title: Single-cell RNA sequencing of adult mouse fibrotic kidney induced by unilateral uretral obstruction

status: Public on May 08 2024

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

institute: Instituto de Neurociencias (CSIC-UMH)

summary: We performed single-cell RNAseq for adult mouse fibrotic kidney to characheterize how epithelial to mesenchymal transition program is implemented at single tubular cells resolution during the course of renal intrestitial fibrosis

overall_design: 12 weeks old males mice were subjected to SHAM sergery (CTR) or to unilateral ureteral obstruction (UUO) to indice renal interstitial fibrosis. 1UUO and SHAM kidneys were harvested and disregated into single cell preparations contaning all kidney cell types. 10X Chromium were used to  prepare cDNA libraries. Two UUO and one SHAM cDNA libraries were obtained  sequenced.

first: Nitin

last: Narwade

first: Khalil

last: Youssef


title: Single-cell RNA profiling of mammary gland tumours in MMTV-PyMT mouse model of breast cancer.

country: Spain

type: Expression profiling by high throughput sequencing

summary: Here, we use single cell sequencing to delineate the heterogeneity of tumours from the genetically engineered MMTV-PyMT mouse model of breast cancer (MMTV-PyMT::K14Cre::Rosa-tdTomato mice).

overall_design: Mammary tumours were collected from 13-14-week-old MMTV-PyMT female mice and were subjected to single cell expression profiling to address heterogeneity in metastatic breast cancer.

first: Angel

last: MARQUEZ-GALERA

middle: K

last: YOUSEFF

first: Jose

middle: P

last: LOPEZ-ATALAYA

first: M

middle: A

last: NIETO


title: Canid alphaherpesvirus 1 infection affects the gene expression and secretome profile of canine adipose-derived mesenchymal stem cells in vitro

status: Public on May 17 2024

city: Zagreb

first: Marina

last: Prišlin

address: Savska cesta 148

department: Virology Department

country: Croatia

institute: Croatian Veterinary Institute

summary: Canine adipose  -derived mesenchymal stem cells (cAD-MSCs) demonstrate promising tissue repair and regeneration capabilities. However, the procurement and preservation of these cells or their secreted factors for therapeutic applications pose a risk of viral   contamination, and the consequences on cAD-MSCs remain unexplored. Consequently, this research sought to assess the impact of Canid alphaherpesvirus 1 on the functional attributes of cAD-MSCs, including gene expression profiles and secretome composition. To this end, abdominal fat tissue from twelve healthy dogs was harvested to isolate cAD-MSCs. These samples were tested for CHV contamination before introducing a wild-type CHV strain via serial passages. Following CHV infection, RT-PCR arrays and LC-MS/MS assessments enabled gene expression analysis and the secretome's proteomic landscape, respectively. The study established that the initial cAD-MSCs populations were devoid of CHV. Upon exposure to the virus, cAD-MSCs exhibited susceptibility, leading to notable modifications in gene expression and secretome profile. These changes reflected their intrinsic properties, such as stemness, differentiation potential, structural integrity, proliferative capacity, survival, directional migration, and immune-modulatory functions, depriving their regenerative efficacy  . Despite the absence of pre-existing contamination, the outcomes underscore the imperative of routine viral screening   prior to therapeutic use, particularly CHV. Moreover, these findings provide insights into the pathogenic mechanisms of CHV and the intricate interactions between canine stem cells and viruses.

overall_design: Twelve biological replicates are studied in two different cell conditions, before and after infection with canine herpesvirus (Varicellovirus canidalpha1).

first: Dragan

last: Brnić


title: SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE

status: Public on Jun 04 2024

city: Boston

first: Neta

last: Rosenzweig

state: Massachusetts

address: 60 Fenwood Road, 10002K, Brigham and Women’s Hospital

country: USA

institute: Brigham and Women's Hospital, Harvard Medical School

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: Context dependent activity of p63-bound gene regulatory elements

city: Albany

first: Morgan

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

summary: Assessing the contribution of the p63 binding motif on p63-dependent enhancer activity in 5 different cellular contexts.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Implemented STARR-seq MPRA method (Arnold et al., 2013) to assay 17,310 unique enhancers. The library pool included 5 variants of each enhancer: wild-type, p63RE motif mutant, p63RE shuffle, p63RE flanking region shuffle, and a fully shuffled enhancer sequences. Each fragment tested included 119-120 nt of the enhancer centered around p63RE. All enhancers were assayed in several epithelial cell lines or their derivatives: MCF10A, MCF10A p53KO, HaCaT, SCC25, MCF10A GUS overexpression, MCF10A TAp63β overexpression. Plasmid pool 1 was transfected into all cell types except for HaCaT replicates 1 and 2 where plasmid pool 2 was transfected.

first: Abby

last: McCann

first: Gabriele

last: Baniuyte


title: Effect of inulin on extracellular vesicles microRNAs in milk from dairy cows with sub-clinical mastitis

status: Public on May 31 2024

city: Beijing

first: Wanjie

last: Yu

address: No. 2 Yuanmingyuan West Road

country: China

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Milk contains microRNAs (miRNAs) that are protected by extracellular vesicles (EV). Beyond variations among individuals, the nutritional conditions of cattle play a role in shaping these milk miRNA profiles. This study explored milk-derived EV-miRNA variations induced by inulin supplementation and analyzed involved pathways. Fourteen lactating cows with sub-clinical mastitis were equally and randomly divided into an inulin and a control group. Cows in the inulin group received 300 g/d inulin, while the control group did not. After one week of adaptation and five weeks of treatment, milk-derived EV-miRNAs from cows were isolated. Differentially expressed (DE) miRNAs were identified via high-throughput sequencing. Functional enrichment analyses, including Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, were conducted to examine the target genes of DE miRNAs. Inulin supplementation did not significantly alter miRNA length, the number of known miRNAs, or the read number of small RNAs.


title: Girolline is a sequence-context specific modulator of eIF5A activity

status: Public on Jun 10 2024

city: Wako-shi

first: Tilman

last: Schneider-Poetsch

email: tilman@cal.berkeley.edu, tsp@riken.jp

state: Saitam

address: 2-1 Hirosawa

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary: Natural products have a long history of providing potent probes into protein biosynthesis, with  numerous molecules serving as valuable therapeutics. The marine natural product girolline has  been described as an inhibitor of protein synthesis. Here, we demonstrate that it is not a general  translation inhibitor but represents a sequence-specific modulator of translation factor eIF5A.  Girolline interferes with ribosome-eIF5A interaction and induces ribosome stalling, primarily on  AAA-encoded lysine. Our data furthermore indicate that eIF5A plays a physiological role in  ribosome-associated quality control (RQC) and is important in maintaining the efficiency of  translational progress. Girolline, therefore, provides a potent tool compound for understanding  the interplay between protein production and quality control in a physiological setting and offers  a new and selective means of modulating gene expression.

overall_design: Ribosome profiling and RNA-Seq of human cells treated with girolline

first: Yongjun

last: Dang

first: Mayumi

last: Arata

first: Yuichi

last: Shichino

first: Ali

last: Al-Mourabit

first: Daniel

last: Romo

first: Jun

middle: O

last: Liu

first: Shintaro

last: Iwasaki

first: Minoru

last: Yoshida


title: A Dataset Examining Technical Factors on Fixed Whole Blood Single-Cell RNA-Seq

status: Public on May 06 2024

city: Melbourne

middle: Victor

last: Brown

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: High-throughput sequencing technologies have enabled many biological discoveries; nevertheless, the resolution of bulk RNA sequencing is insufficient to elucidate the heterogeneity at the single-cell level. Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for disentangling this complexity.. A major challenge in scRNA-Seq of blood is the analysis of granulocytes. These cells are pivotal to immunological responses but are recalcitrant to isolation from blood without inducing activation artifacts, thereby perturbing their transcriptomic integrity.. The difficulty of granulocyte handling for scRNA-Seq necessitate immediate processing of samples, a workflow incompatible with the logistical demands of large-scale, multi-centric studies. Innovations in commercial fixed scRNA-Seq methodologies promise to ameliorate these limitations by preserving RNA integrity post-fixation. Our investigation evaluates two such commercial kits for fixed scRNA-Seq. Our overall goal was to determine feasibility for distributed collection and centralised processing of fixed whole blood samples.

overall_design: The dataset consists of 2 technology platforms; Honeycomb HIVE v1 and 10x Genomics Flex v1. This consists of 2 batches of HIVE and 4 batches for 10x Genomics. In total there are 18 samples; 2 for HIVE and 16 for Flex. The underlying samples are red blood cell depleted whole blood from healthy donors (Figure 1). For 10x Genomics Flex batch 3, we received a replacement set of library preparation reagents due to poor performance of this batch “batch 3A”. As instructed by 10x Genomics field application specialist we performed a second capture reaction of remaining material from batch 3A = “batch 3B”.

middle: V

first: Agnieszka

last: Swierczak

first: Yue

last: You

first: Yupei

first: Daniela

last: Amann-Zalcenstein

first: Peter

last: Hickey

first: Arthur

last: Hsu

first: Matt

last: Ritchie

first: Monther

last: Alhamdoosh

first: Judith

last: Field

first: Rory

last: Bowden


title: PDGFRa signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking (RNA-seq)

status: Public on May 02 2024

city: Aurora

first: Katherine

middle: Ann

last: Fantauzzo

state: CO

address: 12801 East 17th Avenue, MS 8120

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

summary: Signaling through the platelet-derived growth factor receptor alpha (PDGFRa) plays a critical role in craniofacial development, as mutations in PDGFRA are associated with cleft lip/palate in humans and Pdgfra mutant mouse models display varying degrees of facial clefting. Phosphatidylinositol 3-kinase (PI3K)/Akt is the primary effector of PDGFRa signaling during skeletal development in the mouse. We previously demonstrated that Akt phosphorylates the RNA-binding protein serine/arginine-rich splicing factor 3 (Srsf3) downstream of PI3K-mediated PDGFRa signaling in mouse embryonic palatal mesenchyme (MEPM) cells, leading to its nuclear translocation. We further showed that ablation of Srsf3 in the murine neural crest lineage results in severe midline facial clefting, due to defects in proliferation and survival of cranial neural crest cells, and widespread alternative RNA splicing (AS) changes. Here, we sought to determine the molecular mechanisms by which Srsf3 activity is regulated downstream of PDGFRa signaling to control AS of transcripts necessary for craniofacial development. We demonstrated via enhanced UV-crosslinking and immunoprecipitation (eCLIP) of MEPM cells that PDGF-AA stimulation leads to preferential binding of Srsf3 to exons and loss of binding to canonical Srsf3 CA-rich motifs. Through the analysis of complementary RNA-seq data, we showed that Srsf3 activity results in the preferential inclusion of exons with increased GC content and lower intron to exon length ratio. Moreover, we found that the subset of transcripts that are bound by Srsf3 and undergo AS upon PDGFRa signaling commonly encode regulators of PI3K signaling and early endosomal trafficking. Functional validation studies further confirmed that Srsf3 activity downstream of PDGFRa signaling leads to retention of the receptor in early endosomes and increases in downstream PI3K-mediated Akt signaling. Taken together, our findings reveal that growth factor-mediated phosphorylation of an RNA-binding protein underlies gene expression regulation necessary for mammalian craniofacial development.

