title: Transcriptional Profiling of SARS-CoV-2 and IAV across Syrian golden hamster brain regions and peripheral tissues at early and late time points post-infection

status: Public on Jun 07 2022

first: Justin

last: Frere

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

summary: Here, we systemically profile transcriptional responses to SARS-CoV-2 and IAV in the Syrian golden hamster infection model at 3 and 31 days post-infection. In doing this, we are able to benchmark SARS-CoV-2-induced host-responses against those induced by IAV and highlight unique pathologies that occur in response to SARS-CoV-2 at the peak of infection and following viral clearance. Through profiling of neural (olfactory bulb, medial prefrontal cortex, thalamus, striatum, cerebellum, trigeminal ganglion) and peripheral organ (lung, heart, kidney) tissues, we are able to show that while both viruses are able to induce systemic IFN-I responses and immune activation during acute infection, SARS-CoV-2 induces a uniquely localized and persistent inflammatory phenotype in the olfactory bulb that persists out to 31 days post-infection.

overall_design: RNA-sequencing of SARS-CoV-2-, IAV-, and mock-treated hamster organ tissues at 3 and 31 days-post-infection to allow differential expression analysis among infection groups and time points.

first: Benjamin

last: tenOever


title: Gene expression profiles of colorectal cancer tissues and tumor-adjacant tissues reveal key genes that participate in oncogenic activities

city: Changsha

first: Kuijie

last: Liu

state: Hunan

address: 139 Renmin Middle Road

department: Department of General Surgery

country: China

institute: The Second Xiangya Hospital

type: Expression profiling by high throughput sequencing

summary: To investigate the key genes involved in the inception and progression of colorectal cancer, we obtained tumor and tumor-adjacant tissues from CRC patients who underwent surgical resection and sent them to high-throughput sequencing. In this study, we compared the gene expression profiles of tumor tissues and normal tissues, aiming at identifying differentially expressed genes.  Our study revealed a set of differentially expressed genes that may participate in the oncogenic activities during CRC inception and development.

overall_design: We sequenced RNA from the colorectal cancer tissues and normal tissues of two patients. Two replicates per sample were included

first: Yuhong

last: Jiang

first: Xiaobo

last: Wang

first: Lun

last: Li

first: Jun

last: He

first: Qianqian

last: Jin

first: Dongju

last: Long

first: Chao

first: Weihan

last: Zhou


title: Sensory neurons display cell-type specific vulnerability to loss of axon-glia interactions

status: Public on Jun 06 2022

city: Chicago

first: Benayahu

last: Elbaz

state: Illinois

address: 303 E. Chicago Ave. Ward 7-641. Chicago, IL 60611

department: Neurology

country: USA

institute: Northwestern University

summary: In this study we characterized the transcriptional response of sensory neurons to PNS demyelination caused by genetic ablation of glial cells

overall_design: The sciatic nerve and DRG L3-L5 were harveted at no disease, peack disease (PID21) and during the recovery (PID42). Total RNA was purified from the tissues and subjected to bulk-RNA-seq


title: Quantitative analysis of hippocampal transcriptomes of naïve and post-status epilepticus (SE) mouse with or without levetiracetam (LEV).

status: Public on Jun 09 2022

city: Sanuki

first: Rie

last: Komori

department: Kagawa School of Pharmaceutical Sciences

country: Japan

institute: Tokushima Bunri University

summary: LEV is known to be involved in neuroprotection via anti-angiogenesis and anti-inflammatory activities against blood-brain barrier dysfunction in the acute phase of epileptogenesis after SE, but the mechanism remains unclear. The purpose of this study is to comprehensively examine the gene expression in hippocampus of LEV-treated and untreated pilocarpine induced (PILO-) SE mouse in order to understand the whole process of early epileptogenesis.

overall_design: PILO-SE mice were treated with LEV  (n=2).

first: Taira

last: Matsuo

first: Ritsuka

last: Hashimoto

first: Sizuka

last: Kubo

first: Chihiro

last: Kozawa

first: Tomomi

last: Kono

first: Yasuhiro

last: Ishihara

first: Kouichi

last: Itoh


title: Single cell RNA sequencing of P10 and adult vomeronasal organ of OMPCreR26AP2e and Controls

city: Albany

first: Paolo

middle: E

last: Forni

state: New York

address: 1400 Washington Avenue

institute: University at Albany

summary: Neuronal identity dictates the position in an epithelium, and the ability to detect, process, and transmit specific signals to specified targets. Traditionally, transcription factors (TFs) determine cellular identity via direct modulation of genetic transcription and recruiting chromatin modifiers. However, our understanding of the mechanisms that define neuronal identity and their magnitude remains a critical barrier to elucidate the etiology of congenital and neurodegenerative disorders. The structure of the rodent vomeronasal organ provides a unique system to examine in detail the molecular mechanisms underlying the differentiation and maturation of chemosensory neurons (VSNs). Here we demonstrated that the identity of postmitotic/maturing VSNs and vomeronasal dependent behaviors can be reprogrammed through the rescue of AP-2e expression in the AP-2eNull mice and by inducing ectopic AP-2e expression in mature apical VSNs. Our data suggest that the transcription factor AP-2e directly controls the expression of batteries of vomeronasal genes.

overall_design:
We employed single-cell RNA sequencing (scRNA-seq) to understand  the molecular differences between apical and basal VSNs and the effect of ectopically expressed Tfap2e/AP-2e in underlying cell fate specification of two major types of vomeronasal neurons in mice at two different stages of life, P10 and 3mo adult, to understand acute and long-term effects of ectopic AP-2e expression on the vomeronasal epithelium. The frozen single-cell sustpension was sent to Singulomics for high-throughput single-cell sequencing using the 10x Genomics Chromium Platform.
contributor: Singulomics Corporation, Bronx, NY

first: Jennifer

middle: M

last: Lin

first: Ed

middle: Z

last: Taroc

first: Raghu

middle: R

last: Katreddi


title: Hypoxia-mediated stabilization of HIF1A in prostatic intraepithelial neoplasia promotes cell plasticity and malignant progression

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Prostate cancer (PCa) is a leading cause of cancer-related deaths. The slow evolution of precancerous lesions to malignant tumors provides a broad time-frame for preventing PCa. To characterize prostatic intraepithelial neoplasia (PIN) progression, we conducted longitudinal studies on Pten(i)pe-/- mice which recapitulate prostate carcinogenesis in humans. We discovered that early PINs are hypoxic and that hypoxia-inducible factor 1 alpha (HIF1A) signaling is activated in luminal cells, which enhances malignant progression. Luminal HIF1A dampens immune surveillance and drives luminal plasticity leading to the emergence of cells with selective Transglutaminase 2 (TGM2) expression and impaired androgen signaling. Importantly, elevated TGM2 levels in PCa patients are associated with shortened progression-free survival after prostatectomy. Finally, we show that pharmacologically inhibiting HIF1A impairs cell proliferation and induces apoptosis in PINs. Therefore, our study demonstrates that HIF1A is a target for PCa prevention, and that TGM2 is a promising prognostic biomarker of early relapse after prostatectomy.

overall_design: The aim was to determine the HIF1A cistrome in mouse prostate adenocarcinoma cells. Myc-CaP cells were treated with DMOG (HIF1A stabilizer) at a concentration of 1.0 mM for 6h. 3 samples were analyzed: 1 replicate of DMOG-treated Myc-CaP cells with 50 µg of chromatin immunoprecipitated using 5 µg of HIF1A antibody; 1 replicate of DMOG-treated Myc-CaP cells with 50 µg of chromatin immunoprecipitated using 5 µg of rabbit IgG (negative control); 1 replicate of non-immunoprecipitated chromatin (control).

first: Mohamed

middle: A

last: Abu el Maaty

first: Gilles

last: Laverny

first: Daniel

last: Metzger

last: Ye


title: Regulation of both transcription and RNA turnover contribute to germline specification

status: Public on Jun 10 2022

city: La Jolla

first: Kun

last: Tan

state: CA

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

summary: The nuanced mechanisms driving primordial germ cells (PGC) specification remain incompletely understood since genome-wide transcriptional regulation in developing PGCs has previously only been defined indirectly. Here, using SLAMseq analysis, we determined genome-wide transcription rates during the differentiation of embryonic stem cells (ESCs) to form epiblast-like (EpiLC) cells and ultimately PGC-like cells (PGCLCs). This revealed thousands of genes undergoing bursts of transcriptional induction and rapid shut-off not detectable by RNAseq analysis. Our SLAMseq datasets also allowed us to infer RNA turnover rates, which revealed thousands of mRNAs stabilized and destabilized during PGCLC specification. mRNAs tend to be unstable in ESCs and then are progressively stabilized as they differentiate. For some classes of genes, mRNA turnover regulation collaborates with transcriptional regulation, but these processes opposed each other in a surprisingly high frequency of genes. To test whether regulated mRNA turnover has a physiological role in PGC development, we examined 3 genes that we found were regulated by RNA turnover: Sox2, Klf2, and Ccne1. Circumvention of their regulated RNA turnover severely impaired the ESC-to-EpiLC and EpiLC-to-PGCLC transitions. Our study demonstrates the functional importance of regulated RNA stability in germline development and provides a roadmap of transcriptional and post-transcriptional regulation during germline specification.

overall_design: Mouse ES cells were induced to differentiate into EpiLCs and PGCLCs, as previously described (Hayashi et al., 2011). ESC, EpiLC, and purified PGCLC were collected for SLAMseq analysis. Libraries were prepared using the Quant-seq mRNA 3′ end library preparation kit (Lexogen) according to the manufacturer’s instructions. Sequencing was performed using a Illumina HiSeq 4000 in the SR100 mode.

first: Miles

middle: F

last: Wilkinson


title: A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

country: Netherlands

institute: Amsterdam University Medical Centers

summary: Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigated the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We found that ~82% of SARS-CoV-2 S-reactive B cells show a naive phenotype, which represents an unusually high fraction of total human naive B cells (~0.1%). Approximately 10% of these naive S-reactive B cells shared an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.

overall_design:
Single-cell transcriptomics experiment on SARS-CoV-2-Spike specific B cells from blood samples of 10 healthy donors unvaccinated and unexposed to SARS-CoV-2 *** Raw data not available due to patient privacy concerns ***
---------------------------------------
Authors state "raw data not available due to patient privacy concerns".

first: Mathieu

last: Claireaux

first: Tom

middle: G

last: Caniels

first: Gius

last: Kerster

first: Barbera

middle: C

last: van Schaik

first: Perry

middle: D

last: Moerland

first: Rogier

middle: W

last: Sanders

first: Marit

middle: J

last: van Gils


title: Endometrial gland impacts on stromal cell decidualization

city: columbia

first: Hongyu

last: Liu

state: mo

address: 920 east campus drive.

