title: Dual roles of the Arabidopsis PEAT complex in histone H2A deubiquitination and H4K5 acetylation [RNA-seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. We found that UBP5, an ubiquitin-specific protease, interacts with a previously identified PEAT (PWWP-EPCR-ARID-TRB) complex to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. Moreover, our results indicated that the histone acetyltransferases HAM1 and HAM2 (HAM1/2), catalytic subunits of the NuA4 histone acetyltransferase complex, are also part of the PEAT complex at PEAT target genomic loci. Within the PEAT complex, the PWWP components (PWWP1, PWWP2 and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. This study identifies previously unknown regulators of H2A deubiquitination and H4K5 acetylation and illustrates how these processes collaborate at the whole-genome level.

overall_design: Examination of the mRNA expression of 12-day-old wild type and five mutants in Arabidopsis

first: Xin-Jian


title: The impact of the SCFA crotonate on Candida albicans and macrophage transcriptomes

status: Public on Oct 02 2023

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

type: Expression profiling by high throughput sequencing

summary: The effects of the SCFA crotonate on fungal and host transcriptomes were addressed, following infection of mouse bone marrow-derived macrophages(BMDMs) with Candida albicans.

overall_design: Macrophages were challenged with Candida albicans and fungal and macrophage samples taken at 1 and 3 h following the challenge.

first: Jiyoti

last: Verma

first: Ana

last: Traven

first: Tim

last: Tucey


title: Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon expression and impairs the infectivity of live-attenuated rotavirus vaccines [hALI_Ch]

city: St. Louis

first: L.

middle: David

last: Sibley

state: MO

address: 425 S. Euclid Ave

department: Molecular Microbiology

country: USA

institute: Washington University School of Medicine

summary:
We developed a stem cell-derived culture system for C. hominis using human enterocytes differentiated under air-liquid interface (ALI) conditions. Human ALI (hALI) cultures supported robust growth and complete development of C. hominis in vitro including all life cycle stages.
C. hominis infection induced a strong interferon response from enterocytes, likely driven by an endogenous dsRNA virus in the parasite. Prior infection with Cryptosporidium induced type III IFN secretion and consequently blunted infection with Rotavirus, suggesting such co-infections may alter vaccine efficacy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hALI infected with C. hominis for 24h or without infection.

first: Valentin

last: Greigert

first: Iti

last: Saraav

first: L

middle: D


title: Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon expression and impairs the infectivity of live-attenuated rotavirus vaccines.

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

overall_design: Refer to individual Series


title: Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis

city: Solna

first: Kristiina

last: Tammimies

address: Visiongatan 4

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

summary: Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level. HNRNPU downregulation leads to altered neurogenesis and an increased fraction of neural progenitors in the maturing neuronal population. We conclude that, HNRNPU locus is involved in delayed commitment of neural progenitors to neuronal maturation in cell types with hindbrain profile.

overall_design: Two different HNRNPU locus deficient hindbrain neuronal culture models were compared with control samples (3-5 technical replicates). ***The submitters are not legally permitted to submit the raw data to GEO or a restricted-access database such as dbGaP or EGA. Therefore, raw data is not provided.

first: Francesca

last: Mastropasqua

first: Marika

last: Oksanen

first: Cristina

last: Soldini

first: Shemim

last: Alatar

first: Abishek

last: Arora

first: Roberto

last: Ballarino

first: Maya

last: Molinari

first: Federico

last: Agostini

first: Axel

last: Poulet

first: Michelle

last: Watts

first: Ielyzaveta

last: Rabkina

first: Martin

last: Becker

first: Danyang

last: Li

first: Britt-Marie

last: Anderlid

first: Johan

last: Isaksson

first: Karl

last: Lundin Remnelius

first: Mohsen

last: Moslem

first: Yannick

last: Jacob

first: Anna

last: Falk

first: Nicola

last: Crosetto

first: Magda

last: Bienko

first: Emanuela

last: Santini

first: Anders

last: Borgkvist

first: Sven

last: Bölte


title: Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon expression and impairs the infectivity of live-attenuated rotavirus vaccines [hALI_Cp]

first: L.

last: Sibley

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hALI infected with C. parvum for 24h, or without infection.

first: Valentin

last: Greigert

first: Iti

last: Saraav

first: L


title: SKP2 knockout in Rb1/p53 deficient transgenic mouse models of osteosarcoma induces macrophage infiltration and drives transcription of genes with favorable prognosis in patients

city: The Bronx

first: Alexander

last: Ferrena

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: To study SKP2 in osteosarcoma, we generated a Skp2 KO line and a Skp2 intact line of transgenic OS mouse models: germline Skp2 knockout (“TKO”: Osx1-Cre;Rb1lox/lox;p53lox/lox;SKP2) versus Skp2 intact (“DKO”: Osx1-Cre;Rb1lox/lox;p53lox/lox). We then performed bulk RNAseq of the SKP2 KO vs SKP2 intact OS.

overall_design: Comparative transcriptomics for SKP2 KO versus SKP2 intact transgenic osteosarcoma tumor models

first: Jichuan

last: Wang

first: Bang

last: Hoang

first: Deyou

last: Zheng


title: Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics

status: Public on Oct 03 2023

city: Cambridge

first: Andrew

middle: James Charles

last: Russell

address: 415 Main St

institute: Broad Institute of MIT and Harvard

summary: Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed. Missing from these measurements, however, is the ability to routinely and easily spatially localise these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are ‘tagged’ with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as input into a wide variety of single-nucleus profiling assays. We used Slide-tags to profile two different stages of development in the mouse brain.

overall_design: Slide-tags was used to spatially barcode nuclei from 20-micron thick fresh frozen tissue sections. These spatially barcoded nuclei were then used as input for 10x Genomics Chromium v3.1 snRNA-seq.

first: Fei

last: Chen

first: Evan

last: Macosko

first: Jackson

last: Weir

first: Naeem

last: Nadaf


title: Gene expression profile at single nuclei level of brain tissues from diabetic mice exposed to acute or recurrent hypoglycemia.

city: Lausanne

first: Flavia

last: Marzetta

address: Quartier Sorge - Batiment Genopode

country: Switzerland

institute: Swiss Institute of Bioinformatics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The brain is an important controller of glucose homeostasis and mediates counterregulatory responses to hypoglycemia. We used single-nuclei transcriptomics to study the mechanisms of defective hypoglycaemia counter-regulation in brain in a model of diabetic mice exposed to acute or recurrent hypoglycemia.

overall_design: Single nuclei were isolated from hypothalamus and cortex tissues of diabetic mice subjected to recurrent (RH) or acute hypoglycemia (AH) and used to generate transcriptome profiles.

first: Judit

last: Castillo Armengol

first: Ana

last: Rodriguez Sanchez-Archidona

first: Bernard

last: Thorens


title: Effector Memory T cells induce DC-intrinsic DNA damage and a non-canonical STING pathway during innate inflammation [ATAC]

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: Ohio

address: 250 Albert Sabin Way

department: Immunology

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: A breach in tolerance to self-antigens induces expansion of autoreactive T cells, ultimately leading to autoimmune inflammation. While autoreactive T cells are principal drivers of autoimmunity, tissue pathology is alternatively driven by innate cytokines, indicating that autoreactive T cells can induce innate inflammation. This study has led to the discovery that effector memory T (Tem) cells trigger double stranded breaks via mitochondrial ROS production in interacting DCs. Consequently, initiation of the DNA damage response leads to activation of a cGAS-independent, STING-TRAF6-NFkB signaling axis. STING deficient DCs display significant defects in transcriptional induction and functional production of IL-1b and IL-6 following their interaction with Tem cells, both in vitro and in vivo. The discovery of Tem induced innate inflammation through DNA damage and a non-canonical STING-mediated NFkB activation presents this pathway as a potential target to alleviate T cell driven autoimmune inflammation.

overall_design: WT or STING golden ticket BMDCs were co-cultured with in vitro generated effector memory T (Tem) cells + anti-CD3 for 1 hour. BMDCs were then sorted away from Tem cells and submitted for sequencing. Control samples include WT and STING golden ticket sorted BMDCs previously cultured with Tem cells - anti-CD3 (unstimulated).

first: Hannah

middle: E

last: Meibers

last: VonHandorf

first: Omer

last: Donmez

first: Matthew

last: Weirauch


title: TMIGD2 is a leukemic stem cell-specific surface marker in human acute myeloid leukemia

city: bronx

first: Hao

last: Wang

address: 1300 morris park ave, Forch 405

summary:
To comprehensibly understand the genes and pathways associated with TMIGD2 expression in CD34-expressing leukemia cells,
RNA-seq was conducted on FACS-purified CD34+TMIGD2+ and CD34+TMIGD2- subfractions of six primary AML specimens.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD34+TMIGD2+ and CD34+TMIGD2- primary AML cells.

first: Wang

last: Hao

first: Galbo

last: Phillip

first: Zheng

last: Deyou

first: Zang

last: Xingxing


title: RNA-Seq of X-ray irradiated planarians

city: Sagamihara

first: Makoto

last: Kashima

state: Kanagawa

address: 5-1-16, Fuchinobe

country: Japan

institute: Aoyama Gakuinn University

summary: Time-course RNA-Seq of X-ray irradiated planarians Dugesia japonica.

overall_design: Irradaited planarians were sampled at 0 (without irradiation), 1, 3, 5, and 7 days post irradiation with three biological replicates.

first: Yuki

last: Sato


title: Mitochondrial gene expression is required for platelet function and blood clotting

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

summary: Platelets are anucleate blood cells that contain mitochondria, that regulate blood clotting in response to injury. Mitochondria contain their own gene expression machinery which relies on nuclear encoded factors for the biogenesis of the oxidative phosphorylation (OXPHOS) system to produce energy, ions and metabolites required for thrombosis. The autonomy of the mitochondrial gene expression machinery from the nucleus is not known and platelets provide a valuable model to understand the importance of mitochondrial gene expression in anucleate cells. We generated three different platelet-specific conditional knockout mouse models, each lacking a gene that is essential for mitochondrial gene expression at the level of RNA processing, stability and translation (Elac2Pf4∆/Pf4∆, Ptcd1Pf4∆/Pf4 and Mtif3Pf4∆/Pf4∆). Loss of ELAC2, PTCD1 or MTIF3, leads to increased megakaryocyte ploidy, elevated circulating levels of reticulated platelets, thrombocytopenia and consequent extended bleeding time. Loss of ELAC2, PTCD1 and MTIF3 reduced agonist induced platelet activation. Transcriptomic and proteomic analyses showed that mitochondrial gene expression and protein synthesis facilitate fibrinolysis, haemostasis and blood coagulation in response to injury.

