title: Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate motor cortex [Macaque]

status: Public on Oct 31 2023

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome, and chromosomal conformation profiles from a total of over 180,000 cells. For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes and that epigenetic status at distal candidate cis-regulatory elements (cCREs) evolves faster than promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity helps uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.

overall_design:
The motor cortex of  Macaque were disected and nuclei were prepared for library preparation. In-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.  The snm3C-seq samples followed the library preparation protocol detailed previously. This protocol has been automated using the Beckman Biomek i7 instrument to facilitate large-scale applications. The snm3C-seq libraries were sequenced on an Illumina NovaSeq 6000 instrument, utilizing one S4 flow cell per 16 384-well plates and employing a 150 bp paired-end mode.

This study includes samples in the following series:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241339
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219006
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219113
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219198
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219263

first: Wenliang

last: Wang

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Huaming

last: Chen


title: Affymetrix array expression data from colon polyps

status: Public on Aug 09 2023

city: Baltimore

first: Yuba

last: Bhandari

state: MD

address: 1650 Orleans Street

country: USA

institute: The Johns Hopkins University School of Medicine

summary:
The tubular adenoma sample cohort (accrued by Janssen Pharmaceuticals) consisted of 127 high-risk baseline adenoma samples acquired retrospectively by Avaden Biosciences. High risk patients are defined here as presenting a tubular adenoma ? 10mm, 3 or more adenomas, adenomas with villous histology or adenomas showing high-grade dysplasia based on Lieberman et al.
Patients with familial adenomatous polyposis (FAP) and Lynch syndrome were excluded. All patients received at least one baseline colonoscopy for which clinical and pathological records were available. Adenoma tissue was available as archival, formalin-fixed, paraffin-embedded (FFPE) blocks.

overall_design: Expression dataset (N=61 samples) for the colon polyps was derived using Affymetrix Array platform (HT HG-U133 Plus PM) and was processed using affy package with Robust Multichip Average (RMA) normalization.

first: Vinod

last: Krishna

first: Rachael

last: Powers

first: Sehej

last: Parmar

first: Sara-Jayne

last: Thursby

first: Ekta

last: Gupta

first: Ozlem

last: Kulak

first: Prashanth

last: Gokare

first: Joke

last: Reumers

first: Liesbeth

last: Van Wesenbeeck

first: Kurtis

middle: E

last: Bachman

first: Stephan

middle: B

last: Baylin

first: Hariharan

last: Easwaran


title: Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Single-cell RNA sequencing of Drosophila embryonic heart

status: Public on Aug 07 2023

first: Hangnoh

last: Lee

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

type: Expression profiling by high throughput sequencing

summary: Single-cell RNA sequencing was performed on embryonic Drosophila heart cells. Analysis of single-cell RNA sequence (scRNA-seq) data at timepoints prior to migration of cardiac progenitor cells through to heart tube closure (embryonic stages 13, 14-early, 14-late, 15 and 16) revealed several interesting findings. We found specification of cardiac cell types takes place early, before stage 13, with biggest changes in transcriptomic profiles detected once cells had settled at the midline for further cardioblast maturation. Throughout development, our data identified multiple cell types, covering cardioblasts and five types of pericardial cells including a neural cardiac cell type. The scRNA-seq data further revealed a combination of first and second heart fields during heart development in fly. Further, we uncovered new cell type-specific markers discerning the different cardiac cell types. And we identified signaling pathways key to heart cell maturation, which are conserved from fly to human.

overall_design: We collected fresh embryonic heart cells from stage 13 to stage16 by FACS and prepared single-cell RNA library according to the manufacturer's protocol (10X Genomics, CA, USA), and samples were sequenced by Illumina HiSeq platform (carried out by Novogene, CA).

first: X

last: Huang

first: Y

last: Fu

first: H

first: P

last: Zhang

first: Z

last: Han


title: Effect of LIPUS & Piezoelectric Membranes for  of Macrophage Polarization

status: Public on Jul 31 2023

city: Shanghai,

first: Ting

last: Jiang

address: Quxi Road No. 500

country: China

institute: Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Effect of Low-intensity pulsed ultrasound (LIPUS) assisted BT/MWCNTs/Col (BMC) membrane on gene expression during  immune response  of macrophages (Raw 264.7).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of Raw264.7 under different conditions (control, BMC, BMC+lipus)

first: Ningjuan

last: Ouyang


title: Alalysis of gene expression sigunature in WT and Menin KO CD8 T cells.

status: Public on Jul 12 2023

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

summary: To elucidate the effect of menin on the differentiation of CD8 T cell, the gene expression were measured in WT and Menin KO CD8 T cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Menin KO CD8 T cells at indicated days after TCR stimulation.


title: Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation

status: Public on Jul 15 2023

city: Munich

first: Louis

last: Kuemmerle

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Centre Munich

summary: The bone marrow in the skull is important for shaping immune responses in the brain and meninges, but its molecular makeup in comparison to other bones in mice and humans remains unclear. Here, we show that the skull has the most distinct transcriptomic profile compared to other bones in states of health and injury, characterized by a late-stage neutrophil phenotype. In humans, proteome analysis reveal that the skull marrow is the most distinct, with differentially expressed neutrophil-related pathways and a unique synaptic protein signature. 3D imaging demonstrates the structural and cellular details of human skull-meninges connections compared to veins. Lastly, using TSPO-PET imaging, we show that the skull bone marrow reflects inflammatory brain responses with a disease-specific spatial distribution in patients with various neurological disorders. The unique molecular profile, anatomical, and functional connections of the skull show its potential as a new site for diagnosing, monitoring, and treating brain diseases.

overall_design: A single-cell RNA sequencing experiment was conducted using 10x Genomics technology on samples from three distinct groups, which included six bones, meninges, and the brain. The study comprised three groups: those that underwent MCAo surgery, those that underwent sham surgery, and a group of naive animals. Each sample consisted of cells pooled from three animals, with a total of 32 samples utilized. The MCAo surgery group contributed 2 samples, each consisting of cells pooled from 3 different animals. The sham and naive groups served as control groups. In addition to the single-cell RNA sequencing, bulk RNA sequencing experiments were conducted using the Illumina ligation stranded mRNA preparation kit. These experiments involved samples from the six bones under the three conditions (naive, sham, and MCAo). Separate measurements were taken for 4-6 animals per condition, yielding a total of 95 samples. Furthermore, bulk RNA sequencing was carried out using Smart-seq2 for mini-bulks of about 50 CD45+/Cd11b+ sorted immune cells each from the skull and femur. These samples were taken from wildtype animals (5 in total) and 5xFAD animals (3 in total), amassing 168 samples overall, with approximately 20 samples per animal.

first: Zeynep

middle: I

last: Kolabas

first: Robert

last: Perneczky

first: Benjamin

last: Förstera

first: Selin

last: Ulukaya

first: Mayar

last: Ali

first: Saketh

last: Kapoor

first: Laura

middle: M

last: Bartos

first: Maren

last: Büttner

first: Ozum

middle: S

last: Caliskan

first: Zhouyi

last: Rong

first: Hongcheng

last: Mai

first: Luciano

last: Höher

first: Denise

last: Jeridi

first: Muge

last: Molbay

first: Igor

last: Khalin

first: Ioannis

middle: K

last: Deligiannis

first: Moritz

last: Negwer

first: Kenny

last: Roberts

first: Alba

last: Simats

first: Olga

last: Carofiglio

first: Mihail

last: Todorov

first: Izabela

last: Horvath

first: Furkan

last: Ozturk

first: Selina

last: Hummel

first: Gloria

last: Biechele

first: Artem

last: Zatcepin

first: Marcus

last: Unterrainer

first: Johannes

last: Gnörich

first: Jay

last: Roodselaar

first: Joshua

last: Shrouder

first: Pardis

last: Khosravani

last: Tast

first: Lisa

last: Richter

last: Díaz-Marugan

first: Doris

last: Kaltenecker

first: Laurin

last: Lux

first: Ying

last: Chen

first: Shan

last: Zhao

first: Boris-Stephan

last: Rauchmann

first: Michael

last: Sterr

first: Ines

last: Kunze

first: Karen

last: Stanic

first: Simon


title: Tracking B Cell Responses to the SARS-CoV-2 mRNA-1273 Vaccine

status: Public on Jul 07 2023

city: Bethesda

first: Susan

last: Moir

address: 9000 Rockville Pike, 10/6A02

department: NIAID

institute: NIH

summary: The COVID-19 pandemic left an unprecedented social and economic impact on the world. This rapidly evolving global instigated a worldwide effort to develop an effective vaccine. Despite the generation of a protective antibody response in most individuals after two doses of an anti-spike mRNA vaccine, some studies have shown that a poorer response is elicited in some individuals, particularly those that are immunocompromised or elderly. To gain further insight into the cellular mechanisms driving B cell evolution in response to vaccination against SARS-CoV-2, we performed longitudinal single-cell transcriptomic, epitope sequencing (CITE-seq), and repertoire profiling of three COVID-19 vaccinees. Spike-specific (S-2P+) B cells showed early immune activation at v1D14 (14 days after vaccine dose 1) and accumulation of somatic hyper mutation (SHM) up to v2M6 (months 6). At v2D6, the S-2P+ cells expanded into memory B cell (MBC) cluster 5 with a dynamic kinetics over time. At v2M6, majority of S-2P+ cells were into resting memory (RM) subset within cluster 5. Analysis of B cell receptor (BCR) repertoire showed selection of genes commonly detected in neutralizing monoclonal antibodies from COVID-19 patients. Tracking of S-2P+ B cell response showed clonal association between earlier activated CD38+ memory, as well as tissue-like memory, with RM B cells at v2M6. These clones showed evolving signal with progressive accumulation of SHM over time. The presence of early plasmablast (PB) within these clones corroborates our previous report that associates PB response with sustained immunity. This integrated analysis allowed us to characterize the transcriptional activity underpinning the development of B cells involved in inducing an immune response to the COVID-19 vaccine.

overall_design: B cells of COVID-uninfected individuals who received Moderna mRNA-1273 vaccine were isolated from thawed cryopreserved PBMC. Spike-specific and non-specific B cells, and total plasmablast were sorted. Cells from all individuals were pooled evenly before cell sorting. Multiple cell pools were prepared, such that cells from the same donors but different time points were in different pools. After cell sorting, cell pools were Fc blocked, CITE-seq and hashtag stained with custom TotalSeq-C cocktail antibodies. Single-cell gene expression (GEX), cell surface protein (ADT) and B cell receptor (BCR) libraries were prepared as instructed by 10x Genomics Single Cell Immune Profiling kit v.2 user guide and sequenced on Illumina NovaSeq 6000 platform. Cells from each donor were demultiplexed in silico using donor-specific single nucleotide polymorphism (SNP) information collected during data analysis. Data were analyzed using Seurat package in R.

