening of a barcoded library in cells treated with standard of care neuroblastoma drugs

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Neuroblastoma cells were treated with a barcoded library of >600 genes and one of several standrard of care neuroblastoma compounds (or vehicle control)

overall_design:
Sequencing of gRNAs of each cell line treated with the barcoded library and a standard of care compound or vehicle control
The sequencing data (gRNA abundance data in drug-treated cells) are analyzed with a de facto tool called MAGeCK. This tool is standard and outputs data for all measured gRNA abundances for all perturbation conditions (drug treatments in our case) for all samples. The detailed description can be found at https://sourceforge.net/p/mageck/wiki/output/


title: Neural adaption in midbrain GABAergic cells contributes to high-fat-diet induced obesity

city: HangZhou

first: hao

last: wu

address: YuHang street

institute: Zhejiang University

summary: Overeating disorders significantly contribute to worldwide incidences of obesity. Available treatments are limited. Here, we discovered that long-term chemogenetic activation of ventrolateral periaqueductal gray (vlPAG) GABAergic cells rescue obesity of high-fat diet induced obesity (DIO) mice. This was associated with the recovery of enhanced mIPSCs, decreased food intake, increased energy expenditure, and inguinal white adipose tissue (iWAT) browning. In vivo calcium imaging confirmed vlPAG GABAergic suppression for DIO mice, with corresponding reduction in intrinsic excitability. Single-nucleus RNA sequencing identified transcriptional expression changes in GABAergic cell subtypes in DIO mice, highlighting Cacna2d1 as of potential importance. Overexpressing Cacna2d1 in vlPAG GABAergic cells of DIO mice rescued enhanced mIPSCs and calcium response, reversed obesity, and therefore presented here as a potential target for obesity treatment.

overall_design: To explore changes in the gene expression profile of vlPAG GABAergic cells in DIO mice, we collected the vlPAG from mice fed with either 7 weeks of HFD or normal chow and performed single cell nucleus sequencingSingle-nuclei suspensions were loaded to 10X Chromium to capture 8000 single cells using a 10X Genomics Chromium Single-Cell 3' kit (V3) according to the manufacturer's instructions.

first: Hao

last: Wu

first: Xiaomeng


title: Single cell RNA sequencing of immune cells from lenvatinib-resistant mouse HCC model after lenvatinib or combined lenvatinib and CDK4/6 inhibitor palbociclib treatment

city: Shatin

first: Karl Kam Hei

last: So

state: New Territories

address: 608A, Lo Kwee-Seong Integrated Biomedical Sciences Building, The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We used single-cell RNA sequencing (scRNA seq) to elucidate the alterations of tumor microenvironment upon combined treatment of lenvatinib and palbociclib (combo).

overall_design: Single-cell RNA-seq of CD45+ immune cells from lenvatinib-resistant Trp53KO/MYCOE-induced mouse HCC model treated with lenvatinib or combined treatment of lenvatinib and palbociclib

first: Carmen Oi Ning

last: Leung

first: Terence Kin Wah


title: Effect of depletion of S100A16 on gene expression during lipid accumulation of  primary hepatocytes

status: Public on Sep 26 2023

city: Nanjing

first: Wen-Song

last: Zhang

state: Jiangsu

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Alcoholic liver disease (ALD) encompasses conditions ranging from simple steatosis to cirrhosis and even liver cancer. It has gained significant global attention in recent years. Despite this, effective pharmacological treatments for ALD remain elusive, and the core mechanisms underlying the disease are not yet fully comprehended. S100A16, a newly identified calcium-binding protein, is linked to lipid metabolism. Our research has discovered elevated levels of the S100A16 protein in both serum and liver tissue of ALD patients. A similar surge in hepatic S100A16 expression was noted in a Gao-binge alcohol feeding mouse model. S100a16 knockdown alleviated ethanol-induced liver injury, steatosis and inflammation. Conversely, S100a16 transgenic mice showed aggravating phenomenon. Mechanistically, we identify mesencephalic astrocyte-derived neurotrophic factor (MANF) as a regulated entity downstream of S100a16 deletion. MANF inhibited ER-stress signal transduction induced by alcohol stimulation. Meanwhile, MANF silencing suppressed the inhibition effect of S100a16 knockout on ethanol-induced lipid droplets accumulation in primary hepatocytes. Our data suggested that S100a16 deletion protects mice against alcoholic liver lipid accumulation and inflammation dependent on upregulating MANF and inhibiting ER stress. This offers a potential therapeutic avenue for ALD treatment.

overall_design: To investigate the function S100A16 in the regulation of lipid accumulation,we isolated primary hepatocytes from alcohol-fed WT and S100a16KO+/- mice . We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

first: Dan

first: Rihua

first: Xiaoxuan

last: Qin

first: Jizheng

first: Yifang

last: Hu

first: Shan

last: Lu

first: Jingbao

last: Kan

first: Yaoqi

last: Ge

first: Ke

last: Jin

first: Yun

last: Liu


title: Evolutionary innovation through transcription factor rewiring in microbes is shaped by levels of transcription factor activity, expression, and existing connectivity

city: Bath

first: Matthew

middle: J

last: Shepherd

state: Somerset

address: University of Bath, Claverton Down

department: Department of Life Sciences

country: United Kingdom

institute: University of Bath

summary: The survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way to achieve this is via change to gene regulatory network (GRN) connections – known as rewiring – that facilitate novel interactions and innovation of transcription factors. To understand the success of rapidly adapting organisms, we therefore need to determine the rules that create and constrain opportunities for GRN rewiring. Here, using an experimental microbial model system based on the soil bacterium Pseudomonas fluorescens, we reveal a hierarchy among transcription factors that are rewired to rescue lost function, with alternative rewiring pathways only unmasked after the preferred pathway is eliminated. We identify three key properties - high activation, high expression, and pre-existing low-level affinity for novel target genes – that facilitate transcription factor innovation. Ease of acquiring these properties is constrained by pre-existing GRN architecture, which was overcome in our experimental system by both targeted and global network alterations. This work reveals the key properties that determine transcription factor evolvability, and as such, the evolution of GRNs.