overall_design: RNA sequencing and differential gene expression performed on megakaryocytes, resting platelets and activated platelets in PTCD1, MTIF3 and ELAC2 knockout and wild type mice.

first: Tara

middle: R

last: Richman

first: Judith

middle: A

last: Ermer

first: Jessica

last: Baker

first: Benjamin

last: Kile

last: Lindon

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: Single-cell RNA sequencing of human prostate basal epithelial cells reveals zone-specific cellular populations and gene expression signatures

city: Chicago

first: Donald

last: Vander Griend

state: IL

address: 909 S. Wolcott Ave, COMRB Room 5051

department: Pathology

institute: The University of Illinois at Chicago

summary: Prostatic basal cells have been implicated in differentiation and proliferation during prostate development and regeneration; however, the contribution of zonal variation and the critical role of basal cells in prostatic disease etiology is not well understood. Using single-cell RNA sequencing of primary prostate epithelial cultures, we elucidated organ-specific, zone-specific, and cluster-specific gene expression differences in basal cells isolated from human prostate and seminal vesicle (SV).

overall_design: scRNA-seq was performed on 8 biopsies from a single patient: 2 replicates of biopsies from the prostatic central zone (CZ), peripheral zone (PZ), and transition zone (TZ) plus seminal vesicle (SV).

first: Jordan

last: Vellky

first: Jenny

last: Drnevich


title: MicroRNA-92b in the skeletal muscle regulates exercise capacity via modulation of glucose metabolism

status: Public on Oct 01 2023

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

country: China

institute: shenzhen people's hospital

summary: Background: Exercise mimetics is a proposed class of therapeutics that specifically mimics or enhances the therapeutic effects of exercise. Muscle glycogen and lactate extrusion are critical for physical performance. The mechanism by which glycogen and lactate metabolism are manipulated during exercise remains unclear. This study aimed to assess the effect of miR-92b on the upregulation of exercise training-induced physical performance.  Methods: Adeno-associated virus (AAV)-mediated skeletal muscle miR-92b overexpression in C57BLKS/J mice, and global knockout of miR-92b mice were used to explore the function of miR-92b in glycogen and lactate metabolism in skeletal muscle. AAV-mediated UGP2 or MCT4 knockdown in WT or miR-92 knockout mice was used to confirm whether miR-92b regulates glycogen and lactate metabolism in skeletal muscle through UGP2 and MCT4. Body weight, muscle weight, grip strength, running time and distance to exhaustion, and muscle histology were assessed. The expression levels of muscle mass-related and functionrelated proteins were analysed by immunoblotting or immunostaining. Results: Global knockout of miR-92b resulted in normal body weight and insulin sensitivity, but higher glycogen content before exercise exhaustion (0.8538 ± 0.0417 vs 1.043 ± 0.040, **P=0.0087), lower lactate levels after exercise exhaustion (4.133 ± 0.2589 vs 3.207 ± 0.2511, *P=0.0279), and better exercise capacity (running distance to exhaustion, 3616 ± 86.71 vs 4231 ± 90.29, ***P=0.0006; running time to exhaustion, 186.8 ± 8.027 vs 220.8 ± 3.156, **P=0.0028), as compared to those observed in the control mice. Mice skeletal muscle overexpressing miR-92b (both miR-92b-3p and miR-92b-5p) displayed lower glycogen content before exercise exhaustion (0.6318 ± 0.0231 vs 0.535 ± 0.0194, **P=0.0094), and higher lactate accumulation after exercise exhaustion (4.5 ± 0.2394 vs 5.467 ± 0.1892, *P=0.01), and poorer exercise capacity (running distance to exhaustion, 4005 ± 81.65 vs 3228 ± 149.8, ***P＜0.0001; running time to exhaustion, 225.5 ± 7.689 vs 163 ± 6.476, **P=0.001). Mechanistic analysis revealed that miR-92b-3p targets UDP-glucose pyrophosphorylase 2 (UGP2) expression to inhibit glycogen synthesis, while miR-92b-5p represses lactate extrusion by directly target monocarboxylate transporter 4 (MCT4). Knockdown of UGP2 and MCT4 reversed the effects observed in the absence of miR-92b in vivo.  Conclusions: This study revealed regulatory pathways, including miR-92b-3p/UGP2/glycogen synthesis and miR-92b-5p/MCT4/lactate extrusion, which could be targeted to control exercise capacity.

first: Guangyan

first: Xinyu

last: Wang


title: Stem cell-derived human liver organoids to model the progression of inflammatory and fibrotic injury in non-alcoholic fatty liver disease

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

summary: Chronic liver injury promotes fibrosis, which can progress to cirrhosis, a major cause of morbidity and mortality worldwide. Resolving the cell-type-specific transcriptional changes orchestrating this transformation remains challenging. Recent advances in differentiation protocols allow the generation of multi-lineage human liver organoids (HLOs) from human pluripotent stem cells (hPSCs), providing a new model system to study evolving liver injury. We differentiated hPSCs into HLOs and defined optimal 3D culture conditions for liver injury induction. We modeled steatohepatitis through treatment with palmitic acid (PA) and fibrotic injury through treatment with transforming growth factor beta 1 (TGF-β1). For each injury type, we evaluated the development of fibrosis and inflammation by monitoring changes in morphology, gene expression, and histology. We then performed single-cell RNA-sequencing (scRNA-seq) to investigate cell-type diversity in healthy organoids at different time-points and to understand how TGF-β1- and PA-mediated injury affects each cell type. We observed transcriptional response signatures in injured HLOs to be both cell-type- and injury-specific. TGF-β1 treatment expanded hepatic stellate cell (HSC)-like populations and remodeled cell-cycle patterning. Gene set scoring revealed increased fibroblast activity with TGF-β1 treatment, while PA treatment was associated with inflammatory activity. Differential gene expression analysis at the subpopulation level showed induced profibrotic and extracellular matrix-remodeling pathways with TGF-β1 and non-alcoholic fatty liver disease (NAFLD) expression signatures with PA treatment. Evaluation of receptor and ligand expression defined hepatocyte-, cholangiocyte-, and HSC-like cell-cell interactions induced upon TGF-β1 treatment, an effect not observed with PA treatment. Tracing the changes at receptor-ligand pair resolution revealed specific COL1A1-Integrin complex interactions with TGF-β1 treatment and inflammation-specific interactions including CXCR7 and HLA-C with PA treatment. Treatment of HLOs with PA and TGF-β1 also demonstrated a sequential increase in expression of gene sets that predict clinical disease progression in non-alcoholic steatohepatitis (NASH). Our results demonstrate the applicability of hPSC-derived HLOs as a dynamic in vitro 3D human liver model system for the study of fibrotic and inflammatory liver injury.

overall_design: hPSC-derived HLOs cultured on an orbital shaker (OS) were stimulated with TGF-β1 (10 ng/ml) or PA (500 µM) for five days and subjected to scRNAseq at day 25. Additionally, naive (untreated) HLOs cultured on ultra-low attachment (ULA) plates were analyzed by scRNAseq at day 21 and day 34 of the differentiation protocol.

first: Anja

last: Hess

last: Gentile

first: Raza

middle: U

last: Rahman

middle: C


title: Loss of Feedback Regulation between FAM3B and Androgen Receptor Driving Prostate Cancer Progression

city: New Orleans

first: Yan

last: Dong

address: 1700 Tulane Ave

institute: Tulane University

summary: TMPRSS2-ERG gene fusion is one of the most frequent genetic alterations in prostate cancer (PC). Through a systematical survey of the loss of interstitial genes and patient outcomes, we nominated FAM3B as the top-ranked interstitial genes whose loss is associated with a poor prognosis. Using cultured cells, patient- and cell-line-derived xenograft models in gonad-intact or castrated host, and genetically engineered mouse models with FAM3B overexpression, knockdown, or knockout, we defined a driver role of FAM3B loss in prostate cancer progression. By performing RNA-seq analysis in two pre-clinical models with ectopic FAM3B expression or FAM3B knockdown, we identified that the androgen response pathway was commonly modulated by FAM3B in these two models. Further validation studies showed that FAM3B inhibites AR activity.

overall_design: FAM3B-inducible-expressing C4-2 cells and the control cells were treated with 200 ng/ml doxycycline for 48 hours. Total RNA was isolated from these cells and castration-resistant control-shRNA- or FAM3B-shRNA-expressing VCaP tumors using the TRIzol reagent. RNA integrity was assessed using an Agilent Bioanalyzer. The RNA samples from C4-2 cells were sent to Novogene for polyA-selected, 150-base paired-end RNA sequencing on an Illumina platform, and those from the VCaP tumors were sent to the Beijing Genomics Institute for polyA-selected, 100-base paired-end stranded RNA sequencing on the DNBSEQ platform.

first: Tianfang

last: Ma


title: Gene expression analysis of sorted murine B16-F10 melanoma tumor derived endothelial cells

city: Leuven

first: Patrizia

last: Agostinis

address: Herestraat 49 - box 802

department: Cellular and Molecular Medicine

country: Belgium

institute: VIB-KU Leuven

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 8,644 genes in 50 non-small cell lung cancer (NSCLC) cases, which had been consecutively operated on within a defined short period of ti

overall_design: 250,000 B16-F10 melanoma cells were subcutaneously implanted in the right flank of C57B6 mice (WT and ATG5-BECKO). Tumors were digested 18 days post grafting using collagenase digestion. From digested tumors, immune cells were depleted by Miltenyi magnetic beads labelled with anti CD45 and subsequently endotheilal cells were enriched by Miltentyi magantic beads labelled with anti CD31. The cell pellets obtained after enrichment of CD31+ endothelial cells was stained with fluroscently labelled antiobodies and pure endothelial cells were sorted as Live CD45-CD31+ cells.

first: Agostinis

last: Patrizia


title: The role of TP63 fusion in mouse lymphomagenesis

city: BOSTON

first: Gongwei

last: Wu

address: 450 Brookline Ave, SM1022, Dana-Farber Cancer Institute

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Patients with lymphoma harboring TP63 rearrangements have aggressive clinical course and dismal prognosis with no target therapy available. Thus, there is an urgent need to elucidate the molecular mechanisms and to develop novel therapeutic options for these patients. We then generated a TBL1XR1::TP63 fusion knockin trangenic mouse model and crossed with CD2/iCre mouse. This project is to study the role and function of TP63 fusion in mouse lymphomagenesis.

overall_design: Four mouse lymphoma samples were performed conventional RNAseq.