first: Felipe

last: Assis

first: Kenneth

last: Hoehn

first: Xiaozhen

last: Zhang

first: Omar

last: El Merhebi

first: Lela

last: Kardava

first: Connor

last: Smith

first: Clarisa

last: Buckner

first: Wei

last: Wang

first: Vicky

first: Paul

last: Schaughency

first: Foo

last: Cheung

first: Justin

last: Lack

first: Steven

last: Kleinstein


title: First-line durvalumab and tremelimumab with chemotherapy in RAS-mutated metastatic colorectal cancer: a phase 1b/2 trial

status: Public on Jul 05 2023

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231


title: First-line durvalumab and tremelimumab with chemotherapy in RAS-mutated metastatic colorectal cancer: a phase 1b/2 trial [RNA-Seq]

summary: While patients with microsatellite instable, metastatic colorectal cancer (CRC) benefit from immune checkpoint blockade, chemotherapy with targeted therapies remains the only therapeutic option for microsatellite stable (MSS) tumors. The single arm, phase IB/II MEDITREME trial evaluates safety and efficacy of durvalumab plus tremelimumab in combination with mFOLFOX6 chemotherapy in first line, in 57 patients with RAS-mutant unresectable mCRC. Safety was primary objective of phase IB and no safety issue was observed. The primary objective of phase II was efficacy in terms of 3-month PFS in MSS patients, which was met with a 3 month PFS of 90.7% [95% CI: 79.2-96%]. For secondary objective, response rate was 64.5%, median PFS was 8.2 months [95% CI: 5.9–8.6] and overall survival was not reached in MSS patients.  Higher tumor mutational burden and a lower degree of genomic instability in responder patients. Integrated transcriptomic analysis underlined that high immune signature, and low epithelio-mesenchymal transition were associated with better outcome. Immunomonitoring showed induction of neoantigen and NY-ESO1 and TERT blood tumor specific T cell response associated with better PFS. The combination of durvalumab-tremelimumab with mFOLFOX6 was tolerable with promising clinical activity in MSS mCRC.

overall_design: We performed gene expression profiling analysis using RNA-seq data from 34 patients splited into responders and non-responders

last: Ghiringelli

first: Marion

last: Thibaudin

first: Caroline

last: Truntzer


title: Arid1a in mouse embryonic cells

status: Public on Jul 24 2023

city: Shanghai

first: Ze-guang

last: Han

address: 800 Dongchuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by high throughput sequencing


title: Single-cell Transcriptomic Architecture Reveals Dynamic Heterogeneity and Intracellular Crosstalk Features Which Triggers Liver Mallory-Denk Bodies Pathogenesis

status: Public on Jun 21 2023

city: Guangzhou

first: Hui

last: Liu

address: Xinzao Road No.1

institute: Guangzhou Medical University

summary: Liver cell injury causes balloon hepatocytes and Mallory-Denk Bodies (MDBs) formation impeding liver parenchymal regeneration. MDBs are an intracellular deposition of misfolded protein and typical features of distinct chronic liver disease. Therefore, a comprehensive understanding of cellular heterogeneity and intercellular signaling of MDBs formation is essential to elucidate the mechanisms driving MDBs formation and chronic liver disease progression and to develop therapeutic approaches.

overall_design: Herein, we performed single-nucleus RNA-sequencing (snRNA-seq) to illustrate the comprehensive transcriptomic landscape and intercellular ligand-receptor signaling on the fractionations isolated from healthy and MDB-forming mouse livers induced following DDC. In addition, we applied an MDB-forming cell model induced by cytokines combined clinical hepatocellular carcinoma specimen which had formed MDBs to further verify the potential MDB-forming markers. The results of the analyses were validated using typical MDB-related immunofluorescence staining, bulk transcriptomic datasets, and functional experiments in vitro and in vivo.

first: Rong

first: Menghua

last: He

first: Bei

last: Zhong

first: Jun

last: Dong

first: Xinyu

last: Yang

first: Jiangtao

last: Jia

first: Zixuan

last: Fang

first: Jiayi

last: Pan

first: Wuyi

last: Zeng

first: Jiashan

first: Xinghua


title: Genetic activation of glycolysis in osteoblasts preserves bone mass in type I diabetes

status: Public on Jun 20 2023

city: PHILADELPHIA

first: XING`

last: JI

state: PA

address: 3401 Civic Center Blvd

institute: Children's hospital of Philadelphia


title: Genetic activation of glycolysis in osteoblasts preserves bone mass in type I diabetes [bulkRNA-seq]

summary: Type I diabetes (T1D) impairs bone accrual in patients, but the mechanism is unclear.  Here in a murine monogenic model for T1D, we demonstrate that diabetes suppresses bone formation resulting in a rapid loss of both cortical and trabecular bone.  Single-cell RNA sequencing uncovers metabolic dysregulation in bone marrow osteogenic cells of the diabetic mice.  In vivo stable isotope tracing reveals impaired glycolysis in diabetic bone that is highly responsive to insulin stimulation.  Remarkably, deletion of the insulin receptor reduces cortical but not trabecular bone.  Increasing glucose uptake by overexpressing Glut1 in osteoblasts exacerbates bone defects in T1D mice.  Conversely, activation of glycolysis by Pfkfb3 overexpression preserves both trabecular and cortical bone mass in the face of diabetes.  The study identifies defective glucose metabolism in osteoblasts as a pathogenic mechanism for osteopenia in T1D, and furthermore implicates boosting osteoblast glycolysis as a potential anabolic therapy.

overall_design: WT and Akita at 20 weeks, n=4 for each genotype

first: Xing

last: Ji

first: Fanxin

last: Long


title: Single-Cell Analysis Uncovers Dramatic Alteration of Microglia Heterogeneity after Ischemic Stroke

status: Public on Jun 14 2023

first: Yueman

last: Zhang

address: 160 Pujian Rd

institute: Department of Anesthesiology,  Renji Hospital, School of Medicine Shanghai Jiao Tong University, China

summary: Microglia are resident myeloid cells in the central nervous system (CNS) that regulate homeostasis and protect CNS from damage and infection. The phenotype of microglia is critical in regulating the propagation and resolution of inflammatory responses after ischemic stroke. However, little is known of its complexity and heterogeneity in the above context. Here, using single-cell RNA sequencing (scRNA-seq) of over 11,000 cells from the mice ischemic brain tissues, we demonstrated a previously undefined molecular heterogeneity among microglia clusters following ischemic stroke.

overall_design: To characterize the cell types and phenotypic changes involved in ischemic injury, we sorted a total of 11,226 single cells from sham or MCAO mice brain (n=3/group). All cells were sequenced using a modified BD Rhapsody scRNA-seq protocol after filtering

first: Yunlu

last: Guo

first: Tingting

last: Huang


title: Insights into intestinal neuroendocrine tumors in relation to normal human EEC differentiation [ChIPseq]

status: Public on Apr 29 2026

city: Brookline

first: Ramesh

middle: A

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

institute: DFCI

summary: Mutationally silent small intestinal neuroendocrine tumors (SI-NETs) characterized by few recurrent alterations, such as those that inactivate the cyclin-dependent kinase (CDK) inhibitor CDKN1B in <10% of cases are not well defined at the molecular level. Since the native enteroendocrine cells (EECs), which these tumors resemble, are scarce; the lack of reference data from normal EECs limits identification of gene and cis-element dysregulation in SI-NETs. We established transcriptional landscapes (RNA-seq) in bulk cultures and at single-cell (sc) resolution during the trajectory of normal human EEC differentiation from ileal stem cells in vitro (PMID 38733993). We compared the findings in SI-NETs against the novel reference profiles of normal human EEC differentiation and maturation. SI-NETs correspond principally to mature EC cells, with discernible features of non-EC and progenitor cells; persistent expression of the latter genes likely contributes to malignant properties. Underlying this aberrant expression pattern we found diverse SI-NET enhancers. EECs normally differentiate through an intermediate HES6hi/ASCL1+ oscillatory state before NEUROD1+ pre-terminal cells emerge; ASCL1 expression then persists only in mature EC cells. In contrast, although SI-NETs express NEUROD1, they strictly lack ASCL1 and other genes normally co-expressed with ASCL1. Notably, ASCL1 and loci encoding transcription factors that define non-EC cell types (ISL1, ARX, PAX6, PDX1) are marked with H3K27me3, signifying epigenetic silencing. SI-NETs express CDKN1B but other CDK inhibitors, e.g., CDKN2A and CDKN1C, are epigenetically silenced, suggesting that tumor cells may especially depend on wild-type CDKN1B function. Chromatin and transcriptional features of SI-NETs, revealed for the first time with respect to normal EEC differentiation, will help identify tumorigenic pathways and candidate therapeutic targets.

overall_design: Chromatin obtained from 100µ frozen sections and immunoprecipitated for H3K27ac, H3K4me3 and H3K27me3

first: Pratik

middle: N

last: Singh


title: Brain and blood single-cell transcriptomic analysis in acute and subacute phases after experimental stroke

city: New York

first: Josef

last: Anrather

state: NY

address: 407 East 61st Street

department: BMRI

institute: Weill Cornell Medical College

summary: The secondary immune response to ischemic stroke progresses for days to weeks and involves glial and brain endothelium activation, recruitment of peripheral immune cells, and release of cytokines and chemokines. Whereas there is evidence that the acute inflammatory response contributes to the progression of ischemic brain injury, on the other hand, recent research points at a more multifaceted role of immune cells in brain ischemia, where immune cells participate in repair processes during the sub-acute and chronic stages. Here we used single-cell sequencing to gain deeper insights into the impact of ischemic stroke on signature and the heterogeneity of brain immune cells, endothelial cells and circulating leukocytes in mice.

overall_design: Single-cell RNA profiling of CD45intermediate and CD45high immune cells and CD45negative/Ly6chigh endothelial cells isolated from mice 2 and 14 days after transient middle cerebral artery occlusion or sham surgery. Single-cell RNA profiling of peripheral blood leukocytes from mice 2 and 14 days after transient middle cerebral artery occlusion or sham surgery.

first: Lidia

last: Garcia-Bonilla

first: Gianfranco

last: Racchumi


title: Revealing the Pathogenesis of Keloids Based on the Status: Active vs Inactive

status: Public on Jun 01 2023

city: Seoul

first: Sejin

last: Oh

address: 81 Irwon-ro Gangnam-gu

country: South Korea

institute: Samsung Medical Center

summary: Multiomics analysis demonstrated the distinct expression profile of active and inactive keloids. Clinically, these findings may provide the future appropriate directions for treatment of keloids depending on their activity and characteristics.