overall_design: RNAseq samples - Pseudomonas fluorescens, whole bacterial cell transcriptome, RNA extraction during logarithmic growth in shaking LB broth. Biological triplicate RNA samples, ribodepleted.

first: Aidan

last: Pierce

first: Tiffany

middle: B

last: Taylor


title: The CCR4-NOT complex suppresses untimely translational activation of maternal mRNAs.

city: Kunigami-gun

first: Tadashi

last: Yamamoto

state: Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology

summary: Control of mRNA poly(A) tail has central role to regulate mRNA metabolism: translation efficiency and mRNA stability. Gene expression in maturing oocytes largely relies on the regulation of mRNA metabolism as they are transcriptionally silent. The CCR4-NOT complex is a major deadenylase for mammals and regulates poly(A) tails of maternal mRNAs, however their function to translational regulation was not well understood. Here we show that CCR4-NOT suppresses translational activity of maternal mRNAs during oocyte maturation. Oocytes which lack entire deadenylase activity of CCR4-NOT by genetic deletion of its catalytic subunits: CNOT7 and CNOT8 showed increase of both expression of maternal mRNAs and translational activity of them during oocyte maturation.

overall_design: Comparative gene expression analysis using RNA-seq data from CNOT7&8 KO oocytes and Zp3-Cre control.

first: Shou

last: Soeda


title: Niclosamide as a chemical probe for analyzing SARS-CoV-2 modulation of host cell lipid metabolism

city: Gainesville

first: Rhoel

last: Dinglasan

address: 2055 Mowry Rd

institute: University of Florida

summary:
Purpose: The global effort to combat COVID-19 rapidly produced a shortlist of approved drugs with anti-viral activities for clinical repurposing. However, the jump to clinical testing was lethal in some cases since a full understanding of the mechanism of antiviral activity as opposed to inherent toxicity for these drugs was lacking. We used parallel lipidomic and transcriptomic analyses to investigate the effect of Niclosamide (NIC), a poorly soluble anti-helminth drug identified for repurposed treatment of COVID-19, on SARS-CoV-2 infected Vero E6 cells.
Methods: A time of addition study was performed on VeroE6 cells to gain mRNA profiles of 16 and 48h SARS-CoV-2 and/or niclosamide infected cells in triplicate, using an Illumina NovaSeq6000 platfrom. Sequence reads that passed quality filters were analyzed by featurecounts and DESeq2.
Results: Herein, we identified and characterized autophagic or lipophagic pathways (and wider linked cellular networks) that are targeted by NIC in the presence and absence of a SARS-CoV-2 infection. We used the lipid and gene expression signatures induced by this anti-parasitic compound to detect pathways that are predicted to either lead to direct antiviral effects or to cellular dysregulation and cell death.
Conclusions: NIC treatment reduced the abundance of phosphatidylethanolamines (PE), a known activator of autophagy, only after establishment of SARS-CoV-2 infection. Countering SARS-CoV-2 subversion of lipid metabolism by NIC through the activation of PE may lead to a focused screen for approved, more druggable compounds that can suppress viral replication in COVID-19 patients.

overall_design: Vero E6 cell mRNA profiles at 0h, 16h or 48h treated and/or infected with NIC or SARS-CoV-2

first: Heather

last: Coatsworth

first: Jasmine

last: Ayers


title: MYC overexpression and SMARCA4 loss cooperate to drive medulloblastoma formation in mice

city: Hamburg

first: Ulrich

last: Schüller

address: Martinistraße 52

institute: University Medical Center Hamburg-Eppendorf

summary: Group 3 medulloblastoma is one of the most aggressive types of childhood brain tumors. Roughly 30% of cases carry genetic alterations in MYC, SMARCA4, or both genes combined. While overexpression of MYC has previously been shown to drive medulloblastoma formation in mice, the functional significance of SMARCA4 mutations and their suitability as a therapeutic target remain largely unclear. To address this issue, we combined overexpression of MYC with a loss of SMARCA4 in granule cell precursors. Both alterations did not increase proliferation of granule cell precursors in vitro. However, combined MYC overexpression and SMARCA4 loss successfully induced tumor formation in vivo after orthotopic transplantation in recipient mice. Resulting tumors displayed anaplastic histology and exclusively consisted of SMARCA4 negative cells although a mixture of recombined and non-recombined cells was injected. These observations provide first evidence for a tumor-promoting role of a SMARCA4 deficiency in the development of medulloblastoma. In comparing the transcriptome of tumors to the cells of origin and an established Sonic Hedgehog medulloblastoma model, we gathered first hints on deregulated gene expression that could be specifically involved in SMARCA4/MYC driven tumorigenesis. Finally, an integration of RNA sequencing and DNA methylation data of murine tumors with human samples revealed a high resemblance to human Group 3 medulloblastoma on the molecular level. Altogether, the development of SMARCA4-deficient medulloblastomas in mice paves the way to deciphering the role of frequently occurring SMARCA4 alterations in Group 3 medulloblastoma with the perspective to explore targeted therapeutic options.