first: Wu

last: Gongwei

first: Tayla

middle: B

last: Heavican-Foral


title: Effect of TMIGD2 knockdown on gene expression in HEL cell line

first: Hao

summary: To investigate the effect of TMIGD2 on transcriptional functions in human AML cell line, we performed gene expression profiling analysis using data obtained from RNA-seq of HEL cells upon TMIGD2 knockdown.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for shCtrl versus shTMIGD2 HEL cells.

first: Phillip

last: Galbo

first: Deyou

last: Zheng

first: Xingxing

last: Zang


title: The Rogdi Knockout Mouse is a Model for Kohlschütter–Tönz Syndrome

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

country: France

institute: IGBMC/PHENOMIN-ICS

summary: Kohlschütter–Tönz syndrome (KTS) is a rare autosomal recessive disorder characterized by severe intellectual disability, early-onset epileptic seizures, and amelogenesis imperfecta. Loss of ROGDI expression likely produces these severe patient defects. Here we present a novel Rogdi mutant mouse demonstrating Rogdi-/- loss of function recapitulates most KTS patient symptoms. Mutants displayed pronounced pentylenetetrazol-induced seizures confirming epilepsy susceptibility. Spontaneous locomotion and circadian activity tests demonstrate Rogdi mutant hyperactivity mirroring patient spasticity. Object recognition impairment indicates memory deficits. Rogdi-/- mutant enamel was markedly less mature. Scanning electron microscopy confirmed its hypomineralized/hypomature crystallization, as well as its low mineral content. Transcriptomic RNA sequencing of postnatal day 5 lower incisors showed downregulated enamel matrix proteins Enam, Amelx, and Ambn. Enamel crystallization is highly pH-dependent as an acidic pH is required to accelerate matrix protein degradation and to promote mineralization. Rogdi-/- teeth exhibit no signs of cyclic dental acidification. Additionally, expression changes in Wdr72, Slc9a3r2, and Atp6v0c were identified as potential contributors to these tooth acidification abnormalities. These proteins interact through the acidifying V-ATPase complex.  Here we present the Rogdi-/- mutant as a novel model deciphering partially KTS pathophysiology. Rogdi-/- mutant defects in acidification might explain the unusual combination of enamel and neurological rare disease symptoms.

overall_design: To investigate the role of ROGDI, A mouse mutant model of Rogdi inactivation was generated at the Institut Clinique de la Souris (ICS), Illkirch, France. independent lower incisors of PN5 male Rogdi mutants and WT controls were analyzed by high throughput RNA sequencing (RNA-seq). Bioinformatic analysis were performed selecting significant genes using p-value < 0.05 and absolute value of log2 Fold-Change > 0.3.

first: Alexandra

last: Jimenez-Armijo

first: Agnès

last: Bloch-Zupan


title: RNA-sequencing (RNAseq) of human small airway epithelial cells treated with neutrophil extracellular traps

city: GuangZhou

first: Zhongji

address: No.151 Yanjiang West Road, Yuexiu District, Guangzhou City, Guangdong Province

department: Pediatrics

institute: the First Affiliated Hospital of Guangzhou Medical University

summary: Previous studies have shown that NETs expression levels are increased in patients or mouse models of several airway diseases, such as asthma, COPD, and cystic fibrosis. However, little is known about the effects of NETs on airway epithelial cells. In this study, we used transcriptome sequencing and bioinformatics analysis to investigate the role of NETs in small airway epithelial cells.  This study advances our understanding of the effects of NETs on airway epithelial cells and provides valuable insights into the pathogenesis of airway diseases. Our findings may contribute to the development of new therapeutic strategies for airway diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NETs treated-SAECs and untreated SAECs

first: Dehui

last: Chen

first: Xiaowen


title: Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition [bulkRNA-seq]

city: Bethesda

first: Dawn

last: Watkins-Chow

state: Maryland

address: 9000 Rockville Pike

institute: NIH

summary: Comparative gene expression profiling analysis of bulk RNA-seq data for control 501mel cells compared to transient knockdown with two different TBX3 siRNAs

overall_design: 501mel human melanoma cells were transfected with either siCtrl or siTBX3 for 24h to contrast global gene expression differences in control versus knockdown. Three biological replicates of each condition were harvested for RNA extraction and bulk RNA sequencing

first: Stacie

middle: K

last: Loftus

first: Matthew

middle: H

last: Berns

first: William

last: Pavan


title: A common graft formation pathway in Norway spruce and Arabidopsis thaliana identifies the PAT gene family as conserved regulators of tissue attachment and wound healing [RNAseq: Hornome-Treatment-samples]

city: Uppsala

first: Ai

last: Zhang

state: Uppsala

address: Biocenter, Almas allé 5

department: Plant Biology

institute: SLU

summary: The widespread use of plant grafting has enabled different plants to join and combine their best properties to improve stress tolerance, growth and yields. Grafting is commonly performed between closely related eudicots or gymnosperms where mechanisms permit tissue fusion yet limit success as plants become unrelated. To investigate these aspects, we developed a micrografting method using young conifer tree seedlings that enabled divergent conifer members to successfully graft. Conifer grafts showed rapid connection of phloem and xylem at the junction, while a genome-wide transcriptome analysis of the Picea abies (Norway spruce) healing junction revealed differential expression of thousands of genes including those related to auxin response and cell wall biogenesis. We compared these genes to those induced during Arabidopsis thaliana graft healing and found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis revealed that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a central hub during Picea grafting and was also induced during Arabidopsis grafting. Arabidopsis mutants lacking PATs failed to attach tissues or successfully graft, while complementing Arabidopsis PAT mutants with the Picea abies PAT1 homolog could rescue tissue attachment and enhance callus formation. Together, our data demonstrate a competency for young tissues to graft to distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration in eudicots and gymnosperms.

overall_design: Two-week-old spruce seedlings were selected for hormonal treatment. Spruce seedlings were treated with either BAP, IAA, or a combination of BAP and IAA hormones. The hormone concentrations were BAP 135 mM, IAA 50 mM, BAP 135 mM + IAA 50 mM. 20 μl of hormone dissolved in 70% ethanol was quickly mixed with a small amount of lanolin. The hormone lanolin paste was then applied to the middle hypocotyl region of the seedlings, approximately 1.5 cm below the needles. The treated area (8-10 mm in length) was wrapped in aluminum foil.

first: Ming

last: Feng

first: Van

last: Nguyen

first: Anchal

last: Bisht

first: Curt

last: Almqvist

first: Lieven

last: De Veylder

first: Annelie

last: Carlsbecker

first: Charles

middle: W

last: Melynk


title: A common graft formation pathway in Norway spruce and Arabidopsis thaliana identifies the PAT gene family as conserved regulators of tissue attachment and wound healing [RNAseq: Grafted-samples]

overall_design: Graft junction libraries: Samples were collected from both ungrafted (intact) and grafted Picea abies above and below the graft junction at 0, 1, 3, 7,14 and 28 days after grafting. Approximately 1 mm of tissues from scions or rootstocks or 2 mm from intact plants.


title: Sexually dimorphic impact of constitutive androstane receptor activation in mouse liver

city: Toulouse

first: Sandrine

last: Ellero-Simatos

address: 180 chemin de Tournefeuille

institute: INRAe

summary: The constitutive androstane receptor (CAR) is a nuclear receptor able to recognize a large panel of drugs leading to the modulation of the expression of its target genes involved in xenobiotic detoxication and energy metabolism. CAR hepatic activity is thought to be higher in women than in men, but its target genes and metabolic role in female mice have never been thoroughly studied. Here, we investigated the liver gene expression in Car+/+ vs Car-/- male and female C57Bl6/J mice treated with the CAR-specific agonist, 1,4-bis[2-(3,5-dichloropyridyloxy)] benzene (TPOBOP), or with Corn Oil

overall_design: Car+/+ and Car-/- littermate mice were separated by sex and genotype at 4 weeks and randomly allocated to the different experimental groups: Male Car+/+ Corn Oil (M Car+/+ CO, n=6), Male Car+/+ TCPOBOP  (M Car+/+ TCPOBOP, n=6), Male Car-/- Corn Oil (M Car-/- CO, n=6), Male Car-/- TCPOBOP  (M Car-/- TCPOBOP, n=6), Female Car+/+ Corn Oil (F Car+/+ CO, n=6), Female Car+/+ TCPOBOP  (F Car+/+ TCPOBOP, n=6), Female Car-/- Corn Oil (F Car-/- CO, n=6), Female Car-/- TCPOBOP  (F Car-/- TCPOBOP, n=6) (one cage per group). Mice included in TCPOBOP groups received a daily intraperitoneal injection of 1,4-bis[2-(3,5-dichloro pyridyloxy)]Benzene (TCPOBOP, Sigma Aldrich) diluted in corn oil at 3mg/kg for 4 days while CO mice received corn oil only (Sigma Aldrich). At ZT16 (6 hours after the last TCPOBOP injection), mice were anesthetized with Isoflurane and Xylasine (2%, 2mg/kg) and liver samples were collected.