overall_design: We aimed to profile the transcriptomics of FBs and vascular endothelial cells (VECs) of keloids according to their clinical activity and location within the keloid lesion. Tissue samples were collected (keloid based on its activity (active and inactive), mature scar (MS) from keloid patients and normal scar (NS) from non-keloid patients). Multiomics assessment was performed by using single-cell RNA sequencing and multiplex immunofluorescence. Increased mesenchymal FBs was the main feature in keloid patients.

first: Jong Hee

last: Lee

first: Eunhye

last: Yeo


title: Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1

city: Istanbul

first: mehmet

last: tardu

address: Beyazit campus

department: Biology

country: Turkey

institute: Istanbul University

summary: Ribosome dynamics during mRNA translation elongation regulate mRNA stability. Yet, known regulators of ribosome transit, such as codon usage, cannot fully explain transcriptome-wide decay rates. Here, we demonstrate that nascent polypeptide folding modulates elongation rates, with Zuotin (Zuo1) serving as an essential mediator. Using reporter constructs encoding co-translationally unstructured proteins and RNA sequencing under proteotoxic stress, we show that Zuo1 is required for selective destabilization of transcripts whose nascent peptides fail to fold properly. This process relies on the co-translational mRNA decay factor Not5, which detects slowed ribosomes. 35S labeling indicates that nascent peptide folding defects correlate with reduced elongation rates in a Zuo1-dependent manner, and ribosome profiling reveals that global protein misfolding induces Zuo1-dependent ribosome pausing. These findings position Zuo1 as a key mediator linking nascent peptide folding status to ribosome dynamics and mRNA stability. Furthermore, this work suggests an expanded role for Not5 beyond codon optimality sensing.

overall_design: mRNA-seq and Ribosome profiling of exponentially growing (OD600 = 0.6) Saccharomyces cerevisiae cells were performed by deep sequencing , in two biological replicates, using Illumina HiSeq-4000 platform.

first: Suhee

last: Chang

first: Ryan

last: Kawalerski

first: Mehmet

last: Tardu

first: Sophie

last: Martin

first: Kristin

last: Koutmou

first: Jeff

last: Coller


title: Sites of transcription initiation drive mRNA isoform selection [FLAMseq]

status: Public on May 10 2023

city: Basel

first: Valérie

last: Hilgers

address: Mattenstrasse 28

department: Deparment of Biomedicine

country: Switzerland

institute: University Basel

summary: The generation of distinct messenger RNA isoforms through alternative splicing and alternative 3' end formation influences the expression and function of genes, often in a cell-type specific manner. Here, we quantitatively assess the regulatory relationships between transcription initiation and co-transcriptional processing steps, particularly 3' end formation. Applying multiple long-read-sequencing approaches to obtain an assembly accurately representing even the longest mRNA isoforms from end-to-end, we quantify mRNA isoform choice in Drosophila and human tissues, including the transcriptionally complex nervous system. We find that in Drosophila brains as well as in human cerebral organoids, 3' end site choice is globally influenced by the site of transcription start. We define a subset of TSSs, “dominant promoters” that impose a transcriptional constraint to predetermine splice and polyadenylation variants, which are characterized by specific epigenetic signatures. In vivo deletion or overexpression of dominant promoters disrupted the 3' end expression landscape. Our study demonstrates the crucial impact of transcription initiation site choice on the regulation of transcript diversity and tissue identity.

overall_design: FLAM-sequencing of wild type (w1118) Drosophila melanogaster heads, 3 replicates

first: Carlos

last: Alfonso-Gonzalez

first: Ivano

last: Legnini

first: Sarah

last: Holec

first: Laura

last: Arrigoni

first: Ulrike

last: Bönisch

first: Agnieszka

last: Rybak-Wolf

first: Nikolaus

last: Rajewsky


title: Moderate intrinsic phenotypic alterations in C9orf72 ALS/FTD iPSC-microglia despite the presence of C9orf72 pathological features

status: Public on May 23 2023

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N. Fifth Street

institute: TGen

summary: To differentiate, characterize and examine intrinsic phenotypes of C9orf72 ALS/FTD patient-derived induced pluripotent stem cells into microglia (iPSC-MG). Moderate molecular and functional differences were observed in C9orf72 iPSC-MG mono-cultures despite the presence of C9orf72 pathological features.

overall_design:
Gene expression profiling analysis of control and C9orf72 ALS/FTD iPSC derived MG mono-cultures.  For figure 1 - we compared the iPSC-MG gene expression profile to iPSC derived cortical neurons.
We also performed gene expression profiling analysis of LPS and Ab treated control and C9orf72 ALS/FTD iPSC derived MG mono-cultures.

first: Ileana

last: Lorenzini

last: Pevey


title: Sites of transcription initiation drive mRNA isoform selection

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens


title: Hepatic irradiated pigs develop radiation induced veno-occlusive liver disease with ferroptosis

status: Public on Apr 04 2023

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: In this study, we performed a dose escalation study of whole-liver irradiation in miniature pigs and established a novel pig model for the severe form of RILD largely resembling the clinical and histological features of the human diseases, especially VOD and hepatic necrosis. Furthermore, taking advantage of serial liver biopsy in large-sized animal, we dissected the dynamics of cellular events essential for irreversible liver dysfunction in RILD. Unexpectedly, ferroptosis was also detected in irradiated pig liver samples.

overall_design: We performed a whole-genome RNA-sequencing analysis of irradiated livers from the 20Gy, 30Gy,40Gy treated and control pigs

first: Yifan

last: Wang

first: Qiang

last: Zheng

first: Zhen

last: Sun

first: Ludi

last: Zhang

first: Xiujun

last: Cai


title: Single-cell analyses reveal the dynamic functions of Itgb2+ microglia subclusters at different stages of cerebral ischemia-reperfusion injury in transient middle cerebral occlusion mice model

status: Public on Mar 21 2023

city: guangzhou

first: Fanning

last: Zeng

state: Guangdong

address: Nanshitou Street, Haizhu District

department: Department of Anesthesiology

institute: Zhujiang hospital, Southern Medical University

summary: The underlying pathophysiological mechanisms of cerebral ischemia-reperfusion injury (CIRI) is intricate, and current studies suggest that neuron, astrocyte, microglia, endothelial cell, and pericyte all have different phenotypic changes of specific cell types after ischemic stroke. And microglia account for the largest proportion after CIRI. Previous transcriptomic studies of ischemic stroke have typically focused on the 24 hours after CIRI, obscuring the dynamics of cellular subclusters throughout the disease process. Therefore, traditional methods for identifying cell types and their subclusters may not be sufficient to fully unveil the complexity of single-cell transcriptional profile dynamics caused by an ischemic stroke. In this study, to explore the dynamic transcriptional profile of single cells after CIRI, we used scSTAR, a new bioinformatics method, to analyze the single cell transcriptional profile of day 1, 3 and 7 of transient middle cerebral artery occlusion (tMCAO) mice. Combining our bulk RNA sequence and proteomics data, we found that the Itgb2+ subclusters of microglia exhibited specific functions at three different time points after the tMCAO. Our further analysis revealed that the Itgb2+ microglia subcluster was mainly involved in energy metabolism, cell cycle, angiogenesis, neuronal myelin formation and repair at 1, 3 and 7 days after tMCAO, respectively. Our results suggested that Itgb2+ microglia act as a time-specific multifunctional immunomodulatory subcluster during CIRI, and the underlying mechanisms remain to be further investigated.

overall_design: Single-cell sequencing of the ipsilateral cerebral hemispheres of mice at 1, 3, 7 days after tMCAO and at day 7 of sham group.

first: Jun

last: Cao

first: Zexuan

last: Hong

first: Yujun

last: Liu

first: Jie

last: Hao

first: Zaisheng

last: Qin

first: Xin

last: Zou

first: Tao

last: Tao


title: Characterization of molecular changes associated with aging in the mouse cochlear lateral wall

status: Public on Feb 18 2023

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study is to identify key molecular regulators that change in the cochlear lateral wall as a function of aging

overall_design: Three experimental replicates of lateral wall (LW) from young (2 months) and old (2.5 years) CBA/CaJ mice were compared by RNAseq analysis

first: Hainan

last: Lang

middle: L

first: Clarisse

last: Paganiban

first: Kenyaria

last: Noble


title: Coordinated chemokine expression defines macrophage subsets across tissues

status: Public on Mar 02 2023

city: Lebanon

first: Claudia

middle: V

last: Jakubzick

state: NH

address: 1 Medical Center Drive, Rm 626 W Borwell, PO#1250960

department: Microbiology and Immunology

institute: Dartmouth College

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

Lung-resident macrophages, which include alveolar macrophages and interstitial macrophages (IMs), exhibit a high degree of diversity, generally attributed to different activation states, and often complicated by the influx of monocytes into the pool of tissue-resident macrophages. To gain a deeper insight into the functional diversity of IMs, here we perform comprehensive transcriptional profiling of resident IMs and reveal ten distinct chemokine-expressing IM subsets at steady state and during inflammation. Similar IM subsets that exhibited coordinated chemokine signatures and differentially expressed genes were observed across various tissues and species, indicating conserved specialized functional roles. Other macrophage types shared specific IM chemokine profiles, while also presenting their own unique chemokine signatures. Depletion of CD206hi IMs in Pf4creR26EYFP+DTR and Pf4creR26EYFPCx3cr1DTR mice led to diminished inflammatory cell recruitment, reduced tertiary lymphoid structure formation and fewer germinal center B cells in models of allergen- and infection-driven inflammation. These observations highlight the specialized roles of IMs, defined by their coordinated chemokine production, in regulating immune cell influx and organizing tertiary lymphoid tissue architecture.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

last: Li

first: Arlind

last: Mara

first: Shawn

middle: C

last: Musial

first: Fred

middle: W

last: Kolling

first: Sophie

last: Gibbings

first: Nikita

last: Gerebtsov


title: Molecular Signatures and Functional Analysis of Secondary Hair Follicles in Cashmere Goat During Annual Cashmere Growth

status: Public on Jan 31 2023

city: Shenyang

first: Huiling

last: Xue

address: 120 Dongling Road,110866 Shenyang,China

institute: Shenyang Agricultural University

summary:
Secondary hair follicles (SHFs) produce the cashmere of goats. In the present study, SHF clusters were isolated under the microscope by cutting out the epidermis and removing the connective tissues. RNA sequencing was performed on the collected SHFs.
Through genome-wide transcriptomic analysis, we discovered and characterized differentially expressed molecular signatures across the annual growth cycle of cashmere and demonstrated their differential expression features and importance in cashmere growth.