overall_design:
We cultured granule cell precursors isolated from Math1-creERT2::Smarca4fl/fl mice at P7 after tamoxifen-induced loss of SMARCA4 (injection at P3) and performed transduction with a lentiviral construct to drive overexpression of MYC.
These cells were transplanted into the cerebella of CD1nu/nu recipient mice, which successfully drove tumor formation.
Bisulphite converted DNA from three of these MYC/SMARCA4 tumors was hybridised to the Illumina Infinium Mouse Methylation BeadChip for a subsequent comparison to published global DNA methylation profiles of human tumors. Tumors 1,2,3 in this series correspond to tumors 1,3,4 in RNA sequencing analysis within the same project (GSE235625).

first: Carolin

last: Göbel

first: Shweta

last: Godbole

first: Melanie

last: Schoof

first: Dörthe

last: Holdhof

first: Catena

last: Kresbach

last: Loose


overall_design:
We cultured granule cell precursors isolated from Math1-creERT2::Smarca4fl/fl mice at P7 after tamoxifen-induced loss of SMARCA4 (injection at P3) and performed transduction with a lentiviral construct to drive overexpression of MYC.
These cells were transplanted into the cerebella of CD1nu/nu recipient mice, which successfully drove medulloblastoma formation.
To analyze gene expression profiles of MYC/SMARCA4 tumors, we performed RNA sequencing of four tumors using RNA derived from FFPE punches.
As a validation, we simultaneously sequenced three samples of the previously established SHH medulloblastoma model Math1-cre::Smofl/wt. Moreover, we included samples derived from Math1-creERT2::Smarca4fl/fl cerebella at P7 as a control. Tumors 1,3,4 in this series correspond to tumors 1,2,3 in DNA methylation analysis within the same project (GSE235924).


title: Isoform-resolved transcriptome of the human preimplantation embryo [PacBio]

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Human preimplantation development is a complex process involving extensive remodeling of gene expression. However, the preimplantation embryo transcriptome has only been annotated using short-read sequencing, which fails to capture full-length mRNAs and associated isoform diversity. We present a novel human embryo transcriptome using integrated long- and short-read RNA sequencing data. Our analysis reveals a total of 110,212 novel isoforms transcribed from known genes containing either a novel combination of known splice sites or at least one novel splice site, and 17,964 isoforms transcribed from completely novel genes located either in antisense direction of known genes or in intergenic space.

overall_design: RNA sequencing data was generated from a total of 73 human embryos across six pre-implantation stages: 13 zygotes (1C), 13 2-cell (2C) embryos, 16 4-cell (4C) embryos, 15 8-cell (8C) embryos, 3 morulae and 13 blastocysts. For each embryo, mRNA was extracted and converted to full-length cDNA, and used to generate Illumina RNA-Seq data, generating an average of 58.6 million paired end reads per sample. The same cDNA samples were used for SMRT-seq, pooling together low-yield samples to obtain enough mass for long-read sequencing. This resulted in a total of 10,139,308 full-length nonchimeric (FLNC) reads across 10 Sequel II SMRTcells, with an average cDNA length of 1,332 bp.

first: D

last: Torre

first: N

last: Francoeur

first: Y

last: Kalma

last: Ben-Yosef

first: R


title: Isoform-resolved transcriptome of the human preimplantation embryo

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


title: Isoform-resolved transcriptome of the human preimplantation embryo [Illumina]


title: Antitumor effects of PRMT5 inhibition in sarcomas [RNA-seq]

status: Public on Sep 25 2023

city: Bordeaux

first: Amandine

last: Crombe

address: 229 cours de l'Argonne

institute: Institut Bergonié

summary: Patients with advanced soft-tissue sarcomas (STSs) have few therapeutic options. Protein arginine methyltransferase 5 (PRMT5), an anticancer target, has been extensively investigated in recent years in epithelial tumors. To date, no data related to the biological role of PRMT5 inhibition and its potential effect as a treatment in STS have been reported. To investigate the therapeutic potential of PRMT5 targeting in STS, we first evaluated the prognostic value of PRMT5 expression in 2 different cohorts of patients with STS. We then used the potent and selective GSK3326595 (GSK595) compound to investigate the antitumor effect of the pharmacological inhibition of PRMT5 in vitro via MTT, apoptosis, cell cycle, clonogenicity and proliferation assays. In vivo studies were performed with two animal models to evaluate the effects of GSK595 on tumor growth. The mechanisms of action were investigated by RNA sequencing, metabolic pathway analysis, Western blotting and glucose uptake/lactate production assays. High PRMT5 gene expression levels were significantly associated with worsened metastasis-free survival of STS patients. GSK595 decreased the global symmetric dimethylarginine level, the proliferation rate and clonogenicity of STS cell lines in vitro and tumor growth in vivo. Moreover, PRMT5 inhibition regulated aerobic glycolysis through downregulation of key enzymes of glycolysis as well as glucose uptake and lactate production. The present study demonstrated that PRMT5 regulates STS cell metabolism and thus represents a potential therapeutic target for STS. Additional studies in diverse sarcoma subtypes will be essential to confirm and expand upon these findings.

overall_design: To decipher the mechanism of action of PRMT5 inhibition in STS cell lines, we explored the transcriptomic changes in IB111 cells after 10 days of treatment by RNA sequencing. IB111 cells were untreated or treated with GSK595 at the IC50 every 3 days for 10 days in triplicate. RNA was then extracted and sequenced on a NovaSeq6000 S2 platform.