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition

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: TGF-β regulated RNA-binding proteins control endothelial function and mesenchymal transition in cardiac endothelial cells [RNA-seq]

city: Mannheim

first: Joerg

last: Heineke

address: Ludolf-Krehlstr. 7-11 Tridomus B

department: Cardiovascular Physiology

country: Germany

institute: Medical Faculty of Mannheim Heidelberg University

summary: Endothelial to mesenchymal transition (EndoMT) plays a key role in heart development, but is also implicated in cardiovascular diseases in postnatal life. While the roles of TGF-β as inducer of EndoMT on the transcriptional level are well characterised, its post-transcriptional regulatory mechanisms remain largely unknown.  Here, we identified global changes in the endothelial mRNA bound proteome upon TGF-β stimulation using RNA interactome capture. Characterisation of TGF-β regulated RNA binding proteins (RBPs) revealed heterogeneous nuclear ribonucleoprotein H1 (hnRNP H1) and Cold Shock Domain Containing E1 (Csde1) as key regulators of endothelial function and EndoMT. We profiled TGF-β driven changes in the RNA binding patterns of hnRNP H1 and Csde1 and found that they dynamically bind and regulate specific subsets of functionally connected RNAs related to mesenchymal activation upon TGF-β stimulation. Together, we show that RBPs play a key role in EndoMT and that the RBPs hnRNP H1 and Csde1 maintain endothelial cell function and counteract mesenchymal activation.

overall_design: RNA seq siCtl vs sihnRNP H1 or siCsde1, with and without TGF-β stimulation

first: Rhys

last: Wardman

first: Merve

last: Keles


title: HMGA1 Chromatin Regulators Drive MPN Progression [ChIP-Seq]

status: Public on Oct 05 2023

city: BALTIMORE

first: Linda

last: Resar

address: 720 Rutland Avenue

department: Department of Medicine / Division of Hematology

institute: Johns Hopkins University

summary: Myeloproliferative neoplasms (MPN) transform to myelofibrosis (MF) and highly lethal acute myeloid leukemia (AML), although actionable mechanisms driving progression remain elusive. The HMGA1 chromatin regulator is up-regulated during MPN progression with highest levels after transformation. HMGA1 depletion in JAK2V617F MPN AML cell lines disrupts proliferation, clonogenicity, and leukemic engraftment. Surprisingly, loss of just a single Hmga1 allele prevents progression to MF in JAK2V617F transgenic mice, decreasing blood counts and expansion in stem and myeloid progenitors while preventing splenomegaly and fibrosis within the spleen and bone marrow. RNA sequencing revealed HMGA1-dependent transcriptional networks that govern proliferation (E2F, G2M, mitosis, MYC targets) and cell fate, including the GATA2 master regulatory gene. Silencing GATA2 recapitulates phenotypes observed with HMGA1 depletion whereas GATA2 re-expression partially rescues leukemogenesis. HMGA1 transactivates GATA2 through sequences near the developmental enhancer (+9.5), increasing chromatin accessibility and recruiting active histone marks. Further, HMGA1 transcriptional networks, including GATA2, are activated in human MF after leukemic transformation. Further, HMGA1 depletion synergizes with the JAK2 inhibitor, ruxolitinib, to prolong survival in murine MPN AML. These findings illuminate HMGA1 as a key epigenetic switch required for MPN transformation and promising therapeutic target to treat or prevent disease progression.

overall_design: HMGA1-ChIP sequencing (ChIPseq) was performed with DNA from of DAMI cell lines

first: Leslie

last: Cope


title: WhiB1 transcriptone in response to NO stress

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary: Mycobacterium tuberculosis is the etiological agent of tuberculosis. Mtb is an efficient pathogen partially due to its ability to adapt to the disparate conditions encountered during the course of infection. NO is one of the potent antimicrobial chemicals produced in hosts to tackle pathogens. Mtb is known to respond swiftly to NO-stress. Since, WhiB1 is [4Fe-4S] cluster containing transcription factor with high sensitivity to NO, we evaluate the role of WhiB1 in regulating the cellular transcriptional profile of Mtb in presence or absence of NO.

overall_design: This study involves determining the mRNA transcriptome profiles for WT and whiB1 knockdown; grown under standard in vitro conditions (7H9+ADS+Tween80 at 37°C and 180 rpm) in presence or absence of NO (DETA-NO). Knockdown was obtained by addition of 200 ng/ml anhydrotetracycline (ATc).  Two independent experiments were done for each of the strains.

first: Sakshi

last: Kohli

first: Nitish

last: Malhotra

first: Aswin

middle: S

last: Seshasayee


title: A CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in Arabidopsis

city: LAUSANNE

first: JOAQUIN

last: CLUA

address: BIOPHORE

department: DBMV

institute: UNIL

summary: Phosphate is an essential macronutrient required for plant growth and development. However, it is present at suboptimal levels in many terrestrial ecosystems. To ameliorate this limitation, plants have evolved developmental and physiological mechanisms known as phosphate starvation responses (PSR). One of the main PSR in Arabidopsis thaliana is a deep restructuration of the root system architecture, which includes a reduction in primary root growth resulting in a shallower root system better adapted to explore the nutrient-rich topsoil. Intense research over the last years has shown that this developmental change is dependent on the accumulation and redistribution of iron (Fe) at the root tip, which in turn, participates in Fenton reactions and generates reactive oxygen species that affect meristem function and cell elongation. We have recently identified and characterized a cytochrome-containing protein in A. thaliana, named CRR, which is involved in the primary root growth response to phosphate starvation. Our results showed that CRR is an ascorbate-dependent ferric-reductase whose expression levels modulates iron distribution pattern in the root, affecting meristem function and cell elongation. Moreover, this activity also has shown to be critical for iron toxicity tolerance since CRR determines the transport rate of iron from root to shoot.

overall_design: Arabidopsis thaliana seedlings Col-0 or a line over-expressing CRR (CRR OE), were grown on plus (+Pi; control condition) or minus (-Pi) phosphate conditions for 7 days and root tissue was used for the transcriptomic analysis

first: Joaquin

last: Clua

first: Jonatan

last: Montpetit

first: Yves

last: Poirier


title: RNA-sequencing of Mtb H37Rv, MtbΔiscS, iscS complemented, Mtb-sufS knockdown, ΔiscS-sufS knockdown

summary: Iron-sulfur (Fe-S) cluster containing proteins are a subset of proteins with crucial functions in the maintenance of cellular physiology throughout all kingdoms of life. The systems involved in the biogenesis and repair of Fe-S clusters hence plays important role in fine-tuning the availability and functionality of Fe-S proteins. Two of the systems known in bacteria are, Isc and Suf. Compared to the facultative anaerobe, E. coli, which codes for the two multi-genic Fe-S biogenesis systems; Mtb Fe-S biogenesis machinery is skewed with a multi-genic Suf system (sufRBDCSUT) and a single gene of Isc system (iscS). Several Fe-S proteins are deployed by Mtb to maintain cellular homeostasis and survival in a hostile host environment. Hence, we determine the transcriptome of Mtb on depletion of the two key enzymes of Fe-S biogenesis- IscS and sufS, that could help understand the role and regulation between the two systems in the human pathogen Mtb.

overall_design: This study involves determining the mRNA transcriptome profiles for the strains Mtb H37Rv, MtbΔiscS, iscS complemented, Mtb-sufS knockdown, ΔiscS-sufS knockdown; grown under standard in vitro conditions in 7H9+ADS+Tween80 at 37°C and 180 rpm, till cultures reached ~0.4 OD600. Knockdown was obtained by addition of 200 ng/ml anhydrotetracycline (ATc). Three independent experiments were done for each of the strains.

first: Mayashree

last: Das


title: Inflammasome activation drives inflammation in hidradenitis suppurativa skin

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Treatment for the debilitating, chronic skin disease hidradenitis suppurativa (HS) is grossly inadequate. A better understanding of its pathogenesis is required to design new therapeutic strategies. Despite an incidence of approximately 1 in 200, HS is underrecognized and underdiagnosed, with a high morbidity and poor quality of life, which may last decades. In this study we first employed single cell RNA sequencing to analyse gene expression in immune cells isolated from HS lesions compared with healthy control skin. We identified 30 unique immune cell clusters, with a significant enrichment in the frequency of plasma cells, Th17 cells and a subset of dendritic cells (DC) in HS skin. These findings were validated by flow cytometry, which revealed a significant increase in infiltrating immune cells in HS skin, including T cells, B cells, neutrophils, dermal macrophages and DC. The sequencing analysis revealed that the immune transcriptome in HS skin was distinct and much more heterogenous, when compared with healthy skin. Genes and pathways associated with Th17 cells and IL-17, IL-1β, and the NLRP3 inflammasome were enhanced in HS skin, particularly in samples with a high inflammatory load. Inflammasome constituent genes principally mapped to Langerhans cells and a subpopulation of DC. A skin explant model showed that culture of HS skin with an NLRP3 inflammasome inhibitor reduced the inflammatory response, with significant reduction of IL-1β and IL-17A as well as other key mediators of inflammation. These data provide a rationale for targeting the IL-17 pathway in HS, particularly upstream at the NLRP3 inflammasome.

overall_design: Skin samples from HS or healthy control skin was digested into a single cell suspension. Samples were resuspended in CryoStor cyropreservation media and frozen at -80 degrees. Once thawed, live cells were FACS sorted into CD45+ cells and 10X Genomics scRNA-seq was performed.

first: Barry

last: Moran

first: Conor

middle: M

last: Smith

first: Alexandra

last: Zabarowski

first: Mark

last: Ryan

first: Jozsef

last: Karman

first: Robert

last: Dunstan

first: Kathleen

first: Roisin

last: Hambly

first: Jana

last: Musilova

first: Aurelie

last: Fabre

first: Margaret

last: O'Donnell

first: Kingston

last: Mills

first: William

last: Housley

first: Desmond

last: Winter

first: Brian

last: Kirby

first: Jean

last: Fletcher


title: TGF-β regulated RNA-binding proteins control endothelial function and mesenchymal transition in cardiac endothelial cells

first: Joerg

last: Heineke


title: Protoplast data: suberized exodermis is required for tomato drought tolerance

city: Davis

first: Siobhan

last: Brady

state: California

address: One Shields

department: Plant Biology and Genome Center

institute: UC Davis

summary: This experiment aimed to identify protoplast-induced genes in tomato seedling, for future use in single cell datasets.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tomato seedling roots (protoplasted vs non-protoplasted).

first: Alex

last: Canto-Pastor


title: Single cell data: suberized exodermis is required for tomato drought tolerance

summary: Single cell datasets of tomato (Solanum lycopersicum) seedling roots grown in MS plates.

overall_design: single-cell RNA-sesq


title: Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition [scRNA-seq]

first: Dawn

last: Watkins-Chow

summary: We used single-cell RNA-sequencing (scRNA-seq) of melanocytes isolated from two distict red hair color (RHC) mouse models for comparison with and black hair color, functional MC1R signaling, to reveal a Pheomelanin Gene Signature (PGS) of differentially expressed genes in RHC melanocytes.

overall_design: Melanocytes were derived from the dorsal skin of postnatal day 3 old mice and FACS was used to enrich melanocytes for scRNA-seq. A total of 4 samples were used in two pairwise batches: a Lethal yellow (Ay) mouse for comparison with a nonagouti (a/a) control littermate harvested and sequenced in parallel; and a Recessive yellow (Mc1rE) sample for comparison with a nonagouti (a/a) control sample harvested and sequenced in parallel.

first: Stacie

last: Loftus

first: Matthew

last: Berns

last: Pavan


title: The role of GSK3 on macrophage re-programming by high-dose methotrexate

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary: Macrophage phenotypic and functional heterogeneity derives from tissue-specific transcriptional signatures shaped by the local microenvironment. M-CSF drives the generation of human monocyte-derived macrophages with a potent anti-inflammatory activity upon stimulation. One-carbon metabolism (OCM) is a complex network of biosynthetic pathways that includes de novo biosynthesis of purines and thymidylate, amino acid metabolism, and methylation reactions. Methotrexate (MTX) is an anti-folate drug used for Acute Lymphoblastic Leukemia treatment. We explored the molecular impact of blocking GSK3 a/b on the transcriptional effect of high-doses of MTX in M-CSF-primed human monocyte derived macrophages.