institute: university of missouri

summary: Uterine glands and, by inference, their secretions impact uterine receptivity, blastocyst implantation, stromal cell decidualization, and placental development. Changes in gland function across the menstrual cycle are impacted by steroid hormones, estrogen and progesterone, as well as stroma-derived factors. Using an endometrial epithelial organoid (EEO) system, transcriptome and proteome analyses identified distinct responses of the EEO to steroid hormones and prostaglandin E2 (PGE2). Notably, steroid hormones and PGE2 modulated the basolateral secretion of EEO proteins, where cystatin C (CST3) was significantly increased by progesterone and PGE2. CST3 treatment of decidualizing stromal cells significantly decreased the decidualization markers PRL and IGFBP1. The attenuation of stromal cell decidualization via CST3 suggests a role for uterine gland-derived proteins in controlling the extent of decidualization. These findings provide evidence that uterine gland-derived factors directly impact stromal cell decidualization, which has strong implications for better understanding pregnancy establishment and female fertility in humans.

overall_design: Pair-end sequencing was performed on hormone treated EEO derived from three donors. FastQC (v 0.11.9) and MultiQC (v 1.10.1) were used to evaluate the quality of the sequence. Trimmomatic (v 1.10.1) was used to remove adapters and low-quality bases from the reads. Trimmed reads were aligned to the human genome (GRCh38) with STAR aligner (v 2.7.9a) (average unique mapping rate of 89.21% and read length of 200 bp). Gene quantification was calculated by using featureCounts from Subread package (v 2.0.3). Counts extracted from featureCounts were used to perform differential gene analysis in R (version 4.0.2) using DESeq2 (v 1.30.1).

first: Harriet

last: Fitzgeralda


title: ISR8 / IRF1-AS1 is relevant for IFNα and NF-κB responses

status: Public on Jun 03 2022

city: Pamplona

first: Puri

last: Fortes

address: Pio XII 55

country: Spain

institute: CIMA/UNAV

summary: The study of the interferon (IFN) α-induced cell transcriptome has shown altered expression of several long non-coding RNAs (lncRNAs). ISR8 / IRF1-AS1 (IFN stimulated RNA 8), located close to IFN regulatory factor 1 (IRF1) coding gene, transcribes a lncRNA induced at early times after IFNα treatment or IRF1 or NF-κB activation. Depletion or overexpression of ISR8 RNA does not lead to detected deregulation of the IFN response. Surprisingly, disruption of ISR8 locus with CRISPR-Cas9 genome editing results in cells that fail to induce several key ISGs and pro-inflammatory cytokines after a trigger with IFNα or overexpression of IRF1 or the NF-κB subunit RELA. This suggests that the ISR8 locus may play a relevant role in IFNα and NF-κB pathways. Interestingly, IFNα, IRFs and NF-κB-responding luciferase reporters are normally induced in ISR8-disrupted cells when expressed from a plasmid but not when integrated into the genome. Therefore, IFNα and NF-κB pathways are functional to induce the expression of exogenous episomic transcripts but fail to activate transcription from genomic promoters. Transcription from these promoters is not restored with silencing inhibitors, by decreasing the levels of several negative regulators or by overexpression of inducers. Transcriptome analyses indicate that ISR8-disrupted cells have a drastic increase in the levels of negative regulators such as XIST and Zinc finger proteins. Our results agree with ISR8 loci being an enhancer region that is fundamental for proper antiviral and proinflammatory responses. These results are relevant because several SNPs located in the ISR8 region are associated with chronic inflammatory and autoimmune diseases including Crohn’s disease, inflammatory bowel disease, ulcerative colitis or asthma.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HeLa cells and its CRIPSR-KD derivative treated or not with IFNa (pNISR8).

first: Marina

last: Barriocanal


title: RNA-Seq of NIH-3T3 cells treated with CMA modulators

city: Bronx

first: Mericka

last: McCabe

state: NY

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: Transcriptomics of NIH-3T3 cells treated with CMA activators to evaluate gene expression changes

overall_design: Four samples; No treatment (control) and three treatment conditions (AR7, CA39, and CA77)

first: Ana

last: Cuervo

first: Fernando

last: Macian


title: RNA-Seq of NIH-3T3 cells treated with atypical RARa modulators

summary: Transcriptomics of NIH-3T3 cells treated with typical or atypical RARa modulators to evaluate genetic changes induced by chemical modification of RARa signalling

overall_design: Three samples; No treatment (control) and two treatment conditions (AR7 and BMS614)


title: Next Generation Sequencing of wild-type and ORP4L knock-in murine T-cells Transcriptomes

status: Public on Jun 04 2022

city: Guangzhou

first: Wenbin

last: Zhong

address: No.601, West Huangpu Avenue

institute: Jinan University

summary:
Purpose: The goals of this study is to determine whether specific gene sets are dysregulated in the murine ORP4L knock-in T-cells, as compared to wild-type T-cells.
Methods: T-cell mRNA profiles of wild-type and ORP4L knock-in mice were generated by deep sequencing, using Illumina NovaSeq 6000 sequencer for 318 cycles.Reads that passed the Illumina quality filters were kept for the subsequent analyses. Adapters were trimmed from the reads, and reads shorter than 17 nt were discarded. The reads were mapped to the Mouse mRNA reference database using FANSe3 algorithm on Chi-Cloud NGS Analysis Plantform.
Results: We use edgeR to analysis ORP4 kncok-in vs. wild-type，with a |log2 (FoldChange)| > 1 and p value <0.01. Hierarchical clustering of differentially expressed genes uncovered a total of 970 differentially expressed genes (DEGs) , of which 539 were down-regulated and 431 up-regulatedseveral.
Conclusions: Our study represents the first detailed analysis of transcriptomes that promote T-cell malignant transformation driven by oncogene ORP4L in mice.

overall_design: Examination of transcriptomes in T-cells from wild-type and ORP4L knock-in mice.

first: Daoguang

last: Yan

first: Huanzhao

last: Chen


title: single cell RNA sequencing of adult (P60) vomeronasal organ

first: Paolo

last: Forni

department: Department of Biological Sciences

summary: The vomeronasal organ of mice consists of two major types of vomeronasal sensory neurons (VSNs) expressing either receptors of the V1R or V2R family.  V1R and V2R VSNs form from a common pool of progenitors but have distinct differentiation programs. We analyzed single cell RNA sequencing data of adult VNO and identified differential expression of Notch1 receptor and Dll4 ligand among the neuronal precursors at the VSN dichotomy. We further demonstrated that Notch signaling is required for effective differentiation of V2R+ basal VSNs.

overall_design:
We employed single-cell RNA sequencing (scRNA-seq) technique to understand the mechanisms underlying cell fate specification of two major types of vomeronasal neurons in mice. As adult neurogenesis happen through out the life at marginal zones of the vomeronasal sensory epithelium in mice, we chose postnatal day 60 to do scRNA-seq in order to collect cells ranging from neuronal progenitors, to immature and mature vomeronasal neurons and non-neuronal cells of both sensory and non-sensory epithelium. The frozen single cell suspension was sent to Singulomics for high-throughput single-cell gene expression profiling using the 10x Genomics Chromium Platform.
Contributor: Singulomics Corporation, Bronx, NY

first: Raghu Ram

last: Katreddi

first: Jennifer

last: Lin

first: Ed

last: Taroc

first: Sawyer

last: Hicks


title: Overlapping and distinct functions between ERα and ERβ homodimers and corresponding transcriptomes in the same cellular context

city: Stockholm

first: Dandan

last: Song

address: Tomtebodavägen 23

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: The two estrogen receptors, ERα and ERβ function as ligand-inducible transcription factors. Most in vitro studies have reported that ERα drives breast cancer growth whereas ERβ, if expressed, suppresses growth. To dissect function and gene expression profile regulated by ERα or ERβ, respectively, we generated a novel cell model expressing only ERβ, by applying CRISPR-cas9 to delete ERα in MCF7 cells with stable Tet-Off-inducible ERβ expression. This model with ERβ expression only, exhibited regulation of known estrogen responsive genes in a ligand-dependent manner. By cell proliferation assay, we found that either ER was required for proliferation, and that while E2 increased proliferation of ERα (only) MCF7, it reduced proliferation of ERβ (only) MCF7 cells. RNA-Seq analysis revealed 768 and 984 specific target genes regulated by ERα and ERβ in response to E2, respectively. Furthermore, functional enrichment analysis showed that the two ER isoforms regulated cell proliferation in opposite direction. In conclusion, within the same cellular context the two ERs regulated cell proliferation in opposite manner by regulating distinct sets of target genes in response to E2. The novel developed cell model provides a novel and valuable resource to further complement the mechanistic understanding of the two different ER isoforms.

overall_design: mRNA profiles of MCF7 tetoff cell model upon E2/vehicle treatment

first: Cecilia

last: Williams


title: Ileal S100A9 expression distinguishes Crohn’s disease patients by age at diagnosis

status: Public on Jun 02 2022

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Crohn’s disease (CD) is a debilitating gastrointestinal disorder that can impact the entirety of the GI tract. While substantial progress has been made in the medical management of CD, it remains incurable, frequently relapses, and is a significant financial and medical burden. The pathophysiology of CD is not well understood, but it is thought to arise in genetically susceptible individuals upon an environmental insult. Further elucidation of the disease etiology promises to expose additional therapeutic avenues, with the hope of reducing the burden of CD. One approach to understanding disease pathophysiology is to identify clinically relevant molecular disease subsets using transcriptomics. In this report, we use hierarchical clustering of the ileal transcriptomes of 34 patients to identify two CD subsets. Clinically, these clusters differed in the age of the patients at CD diagnosis, suggesting that age of disease onset impacts the pathophysiology of the disease. We found that the ileal transcriptomes of the early diagnosis cluster are enriched in inflammatory transcripts, including S100A9, which encodes a calprotectin subunit. Furthermore, levels of S100A9 distinguished individuals diagnosed before the age of 30 from those diagnosed after 30. Together, these findings suggest that medical management of CD patients should consider their age at diagnosis and therapeutic blockade of calprotectin may be beneficial in patients diagnosed earlier in life.

overall_design: Gene expression profiles from the surgically resected, diseased, ileal tissue of 34 Crohn's disease patients were generated by deep sequencing.

first: Melanie

last: Eshelman

first: Walter

last: Koltun

first: Gregory

middle: S

last: Yochum


title: Bona fide and bystander memory B cell subsets colonize the lung peribronchial niche upon viral infection

city: Marseille

first: Lionel

last: Spinelli

address: Avenue de Luminy

institute: CIML

summary: Memory B cells (MBCs) are key cellular components of long-term humoral immunity that dominate recall responses by rapidly differentiating into effector cells. As the biology of MBCs has been mainly studied in the context of model antigen immunizations, the dynamics of these cells during infection remains largely unexplored. Here, we combined influenza and SARS-CoV-2 infection models with fluorescent-reporter mice to identify MBCs regardless of antigen-specificity. scRNA-seq analysis and confocal imaging revealed that two main transcriptionally distinct subsets of MBCs colonize the lung airways after infection. These subsets were class-switched, somatically mutated and preferentially differentiated into plasma rather than germinal center cells upon activation. Combined analysis of antigen-specificity and B cell receptor repertoire unveiled a highly permissive selection process that segregated these subsets into “bona fide” virus-specific MBCs and “bystander” MBCs with no apparent specificity for eliciting viruses. Thus, diverse transcriptional programs in MBCs are not linked to specific effector fates but rather to divergent strategies of the immune system to simultaneously provide rapid protection from re-infection while diversifying the initial B cell repertoire.

overall_design: Memory B cells were FACS-sorted from lungs, mediastinal lymph nodes, or spleen of Aicda-Cre-ERT2 x Rosa26-LSL-eYFP mice 70 days after intranasal infection with influenza A virus PR8 H1N1 strain, and subjected to single-cell RNA-seq by either droplet-based 10x Genomics 5'-end protocol, or plate-based FB5P-seq 5'-end protocol.

first: Mauro

last: Gaya

first: Pierre

last: Milpied

first: Claude

last: Grégoire

first: Laurine

last: Gil

first: Chuang

last: Dong


title: Maladaptive Positive Feedback Production of ChREBPβ Drives Glucotoxic β-Cell Failure

city: New York

first: Donald

middle: K

last: Scott

address: 1428 Madison Avenue

department: Diabetes Obesity and Metabolism Institute

institute: MSSM

summary:
Purpose: Test the role of ChREBPbeta in pancreatic beta cells using tools that distinguish ChREBPalpha and ChREBPbeta and loss and gain of function experiments, confirming its role in glucose toxicity and finding mitigation strategies.
Methods: INS-1 832/13 cells cultured in 2 mM or 11 mM glucose were transduced with adenoviruses expressing GFP as control or ChREBPbeta. After 48 h, RNA was isolated and amplified via the NuGEN Ovation RNA-Seq System V2 prior to RNA sequencing. Human islets from non-diabetic and T2D subjects were transduced with adenovirus ZSGreen and cell sorted. RNA was isolated and subjected to RNAseq.
Results: Overexpression of ChREBPbeta led to increased expression of cell cycle and apoptotic genes and a decrease in beta cell maturity genes. T2D human beta cells expressed an increased ratio of ChREBPbeta to ChREBPalpha compared to non-diabetics.
Conclusions: ChREBPbeta is necessary for adaptive beta cell expansion, but drives glucose toxicity when overexpressed, mimicking the graded effect of Myc overexpression in beta cells.

overall_design: RNAseq: INS-1 832/13 cells were cultured in 2 or 11 mM glucose transduced with control (GFP) or ChREBPbeta-expressing adenoviruses for 48 h.


title: Time series mRNA abundance measurement triggered by ActinomycinD treatment in patient iPSC derived neurons

status: Public on Jun 01 2022

city: Boston

first: Xianjun

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

summary: We measured bulk mRNA abundance in Ngn2 induced patient derived cortical neurons in synucleinophaty models. ActD shuts off the transcription allowing us to measure mRNA decay.

overall_design: Biological samples: SNCA 2 copy neurons and SNCA 4 copy neurons, Treatment: ActD(10 ug/ml), Collection times: 0,1,3,6,12 hour after ActD tretment, Perturbation: SNCA preformed fibril addition(5 ug/ml)

first: Erinc

last: Hallacli


title: Mechanism of abnormal coagulation induced by tigecycline in cancers

city: Shanghai

first: Dawei

last: Wang

address: 197 Ruijin Road II

institute: Shanghai Jiao Tong University School of Medicine

summary: Tigecycline is a broad-spectrum active intravenous antibiotic that is also active against methicillin-resistant staphylococcus aureus. In Phase 3 and 4 clinical trials, increased all-cause mortality was observed in patients treated with tigecycline compared to patients in the control group. The reason for the increase is not yet clear. In this study, we found tigecycline could cause abnormal coagulation in tumor patients, especially in patients with hematological malignancies. The main manifestations were decreased fibrinogen and prolonged activated prothrombin time (APTT), thrombin time (TT) and D-dimer. In addition, functional studies have found that tigecycline could inhibit platelet adhesion and aggregation, and the patient's coagulation function could gradually recover after discontinuation. Gene sequencing results suggested that tigecycline could significantly regulate the expression of genes related to platelet function pathways, and could increase the incidence of single nucleotide polymorphisms and the number of alternative splices in CHO cells with tigecycline treatment. Abnormal platelet function and low numbers are common in patients with hematological malignancies. Our study could explain the mechanism of abnormal coagulation caused by tigecycline. At the same time, a warning should be given when doctors applied tigecycline to cure infections in tumor patients.

overall_design: The CHO cells treated with tigecycline (0 mg/ml and 0.2 mg/ml) for 48 h was used for RNA sequencing.

first: Yujun

last: Dai


title: Exosomal microRNA expression profiles of NASH: normal vs. NASH

city: GuangZhou

first: zhiping

last: wan

institute: Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Non-alcoholic fatty liver disease (NAFLD) is a predominant form of chronic liver disease, affecting nearly 25 % of the global population. The progression from steatosis to nonalcoholic steatohepatitis (NASH) in NAFLD patients is one of the major causes of liver-related death worldwide. We assessed the miRNA expression profiles of the exosomes derived from the peripheral blood of NASH patients or healthy controls.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for exosomes derived from the peripheral blood of NASH patients or healthy controls.

first: Zhiping

last: Wan

first: Xiaoan

last: Yang

first: Xiaoquan

last: Liu

first: Yinfang

last: Sun

first: Piaojian

last: Yu

first: Fen

last: Xu

first: Hong

last: Deng


title: APEX-seq performed for DDX3X and DDX3Y without arsenite treatment

city: philadelphia

first: Fange

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

summary: Sex differences are pervasive in human health and disease. One of the major keys to sex-biased differences lies in the sex chromosomes, which encode a group of sex-specific protein homologs. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs remains elusive. One pair of sex chromosome-encoded proteins are the RNA helicases DDX3X and DDX3Y. DDX3X and DDX3Y can both form stress granules (SGs) under different types of stress. SGs are composed of a stable core structure, they are surrounded by a dynamic shell with assembly, disassembly, and transitions of proteins and RNA between the core and shell. Different SGs have distinct proteins and RNA constituents, which raises the possibility that different SGs might perform different biological functions. Previously, we performed APEX-seq to explore the RNA compositions in DDX3X and DDX3Y SGs, however, the difference between the mRNA partner of DDX3X and DDX3Y without stress treatment is still uncharted. Therefore, we applied the APEX-seq to cytosome diffused DDX3X and DDX3Y.

overall_design: RNA-seq after streptavidin beads pulldown of biotion labeled RNA for APEX2-EGFP, APEX2-DDX3X and APEX2-DDX3Y without stress treatment in HeLa cells

first: Kathy

first: Hui

last: Shen


title: Single-cell RNA sequencing unveils the clonal and transcriptional landscape of cutaneous T-cell lymphomas

city: Pittsburgh

first: Patrizia

last: Fuschiotti

address: 200 Lothrop St

institute: University of Pittsburgh

summary: Mycosis fungoides (MF) is the most common subtype of cutaneous T-cell lymphoma, arising from clonal expansion of transformed skin-homing memory T cells. However, the lack of specific markers for malignant lymphocytes prevents distinguishing them from benign T cells in the tumor microenvironment (TME) of MF, thus delaying diagnosis and development of specific treatment, which results in poor clinical outcomes. Here we employed recent advances in single-cell RNA-sequencing to establish the transcriptome of expanded T-cell clones directly in advanced-stage MF skin tumors, allowing the transcriptional profiles of malignant and reactive T lymphocytes to be distinguished. Our analysis identified multiple non-overlapping expanded T-cell clonotypes within individual MF tumors, which included malignant and reactive clones. Heterogeneity among samples was observed not only in the number of expanded clonotypes but also in their TCR specificity and gene expression. While patient-specific tumorigenic pathways were up-regulated by the malignant clones, we also identified a common gene expression that included genes associated with cancer cell metabolism, de novo nucleotide biosynthesis, and invasion. Most non-malignant clones originated from CD8+ T cells and commonly presented an exhausted immune phenotype and activated Th1/Th2 pathways. While non-clonal infiltrating CD4+ and CD8+ lymphocytes from all tumors shared anti-inflammatory and immunosuppressive pathways, patient-specific mechanisms included the TNFR2 signaling cascade, ferroptosis, and cytotoxic pathways by gamma/delta T cells. Thus, scRNAseq reveals new insights in MF pathogenesis by providing an unprecedented report of the transcriptomes of malignant and reactive T cells in the TME of individual patients and offers novel prospective targets for personalized therapy.

overall_design: 4 MF samples and 4 normal samples were analyzed for gene expression and TCR expression. 4 SZ samples and 3 healthy PBMC samples were analyzed for gene expression and TCR expression. 2 blood/skin samples from same patient were analyzed.

first: Alyxzandria

last: Gaydosik

first: Connor

last: Stonesifer

first: Larisa

last: Gerskin


title: Adaptation of Geobacter sulfurreducens to grow with fumarate only and its impact on the transcriptome

city: Wuhan

first: Pier-Luc

last: Tremblay

state: Hubei

address: 122 Luoshi Road

department: School of Chemistry, Chemical Engineering and Life Science

institute: Wuhan University of Technology

summary: The expression profile of adapted G. sulfurreducens strain T9-1 grown with 40 mM fumarate without any other substrate versus the expression profile of G. sulfurreducens PCA (wild type) grown with 10 mM acetate and 40 mM fumarate

overall_design: Illumina RNA-seq of total RNA extracted from G. sulfurreducens wild type grown anaerobically in NB medium with 10 mM acetate and 40 mM fumarate. Illumina RNA-seq of total RNA extracted from G. sulfurreducens strain T9-1 evolved by adaptive laboratory evolution to grow anaerobically in NB medium with only 40 mM fumarate. The adapted strain was transferred nine times in the fumarate-only medium and Total RNA was extracted from T9-1 performing fumarate disproportionation

first: Xiao-Chen

last: Shi

first: Tian

last: Zhang


title: Molecular signatures of in-situ to invasive progression for basal-like breast cancers: An integrated mouse model and human tumor study [CGH]

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

type: Genome variation profiling by genome tiling array

summary:
This study identifies progression in breast ductal carcinoma in situ (DCIS) as it progresses towards triple negative invasive breast cancer (TNBC).
Bulk DNA arrayCGH was performed on the C3Tag genetically engineered mouse model that forms human breast-like DCIS and TNBC.

overall_design: Charles, M, Perou

first: Aatish

last: Thennavan


title: Molecular signatures of in-situ to invasive progression for basal-like breast cancers: An integrated mouse model and human tumor study [mouse]

summary: This study identifies progression in breast ductal carcinoma in situ (DCIS) as it progresses towards triple negative invasive breast cancer (TNBC).

overall_design: Single cell RNA sequencing (scRNAseq) and bulk RNA sequencing was performed on the C3Tag genetically engineered mouse model that forms human breast-like DCIS and TNBC. Bulk RNA sequencing was performed on RNA harvested from 10 archival formalin-fixed paraffin embedded (FFPE) pairs comprising of estrogen receptor (ER) positive (ER+) and ER- subsets of DCIS.


title: Characterisation of the temporal hepatic transcriptome at subcellular level

city: Lausanne

first: Felix

last: Naef

state: Vaud

address: AAB 040 Station 15

department: Institute of Bioengineering

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne

summary: In eukaryotes, RNA is synthesized in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, generating daily fluctuations of RNA accumulation and impacting the distribution of transcripts in different subcellular compartments. Here, we performed a comprehensive analysis of nuclear and cytoplasmic, polyA and total, transcriptomes of mouse livers sampled along the daily cycle. These data provide a genome-wide temporal inventory of RNA subcellular enrichments, and revealed specific signatures of splicing, nuclear export and cytoplasmic mRNA stability related to transcript and gene lengths. Combined with a mathematical model describing rhythmic RNA profiles , we could test the rhyhtmicity of export rates and cytoplasmic degradation rates of ~1400 genes. While nuclear export times  are usually much shorter than cytoplasmic half-lives, we found that that nuclear export contributes to the modulation and generation of rhythmic profiles of ~10% of the cycling nuclear mRNAs. This study provides an estimation of the nuclear and cytoplasmic life times in the liver  and contributes to a better understanding of the dynamic regulation of the transcriptome during the feeding-fasting cycle.

overall_design: RNA-seq of mouse liver tissues sampled during the diurnal cycle (6 time points, 2 WT and 2 Cry1/Cry2 KO animals per time points), at ZT0, 4, 8, 12, 16 and 20. ZT0 is the onset of the light phase (rest phase, without food access) and ZT12 is onset of the dark phase (active phase, with food access). RNA from nuclear fraction, cytoplasmic fraction and total liver tissue were sequenced

first: Clémence

last: Hurni

first: Benjamin

last: Weger

first: Cédric

last: Gobet


title: Molecular signatures of in-situ to invasive progression for basal-like breast cancers: An integrated mouse model and human tumor study [human]

overall_design:
Single cell RNA sequencing (scRNAseq) and bulk RNA sequencing was performed on the C3Tag genetically engineered mouse model that forms human breast-like DCIS and TNBC. Bulk RNA sequencing was performed on RNA harvested from 10 archival formalin-fixed paraffin embedded (FFPE) pairs comprising of estrogen receptor (ER) positive (ER+) and ER- subsets of DCIS.

**Submitter declares that the raw data are being deposited in dbGaP (phs002443.v1.p1) due to patient privacy concerns**


title: Molecular signatures of in-situ to invasive progression for basal-like breast cancers: An integrated mouse model and human tumor study

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A novel tubulin binding molecule drives differentiation of acute myeloid leukaemia cells

city: oxford

first: Thomas

last: Jackson

address: weatherall institute of molecular medicine

department: paediatrics

country: United Kingdom

institute: University of Oxford

summary: Acute Myeloid Leukaemia (AML) continues to have a poor prognosis, especially in the elderly. One reason for this is that many treatment regimens are not well tolerated by elderly patients. Much current focus is on the development of therapies that can target specific vulnerabilities of AML while having fewer toxic side effects. However, despite much recent progress in developing better drugs, many patients with AML still die within a year of diagnosis, partly due to the fact that it is difficult to identify therapeutic targets that are effective across multiple AML subtypes. One common factor across AML subtypes is the presence of a block in differentiation. Thus screening for compounds that can overcome this block in genetically diverse AML models should allow for the identification of agents that are not dependent on a specific mutation for their efficacy. Here, we used a phenotypic screen to identify novel compounds that stimulate differentiation in several AML cell lines. Lead compounds were shown to decrease tumour burden and to increase survival in vivo. Using multiple complementary target deconvolution approaches, these compounds were revealed to be anti-mitotic tubulin disruptors that cause differentiation by inducing a G2-M mitotic arrest. Together, these results reveal a novel function for tubulin disruptors in causing differentiation of AML cells.

overall_design: Examiniation of the tracritpiomic respoinse of HL-60 cells to novel compounds.

first: Aini

last: Vuorinen

first: Laia

last: Josa-Culleré

first: Katrina

last: Madden

first: Daniel

last: Conole

last: Cogswell

first: Isabel

middle: L

last: Wilkinson

first: Laura

last: Kettyle

first: Douzi

first: Alison

last: O’Mahoney

first: Deanne

last: Gracias

first: Lorna

last: McCall

first: Robert

last: Westwood

first: Georg

last: Terstappen

first: Stephen

last: Davies

first: Edward

last: Tate

first: Graham

last: Wynne

first: Paresh

last: Vyas

first: Angela

last: Russell

last: Milne


title: PD-1 directed immunotherapy alters Tfh and humoral immune responses to seasonal flu vaccine

city: New York City

first: Ramin

last: Herati

address: 429 E. 29th Street, room 308

institute: NYU School of Medicine

summary: Anti-PD-1 (aPD1) immunotherapy likely affects other immune cells including follicular helper CD4 T cells (Tfh) involved in germinal center (GC) responses.  Little is known, however, about the effects of anti-PD-1 immunotherapy on non-cancer immune responses in humans. To investigate this question, we examined the impact of aPD1 immunotherapy for cancer on the Tfh-B cell axis responding to unrelated viral antigens. Following influenza vaccination, a subset of adults receiving aPD1 had more robust circulating Tfh (cTfh) responses than adults not receiving immunotherapy, and cTfh responses correlated with plasmablasts. PD-1 pathway blockade also resulted in transcriptional signatures of increased cellular proliferation in cTfh and responding B cells compared to controls.

overall_design: Comparison of 4 immune subsets before and after influenza vaccination in the setting of anti-PD1 immunotherapy

first: David

last: Knorr

last: Vella

first: Luisa

middle: V

last: Silva

first: Lakshmi

last: Chilukuri

first: Sokratis

last: Apostolidis

first: Alexander

last: Huang

last: Muselman

first: Sasikanth

last: Manne

first: Oliva

last: Kuthuru

first: Ryan

middle: P

last: Staupe

first: Sharon

last: Adamski

first: Senthil

last: Kannan

first: Raj

last: Kurupati

first: Hildegund

last: Ertl

first: Jeffrey

last: Wong

first: Stylianos

last: Bournazos

first: Lynn

last: Schuchter

first: Ritesh

last: Koetcha

first: Samuel

last: Funt

first: Martin

middle: H

last: Voss

last: Motzer

first: Chung-Han

last: Lee

first: Dean

last: Bajorin

first: Tara

last: Mitchell

last: Ravetch

first: E

last: Wherry


title: Gene expression changes in THP1 AML cells following Withaferin A exposure

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

summary: Connectivity map analysis using an AML-specific cMYB gene signature (Walf-Vorderwulbecke et al. Leukemia. 2018;32(4):882-889.  10.1038/leu.2017.317) identified withaferin A (WFA) as a candidate cMYB deregulating agent in AML. In order to validate the predicted effect of WFA on cMYB function, RNAseq analysis was performed on THP1 cells following exposure to DMSO or 1mM WFA for 6 hours.

overall_design: Total cellular RNA was purified from DMSO and 1mM WFA treated THP1 samples from three independent experiments

first: Katherine

last: Clesham

first: Jasper

last: de Boer


title: APEX-seq Captures the Protein-RNA Interaction Patterns of DDX3X and DDX3Y

first: Fange

last: Liu

summary: Although stress granules (SGs) are composed of a stable core structure, they are surrounded by a dynamic shell with assembly, disassembly, and transitions of proteins and RNA between the core and shell. Different SGs have distinct proteins and RNA constituents, which raises the possibility that different SGs might perform different biological functions. The RNA compositions of DDX3X- or DDX3Y-positive SGs are not known, nor is it known what differential effects DDX3X or DDX3Y may exert on these RNA components. To understand the biological function and the compositional differences between DDX3X- or DDX3Y-positive SGs, we first determined the RNA constituents in these SGs using an adapted Ascorbate-peroxidase (APEX)-based proximity labeling method. APEX converts exogenously supplied biotin-phenol (BP) to biotin-phenoxyl radicals, which in turn covalently labels protein and RNA in nanometers. APEX-mediated biotinylation has been widely used in studies of protein-protein interactions and recently in studying protein-RNA interactions. Here, we applied the APEX-mediated biotinylation in DDX3X and DDX3Y SGs to dissect their different RNA composition.

overall_design: RNA-seq after streptavidin beads pulldown of biotin-labeled RNA for APEX2-EGFP, APEX2-DDX3X, and APEX2-DDX3Y transient expression HeLa cells with arsenite treatment.

first: Kathy

first: Hui

last: Shen


title: HIGH-RISK SUBTYPES OF CHRONIC LYMPHOCYTIC LEUKEMIA ARE DETECTABLE AS EARLY AS 16 YEARS BEFORE DIAGNOSIS

city: Rotterdam

first: Anton

middle: W.

last: Langerak

address: Doctor Molewaterplein 40

institute: Erasmus MC

summary: Chronic lymphocytic leukemia (CLL) is preceded by monoclonal B-cell lymphocytosis (MBL), a CLL precursor state with a prevalence of up to 12% in aged individuals. However, the duration of MBL and the mechanisms of its evolution to CLL remain largely unknown. In this study, we sequenced the B-cell receptor immunoglobulin heavy chain (BcR IGH) gene repertoire of 124 CLL patients and 118 matched controls in blood samples taken up to 22 years prior to diagnosis. Significant skewing in the BcR IGH gene repertoire was detected in the majority of patients, even before the occurrence of lymphocytosis and irrespective of the clonotypic IGH variable gene somatic hypermutation status. Furthermore, in 14 CLL patients we identified dominant clonotypes belonging to major stereotyped subsets associated with poor prognosis up to 16 years before diagnosis. In 22 patients with longitudinal samples, the skewing of the BcR IGH gene repertoire increased significantly over time to diagnosis or remained stable at high levels. For 14/16 patients with available samples at diagnosis, the CLL clonotype was already present in the pre-diagnostic samples. Overall, our data indicate that the pre-clinical phase of CLL could be longer than previously thought, even in adverse-prognostic cases.

overall_design: B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of pre-diagnostic and diagnostic samples of CLL patients and matched controls.

first: A

first: P

middle: M

last: Kolijn


title: Reversal of Synapse Loss in Alzheimer Mouse Models by Targeting mGluR5 to Prevent Synaptic Tagging by C1q

city: New Haven

first: Stephen

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

institute: Yale University

summary:
Longitudinal PET imaging of Alzheimer models reveals synaptic rescue by an mGluR5 modulator with selective normalization of neuronal transcriptomes.
Alzheimer’s disease symptoms are initiated by synapse loss in the setting of microglial reactivity, but the basis for immune mediator attack on synapses is not clear. The mGluR5 silent allosteric modulator (SAM), BMS-984923, prevents Alzheimer’s triggered aberrant synaptic signaling while preserving physiological Glu activation. Here, we show that oral BMS-984923 effectively occupies brain mGluR5 sites visualized by [18F]FPEB PET at doses 250-fold below adverse effect doses in rodent and non-human primate. For aged transgenic and double knock-in mouse Alzheimer’s models, SV2A PET imaging with [18F]SynVesT-1 reveals cortical and hippocampal synapse density decreases, which are fully recovered by SAM treatment. The disease-modifying benefit persists after drug washout. Tau accumulation in double knock-in mice is also reduced by SAM treatment. Single nuclei transcriptomics demonstrate that SAM treatment normalizes expression patterns to a much greater extent in neurons than glia. Production of the microglial mediator, C1q, is not altered by the mGluR5 compound, but Alzheimer gene-dependent C1q localization to synapses and synaptic engulfment are prevented. Thus, selective modulation of mGluR5 reverses neuronal gene expression changes to protect synapses from damage by microglial mediators.

overall_design: An examination of silent allosteric modulator (SAM) of mGluR5, BMS-984923, binding effecacy at target receptors in rodent and non-human primate as well as it structural and functional effect in 2 rodent models of Alzheimeris disease.

first: Joshua

last: Spurrier

first: LaShae

last: Nicholson

first: Xiotian

middle: T

last: Fang

first: Austin

last: Stoner

first: Takuya

last: Toyonaga

first: Daniel

last: Holden

first: Timothy

last: Siegert

first: William

last: Laird

first: Mary

last: Allnutt

first: Marius

last: Chiasseu

first: Harrison

last: Brody

first: Hideyuki

last: Takahashi

first: Sarah

last: Nies

first: Azucena

last: Canamas

first: Pragalath

last: Sadasivam

first: Supum

first: Songye

last: Li

first: Le

last: Zhang

first: Yiyun

last: Huang

first: Richard

middle: E

last: Carson

first: Zhengxin

last: Cai

last: Strittmater


title: Prostaglandin E1 attenuates AngII-induced cardiac hypertrophy via EP3 receptor activation and Netrin-1upregulation

first: Yejiao

last: Shen

address: 241 West Huaihai Road

institute: Shanghai Jiaotong University affiliated chest hospital

summary: Aims: Pathological cardiac hypertrophy induced by activation of the renin–angiotensin–aldosterone system (RAAS) is one of the leading causes of heart failure. However, in current clinical practice, the strategy for targeting the RAAS is not sufficient to reverse hypertrophy. Here, we investigated the effect of prostaglandin E1 (PGE1) on angiotensin II (AngII)-induced cardiac hypertrophy and potential molecular mechanisms underlying the effect.   Methods and Results: Adult male C57 mice were continuously infused with AngII or saline and treated daily with PGE1 or vehicle for two weeks. Neonatal rat cardiomyocytes were cultured to detect AngII-induced hypertrophic responses. We found that PGE1 ameliorated AngII-induced cardiac hypertrophy both in vivo and in vitro. The RNA sequencing (RNA-seq) and expression pattern analysis results suggest that Netrin-1 (Ntn1) is the specific target gene of PGE1. The protective effect of PGE1 was eliminated after knockdown of Ntn1. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the PGE1-mediated signaling pathway changes are associated with the mitogen-activated protein kinase (MAPK) pathway. PGE1 suppressed AngII-induced activation of the MAPK signaling pathway, and such an effect was attenuated by Ntn1 knockdown. Blockade of MAPK signaling rescued the phenotype of cardiomyocytes caused by Ntn1 knockdown, indicating that MAPK signaling may act as the downstream effector of Ntn1. Furthermore, inhibition of the E-prostanoid (EP)3 receptor, as opposed to the EP1, EP2, or EP4 receptor, in cardiomyocytes reversed the effect of PGE1, and activation of EP3 by sulprostone, a specific agonist, mimicked the effect of PGE1.  Conclusion: In conclusion, PGE1 ameliorates AngII-induced cardiac hypertrophy through activation of the EP3 receptor and upregulation of Ntn1, which inhibits the downstream MAPK signaling pathway. Thus, targeting EP3, as well as the Ntn1–MAPK axis, may represent a novel approach for treating pathological cardiac hypertrophy.

overall_design: Cardiac mRNA profiles of C57 mice treated with saline, AngII and AngII + PGE1

first: Xia

last: Wang

first: Xin

last: Pan

first: Xiaoxiao

last: Yang

first: Jiali


title: The N6-methyadenosine (m6A) levels in PC9 cell lines.

city: Hamamatsu

first: Kazuo

last: Tsuchiya

department: Tumor pathology

institute: Hamamatsu University School of Medicine

summary:
ALKBH5 (AlkB homolog 5) has been identified as a eukaryotic demethylase, which catalyzes N6 adenosine. N6-methyladenosine (m6A) is oxidatively demethylated by ALKBH5 with α-ketoglutarate as a substrate and Fe (II) as a coenzyme.
We used microarrays to detail the differential gene expression by ALKBH5 knockdown in lung cancer cell lines.

overall_design: Total RNA were extracted from ALKBH5 knockdown PC9 cells at 96 h after transfection. We used the two different sequences for the one target gene, to minimize off-target effects. Cells were cultured for 24 hours prior to transfection and transfected with 15 nM of final concentrations of siRNAs.

first: Yuji

last: Iwashita

first: Haruhiko

last: Sugimura


title: Next Generation Sequencing Identifies Biased Light Chain Usage and Evidence of Light Chain Gene Replacement in phosphatidylcholine (PtC)-specific CD5+  B cells from dnRAG1 and VH12 mice.

city: Omaha

first: Patrick

last: Swanson

state: NE

address: 2500 California Plaza

department: Medical Microbiology and Immunology

institute: Creighton University School of Medicine

summary: B cells reactive toward phosphatidylcholine (PtC) are enriched in the B1 B cell subset, and express predominantly one of two VH/Vk combinations to confer this specificity: VH12/Vk4/5H and VH11/Vk9.  Studies of transgenic mice expressing the VH12 heavy chain (VH12 mice) suggest two major checkpoints for light chain expression in this system: the first involves selection of V-J rearrangements which encode a “permissive” light chain that can functionally pair with the VH12 heavy chain; the second involves receptor editing to salvage non-PtC reactive B cells to acquire a permissive light chain that confers PtC reactivity.  If this model is correct, impairing receptor editing should reduce the frequency of PtC-reactive B1 B cells in VH12 mice.  To test this possibility, we bred VH12 mice to transgenic mice expressing a catalytically inactive form of RAG1 (dnRAG1 mice) which show a defect in receptor editing.  Interestingly, dnRAG1 expression in VH12 mice enforces development of PtC-reactive B1 B cells, rescuing the loss of splenic B cells observed in VH12 mice.  These data suggest receptor editing normally functions to remove a large portion of PtC-specific B cells in VH12 mice.  Deep sequencing of the expressed light chain repertoire of PtC-reactive and non-reactive B cells in VH12 mice revealed that PtC-reactive B cells predominantly expressed the Vk4/5H (IGKV4-91) light chain gene, whereas PtC-non-reactive B cells expressed a broader, yet restricted, set of light chain genes.  This analysis also revealed a low frequency of in-frame hybrid light chain genes appearing to originate via Type 2 gene replacement, which we show can originate from template switching during PCR.

overall_design: The sequencing libraries were generated from total RNA extracted from 60 samples. 24 samples were analyzed in the first round, these were comprised of 3 independent biological replicates for 8 unqiue cell populations from the spleens of 4 geneotypes of mice. For the second round 36 samples were anlysed, comprised of 3 independent biological replicates for 12 unique cell populations from the bone marrow and spleen of 2 genotypes of mice.

first: Alexandra

middle: N

last: Worth

first: Victoria

last: Palmer

first: N

last: Schabla

first: Greg

middle: A

last: Perry

first: Anna

last: Fraser-Philbin


title: Expression data from lung cancer cell lines


title: Silica materials effect on Bhas 42 cell transformation

city: Vandœuvre-lès-Nancy

first: Hélène

last: Dubois-Pot-Schneider

address: Site CRAN/Faculté de Médecine - Bâtiment D, 1er étage 9 avenue de la Forêt de Haye, BP 184

department: CRAN

institute: Université de Lorraine - UMR7039 CRAN

summary: Gene expression profile analysis allowed to identify a panel of genes characteristic of silica materials effect on transformation process.

overall_design: We performed transcriptomic analysis with NM-203 (1 µg/cm²; 2 µg/cm² and 5 µg/cm²), Min-U-Sil 5, DE (diatomaceous earth) and TPA (12-O-tetradecanoylphorbol-13-acetate).  Four independent experiments were performed

first: Anais

last: Kirsch

first: Yves

last: Guichard


title: Lactic Acid as an Epigenetic Metabolite in Glioblastoma

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: We investigate the role of lactic acid in GBM cells as an epigenetic metabolite in the regulation of pro-survival gene expression.

overall_design: KNS42, GBM22 and GBM43 cells were starved (0.5mM Glucose; 0.5mM Glutamate media) for 24h with or without L-lactic acid for 24h. Thereafter, cells were harvested and subjected to RNA extraction and submitted for microarray analysis.

first: Consuelo

last: Torrini

first: Markus

last: Siegelin


title: Chronic Dosed-Feed Toxicity/Carcinogenicity Study of 2-Hydroxy-4-Methoxybenzophenone (HMB, C10260; CAS No. 131-57-7) in Sprague-Dawley rats (G822872B)

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

summary: 2-Hydroxy-4-methoxybenzophenone (HMB) is an approved Food and Drug Administration (FDA) over-the-counter Category I product considered to be a deterrent to ultraviolet (UV) radiation-induced skin cancer. HMB is used in pharmaceuticals, plastic products, fabric coatings, finishes, and cosmetics. Exposure to HMB occurs through both occupational and consumer routes. HMB is used in skin moisturizing products and sunscreen lotions. In plastics manufacturing, HMB is used in surface coatings and polymers including ABS resins, cellulosic esters, polyesters, polystyrenes, rubber, flexible and rigid vinyl, and vinylidene chloride. HMB readily penetrates the skin and bioaccumulates in lipid-rich tissues. Uptake from the gastrointestinal tract is rapid. This study will characterize the toxicologic and carcinogenic potential of HMB administered in dosed feed to Sprague-Dawley rats given its potential for widespread human exposure as a broad-spectrum sunscreen.

overall_design: Following 13 weeks of treatment (0 and 10000 ppm groups), rat were sacrificed and the liver removed and sectioned with one section taken for histopathology and one section placed in RNAlater and treated according to the manufacturer's protocol. The sample placed in RNAlater was minced into 2-3 mm pieces, maintained on wet ice until the end of necropsy, and subsequently refrigerated overnight. The liver samples were then  frozen in liquid nitrogen and maintained at  -80 degrees centigrade until shipped frozen to an NTP-designated laboratory for RNA extraction and microarray assessment using the Affymetrix GeneChip® Rat Genome 230 2.0 array.


title: Temporally-Divergent Regulatory Mechanisms Govern Neuronal Diversification and Maturation in the Neocortex [scATAC-seq]

status: Public on May 31 2022

city: Cambridge

first: Paola

last: Arlotta

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. The regulatory strategies that neurons use during progressive development and maturation remain unclear. We present an integrated single-cell epigenomic and transcriptional analysis of individual classes of neurons from both mouse and marmoset neocortex, sampled during both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We find that in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use molecular regulatory programs with broader tissue distribution and greater evolutionary conservation. In contrast, programs that are active during later neuronal maturation implement more brain- and neuron-specific mechanisms showing greater evolutionary divergence. Our work uncovers a temporally-regulated shift in regulatory choices, likely reflecting unique evolutionary constraints on distinct events of neuronal development in the neocortex.

sample_organism:
Callithrix jacchus
Mus musculus

platform_organism:
Callithrix jacchus
Mus musculus

overall_design: Examination of the regulatory strategies governing neuronal development in mouse and marmoset neocortex across timepoints

first: Wen

last: Yuan

first: Sai

last: Ma

first: Juliana

middle: R

last: Brown

first: Kwanho

last: Kim

first: Vanessa

last: Murek

first: Lucia

last: Trastulla

first: Alexander

last: Meissner

first: Simona

last: Lodato

first: Ashwin

last: Shetty

first: Joshua

middle: Z

last: Levin

first: Jason

last: Buenrostro

first: Michael

last: Ziller


title: Temporally-Divergent Regulatory Mechanisms Govern Neuronal Diversification and Maturation in the Neocortex [scRNA-seq]

middle: D


title: Temporally-Divergent Regulatory Mechanisms Govern Neuronal Diversification and Maturation in the Neocortex [snRNA-seq]

middle: J


title: Temporally-Divergent Regulatory Mechanisms Govern Neuronal Diversification and Maturation in the Neocortex

type: Methylation profiling by high throughput sequencing


title: Temporally-Divergent Regulatory Mechanisms Govern Neuronal Diversification and Maturation in the Neocortex [ATAC-seq]


title: Temporally-Divergent Regulatory Mechanisms Govern Neuronal Diversification and Maturation in the Neocortex [RNA-seq]


title: RNA-seq analyses of mouse retinal pigment epithelium cells

city: Hong Kong

first: Wenjun

last: Xiong

state: Hong Kong SAR

address: Block2-315Room, To Yuen Building, City University, of  Hong Kong, 31 To Yuen Street, Kowloon Tong, Kowloon

country: Hong Kong

institute: City University of Hong Kong

summary: The retinal pigment epithelium (RPE) is a monolayer of polarized epithelial cells lying between the retina and the choroid/sclera, with a major function in supporting photoreceptor homeostasis, but the role of RPE in eye size regulation is yet to be further explored. it was recently reported that selective deletion of Low density lipoprotein receptor-related protein 2 (Lrp2) in the mouse RPE resulted in large eyes, similar to the phenotypes of Lrp2 whole eye knockout mice, suggesting that the RPE is the tissue in which LRP2 functions. Here, to investigate which downstream pathways of Srebp2 and Lrp2 are responsible for regulating eye growth, we performed RNA-seq analysis with the mouse RPE tissues. Postnatal day 0 (P0) mice were injected with AAV8-Best1-GFP/nSrebp2/ctrl sh/Lrp2 sh1/Lrp2 sh2 viruses to overexpress the constitutively active form of Srebp2 or to knockdown Lrp2 in the RPE specifically. At P14, RPE cells were carefully dissociated for RNA extraction. Via RNA-seq analysis and functional validation, we identified that Bmp2 is the target and the effector of the Srebp2-Lrp2 pathway.  Overall, the present study unveils an essential role of RPE in regulating eye size via the Srebp2-Lrp2-Bmp2 signaling pathway, shedding light on the underlying mechanism of eye size control.

overall_design: Retinal pigment epithelium (RPE) mRNA profiles of postnatal day 14 mice injected with AAV8-Best1-GFP/nSrebp2/ctrl sh/Lrp2 sh1/Lrp2 sh2 viruses


title: Immune tolerance of food is mediated by multiple layers of CD4+ T cell dysfunction

city: Minneapolis

first: Adam

last: Herman

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Gastrointestinal health depends on the adaptive immune system tolerating the foreign proteins in food1,2. This tolerance is paradoxical because the immune system normally attacks foreign substances by generating inflammation. Here, we addressed this conundrum by using a sensitive cell enrichment method to assess how CD4+ helper T cells respond to peptides from food. Polyclonal CD4+ T cells responded to food peptides, including a natural one from gliadin, by proliferating weakly in secondary lymphoid organs of the gut-liver axis due to the action of regulatory T cells. A few food-specific T cells then differentiated into T follicular helper cells that promoted a weak antibody response. Most cells, however, lacked T helper lineage markers and became either naïve-like or T follicular helper-like anergic cells both with limited capacity to migrate to the lamina propria and form Th1 cells. Eventually, many of the T helper lineage-negative cells became Treg cells themselves via an IL-2-dependent mechanism. Our results indicate that food peptide-specific CD4+ T cells do not cause immunopathology because they are activated in a Treg cell-generated environment to become hyporesponsive cells that do not drive inflammation and are prone to become peripheral Treg cells.

overall_design: Secondary lymphoid organ CD4 T cells from mice fed on days 0, 2, and 4 (3X) or else days 0, 2, 4, 6, 8, and 10 (6X) with 2W peptide alone, or fed days 0, 2, and 4 with 2W peptide plus cholera toxin (CT), or continuously fed gliadin protein for 1 week (Gliadin), or infected with 2W-expressing Listeria monocytogenes (eLm2), or immunized with 2W peptide plus CFA (CFA) were isolated either 2 days after the last feeding or 1 week after immunization or infection. 2W:I-Ab or gliadin peptide:I-Ab tetramer-binding T cells were subsequently purified by Fluorescence Activated Cell Sorting from experimental mice. As  controls, tetramer-negative CD44lo naïve CD4 T cells were also sorted from normal healthy mice (untreated), or from mice infected 7 days earlier with 2W-expressing Listeria monocytogenes (neLm1), or from mice infected for >30 days with either 2W-expressing Listeria monocytogenes (nmLm1) or 2W-expressing Influenza A virus (nmIAV2). Each cell experimental group was incubated with a unique hashtag antibody prior to 10X Genomics scRNA-Seq analysis.

first: Sung-Wook

last: Hong

first: Peter

last: Krueger

first: Kevin

middle: C

last: Osum

first: Thamotharampillai

last: Dileepan

first: Daniel

last: Mueller

first: Marc

last: Jenkins


title: Single cell sequencing of mucosal brushings from human nasal polyp

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

summary: Allergic nasal polyposis is a chronic type 2 inflammatory condition of the upper respiratory tract. We characterize nasal polyps from 5 subjects using single-cell RNA-sequencing, identifying “allergic” tuft cells, characterized by increased expression of the prostaglandin synthetic pathway, in association with a PGE2-activated gene signature.

overall_design: 5 individual polyp brushings

first: Erin

last: Gordon

first: Maya

last: Kotas

first: Max

last: Seibold


title: Temporally-Divergent Regulatory Mechanisms Govern Neuronal Diversification and Maturation in the Neocortex [WGBS]

first: Paola

last: Arlotta

first: Wen

last: Yuan

first: Sai

last: Ma

first: Juliana

last: Brown

first: Kwanho

last: Kim

first: Vanessa

last: Murek

first: Lucia

last: Trastulla

first: Alexander

last: Meissner

first: Simona

last: Lodato


title: Fatty acid oxidation protects cancer cells from apoptosis through increasing mitochondrial membrane lipids

city: Duarte

first: Yi-Jia

last: Li

address: 1500 E Duarte Rd

institute: Beckman Research Institute at City of Hope Cancer Center

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

overall_design: Refer to individual Series


title: Fatty acid oxidation protects cancer cells from apoptosis through increasing mitochondrial membrane lipids [STAT3]

summary: Overcoming resistance to chemotherapies remains a major unmet need for cancers such as triple negative breast cancer (TNBC). Therefore, mechanistic studies to provide insight for drug development are urgently needed to overcome TNBC therapy resistance. Recently, an important role of fatty acid β-Oxidation (FAO) in chemoresistance has been shown. But how FAO might mitigate tumor cell apoptosis by chemotherapy is unclearknown. Here, we show that elevated FAO activates STAT3 by acetylation via elevated acetyl-CoA.  Acetylated STAT3 upregulates expression of long-chain acyl-CoA synthetase 4 (ACSL4), resulting in increased phospholipid synthesis. Elevating phospholipids in mitochondrial membranes leads to heightened mitochondrial integrity, which in turn overcomes chemotherapy-induced tumor cell apoptosis. Conversely, in both cultured tumor cells and xenograft tumors, enhanced cancer cell apoptosis by inhibiting ASCL4 or specifically targeting acetylated-STAT3 is associated with a reduction in phospholipids within mitochondrial membranes. This study demonstrates a critical mechanism underlying tumor cell chemoresistance.

overall_design: The differental expression of lipid metabolic gene in  MDA-MB-231-R (paclitaxel-resistant) cells expressing wild type and acetylation-deficient K685R STAT3.

first: Hua

last: Yu


title: Single cell transcriptomics reveals HIV viral transcription and compartmentalized immune perturbations in the CNS of people with HIV despite antiretroviral treatment

first: Jun

last: Zhao

state: CT

address: 300 George Street

department: Pathology/Immunology

summary: Single cell RNA sequencing of blood and CSF in people with HIV on ART compared to uninfected controls.

overall_design: We performed scRNA-seq analysis of blood and CSF from people with HIV and controls

first: Shelli

middle: F

last: Farhadian

first: Yuval

last: Kluger

first: Ofir

last: Lindenbaum

first: Michael

last: Corley


title: Bone morphogenetic protein-2 (BMP2) and estradiol-17β (E2)-induced changes in ovarian transcriptome during primordial follicle formation in the mouse ovary

first: Shyamal

middle: K.

last: Roy

address: 984515 Nebraska Medical Center

department: Ob/Gyn

institute: University of Nebraska Medical Center

summary: Estradiol-17β (E2) has been shown to promote primordial follicle (PF) formation and to involve BMP2 as a downstream effector to promote PF in the hamsters. However, the molecular mechanism whereby these factors regulate ovarian somatic cells to pre-granulosa  cells (preGC) transition leading to PF formation remains unclear. The objective of this study was to determine whether BMP2 and/or E2 would regulate the expression of specific ovarian transcriptome during preGC transition and PF formation in the mouse ovary. BMP2 mRNA level increased during the period of PF formation with concurrent presence of BMP2 protein in ovarian somatic cells. E2 but not BMP2 exposure led to increased expression of ovarian BMP2 mRNA, and the effect of E2 could not be suppressed by LDN 193189 (LDN). Either BMP2 or E2 stimulated PF formation without inducing apoptosis. RNAseq analysis of ovaries exposed to exogenous BMP2 or E2 revealed differential expression of several thousand genes. Most of the differentially expressed genes (DEG), which were common between BMP2 or E2 treatment demonstrated concordant changes, reinforcing the idea of cooperativity between E2 and BMP2 during PF formation. Further, we have Identified E2, in cooperation with BMP2, could affect the expression of three major transcription factors GATA2, GATA4 and EGR2 and one serine protease, hepsin in preGC during PF formation. Taken together, results of this study suggest that E2 and BMP2 may regulate ovarian gene expression that promote somatic cells to preGC transition and PF formation in the mouse ovary.

overall_design: RNA-seq was performed on E16 embryonic ovaries cultured for 24 hours with either vehicle, or bone morphogenetic protein 2 (BMP2) or estradiol-17β (E2).

first: Prabuddha

last: Chakraborty

first: Rebecca

last: Anderson

middle: K


title: Fatty acid oxidation protects cancer cells from apoptosis through increasing mitochondrial membrane lipids [PS-ac-peptide]

overall_design: The differental expression of lipid metabolic gene in  MDA-MB-231-R (paclitaxel-resistant) xenograft tumors that had been treated with HBSS or PS-acet-STAT3 peptide every other day for 14 days.


title: Next Generation Sequencing (NGS) for quantitative transcriptomic analysis of Francisella strains (Francisella novicida, ribD-deficient Francisella novicida , Francisella tularensis)

city: Ube-shi

first: Kensuke

last: Shibata

state: Yamaguchi

address: 1-1 Minami-Kogushi 1-chome

institute: Yamaguchi univeristy

summary:
To understand differences of gene expression profiles between Francisella strains
RNA profiles of Francisella strains were generated by deep sequencing, in triplicate, using NovaSeq6000. qRT–PCR validation was performed using SYBR Green assays.
Our study represents the first detailed differential transcriptomic analysis of Francisella strains , with biologic replicates, generated by RNA-seq technology.

sample_organism: Francisella tularensis subsp. tularensis SCHU S4

sample_organism: Francisella tularensis subsp. novicida U112

overall_design: mRNA profiles of Francisella strains were generated by deep sequencing, in triplicate, using NovaSeq6000.

first: Takashi

last: Shimizu


title: Naa50 regulates tapetum degradation

city: Linfen

first: lin

middle: jin

last: feng

state: Shanxi

address: gongyuan 1 street

department: College of Life Sciences

institute: Shanxi Normal University

summary: N-terminal acetylation of proteins is a key modification in eukaryotes; however, our understanding of its biological function in plants is limited. Naa50 is the catalytic subunit of the protein N-terminal acetyltransferase NatE complex. We previously showed that the absence of Naa50 led to sterility in Arabidopsis thaliana. In the present study, we show that a lack of Naa50 in Arabidopsis resulted in collapsed and sterile pollen grains. Further study revealed that the mutation of Naa50 accelerated programmed cell death in the tapetum. Expression pattern analysis showed that Naa50 was specifically expressed in tapetal cells from anthers at stages 9–11 of pollen development, when tapetal programmed cell death occurs. Reciprocal cross analyses indicated that the male sterility of naa50 plants was due to sporophytic effects. Transcriptome sequencing of closed buds showed that the deletion of Naa50 resulted in up-regulation of the cysteine protease-coding gene CEP1 and impaired the expression of several genes that function in pollen wall deposition and pollen mitosis. Our findings suggest that Naa50 regulates cell degradation in the tapetum during anther development and plays an important role in pollen development by affecting several pathways.

overall_design: There were six samples in total. Wild-type and naa50-1 have three biological replicates each.

first: Jinlin

last: Feng

first: Minghui

last: Qin

first: Lixia

last: Yao

first: Rong

last: Han

first: Ligeng

last: Ma


title: RNA-seq: Transcriptome profile between wild type control and Alk-YS mutant in the Drosophila larval CNS.

city: Gothenburg

first: Ruth

last: Palmer

address: Medicinaregatan 9A, Shalgrenska Academy

department: Medical Biochemistry & Cell Biology

institute: Gothenburg University

summary: We assessed the differential expression of genes in the Drosophila larval CNS for the Alk mutant and control to understand how the transcriptional responce in Alk-YS mutant.

overall_design: Two groups of Drosophila larval CNS (Alk mutant and control) with three biological replicates per group

first: Badrul

last: Arefin


title: Postweaning iron deficiency in rats alters reelin expression in the nucleus accumbens

city: Otsu

first: Noriko

last: Nishikura

state: Shiga

address: Seta Tsukinowa

department: Department of Anatomy and Cell Biology

institute: Shiga University of Medical Science

summary: Background: Epidemiological research indicates that iron deficiency (ID) in infancy correlates with long-term cognitive impairment and behavioral disturbances, despite therapy. However, the mechanisms underlying these effects are unknown.  Objective: We investigated how ID affected postweaning behavior and monoamine concentration in rat brains to determine whether ID during the juvenile period affected gene expression and synapse formation in the prefrontal cortex (PFC) and nucleus accumbens (NAcc).  Methods: Fischer344/Jcl male rats aged 21–39 days were fed low-iron diets (0.35 mg/kg iron; ID group) or standard AIN-93 G diets (3.5 mg/kg iron; control group). The locomotor activity of male offspring was evaluated by the open field and elevated plus maze tests at ages 8 and 12 weeks. Monoamine concentrations in the PFC, NAcc, caudate-putamen, ventral midbrain, dorsal midbrain, and pons were analyzed. Comprehensive gene expression analysis was performed in the PFC and NAcc at age 13 weeks. Finally, we investigated synaptic density in the PFC and NAcc by synaptophysin immunostaining.  Results: Behavioral tests revealed significant interactions between age and iron consumption for the total distance traveled and the distance traveled in the peripheral area (p < 0.05), indicating that ID during the juvenile period affected hyperactivity and that this persisted to adulthood. At age 13 weeks, the ID group had increased levels of both dopamine and the metabolites of dopamine and serotonin in the NAcc. Comprehensive gene expression analysis and immunostaining showed decreased Reelin gene expression (adjusted p < 0.01) and significantly increased spine density in the NAcc in the ID group compared with the control group (p < 0.01).  Conclusions: ID during the postweaning juvenile period led to long-term hyperactivity, monoamine disturbance in the brain, and downregulation of Reelin expression in the NAcc despite complete iron repletion. Epigenetic modification of Reelin genes may be involved in synaptic plasticity in the NAcc.

overall_design: Fischer344/Jcl male rats aged 21-39 days were fed low-iron diets

first: Yasuhiro

last: Uchimura


title: Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution

city: San Francisco

first: Zev

last: Gartner

state: CA

address: 600 16th St. Room GH-N512E Box 2280

department: Pharmaceutical Chemistry

institute: University of California San Francisco

summary: To identify inter-individual differences in transcriptional cell state in the human breast, we performed scRNAseq analysis on 86,136 cells collected from 28 healthy premenopausal donors who underwent reduction mammoplasty surgery. To obtain an unbiased snapshot of the epithelium and stroma, we collected live (DAPI negative) / singlet cells from all samples by fluorescence activated cell sorting (FACS). For a subset of samples, we also collected purified epithelial cells or purified luminal and basal/myoepithelial cells. We used MULTI-seq barcoding and in silico genotyping for sample demultiplexing to minimize technical variability between samples.

overall_design:
Single-cell expression profiles in 28 healthy reduction mammoplasty tissue samples.
The samples named Set 1 - Set 17 are each from an individual sample, enriched by cell sorting (see the Sample Characteristics "sort gate" field).
The samples named Set 18 - Set 22 are barcoded/multiplexed samples, each run on one lane of a 10X run (see the Sample Characteristics "number of multiplexed samples" field). Some samples were run across multiple lanes (e.g. individual samples and multiplexed samples were run across multiple sort gates, some samples were included in both multiplexed and individual lanes) as an experimental control.

first: Z

first: L

last: Murrow


title: Single-cell analysis implicates Th17 to Th2 cell plasticity in the pathogenesis of palmoplantar pustulosis

city: London

first: Dan

last: McCluskey

address: Guy's Hospital

institute: King's College London


title: The heterogeneity of smooth muscle cells in aortic dissection was determined by single-cell sequencing

status: Public on May 30 2022

city: Taizhou,  Zhejiang Province

first: Cheng

last: Xu

address: Department of Cardiology, Taizhou Hospital, Wenzhou Medical University, 150 Ximen Street, Linhai 317000, P.R. China

institute: Taizhou Hospital Affiliated to Wenzhou Medical University

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on apoE mice after infused for 7 days with angiotensin II（Ang II ）(2500ng/kg/min)or saline. Aortas（4 aortas in control group  were pooled together as one sample and 3 aortas in experimental group were pooled together as another sample respectively） were collected 7 days after AD induction and processed for sequencing. These data provide high-resolution insight into the complexity and heterogeneity of vascular smooth muscle cell.

first: Xiaowei

last: Liu

first: Xiaofeng

last: Chen


title: Purification of Human iPSC-derived Cardiomyocytes in a Large Scale Using MicroRNA Switch and Magnetic-activated Cell Sorting

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

summary: We showed novel synthetic microRNA (miRNA) switch system, which can purify large quantities of iPSC-CMs using magnetic-activated cell sorting (MACS). We used miR-208a, which is specifically expressed in cardiomyocytes, as a specific miRNA of CMs, and CD4 as a selection marker for MACS. We synthesized a miRNA switch encoding CD4 tagged with complementary sequences against miR-208a (miR-208a CD4 switch). We transfected this switch into differentiated cells, and easily got efficiently purified CMs in a large scale with MACS. In addition, we demonstrated that purified cells were shown to be engrafted as CMs in mouse hearts.

overall_design: 201B7 iPSCs, N=2  201B7-derived CMs at day20 purified by miR-208a CD4 switch and MACS, N=2  201B7-derived CMs at day20 purified by antibodies

first: Takeshi

last: Hatani

first: Chikako

last: Okubo

first: Narita

last: Megumi


title: transcriptome analysis  of whole lung tissue from anti-PD-1 therapy-treated mice

first: Hirotake

last: Tsukamoto

state: Sakyo-Ku

address: 53 Kawahara-cho Shogoin

department: Center for Cancer Immunotherapy and Immunobiology

summary: IIn contrast to the young mice treated with anti-PD-1 therapy, aged mice exhibited immune-related adverse event (irAE)-like symptoms in the lung when treated with anti-PD-1 therapy. To understand the molecular events underlying the development of anti-PD-1 therapy-induced irAE, we employed deep RNA sequencing of whole lung transcript from anti-PD-1 therapy-treated young and aged mice. In order to further evaluate the effect of IL-21 signal on PD-1-blockade-mediated immune response, gene expression profile in lung tissue from aged mice twith the blockade of IL-21 activity was also assessed.

overall_design: Whole lung transcripts were obtained from melanoma-bearing young or aged mice treated anti-PD-1 Ab, aged mice treated with rat control Ab, and aged mice similtaneously treated with anti-PD-1 Ab and anti-IL-21 receptor in vivo. Each gene expression profile was analyzed by RNA sequencing, and the differential gene expressions in whole lung tissues among those stimulatory conditions were assessed.


title: Relieving Dyrk1a repression of MKL1 corrects developmental defects in infantile megakaryocytes

status: Public on May 29 2022

city: Charlottesville

first: Robert

last: Cornelison

state: VA

address: 345 Crispel Drive

department: Pathology

institute: University of Virginia School of Medicine

summary: Adult and fetal megakaryocytes are morphologically different. These differences contribute to neonatal thrombocytopenia in premature neonates and in neonates after infection and also contribute to poor megakaryocytes engraftment after umbilical cord blood transplant. We found that Dyrk1a kinase inhibition shift the fetal megakaryocytes phenotype toward adult phenotype. This effect is mediated by MKL1 the master regulator of megakaryocytes morphogenesis. To identify differences between adult and fetal megakaryocytes we performed RNA seq of adult derived megakaryocytes and fetal derived megakaryocytes treated and untreated with Dyrk inhibitors. Through this approach we identified cohorts of genes co-regulated in adult megakaryocytes and fetal megakaryocytes treated with the dyrk inhibitors. More importantly, we found that the dyrk inhibition in fetal megakaryocytes leads to upregulation of a significant number of MKL1 target genes.

overall_design: Comparison of transcription changes in megakaryocytes treated with Dyrk inhibitor harmine for 11 days.

first: Kamaleldin

last: Elagib

first: Hui

last: Li

first: Adam

last: Goldfarb


title: Markers of endothelial glycocalyx dysfunction in Clarkson disease

city: Bethesda

first: Katherine

last: Hornick

state: MD

address: 10 Center Dr, Building 29B

department: Integrated Data Sciences Section (IDSS)

institute: NIAID

summary:
Background
Clarkson disease is a rare idiopathic condition marked by transient, relapsing-remitting episodes of systemic microvascular hyper-permeability, which liberates plasma fluid and macromolecules into the peripheral tissues. This pathology manifests clinically as the abrupt onset of hypotensive shock, he-moconcentration, and hypoalbuminemia.
Methods
We analysed endothelial glycocalyx (eGCX)-related markers in plasma from patients with SCLS dur-ing acute disease flares and convalescence by ELISA and comprehensive proteomic profiling. eGCX-related components and gene expression in cultured endothelial cells were evaluated by RNA-sequencing, real-time PCR, and fluorescence.
Results
Serum levels of eGCX-related core components including hyaluronic acid (HA) and/or the core pro-teoglycan soluble syndecan-1 (sCD138) were elevated at baseline and during acute SCLS flares.  Se-rial measurements in several patients demonstrated that sCD138 levels peaked during the recovery (post-leak) phase of the illness. Proteomic analysis of matched acute and convalescent SCLS plasma revealed increased abundance of eGCX-related proteins, including glypicans, thrombospondin-1 (TSP-1), and eGCX-degrading enzymes in acute plasma compared to remission plasma. Abundance of endothelial cell damage markers did not differ in acute and baseline plasma. Expression of several eGCX-related genes and surface carbohydrate content in endothelial cells from patients with SCLS did not differ significantly from that observed in healthy control cells.
Conclusions
eGCX dysfunction, but not endothelial injury, may contribute to clinical symptoms of acute SCLS.
Serum levels of of eGCX components including sCD138 may be measured during acute episodes of SCLS to monitor clinical status and therapeutic responses.

overall_design: Blood outgrowth endothelial cells (BOECs) were cultured from whole blood samples from 5 systemic capillary leak syndrome (SCLS) patients and 6 controls

first: Zhihui

last: Xie

first: Margne

last: Børset

first: Kjell

last: Svéen

first: Ole

middle: W

last: Bøe

first: Eunice

last: Chan

first: Justin

middle: B

last: Lack

first: Franco

last: Verlicchi

first: A

last: Eisch

first: Remo

last: Melchio

first: Arkadiusz

last: Dudek

first: Kirk

last: Druey


title: Follicular lymphoma microenvironment characteristics associated with tumor cell mutations and MHC class II expression

status: Public on May 28 2022

city: Houston

first: Michael

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

summary: Follicular lymphoma (FL) is a B-cell lymphoma with a complex tumor microenvironment that is rich in non-malignant immune cells. We applied single-cell RNA-sequencing to characterize the immune microenvironment of FL. This provides a classification framework of the FL microenvironment, their association with FL genotypes and antigen presentation, and informs different potential immunotherapeutic strategies.

overall_design:
scRNA-seq of 20 FL lymph node biopsies and three reactive lymph nodes (RLN) using the 10X Chromium platform to profile the transcriptome in addition to T-cell receptor (TCR) and immunoglobulin (Ig) repertoires.

**RAW data has been uploaded to EGA. Accession EGAS00001006052.**


title: Identification of a LncRNA EPR—>METTL7A1 pathway modulating  translation of select genes (Total RNA)

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: EPR is a long non-coding RNA (lncRNA) that controls cell proliferation in mammary gland cells by regulating gene transcription and, here, we report on Mettl7a1 as a target of EPR. We show that the lncRNA induces Mettl7a1 transcription by remodeling the 3-dimensional chromatin structure at the Mettl7a1 locus. Our data indicate that METTL7A1 participates in the EPR-dependent pathway that antagonizes TGF-β signaling. METTL7A1 is absent in tumorigenic murine mammary gland cells and its human ortholog (METT7A) is downregulated in breast cancers. Importantly, expression of METTL7A1 in 4T1 tumorigenic cells reduces their transformation potential, and the putative methyltransferase activity of METTL7A1 appears dispensable for its biological functions. METTL7A1 is a cytoplasmic protein and, from a mechanistic perspective, interacts with factors implicated in the early steps of mRNA translation, associates with ribosomes, and affects the levels of select proteins without substantial changes in mRNA abundance. Our data suggest the possibility that METTL7A1 conveys the transcriptional regulation operated by EPR into specific changes of mRNA translation.

overall_design: High-quality RNA was extracted from either mock or METTL7A1-overexpressing 4T1 cells (biological triplicates for each experimental condition), and a total of six libraries were prepared using standard Illumina Stranded Total RNA Prep with Ribo-Zero Plus protocol and sequenced on Illumina NovaSeq 6000.

first: Paola

last: Briata

first: Luca

last: Caputo

first: Ettore

last: Zapparoli

first: Gabriele

last: Bucci

first: Roberto

last: Gherzi


title: Identification of a LncRNA EPR—>METTL7A1 pathway modulating  translation of select genes (3C-Seq)

overall_design: Chromosome Conformation Capture (3C) analysis coupled to high throughput sequencing (3C-Seq) to characterize the spatial interaction within Mettl7a1 locus using the EPR-bound Mettl7a1 promoter region as viewpoint in mock and NMuMG-EPR cells

first: Pier

middle: L

last: Puri


title: An herbal medicine-based formula affected the epithelial cell line, BEAS-2B, genes expression.

status: Public on May 27 2022

city: Taipei

first: Zi-yi

last: Huang

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City 112304, Taiwan

department: School of Life Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Coronavirus Disease 2019 (COVID-19) remains a threat on the fatal ARDS with an incidence rate of 41.8%, or irreversible pulmonary fibrosis, without specific effective therapeutic drugs. The infection causes dysregulation of the immune system with a cytokine storm in lung tissue. To define the drug candidate of Virofree to COVID-19 induced-ARDS, we treated 66.67 ug/ml and 500 ug/ml in epithelial cell line, BEAS-2B, and compared the PBS control group to obtain Virofree expression profiles.

overall_design: Examination of 2 different concentrations of Virofree in BEAS-2B cells.

first: Ly

middle: H

last: Doan

first: Zi-Yi

first: Anh

last: Nguyen


title: Descriptive Transcriptome Analysis of Tendon Derived Fibroblasts Following In-Vitro Exposure to Advanced Glycation End Products

city: WEST LAFAYETTE

first: Chad

last: Carroll

state: IN

address: 800 W Stadium Ave

institute: Purdue University

summary: Tendon pathologies affect a large portion of people with diabetes. This high rate of tendon pain, injury, and disease appears to manifest independent of well-controlled HbA1c and fasting blood glucose. Advanced glycation end products (AGEs) are elevated in the serum of those with diabetes. In vitro, AGEs severely impact tendon fibroblast proliferation and mitochondrial function. However, the extent that AGEs impact the tendon cell transcriptome has not been evaluated. The purpose of this study was to investigate transcriptome-wide changes that occur to tendon-derived fibroblasts following treatment with AGEs. We propose to complete a descriptive approach to pathway profiling to broaden our mechanistic understanding of cell signaling events that may contribute to the development of tendon pathology. Rat Achilles tendon fibroblasts were treated with glycolaldehyde-derived AGEs (200μg/ml) for 48 hours in normal glucose (5.5mM) conditions. In addition, total RNA was isolated, and the PolyA+ library was sequenced. We demonstrate that tendon fibroblasts treated with 200μg/ml of AGEs differentially express 2,159 gene targets compared to fibroblasts treated with an equal amount of BSA-Control. Additionally, we report in a descriptive and ranked fashion 21 implicated cell-signaling pathways. We demonstrate that tendon fibroblasts treated with 200μg/ml of AGEs differentially express 2,159 gene targets compared to fibroblasts treated with an equal amount of BSA-Control. Additionally, we report in a descriptive and ranked fashion 21 implicated cell-signaling pathways. Our findings suggest that AGEs disrupt the tendon fibroblast transcriptome on a large scale and that these pathways may contribute to the development and progression of diabetic tendinopathy. Specifically, pathways related to cell cycle progression and extracellular matrix remodeling were affected in our data set and may play a contributing role in the development of diabetic tendon complications.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tendon-derived cells treated with glycolaldehyde-derived advanced glycation end-products

first: Shivam

last: Patel

first: Christopher

last: Mendias


title: Identification of a LncRNA EPR—>METTL7A1 pathway modulating  translation of select genes

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

overall_design: Refer to individual Series


title: Nuclear factor AP2X-4 governs the expression of cell cycle and life stage regulated genes and is critical for Toxoplasma growth

city: Wuhan

first: Bang

last: Shen

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

summary: RNA-seq were performed to compare the transcriptomic differences between KOX-4 strain (ME49ΔAP2X-4) and its wild type ME49

overall_design: mRNA profiles of KOX-4 strain (ME49ΔAP2X-4) and wide type ME49

first: Jingwen

last: Zhang

first: Fuqiang

last: Fan

first: Lihong


title: Insulin-stimulated glucose uptake in recombinant MMP12 treated 3T3-L1 cells

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: Pharmacy Building, 1601 SW Jefferson Way

department: Pharmaceutical Sciences

institute: Oregon State University

summary: Microbiota contributes to induction of type 2 diabetes by high-fat/high-sugar (HFHS), but which organs/pathways are impacted by microbiota remains unknown. Using multi-organ network and transkingdom analyses, we found that microbiota-dependent. impairment of OXPHOS /mitochondria in white adipose tissue (WAT) plays a primary role in regulating systemic glucose metabolism. The follow-up analysis established that Mmp12+ macrophages link microbiota-dependent inflammation and OXPHOS damage in WAT. Moreover, the molecular signature of Mmp12+ macrophages in WAT was associated with insulin resistance in obese patients. Next, we tested functional effects of MMP12 and found that Mmp12 genetic deficiency or MMP12 inhibition improved glucose metabolism in conventional, but not in germfree mice. MMP12 treatment induced insulin resistance in adipocytes. TLR2-ligands present in Oscillibacter valericigenes bacteria, which are expanded by HFHS, induce Mmp12 in WAT macrophages in a MYD88-ATF3-dependent manner. Thus, HFHS induces Mmp12+ macrophages and MMP12, representing a microbiota-dependent bridge between inflammation and mitochondrial damage in WAT and causing insulin resistance. doi: https://doi.org/10.1084/jem.20220017

overall_design: in vitro stimulation of adipocytes with or without insulin and/or Mmp12 recombinant protein [rMmp12]. 5 biological replicates of each group

first: Natalia

last: Shulzhenko