first: Stephanie

last: Verbeke

first: Aurélien

last: Bourdon

first: Jean-Philippe

last: Guégan

first: Laura

last: Leroy

first: Vanesssa

last: Chaire

first: Elodie

last: Richard

first: Alban

last: Bessede

first: Antoine

last: Italiano


title: Transcriptomic response of Mycobacterium tuberculosis to artemisinin, Artemisia annua extract, and Artemisia afra extract

city: Worcester

first: Scarlet

last: Shell

state: Massachusetts

address: 60 Prescott St, WPI

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

summary: We sought to determine the transcriptomic impacts of artemisinin, Artemisia annua extract, and Artemisia afra extract on M. tuberculosis. Log phase cultures were treated with lethal doses for four hours or with inhibitory or sub-inhibitory doses for 24 hours. RNA was collected from untreated controls at the same timepoint.

overall_design: M. tuberculosis strain mc26230 (H37Rv ΔRD1 ΔpanCD) was treated with artemisinin or with dichloromethane extracts of A. annua or A. afra at three different doses. A lethal dose (2X MIC) was applied for four hours, and inhibitory (MIC or 1.33X MIC) and sub-inhibitory doses (0.5X MIC) were applied for 24 hours. Untreated cultures were harvested after 4 and 24 hours for comparison. All treatments were done in quadruplicate.

first: Maria

middle: N

last: Alonso

first: Junpei

last: Xiao


title: Antitumor effects of PRMT5 inhibition in sarcomas

summary: Patients with advanced soft-tissue sarcomas (STSs) have few therapeutic options. Protein arginine methyltransferase 5 (PRMT5), an anticancer target, has been extensively investigated in recent years in epithelial tumors. To date, no data related to the biological role of PRMT5 inhibition and its potential effect as a treatment in STS have been reported.  To investigate the therapeutic potential of PRMT5 targeting in STS, we first evaluated the prognostic value of PRMT5 expression in 2 different cohorts of patients with STS. We then used the potent and selective GSK3326595 (GSK595) compound to investigate the antitumor effect of the pharmacological inhibition of PRMT5 in vitro via MTT, apoptosis, cell cycle, clonogenicity and proliferation assays. In vivo studies were performed with two animal models to evaluate the effects of GSK595 on tumor growth. The mechanisms of action were investigated by RNA sequencing, metabolic pathway analysis, Western blotting and glucose uptake/lactate production assays.  High PRMT5 gene expression levels were significantly associated with worsened metastasis-free survival of STS patients. GSK595 decreased the global symmetric dimethylarginine level, the proliferation rate and clonogenicity of STS cell lines in vitro and tumor growth in vivo. Moreover, PRMT5 inhibition regulated aerobic glycolysis through downregulation of key enzymes of glycolysis as well as glucose uptake and lactate production.  The present study demonstrated that PRMT5 regulates STS cell metabolism and thus represents a potential therapeutic target for STS. Additional studies in diverse sarcoma subtypes will be essential to confirm and expand upon these findings.

overall_design: To decipher the mechanism of action of PRMT5 inhibition in STS cell lines, four sarcoma cell lines (the IB111, IB114, IB115, and IB128 cells) were untreated or treated with GSK595 at IC80 every 3 days for 10 days and RNA were analyzed by Nanostring assay using an nCounter Metabolic Pathways Panel in the nCounter Max Analyzer.


title: The Hypoxia-regulated Ectonucleotidase CD73 is a Host Determinant of HIV Latency

first: Hannah Sabeth

last: Sperber

overall_design: Refer to individual Series


title: Lung emphysema can be elicited by nanoparticle triggered, p38 MAPK mediated virus reactivation

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Environmental particle inhalation and persistent herpesvirus infection are omnipresent and associated with chronic lung diseases. Previously, we showed that pulmonary exposure to soot-like carbonaceous nanoparticles (CNP) or fibre-shaped engineered double-walled carbon nanotubes (DWCNT) induced an increase of lytic virus protein expression in latently murine gammaherpesvirus 68 (MHV-68) infected mouse lungs, with a similar pattern as acute infection suggesting virus reactivation. However, the molecular mechanisms underlying herpesvirus reactivation as well as herpesvirus reactivation associated disease exacerbation caused by particle exposure remain unclear.  Here, we investigated the effects of environmental relevant repeated particle exposure and herpesvirus reactivation mechanistically, and therapeutically.  In the MHV-68 mouse model, we identified elevated lung inflammation and emphysema-like injury after repetitive CNP exposure. We further uncovered that CNP reactivated latent herpesvirus mainly in CD11b+ macrophages. Mechanistically, ERK1/2, JNK and p38 MAPK were rapidly activated after CNP and DWCNT exposure in persistently MHV-68 infected bone marrow-derived macrophages, followed by upregulation of viral gene expression and increased viral titer but without generating a pro-inflammatory transcriptional signature. Pharmacological inhibition of p38 activation abrogated CNP but not DWCNT triggered virus reactivation. In vivo, p38 inhibitor pretreatment of latently infected mice also attenuated CNP exposure induced MHV-68 reactivation. Our findings suggest that particle pollution is an environmental challenge to trigger herpesvirus reactivation and related chronic lung disease by activating latent herpesvirus via p38 MAPK dependent signalling. Pharmacological p38 inhibition might serve as a protective target to alleviate particle exposure related chronic lung disease exacerbations.