overall_design: mRNA profiles of human monocyte-derived macrophages exposed to MTX and/or CHIR99021 for 48h. Monocytes were cultured for 5 days containing M-CSF (10 ng/ml) to generate M-CSF-polarized macrophages (M-MØ). M-CSF was added every two days. DMSO, Methotrexate (MTX, 5 µM), CHIR99021 (CHIR, 10 µM) or both (MTX+CHIR) were added once on 5 day-differentiated macrophages, and treatment maintained for 48h.

first: Rodolfo

middle: I

last: Ríos

first: Mónica

middle: T

last: Torresano

middle: P

last: Kröger


title: RNA sequencing of gastric epithelial cells treated with bacteria

city: Tokyo

first: Yoku

last: Hayakawa

state: TOKYO

address: 7-3-1, Hongo, Bunkyo-ku, Clinical Research Center 4F, Room 425

institute: University of Tokyo

summary: We treated AGS cell line with Helicobacter pylori, Fusobacterium nucleatum, and Neisseria subflava, and extracted RNA after 4 hours. RNAs were applied to RNA sequencing analysis to investigate bacteria-specific effects on gastric epithelial cells.

overall_design: Examination of transcriptomic analysis on bacteria-treated AGS cells.

first: Ryota

last: Niikura

first: Naoyoshi

last: Nagata

first: Mitsuhiro

last: Fujishiro


title: Dgcr8 function in the anterior second heart field

city: Bronx

first: Silvia

middle: Elisa

last: Racedo

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

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

summary:
Morphogenesis of the heart is a complex process that relies on the precise gene expression and gene expression regulators during embryonic development. Dgcr8 is a gene involved in cardiac morphogenesis and it is in the chromosomal region deleted in 22q11.2DS patients. In order to study Dgcr8 function on heart development, we inactivated this gene in the cardiac progenitor cells of mouse embryos and did expression profiling of the long RNAs and miRNAs.
We used microarrays to detail the global programme of gene expression downstream of DGCR8 underlying cardiac development.

platform_organism:
Mus musculus
synthetic construct

overall_design: Mouse embryos were used at embryonic day E9.5 to microdisect two different cardiac tissues, the cardiac progenitor cells located at the back of the heart tube (aSHF) and the outflow tract and right ventricle (OFT-RV) from the heart tube itself. Several pools of each tissue from wild type or mutants embryos were processed for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain pools combining several embryos of the same genotype per replicate in order to obtain a more accurate representation of the expression profile in the embryo population. To that end, we have pooled embryos of the same genotype from at least five different litters. Thirty different pools were obtained, one per array described in the sample list.

first: Bernice

last: Morrow


title: Astrocytes of the optic nerve exhibit a region-specific and temporally distinct response to elevated intraocular pressure

city: Oxford

first: Amélie

last: Julé

address: Roosevelt Drive, Headington

country: United Kingdom

institute: Kennedy Institute of Rheumatology (KIR)

summary: The optic nerve is an important tissue in glaucoma and the unmyelinated nerve head region remains an important site of many early neurodegenerative changes.  In humans and mice, astrocytes constitute the major glial cell type in the region, and in glaucoma they become reactive, influencing the optic nerve head (ONH) microenvironment and disease outcome. To determine the response of ONH astrocytes in glaucoma, we studied their transcriptional response to an elevation in intraocular pressure (IOP) induced by the microbead occlusion model. We also assessed the response of astrocytes in the more distal myelinated optic nerve proper (ONP). In this experimental model, astrocytes of the optic nerve exhibited a region-specific and temporally distinct response: ONH astrocytes showed very few early transcriptional changes and ONP astrocytes demonstrated substantially larger changes over the course of the experiment.

overall_design: We studied the transcriptional response of ONH and ONP astrocytes to an elevation in IOP induced by the microbead occlusion model. Mice were sacrificed at day 0 (untreated), day 7 or day 30 post-injection. To specifically isolate astrocyte mRNA from the dissected tissues, we used the ribotag method to genetically tag ribosomes in astrocytes, which enabled purification of astrocyte-associated mRNA throughout the entire cell, including the fine processes, for bulk RNA-sequencing.

first: Arpan

middle: G

last: Mazumder

first: Daniel

last: Sun


title: PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors [RNA-seq]

status: Public on Sep 30 2023

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a FP-RMS mouse model driven by P3F expression and Cdkn2a loss in endothelial cells. Additionally, we show that P3F expression in TP53-null human iPSCs blocks endothelial-directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.

overall_design: RNA was harvested at Day 0 and Day 15 of a 14 day Endothelial differentiation protcol. Cells were transduced with P3F or left untreated at Day 5 of the protocol so that we could deteremine the effect of enforced P3F expression on endothelial differentiation

first: Madeline

last: Searcy

first: Kate

last: Gadek

first: Bradley

last: Stevens

first: Randolph

last: Larsen

first: Mark

middle: E

last: Hatley


title: LncRNA DCRT protects against dilated cardiomyopathy via binding to PTBP1 (Iso-seq)

city: WUHAN

first: heng

middle: zhi

last: du

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

institute: Wuhan Tongji Hospital

summary: Dilated cardiomyopathy (DCM) is characterized by left ventricular dilation and continuous systolic dysfunction. Mitochondrial impairment is critical in DCM, but the mechanism remains to be elucidated. Here we explored the cardio-protective role of a heart-enriched long non-coding RNA (lncRNA), named dilated cardiomyopathy repressive transcript (DCRT), via maintaining mitochondrial function. We found the lncRNA DCRT was highly enriched in normal heart tissue and its expression was significantly down-regulated in myocardium of DCM patients. DCRT knockout in mice spontaneously developed cardiac dysfunction with cardiac enlargement and mitochondrial impairment. DCRT transgenic or overexpressed mice attenuated cardiac dysfunction induced by transverse aortic constriction (TAC) treatment.

overall_design:
In order to study lncDCRT knockout effect on alternative splicing in AC16 cell lines. We constructed DCRT-knockout (DCRT-KO) cell lines using human cardiomyocyte AC16 via CRISPR-Cas9 strategy. Single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) was performed to detect all the alternative splicing events in DCRT-KO and WT cells

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first: Hengzhi

last: Du

first: Yanru

last: Zhao


title: TGF-β regulated RNA-binding proteins control endothelial function and mesenchymal transition in cardiac endothelial cells [RIP-seq]

first: Joerg

last: Heineke

overall_design: RIP-Seq, input vs Csde1 and hnRNP H1, non-stimulated vs TGF-β (24h, 10 ng/ml)

first: Rhys

last: Wardman

first: Merve

last: Keles


title: PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors [Cut&Run]

overall_design: CUT&RUN for FOXO1, H3K27ac, and IgG (negative control) was harvested at Day 0 and Day 15 of a 14 day Endothelial differentiation protcol. Cells were transduced with P3F or left untreated at Day 5 of the protocol so that we could determine the effect of enforced P3F expression on H3K27ac changes and identify loci where P3F binds

first: Yang

last: Zhang


title: The tumor-derived cytokine Chi3l1 induces neutrophil extracellular traps that promote T cell exclusion in triple-negative breast cancer

city: Montreal

first: Sherif

middle: Samer

last: Attalla

state: Quebec

address: 1160 Ave. Pine W

department: Goodman Cancer Institute

country: Canada

institute: McGill

summary: With the rise of immunotherapies as a treatment option for various cancers, there is a critical need to understand the mechanisms through which cancers evade the immune system. In a subset of poor outcome Triple Negative Breast Cancers, cytotoxic T cells are excluded from the tumor nest and restricted to the surrounding stroma, a phenomenon known as stromal restriction. Data from genetically engineered mouse models and human tumors identified that the secreted cytokine Chitinase-3 like 1 regulates the spatial positioning of T cells in several tumor types including breast, lung and colon. We further demonstrate that Chi3l1 regulates the spatial exclusion of T cells through the direct induction and deposition of neutrophil extracellular traps. Given the importance T cell infiltration in the immune elimination of nascent tumors, the future targeting of Chi3l1 should improve immunotherapy efficacy and outcomes in patients with tumors characterized by a T cell excluded microenvironment.

overall_design: MIC mice were induced with doxyxycline in their drinking water (2mg/mL). The hyperplastic mammary gland was harvested.RNA was extracted and sequenced

first: Tarek

last: Taifour

first: Dongmei

last: Zuo

first: Yu

last: Gu

first: Virginie

last: Sanguin-Gendreau

first: Hailey

last: Proud

first: Emilie

last: Solymoss

first: Tung

last: Bui

first: Hellen

last: Kuasne

first: Vasilios

last: Papavasiliou

first: Chun

last: Lee

first: Suchitra

last: Kamle

first: Peter

last: Siegel

first: Jack

middle: A

last: Elias

first: Morag

last: Park

first: William

last: Muller


title: Single-cell analysis of Diphtheria, Tetanus, and Pertussis (DTP)-vaccinated repertoire

city: Suita

first: Daron

last: Standley

state: Osaka

address: Yamadaoka 3-1

department: Genome Informatics

institute: Osaka University

summary: Diphtheria, tetanus, and pertussis (DTP) are infectious diseases caused by toxin-producing bacteria that can be fatal, especially in children. Despite the availability of combined DTP vaccines for more than 60 years, a comprehensive understanding of how human antibodies respond to DTP vaccination, which helps further improve the vaccine remains elusive. Here, we aimed to characterize toxin-specific antibody repertoires following DTP vaccination. To this end, CD19+CD27+ antigen-experienced B cells obtained from four healthy donors 7-days post vaccination were sorted for toxin-binding and non-toxin-binding B cells, using each of the DTP recombinant toxins (DT, TT, and PT) as fluorescent bait. 10X single-cell immune profiling was then performed, followed by in silico antibody sequence clustering.

overall_design: Antigen-experienced B cells (CD19+CD27+) from four healthy donors vaccinated by Diphtheria, Tetanus, and Pertussis (DTP) vaccine booster were sorted using FACS to obtain DT, TT, or PT binding cells, as well as DTP non-binding cells (NEG). Donor information was retained using Cell Hashtag. Samples were analyzed for scRNA-Seq with additional Feature Barcode and VDJ sequencing.