overall_design: RNA-seq was performed on iMEPM cells with stably integrated scramble shRNA or Srsf3 shRNA.  Both conditions were tested in the presence and absence of PDGF-AA ligand treatment.

first: Thomas

middle: E

last: Forman

first: Marcin

last: Sajek

first: Eric

middle: D

last: Larson

first: Neelanjan

last: Mukerhjee


title: PDGFRa signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking (eCLIP)

overall_design: eCLIP was performed for Srsf3 on iMEPM cells in the presense or absence of PDGF-AA ligand treatment


title: PDGFRa signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking


title: Gene exprssion profile at single nucleus level of liver tissue from mice infected with dengue virus

status: Public on May 01 2024

city: beijing

first: qian

last: chen

address: No. 5, Panjiayuan South

institute: PUMC

summary: Severe dengue fever is associated with different degrees of liver injury. We used single nucleus RNA sequencing (snRNA-seq) to analyze the genetic changes in different cells of liver tissue after dengue virus infection.

overall_design: The experimental group was divided into uninfected group and dengue virus infected group including NGC and N10 group. On the 6th day after infection, single nucleus RNA sequencing was performed on the liver tissues of the above three groups.

first: Qian

last: Chen

first: YiZhen

last: Yuan

first: FangZhou

last: Cai

first: Wei

last: Wang


title: Investigating determinants of aneuploidy toxicity using gene duplication in Saccharomyces cerevisiae

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

summary: Aneuploidy has a myriad of consequences for health and disease, yet models of aneuploidy toxicity are still widely debated. To distinguish the effects of specific genes from the generalized burden of chromosome amplification, we measured the effects of duplicating individual genes in euploid cells as well as in select aneuploids using a barcoded plasmid library. We analyzed the responses of cells with and without extra chromosomes, as well as those with and without RNA-binding protein Ssd1. Deletion of Ssd1 sensitizes cells to chromosome amplification, but the source of this vulnerability is not known. Results of this experiment were used to interrogate determinants of aneuploidy toxicity, test models of Ssd1 dependence, and identify vulnerabilities of sensitized (ssd1-) and wild-type aneuploids. We also used the fitness effects of gene duplication in euploid cells to model the cost associated with chromosome duplication.

overall_design: Euploid and select aneuploid yeast strains (haploids with one additional copy of chromosomes IV, VII, XII, and XV, respectively) with and without the RNA-binding protein SSD1 were transformed with a barcoded CEN plasmid library. For each strain, we took samples at generation 0 (start of experiment) and generation 10 (and/or generation 5 for a subset of strains) to quantify the effects of gene duplication on fitness. Each strain was measured in at least biological triplicate (4 replicates from 2 independent transformations of the plasmid library in Batch 1 and 3 replicates from 3 independent transformations in Batch 2).

first: H

last: Dutcher

first: Julie

last: Rojas


title: Genomic context-dependent histone H3K36 methylation by Drosophila methyltransferases

status: Public on May 07 2024

city: Munich

first: Muhunden

middle: Nallappa

last: Jayakrishnan

state: Munich (city)

address: 57 Nusselstrasse, 57

department: Molecular Biology

country: Germany

institute: Biomedical Center, Ludwig Maximilians University Munich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: How different histone methyltransferases (HMT) cooperate to progressively catalyze different methylation states of the same residue as well the functional consequences of the different methylation states are not well known. Here, we address in the context of Drosophila H3K36 methylation by using single and combinatorial RNAi of HMTs along with genome-wide MNase-ChIPseq analyses. Our study reveals that K36me1/2/3 each mark distinct chromatin compartments. Each HMT predominantly contributes to only one modification state, however our approach also identifies context-dependent cooperative and compensative patterns. Further, correlating changes in K36me1/2/3 to reader binding reveals that K36me2/3 can redundantly contribute to faithful reader binding ensuring robustness.

overall_design:
MNase Chromatin Immunoprecipitation DNA Sequencing (ChIP-seq) for K36me1/2/3, K27me3, K9me2, HMTs(ePol, Mes4) and readers (JASPer/PW, Msl3) in RNAi treated (10/7 days; RNAi targets - GST/GFP=Control, Set2, NSD,Ash1, Comb=Set2+NSD) S2 cells.

UPDATE: [Jan-15-2025] The processed data files for the ChIP-seq Samples were replaced.

first: Silke

last: Krause

first: Roshni

last: Shetty


title: Integrating Tumor and Healthy Epithelium in a Microphysiology Multi-compartment Approach to Study Renal Cell Carcinoma Pathophysiology

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

institute: University Medicine Greifswald

summary: The advent of micro-physiological systems (MPS) in biomedical research has enabled the introduction of more complex and relevant physiological into in vitro models. The recreation of complex morphological features in three-dimensional environments can recapitulate otherwise absent dynamic interactions in conventional models. In this study we developed an advanced in vitro Renal Cell Carcinoma (RCC) that mimics the interplay between healthy and malignant renal tissue. Based on the TissUse Humimic platform our model combines healthy renal proximal tubule epithelial cells (RPTEC) and RCC. Co-culturing reconstructed RPTEC tubules with RCC spheroids in a closed micro-perfused circuit resulted in significant phenotypical changes to the tubules. Expression of immune factors revealed that interleukin-8 (IL-8) and tumor necrosis factor-alfa (TNF-α) were upregulated in the non-malignant cells while neutrophil gelatinase-associated lipocalin (NGAL) was downregulated in both RCC and RPTEC. Metabolic analysis revealed that RCC prompted a shift in the energy production of RPTEC tubules, inducing glycolysis, in a metabolic adaptation that likely supports RCC growth and immunogenicity. In contrast, RCC maintained stable metabolic activity, emphasizing their resilience to external factors. RNA-seq and biological process analysis of primary RTPTEC tubules demonstrated that the 3D tubular architecture and MPS conditions reverted cells to a predominant oxidative phosphorylate state, a departure from the glycolytic metabolism observed in 2D culture. This dynamic RCC co-culture model, approximates the physiology of healthy renal tubules to that of RCC, providing new insights into tumor-host interactions. Our approach can show that an RCC-MPS can expand the complexity and scope of pathophysiology and biomarker studies in kidney cancer research.

overall_design: This study aimed to reconstruct renal tubules using RPTEC_TERT1 cells embedded in a collagen type I matrix and to generate RCC spheroids employing CAKI-1 cells in an agar/collagen matrix within the Humimic chip2 Microphysiology System (MPS). Additionally, the impact of dynamic culture on RPTEC physiology was assessed by culturing primary RPTEC cells in both conventional 2D formats and the MPS without RCC spheroids. The experiment included three conditions: (1) Renal tubules only, (2) RCC spheroids only, and (3) Renal tubules and RCC spheroids in co-culture, all cultured in the MPS for 5 days. Cell and supernatant samples were collected from each condition for analysis. The anticipated outcomes include successful renal tubule reconstruction, RCC spheroid formation, and insights into the influence of dynamic culture on RPTEC physiology.

first: Maryna

last: Somova

first: Adventina

last: Padmyastuti

first: Jens

last: Ehrdardt

first: Janosch

last: Schoon

first: Ingmar

last: Wolff

first: Martin

last: Burchardt

first: Cindy

last: Roennau

first: Pedro

last: Pinto


title: Transcriptomic data from a clinical cohort of men who have sex with men (MSM) and controls.

status: Public on Jun 20 2024

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: These samples are part of large study to understand the rectal mucosal immune environment among MSM.

overall_design: 140 rectal biopsies from MSM and contols subjects from various Race, Age and Infection status groups. 57 samples previously submitted in GSE211922 (see below table of reanalyzed samples).

first: S

last: Smith

first: Phillip

middle: M

last: Murray

first: Praveen

last: Amancha

first: Cassie

middle: G

last: Ackerley

first: Vanessa

last: Van Doren

first: Yi-Juan

last: Hu

first: Robert

last: Archer

middle: R

last: Johnson

first: Steven

last: Bosinger

first: Rama

last: Amara

first: Colleen

middle: F

last: Kelley


title: Global mRNA profiling reveals the effect of boron as a crop protection tool against Sclerotinia sclerotiorum

status: Public on Apr 22 2024

city: Winnipeg

first: Mark

last: Belmonte

state: MB

address: 50 Sifton Road

country: Canada

institute: University of Manitoba

summary: Sclerotinia sclerotiorum, the causal agent of white mould, is a necrotrophic fungal pathogen responsible for extensive crop loss. Current control options rely heavily on the application of chemical fungicides that are becoming less effective and may lead to the development of fungal resistance. In the current study, we used a foliar spray application of boron to protect Brassica napus (canola) from S. sclerotiorum infection using whole plant infection assays. Application of boron to aerial surfaces of the canola plant reduced the number of S. sclerotiorum forming lesions by 87% compared to an untreated control. We used dual RNA sequencing to profile the effect of boron on both the host plant and fungal pathogen during the infection process. Differential gene expression analysis and gene ontology term enrichment further revealed the mode of action of a foliar boron spray at the mRNA level. A single foliar application of boron primed the plant defense response through the induction of genes associated with systemic acquired resistance while an application of boron followed by S. sclerotiorum infection induced genes associated with defense-response-related cellular signalling cascades. Additionally, in S. sclerotiorum inoculated on boron-treated B. napus, we uncovered gene activity in response to salicylic acid breakdown, consistent with salicylic-acid-dependent systemic acquired resistance induction within the host plant. Taken together, this study demonstrates that a foliar application of boron results in priming of the B. napus plant defense response, likely through systemic acquired resistance, thereby contributing to increased tolerance to S. sclerotiorum infection.

sample_organism:
Brassica napus
Sclerotinia sclerotiorum

platform_organism:
Brassica napus
Sclerotinia sclerotiorum

overall_design: Whole Brassica napus plants were treated with boron, boscalid, or water before being inoculated with Sclerotinia sclerotiorum. Three leaves were collected and pooled to form a single biological replicate. Tissue was collected from both infected and uninfected plants for each treatment. Three biological replicates were sampled per treatment/infection status.

first: Natalie

middle: L

last: Cale

first: Philip

last: Walker

first: Sanjana

last: Sankar

first: Sean

last: Robertson

first: Olivia

last: Wilkins


title: Activation of MEK‐ERK‐c‐MYC signaling pathway promotes splenic M2 macrophage polarization to inhibit PHcH-liver cirrhosis

status: Public on Apr 27 2024

city: Xi’an

first: wang

middle: gui

last: hu

address: No.157#, The West 5th Road

department: The Second Affiliated Hospital

institute: Xi'an Jiaotong University

summary: Portal hypertension combined with hypersplenism (PHcH) is the main cause of hypocytosis and esophagogastric variceal hemorrhage in patients with liver cirrhosis. Activated macrophages that destroy excess blood cells are the main cause of hypersplenism, but the activating pathway is not very clear. This study aims to investigate the activation types of splenic macrophages and their activation mechanisms, to provide experimental evidence for the biological treatment of splenomegaly, and aiming to find a strategy to improve liver fibrosis and inflammation by intervening in splenic immune cells. This study revealed the occurrence of M2 type polarization of macrophages and upregulation of c-Myc gene expression in the PH spleen. RNAseq, protein chip, western blot, and chip-seq were performed on macrophages and the in vitro MEK inhibitor rafametinib was used. Carbon tetrachloride and thioacetamide induced mouse cirrhosis models were separately constructed. c-Myc gene knockout in splenic macrophages reduced M2 type polarization and exacerbated liver fibrosis inflammation. c-Myc activated the MAPK signaling pathway and upregulated the expression of IL-4 and M2 related genes in PH hypersplenism through the MEK-ERK-c-Myc axis. In addition, the c-Myc gene exerted anti-inflammatory effects by upregulating IL-4-mediated signal transduction to promote M2 type differentiation and anti-inflammatory cytokine secretion. Therefore, the induction of macrophage depolarization might represent a new therapeutic approach in the cure of PH hypersplenism, making c-Myc a potential candidate for macrophage polarization therapy.

overall_design:
Fresh human normal spleen samples (n = 15) were obtained from patients with traumatic splenic rupture who underwent splenectomy (Nor group); splenic samples (n = 36) of hepatitis B cirrhosis, accompanied by PH were obtained from patients with PH hypersplenism who underwent splenectomy (PH group).Study on the mechanism of C-myc gene involvement in M2 macrophage regulation in patients with PH splenomegaly .
This study primers macrophage specific C-Myc KO mice and constructs two liver fibrosis models, CCL4 and TAA, to verify the polarization characteristics and specific mechanism changes of mouse spleen macrophages after C-Myc gene KO.
mether: qPCR、WB、IHC、FACS、RNAseq, protein chip, western blot, and chip-seq were performed on macrophages and the in vitro MEK inhibitor rafametinib

first: G

middle: H

last: Wang

first: W

last: Dong

first: H

last: Zhang

first: C

middle: Y


title: Site saturation mutagenesis of 500 human protein domains

city: Barcelona

first: Antoni

last: Beltran

address: Dr Aiguader, 88

institute: CRG Barcelona

summary: Missense variants that change the amino acid sequences of proteins cause one third of human genetic diseases. Tens of millions of missense variants exist in the current human population, with the vast majority having unknown functional consequences. Here we present the first large-scale experimental analysis of human missense variants. Using DNA synthesis and cellular selection experiments we quantify the impact of >500,000 variants on the abundance of >500 human protein domains. This dataset, Domainome 1.0, reveals that >60% of disease-causing variants destabilize proteins. The contribution of stability to protein fitness varies across proteins and diseases, and is particularly important in recessive disorders. Combining experimental stability measurements with large language models we annotate functionally important sites across domains. Fitting energy models to the data demonstrates the conservation of mutation effects in homologous domains and allows stability to be accurately predicted for entire domain families. Domainome 1.0 demonstrates the feasibility of assaying human protein variant effects at scale and provides a large consistent reference dataset for clinical variant interpretation and the training and benchmarking of computational methods.

overall_design: We designed site saturation mutagenesis variant libraries of >500 protein domains, and selected them using an in cell abundance assay to measure the effects of mutations on protein abundance.

first: Ben

last: Lehner


title: The post-septic peripheral myeloid compartment reveals unexpected diversity in myeloid-derived suppressor cells

status: Public on Apr 17 2024

city: Gainesville

first: Rhonda

last: Bacher

address: 2004 Mowry Rd.

institute: University of Florida

summary: Sepsis engenders distinct host immunologic changes that include the expansion of myeloid-derived suppressor cells (MDSCs). These cells play a physiologic role in tempering acute inflammatory responses but can persist in those patients who develop chronic critical illness. The origins and lineage of these MDSC subpopulations were previously assumed to be linear, discrete, and unidirectional; however, these cells exhibit a dynamic phenotype with considerable plasticity. Using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) followed by transcriptomic analysis, we identify a unique lineage and differentiation pathway for MDSCs after sepsis and describe a novel MDSC subpopulation. Additionally, we report that the heterogeneous response of the myeloid compartment of blood to sepsis is dependent on clinical outcome.

overall_design:
A mixture of whole blood myeloid-enriched and Ficoll-enriched peripheral blood mononuclear cells from 4 early septic patients (day 4), 10 late septic patients (post-sepsis day 14-21, RAP n=5 and CCI n=5) and 12 healthy subjects underwent Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq).
ADT; Oligo Sequence
Biolegend_307663_C0159 HLADR; AATAGCGAGCAAGTA
Biolegend_300479_C0034 CD3; CTCATTGTAACTCCT
Biolegend_323053_C0392 CD15; TCACCAGTACCTAGT
Biolegend_351356_C0390 CD127; GTGTGTTGTCCTATG
Biolegend_353747_C0140 CD183; GCGATGGTAGATTAT
Biolegend_392909_C0166 CD66B; AGCTGTAAGTTTCGG
Biolegend_300567_C0072 CD4; TGTTCCCGCTCAACT
Biolegend_301859_C0081 CD14; TCTCAGACCTCCGTA
Biolegend_353440_C0143 CD196; GATCCCTTTGTCACT
Biolegend_302649_C0085 CD25; TTTGTCCTGTACGCC
Biolegend_301359_C0161 CD11B; GACAAGTGATCTGCA

first: Efron

last: Phil

first: Bacher

last: Rhonda


title: G3BP1 Ribonucleoprotein Complexes Regulate Focal Adhesion Protein Mobility and Cell Migration [Ribo-Seq]

status: Public on Apr 20 2024

city: New Haven

first: Liana

last: Boraas

state: CT

address: 300 George Street, Room 752: Loria Center

institute: Yale University

summary: The subcellular localization of mRNAs plays a pivotal role in biological processes, including cell migration. For instance, β-actin mRNA and its associated RNA binding protein (RBP), ZBP1/IGF2BP1, are recruited to focal adhesions (FAs), to support localized β-actin synthesis, crucial for cell migration. However, whether other mRNAs and RBPs also localize at FAs remains unclear. Here, we identify hundreds of mRNAs that are enriched at FAs (FA-mRNAs). FA-mRNAs share characteristics with stress granule (SG) mRNAs and are found in ribonucleoprotein (RNP) complexes with the SG RBP. Mechanistically, G3BP1 binds to FA proteins in an RNA-dependent manner, and its RNA-binding and dimerization domains, essential for G3BP1 to form RNPs in SG, are required for FA localization and cell migration. We find that G3BP1 RNPs promote cell speed by enhancing FA protein mobility and FA size. These findings suggest a previously unappreciated role for G3BP1 RNPs in regulating FA function under non-stress conditions.

overall_design: Ribosome profiling from whole cell or isolated focal adhesions from HUVECS (human umbilical vein endothelial cells) or HDFs (Human dermal fibroblasts). Ribosomes in active translation were isolated and the ribosome protected fragments were sequenced

first: Mengwei

last: Hu

first: Pieter

last: Martino

first: Lauren

last: Thornton

first: Charles

last: Vejnar

first: Gang

last: Zhen

first: Longhui

last: Zeng

first: Dylan

last: Parker

first: Andy

last: Cox

first: Antionio

middle: J

last: Giraldez

first: Xiaolei

last: Su

first: Christine

last: Mayr

first: Siyuan

first: Stefania

last: Nicoli


title: G3BP1 Ribonucleoprotein Complexes Regulate Focal Adhesion Protein Mobility and Cell Migration [RNA-seq]

overall_design: Poly-A-sequencing from whole cell or isolated focal adhesions from HUVECS (human umbilical vein endothelial cells) or HDFs (Human dermal fibroblasts)

middle: C

first: Antonio

last: Wang


title: RNA sequencing of gonad tissue of Nothobranchius furzeri at different age in males and females

status: Public on Apr 15 2024

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: Quantification of gene expression at different dvelopmental stages of the short-lived killifish Nothobranchius furzeri GRZ strain.

overall_design: Four developmental stages of the GRZ strain were analyzed with RNA-seq. Stages and number of samples: at 10 days post fertilization (dpf, whole embryos), 6 samples; at the day of hatch (0dph), 5 samples; at 3 days post hatching (3dph, trunk of fry), 6 samples; and at 3 months post hatching (3mph, gonads), 2 samples.

first: Nils

last: Hartmann

first: Andreas

last: Petzold

first: Marco

last: Groth


title: G3BP1 Ribonucleoprotein Complexes Regulate Focal Adhesion Protein Mobility and Cell Migration

first: Liana

last: Boraas

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

overall_design: Refer to individual Series


title: Bleximenib, the novel menin-KMT2A inhibitor JNJ-75276617, impairs long-term proliferation and immune evasion in acute myeloid leukemia

status: Public on Apr 29 2024

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

country: Netherlands

institute: UMCG

summary: Acute myeloid leukemia (AML) remains challenging to treat, which in part relates to genetic heterogeneity of the disease, to the protective tumor microenvironment driving resistance to therapy, and also to immune evasion characteristics of leukemic cells. Targeting epigenetic programs in AML provides an attractive opportunity to impair long-term proliferation and induce differentiation. The novel inhibitor JNJ-75276617 (bleximenib) targets the menin-KMT2A interaction and provides preclinical efficacy in AML (Kwon et al1). Here, we provide mechanistic insight in how JNJ-75276617 impairs proliferation and drives differentiation of primary AML patient cells. A large-scale drug screen was set up in which genetic alterations and quantitative proteomics were compared with drug sensitivity in a preclinical setting, which revealed that granulocyte macrophage progenitor (GMP)-like AMLs display the greatest sensitivity. Furthermore, we identified that NPM1c/DNMT3Amut AMLs are sensitive, and some NPM1wt AML subtypes without KMT2A-MLLT3 rearrangements benefit from menin-KMT2A inhibition. Genome-wide ChIP-seq studies revealed patient-specific epigenetic alterations upon JNJ-75276617 treatment, uncovering a striking upregulation of MHC class I and class II expression as a consequence of epigenetic changes upon menin-KMT2A inhibition, independent of MEIS1 loss but involving CIITA activation. Functionally, this results in enhanced sensitivity of leukemic blasts to T cell-mediated cytotoxicity in allogeneic and autologous settings. Our data indicate that JNJ-75276617 provides a potential therapeutic approach whereby not only proliferation is impaired and differentiation is induced, but whereby therapeutic benefit might also be achieved by reactivating the antigen presentation machinery.

overall_design: Samples were treated for 4 days with 0.03/0.3 µM JNJ-75276617 followed by crosslinking and performance of ChIP and sequencing

first: Shanna

last: Hogeling

first: Jan Jacob


title: Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus

status: Public on Apr 23 2024

city: Cambridge

first: Allison

last: Coe

state: MA

address: 15 Vassar St

department: Civil and Environmental Engineering

institute: Massachusetts Institute of Technology

summary: Prochlorococcus is found throughout the euphotic zone in the oligotrophic open ocean. Deep mixing and sinking in aggregates or while attached to particles can, however, transport cells below this sunlit zone, depriving them of light for extended periods of time and influencing their circulation via ocean currents. Viability of these cells over extended periods of darkness could shape the ecology and evolution of the Prochlorococcus collective. We have shown that when co-cultured with a heterotrophic microbe and subjected to repeated periods of extended darkness, Prochlorococcus cells develop a heritable dark-tolerant phenotype – through an apparent epigenetic mechanism – such that they survive longer periods of darkness. Here we examine this adaptation at the level of physiology and metabolism in co-cultures of dark-tolerant and parent strains of Prochlorococcus, each grown with the heterotroph Alteromonas under diel light:dark conditions. The relative abundance of Alteromonas is higher in dark-tolerant than parental co-cultures, while dark tolerant Prochlorococcus cells are also larger, contain less chlorophyll, and are less synchronized to the light:dark cycle. Meta-transcriptome analysis of the cultures further suggests that dark-tolerant co-cultures undergo a coupled shift in which Prochlorococcus uses more organic carbon and less photosynthesis, and Alteromonas uses more organic acids and fewer sugars. Collectively, the data suggest that dark adaptation involves a loosening of the coupling between Prochlorococcus metabolism and the light:dark cycle and a strengthening of the coupling between the carbon metabolism of Prochlorococcus and Alteromonas.

sample_organism:
Alteromonas macleodii
Prochlorococcus marinus str. NATL2A

overall_design: To investigate dark-tolerance in Prochlorococcus, we obtained a dark-tolerant strain (as first described in Coe et al 2021) by subjecting exponentially growing co-cultures of Prochlorococcus NATL2A with Alteromonas macleodii MIT1002 on a 13:11 light:dark cycle to 3 days of darkness, and then returned them to 13:11 light:dark. Once cells resumed growth and reached late exponential growth, they were transferred into fresh media and the process was repeated until cells resumed growth within 1-2 days after dark exposure, at which point they were defined as dark-tolerant. We then examined gene expression differences in both Prochlorococcus and Alteromonas using RNA-seq for parental and dark-tolerant cell lines every 4-5h over a full 13:11 light:dark cycle.  Samples include triplicate biological replicates at multiple time points over a 13:11 light:dark cycle with a repeating timepoint at sunrise.

first: Rogier

last: Braakman

first: Steven

last: Biller

first: Aldo

last: Arellano

first: Christina

last: Bliem

first: Nhi

middle: N

last: Vo

first: Konnor

last: von Emster

first: Elaina

last: Thomas

first: Michelle

last: DeMers

first: Claudia

last: Steglich

first: Jef

last: Huisman

first: Sallie

middle: W

last: Chisholm


status: Public on Apr 24 2024

first: wang

last: hu

first: G

last: Wang

first: W

last: Dong

first: H

last: Zhang

first: C


title: Single-cell analysis reveals Mycobacterium tuberculosis ESX-1–mediated accumulation of permissive macrophages in infected mouse lungs

city: San Francisco

first: Leah

last: Dorman

state: CA

address: 499 Illinois St

department: Data Science

institute: CZBiohub

summary: Mycobacterium tuberculosis (MTB) infects and replicates in lung mononuclear phagocytes (MNPs) with astounding ability to evade elimination. A virulence determinant that contributes to MTB’s ability to survive within MNPs is ESX-1, a type VII secretion system. However, how MTB virulence factors influence mononuclear cell recruitment and/or differentiation remains unknown. Here, using single-cell RNA sequencing, we studied the role of ESX-1 in MNP heterogenicity and response in mice and murine bone marrow-derived macrophages. We found that ESX-1 is required for MTB to recruit diverse MNP subsets with high MTB burden. Further, MTB induces an anti-inflammatory signature that may lead to more permissive MNPs. Spatial transcriptomics revealed an upregulation of anti-inflammatory signals in MTB lesions, where monocyte-derived macrophages concentrate near MTB-infected cells. Together, our findings suggest that MTB ESX-1 mediates the recruitment and differentiation of anti-inflammatory MNPs, which MTB can infect and manipulate for survival.

overall_design: Bonemarrow-derived macrophages were matured, infected with H37Rv-dsRed or H37Rv-deltaRD1-dsRed, and compared to control for 24hours- cells were sorted for live infected and bystander cells, labeled using MultiSeq method, and processed with manufacturer's protocol for 10X single cell library preparation with modification given the labels. There are two other cell types in this experiment (PBMC and THP-1) that are not part of the noted project.

first: Shoshana

middle: B

last: Zha

first: Weihao

last: Zheng

first: Michael

last: Borja

first: Norma

last: Neff

first: Angela

last: Pisco


title: Transcriptomic changes in the ovine caruncular endometrium following imbalanced nutrition and FSH-induced ovarian hyperstimulation

status: Public on Apr 19 2024

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Imbalanced nutrition and exogenous gonadotrophins affect uterine function and morphology. In sheep, FSH-induced superovulation causes morphological alterations in the uterus, leading, i.e., to an increase in lipid droplets. Similarly, depending on diet, FSH treatment alters the expression of estrogen and progesterone receptors and of adhesion molecules. To broad the knowledge regarding imbalanced nutrition and carry-over effects of superovulation induced with FSH in the caruncular endometrium, deep RNA sequencing (NGS, RNA-Seq) was applied, followed by functional analysis. Ewes (n = 3-5/group) were divided as follows: control fed (CF), overfed (OF), and underfed (UF), and each group was further treated with FSH (superovulated (SOV)) or saline (negative controls (CONT)). Samples were collected on day 10 of diestrus. Furthermore, samples from CF_CONT were collected on day 5 to assess time-dependent changes. The 1484 differentially expressed genes (DEGs, P < 0.01, FDR < 0.05) identified between CF_CONT animals at days 5 and 10 were associated with increased immune activity and cellular metabolic processes and decreased cellular proliferation. In CONT animals, unbalanced nutrition (i.e., both OF and UF) was associated with enrichment of terms associated with cell adhesion and differentiation, immune response and angiogenesis. As for carry-over effects of FSH, higher number of DEGs were found for CF animals (1374), than in OF (168) or UF (18) samples, associated with dysregulation of cell cycle and hormonal sensitivity. The absence of genes concomitantly affected by SOV at all different feeding regimes suggested multidirectional and body condition-dependent effects of FSH in caruncular transcriptome. Both body condition and SOV appear to affect the homeostasis of the ovine caruncles, possibly involving the modulation of uterine receptivity.

overall_design: A total of 29 ewes were used in the present work. Ewes (n=3-5/group) were divided into control fed (CF, 100% of National Research Council requirements ), overfed (OF, 200% of National Research Council requirements), and underfed (UF, 60% of National Research Council requirements), with each group further divided between superovulated (SOV; FSH, 5mg/injection on day 13, 4mg/injection on day 14 and 3mg/injection on day 15 of estrus cycle.) or control (C; saline, 10 ml of 0.9% NaCl in water ). Samples were collected on days (d) 5 and 10 of diestrus in the next estrous cycle.

first: Mariusz

middle: P

last: Kowalewski

first: Özlem

last: Bedir

first: Miguel

last: Tavares Pereira

first: Hubert

last: Rehraurer

first: Anna

last: Grazul-Bilska


title: Enhancing Precise Genome Editing in Human Pluripotent Stem Cells through Dual Inhibition of DNA Damage Response and Repair Pathways

city: Seoul

first: Hyuk-Jin

last: Cha

address: 215-20 Gwan-ak ro Gwan-ak gu

country: South Korea

institute: Seoul National University


title: Effect of Dhps deletion in epithelial cells and Citrobacter rodentium infection on the transcriptome of the colonic mucosa

status: Public on Apr 08 2024

city: Nashville

first: guoqiang

last: Gu

state: Tennessee

address: 9415D Medical Research Building IV

department: Department of Cell and Developmental Biology

institute: Vanderbilt University Medical Center

summary: We previously reported that hypusination in myeloid cells is required to limit the development of pathogenic bacteria in the gastrointestinal tract, including Helicobacter pylori for the stomach and C. rodentium in the colon. The aim of the present study was to investigate the role of epithelial hypusination on C. rodentium pathogenicity

overall_design: Dhps<fl/fl> mice and Dhps<fl/fl>;Vil1<cre/+> mice were infected or not with Citrobacter rodentium (5X108 bacteria/mouse) for 14 days. RNA was extracted from the colon and RNA sequencing was performed

first: Alain

last: Gobert

first: Yu

first: Shilin

last: Zhao

first: Keith

middle: T

last: Wilson


title: Group B Streptococcal transcriptome when interacting with brain endothelial cells

city: Cologne

first: Till

middle: David

last: Sauerwein

address: Gleueler Str. 60

department: Data Science and Services

institute: ZB MED - Information Centre for Life Sciences

summary: We have conducted RNA-seq analysis on Group B Streptococcus (GBS) when interacting with human stem-cell (hSC) derived BECs. The study contains a control group for GBS and a control group for BECs each with three biological replicates. The last group contains GBS infection BECs and also has three replicates.

sample_organism:
Streptococcus sp. 'group B'
Homo sapiens

overall_design: Dual RNA-sequencing analysis of Group B Streptococcus infection Brain-like endothelial cells generated from induced pluripotent stem cells (iPSC-BECs)

first: Bailey

middle: E

last: Bridgers

first: Madelyn

last: Armstrong

first: Eric

last: Espinal

first: Mustafa

last: Divyapicigil

first: Thomas

middle: A

last: Hooven

first: Alexander

last: Westermann

first: Konrad

middle: U

last: Foerstner

first: Alexandra

last: Schubert-Unkmeir

first: Brandon

last: Kim

first: Nadine

last: Vollmuth

first: Abigail

last: Gildea

first: Jacob

last: Wood

first: Guilia

last: Barbieri


first: Leah

last: Dorman

overall_design: Single cell suspension from harvested lungs from C57BL/6 uninfected or infected with H37Rv-mCherry for 28 days were stained and sorted to obtain live tissue CD45+ infected cells and bystander (mCherry negative)/uninfected cells - these were processed with manufacturer's protocol for 10X single cell library preparation.

first: Shoshana

last: Zha

first: Weihao

last: Zheng

first: Michael

last: Borja

first: Norma

last: Neff

first: Angela

last: Pisco


title: miR-141-3p regulates the expression of corneal epithelial differentiation

city: Mexico City

first: Federico

last: Castro-Muñozledo

address: Av Instituto Politecnico Nacional 2508, San Pedro Zacatenco

department: Cell Biology

country: Mexico

institute: CINVESTAV

summary: Corneal epithelial RCE1(5T5) cells follow a sequential process that leads to the formation of a 4-5 layered stratified epithelium with a gene expression pattern similar to that shown in primary cultures of corneal epithelial cells. We have previously identified three different developmental stages during the differentiation of the rabbit corneal epithelial cell line RCE1(5T5). In this analysis we describe the participation of miR-141-3p as a regulator of the proliferative phenotype and its participation on maintaining differentiation of corneal eptihelial cells.

overall_design: To evaluate the participation of miR-141 on corneal epithelial differentiation, we obtained the transcriptome of four samples of rabbit corneal epithelium formed by RCE1(5T5) cells at three distinct stages of the differentiation program and RCE1(5T5) cells transfected with antagomiR-141.

first: Maria-Teresa

last: Ortiz-Melo

first: María-Jimena

last: Garcia-Murillo

first: Victor

middle: M

last: Salazar-Rojas

first: Jorge

last: Campos-Contreras

last: Castro-Munozledo


title: In vitro drug screening of RAF/MEK/ERK Inhibitors in two PDA Cell Lines

status: Public on Apr 28 2024

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: In this study 14 different RAF, MEK, or ERK inhibitors were tested in ASPC1 and PANC1 PDA cell lines

overall_design: Panc-1 and AsPC-1 pancreatic cancer cells were cultured in 96-well tissue culture-treated plates at optimized density, in 100 μl of their optimal media. After 24 h of incubation, the plates were treated with following

first: Urszula

last: Wasko

first: Mallika

last: Singh

first: Andrea

last: Califano

first: Kenneth

last: Olive


title: Characterization of mast cells from human umbilical cord blood

status: Public on Apr 30 2024

city: Jeddah

first: Sherin

last: Bakhashab

address: Abdullah Sulyman

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

summary:
Mast cells are tissue-resident innate immune cells that express high affinity to receptor immunoglobulin E and responsible for host defense and array of diseases relate to immune system.
We aim to characterize the function of human umbilical cord blood-dervied mast cells (hCBMCs).

overall_design: CD34+ cells were isolated from human umbilical cord blood and differentiated into mast cells using rhIL-6 and rh-SCF for 6-8 weeks. Total RNA was extracted from hCBMCs and CD34- cells and hybridized using Affymetrix Human Gene ST 1.0 arrays.

first: Ghalya

last: Banafea

first: Farid

last: Ahmed

first: Haneen

last: Alsehli

first: Huda

middle: F

last: Alshaibi

first: Nadia

last: Bagatian

first: Ohoud

last: Subhi

first: Kalamegam

last: Gauthaman

first: Mahmood

last: Rasool

first: Hans-Juergen

last: Schulten

first: Peter

last: Pushparaj


title: Trancriptome analysis of tumor tissue to search for the associations between USP8 mutation status, molecular markers of pituitary adenomas, and clinical, and diagnostic parametres of Cushing disease

status: Public on Apr 11 2024

city: Saint-Petersburg

first: Elena

last: Nerubenko

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Center

summary: In this work we employed the comprehensive evaluation of clinical data of the cohort of CD patients along with the sequencing of 14 exon of USP8 to estimate the prevalence of USP8 mutations in our cohort and transcriptome analysis of tumor tissue to search for the associations between USP8 mutation status, molecular markers of pituitary adenomas, and clinical and diagnostic parameters of Cushing’s syndrome including hormonal secretion, tumor size, aggressiveness, and SSRT2/SSRT5 expression.

overall_design: The RNA were extracted from  pituitary tumor brain tissue after transfenoidal surgery from alive patients. Under investigation were patients carrying the USP8 mutation and patients carrying the wild type of the gene.

middle: S

first: Oksana

last: Ivanova

middle: V

last: Ignatieva

first: Renata

middle: I

last: Dmitrieva

first: Ulyana

last: Tsoy


title: Australian Chronic Allograft Dysfunction II

status: Public on Apr 05 2024

city: Westmead

first: Harry

last: Robertson

state: NSW

address: 176 Hawkesbury Rd

department: Centre for Transplant and Renal Research

institute: Westmead Institute for Medical Research

summary: The Australian Chronic Allograft Dysfunction (AUSCAD) study is an ongoing single centre cohort study at Westmead hospital in Australia. In this section of the study, we aimed to identify biomarkers for chronic allograft dysfunction in kidney transplant recipients. Our study recruited 136 patients, each having protocol renal allograft biopsies taken pre transplantation.

overall_design: 136 patients had renal allograft back table biopsies collected pre-transplant at Westmead hospital. A combined criteria was used to classify the early function of the graft as either immediate or delayed. Kidney biopsy specimens were left in RNAlater (Sigma-Aldrich) overnight at 4°C before removal and storage at -80°C until RNA extraction. Specimens were chemically and physically lysed by using 2-Mercaptoethanol (Sigma-Aldrich) and TissueLyser II (Qiagen, Germany), follow by RNA extraction using AllPrep DNA/RNA/microRNA and MiniElute clean- up kits (Qiagen, Germany). All RNA samples were frozen and stored at -80°C and then sent in bulk to the Australian Genome Research Facility (AGRF, Melbourne, Australia). Sample QC and library preparation were performed in-house, and the resultant libraries sequenced using the NovaSeq 6000 platform (Illumina)

first: Jennifer

last: Li

first: Elivira

last: Jiminez-Vera

first: Natasha

last: Rogers

first: Ellis

last: Patrick

first: Philip

last: O'Connell


title: Base editing of Ptbp1 in neurons alleviates symptoms in a Parkinson’s disease mouse model

status: Public on Apr 02 2024

first: Desiree

last: Boeck

institute: University of Zurich

summary: Parkinson’s disease (PD) is a multifactorial disease caused by irreversible progressive loss of dopaminergic neurons. Recent studies reported successful conversion of astrocytes into dopaminergic neurons by repressing polypyrimidine tract binding protein 1 (PTBP1), which led to a rescue of motor symptoms in a mouse model for PD. However, the mechanisms underlying this cell type conversion remain underexplored and controversial. Here, we devised a strategy using adenine base editing to effectively knockdown PTBP1 in astrocytes and neurons in a PD mouse model. Using AAV delivery vectors at a dose of 2´108 vg per animal, we found that Ptbp1 editing in neurons, but not astrocytes, of the substantia nigra pars compacta and striatum resulted in the formation of tyrosine hydroxylase (TH)+ cells and the rescue of forelimb akinesia and spontaneous rotations. Phenotypic analysis of TH+ cells indicates that they originated from non-dividing neurons and acquired dopaminergic neuronal markers upon PTBP1 downregulation. While further research is required to fully understand the origin, identity, and function of these newly generated TH+ cells, our study reveals that the downregulation of PTBP1 can reprogram neurons to mitigate symptoms in PD mice.

overall_design: in vitro NGS data of base editing experiments (from 3 biological replicates )

last: Böck

first: Maria

last: Wilhem

first: Tommaso

last: Patriarchi

first: Gerald

last: Schwank


title: TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states [RNA-seq - day 10 earclips]

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

summary: Mutations in cancer risk genes increase susceptibility, but not all carriers develop cancer. Indeed, while DNA mutations are necessary drivers of cancer, only a small subset of mutated cells go on to cause the disease. To date, the mechanisms underlying individual cancer susceptibility remain unclear. Here, we took advantage of a unique mouse model of intrinsic developmental heterogeneity (Trim28+/D9) to investigate whether early-life epigenetic variation influences cancer susceptibility later in life. We found that heterozygosity of Trim28 is sufficient to generate two distinct early-life epigenetic states associated with differing cancer susceptibility. These developmentally primed states exhibit differential methylation patterns at typically silenced heterochromatin, detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential, frequently mutated in human cancers and correlated with poor prognosis. This study provides genetic evidence that intrinsic developmental heterogeneity can prime individual, lifelong cancer susceptibility.

overall_design: RNA sequencing of day 10 ear clips from WT and Trim28 animals

first: Ilaria

last: Panzeri

first: J

last: Pospisilik


title: MYT1L deficiency impairs excitatory neuron trajectory during cortical development [E14]

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

institute: Washington University in St. Louis

summary: Mutations that reduce the function of MYT1L, a neuron-specific transcription factor, are associated with a syndromic neurodevelopmental disorder. Furthermore, MYT1L is routinely used as a pro-neural factor in fibroblast-to-neuron transdifferentiation. MYT1L has been hypothesized to play a role in the trajectory of neuronal specification and subtype specific maturation, but this hypothesis has not been directly tested, nor is it clear which neuron types are most impacted by MYT1L loss. In this study, we profiled 412,132 nuclei from the forebrains of wild-type and MYT1L-deficient mice at three developmental stages: E14 at the peak of neurogenesis, P1 when neurons in the six cortical layers have been born, and P21 when neurogenesis is complete and neurons are maturing, to examine the role of MYT1L levels in the trajectory of neuronal development. We found that MYT1L deficiency significantly disrupted the relative proportions of cortical excitatory neurons. Changes in gene expression were concentrated in excitatory neurons, suggesting that transcriptional effects of MYT1L deficiency are largely due to disruption of neuronal maturation programs. Most effects on gene expression were cell autonomous and persistent through development. In addition, while MYT1L can both activate and repress gene expression, the repressive effects were most sensitive to haploinsufficiency, and thus more likely mediate MYT1L syndrome. These findings illuminate the intricate role of MYT1L in orchestrating gene expression dynamics during neuronal development, providing insights into the molecular underpinnings of MYT1L syndrome.

overall_design: Samples for snRNAseq were collected at three key developmental timepoints: E14, P1, and P21. At E14, forebrains were dissected from MYT1L WT, Het, and KO mice, with three replicates per genotype. These E14 samples included a mix of males and females for each genotype. For P1 samples, forebrains were harvested from 8 WT mice (5 male, 3 female) and 4 Het mice (3 male, 1 female). At P21, cortices were colleced from 6 WT animals (3 male, 3 female) and 6 Het animals (3 male, 3 female). Across all time points, nuclei were isolated from the dissected tissues. Library preparation was carried out using the Scale Biosciences Single Cell RNA Kit, with samples batched by age.

first: Allen

last: Yen

first: Simona

last: Sarafinovska

first: Xuhua

last: Chen

first: Dominic

last: Skinner

first: Fatjon

last: Leti

first: MariaLynn

last: Crosby

first: Jessica

last: Hoisington-Lopez

first: Yizhe

last: Wu

first: Jiayang

first: Zipeng

first: Kevin

middle: K

last: Noguchi

first: Robi

last: Mitra


title: TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states [RNA-seq - matched healthy and tumor tissues]

overall_design: RNA sequencing of matched healthy and tumor tissues from multiple organs of Trim28 animals


title: The architecture of the Porcine deltacoronavirus RNA genome inside virions by vRICseq

status: Public on Apr 10 2024

city: Wuhan

first: Dengguo

last: Wei

state: Hubei Province

address: Huazhong Agricultural University, Hongshan District, Wuhan City, Hubei Province

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

summary: Porcine deltacoronavirus (PDCoV) is a newly emerging and special delta coronavirus, which infect mammals such as pigs, cattle and humans, as well as chickens and birds. Exploring RNA structures in the viral genome benefits the understanding of the role of RNA in the lifecycle of viruses. In this study, vRIC-seq is employed to analyze the RNA-RNA interaction in the whole genome structure of PDCoV in virions. About 12.87 and 13.52 million paired reads are obtained in two biological replicates, respectively, with 17.9% and 14.8% of them are identified as valid chimeric reads. These are employed to predict the RNA secondary structure, which is compact and highly structured. A twisted-cyclized conformation is observed in the RNA-RNA interaction map of PDCoV for the first time. 77 multi-way junctions are evenly distributed in the PDCoV genome. Our work provides fundamental structural insights that are essential for understanding the genomic structure and function, genetic evolution, and packaging characteristics of PDCoV.

overall_design: The whole genome structure of PDCoV (ID: KT336560) was probed by vRIC-seq.

first: Ju

last: Sun

first: Zhiyuan

last: Huang

first: Lei

first: Liangrong

last: Guo

first: Yuxiang

last: Wang

first: Yingxiang

last: Deng

first: Guoyue

last: Liu

first: Zi

last: Wen


title: Ectopic expression of transcriptional regulatory proteins reveals two classes of late genes during chlamydial development, corresponding to the IB and EB cell type.

status: Public on Apr 01 2024

city: Moscow

first: Scott

middle: Stephen

last: Grieshaber

state: ID

address: 875 Perimeter Drive MS 3051

department: Biological Sciences

institute: University of Idaho

summary: The bacteria in the chlamydiales order are obligate intracellular parasites of eukaryotic cells. They are reliant on an infectious cycle consisting of at least three phenotypically distinct cell forms termed the reticulate body (RB), the intermediate body (IB) and the elementary body (EB). The EB is infectious but does not replicate. The RB replicates in the host cell but is non-infectious, while the IB is an intermediate form that transitions to the EB form. Within this order, the genus Chlamydia contains the causative agents of a number of important pathogens of humans. C. psittaci causes zoonotic infections resulting in pneumonia, while C. pneumoniae is a human pathogen that causes respiratory disease and is linked to atherosclerosis. Biovars of C. trachomatis are the causative agents of trachoma, the leading cause of preventable blindness worldwide, as well as sexually transmitted infections with the potential to cause pelvic inflammatory disease and infertility. Irrespective of the resulting disease, all chlamydial species share the same obligate intracellular life cycle and developmental cell forms. In this study we investigated the role of four transcriptional regulators on chlamydial gene expression and completion of the developmental cycle. We ectopically expressed the transcriptional repressor Euo, each of the two nucleoid associated proteins HctA and HctB and the two component sensor kinase CtcB in the RB. All four blocked development of infectious EBs. Transcriptional analysis using RNA-seq and differential expression clustering revealed three classes of gene expression. FISH analysis demonstrated that these classes corresponded to distinct cell forms revealing the gene expression profile of the RB, IB and EB developmental forms. Additionally, these data revealed that the genes for the T3SS were cell type restricted. The structural genes for the T3SS were expressed primarily in the IB while the two translocons were expressed in distinct cell types one in the RB and the other in the EB. Overall these data show that the chlamydial developmental cycle produces three distinct regulons corresponding to the RB, IB and EB cell forms and that the T3SS is expressed in a cell form specific manner suggesting defined functional roles for the T3SS in specific cell forms.

overall_design: RNA-seq analysis of Chlamydia trachomatis ectopicaly expressing the regulatory proteins, Euo, HctA, CtcB and HctB

first: Nicole

first: Cody

last: Appa

first: Anders

last: Omsland


title: The 24-Hour Time Course of Integrated Molecular Responses to Resistance Exercise in Human Skeletal Muscle Implicates MYC as a Hypertrophic Regulator

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: Molecular control of recovery after exercise in muscle is temporally dynamic. A time course of biopsies around resistance exercise (RE) combined with -omics is necessary to better comprehend the molecular choreography of skeletal muscle adaptation in humans. We collected vastus lateralis biopsies before and 30 minutes, 3-, 8-, and 24 hours after acute RE. RNA-sequencing defined the transcriptome and a time-point matched biopsy only group were controls. DNA methylomics and computational approaches complimented the transcriptome data. Moreover, we tested whether cyclic transient overexpression of transcription factor MYC for 4 weeks were sufficient to induce skeletal muscle hypertrophy in female mice.

overall_design: Thirteen recreationally active volunteers volunteered to participate in the study. Eight in the RE group (age of 32±5 years, height of 181±9 cm, weight of 83±8 kg, and body mass index (BMI) of 25.3±2.0), and five in the CON group (age of 30±4 years, height of 177±5 cm, weight of 85±12 kg, and finally a BMI of 27.3±3.6).  Following an overnight fast, volunteers consumed a standardized amount of liquid formula for breakfast. One hour after the breakfast, skeletal muscle biopsies were collected from the vastus lateralis using a Bergström needle. Ninety minutes after breakfast, volunteers started a 45 minute standardized RE session (7 reps x 7 set on leg press and leg extension machines; RE group) or rested for 45 minutes (CON group). Biopsies were again collected at 30 minutes, 3-, 8-, and 24 hours after exercise cessation. Biopsies were time point matched in the CON group. A standardized lunch was administered following the biopsy at 3 hours post RE. Following the 8-hour biopsy, volunteers were sent home overnight and instructed to eat a healthy dinner. The morning after, volunteers again received a standardized breakfast prior to donating their final biopsy, 24 hours after RE. Approximately 25 mg of muscle tissue from each biopsy was homogenized in TRI Reagent (Sigma-Aldrich, St Louis, MO, USA). RNA isolated using bromochloropropane and centrifugation. Next, the RNA was processed using Direct-zol filter columns (Zymo Research, Irvine, CA, USA). Finally, the RNA was treated with DNAse and eluted in DEPC-treated water prior to storage at -80°C. The concentration and purity of the RNA were determined using a BioTek PowerWave XS microplate reader (BioTek Instruments Inc., Winooski, VT, USA). mRNA library preparation was done using Poly A enrichment, followed by RNA sequencing by an Illumina NovaSeq 6000 (Novogene Corp. Inc., Sacramento, CA, USA) using 150 bp paired-end sequencing.

first: Sebastian

last: Edman

first: Ronald

middle: G

last: Jones III

middle: R

last: Murach

first: Ferdinand

last: von Walden


title: MYT1L deficiency impairs excitatory neuron trajectory during cortical development

first: Joseph

last: Dougherty

department: Genetics

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

overall_design: Refer to individual Series


title: Plasma amino acids regulate pancreatic acinar cell proliferation and size via mTORC1 and YAP/TAZ signaling pathways

status: Public on Mar 30 2024

first: Wenbiao

last: Chen

address: 743 Robinson Research Building

department: MPB

institute: Vanderbilt Univ School of Medicine

summary: Pancreas volume or mass varies more than 3-fold among adult humans. The heterogeneity is likely the result of genetics, diseases, and nutrition. Dietary protein intake and blood amino acid levels are known to affect pancreas mass, but the underlying mechanism is not well understood. The goal of this study is to determine how increased blood amino acid level (hyperaminoacidemia) induces pancreas expansion.Multiple complementary mouse and zebrafish models were used to study the impact of hyperaminoacidemia on pancreatic mass, acinar cell size and proliferation. Blood amino acid levels were manipulated by dietary protein content, or by pharmacologic or genetic interruption of glucagon signaling (IGS). The activation of mammalian target of rapamycin complex 1 (mTORC1) and Yes-associated protein 1 (YAP) were determined by pS6 and YAP staining. Sirolimus administration in mice and knockdown of solute carrier family 38 member 5b (slc38a5b) and yap/taz in zebrafish were used to determine the role of mTORC1, SLC38A5 and YAP/TAZ in acinar cell proliferation and pancreas expansion. We found that the IGS-induced pancreas expansion was the result of acinar cell proliferation and hypertrophy. Hyperaminoacidemia was the likely mediator as pancreas expansion was blunted by a low protein diet in mice and by knocking down the most highly expressed amino acid transporter gene, slc38a5b, in zebrafish lacking both glucagon receptor genes (gcgr-/-). In GCGR-Ab treated mice, inhibition of mTORC1 attenuated both hyperplasia and hypertrophy of acinar cells. There was a gene expression signature of YAP activation in acinar cells, consistent with increased YAP-expressing acinar cells in GCGR-Ab treated mice and increased fraction of acinar cells with nuclear YAP1 in gcgr-/- zebrafish. Knocking down yap1 or taz decreased mTORC1 activity and acinar cell hyperplasia and hypertrophy in gcgr-/- zebrafish. Hyperaminoacidemia leads to acinar cell proliferation and hypertrophy via activation of both mTORC1 and YAP pathways. The study discovered a previously unrecognized role of the YAP/Taz pathway in hyperaminoacidemia-induced acinar cell hypertrophy and hyperplasia.

overall_design: To investigate the interruption of glucagon signaling, C57BL/J6 mice were intraperitoneally injected with  monoclonal antibody targeting the glucagon receptor (GCGR-Ab) or IgG . Next, we perform gene xpression analysis from the RNA-seq data of 5 GCG-Ab treated samples and 4 IgG treated samples.

first: Chunhua

last: Dai

first: Yulong

last: Gong

first: Yue

last: Zhang

first: Amber

last: Bradley

first: Zihan

last: Tang

first: Katelyn

last: Sellick

first: Shristi

last: Shrestha

first: Erick

last: Spears

first: Brittney

last: Covington

first: Jade

last: Stanley

first: Regina

last: Jenkins

first: Tiffany

last: Richardson

first: Rebekah

last: Brantley

first: Katie

last: Coate

first: Diane

middle: C

last: Saunders

first: Jordan

last: Wrights

first: Marcela

last: Brissova

first: Danielle

last: Dean

first: Alvin

last: Powers


title: MYT1L deficiency impairs excitatory neuron trajectory during cortical development [P21]

first: Joseph

last: Dougherty

first: Allen

last: Yen

first: Simona

last: Sarafinovska

first: Xuhua

last: Chen

first: Dominic

last: Skinner

first: Fatjon

last: Leti

first: MariaLynn

last: Crosby

first: Jessica

last: Hoisington-Lopez

first: Yizhe

last: Wu

first: Jiayang

first: Zipeng

last: Li

first: Kevin

last: Noguchi

first: Robi

last: Mitra


title: Single-cell analysis reveals Mycobacterium tuberculosis ESX-1–mediated accumulation of permissive macrophages in infected mouse lungs

first: Leah

last: Dorman

institute: CZBiohub

summary: Mycobacterium tuberculosis (MTB) infects and replicates in lung mononuclear phagocytes (MNPs) with astounding ability to evade elimination. A virulence determinant that contributes to MTB’s ability to survive within MNPs is ESX-1, a type VII secretion system. However, how MTB virulence factors influence mononuclear cell recruitment and/or differentiation remains unknown. Here, using single-cell RNA sequencing, we studied the role of ESX-1 in MNP heterogenicity and response in mice and murine bone marrow-derived macrophages. We found that ESX-1 is required for MTB to recruit diverse MNP subsets with high MTB burden. Further, MTB induces an anti-inflammatory signature that may lead to more permissive MNPs. Spatial transcriptomics revealed an upregulation of anti-inflammatory signals in MTB lesions, where monocyte-derived macrophages concentrate near MTB-infected cells. Together, our findings suggest that MTB ESX-1 mediates the recruitment and differentiation of anti-inflammatory MNPs, which MTB can infect and manipulate for survival.

overall_design: Single-cell suspension from harvested lungs from C57BL/6 uninfected or infected with H37Rv or H37Rv-deltaEccD for 28 days were stained and index sorted to obtain live CD11b and/or c infected cells and bystander into 384 well plates - these were processed by smartseq2.

first: Shoshana

middle: B

last: Zha

first: Weihao

last: Zheng

first: Michael

last: Borja

first: Norma

last: Neff

first: Angela

last: Pisco


title: TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states

status: Public on Mar 29 2024

first: Luca

last: Fagnocchi

type: Methylation profiling by genome tiling array

first: Ilaria

last: Panzeri

first: J

last: Pospisilik


title: Australian Chronic Allograft Dysfunction III

first: Harry

last: Robertson

summary: The Australian Chronic Allograft Dysfunction (AUSCAD) study is an ongoing single centre cohort study at Westmead hospital in Australia. In this section of the study, we aimed to identify biomarkers for allograft rejection in kidney transplant recipients, 3-months after their transplant. Our study recruited 123 patients, each having protocol renal allograft biopsies taken 3-months post transplantation.

overall_design:
123 patients had renal allograft biopsies collected 3 months post-transplant at Westmead hospital. One core was used for sequencing, the other was analysed by a single pathologist at Westmead. The banff19 classification system was used for diagnosis. For the purpose of this study, a combined criteria of ABMR and TCMR was classified at Rejection (Rej). Biopsies with no evidence of rejection were treated as the control group (Nill).
Kidney biopsy specimens were left in RNAlater (Sigma-Aldrich) overnight at 4°C before removal and storage at -80°C until RNA extraction. Specimens were chemically and physically lysed by using 2-Mercaptoethanol (Sigma-Aldrich) and TissueLyser II (Qiagen, Germany), follow by RNA extraction using AllPrep DNA/RNA/microRNA and MiniElute clean- up kits (Qiagen, Germany). All RNA samples were frozen and stored at -80°C and then sent in bulk to the Australian Genome Research Facility (AGRF, Melbourne, Australia). Sample QC and library preparation were performed in-house, and the resultant libraries sequenced using the NovaSeq 6000 platform (Illumina)

first: Jennifer

first: Elivira

last: Jiminez-Vera

first: Natasha

last: Rogers

first: Ellis

last: Patrick

first: Philip

last: O'Connell


title: Single-cell analysis reveals Mycobacterium tuberculosis ESX-1-mediated accumulation of permissive macrophages in infected mouse lungs

relation:
SuperSeries of: GSE263880
SuperSeries of: GSE263882
SuperSeries of: GSE263891


title: Paired analysis of host and pathogen genomes identifies determinants of human tuberculosis

city: Boston

first: Xin

last: Wang

address: 677 Huntington Ave

institute: Harvard University School of Public Health

summary: The outcome of an infectious disease exposure is the result of interactions between host and pathogen and can depend on genetic variations in both. We explored this relationship in tuberculosis (TB) by conducting a genome-to-genome (g2g) study of paired human and Mycobacterium tuberculosis (Mtb) genomes from a cohort of 1556 TB patients in Lima, Peru. We identified an association between a human intronic variant (rs3130660, OR = 10.06, 95% CI: 4.87 - 20.77, P = 7.92 ⨉ 10-8 ) in the FLOT1 gene and a subclade of Mtb Lineage 2 (g2g-L2). We assessed this interaction in a Mtb-macrophage infection model between bacterial and host genetic backgrounds. We found that expression of FLOT1 and other genes in the MHC class-I region are differentially modulated by g2g-L2 compared to nearest neighbor strains. We also found distinct inflammatory responses with different host genetic backgrounds, with hosts carrying the A allele of rs3130660 inducing stronger type I and II interferon (IFN) gene signatures than hosts carrying only the T allele. TB infection with g2g-L2 strains shift macrophage responses away from this IFN signaling. In vitro analyses show that the g2g-L2 strains are distinguished by altered redox states and resistance to reductive stress and that these phenotypes result from a single mutation in thioredoxin reductase (trxB2, T2N). We also investigated this association in a 2020 cohort of 699 patients with TB recruited during the COVID-19 pandemic. Between 2010 and 2020, the prevalence of the g2g-L2 strain almost doubled, nearly fully replacing the other co-circulating L2 strains. However, g2g-L2 infection was not associated with rs3130660 in this cohort. These data raise the possibility of a more dynamic landscape of interacting host, pathogen and environmental risk factors than previously expected for TB.

overall_design: We obtained macrophages from three randomly selected Peruvian donors from our cohort who carried the risk allele A (rs3130660-AT) and three donors who did not (rs313060-TT). We infected these monocyte-derived donor macrophages (MDMs) with three g2g-L2 strains and three non-g2g-L2 strains with similar in vitro growth characteristics, and measured macrophage transcriptional responses by RNA-sequencing

first: Nicole

last: Howard

first: Qingyun

last: Liu

first: Yang

last: Luo


title: From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [scRNAseq]

city: Paris

first: Anne-Hélène

last: Monsoro-Burq

state: Ile-de-France

address: 26 rue d'Ulm

country: France

institute: Curie Institute

summary: Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices governing the emergence of neural crest heterogeneity from the ectoderm remains elusive. Gene regulatory networks govern these steps of embryonic development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning strategies and experimental validation to provide a comprehensive gene regulatory network driving vertebrate neural crest fate diversification, from induction to early migration stages. Transcription factor connectome and bifurcation analyses demonstrate emergence of early neural crest fates at the neural plate stage, alongside an unbiased multipotent neural crest lineage persisting until after epithelial-mesenchymal transition. We also define a new and transient neural border zone state, preceding choice between neural crest and placodes during gastrulation. Theis combination of experimental tests, with Machine Learning broadly applicable to single cell transcriptomics, deciphers the circuits driving cranial and vagal neural crest formation and provides a general model for investigating vertebrate GRNs in development, evolution and disease.

overall_design: We sequenced the RNA-libraries for the developmental stages NF8 to NF22 used in (Briggs et al., 2018). For sequencing we used two flow cells (two lanes each) of NovaSeq S2 at 100 cycles setting generating a total of 12 billion reads.

first: Aleksandr

last: Kotov

first: Mansour

last: Alkobtawi

first: Subham

last: Seal

first: Vincent

last: Kappes

first: Sofia

last: Medina

first: Hugo

last: Arbes

first: Richard

last: Harland

first: Leon

last: Peshkin

first: Anne-Helene


title: Functional omics of ORP7 in primary endothelial cells

status: Public on Mar 19 2024

city: Helsinki

first: Juuso

last: Taskinen

address: Tukholmankatu 8

country: Finland

institute: Minerva Foundation Institue for Medical Research

summary: Many members of the oxysterol binding protein related protein (ORP) family have been characterized in detail over the past decades, but the lipid transport and other functions of ORP7 still remain elusive. What is known about ORP7 points toward an endoplasmic reticulum and plasma membrane-localized protein, which also interacts with GABARAPL2 and unlipidated LC3B, suggesting a further autophagosomal/lysosomal association. Functional roles of ORP7 have been suggested in cholesterol efflux, hypercholesterolemia, and macroautophagy. We performed a hypothesis-free omics analysis of chemical ORP7 inhibition utilizing transcriptomics and lipidomics as well as proximity biotinylation interactomics to characterize ORP7 functions in a primary cell type, human umbilical vein endothelial cells (HUVECs). Moreover, assays on metrics such as angiogenesis, cholesterol efflux and lipid droplet quantification were conducted. Pharmacological inhibition of ORP7 lead to an increase in gene expression related to lipid metabolism and inflammation, while genes associated with cell cycle and cell division were downregulated. Lipidomic analysis revealed increases in ceramides, lysophosphaditylcholines, as well as saturated and monounsaturated triacylglycerols. Significant decreases were seen in all cholesteryl ester and in some unsaturated triacylglycerol species, compatible with the detected decrease of mean lipid droplet area. Along with the reduced lipid stores, ABCG1-mediated cholesterol efflux and angiogenesis decreased. Interactomics revealed an interaction of ORP7 with AKT1, a central metabolic regulator. The transcriptomics results suggest an increase in prostanoid as well as oxysterol synthesis, which could be related to the observed upregulation of proinflammatory genes. We envision that the defective angiogenesis in HUVECs subjected to ORP7 inhibition could be the result of an unfavorable plasma membrane lipid composition and/or reduced potential for cell division. To conclude, the present study suggests multifaceted functions of ORP7 in lipid homeostasis, angiogenic tube formation and gene expression of lipid metabolism, inflammation and cell cycle in primary endothelial cells.

overall_design: HUVEC cells were treated with a 10 micro molar concentration of ORP7 inhibitor CpdG or 1:1000 v/v% of DMSO for 24 hours. HUVECs lentiviral transfected with a ORP7-mycBirA or an empty mycBirA vector

middle: H

first: Minna

last: Holopainen

first: Hanna

last: Ruhanen

first: Reijo

last: Käkelä

first: Vesa

last: Olkkonen


title: IMMUNE-RESPONSIVE GENE 1 REGULATES ATHEROSCLEROTIC PLAQUE INFLAMMATION II

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

summary: Atherosclerosis is the major underlying cause of cardiovascular disease (CVD) mortality and is fueled by a failure to resolve inflammation within the vessel wall1. The mechanisms underpinning sustained inflammation within this microenvironment are not fully elucidated. A more comprehensive understanding of the immunoregulatory pathways modulating inflammation in this context holds the potential to inform the development of more specific therapies. Immune responsive gene 1 (Irg1) is an enzyme that diverts cis-aconitate from the TCA cycle and produces the metabolite itaconate, which elicits immunological tolerance in the context of microbial infection2–4. We hypothesized that the IRG1-itaconate axis restricts inflammation in the atherosclerotic plaque.

overall_design:
Formation of atherslerotic plaque was induced in mice by placing them on Western Diet. Aorta's were removed and single-cell suspensions of the aortic arch were made and CD45+immune cells were isolated by staining (anti-CD45 PerCp-Cy5.5, BioLegend) and flow sorting viable (fixable viability dye e780, eBioscience) single cells on a Facs Aria II cytometer (BD) equipped with a 100 µm nozzle. Next scRNA seq was performed and analyzed.
ADT/HTO Barcode sequence hashtagged samples
CMO301 ATGAGGAATTCCTGC WT_mouse_1
CMO302 CATGCCAATAGAGCG WT_mouse_2
CMO303 CCGTCGTCCAAGCAT WT_mouse_3
CMO304 AACGTTAATCACTCA WT_mouse_4
CMO305 CGCGATATGGTCGGA WT_mouse_5
CMO306 AAGATGAGGTCTGTG KO_mouse_1
CMO307 AAGCTCGTTGGAAGA KO_mouse_2
CMO308 CGGATTCCACATCAT KO_mouse_3
CMO309 GTTGATCTATAACAG KO_mouse_4
CMO310 GCAGGAGGTATCAAT KO_mouse_5
CMO301 ATGAGGAATTCCTGC WT+DMSO_mouse_1
CMO302 CATGCCAATAGAGCG WT+DMSO_mouse_2
CMO303 CCGTCGTCCAAGCAT WT+DMSO_mouse_3
CMO304 AACGTTAATCACTCA WT+DMSO_mouse_4
CMO308 CGGATTCCACATCAT KO+DMSO_mouse_1
CMO309 GTTGATCTATAACAG KO+DMSO_mouse_2
CMO310 GCAGGAGGTATCAAT KO+DMSO_mouse_3
CMO311 GAATCGTGATTCTTC KO+DMSO_mouse_4
CMO312 ACATGGTCAACGCTG KO+DMSO_mouse_5
CMO305 CGCGATATGGTCGGA KO+4OI_mouse_1
CMO306 AAGATGAGGTCTGTG KO+4OI_mouse_2
CMO308 CGGATTCCACATCAT KO+4OI_mouse_3
CMO309 GTTGATCTATAACAG KO+4OI_mouse_4

first: Fazli

last: Bozal

first: Yannick

last: Cyr

first: Jose

last: Duran

first: Kathryn

middle: J

last: Moore


title: TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states [DNA methylation array - d10earclips_2nd cohort]

first: Luca

last: Fagnocchi

overall_design: Comparison of DNA methylation profiles by array of 10 days old mouse ear clips, between 2 genotypes (WT, Trim28) - 2nd cohort

first: Ilaria

last: Panzeri

first: J

middle: A

last: Pospisilik


title: TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states [DNA methylation array - healthyTissues]

overall_design: DNA methylation profiles by array of different tissues from Trim28-Light and -Heavy animals


title: From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [morpholinoRNAseq]

first: Anne-Hélène

last: Monsoro-Burq

overall_design: There are 10 samples for pax3, zic1 and tfap2e MO. Two replicates for zic1 and tfap2e and one replicate for pax3. Previously validated antisense morpholino oligonucleotides (MO) were used to block pax3 and tfap2e expression (GeneTools). 20 ng of pax3 MO (Monsoro-Burq et al., 2005) or tfap2e MO (Hong et al., 2014) were injected into one blastomere of two-cell stage X. laevis embryos, according to the assay. At the desired stage, one anterior NB (stage 14) or one NC (stage 17) was dissected from the injected side and used for RNA extraction and cDNA library preparation, which were then used for small RNA-seq (Fig S8). The resulting 100 bp paired-end sequencing reads were aligned to the X. laevis genome version 9.2 using STAR and the count reads were analyzed using String Tie.

first: Aleksandr

last: Kotov

first: Mansour

last: Alkobtawi

first: Subham

last: Seal

first: Vincent

last: Kappes

first: Sofia

last: Medina

first: Hugo


title: Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts

status: Public on Mar 28 2024

city: Cambridge

first: Jessica

last: Mitchell

state: Massachusetts

address: 16 Divinity St, Biolabs # 3102

department: Department of Organismic and Evolutionary Biology

institute: Harvard University

summary: Biological carbon fixation is foundational to the biosphere. Most autotrophs are thought to possess one carbon fixation pathway. The hydrothermal vent tubeworm Riftia pachyptila’s chemoautotrophic symbionts, however, possess two functional pathways: the Calvin Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. Little is known about how Riftia’s symbionts and related organisms coordinate the functioning of these two pathways. Here we investigated net carbon fixation rates, transcriptional/metabolic responses, and transcriptional co-expression patterns of Riftia pachyptila’s endosymbionts by incubating tubeworms at environmental pressures, temperature, and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes, suggesting distinctive yet complementary roles in metabolic function. Net carbon fixation rates were also exemplary, and accordingly we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.

overall_design: In order to investigate the symbiont's  response to varying conditions in our high pressure aquaria, we looked at the gene expression profiles of symbionts sampled from individual worms that were in these aquaria. These data  include three samples (from three worms) from each experimental aquaria representing 10 different conditions, so 30 metatranscriptomes in total.

first: Adam

last: Freedman

first: Jennifer

last: Delaney

first: Peter

last: Girguis


title: IMMUNE-RESPONSIVE GENE 1 REGULATES ATHEROSCLEROTIC PLAQUE INFLAMMATION III

first: Michael

last: Gildea

overall_design: Formation of atherslerotic plaque was induced in mice by placing them on Western Diet. Aorta's were removed and single-cell suspensions of the aortic arch were made and CD45+immune cells were isolated by staining (anti-CD45 PerCp-Cy5.5, BioLegend) and flow sorting viable (fixable viability dye e780, eBioscience) single cells on a Facs Aria II cytometer (BD) equipped with a 100 µm nozzle. Next scRNA seq was performed and analyzed.

first: Fazli

last: Bozal

first: Yannick

last: Barcia Duran


title: Sef1-dependent gene expression in Saccharomyces cerevisiae

status: Public on Mar 25 2024

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: To understand the gene expression in Saccharomyces cerevisiae under fermentative and respiraotry conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of S. cerevisiae wild type, sef1 deletion, and hyperactive SEF1-VP16 mutants under the YPD and YPGly conditions.

overall_design: Cells from overnight YPD cultures were diluted into YPD and YPGly at a cell density of 0.2 OD per ml and incubated at 30°C for 5.5 h. Four biological replicates fro each strain under each condition were preprared.

first: Jun-Yi

last: Leu


title: Comparison of gene expression in the nucleus accumbens of rats expressing or not the conditioned place preference to cocaine [CPPE, nCPPE, Saline after cocaine reinstatement]

status: Public on Mar 11 2024

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: Substance use disorder emerges in a small proportion of drug users and has the characteristics of a chronic relapsing pathology. The objective of our study was to demonstrate and characterize the variability in the expression of the reinforcing effects of cocaine in the conditioned place preference (CPP) paradigm. An unbiased cocaine-CPP paradigm in Sprague-Dawley rats with an extinction period of 12 days and reinstatement was conducted. We developed a statistical model to distinguish rats that express or do not express cocaine-induced place preference. Two groups of rats were identified: rats that did express reinforcing effects (CPP expression (CPPE), score > 102 s) and rats that did not (no CPP expression (nCPPE), score between −85 and 59 s). These two groups did not show significant differences in a battery of behavioral tests. To identify differentially expressed genes in the CPPE and nCPPE groups, we performed a whole-transcriptome RNA-sequencing analysis in the nucleus accumbens (Nac) 24 h after the CPP test. Four immediate early genes (Fos, Egr2, Nr4a1 and Zbtb37) were differentially expressed in the Nac of CPPE rats after CPP memory retrieval. Variability in cocaine-induced place preference persisted in the CPPE and nCPPE groups after the extinction and reinstatement phases. Transcriptomic differences observed after reinstatement were distinct from those observed immediately after CPP memory retrieval. These new findings provide insights into the identification of mechanisms underlying interindividual variability in the response to cocaine's reinforcing effects.

overall_design: Cocaine CPP was performed in 8-week-old Sprague-Dawley rats, after a 12 days extinction phase cocaine reinstatement was conducted and the nucleus accumbens transcriptomes of CPPE, nCPPE and Saline rats were compared.

first: Luisa

last: Atehortua Martinez

first: Nawel

last: Mekdad

first: Emmanuel

last: Curis

first: Claire

last: Larrieu

first: Cindie

last: Courtin

first: Laurent

last: Jourdren

first: Corinne

last: Blugeon

first: Jean

middle: L

last: Laplanche

first: Bruno

last: Megarbane

first: Cynthia

last: Marie-Claire

first: Nadia

last: Benturquia


title: IMMUNE-RESPONSIVE GENE 1 REGULATES ATHEROSCLEROTIC PLAQUE INFLAMMATION I

first: Michael

last: Gildea

overall_design:
PBMCs were treated with 4O1 and CVD plasma, plasma only or no plasma. After 4 hours, cells were harvest and subjected to scRNAseq
ADT/HTO Barcode sequence hashtagged samples
HT1 GTCAACTCTTTAGCG No_plasma_sample_1
HT2 TGATGGCCTATTGGG No_plasma_sample_2
HT3 TTCCGCCTCTCTTTG No_plasma_sample_3
HT4 AGTAAGTTCAGCGTA No_plasma_sample_4
HT1 GTCAACTCTTTAGCG plasma_sample_1
HT2 TGATGGCCTATTGGG plasma_sample_2
HT3 TTCCGCCTCTCTTTG plasma_sample_3
HT4 AGTAAGTTCAGCGTA plasma_sample_4
HT1 GTCAACTCTTTAGCG Plasma+4OI_sample_1
HT2 TGATGGCCTATTGGG Plasma+4OI_sample_2
HT3 TTCCGCCTCTCTTTG Plasma+4OI_sample_3
HT4 AGTAAGTTCAGCGTA Plasma+4OI_sample_4

last: Cyr

first: Jose

last: Duran

first: Kathryn

last: Moore


title: From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [ChIPseq]

first: Anne-Hélène

last: Monsoro-Burq

sample_organism:
Xenopus laevis
Xenopus tropicalis

platform_organism:
Xenopus laevis
Xenopus tropicalis

overall_design: There are 23 samples for 3 Transcription factors (Pax3, Tfap2a, Tfap2e) with 3 replicates for Pax3 and Tfap2a. Chromatin immunoprecipitation assay was performed according to Wills et al., 2014. Embryos were injected in both blastomeres at two-cell stage with trace amounts of mRNA encoding Pax3-FLAG-HA (75 pg), Tfap2a-FLAG or Tfap2e-FLAG. Injected embryos were collected at mid-neurula stage 14 (Pax3 and Tfap2a, 100 embryos/condition) or at NC migratory stage 19 (Tfap2e, 100 embryos/condition). Sonication was performed using a 3.2 mm tapered microtip for 13 mm horn (Branson 450 sonicator). Anti-FLAG (Sigma F3165) and magnetic beads (Invitrogen, 10002D) were added separately to the chromatin.

first: Aleksandr

last: Kotov

first: Mansour

last: Alkobtawi

first: Subham

last: Seal

first: Vincent

last: Kappes

first: Sofia

last: Medina

first: Hugo

last: Arbes

first: Richard

last: Harland

first: Leon

last: Peshkin

first: Anne-Helene


title: IMMUNE-RESPONSIVE GENE 1 REGULATES ATHEROSCLEROTIC PLAQUE INFLAMMATION

status: Public on Mar 18 2024

overall_design: Refer to individual Series


title: Effect of ATRA on HH, Hut78 and NB4 cells

city: Shanghai

first: Chenhui

last: Luo

address: Shanghai Jiao Tong University School of Medicine

summary: Cutaneous T-cell lymphoma (CTCL) is a highly heterogeneous non-Hodgkin lymphoma.While retinoids analog including ATRA have been used to treat CTCLs for decades, their mechanism of action and the role of RA-RARα signaling remain poorly understood.Thus,we treated CTCL cells with ATRA.In parallel, we treated acute promyelocytic leukemia (APL) cell line NB4 with ATRA followed by RNA-seq analysis.Total RNA was prepared from biological duplicate plates of cells and subjected to bulk RNAseq. 150-bp paired-end sequencing was performed on the BGISEQ-500.

overall_design: HH, Hut78 and NB4 cells were treated with 1 µM of ATRA for 6 hours (n=2 for each group).Total RNA extraction were used for RNA-seq.