overall_design: Gene expression profiling analysis of RNA-seq data for cashmere follicles during annual cashmere growth. RNA sequencing was performed using Illumina HiSeq 4000 platform across six time points, each with two biological replicates (male and female), representing phases of anagen (May and September), catagen (November and December) and telogen (February and March).

first: Minglin

last: Wang

first: Zehao

first: Yanlei

first: Shengda

last: Sheng


title: Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Lymphoma

status: Public on Jan 25 2023

city: Freiburg

first: Julian

last: Wolf

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: This study characterizes the transcriptional profile and the cellular tumor microenvironment of conjunctival lymphoma and identifies prognostically relevant biomarkers. 10 formalin-fixed and paraffin-embedded conjunctival lymphoma and 8 healthy conjunctival specimens were analyzed by MACE RNA sequencing. The 3,417 upregulated genes in conjunctival lymphoma were involved in processes such as B cell proliferation and Rac protein signaling, whereas the 1,188 downregulated genes contributed most significantly to oxidative phosphorylation and UV protection. The tumor microenvironment, as determined by deconvolution analysis, was mainly composed of multiple B cell subtypes which reflects the tumor’s B cell lineage. However, several T cell types, including T helper 2 cells and regulatory T cells, as well as innate immune cell types, such as anti-inflammatory macrophages and plasmacytoid dendrit-ic cells, were also strongly enriched in conjunctival lymphoma. A 13-biomarker prognostic panel, including S100A8 and S100A9, classified ocular and extraocular tumor recurrence, exceeded prognostic accuracy of Ann Arbor and AJCC staging, and demonstrated prognos-tic value for patient survival in 21 different cancer types in a database of 12,332 tumor pa-tients. These findings may lead to new options of targeted therapy and may improve prog-nostic prediction for conjunctival lymphoma.

overall_design: MACE RNA sequencing of 10 conjunctival lymphoma and 8 healthy conjunctiva samples

first: Rozina

last: Hajdu

first: Thomas

last: Reinhard

first: Günther

last: Schlunck

last: Auw-Hädrich

first: Clemens

last: Lange


title: Investigating microenvironment in MDS

city: Taipei

first: Yu-Hung

address: N0 7, Chung-Shan South Rd

country: Taiwan

institute: National Taiwan University Hospital

summary: High BM plasma S100A8/A9 is associated with a perturbed microenvironment and poor prognosis in myelodysplastic syndromes

overall_design: mRNA profiles of 215 MDS patients using RNA-seq

first: Hwei-Fang

last: Tien

first: Wen-Chien

last: Chou

first: Chien-Chin

last: Lin


title: Interferon gamma-induction of TH1-like regulatory T cells controls anti-viral responses

status: Public on Jan 23 2023

city: Pittsburgh

first: Jian

last: Cui

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

summary: Regulatory T cells (Tregs) are an immunosuppressive population that are required to maintain peripheral tolerance and prevent tissue damage during immunopathology, via anti-inflammatory cytokines, inhibitor receptors and metabolic disruption. We report that Tregs acquire an effector-like state, yet remain stable and functional, when exposed to IFNγ during chronic infection with lymphocytic choriomeningitis (LCMV) and Influenza A virus (IAV). Mechanistically, Treg-restricted-deletion of the IFNγ receptor 1 (IFNGR1), but not the IL12 receptor, prevented TH1-like polarization (decreased expression of T-bet, CXCR3 and IFNγ) and promoted TH2-like polarization (increased expression of GATA-3, CCR4 and IL4). TH1-like Tregs limited CD8+ T cell effector function, proliferation and memory formation during chronic and acute infection. These findings provide fundamental insights into how Tregs sense inflammatory cues from the environment (IFNγ) during viral infection to provide immune guidance to the effector T cell response, to prevent prolonged immunoinflammatory responses and shape the quality of the memory response.

overall_design: Our goal was to determine how Tregs become specialized in response to inflammation in vivo and the consequential impact on primary and secondary responses to viral infection. We report that viral infection promotes TH1-like differentiation of Tregs in vivo. Since TH1 cells produce IFNγ, we asked if IFNγ promoted TH1-like polarization in Tregs. Surprisingly, Ddeletion of the IFNγ receptor (IFNGR1), but not the IL12 receptor (IL12RB2), from Tregs robustly prevented TH1 polarization and consequently induced TH2 polarization. TH2-like Ifngr1-deficient Tregs were unable to adequately limit the T cell anti-viral response and CD8+ T cell effector memory, and central memory, formation. Our study uncovers a unique mechanism underlaying how Tregs respond to inflammation to program their immunosuppressive function appropriately and limit excessive immunoinflammatory responses.

first: Angela

last: Gocher-Demske

first: Dario

last: Vignali


title: Postnatal lung development under the influence of pulmonary hypoperfusion

status: Public on Jan 18 2023

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

summary: We reported the RNAseq analyses of lungs tissues in neonatal SD rats with or without reduced pulmonary blood flow. Lung hypoperfution was induced by causing the supravalvular pulmonary stenosis through performing pulmonary artery banding surgery within 24 hours postnatally (P1). RNAseq analyses of the upper lobe of the right lung tissues was generated at P7 from 5 sham-operated rats and 4 pulmonary artery banding rats (1 rat dead before sample collection). The results revealed that there were 2666 differentially expressed genes between PAB and sham group at P7, among which 1255 were upregulated and 1411 were downregulated.

overall_design: RNAseq analyses of the upper lobe of the right lungs tissues in PAB and sham-operated neonatal rats.

first: Lijun

last: Chen

first: Lincai

last: Ye

first: Qi

last: Sun


title: Congenital heart disease associated bronchopulmonary dysplasia and its underlying mechanisms

summary: We reported the RNAseq analyses of lungs tissues in neonatal SD rats with or without reduced pulmonary blood flow(RPF). RPF was induced by causing the supravalvular pulmonary stenosis through pulmonary artery banding within 24 hours postnatally (P1). RNAseq analyses of the upper lobe of the right lung tissues was generated at P14 from 5 sham-operated rats and 5 PAB rats. The results revealed that there were 2013 differentially expressed genes between PAB and sham group at P7, among which 936 were upregulated and 1077 were downregulated. GO and KEGG pathway analysis of downregulation of DEGs indicated that abundantly enriched terms of cell migration and metabolism.


title: Profiling placental DNA methylation associated with maternal SSRI treatment during pregnancy

status: Public on Jan 12 2023

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary:
Background:
Selective serotonin reuptake inhibitors (SSRIs), used to treat prenatal maternal depression, have been associated with neurobehavioral disturbances in exposed neonates, though the underlying molecular mechanisms remain poorly understood. In utero exposure to SSRIs may have an effect on DNA methylation (DNAme) in the human placenta, which is an epigenetic mark that is established during development and is associated with gene expression.
Methods:
Chorionic villus samples from 64 human placentas were profiled with the Illumina MethylationEPIC BeadChip and clinical assessments of maternal mood were collected at multiple time points during pregnancy. Case distribution was 20 SSRI-exposed cases and 44 SSRI non-exposed cases.  Maternal depression using a mean maternal Hamilton Depression score >8 to indicate symptomatic depressed mood (“maternally-depressed”) further classified cases into SSRI-exposed, maternally-depressed (n=14); SSRI-exposed, not maternally-depressed (n=6); SSRI non-exposed, maternally-depressed (n=20); and SSRI non-exposed, not maternally-depressed (n=24). To provide a replication cohort, Illumina 450K DNAme profiles were obtained from 34 additional cases from an independent cohort (n=17 SSRI-exposed, n=17 SSRI non-exposed).
Results:
No CpGs were differentially methylated at FDR < 0.05 comparing SSRI-exposed to non-exposed placentas, while adjusting for mean maternal Hamilton Depression score, nor comparing SSRI-exposed maternally-depressed to SSRI-non-exposed maternally-depressed cases. At a relaxed threshold of FDR < 0.25, five CpGs were differentially methylated (|Δβ| > 0.03) by SSRI exposure status. Four of these CpGs were covered by the 450K array and were examined in the replication cohort, but none replicated. Amongst SSRI non-exposed cases, No CpGs were differentially methylated (FDR < 0.25) comparing maternally depressed to not depressed cases. In sex-stratified analyses for SSRI-exposed versus non-exposed cases (females n=31; males n=33), three additional CpGs in females, but none in males, were differentially methylated at the relaxed FDR < 0.25 cut-off.
Conclusions:
We did not observe large-scale alterations of DNAme in placentas exposed to maternal SSRI treatment compared to placentas with no SSRI exposure. We also found no evidence for altered DNAme in maternal depression-exposed versus depression non-exposed placentas. This novel work in a prospectively-recruited cohort with clinician-ascertained SSRI exposure and mood assessments would benefit from future replication.

overall_design: Participants were recruited as part of a prospective, longitudinal cohort approved by the University of British Columbia/ Children’s and Women’s Health Centre of British Columbia research ethics board: H12-00733 (27), and written informed consent was obtained from all mothers; all procedures complied with the ethical standards on human experimentation and with the Helsinki Declaration of 1975, as revised in 2008. This specific study was additionally approved under certificate H16-02280.  64 pregnant individuals with and without prenatal diagnoses of depression, and with/without SSRI treatment plans were recruited at the British Columbia Women’s Hospital (BCWH) in the 20th week of gestation. Depression was defined as clinician-assessed depression. SSRI-exposure was defined as treatment with one of fluoxetine, paroxetine, sertraline, citalopram, escitalopram, or venlafaxine for at least 75 days including the 3rd trimester.

first: Amy

last: Inkster

first: Chaini

last: Konwar

first: Maria

last: Peñaherrera

first: Ursula

last: Brain

first: Almas

last: Khan

first: E

last: Price

first: Johanna

last: Schuetz

first: Élodie

last: Portales-Casamar

first: Amber

last: Burt

first: Carmen

middle: J

last: Marsit

first: Cathy

last: Vaillancourt

first: Tim

middle: F

last: Oberlander

middle: P


title: WT and p27KO

status: Public on Jan 09 2023

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

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


title: RNA-seq of WT and p27KO

summary: Cell differentiation involves profound changes in global gene expression that often have to occur in coordination with cell cycle exit. Because cyclin-dependent kinase inhibitor p27 reportedly regulates proliferation of neural progenitor cells in the subependymal neurogenic niche of the adult mouse brain, but can also have effects on gene expression, we decided to molecularly analyze its role in adult neurogenesis and oligodendrogenesis. At the cell level, we show that p27 restricts residual cyclin-dependent kinase activity after mitogen withdrawal to antagonize cycling, but is not essential for cell cycle exit. Contrasting gene expression with chromatin accessibility, we find that p27 is coincidentally necessary to globally repress many genes involved in the transit from multipotentiality to differentiation, including those coding for neural progenitor transcription factors SOX2, OLIG2, and ASCL1. Our data reveal both direct association of p27 with regulatory sequences in the three genes and an additional hierarchical relationship where p27 repression of the Sox2 gene leads to reduced levels of SOX2-downstream targets Olig2 and Ascl1. In vivo, p27 is also required for the regulation of the proper level of SOX2 necessary for neuroblasts and oligodendroglial progenitor cells to timely exit cell cycle in a lineage-dependent manner.

overall_design: 3 DIV proliferating WT and p27KO neurospheres and WT and p27KO NPs at the onset of differentiation (2+1 DIV) were harvested for RNA extraction. Between 2 and 3 biological replicates per condition and genotype.

first: Ana

last: Domingo-Muelas

first: Jose

last: Morante-Redolat

first: Verónica

last: Moncho-Amor

last: Jordán-Pla

first: Robin

last: Lovell-Badge

first: Isabel

last: Farinas


title: Defining the age-dependent and tissue-specific circadian transcriptome in male mice

status: Public on Jan 10 2023

city: Gainesville

first: Karyn

last: Esser

state: Florida

address: 1345 Center Drive

department: PHYSIOLOGY & FUNCTIONAL GENOMICS

institute: University of Florida

summary: Cellular circadian clocks direct a daily transcriptional program that supports homeostasis. Emerging evidence supports age-associated changes in circadian functions. To define age-dependent changes at the systems level, we profiled the circadian transcriptome in the hypothalamus, lung, heart, kidney, skeletal muscle, and adrenal gland in 3 age groups. We found age-dependent and tissue-specific clock output changes. Aging reduced the number of rhythmically expressed genes (REGs), indicative of weakened circadian control. Many genes gained rhythmicity in old tissues, reflecting an adaptive response. REGs were enriched for the hallmarks of aging, adding a new dimension to understanding aging. Differential gene expression analysis found that there were temporally distinct clusters of genes in tissue-specific manner. This novel analysis extends the landscape of the understanding of aging. Increased daily gene expression variability is a common feature of aged tissues. Our data highlight the impact of aging on circadian function and temporal changes in gene expression.

overall_design: Hypothalamus, lung, kidney, skeletal muscle, heart, and adrenal gland tissues from Young (6mo), Aged (18mo), and Old (27mo) male mice were collected every 4h for 48h to characterize the circadian transcriptome changes with age. Two samples per age were collected and pooled for RNAseq analysis.

first: Christopher

last: Wolff

first: Miguel

last: Gutierrez-Monreal

first: Lingsong

last: Meng

first: Xiping

last: Zhang

first: Lauren

last: Douma

first: Hannah

last: Costello

first: Collin

last: Douglas

first: Elnaz

last: Ebrahimi

first: Bryan

last: Alava

first: Andrew

last: Morris

first: Mehari

last: Endale

first: G

last: Crislip

first: Kit-yan

last: Cheng

first: Elizabeth

last: Schroder

first: Brian

last: Delisle

last: Bryant

first: Michelle

last: Gumz

first: Zhiguang

last: Huo

last: Liu


title: Foxp3 promotes macrophage phagocytosis in AIS

status: Public on Dec 31 2022

city: Guangzhou

first: Mengyan

last: Hu

address: Tianhe Road

institute: Sun Yat-sen University


title: ATAC-seq of WT and p27KO

first: Antonio

last: Jordan

overall_design: Nuclei from 3 DIV proliferating WT and p27KO neurospheres and WT and p27KO NPs at the onset of differentiation (2+1 DIV) were harvested for ATAC preparaton. Between 2 and 3 biological replicates per condition and genotype.

first: Ana

last: Domingo-Muelas

first: Jose

last: Morante-Redolat

first: Verónica

last: Moncho-Amor

last: Jordán-Pla

first: Robin

last: Lovell-Badge

first: Isabel

last: Farinas


title: Gene expression profile at single cell level of infiltrated macrophages from ischemic brain after stroke

summary: Macrophages play an important role in the pathological process of stroke. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of infiltrated macrophages from ischemic brain after stroke.

overall_design: Infiltrated macrophages from ischemic brain of Foxp3Egfp mice were isolated by Fluorescence-activated cell sorting (FACS) according to low sorting of CD45+CD11b+CD3-F4/80+ cells signal and analyzed using scRNAseq.

first: Wei

last: Cai

first: Zhengqi

last: Lu


title: Massively parallel reporter assays with multi-layer annotation identified cell-type-specific functional variants and genes associated with melanoma (RNA-Seq)

status: Public on Nov 28 2022

city: Rockville

first: Jiyeon

last: Choi

state: Maryland

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

summary: The most recent genome-wide association study (GWAS) of cutaneous melanoma identified 54 risk-associated loci, but functional variants and their target genes for most have not been established. Here, we performed massively parallel reporter assays (MPRA) using malignant melanoma and normal melanocyte cells and further integrated multi-layer annotation to systematically prioritize functional variants and susceptibility genes from these GWAS loci. Of 1,992 risk-associated variants tested in MPRA, we identified 285 from 42 loci (78% of the known loci) displaying significant allelic transcriptional activities in either cell type (FDR < 1%). We further characterized MPRA-significant variants by motif prediction, epigenomic annotation, and statistical/functional fine-mapping to create integrative variant scores, which prioritized one to six plausible candidate variants per locus for the 42 loci and nominated a single variant for 43% of these loci. Overlaying the MPRA-significant variants with genome-wide significant expression or methylation quantitative trait loci (QTLs) from melanocytes or melanomas identified candidate susceptibility genes for 60% of variants (172 of 285 variants). CRISPRi of top-scoring variants validated their cis-regulatory effect on the eQTL target genes, MAFF (22q13.1) and GPRC5A (12p13.1). Finally, we identified 36 melanoma-specific and 45 melanocyte-specific MPRA-significant variants, a subset of which are linked to cell-type-specific target genes. Analyses of transcription factor availability in MPRA datasets and variant-transcription factor interaction in eQTL datasets highlighted the roles of transcription factors in cell-type-specific variant functionality. In conclusion, MPRA along with variant scoring effectively prioritized plausible candidates for most melanoma GWAS loci and highlighted cellular contexts where the susceptibility variants are functional.

overall_design: Whole transcriptome RNA-sequencing of UACC903 human melanoma cell lines (n = 3 biological replicates) and C283T human immortalized normal melanocytes (n = 3 biological replicates)

first: Erping

last: Long

first: Jinhu

last: Yin

first: Karen

last: Funderburk

first: Kevin

last: Brown


title: Massively parallel reporter assays with multi-layer annotation identified cell-type-specific functional variants and genes associated with melanoma (MPRA)

overall_design: Targeted amplicon RNA-sequencing of ectopic luciferase constructs with sequence tags transfected into UACC903 human melanoma cell lines (n = 8 biological replicates) and C283T human immortalized normal melanocytes (n = 5 biological replicates) together with amplicon DNA sequncing of input luciferase constructs for normalization control (n = 3 biological replicates)


title: Pioneering function of Yap and Taz in promoting osteogenesis of neural crest cells by preventing chondrogenesis

status: Public on Nov 02 2022

city: Houston

first: Jun

last: Wang

state: TX

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

summary: Neural crest cells (NCCs) are multipotent stem cells with a remarkable ability to differentiate into multiple cell lineages, including osteoblasts and chondrocytes. NCCs contribute to the majority of craniofacial skeleton, yet the molecular mechanisms regulating NCCs diversification into osteoblasts or chondrocytes remain poorly understood. We found that Yap and Taz function redundantly as key determinants of the osteogenesis versus chondrogenesis fate decision and differentiation in NCCs in vitro, ex vivo and in vivo, and Yap/Taz-deficiency in NCCs resulted in a switch from osteogenesis to chondrogenesis. Comprehensive analysis of unbiased datasets including CUT&RUN-seq and RNA-seq indicated that Yap/Taz directly regulate key genes that govern osteogenesis and chondrogenesis. During NCC-derived osteogenesis, Yap/Taz promote expression of osteogenic genes such as Runx2 and Sp7 but repress expression of chondrogenic genes such as Sox9 and Col2a1. Further, we found Yap/Taz directly interact with β-catenin in NCCs to coordinately promote osteoblast differentiation and repress chondrogenesis. Together our data indicate that Yap/Taz promote osteogenesis in NCCs by preventing chondrogenesis, partly through interactions with the Wnt-β-catenin pathway.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design:
1. We performed CUT&RUN in O9-1 neural crest cells using Yap, IGG and H3K27me3 antibodies, followed by sequencing.

2. O9-1 cells were cultured under conditioned basal medium. Then the cells were seperated into 2 group: one group used for Yap/Taz dKD and the other group used as control. For the siRNA-mediated KD of Yap and Taz, O9-1 cells were plated at 50% confluency in the conditioned basal media and transfected with siRNA SMART pools of Yap (Dharmacon, L-046247-01-0005), Taz (Dharmacon, L-041057-01), and nontargeting siRNA (Dharmacon, D-001810-04-05) for 48 h according to the guidelines of the RNAiMAX transfection procedure (Life Technologies, 13778075) and cultured to 80% confluency. Then the cells were harvested and used for CUT&Tag experiment.

first: Xiaolei

last: Zhao

first: Li

last: Tang


title: Staphylococcus aureus infection induces the production of the neutrophil chemoattractants CXCL1, CXCL2, CXCL3, CXCL5, CCL3, and CCL7 by osteoblasts

status: Public on Nov 12 2022

city: Charlotte

first: Morgan

middle: Brittany

last: Johnson

state: North Carolina

address: 9201 University City BLVD

department: Biological Sciences

institute: University of North Carolina at Charlotte

summary: Staphylococcus aureus is the principal causative agent of osteomyelitis, a serious bacterial infection of bone that is associated with progressive inflammatory damage.  Bone-forming osteoblasts have increasingly been recognized to play an important role in the initiation and progression of detrimental inflammation at sites of infection, and have been demonstrated to release an array of inflammatory mediators and factors that promote osteoclastogenesis and leukocyte recruitment following bacterial challenge.  In the present study, we describe elevated bone tissue levels of the potent neutrophil-attracting chemokines, CXCL1, CXCL2, CXCL3, CXCL5, CCL3, and CCL7, in a murine model of post-traumatic staphylococcal osteomyelitis.  RNA-Seq gene ontology analysis of isolated primary murine osteoblasts showed enrichment in differentially expressed genes involved in cell migration and chemokine receptor binding and chemokine activity following S. aureus infection, and a rapid increase in the expression of mRNA encoding CXCL1, CXCL2, CXCL3, CXCL5, CCL3, and CCL7, in these cells.  Importantly, we have confirmed that such upregulated gene expression results in protein production with the demonstration that S. aureus challenge elicits the rapid and robust release of these chemokines by osteoblasts and does so in a bacterial dose-dependent manner.  Furthermore, we have confirmed the ability of soluble osteoblast-derived chemoattractants to elicit the migration of a neutrophil-like cell line.  As such, these studies demonstrate the robust production of CXCL1, CXCL2, CXCL3, CXCL5, CCL3, and CCL7, by osteoblasts in response to S. aureus infection, and the release of such neutrophil-attracting chemokines provides an additional mechanism by which osteoblasts could drive the inflammatory bone loss associated with staphylococcal osteomyelitis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for uninfected and S. aureus infected murine osteoblasts

first: Sophie

last: Sipprell

first: M

first: Whitney

last: Leach

first: Samantha

last: Suptela

first: Ian

last: Marriott


title: 3D ECM-rich environment sustains the identity of naïve human iPSCs [Naive_3Dvs2D_p6]

status: Public on Oct 01 2022

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

institute: IBBTEC

summary: The establishment of in vitro naïve human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signaling pathways during maintenance of human naïve pluripotency has been characterized. However, little is known about the role exerted by the extracellular matrix and its three-dimensional organization. Here, using an unbiased and integrated approach combining transcriptional, proteomic and secretome analyses, we found that naïve, but not primed, hiPSC colonies are characterized by a self-organized extracellular matrix (ECM)-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naïve hiPSCs, and also allows direct and timely developmental morphogenesis simply by modulating the signalling environment. Our study opens new perspectives for future applications of naïve hiPSCs to study critical stages of human development in 3D starting from a single cell

overall_design: Comparison of the transcriptomic profile of human naïve iPSCs cultured on feeders or in 3D matrigel (feeder-free). At passage number 6, cells were harvested and a cell sorting was performed to obtain both the bulk population and SUSD2+-only cells. 4 replicates per each sample (bulk or SUSD2+) were collected and total RNA extracted with Qiagen RNeasy Mini Kit.

first: Elisa

last: Cesare

first: Anna

last: Urciuolo

first: Hannah

last: Stuart

first: Erika

last: Torchio

first: Cecilia

last: Laterza

first: Onelia

last: Gagliano

first: Sebastian

last: Martewicz

first: Meihua

last: Cui

last: Manfredi

first: Patrizia

last: Sabatelli

first: Stefano

last: Squarzoni

first: Irene

last: Zorzan

first: Riccardo

last: Massimiliano Betto

first: Graziano

last: Martello

first: Davide

last: Cacchiarelli

first: Camilla

last: Luni

first: Nicola

last: Elvassore


title: Massively parallel reporter assays with multi-layer annotation identified cell-type-specific functional variants and genes associated with melanoma

first: Jiyeon

last: Choi


title: Single-cell transcriptome profiling of primary tumors and paired organoids of pancreatic cancer

status: Public on Oct 04 2022

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

institute: Peking University First Hospital

summary: Pancreatic cancer (PC) is the most lethal common gastrointestinal malignancy with an overall 5-year survival rate of 11%. Recently, a variety of patient-derived models, including patient-derived xenograft (PDX) and cancer organoid models, have paved a way for identifying common responders to chemotherapy. However, the utility of PC organoid for recapitulating hallmarks of corresponding primary tumor at transcriptome level remains to be investigated. We conducted single-cell RNA sequencing (scRNA-seq) for three paired primary tumors and organoids using the 10x Genomics platform to identify common and different phenotypes between them.

overall_design:
All fresh resection specimens and cultured organoids were enzymatically digested to generate single-cell suspensions for scRNA-seq.
-----------------------------------------
Authors state "The corresponding raw data will be submitted to SRA."


title: RNA-Seq of injured mouse hearts depleted for myofibroblast Yap [I]

status: Public on Oct 29 2022

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

summary: A myofibroblast specific tamoxifen inducible Cre was used to assess the contribution of Yap in the mouse heart after myocardial infarction

overall_design: We implemented a Cre-lox system whereby inducible Cre expressed under the myofibroblast specific Periostin promoter is crossed with Yap floxed animals, facilitating inducible depletion of Yap. Mice were siblings with floxed Yap alleles and either a copy of MerCreMer under the endogenous periostin promote or wildtype Periostin. Permenant ligation of the left anterior descending artery or sham surgeries were conducted. Mice were administered tamoxifen citrate diet ad libitum immediately after surgery to promote excession of myofibroblast yap and left ventricles were collected 4 days post injury.

first: M

first: C

last: O'Meara

last: Patterson


title: Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis [RNA-Seq]

status: Public on Apr 28 2026

city: Los Angeles

first: Bishuang

last: Cai

state: CA

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

institute: University of California, Los Angeles

summary: Macrophages are the key players in the pathogenesis of atherosclerosis. Here we explored the role of the endocytic regulator EHD1 in immune responses in macrophages and determined its contribution to atherosclerosis progression. EHD1 expression profile in mouse and human plaques were determined by single cell-RNA sequencing (sc-RNA-seq) and immunofluorescence staining. Bone marrow transplantation (BMT) by transplanting bone marrow cells from Ehd1−/− or littermate wild-type mice to irradiated Ldlr−/− mice was performed to determine the effect of EHD1 deletion on atherosclerosis progression. In vitro mechanistic studies including inflammation signaling and endocytosis assays were performed in bone marrow-derived macrophages. EHD1 expression in macrophages is enhanced as atherosclerosis progresses in both mice and humans. Sc-RNA seq of aortic CD45+ cells demonstrated that EHD1 deletion attenuates pro-inflammatory responses and cell-cell interactions. Mechanistic studies revealed that EHD1 accelerates the endocytic recycling of TNFR2 and activates NF-kB, leading to increased expression of inflammatory cytokines. Moreover, EHD1 interacts with retromer and stabilizes sortilin, a retrograde cargo of retromer and a risk factor for atherosclerosis. Our study reveals novel roles for EHD1-mediated membrane trafficking in macrophage function and paves the way to innovative therapeutic strategies aiming at addressing dysregulated membrane trafficking in atherosclerosis.

overall_design: Mouse BMDMs treated with siEhd1 and incubated with lipopolysaccharide (LPS)

first: Xin

last: Huang


title: Arginine deprivation of ASS1-deficient cancers drives mistranslation and neoepitope production

city: Amsterdam

first: Mrittika

last: Adhikary

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Arginine biosynthesis is frequently suppressed in cancer due to loss of ASS1 expression, rendering cancer cells reliant on extracellular arginine. This feature has propelled the development of systemic arginine depletion strategies, which are clinically safe but have limited clinical benefit. Here, we demonstrate that in conditions of arginine scarcity, cancer cells with low ASS1 expression resort to aberrant mRNA translation in the form of ribosomal frameshifts and amino acid misincorporations. While aberrant proteins originated from most arginine codons, the predominant effect was observed at AGA. This codon preference is caused by a selective decrease in tRNAArg(UCU) levels after arginine deprivation, linked to METTL1-mediated tRNA-modification. Using proteomics and immunopeptidomics, we validated that arginine shortage induces aberrant protein production at the endogenous level. We further demonstrate that such inducible neopeptides are immunogenic, laying the foundation for improved cancer therapy combining systemic arginine depletion strategies with T-cell receptor-based targeting of non-classical neoantigens.

overall_design: RNA sequencing to measure mRNA translation

first: Remco

last: Nagel

first: Adva

last: Kochavi

first: Karine Flem

last: Karlsen

first: Yali

last: Gal-On

first: Maria

last: Klaoudatou

first: Julien

last: Champagne

first: Lorenzo

last: Valcanover

first: Heyilimu

last: Palashati

first: Morten

last: Nielsen

first: Xiaodong

last: Feng

first: Pierre-Rene

last: Körner

first: Lisanne

last: Giebel

first: Weiwen

last: Yang

first: Arno

last: Velds

first: Liesbeth

last: Hoekman

first: Onno

last: Bleijerveld

first: Olaf

last: van Tellingen

first: Johanna

last: Olweus

first: Reuven

last: Agami


title: Roles of Runx2 in chromatin landscape in skeletal development [ChIP-Seq, ATAC-Seq]

status: Public on Sep 06 2022

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

institute: The University of Tokyo

summary: The transcriptional regulator Runx2 has essential roles in chondrocytes and osteoblasts, central to the coordinated development of cartilage and bone. However, the regulatory mechanisms underlying Runx2’s roles in skeletal programming are not well understood. Here, we performed an integrative analysis of Runx2–DNA binding and chromatin accessibility in vivo and identified cell type-distinct chromatin accessibility underlying Runx2 roles in osteoblasts and chondrocytes.

overall_design: Examination of chromatin accessiblity and associataions of transcriptional regulators with DNA in skeletal cells


title: Roles of Runx2 in chromatin landscape in skeletal development

overall_design: Refer to individual Series


title: Systematic variation of RhoA activity reveals an inhibitory impact of active RhoA on the homeostasis and angiogenic capacity of human endothelial cells

status: Public on Jul 06 2022

city: Halle

first: Robert

last: Eckenstaler

address: Kurt-Mothes-Str. 3

department: Institute of Pharmazie

institute: Martin-Luther-University

summary: The small GTPase RhoA regulates a variety of cellular processes, including cell motility, proliferation, survival and permeability. In addition, there are reports suggesting that the RhoA-ROCK axis plays a role in VEGF-mediated angiogenesis, whereas other work has shown opposite effects. To elucidate this conflicting data, we examined HUVEC and HCAEC after stable overexpression (lentiviral transduction) of constitutively active (G14V/Q63L), dominant-negative (T19N), or wild-type RhoA using a variety of in vitro angiogenesis assays (proliferation, migration, tube formation, angiogenic sprouting, endothelial cell viability) and a HUVEC xenograft assay in immune incompetent NSGTM mice in vivo. We observed that expression of active as well as wild-type RhoA but not expression of dominant-negative RhoA significantly increased endothelial cell death as well as inhibited endothelial cell proliferation, migration, tube formation and angiogenic sprouting of endothelial cells in vitro and reduced HUVEC-related angiogenesis in vivo. Inhibition of RhoA by C3 transferase antagonized inhibitory RhoA effects and strongly enhanced VEGF-induced angiogenic sprouting in control-treated cells. In contrast, inhibition of RhoA effectors ROCK1/2 and LIMK1/2 had no significant effect  on RhoA-related effects, but again increased angiogenic sprouting and migration of control-treated cells. In line with these data, VEGF did not activate RhoA in HUVEC as measured by a FRET-based biosensor. Furthermore, global transcriptome and subsequent bioinformatic gene ontology (GO) enrichment analyses revealed that constitutively active RhoA induces a differentially expressed gene pattern that is enriched for GO biological process terms such as mitotic nuclear division, cell proliferation, cell motility and cell adhesion and includes a significant decrease in VEGFR-2 and NOS3 expression. Thus, our data demonstrate that increased RhoA activity has the potential to trigger endothelial dysfunction and anti-angiogenic effects independently of its well-characterized downstream effectors ROCK and LIMK.

overall_design: Three biological replicates were analyzed for each of three different conditions (overexpression of constitutively active RhoA (Q63L) and dominant negative RhoA (T19N) compared to control without overexpression of RhoA).

first: Michael

last: Hauke

first: Anne

last: Ripperger

first: Heike

last: Braun

first: Ralf

last: Benndorf


title: Expression of SARS-CoV-2 proteins in Drosophila heart and blood

status: Public on Aug 24 2022

city: Baltimore

first: Hangnoh

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

summary: We investigated the transcriptomic impact of SARS-CoV-2 proteins in Drosophila malanogaster with a focus on heart development and hemolymph coagulation.

overall_design: RNA-Seq analysis of fly hearts and blood cells (hemocytes) that express either SARS-CoV-2 Nsp6 (heart) or SARS-CoV-2 Orf7a (hemocytes). Hearts or hemocytes that express GFP (heart) or tubulin-Gal4 (hemocytes) were used as controls. The experiments were biologically duplicated/triplicated.

first: Huang

last: Xiaohu

first: Zhu

last: Junyi

first: Han

last: Zhe


title: ROLE OF ENDOPLASMIC RETICULUM STRESS IN  IMPAIRED NEONATAL LUNG GROWTH AND BRONCHOPULMONARY DYSPLASIA

status: Public on Aug 11 2022

city: Milwaukee

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

department: Pediatrics

summary:
Myeloperoxidase (MPO), oxidative stress (OS), and endoplasmic reticulum (ER) stress are all increased in the lungs of neonatal rat pups raised in hyperoxia (HOX, >90% O2), an established model of bronchopulmonary dysplasia (BPD). However, the relationship between OS, MPO, and ER stress has not been examined in HOX rat pups. To determine the relationship between OS, MPO, and ER stress in BPD we treated Sprague-Dawley neonatal rat pups with Tunicamycin (Tun) or with HOX. Tun directly induces ER stress and simplifies neonatal lung alveolarization. Previously, we showed that HOX induces a cycle of destruction that we hypothesize through increased OS, MPO, and ER stress to induce BPD. To inhibit ER stress specifically, we used tauroursodeoxycholic acid (TUDCA), a molecular chaperone. To break the cycle of destruction and reduce OS and MPO we used N-acetyl-lysyltyrosylcysteine-amide (KYC), a systems pharmacology agent. Lung structure was studied morphometrically. ER stress was detected using immunofluorescence (IF), transcriptomic, proteomic, and electron microscopic analyses. Increased ER stress was observed in the lungs of HOX rat pups and also in human BPD lungs by IF. Morphometric and proteomic studies of rat lungs showed that Tun treatment decreased lung complexity and increased ER stress and BPD severity. The fact that TUDCA improved lung complexity in Tun-treated neonatal rat pups, and decreased BPD induced by HOX provides strong support for the idea that ER stress plays a causal role in BPD. Additional support comes from data showing TUDCA decreased lung myeloid cells and MPO levels in the lungs of both Tun- and HOX-treated neonatal rat pups. These data link OS and MPO to ER stress in the mechanisms mediating BPD. KYC's effective inhibition of ER stress in the lungs of Tun-treated rat pups provides additional support for the idea that MPO-induced ER stress plays a direct causal role in BPD. Thus, ER stress appears to expand our proposed cycle of destruction. Our results suggest ER stress evolves from OS and MPO to increase neonatal lung injury and impaired neonatal lung growth and development. The encouraging effect of TUDCA indicates chemical chaperone has the potential in treating BPD.
Using multiomic data to investigate the role of endoplasmic reticulum stress in the development of BPD in rat model.

overall_design: Nursing dams were cared for in a 12-h dark-light cycle and had free access to chow and water. Two or four pregnant rats were used for each experiment, according to the study design. The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10). Oxygen concentrations were continuously monitored with an oxygen sensor (Reming Bioinstruments Co., Redfield, NY). Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity.

first: Kirkwood

last: Pritchard  Jr

first: Xigang

last: Jing

first: Michelle

last: Teng

first: Clive

last: Wells

first: Shuang

last: Jia

first: Jason

last: Jarzembowski

first: Billy

last: Day

first: Stephen

last: Naylor

first: Marty

first: G

middle: G

last: Konduri

first: Ru-Jeng


title: Next Generation Sequencing Facilitates Quantitative Analysis of SPS and Control Rats Model

status: Public on Jun 30 2022

city: Shenyang

first: Fang

last: Han

state: Liaoning

address: No.77 Puhe Road, Shenyang North New Area

institute: China Medical University

summary: In the present study, we used the single prolonged stress (SPS) model to mimic  posttraumatic stress disorder. High-throughput sequencing were utilized to analyze differentially  expressed genes (DEGs) in the hippocampus of control and SPS rats. RNA-seq analysis revealed 230 significantly DEGs between  the control and SPS groups.

overall_design: mRNA profiles of single prolonged stress (SPS) and control rats model


title: Glutamine deprivation enhances directed differentiation of renal organoids

status: Public on Jun 01 2022

city: New York

first: Manoj

last: Kandpal

address: 1230 York Ave

department: Hospital Bioinformatics

institute: Rockefeller University

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


title: Directed differentiation to nephron progenitor cells in the presence and absence of glutamine [RNA Seq 2]

summary: Metabolic pathways driving differentiation into nephron progenitor cells (NPCs) and renal organoids from the pluripotency stage remain poorly understood. In this study, we systematically performed comprehensive metabolite and transcriptome profiling of human pluripotent stem cells (hPSCs) during differentiation into NPCs and further into multicellular organoids. We found activation of distinct metabolic pathways during early-stage progression from hPSCs to NPCs; however, later-stage differentiation from NPCs to organoids, and the intervening developmental stages between them, largely shared similar metabolic profiles. Among the pathways changing in early differentiation, the alanine-aspartate-glutamate and glutamine pathways were found to be significantly altered by both an enrichment and by pathway impact analysis. Moreover, hPSCs survived glutamine deprivation during in vitro differentiation, and NPCs were successfully generated both in the absence and presence of glutamine and glutamate. Surprisingly, glutamine deprivation resulted in enhanced maturation, by accelerating PAX8 expression, and enriching for podocytes as detected through single cell RNA-Seq analysis. Taken together, these findings highlight a critical regulatory role of glutamine metabolism in the derivation of nephron progenitor cells and renal organoids and identify a controlling metabolic pathway of early renal differentiation.

overall_design: Global gene profiling on day 9 of directed differentiation to nephron progenitor cells derived in the presence and absence of glutamine

first: Iman

last: Sarami

last: Wertheim


title: Transcriptomics biomarkers in prostate cancer

status: Public on May 18 2022

city: Créteil

first: Virginie

last: Firlej

address: Ur Trepca

institute: UPEC TrePca

summary:
Prostate cancer (PCa) is the number one cancer in men. It represents a challenge for its management due to its very high incidence but low risk of lethal cancer. Over-diagnosis and over-treatment are therefore two pitfalls. The PSA (Prostate Specific Antigen) assay used for early diagnosis and clinical or molecular prognostic factors are not sufficiently reliable to predict the evolution of the cancer and its lethal or non-lethal character. Although PCa is most often detected at a localised stage, there are almost 30% of metastatic or locally advanced forms for which treatments can slow down the evolution but cannot be curative.
With the use of high-throughput technological tools such as transcriptomics , it is becoming possible to define molecular signatures and identify predictive biomarkers of tumour aggressiveness . Here, we have analyzed 137 samples.

overall_design: array with total RNA were extracted from frozen primary prostatectomie tissue

first: Pierre

last: De la Grange

first: Arturo

last: Londono-Vallejo

first: Yves

last: Allory


title: Directed differentiation to nephron progenitor cells [RNA Seq 1]

overall_design: Global gene profiling on days 0, 1, 3, 4, 6, 7 and 9 during directed differentiation to nephron progenitor cells


title: scRNA sequencing analysis for human ureters and patient derived ureter oragnoid

status: Public on Mar 31 2022

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Tissue engineering offers a promising treatment strategy for ureteral strictures. Successful ureter engineering is necessitated by detailed understanding of the tissue architecture, cellular heterogeneity, and signaling pathways underlying regeneration. We define and spatially map cell populations within the human ureter by using a combinatorial approach: single-cell RNA sequencing, 10X Visium spatial transciptomics, and immunofluorescence. The stromal and urothelial cell populations are analyzed in detail, and we infer potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Specifically, we analyze and experimentally validate the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells support organoid generation in vitro, and accurately predict the differentiation trajectory of basal stem cells, to terminally differentiated umbrella cells, in vivo. Our results highlight essential processes involved in adult ureter tissue homeostasis, and provide a toolkit for guiding ureter tissue engineering.

overall_design: 10 normal human ureters each were subjected to RNA sequencing at single cell resolution on Novaseq using 10X Gemonics library preparation platform. Data was processed using Cellranger 4.0.0 and anayzed using Seurat v3.2.1 to characterize various cell types and understand finer details of the regenrative pathways in the ureter urothelium. This was further explored by analyzing single cell RNA sequencing data from human ureter derived organoid (generated in the same manner as the 10 ureter samples). Freshly processed and thawed tissue sample from the same human subject was used as control to further understand the urothelial regenerative pathways.

first: Byron

last: Lee

first: Emily

middle: E

last: Fink

first: Surbhi

last: Sona


title: Epiregulin is a dendritic cell-derived EGFR ligand that maintains skin and lung fibrosis

status: Public on Dec 09 2022

city: New Haven

first: Ian

last: Odell

state: CT

address: 330 Cedar St. LMP-5040

department: Dermatology

institute: Yale University

summary: Immune cells are fundamental regulators of extracellular matrix (ECM) production by fibroblasts and have important roles in determining extent of fibrosis in response to inflammation. Although much is known about fibroblast signaling in fibrosis, the molecular signals between immune cells and fibroblasts that drive its persistence are poorly understood. We therefore analyzed skin and lung samples of patients with diffuse cutaneous systemic sclerosis, an autoimmune disease that causes debilitating fibrosis of the skin and internal organs. Here we define a critical role of epiregulin – EGFR signaling between dendritic cells and fibroblasts to maintain elevated ECM production and accumulation in fibrotic tissue. Mechanistic studies demonstrate that epiregulin expression marks an inducible state of DC3 dendritic cells triggered by type I interferon. DC3-derived epiregulin activates EGFR on fibroblasts, which drives a positive feedback loop through NOTCH signaling. In well-established mouse models of skin and lung fibrosis, epiregulin was essential for persistence of fibrosis in both tissues, which could be abrogated by epiregulin genetic deficiency or a neutralizing antibody. Notably, therapeutic administration of epiregulin antibody reversed fibrosis in patient skin and lung explants, identifying it as a novel biologic drug target. Our findings reveal epiregulin as a crucial immune signal that maintains skin and lung fibrosis in multiple diseases and is a highly promising antifibrotic target.