first: Dianita

last: Saputri

first: Hendra

last: Ismanto

first: Dendi

last: Nugraha

first: Zichang

last: Xu

first: Yasuhiko

last: Horiguchi

first: Shuhei

last: Sakakibara


title: Elucidation of the mechanism of treatment by TGFβ inhibitors for the IC/PBS mouse model using hydrogen peroxide

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

institute: Kyoto Prefectural University of Medicine

summary: Interstitial cystitis/painful bladder syndrome (IC/PBS) is a chronic disease for which there is no effective treatment.Transforming Growth Factor-β (TGF-β) is thought to be involved in the pathogenesis of IC/PBS, and previous studies have shown that suggested that administration of TGF-β inhibitors significantly ameliorates IC/PBS in a mouse model.However, the molecular mechanism of the therapeutic effect of TGF-β inhibitors on IC/PBS has not been comprehensively analyzed. In this study, we show that TGF-β inhibitor administration ameliorated dysuria in IC/PBS mouse models using hydrogen peroxide through a variety of mechanisms.

overall_design: Three biological replicates were analyzed for each of 3 conditions (control mice, H2O2_saline-treated mice, H2O2_SB431542-treated mice)

first: Hideto

last: Taga


title: Suberized exodermis is required for tomato drought tolerance

first: Siobhan

last: Brady

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

overall_design: Refer to individual Series


title: PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity[Cut&Run]

first: Hongjian

last: Jin

summary: Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a novel FP-RMS mouse model driven by P3F expression and CDKN2A loss in endothelial cells. Additionally, we show that P3F expression in p53 null human iPSCs blocks endothelial directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.

overall_design: We performed CUT&RUN on two distinct mouse models of fusion-positive rhabdomyosarcoma to investigate differences in promoters and enhancer activity with H3K27ac. Comparison of CUT&RUN data from Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP) versus Tek-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (TCP) tumors.

first: Madeline

last: Searcy

first: Randolph

last: Larson

first: Yang

last: Zhang

first: Catherine

middle: J

last: Drummond

first: Bradley

last: Stevens

first: Casey

last: Langdon

first: Katherine

last: Gadek

first: Kyna

last: Vuong

first: Matthew

middle: R

last: Garcia

first: Beisi

first: Darden

last: Kimbrough

first: Nadhir

last: Djekidel

first: Shaina

middle: N

last: Porter

first: Patrick

last: Schreiner

first: Gang

last: Wu

first: Shondra

last: Pruett-Miller

first: Brian

last: Abraham

first: Jerold

last: Rehg

first: Mark

last: Hatley


title: PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity[Hi-C]

first: Hongjian

last: Jin

overall_design: To investigate the effect of cell of origin on tumor chroamtin confirmation we performed HiC on two mouse models of fusion-positive rhabdomyosarcoma from a myogenic (Myf6) and an endothelial (TEK) cell of origin. Comparison of HiC data from Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP) versus Tek-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (TCP) tumors.

first: Madeline

middle: B

last: Searcy


title: Gene expression in hypermorphic vq1, vq10 and vq1vq10 mutant compared to wild type Col-0 plants under normoxia or hypoxia

city: Valencia

first: Jose

last: Leon

address: CPI Edificio 8E, Ingeniero Fausto Elio s/n

institute: IBMCP (CSIC-UPV)

summary: Comparative expression analysis of vq1, vq10 and vq1vq10 versus wild type Col-0 in normoxic plants (at 21% O2) or after hypoxia treatment (4 h at 1% O2).

overall_design: RNA-Seq data from three independent biological replicates for every genotype and condition were used to perform the comparative analysis.

first: José

last: León


title: Early Transient IFN-γ Production-dependent and Independent Mechanisms Underlie the Cross-protectivity of Lung-Resident Memory CD8 T Cells against Respiratory Virus Challenge

city: Shanghai

first: Avon

last: Taylor

address: Caolang Road No.2901

institute: Fudan University

summary: Transcriptome profiling of lung tissues and lung CD8+ TRM during early phase of infection to investigate the mechanism of lung TRM cells during antigen re-exposure within 48hours. After P14 T cell transfer, PR8 infection would not induce P14 TRM cells, while PR8-gp33 would. Comparing the gene expression of lung tissues after LCMV Armstrong challenge at day 30 after PR8 or PR8-gp33 infection would help us understand the function of lung CD8+ TRM cells. Sorted TRM cells from mice challenged with LCMV Armstrong at day 30 after PR8-gp33 infection would reveal the activation mechanism of TRM cells.

overall_design: TCR-transgenic P14 T cells were adoptively transferred to generate immune chimeras. At various time points post LCMV Armstrong infection, P14 Trm cells were sorted from lung BAL based on their surface expression of CD45.1+CD69+CD11a-, and microarray was performed. RNA of lung tissue from sequential infection of PR8 and Armstrong and of PR8-gp33 and Armstrong  was extracted and sent for microarray analysis.

first: Lang

last: Jiang

first: Chen

last: Zhao

first: Zejun

last: Li

first: Xiaoyan

last: Zhang

first: Jianqing

last: Xu


title: PAX3-FOXO1 drives tumor formation from multiple lineages [scRNA-seq]

summary: Comparison of fusion-positive rhabdomyosarcoma tumors from endothelial and myogenic origins to wild-type tissue shows few differences between the two tumors.

overall_design: We performed single cell gene expression profiling analysis fo scRNA-seq data for multiple endothelial cell types and two genetically engineered mouse models of rhabdomyosarcoma.


title: Quantitative analysis of wild type, MiwiΔIns and MiwiR371W round spermatids transcriptomes

city: shanghai

first: Xin

last: Wang

state: shanghai

address: 320 Yue Yang Road, Shanghai 200031

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Analysis of the difference in the transcriptomes (protein-coding gene and transposons) of round spermatids between MiwiΔIns or MiwiR371W and control mice.

overall_design: Examination of transposons and mRNAs in round spermatids isolated from MiwiΔIns or MiwiR371W and control mice.

first: Fengjuan


title: RNAseq analysis of cocaine associated transcriptional dynamics in the thalami of Maged1 WT and cKO mice.

city: Lyon

first: Leonardo

last: Beccari

address: 8 Avenue Rockefeller

institute: Institute NeuroMyoGene (PGNM)

summary: Maged1 inactivation induces insensitivity to cocaine by impairing cocaine-evoked release of dopamine and plasticity in the Nucleus accumbens (NAc). Here we have characterized the chromatin epigenetic and transcriptional alterations associated with chronic cocaine exposure in the paraventricular thalamus (PVT, one of the main regulatory inputs of the Nac) in mice WT or conditional KO for Maged1 activity.

overall_design: We dissected the thalami of WT or Maged1 cKO mice after repeated (5) injections of cocaine or saline vehicle. At least 3 independent biological replicates were processed per each experimental condition.

first: J

last: Cheron


title: Transcriptome analysis of Streptococcus mutans quorum sensing-mediated persisters reveals an enrichment in genes related to stress-defense mechanisms

status: Public on Sep 29 2023

city: Toronto

first: Delphine

last: Dufour

state: Ontario

address: 124 Edward Street

department: Oral Microbiology

institute: Faculty of Dentistry, University of Toronto

summary: Persisters are a small fraction of growth-arrested phenotypic variants that can survive lethal concentrations of antibiotics but are able to resume growth once antibiotics are stopped. Their formation can be a stochastic process or triggered by environmental cues. In the human pathogen Streptococcus mutans, the canonical peptide-based quorum sensing system is an inducible DNA repair system that is pivotal for bacterial survival. Previous work showed that the CSP signaling peptide is a stress-signaling alarmone that promotes the formation of stress-induced persisters. In this study, we exposed S. mutans to the CSP pheromone to mimic DNA damage conditions and isolated the antibiotic persisters by treating the cultures with ofloxacin. Transcriptome analysis was then performed to evaluate the differential gene expression between the normal stationary phase cells and the persisters. RNA-sequencing revealed that triggered persistence was associated with the up-regulation of genes related to several stress-defense mechanisms, notably, multidrug efflux pumps, the arginine deaminase pathway, and the Opu/Opc system. In addition, we showed that inactivation of the VicK kinase of the YycFG essential two-component regulatory system abolished the formation of triggered persisters via the CSP pheromone. These data contribute to the understanding of the triggered persistence phenotype and may suggest new therapeutic strategies for treating persistent streptococcal infections

overall_design: The formation of S. mutans persisters was triggered with a pre-incubation with the CSP quorum sensing pheromone. Persisters were then isolated using the ofloxacin antibiotic. The gene expression profiling of the persisters was compared to the one of CSP-induced untreated cells.

first: Haowen

first: Siew-Ging

last: Gong

first: Celine

last: Levesque


title: PAX3-FOXO1 drives tumor formation from multiple lineages [RNA-seq]

first: Hongjian

overall_design: We performed gene expression profiling analysis fo RNA-seq data for multiple endothelial cell types and two genetically engineered mouse models of rhabdomyosarcoma.

first: Madeline

first: Mark

last: Hatley


title: Maged1 WT and cKO mice

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus


title: Cocaine associated H2AK119ub dynamics in the thalami of Maged1 WT and cKO mice

summary: Maged1 inactivation induces insensitivity to cocaine by impairing cocaine-evoked release of dopamine and plasticity in the Nucleus accumbens (NAc). Here we have characterized the chromatin epigenetic and transcriptional alterations associated with chronic cocaine exposure in the paraventricular thalamus (PVT, one of the main regulatory inputs of the Nac) in mice WT or conditional KO for Maged1 activity. At the epigenetic level, we focused on the analysis of the genomic coverages of the histone post-translational modification H2AK119ub (monoubiquitination of Lysine 119 of H2A; H2Aub), a repressive chromatin mark associated to polycomb (PRC1) –mediated gene repression since Maged1 specifically interact with H2A upon cocaine administration and is required for cocaine-induced increase of H2AK119ub levels in the PVT.

overall_design: We dissected the thalami of WT or Maged1 cKO mice after repeated (5) injections of cocaine or saline vehicle, fixed them in 1%PFA and performed ChIPmentation experiments using the anti-i H2AK119ub antibody (Cell Signaling, 8240S). At least 2 independent biological replicates (derived from 3-4 adult mouse thalami each) were processed per each experimental condition.