overall_design: Ana-1/MHV-68 cells were exposed to CNP, DWCNT, LPS or controls

first: Lianyong

last: Han

first: Verena

last: Haefner

first: Youjia

last: Yu

first: Bing

first: Hongyu

last: Ren

first: Martin

last: Irmler

first: Annette

last: Feuchtinger

first: Ali

middle: O

last: Yildrim

first: Heiko

last: Adler

first: Tobias

last: Stoeger


title: Gene expression profile at single cell level from the colorectal cancer (CRC)

city: Houston

first: Kangyu

last: Lin

address: 1515 Holcombe Blvd

department: Department of Gastrointestinal Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: This study is part of MD Anderson Cancer Center CRC Moon Shot. We used single cell RNAsequencing (scRNA-seq) to analyze the diversity of CRC.

overall_design: Fresh colorectal cancer tissues and adjucent normal tissues from primary and liver/peritnoeum-Met patients were collected for scRNA-seq.

first: Scott

last: Kopetz

first: Shen

last: John Paul


title: Single cell sequencing of mouse gastric cell populations

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

summary: Although gastric cancer is a leading cause of cancer-related deaths, systemic treatment strategies remain scarce. Here, we report the pro-tumorigenic properties of the crosstalk between intestinal tuft cells and type 2 innate lymphoid cells (ILC2) that is evolutionarily optimized for epithelial remodeling in response to helminth infection. We demonstrate that tuft cell-derived interleukin 25 (IL25) drives ILC2 activation, inducing the release of IL13 and promoting tuft cell hyperplasia. This reciprocal tuft cell - ILC2 circuit promotes early gastric metaplasia and tumor formation while genetic ablation of tuft cells, ILC2s or therapeutic targeting of IL13 or IL25 alleviates these phenotypes. Importantly, tuft cell and ILC2 gene signatures predict worsening survival in intestinal-type gastric cancer patients, with ~50% of these tumors showing enrichment for tuft cells and ILC2s. Thus, we reveal an unanticipated function of the tuft cell - ILC2 circuit in promoting multiple steps towards gastric carcinogenesis. Together, this may provide an opportunity to therapeutically inhibit early-stage gastric cancer through repurposing antibody-mediated therapies.

overall_design: Epithelial and immune cells from the stomachs and tumors of Gp130F/F and wildtype Gp130+/+ mice were isolated through flow cytometry and analyzed using scRNAseq.

first: Ryan

last: O’Keefe

first: Annalisa

last: Carli

first: David

last: Baloyan

last: Chisanga

first: Shoukat

last: Afshar-Sterle

first: Moritz

middle: F

last: Eissmann

first: Ashleigh

last: Poh

first: Cyril

last: Seillet

first: Richard

middle: M

last: Locksley

first: Matthias

last: Ernst

first: Michael

last: Buchert


title: The Hypoxia-regulated Ectonucleotidase CD73 is a Host Determinant of HIV Latency [Array]

status: Public on Sep 24 2023

city: Essen

first: Hannah Sabeth

last: Sperber

address: Virchowstr. 171

institute: Essen University Hospital

summary: Deciphering the mechanisms underlying viral persistence is critical to achieving a cure for HIV infection. Here, we implement a systems approach to discover molecular signatures of HIV latently-infected CD4+ T cells, identifying the immunosuppressive, adenosine-producing ectonucleotidase CD73 as a key surface marker of latent cells. Hypoxic conditioning, reflecting the lymphoid tissue microenvironment, increases the frequency of CD73+ CD4+ T cells and promotes HIV latency. Transcriptomic profiles of CD73+ CD4+ T cells favor viral quiescence, immune evasion, and cell survival. CD73+ CD4+ T cells are capable of harboring a functional HIV reservoir and reinitiating productive infection ex vivo. CD73 or adenosine receptor blockade facilitates latent HIV reactivation in vitro, mechanistically linking adenosine signaling to viral quiescence. Finally, tissue imaging of lymph nodes from HIV-infected individuals on antiretroviral therapy reveals spatial association between CD73 expression and HIV persistence in vivo. Our findings warrant development of HIV cure strategies targeting the hypoxia-CD73-adenosine axis.

overall_design: Blood-derived primary CD4+T cells obtained from six healthy individuals were activated in vitro via αCD3/αCD28 bead stimulation and infected with a recombinant HIV dual-reporter virus HIVDFII via spinoculation. Four days post infection, productively- and latently-infected, as well as uninfected cells were purified by fluorescence activated cell sorting. The sorted populations and respective control specimens (untreated samples; unstimulated, infected cells; and stimulated cells without HIVDFII infection) were subsequently subjected to downstream analysis using NanoString hybridization and fluorescence-based digital counting technology allowing for simultaneous detection of 770 mRNA and 30 protein targets.

first: Hannah


title: Modulation of Influenza A virus NS1 expression reveals prioritization of host response antagonism at single-cell resolution

city: Seattle

first: Daniel

last: Blanco-Melo

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: Influenza A virus (IAV) is an important human respiratory pathogen that causes significant seasonal epidemics and potential devastating pandemics. As part of its life cycle, IAV encodes the multifunctional protein NS1, that, among many roles, prevents immune detection and limits interferon (IFN) production. As different host immune pathways exert different selective pressures against IAV as replication progresses, we expect a prioritization in the host immune antagonism by NS1. In this work, we profiled bulk transcriptomic differences in a primary bronchial epithelial cell model facing IAV infections at distinct NS1 levels. We further demonstrated that the intracellular NS1 levels in-part shapes the host response heterogeneity at single cell level. We found that modulation of NS1 levels reveal a ranking in its inhibitory roles: modest NS1 expression is sufficient to inhibit immune detection, and thus the expression of pro-inflammatory cytokines (including IFNs), but higher levels are required to inhibit IFN signaling and ISG expression. Lastly, inhibition of chaperones related to the unfolded protein response requires the highest amount of NS1, often associated with later stages of viral replication. This work demystifies some of the multiple functions ascribed to IAV NS1, highlighting the prioritization of NS1 in antagonizing the different pathways involved in the host response to IAV infection.

overall_design: To better capture the relationship between IAV NS1 expression and the host antiviral response, we characterized the transcriptional landscape of primary bronchial epithelial cells upon infection with wild type and recombinant viruses with varying levels of NS1. We utilized a previously described recombinant virus (lab adapted A/Puerto Rico/8/34 (H1N1)), in which the viral NS1 and NEP open reading frames are separated to enable the insertion of two miRNA targets. We hence compared the NS1 expression levels during active infections via RNA-seq, contrasting IAV-NS1-T with wildtype IAV (IAV-WT) and IAV-ΔNS1, a recombinant virus lacking NS1-specific open reading frame while expressing NEP. In addition, we sought to investigate whether the host antagonism prioritization can also be demonstrated by cell-to-cell NS1 expression heterogeneity during wild-type IAV infection. We employed single cell 3’ RNA-seq technology to characterize both viral transcript abundance and host response in NHBE infected with IAV-WT.

first: Qing

last: Yang

first: Anna

last: Elz

first: Maryline

last: Panis

first: Ting

last: Liu

first: Benjamin

last: Nilsson-Payant


title: RNA-seq of wild type and Slc25a3-deficient CD8 T cells

status: Public on Sep 22 2023

city: Würzburg

first: hao

last: wu

address: Versbacher stress 7-9

institute: institute for systemsimmunology, wurzburg university

summary: RNA-sequencing and analysis of in vitro differentiated CD8 T cells isolated from WT and Slc25a3-fl/fl Cd4-cre mice.

overall_design: Naive T cells were isolated (d0) or activated for 2 days in vitro by anti-CD3 and anti-CD8 antibodies (d2) or followed with 4 days resting in 10 ng/ml IL-2 after activation (d6). Total RNA was harvestred as subjected to bulk RNA-sequncing analysis.

first: Martin

last: Väth

first: Hao

last: Wu


title: IRF1 regulates self-renewal and stress-responsiveness to support hematopoietic stem cell maintenance

city: Lund

first: Alexandra

last: Rundberg Nilsson

address: Klinikgatan 26

department: Experimental Hematology

country: Sweden

institute: Lund University

summary:
The impact of IRF1 loss to hematopoietic stem cells (HSCs).
Transcriptional profiling analysis using data obtained from RNA-seq of HSCs from 6 mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and IRF1 KO HSCs.

last: Karin


title: Single cell sequecing analysis of exhausted CD8 T cell subsets in LCMV-clone13 infected mice

summary: To identify the subsets of exhausted T cells and to analyze the transcriptional-metabolic programs alongside their developmental trajectories at single-cell resolution, we isolated CD44+ PD-1hi CD8+ T cells from chronically infected wild-type (WT) mice 21 days after infection with the ‘clone 13’ strain of lymphocytic choriomeningitis virus (LCMV) by FACs sorting aand performed scRNA-sequencing.

overall_design: C57BL/6 WT Mice were infected with 2x10^6 IU LCMV clone13 after CD4 T cell depletion at d-2 and d0 with 300µg GK1.5 anti-CD4 antibody. At the chronic infection phase (> d21), splenocytes were isolated and CD8+, CD44+, PD-1high cells were sorted using FACS AriaIII.

last: Vaeth

first: Wolfgang

last: Kastenmüller

first: Konrad

last: Knöpper


title: Mutant p53 regulates serine-glycine synthesis and essential amino acids intake

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova


title: Effect of ICSI on gene expression in germline stem cells

status: Public on Sep 21 2023

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Graduate School of Medicine

institute: Kyoto University

summary: To investigate the effect of ICSI in germ cells,  we performed RNA-seq of germline stem cells established from ICSI-derived mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for germline stem cells of  ICSI-derived mice.

first: Yusuke

last: Shiromoto


title: Cell volume controlled by LRRC8A-formed volume-regulated anion channels fine-tunes T cell activation and function

status: Public on Sep 23 2023

city: wuhan

first: zaiqiao

last: sun

institute: wuhan university

summary: To become fully functional effector T cells, naïve T cells undergo a drastic metabolic status shift from quiescence to substantial biosynthesis. The synthesis of biomass initiated by T cell receptor (TCR) signals drives the cell volume increase during T cell activation (T lymphoblast), which resembles the slowest extreme of hypotonic cell swelling. However, the fundamental role of cell volume regulation in TCR signaling during T lymphoblast and its underlying mechanisms remain a long-standing enigma. Here we show that optimal T cell activation and function require appropriate cell volume regulation by regulated volume decrease (RVD) mediated via volume-regulated anion channels (VRACs) during T cell blast. Pharmacological blockade of VRACs and genetic deletion of LRRC8A in T cells, the essential component of VRACs, impair T cell activation and function, particularly under weak TCR stimulation, such as low-affinity TCR-pMHC engagement and unsaturated anti-CD3e crosslinking. Additionally, LRRC8A has distinct influences on mRNA transcriptional profiles driven by various TCR signal strengths, revealing the prominent effects of cell volume regulation for T cell functions. More importantly, LRRC8A-deficient mice have defective antiviral immunity and obstacles in effector-memory transition of CD8+ T cells. Furthermore, LRRC8A escorts the thymic selection of T cells and shapes the T cell repertoire in the thymus. Mechanistically, LRRC8A governs stringent cell volume increase via RVD during T cell blast induced by activation-driven intracellular osmolytes accumulation to keep the proximal TCR signaling molecules at adequate density. T cell blast driven by TCR signal feedbacks to control T cell activation. Together, our results reveal a previously unappreciated layer of T cell activation regulation that LRRC8A acts as a cell volume controlling "valve" to facilitate T cell activation and function

overall_design: To examine whether the TCR signaling controlled by LRRC8A contributes to the formation of TCR repertoire, we performed the TCR sequencing (TCR-seq) analysis of thymocytes from WT (Lrrc8af/f) and LRRC8A KO (Lrrc8af/f; Cd4-Cre) mice.

first: Yuman

last: Wang

first: Zaiqiao

last: Sun

first: Jieming

last: Ping

first: Jianlong

last: Tang

first: Boxiao

last: He

first: Tedingg

last: Chang

first: Qian

last: Zhou

first: Shijie

last: Yuan

first: Zhaohui

first: Xin

last: Li

first: Yan

last: Lu

first: Ran

first: Xi-miao

first: Zheng

first: Lei

last: Yin

first: Ning


title: Effect of ICSI on DNA methylation in germline stem cells.

first: Takashi

type: Methylation profiling by high throughput sequencing

summary: To investigate the effect of ICSI in germ cells,  we performed RRBS of germline stem cells established from ICSI-derived mice.

overall_design: Comparative DNA methylation profiling analysis of RRBS for germline stem cells of  ICSI-derived mice.

first: Yusuke


title: Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [bulkRNAseq_ATRT_cellLines]

status: Public on Sep 20 2023

city: Paris

first: Mamy

middle: Jean de Dieu

last: ANDRIANTERANAGNA

state: Ile de France

address: 26 rue d'Ulm

department: Centre de Recherche

institute: Institut Curie

summary: Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosisand the precise anatomic origin of brain tumors in the Rosa26; Cre-ERT2::Smarcb1flox/flox model. This cross-species analysis points to an extra-cerebral origin for MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway.

overall_design:
To try to understand how NOTCH pathway could actually participate to cell reprogrammation, we treated two SHH ATRT cell lines (CHLA-02, and IC-032) with DAPT, a gamma secretase inhibitor.
3 independant samples of CHLA-02-ATRT and IC-032 cells were treated with DMSO or DAPT at 10 µM for 7 days.
Experiment was designed with 3 replicates for each condition and each cell line.

first: Maria-Jesus

last: Lobon-Iglesias

last: Andrianteranagna

first: Zhi-Yan

last: Han

first: Céline

last: Chauvin

first: Sandrina

last: Turczynski

first: Rachida

last: Bouarich

first: Nicolas

last: Servant

first: Franck

last: Bourdeaut


title: Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [bulkRNAseq_mouseRT_R26]

overall_design: 16 primary RT samples  from 16 different engineered Smarcb1fl/fl;R26-CreERT2 mouse (Han et al., 2016) were collected and analysed by RNA sequencing.

first: Maria

first: Magali

last: Frah


title: Single-cell epigenetic, transcriptional, and protein states of HIV-1-infected cells

city: New Haven

first: Yulong

last: Wei

state: CT

address: 295 Congress Avenue

department: Microbial Pathogenesis

institute: Yale University


title: Single-cell epigenetic, transcriptional, and protein states of HIV-1-infected cells [scATAC-seq]

summary: The heterogeneity and rarity of HIV-1-infected cells hampers effective cure strategies. We used single-cell DOGMA-seq to simultaneously capture transcription factor accessibility, transcriptome, 156 surface proteins, HIV-1 DNA, and HIV-1 RNA from six HIV-1+ individuals during viremia and after suppressive antiretroviral therapy. We identified 252 transcriptionally inactive (HIV-1 DNA+ RNA–) and 270 transcriptionally active (HIV-1 RNA+) HIV-1-infected cells from 82,549 memory CD4+ T cells. We identified increased transcription factor accessibility in HIV-1 DNA+ RNA– cells (RORC) and HIV-1 RNA+ cells (IRF and AP-1), in addition to CNC and MAF in both. Both HIV-1 DNA+ RNA– and HIV-1 RNA+ cells upregulate IKZF3 (Aiolos) that correlates with proliferation of HIV-1-infected cells. We revealed that the heterogeneous HIV-1-infected T cells comprise four distinct immune programs driven by epigenetic regulators – IRF-activation, Eomes-cytotoxic effector, AP-1-migration, and cell death. Our study revealed the single-cell epigenetic, transcriptional, and protein states of transcriptionally inactive and active HIV-1-infected cells.

overall_design: Paired PBMC samples from 6 HIV-1-infected individuals from the Sabes cohort during viremia and after viral suppression and PBMC samples from 4 uninfected controls were processed for DOGMA-seq. Memory CD4+ T cells were isolated from dead-cell removed PBMC by negative selection. Purified memory CD4+ T cells from participants were each stained with uniquely barcoded TotalSeq-A hashing antibodies and pooled. Cells were stained with a panel of 154 cell surface proteins and 9 isotype controls included in TotalSeq-A Human Universal Cocktail. After staining, cells were permeabilized with 0.01% digitonin. Cells were then loaded into the 10x Genomics Chromium Controller for DOGMA-seq (3’ Single Cell 10x Multiome (ATAC + GEX) with feature barcoding). This resulted in libraries for the single cell epigenome, transcriptome, and surface proteome. Six DOGMA-seq runs from virally suppressed HIV-1 infection samples (YW1 – YW6); three DOGMA-seq runs from viremic HIV-1 infection (YW8 – YW10); one DOGMA-seq runs from uninfected controls (HD1). Supplementary file “Participant Hashtags” contains the hashtag IDs for each participant in each pooled samples.

first: Timothy

middle: C

last: Davenport

first: Jack

middle: A

last: Collora

first: Haocong

middle: K

last: Ma

first: Delia

last: Pinto-Santini

first: Javier

last: Lama

first: Ricardo

last: Alfaro

first: Ann

last: Duerr

first: Ya-Chi

last: Ho


title: FGFR3 alterations in bladder cancer stimulate serine synthesis to induce immune-inert macrophages that suppress T-cell recruitment and activation

status: Public on Sep 18 2023

city: Guangzhou

first: Sebastian

last: Ouyang

address: 107 Yanjiangxi Road

department: Dept. of Urology

institute: Sun Yat-sen Memorial Hospital

summary: Metabolic reprogramming of bladder cancer cells driven by mutant FGFR3 increases serine synthesis that suppresses macrophage immunostimulatory functions to generate an immunosuppressive tumor microenvironment, which can be overcome by targeting PI3K.

overall_design: WT and mFgfr3 MB49 cancer cells were inoculated in the C57/BL6 mice, and tumors were harvested for scRNA-seq

first: Yi

first: Ziwei

last: Ou

first: Wenlong

last: Zhong

first: Tianxin

last: Lin

first: Jian

last: Huang


title: Single-cell epigenetic, transcriptional, and protein states of HIV-1-infected cells [scRNA-seq]


title: Osteoarthritis is caused by the loss of chondrogenic stem/progenitor cells at the articular surface.

status: Public on Sep 19 2023

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

institute: The University of Adelaide

summary: Osteoarthritis (OA), which carries an enormous disease burden across the world, is characterised by irreversible degeneration of articular cartilage (AC), and subsequently of bone. The cellular cause of OA is unknown. Here, using lineage tracing in mice, we show that the BMP-antagonist Gremlin 1 (Grem1) marks a novel chondrogenic stem/progenitor (CSP) cell population in the articular surface that generates joint cartilage and subchondral bone during development and adulthood. Notably, this CSP population is depleted when OA-inducing injury is created in two independent models, and with age. OA is also induced by toxin mediated ablation of Grem1 CSP cells in young mice. Transcriptomic analysis and functional modelling in mice revealed articular surface Grem1 CSP cells are dependent on Foxo1; ablation of Foxo1 in Grem1 cells also led to early OA. This analysis identified FGFR3 signalling as a therapeutic target, and injection of its activator, FGF18, caused proliferation of Grem1 CSP cells (but not hypertrophic AC), increased cartilage thickness, and reduced OA pathology. We propose that OA arises from the loss of CSP cells at the articular surface secondary to an imbalance in stem/progenitor cell homeostasis and present a new stem cell progenitor population as a locus for OA therapy.

overall_design: Mice with Grem1-TdT and Lepr-TdT mice were grown to 5-6 weeks of age, and inducted with tamoxifen chow for two weeks. Knee cartileage tissues were processed, sorted, and profiled with single cell transcriptomics

first: Jia

middle: Q

last: Ng

first: Toghrul

last: Jafarov

first: Christopher

last: Little

last: Wang

first: David

last: Haynes

first: Danijela

last: Menicanin

first: Stan

last: Gronthos

first: Daniel

middle: L

last: Worthley

first: Siddhartha

last: Mukherjee


title: N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

summary: Most eukaryotic proteins are N-terminally acetylated, but the functional impact on a global scale has remained obscure. Using genome-wide CRISPR knockout screens in human cells, we reveal a strong genetic dependency between a major N-terminal acetyltransferase and specific ubiquitin ligases. Biochemical analyses uncover that both the ubiquitin ligase complex UBR4-KCMF1 and the acetyltransferase NatC recognize proteins bearing an unacetylated N-terminal methionine followed by a hydrophobic residue. NatC KO-induced protein degradation and phenotypes are reversed by UBR knockdown, demonstrating the central cellular role of this interplay. We reveal that loss of Drosophila NatC is associated with male sterility, reduced longevity, and age-dependent loss of motility due to developmental muscle defects. Remarkably, muscle-specific overexpression of UbcE2M, one of the proteins targeted for NatC KO mediated degradation, suppresses defects of NatC deletion. In conclusion, NatC-mediated N-terminal acetylation acts as a protective mechanism against protein degradation, which is relevant for increased longevity and motility.

overall_design: We performed genome-wide CRISPR knockout screens in human HAP1 cells to better understand genetic dependency of the N-terminal acetyltransferase NatC.

first: Sylvia

last: Varland

first: Thomas

last: Arnesen

first: Charles

last: Boone


title: The role of MDM4 in tumors

status: Public on Sep 17 2023

city: Fuzhou, Fujian, China

first: Jie

last: Liu

address: Shengli Clinical Medical College of Fujian Medical University, Department of Endoscopy, Fujian Provincial Hospital, Fuzhou, China

institute: Fujian Medical University

summary: We transfected GFP and MDM4 into colon cancer cell SW480, and performed transcriptomic analysis.

overall_design: Transcriptomic sequencing was conducted to investigate the effect of MDM4 on transcript levels in colon cancer.