overall_design: Skin biopsies from 5 patients with scleroderma (SSc1-5) and 6 healthy controls (Normal1-6) were analyzed using 10x genomics platform

middle: D


title: Arginase-1 is Required for Macrophage-Mediated Renal Tubule Regeneration

status: Public on Mar 23 2022

first: Leyuan

last: Xu

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

summary: In this study, we compared the transcriptomes of the kidney subjected to unilateral IRI with contralateral nephrectomy (IRI/CL-NX) and the normal healthy control kidney at the single cell level to identify major cell types in the kidney and the differential transcriptional response during kidney repair following IRI.

overall_design: Single cell mRNA profiling of kidneys from wild-type mouse subjected to IRI/CL-NX and normal healthy control mouse

first: Lloyd

last: Cantley


title: Multi-modal analysis of Col1a1-GFP in vitro vs in vivo state

status: Public on Mar 12 2022

city: Iowa City

first: Dakota

last: Jones

state: IA

address: 51 Newton Road

department: Department of Anatomy and Cell Biology

institute: University of Iowa

summary: We performed RNAseq and ATACseq on FACS isolated Col1a1-GFP lung mesenchyme in culture compared to directly sorted from lung tissue

first: Daniel

last: Tschumperlin


title: 3D ECM-rich environment sustains the identity of naïve human iPSCs II

first: Lucio

last: Di Filippo

summary: The establishment of in vitro naïve human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signaling pathways during maintenance of human naïve pluripotency has been characterized. However, little is known about the role exerted by the extracellular matrix and its three-dimensional organization. Here, using an unbiased and integrated approach combining transcriptional, proteomic and secretome analyses, we found that naïve, but not primed, hiPSC colonies are characterized by a self-organized extracellular matrix (ECM)-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naïve hiPSCs, and also allows direct and timely developmental morphogenesis simply by modulating the signalling environment. Our study opens new perspectives for future applications of naïve hiPSCs to study critical stages of human development in 3D starting from a single cell

overall_design: Comparison of the transcriptomic profile of human naïve iPSCs cultured on feeders or in 3D matrigel (feeder-free). At passage number 10, cells were harvested and a cell sorting was performed to obtain both the bulk population and SUSD2+-only cells. 4 replicates per each sample (bulk or SUSD2+) were collected and total RNA extracted with Qiagen RNeasy Mini Kit.

first: Elisa

last: Cesare

first: Anna

last: Urciuolo

first: Hannah

last: Stuart

first: Erika

last: Torchio

first: Cecilia

last: Laterza

first: Onelia

last: Gagliano

first: Sebastian

last: Martewicz

first: Meihua

last: Cui

last: Manfredi

first: Patrizia

last: Sabatelli

first: Stefano

last: Squarzoni

first: Irene

last: Zorzan

first: Riccardo

middle: M

last: Betto

first: Graziano

last: Martello

first: Davide

last: Cacchiarelli

first: Camilla

last: Luni

first: Nicola

last: Elvassore


title: Transcriptome analysis revealed altered response to hypoxia, inflammation and immune regulation in Pdcd10-depleted endothelial cells

first: Lucio

last: Di Filippo

summary: Here we provided novel insights on the physiological functions of PDCD10 by RNA-Seq analysis, profiling Pdcd10-silenced mouse endothelial cells (ECs). We identified 53645 differentially expressed genes (DEGs) in Pdcd10-ECs compared to the respective control cell line, of which 94 reported a p-value Adjusted (pAdj) <0.05. A functional clustered dendogram generated by using ReviGO Gene ontology resource  showed that the DEGs were clustered in cell proliferation, oxidative stress, vascular processes, extra-endothelial cell environment, and immune response gene ontology functions. Moreover, the major cluster of significant genes resulted to significantly enrich specific interesting signaling playing a fundamental role in inflammation and pathogen recognition, such as Hypoxia inducible factor-1 (HIF1α) and Nos2 signaling suggesting the importance of Pdcd10 in these unexplored molecular mechanisms. A validation analysis performed on wild type, Pdcd10-null and Pdcd10-null reconstituted cell lines, were found to be consistent with the sequencing data, revealing that the prioritized genes linked to the mainly meaningful pathways, have a direct functional relation with Pdcd10 expression level modulation.

first: Carmela

last: Fusco

first: Grazia

last: Nardella

last: Difilippo

first: Antonio

last: Petracca

first: Lucia

last: Micale

first: Matteo

last: Malinverno

first: Marco

last: Castori


title: Single-cell RNA-seq reveals immune landscape of pancreatic cancer

status: Public on Sep 13 2022

first: Kai

last: Chen

summary: Pancreatic ductal adenocarcinoma (PDAC) has complex tumor immune microenvironment (TIME), the clinical values of which remains to be explored. This study aimed to delineate the immune landscape of PDAC and determine the clinical value of immune features in TIME. There was a significant difference in immune profiles between PDAC and adjacent normal pancreatic tissues. Several novel immune features were captured by quantitative pathology analysis on mIHC, some of which were significantly correlated to the prognosis of PDAC patients. A risk score-based prognostic model was developed according to these immune features. We also drew a user-friendly nomogram plot to predict the overall survival of patients by combining risk score and clinicopathologic features. Both mIHC and scRNA-seq analyses showed the expression of PD-L1 was scarce in PDAC. We found that PD1+ cells were distributed in different T cell subpopulations, not enriched in a specific subpopulation. In addition, there were other conserved receptor-ligand pairs (CCL5-SDC1/4) besides PD1-PD-L1 interaction between PD1+ T cells and PD-L1+ tumor cells. Our findings reveal the immune landscape of PDAC and highlight the significant value of combined application of mIHC and scRNA-seq in uncovering TIME, which might provide new clues for developing immunotherapy strategies.

overall_design: All H&E stained slides from eighty patients were reviewed for confirming PDAC diagnosis by a pathologist. The corresponding tumor and adjacent noncancerous areas were carefully marked. Duplicated 1.5 mm diameter tissue cores were selectively punched and transferred to recipient tissue array blocks. The tissue microarray (TMA) was set up. For scRNA-seq analysis, a total of six PDAC and six adjacent noncancerous resection specimens were obtained from the Department of General Surgery at Peking University First Hospital. All patients with PDAC did not receive any treatments before collecting specimens.


title: Genome-wide maps of chromatin state in HepG2 cells

status: Public on Mar 01 2022

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

summary: We report the application of chromatin immunoprecipitation sequencing (ChIPseq) and ATAC for high-throughput profiling of histone modifications in HepG2 cells.

overall_design: ChIP-seq were performed with antibodies against acetylated H3K27 (H3K27ac), H3K4me1, and H3K4me3 and evaluated the open chromatin regions by assay for transposase-accessible chromatin with sequencing (ATAC-seq) to detect the genome-wide maps of chromatin state in HCC cells.

first: Zhiao


title: Immune-mediated Tubule Atrophy Promotes Acute Kidney Injury to Chronic Kidney Disease Transition

first: Leyuan

last: Xu

summary: Incomplete repair after acute kidney injury (AKI) is associated with progressive loss of tubular cell function and development of chronic kidney disease (CKD). Here, we compared the kidney single-cell transcriptomes from the mice subjected to either unilateral ischemia-reperfusion kidney injury with contralateral nephrectomy (IRI/CL-NX, in which tubule repair predominates) or unilateral IRI with contralateral kidney intact (U-IRI, in which fibrosis and atrophy predominates) to investigate the mechanism(s) underlying transition to CKD following AKI.

overall_design: 10X Chromium was used to profile mouse kidneys.

first: Xu

last: Leyuan

first: Lloyd

last: Cantley


title: Integrated analysis of single-cell and spatial transcriptomics in keloids

status: Public on Jan 21 2022

city: Seoul

first: Jong Hee

last: Lee

address: 81, Irwon-ro, Gangnam-gu

department: Department of Dermatology

institute: Samsung Medical Center

summary: To uncover the underlying pathophysiology of keloids, we used two technologies, single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST). we focused on the molecular signature of keloids. In this study, we provide the comprehensive transcriptomic atlas of keloids and its matched spatial information, essential to understanding intercellular crosstalk in the skin microenvironments.

overall_design: We employed scRNA-seq on two keloid samples using the platform of 10X Genomics. To further assess the spatial heterogeneity and organization of keloid FBs, we performed ST analysis on tissue from keloid specimens (2 sections from 2 samples including one scRNA-seq paired sample). To confirm the study results, we further applied ST on two independent normal skin sections . Normal skin samples from skin cancer excision were used for ST analysis.

first: Jong

first: Joonho

last: Shim


status: Public on Jan 01 2022

city: Tianjin

first: Shuo

last: Liu

address: 94 Weijin Road

institute: Nankai University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: Analysis of exosomal miRNA in plasma of patients with metastatic and non-metastatic pancreatic cancer. To identify exosomes cargo specific miRNAs promoting cancer metastasis.
Methods: We divide the plasma samples into five groups according to whether they have metastasis and undergo surgery.The five groups are Health(20),Metastasis Pre-operation and Post-operation (14),Non-metastasis Pre-operation and Post-operation(9).Then we collected the exosomes by ultracentrifugation and extracted the small RNA in each sample.Then, we analyzed the expression changes of miRNA by small RNA sequencing.
Result: Different groups have different expression of small RNA. Compared with the non-metastatic group, the expression of miR-92a-3p , miR-148-3p and miR-25-3p increased in the metastatic group.
Conclusion:Exosomal miRNA in pancreatic cancer patient derived plasma were analyze using Hiseq2500 sequencing technique. We identified that miR-92a-3p, miR-148-3p and miR-25-3p enriched in metastatic pancreatic cancer patient plasma derived exosomes.

overall_design: Based on the analysis of exosomal miRNA in plasma samples from 5 different groups to identify the specific exosomal miRNA promoting metastasis.

first: ShiJing

last: yue

last: liu

first: LuHan

last: li