first: L


title: Bacterial mRNA sequencing through targeted rRNA depletion for efficient RNA-seq in varied species and co-cultures

city: Santa Barbara

first: Kellie

last: Heom

address: UC Santa Barbara

department: Chemical Engineering

institute: University of California Santa Barbara

summary: mRNA sequencing in bacteria is challenging due to the abundance of ribosomal rRNA that cannot be easily removed prior to sequencing. While commercially available kits target specific rRNA sequences found in defined lists of common bacterial species, they are frequently inefficient when applied to other divergent species, including those from environmental isolates. Similar to the commercial kits, other common techniques for rRNA depletion typically employ large probe sets that tile full-length rRNA sequences; however, such approaches are both time consuming and expensive when applied to multiple species or complex consortia of non-model microbes. To overcome these limitations, we present EMBR-seq+, which employs less than twenty target oligonucleotides per rRNA molecule, and builds upon our previous rRNA depletion approach, EMBR-seq, through the addition of an RNase H depletion step, to achieve rRNA removal efficiencies of up to 99%. First, we applied EMBR-seq+ to monocultures of Escherichia coli, Geobacter metallireducens, and Fibrobacter succinogenes strain UWB7 to deplete rRNA to approximately 1-7% of the sequencing reads, demonstrating that the new method can be easily extended to diverse bacterial species. Further, in more complex co-cultures between F. succinogenes strain UWB7 and anerobic fungal species, we applied EMBR-seq+ to deplete both bacterial and fungal rRNA, with an approximately 4-fold improved bacterial rRNA depletion efficiency compared to a previous report using a commercial kit, thereby showing that the method can be effectively translated to non-model microbial mixtures. Notably, we also demonstrate that for microbial species with poorly annotated genomes and unknown rRNA sequences, the RNase H depletion component of EMBR-seq+ enables rapid iterations in probe design without requiring to start experiments from total RNA each time, and was key for depleting fungal rRNA to enrich the bacterial mRNA readout in co-cultures. Finally, efficient depletion of rRNA enabled systematic quantification of the reprogramming of the bacterial transcriptome when cultured in the presence of the anerobic fungi, Anaeromyces robustus and Caecomyces churrovis. We observed that F. succinogenes strain UWB7 transcribes nearly 200 carbohydrate-active enzyme (CAZyme) genes in both monoculture and co-culture conditions, with several lignocellulose-degrading CAZymes downregulated in the presence of an anerobic gut fungus. This finding is consistent with the premise that bacteria and fungi specialize in different aspects of biomass breakdown, such that the presence of one regulates the CAZyme production of the other. This also supports previous findings that the fungi release excess reducing sugars in the supernatant, which benefits other members of the microbial community. Thus EMBR-seq+ provides a new and detailed perspective of a rumen microbiome model system by dramatically improving the efficiency of mRNA sequencing, and more generally also enables high-throughput, cost-effective and rapid quantification of the transcriptome to gain functional insights into less-studied and non-model microbial systems.

sample_organism:
Escherichia coli
Fibrobacter succinogenes
Geobacter metallireducens
Anaeromyces robustus
Caecomyces churrovis

overall_design: We developed a method, EMBR-seq+, to efficiently sequence RNA from bacterial samples by depleting rRNA during the RNA library preparation. EMBR-seq+ combines our previous method, EMBR-seq, with RNase H treatment to achieve improved rRNA depletion. We demonstrated that rRNA is depleted to less than 10% of sequencing reads for monocultures of E. coli, G. metallireducens, and F. succinogenes strain UWB7 and less than 25% of bacterial reads for co-cultures of F. succinogenes strain UWB7 with either A. robustus or C. churrovis.

first: Chatarin

last: Wangsanuwat

first: Lazarina

middle: V

last: Butkovich

first: Scott

middle: C

last: Tam

first: Annette

last: Rowe

first: Michelle

last: O'Malley

first: Siddharth

last: Dey


title: Spatial transcriptomics reveals a low extent of transcriptionally active hepatitis B virus integration in patients with HBsAg loss

first: Xiaoqi

last: YU

address: No.197 Ruijin 2nd Road

institute: Ruijin Hospital

summary: Hepatitis B virus (HBV) can integrate into the chromosomes of infected hepatocytes, contributing to the production of hepatitis B surface antigen (HBsAg) and to hepatocarcinogenesis. We performed spatial transcriptomics to investigate the intrahepatic cell heterogeneity and the spatial distribution of transcriptionally active HBV integration events in different phases of chronic HBV infection. Our analysis revealed that transcriptionally active HBV integration occurred in chronically HBV-infected patients in different phases, including those patients with HBsAg loss, and antiviral treatment was associated with a decreased number and extent of viral integrations.

overall_design: Liver biopsies from 18 patients with chronic HBV infection were used for spatial transcriptomics sequencing. EP1-4 were HBeAg-positive patients, EN1-5 were HBeAg-negative patients, OT1-6 were on-treatment patients, SL1-3 were patients with HBsAg loss (SL).

last: Yu

first: Qiming

first: Demin

first: Yongyan

last: Chen

first: Ying

last: Jing

first: Fabien

last: Zoulim

first: Xinxin


title: single cell RNA-Seq of Dugesia japonica

city: Sagamihara

first: Makoto

last: Kashima

address: 5-1-16, Fuchinobe

institute: Aoyama Gakuinn University

summary: A single cell RNA-Seq analysis of Dugesia japonica intact animals by TAS-Seq (Shichino et al, 2022)

overall_design: We conducted scRNA-Seq analysis of cells of approximately 10 μm in diameter such as the neoblasts in D. japonica intact animals using BD Rhapsody scRNA-Seq platform without a fluorescence activated cell sorter.

first: Rei

last: Komura


title: Gcn5- and Bre1-mediated Set2 degradation promotes chronological aging of Saccharomyces cerevisiae

city: wuhan

first: yuchao

last: Mei

address: Bayi Road

department: Colleage of Life Science

institute: Wuhan University


title: Bre1-mediated Set2 protein degradation promotes chronological aging in budding yeast [RNA-seq]

summary: Histone modification affects life span in various organisms. The loss of Histone H3K36 methylation can shorten replicative life span in Saccharomyces cerevisiae. However, budding yeast, as a model organism for aging research, has replicative life span (RLS) and chronological life span (CLS). In this study, we showed that the loss of Histone H3K36 methylation can shorten CLS in Saccharomyces cerevisiae. We identified Ubc3/Bre1 mediates polyubiquitination of Set2 K25 and K530 at log phase and stationary phase, and Bre1 interacts with Ubc3 and Rad6 simultaneously. BRE1 knockout can stabilize Set2 protein to maintain H3K36me3 and regulate the transcription of aging related genes, such as DSE1/DSE2/SUN4/EGT2/SCW11. We also proved that Gcn5-mediated Set2 acetylation regulates Set2 protein stability and chronological aging. Altogether, our study showed that knockout of BRE1 and GCN5 regulate Set2 protein level by mediating the polyubiquitination of Set2 to influence the level of H3K36me3 and the transcription level of aging related genes enriched by H3K36me3, thereby extending the chronological life span.

overall_design: RNA-seq analysis of gene expression in WT, set2-delta and bre1-delta cells of Saccharomyces cerevisiae during chroological aging(Day4 vs Day1).ChIP-seq analysis of H3K36me3 binding in WT and bre1-delta cells Saccharomyces cerevisiae during chroological aging(Day4 vs Day1)

first: Yu-min

last: Li

first: Yu-chao

first: Hai-Ning

last: Du


title: Molecular blueprints for spinal circuit modules controlling locomotor speed

city: Stockholm

first: Abdel

last: El Manira

address: Solnavagen 9

department: Neuroscience

institute: Karolinaska Institutet

summary: The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules, yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm-generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow, intermediate or fast subtypes. Furthermore, we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall, by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function, connectivity and behavior, our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general.

overall_design: To determine whether the functional subtypes of motoneurons and V2a (Chx10+) interneurons are molecularly distinct, we performed single-cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.

first: Irene

last: Pallucchi

first: Maria

last: Bertuzzi

first: David

last: Madrid

first: Pierre

last: Fontanel

first: Shin-ichi

last: Higashijima


title: Preclinical evaluation of the efficacy of anti-human SIRPα antibody for cancer immunotherapy using the MITRG humanized mouse model

city: Kobe

first: Yasuyuki

last: Saito

state: Hyogo

address: 7-5-1, Kusunokicho, Chuo-ku

institute: Kobe University Graduate School of Medicine

summary: Tumor-associated macrophages (TAMs) represent abundantly in the tumor microenvironment (TME) and are thought to be novel targets for cancer immunotherapy. To elucidate the antitumor effects of therapeutics targeting human TAMs in vivo, we have here established a preclinical tumor xenograft model using immunodeficient mice expressing multiple human cytokines (MITRG mice) and examined the anti-tumor effect of anti–human SIRPα antibodies SE12C3, which inhibit the interaction of CD47 on tumor cells and enhance Fcγ receptor-mediated phagocytosis of tumor cells by human macrophages. Humanized immune system (HIS)–MITRG mice particularly facilitate human macrophage differentiation following transplantation of human CD34+ hematopoietic stem and progenitor cells. HIS–MITRG mice promoted the growth of both cell line– and patient–derived B cell lymphoma and infiltration of human TAMs into the tumor. Treatment of rituximab with SE12C3 markedly inhibited B–cell lymphoma growth in HIS-MITRG mice. The inhibition of B–cell lymphoma growth depended on human macrophages and was attributable to the promotion of rituximab–mediated lymphoma cell phagocytosis by human macrophages. In addition, the treatment of rituximab with SE12C3 induced reprogramming of human TAMs towards the pro-inflammatory phenotype in the TME. Furthermore, we demonstrated that the treatment of rituximab with SE12C3 significantly inhibited diffuse large B–cell lymphoma patient–derived tumor growth in HIS–MITRG mice. Together, HIS–MITRG mice provide an excellent mouse model for in vivo preclinical evaluation of the anti-tumor effect of therapeutics targeting human TAMs in the TME, such as anti–human SIRPα antibodies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor-infiltrating macrophages in Raji inoculated HIS-MITRG mice after the treatment with control IgG, rituximab, or rituximab+SE12C3.

first: Rie

last: Iida-Norita


title: Breast cancer remotely imposes a myeloid bias on hematopoietic stem cells by reprogramming the bone marrow niche

city: France

first: Julie

last: Helft

email: gerber.helft@gmail.com, julie.helft@inserm.fr, jason.cosgrove@curie.fr, yoann.missolo-koussou@curie.fr, yohan.gerber@curie.fr

address: 26 Rue D'ulm

institute: Institut Curie

summary: Increased number of circulating myeloid cells is a hallmark of several cancers, however it remains unclear how primary tumors impact on myelopoiesis. Here we show that non-metastatic breast tumors remotely instruct the fate of long-term hematopoietic stem cell (HSCLT) in the bone marrow. We found that HSCLT from tumor bearing mice acquire a myeloid bias persisting upon primary and secondary HSCLT transfer in lethally-irradiated tumor-free animals. By imaging the bone marrow HSC niche, we found that the tumor-bearing status is associated with increased physical interactions between mesenchymal stem/stromal cells (MSC) and HSCLT. Moreover, ex vivo co-culture experiments demonstrate that MSC isolated from tumor-bearing mice increase myeloid differentiation of HSCLT isolated from tumor free mice. In summary, our data reveal that breast cancer remotely promotes myelopoiesis at the earliest stages of hematopoietic differentiation in the bone marrow mesenchymal niche.

overall_design: scRNAseq and bulk RNA seq of bone marrow stromal cells and hematopoietic progenitors sorted from tumor-free or tumor-bearing mice. The aim was to characterize the transcriptomic profile of bone marrow cells in the presence of a localized breast tumor.

first: Yohan

last: Gerber-Ferder

first: Jason

last: Cosgrove

first: Yoann

last: Missolo-Koussou

first: Sonia

last: Lameiras


title: Bre1-mediated Set2 protein degradation promotes chronological aging in budding yeast [ChIP-seq]

first: yuchao

overall_design: ChIP-seq analysis of H3K36me3 binding in WT and bre1-delta cells Saccharomyces cerevisiae during chronological aging (Day4 vs Day1)


title: Single-cell transcriptomics reveals the natural product cannabinoid rewires tumor microenvironment via inhibiting alternative activation of macrophage and synergizes with PD-1 blockade

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

summary: Colorectal tumors often display a suppressive immune microenvironment that limits their response to immunotherapy. Here, we report that Cannabidiol, a natural non-psychoactive constituent of the cannabis plant, inhibits colorectal cancer progression by modulating the suppressive tumor microenvironment. Our single-cell transcriptome sequencing results showed that CBD inhibits M2-polarized macrophages while promoting M1-polarized macrophages, which restores the intrinsic antitumor properties of macrophages to inhibit tumor progression. Mechanistically, CBD inhibits alternative activation of macrophages by inhibiting PI3K-Akt signaling, which shifts cell metabolism from oxidative phosphorylation and fatty acid oxidation to glycolysis. Moreover, CBD-mediated macrophage plasticity enhanced the response to anti-PD1 immunotherapy in xenograft mice. Taken together, our study provides new insights into the antitumor effects of CBD.

overall_design: scRNA-seq profiling of total tumor cells in MC38 mouse transplanted tumor.

first: Xiaofan

last: Sun

first: Lisha

last: Zhou

first: Yi

last: Wang

first: Yang


title: Phase-separated CCER1 coordinates histone-to-protamine transition and fertility

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

summary: Idiopathic fertility disorders are associated with mutations in various genes. Here, we report that coiled-coil glutamate-rich protein 1 (CCER1), a germline-specific and intrinsically disordered protein (IDP), mediates post-meiotic sperm differentiation, while CCER1 deficiency results in defective sperm chromatin compaction and infertility in mice. CCER1 increases transition protein (Tnp1/2) and protamine (Prm1/2) transcription and serves as a multifaceted mediator for multiple epigenetic modification events of histones during the histone to protamine transition (HTP). Immiscible with heterochromatin in the nucleus, CCER1 self-assembles into polymer droplet and acts as a liquid-liquid phase separated condensate in the nucleus. Notably, we identified the loss-of function variants of human CCER1 (hCCER1) in five patients with non-obstuctive azoospermia (NOA) while absent in 2,713 fertile controls. The mutants led to premature termination or frameshift of CCER1 translation and disrupted condensates in vitro. In conclusion, we propose that nuclear CCER1 is a novel phase-separated condensate that links histone epigenetic modifications, sperm HTP transitions, chromatin condensation, and male fertility.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for Ccer1 WT and KO testis.

To confirm the condensate state in the Ccer1 -/- mutants, we took advantage of in situ Hi-C to illustrate the chromatin state in both Ccer1 +/+ and Ccer1-/- sperm at the molecular level."

first: Dongdong

last: Qin

first: Yu

last: Zhang

first: Yayun

last: Gu

first: Shu

first: Wei

last: Xie

first: Zhibin

last: Hu

first: Xin

last: Wu


title: Fibroblasts in heart scar tissue directly regulate cardiac excitability and arrhythmogenesis

status: Public on Sep 28 2023

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Scar tissue that forms in the heart after cardiac injury, comprises an abundant number of non-excitable fibroblasts in close proximity to excitable myocytes, that are embedded within the matrix of the scar. Electrical coupling of fibroblasts and myocytes is known to occur and in vitro  simulation studies have demonstrated that changes in fibroblast membrane potential can lead to myocyte excitability and susceptibility to arrhythmogenesis. However, the physiologic significance of electrical coupling between  myocytes and fibroblasts in scar tissue, in the regulation of cardiac excitability and arrhythmogenesis in vivo is hotly debated and has never been demonstrated. Here, we genetically engineer a mouse that expresses the optogenetic cationic channel ChR2 exclusively in cardiac fibroblasts and not in cardiac myocytes. We subject the animal to cardiac injury and demonstrate that optical stimulation of scar tissue elicits cardiac excitability and induces arrhythmias. Connexin 43 (Cx43) is a gap junctional protein that is the most abundant connexin isoform in the heart and thought to mediate electrical coupling of fibroblasts and myocytes. Using genetic loss of function approaches, we show that Cx43 is not necessary for fibroblast-myocyte electrical coupling in vivo. CRISPR/Cas 9 mediated sequential deletion of the other highly expressed connexins also did not affect electrical coupling of fibroblasts and myocytes. Using computational modeling approaches, we show that gap junctional and non-gap junctional coupling mechanisms synergize in a functionally redundant manner to excite myocytes coupled to fibroblasts. These observations demonstrate that cardiac fibroblasts in scar tissue directly regulate cardiac excitability in vivo and can induce arrhythmogenesis. Our findings throw insight into the importance of electrical coupling of fibroblasts and myocytes in the genesis of scar associated cardiac arrhythmias.

overall_design: Single nuclei RNA sequencing on mouse heart post myocardial infarction day 7

first: Yijie

first: Sivakumar

last: Ramadoss

first: Arjun

last: Deb


title: Defining Spatiotemporal Gene Modules in Liver Regeneration Using Analytical Dynamic Visual Spatial -Omics Representation (ADViSOR)

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: The liver is the only organ with the ability to regenerate following surgical or toxicant insults, and partial hepatectomy (PH) serves as an experimental model of liver regeneration (LR). Dynamic changes in gene expression occur from the periportal to pericentral regions of the liver following PH; thus, spatial transcriptomics, combined with a novel computational pipeline (ADViSOR [Analytic Dynamic Visual Spatial Omics Representation]), were employed to gain insights into the spatiotemporal molecular underpinnings of LR. ADViSOR, comprised of time-interval principal component analysis (TI-PCA) and sliding dynamic hypergraphs (sDyHyp), was applied to spatial transcriptomics data on 100 genes assayed serially through LR, including key components of the Wnt/beta-catenin pathway at critical time points after PH. This computational pipeline identified key functional modules demonstrating cell signaling and cell-cell interactions, inferring shared regulatory mechanisms. Specifically, ADViSOR analysis suggested that macrophage-mediated inflammation is a critical component of early LR and confirmed prior studies showing that Ccnd1, a hepatocyte proliferative gene, is regulated by the Wnt/ß-catenin pathway. These findings were subsequently validated through protein localization which provided further confirmation and novel insights into the spatiotemporal changes in the Wnt/beta-catenin pathway during LR. Thus, ADViSOR may yield novel insights in other complex, spatiotemporal contexts.

overall_design: Two-month-old C57BL/6 mice, purchased from Jackson Laboratory, were subjected to parialt hepatectomy (PH) in which 2/3 of the liver were removed, inducing livering regeneration. Mice were euthanized by isoflurane inhalation and cervical dislocation at the following time points: 0 hours, 24 hours, 48 hours, 72 hours, 14 days, 3 months, and 6 months. Regenerating livers were harvested and the newly regenerated lobes were either paraffin embedded or collected for Molecular Cartography.

first: Anya

last: Singh-Varma

first: Ashti

middle: M

last: Shah

first: Silvia

first: Ruben

last: Zamora

first: Satdarshan

last: Monga

first: Yoram

last: Vodovotz


title: PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity

city: Memphis

first: Hongjian

last: Jin

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Abundant polyadenylation of transcripts and precursor tRNAs in Mycobacterium tuberculosis upon depletion of Rv3907c, the mycobacterial CCA-adding enzyme

city: Lodz

first: Przemysław

middle: Adam

last: Płociński

state: lodzkie

address: Lodowa 106

department: Mycobacterium Physiology and Genetics

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-Seq results accompanying submission of a manuscript: "Depletion of CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs" describing the function of the Rv3907c gene product as a CCA-adding enzyme in Mycobacterium tuberculosis.

sample_organism:
Mycobacterium tuberculosis H37Rv
Mycolicibacterium smegmatis MC2 155

overall_design: Next generation sequencing results are provided in three independent biological replicates for each strain growing in standard 7H9/10% OADC medium. The bacteria were grown to mid-logarythmic phase of growth, when they were collected and total RNA was isolated. The resulting RNA was subjected to ribodepletion with riboPools Pan-Bacteria (siTools Biotech GmbH,Planegg, Germany) and used for preparation of sequencing libraries,generated with a KAPA-stranded RNA Seq kit according to the manufacturer’s protocol (Roche Diagnostics, Rotkreuz, Switzerland) or TruSeq small RNA library preparation kit (Illumina, San Diego, CA, USA). The resulting adapter-ligated, PCR-amplified cDNA libraries were subjected to sequencing on a NextSeq500 sequencer using the NextSeq500/550 v.2 sequencing kit (Illumina, San Diego, CA, USA), and approximately 5 to 10 million paired-end reads were sequenced for each sample for total RNA-Seq and 0.5-2.5mln were sequenced for small RNA libraries. VAHTS mRNA-seq V3 Library Prep Kit for Illumina® (Vazyme, Nanjing, China) with detailed manufacturer's protocol was applied to generate final sequencing libraries for the polyadenylation enriched RNA samples obtained from Mycolicibacterium smegmatis strains.

first: Błaszczyk

last: Ewelina

first: Ewelina

last: Lechowicz

first: Anna

last: Brzostek

first: Bożena

last: Dziadek

first: Małgorzata

last: Korycka-Machała

first: Marcin

last: Słomka

first: Jarosław


title: Human Microglial State Dynamics in Alzheimer's Disease Progression

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute