title: Proteotranscriptomic decoding of the surface-endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche [U87_mRNA_Norm_Hyp]

status: Public on Oct 28 2023

city: Lund

first: Mattias

last: Belting

state: Skåne

address: Barngatan

department: Clinical Sciences Lund

institute: Lund University

summary: Background: Antibody and cell-based immunotherapies, e.g., antibody-drug-conjugates and CAR-T cells, targeted at cell-surface proteins, currently revolutionize clinical oncology. However, target selection warrants a better understanding of the surface-endocytome and how it is modulated by the tumor microenvironment. Here, we unravel the surface-endocytome landscape and its remodeling by hypoxia in primary cultures from glioblastoma (GBM) patients that currently lack targeted therapies. Methods. We employed a comprehensive approach for global and dynamic mapping of surfaceome and endocytosed (endocytome) proteins in primary GBM cultures at normoxia or hypoxia. Selected target candidates were validated by immunofluorescence analyses in patient tumor sections, spheroids, and 2D cultures, and were finally confronted by ADC cytotoxicity studies. Results: We reveal a heterogeneous surface-endocytome profile across GBM cultures from three patients representing different transcriptional subtypes. CD44 emerged as a commonly abundant surfaceome antigen across GBM cultures, and we established a direct correlation between CD44 endocytic activity and ADC cytotoxicity. We elucidate how hypoxia profoundly reshapes the global surface-endocytome, and identify several hypoxia-induced antigens (CXADR, CD47, BSG, CD81, FXYD6), unique to or shared among GBM cultures. Importantly, we highlight the limited correlation between transcriptomics and proteomics, emphasizing the critical role of membrane protein enrichment strategies and targeted mass spectrometry. Conclusions: These studies provide a comprehensive map of the surface-endocytome and its remodeling by hypoxia in GBM as a resource for target discovery. As a proof-of-concept, we validate several proteins, either abundantly expressed in normoxia or induced by hypoxia, for further exploration as potential targets of immunotherapeutic approaches in GBM.

overall_design:
mRNA of normoxic and hypoxic genes expressed in the established U87-MG GBM cell line. Cells were subconfluently seeded, left overnight to attach, and subjected to normoxia (21% O2) or hypoxia (1% O2) for 24 hours. Then, cells were detached and RNA extraction was performed with RNeasy mini quiagen kit as per the manufacturer's instructions.
Each condition was sent in triplicate experiments (3x Normoxia + 3x Hypoxia) and after raw data was received, differentially expressed genes (DEGs) analysis of hypoxic versus normoxic samples was performed.

first: Kelin

last: Gonçalves de Oliveira

first: Anna

last: Bång-Rudenstam

first: Sarah

last: Beyer

first: Axel

last: Boukredine

first: Hugo

last: Talbot

first: Valeria

last: Governa

first: Maria

last: Johansson

first: Ann-Sofie

last: Månsson

first: Karin

last: Forsberg-Nilsson

first: Johan

last: Bengzon

first: Charlotte

last: Welinder

last: Malmström


title: Proteotranscriptomic decoding of the surface-endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche

country: Sweden

type: Expression profiling by high throughput sequencing

summary: Backgroung: Antibody and cell-based immunotherapies, e.g., antibody-drug-conjugates and CAR-T cells, targeted at cell-surface proteins, currently revolutionize clinical oncology. However, target selection warrants a better understanding of the surface-endocytome and how it is modulated by the tumor microenvironment. Here, we unravel the surface-endocytome landscape and its remodeling by hypoxia in primary cultures from glioblastoma (GBM) patients that currently lack targeted therapies. Methods. We employed a comprehensive approach for global and dynamic mapping of surfaceome and endocytosed (endocytome) proteins in primary GBM cultures at normoxia or hypoxia. Selected target candidates were validated by immunofluorescence analyses in patient tumor sections, spheroids, and 2D cultures, and were finally confronted by ADC cytotoxicity studies. Results: We reveal a heterogeneous surface-endocytome profile across GBM cultures from three patients representing different transcriptional subtypes. CD44 emerged as a commonly abundant surfaceome antigen across GBM cultures, and we established a direct correlation between CD44 endocytic activity and ADC cytotoxicity. We elucidate how hypoxia profoundly reshapes the global surface-endocytome, and identify several hypoxia-induced antigens (CXADR, CD47, BSG, CD81, FXYD6), unique to or shared among GBM cultures. Importantly, we highlight the limited correlation between transcriptomics and proteomics, emphasizing the critical role of membrane protein enrichment strategies and targeted mass spectometry. Conclusions: These studies provide a comperehensive map of the surface-endocytome and its remodeling by hypoxia in GBM as a resource for target discovery. As proof-of-concept, we validate several proteins, either abundantly expressed in normoxia or induced by hypoxia, for further exploration as potential targets of immunotherapeutic approaches in GBM.

overall_design:
To unravel the differences between normoxic and hypoxic genes expressed in primary GBM cell lines. The HGCC primary GBM cells U3034-MG, U3047-MG, and U3017-MG were subconfluently seeded, left overnight to attach, and subjected to normoxia (21% O2) or hypoxia (1% O2) for 24 hours. Then, cells were detached and RNA extraction was performed with AllPrep DNA/RNA quiagen mini kit as per the manufacturer's instructions.
Each condition/sample was sent in triplicate experiments (3x Normoxia /cell line + 3xHypoxia/cell line) and after data receival, differentially expressed genes (DEGs) analysis was performed for each hypoxic cell line, compared to their respective normoxic samples.

middle: C


title: scRNA for pansclerotic morphea lesional

status: Public on Oct 19 2023

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

country: USA

institute: University of Michigan

summary: We compared the PSM lesional/non-lesional skin samples with the control skin in the analysis.

overall_design: lesional skin and non-lesional skin from each of the two PSM patients

first: Johann

middle: E

last: Gudjonsson

first: Enze

last: Xing


title: Transcriptome analysis of human mononuclear blood cells post UC-MSC treatment

status: Public on Oct 20 2023

city: Amman

first: Hind

middle: Moh'd

last: Khwaireh

address: Amman,Jordan

department: Cell Therapy Center

country: Jordan

institute: The University of Jordan

summary: Studying the safety and efficacy of two treatment protocols for Multiple sclerosis (MS) patients using Mesenchymal Stromal/Stem Cells MSCs subtype derived from the umbilical cord; UC-MSCs and their secretome

overall_design: Two groups of MS patients were included in the study. Group A consisted of 20 patients, and Group B consisted of 15 patients. In group A, two doses of expanded UC-MSCs were given intrathecally at one-month intervals. While in Group B, a single intrathecal dose was administered. Both groups received conditioned media of the expanded UC-MSCs at three months post first treatment. Adverse events in the form of a clinical checklist and extensive laboratory tests were performed to examine treatment safety. Both groups underwent the Expanded Disability Status Scale (EDSS), MRI, immunology, ophthalmology, psychology, cognitive, and motor tests. Whole transcriptome analysis post-treatment was conducted using a whole transcriptome microarray.

first: Fatima

last: Jamli


title: Modeling dry eye with an air-liquid interface in corneal epithelium-on-a-chip

status: Public on Oct 11 2023

city: Shiga

first: RODI

middle: KADO

last: ABDALKADER

address: 1-1-1 Noji-Higashi, Kusatsu

country: Japan

institute: Ritsumeikan University

summary: Dry eye syndrome (DES) is a complex ocular condition characterized by an unstable tear film and inadequate tear production, leading to tissue damage. Despite its common occurrence, there is currently no comprehensive in vitro model that accurately reproduce the cellular characteristics of DES. Here we modified a corneal epithelium-on-a-chip (CEpOC) model to recapitulate DES by subjecting HCE-T human corneal epithelial cells to an air-liquid (AL) interface stimulus. We then assessed the effects of AL stimulation both in the presence and absence of diclofenac (DCF). Transcriptomic analysis revealed distinct gene expression changes in response to AL and AL_DCF, affecting pathways related to development, epithelial structure, inflammation, and extracellular matrix remodeling. Both treatments upregulated PIEZO2, linked to corneal damage signaling, while downregulating OCLN, involved in cell-cell junctions. They increased the expression of inflammatory genes (e.g., IL6) and reduced mucin production genes (e.g., MUC16), reflecting dry eye characteristics. TGFB1, crucial for corneal wound healing, was slightly downregulated in AL_DCF, potentially affecting wound healing processes rather than reducing inflammation by DCF. Metabolomic analysis showed increased secretion of metabolites associated with cell damage and inflammation (e.g., methyl-2-oxovaleric acid, 3-methyl-2-oxobutanoic acid, lauroyl-carnitine) in response to AL and even more with AL_DCF, indicating a shift in cellular metabolism. This study showcases the utilization of AL stimulus within the CEpOC as a comprehensive approach to faithfully reproduce the cellular characteristics of DES.

overall_design: Next generation sequencing  starting with RNA-seq library construction (TruSeq stranded mRNA LT Sample Prep Kit)  from RNAs in Human corneal epithelial cell line (HCE-T) using NovaSeq 6000.

middle: K


title: GD2-CART cells and iPSC-derived GD2-CART cells (scRNA-Seq)

status: Public on Oct 25 2023

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

institute: Juntendo University

summary: We showed that iPSC-derived GD2-CART therapy for SCLC was more effective than peripheral blood-derived GD2-CART. Here, we investigated the molecular difference between iPSC-derived GD2-CARTs and peripheral blood-derived GD2-CARTs.

overall_design: We performed scRNA sequencing to understand the molecular difference between iPSC-derived GD2-CARTs and peripheral blood-derived GD2-CARTs

first: Shintaro

last: Kinoshita

first: Takaharu

last: Kimura

first: Jun


title: sncRNA in sera from childen with food anaphylaxis and adults with drug anaphylaxis

city: Madrid

first: Vanesa

last: Esteban

state: State...

address: Av. Reyes Catolicos 2

department: Immunology

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz (IIS-FJD), UAM

type: Non-coding RNA profiling by high throughput sequencing

summary: Anaphylaxis is the most severe manifestation of allergic disorders. Currently, an increasing number of cells, pathways and molecules involved in the etiopathogenesis of anaphylaxis are being discovered. However, there are no conclusive biomarkers to confirm its diagnosis. Small non-coding RNAs (sncRNAs) are 18-200 nucleotide molecules that can be divided into: microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), transference RNA derived fragments (tRFs) and YRNA derived fragments (YRFs). These molecules participate in cell-cell communication modulating various physiological processes and have been postulated as non-invasive biomarkers of several pathologies. Therefore, in this study we characterized the serum circulating profile of other   two populations of 5 adults and 5 children with drug- and food- mediated anaphylaxis, respectively. Samples were obtained from each patient under two different conditions: during anaphylaxis and 14 days after the reaction (control).

overall_design: Circulating serum profile of small non-coding RNA were performed at Qiagen Genomics Service by next-generation sequencing


title: Base editing mutagenesis maps functional alleles to tune human T cell activity

city: San Francisco

first: Carl

last: Ward

address: 1650 Owens Street

department: Gladstone-UCSF Institute of Genomic Immunology

institute: Gladstone Institutes

summary: CRISPR-enabled genetic screening is a powerful tool to discover genes that control T cell function and has nominated candidate target genes for immunotherapies1–6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could discover alleles that tune specific phenotypes. DNA base editors are powerful tools to introduce targeted mutations with high efficiency7,8. Here, we develop a large-scale base editing mutagenesis platform with the goal of pinpointing nucleotides encoding amino acid residues that tune primary human T cell activation responses. We generated a library of ~117,000 sgRNAs targeting base editors to protein coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We discovered a broad spectrum of alleles with variants encoding critical residues (in PIK3CD, VAV1, LCP2, PLCG1 and DGKZ and others), comprising both gain-of-function and loss-of-function mutations. We validated the functional effects of diverse alleles and further demonstrated that base edit hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed PAM requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base editing screens in primary immune cells provide biochemical insights with potential to accelerate immunotherapy design.

overall_design: CRISPR base editing screen data in primary human T cells with NGG Cas9 (3 human donors; CBE and ABE; assessing TNFa,IFNg,PD-1,CD25; CD4 T cells) or NG Cas9 (2 human donors; ABE; assessing TNFa; CD4 and CD8 T cells)

first: Ralf

last: Schmidt

first: Rama

last: Dajani

first: Zev

last: Armour-Garb

first: Mineto

last: Ota

first: Vincent

last: Allain

first: Rosmely

last: Hernandez

first: Madeline

last: Layeghi

first: Galen

first: Laine

last: Goudy

last: Wang

first: Yan

middle: Y

last: Chen

first: Chun

middle: J

last: Ye

first: Luke

middle: A

last: Gilbert

first: Justin

last: Eyquem

first: Jonathan

last: Pritchard

first: Stacie

last: Dodgson

first: Alexander

last: Marson


title: Common Mitochondrial Deletions in RNA-Seq: Evaluation of Bulk, Single-Cell and Spatial Transcriptomic Datasets

status: Public on Oct 16 2023

city: Los Angeles

first: Brooke

last: Hjelm

state: CA

address: 1450 Biggy Street

department: Translational Genomics

institute: USC

summary:
To investigate whether large mitochondrial DNA (mtDNA) deletions can be quantified and detected using the high-throughput bioinformatics tool Splice-Break (https://github.com/brookehjelm/Splice-Break2).
This dataset contains 8 human middle temporal gyrus (MTG) samples (from 4 patients) that underwent spatial transcriptomic RNA-Sequencing following 10x Genomics visium protocols as well as 2 samples (from spatial transcriptomics patient 144107/144108) that underwent bulk RNA-Sequencing (one with a ribosomal depletion library preparation and one without).

overall_design: 10x Visium spatial transcriptomics profiles of middle temporal gyrus tissue taken from 4 patient samples (two tissue sections of each), consisting of 2 controls, 1 Alzheimer's Disease (AD), and 1 Parkinson's Disease (PD). Bulk RNA-Sequencing of one patient with no neurodegenerative diagnosis was included for methods comparison.

first: Audrey

last: Omidsalar


title: RNA-seq analysis of Arabidopsis roots of Col-0, fls2 and UBQ10::mCitrine-IMA1 in response to +Fe, +Fe+flg22, -Fe and -Fe+flg22

status: Public on Oct 09 2023

city: La Jolla

first: Ling

last: Zhang

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: We reported the flg22-triggered immune responses in roots affect the iron deficiency responses and may link to the function of FLS2 and IMA1 in the root. To identify the underlying mechanism of how the root transcriptome profiles respond to +Fe, +Fe+flg22, -Fe, -Fe+flg22 respectively, and if the flg22 responses is dependent on the function of FLS2 and IMA1 in the root, we performed an mRNA-seq experiments in Col-0, fls2 and UBQ10::mCitrine-IMA1 with different treatments. The differentially expressed genes in response to +Fe, +Fe+flg22, -Fe, -Fe+flg22 were analyzed.  It has 36 samples in total, with 3 biogical replicates for each condition and each genotype.

overall_design: 7 days old seedling of Col-0, fls2 and UBQ10::mCitrine-IMA1 were grown on +Fe plate and transfer to the liquid medium with +Fe (75µM Fe), +Fe+flg22 (75µM Fe + 100nM flg22), -Fe (50µM FerroZine), -Fe+flg22 (50µM FerroZine + 100nM flg22) and treat for 24 hours, respectively. The root samples were ground in liquid nitrogen and the RNA was extrancted with the SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, Cat. STRN250). The sequencing libraries were generated by the Salk Next Generation Sequencing Core according to Illumina manufacturer’s instructions.

first: Wolfgang

last: Busch

first: Min

last: Cao


title: LMO2 is critical for early metastatic events in breast cancer

status: Public on Oct 08 2023

city: Palo Alto

first: Gunsagar

middle: Singh

last: Gulati

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

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

overall_design: Refer to individual Series


status: Public on Oct 01 2023

city: Braunschweig

first: Elisabeth

last: Haertig

state: Lower Saxony

address: Spielmannstr. 7

department: Microbiology

country: Germany

institute: TU Braunschweig

summary: Light dependent gene expression in D. shibae wildtype compared to the gene expression in the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn. Dinoroseobacter shibae DFL12T (DSM 16493T) and  the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn  were grown in artificial saltwater minimal medium (SWM) in baffled flasks shaking at 180 rpm and 30 °C and incubation was performed under light, dark and bluelight conditions. D. shibae wild type and mutant strain were grown under aerobic conditions up to the mid exponential growth phase (OD578 nM 0.5).

platform_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

first: Alina

last: Rommerskirch

first: Saskia

last: Pucelik

first: Steffi

last: Heyber

last: Härtig

first: Dieter

last: Jahn


title: Identification of a minority population in breast cancer that integrates into the vasculature and initiates metastasis [scRNA-Seq]

summary: Metastasis is responsible for the majority of cancer-related deaths1. Although single-cell RNA sequencing (scRNA-seq) has revealed considerable heterogeneity among tumor cells, identifying the cellular determinants of metastasis has remained challenging. Here, we analyzed scRNA-seq data of primary human breast tumor biopsies and identified a minority population of immature THY1+/VEGFA+ basal epithelial cells that display angiogenic features and are marked by the expression of the oncogene, LMO2. Higher levels of LMO2+ basal cells in human breast tumors correlated with endothelial content and predicted poor distant recurrence-free survival. Using MMTV-PyMT/Lmo2CreERT2 mice, we demonstrate that Lmo2 lineage-traced cells integrate into the vasculature and metastasize to the lung. In human breast tumors, knockdown of LMO2 reduced lung metastasis by affecting multiple steps required for intravasation, leading to a reduced frequency of circulating tumor cells. Mechanistically, we find that LMO2 is a binding partner of STAT3 and is required for STAT3 activation in the presence of the inflammatory cytokines, TNFα and IL6. Collectively, our study identifies a population of metastasis-initiating cells with angiogenic features and establishes the LMO2-STAT3 signaling axis as a therapeutic target in breast cancer metastasis.

overall_design:
Single-cell RNA-sequencing (Smart-seq2) profiles (n = 2,359 cells) of basal (tumor: n = 518, adjacent normal: n = 392), luminal progenitor (tumor: n = 213, adjacent normal: n = 319), mature luminal cells (tumor: n = 354, adjacent normal: n = 356), cancer-associated fibroblasts (CAFs; n = 6), endothelial cells (ECs; n = 126), macrophages (n = 21), CD4 T cells (n = 22), CD8 T cells (n = 21), and B cells (n = 11) from 18 human breast tumor biopsies. This study includes data from GSE138536.
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The authors state that they will "upload the remaining raw data to dbGap".

first: Shaheen

middle: S

last: Sikandar

first: Jane

last: Antony

first: Angera

middle: H

last: Kuo

first: William

last: Ho

first: Soumyashree

last: Das

first: Chloé

middle: B

last: Steen

first: Thiago

middle: D

last: Pereira

first: Dalong

last: Qian

first: Philip

last: Beachy

first: Fredrick

last: Dirbas

first: Kristy

last: Red-Horse

first: Terrence

last: Rabbitts

first: Jean

middle: P

last: Thiery

first: Aaron

middle: M

last: Newman

first: Michael

middle: F

last: Clarke


title: RNA-seq of female gonads isolated from juvenile eif4e1b mutant and wild-type zebrafish

status: Public on Oct 03 2023

city: Vienna

first: Marcus

last: Strobl

address: Campus Vienna Biocenter 1

country: Austria

institute: IMP

summary: The mRNA cap-binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish, we isolated gonads with a high expression of ziwi:GFP (female germline marker) from wild-type and eif4e1b mutant juveniles and performed RNA-seq.

overall_design: We performed differential expression gene analyses of wild-type and eif4e1b mutant gonads (n = 3 biological replicates containing 3 gonads each)

first: Laura

last: Lorenzo-Orts

first: Andrea

last: Pauli


title: Identification of a minority population in breast cancer that integrates into the vasculature and initiates metastasis. [RNA-seq]

first: Gunsagar

last: Gulati

overall_design: Bulk RNA-sequencing profiles (n = 9) of 200,000 MDA-MB-468 cells infected with either pSicoR (control), shLMO2-1, or shLMO2-2 each in triplicates.

first: Shaheen

last: Sikandar

first: Jane

last: Antony


title: Integration of single-nuclei RNA-sequencing and spatial transcriptomics defines the complex microenvironment of NF1-associated plexiform neurofibromas

status: Public on Oct 04 2023

city: Aurora

first: Vladimir

last: Amani

state: CO

address: 12800 East 19th Avenue, Building: RC-1 North; Room: P184402A

institute: University of Colorado Anschutz Medical Campus

summary: Plexiform neurofibroma (PN) are a leading cause of morbidity in Neurofibromatosis Type 1 (NF1), often disfiguring or threatening vital structures. During formation of PN, a complex tumor microenvironment (TME) develops, with recruitment of neoplastic and non-neoplastic cell types being critical for growth and progression. Due to the cohesive cellularity of PN, single-cell RNA-sequencing is difficult and may result in a loss of detection of critical cellular subpopulations, therefor single-nuclei RNA-sequencing (snRNA-seq) was applied retrospectively to 8 frozen PN, a large enough sample cohort required to adequately describe the disease TME. Additionally, 4 frozen PN samples were OCT embedded and spatial transcriptomics (ST) was run, adding morphological context to the transcriptomic data generated. Our snRNA-seq analysis definitively charted the heterogeneous cellular subpopulations in the PN TME, with the predominant fraction being fibroblast-like cells. PN have a remarkable amount of inter-sample homogeneity regarding cellular subpopulation proportions despite being resected from a variety of anatomical locations. ST analysis identified distinct cellular subpopulations which were annotated using snRNA-seq data that correlated with histological features. Schwann cell/fibroblast interactions were further characterized by receptor/ligand interaction analysis (CellChat) that was applied to snRNA-seq data. A high probability of Neurexin 1/Neuroligin 1 (NRXN1/NRGLN1) receptor-ligand crosstalk was predicted between non-myelinated Schwann cells (NM_SC) and fibroblast subpopulations, respectively. We observed aberrant expression of NRXN1 and NRGLN1 in our snRNA-seq data versus normal mouse sciatic nerve. This pathway has never been described in PN but has been observed in other NF1-associated tumors and may indicate a clear and direct communication pathway between putative NM_SC cells of origin and surrounding fibroblasts, potentially driving disease progression. SnRNA-seq integrated with spatial transcriptomics advances our understanding of the complex cellular heterogeneity of PN. These data identify potential novel communication pathways that may drive disease progression, a finding that could provide translational therapy options for patients with these devastating tumors of childhood and early adulthood.

overall_design:
single cell RNA-seq and spatial transcriptomic profiling of plexiform neurofibroma

Please note that the records have been updated with an additional sample record on Mar 20, 2024.

first: Vlad

first: Kent

last: Riemondy

first: Andrew

last: Donson

first: Nicholas

last: Willard


title: A safety screening platform for individualized cardiotoxicity assessment

city: Enschede

first: Carla

last: Cofiño Fabrés

address: Drienerlolaan 5

country: Netherlands

institute: University of Twente

summary:
Cardiotoxicity remains a major cause of drug withdrawal, partially due to lacking predictability of animal models. Additionally, risk of cardiotoxicity following treatment of cancer patients is treatment limiting. It is unclear which patients will develop heart failure following therapy. Human pluripotent stem cell (hPSC)-derived cardiomyocytes present an unlimited cell source and may offer individualized solutions to this problem. We developed a platform to predict molecular and functional aspects of cardiotoxicity. Our platform can discriminate between the different cardiotoxic mechanisms of existing and novel anthracyclines Doxorubicin (DOXO), Aclarubicin (ACLA) and Amrubicin (AMR). DOXO and ACLA unlike AMR substantially affected the transcriptome, mitochondrial membrane integrity, contractile force and transcription factor availability. Cardiomyocytes recovered fully within two or three weeks, corresponding to the intermittent clinical treatment regimen.
Our system permits the study of hPSC-cardiomyocyte recovery and the effects of accumulated dose after multiple dosing, allowing individualized cardiotoxicity evaluation, which effects millions of cancer patients treated with anthracyclines annually.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-CMs in Engineered Heart Tissues treated with DMSO (control), Doxorubicin (DOXO), Aclarubicin (ACLA) or Amrubicin (AMR) for 24h. 3 tissues per condition

first: Verena

last: Schwach

last: Cofiño-Fabres

first: Rolf

last: Slaats

first: Robert

last: Passier


title: Transcriptome profiling in USP7 inhibitor (P22077)-treated H1299 and HeLa cells

status: Public on Sep 30 2023

city: Chungju-si

first: Ji-Hong

last: Lim

state: Chungcheongbuk-do

address: 268 Chungwon-daero

country: South Korea

institute: Konkuk University

summary: To investigate the molecular pathway signature responsive to pharmacological inhibition of USP7, we analyzed transcriptome in P22077 (a USP7 selective inhibitor)-treated H1299 and HeLa cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H1299 and HeLa cells treated with DMSO or P22077

first: Woo-Jin

first: Seonghoon

last: Lee


title: Progestin receptor promotes cell macropinocytosis through CDC42 in pancreatic cancer

status: Public on Sep 27 2023

city: Shanghai

first: yanzhi

last: Gai

address: 800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong university

summary: Endocrine receptors play an essential role in tumor metabolic reprogramming and represent a potential therapeutic approach in pancreatic ductal adenocarcinoma (PDAC). PDAC is characterized by a nutrient-deprived microenvironment, and to support their energetic needs, they can internalize extracellular proteins via macropinocytosis. In this study, we found that progesterone receptor (PGR), a steroid-responsive nuclear receptor, has a higher expression in PDAC tissues from patients and transgenic LSL-KrasG12D/+; LSL-Trp53R172H/+; PDX1-cre (KPC) mice. Moreover, PGR knockdown restrained PDAC cell survival and tumor growth both in vitro and in vivo. Genetic and pharmacological PGR inhibition resulted in dramatically macropinocytosis impairment in PDAC cells and subcutaneous tumor models, which indicates involvement of this receptor in macropinocytosis regulation. Mechanistically, PGR deficiency caused a subsequently decreased expression of CDC42, a key regulator in macropinocytosis. These data deepen our understanding of how endocrine system influences tumor progression via non-classical pathway and provide a novel therapeutic option for patients with PDAC.

overall_design: The cDNA microarrays were performed to investigate the differentially expressed cDNA in PGR-interference AsPC-1 cells compared to control cells.

first: Huizhen

last: Nie

first: Pin

last: Li

first: Yanzhi

first: Hong

last: Pan

first: Yingna

last: Liao

first: Liheng

last: Qian

first: Yifan

last: Zhang


title: Transcriptome analysis of lemon leaves (Citrus limon) infected by Plenodomus tracheiphilus reveals the effectiveness of Pseudomonas mediterranea in priming the plant response to mal secco disease

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

summary: The use of Biological Control Agents (BCAs) to cope diseases has received considerable attention owing to its high efficiency and environmental safety. The aim of our study was to investigate the potential role of the Pseudomonas mediterranea pre-treatments in the response of lemon [Citrus limon (L.) Burm. f.] against mal secco, this being a devastating citrus disease caused by the fungus Plenodomus tracheiphilus. RNAseq analysis revealed that the fungus induced a marked reprogramming of the transcriptome, but P. Mediterranea pre-treatments strongly reduced lemon leaf transcriptome modifications and limited the amount of the fungus DNA inside the plant tissue. Furthermore, P. mediterranea prevented the down regulation of the genes involved in the effector triggered immunity (ETI) and the deregulation of genes involved in the main phytohormone’s biosynthesis and perception. As far as we know, this work represents the first report on the analysis of P. tracheiphilus-lemon plant-BCA interaction at molecular level.

overall_design: Potted lemon 'Femminello Siracusano 2Kr' plants grafted onto Citrus aurantium (sour orange) kept in greenhouses at Agrobiotech srl (Catania) were used for the inoculation tests. The inoculations with the fungal pathogen were carried out by placing 10 µl of the vial suspension of P. tracheiphilus isolated PVCT Pt57 (see paragraph 2.2) on the secondary veins of young but fully expanded leaves; the droplets were then pierced until the leaf was incised with an awl with three entomological needles mounted at the end (Oliveri et al., 2022). Each leaf was inoculated in four spots. In order to evaluate the effect of the treatment with the biocontrol agent, the following theses were defined as follows: 3C thesis,  plants treated with the biocontrol agent three days and one day before H2O inoculation; 3CPt thesis, plants treated with the biocontrol agent three days and one day before P. tracheiphilus inoculation; Pt thesis: plants treated with water three days and one day before P. tracheiphilus inoculation; CK thesis, plants treated and inoculated with dH2O. Six plants were inoculated for each thesis and, in each of these, three branches and at least six leaves per branch, for a total of about 18 leaves per plant. The leaves intended for transcriptomic analysis were collected 7 days after inoculation before symptom appearance.

first: Angelo

last: Sicilia

first: Vittoria

last: Catara

first: Giulio

last: Dimaria

first: Emanuele

last: Scialò

first: Marcella

last: Russo

first: Alessandra

last: Gentile

first: Angela

middle: R


title: Protracted neuronal recruitment in the temporal lobe of young children

status: Public on Sep 26 2023

first: Marcos

middle: Assis

last: Nascimento

address: 35, Medical Center Way

institute: University of California, San Francisco

summary: The human brain's temporal lobe contains the entorhinal cortex (EC), a highly interconnected integrative hub for sensory and spatial information; key for episodic memory formation and the primary source of cortical hippocampal inputs.  The human EC continues to develop during childhood, yet neurogenesis and neuronal migration to the EC are widely considered complete by birth.  Here we show that the human temporal lobe contains many young neurons migrating into the postnatal EC and adjacent regions; with a large tangential stream persisting ~1 year and radial dispersal until ~2-3 years.  In contrast, we found no equivalent postnatal migration in rhesus macaque (Macaca mulatta).  Immunostaining and single-nuclei RNA-seq (snRNA-seq) of ganglionic eminence (GE) germinal zones, EC stream, and postnatal EC reveals that most EC stream migrating cells are derived from the caudal GE and become LAMP5+RELN+ inhibitory interneurons. These late-arriving interneurons could continue to shape the processing of sensory and spatial information well into postnatal life when children are actively interacting with their environment. The EC is one of the first brain regions affected in Alzheimer’s disease and recent work links the decline in cognitive function to the loss of LAMP5+RELN+ cells. Our investigation reveals that many of these cells arrive in the EC through a major postnatal migratory stream in early childhood.

overall_design:
snRNA-seq of snap frozen samples of entorhinal cortex, ganglionic eminences, and the EC stream from 9 human donors (ranging from 23 GW to 27 years of age).
In one multiplexed run, nuclei from 5 donors were pooled together and split in two samples (replicate 1 and replicate 2). A second, non-multiplexed run, consisting of samples from 4 other donors, was carried out as multiple individual samples.

Processed data (count matrices -- after SoupX to attenuate ambient RNA contamination -- , filtered barcodes and genes) is provided here. Raw reads are deposited on dbGaP.

**Submitter declares that the raw data will be deposited in dbGaP due to privacy concerns**

last: Assis Nascimento

first: Sean

last: Biagiotti

first: Vicente

last: Herranz-Pérez

first: Samara

last: Santiago

first: Raymund

last: Bueno

first: Chun

last: Ye

first: Taylor

last: Abel

first: Zhuangzhi

first: Juan

last: Rubio-Moll

first: Arnold

last: Kriegstein

first: Zhengang

last: Yang

first: Jose

last: Manuel Garcia-Verdugo

first: Eric

last: Huang

first: Arturo

last: Alvarez-Buylla

first: Shawn

last: Sorrells


title: In-cell structure analysis of antisense Gadd45α SINEB2-a deletion mutants

status: Public on Sep 19 2023

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Division of Genomic Medicine

institute: RIKEN Center for Integrative Medical Sciences

summary: SINEUPs are SINE repeat element containig long non-coding RNAs (lncRNAs)which positively regulate target mRNA translation at post-transcription level. SINE RNA region is crucial for SINEUP function. To analyze the effect of sequence deletion on RNA secondary structure of SINEB2 RNA derived from mouse natural antisense lncRNA to Gadd45α gene, RNA structure of four deletion mutants were chemically probed inside cells. For this, different structure mutants and target EGFP mRNA plasmids were co-transfected in HEK293 cells and icSHAPE libraries were prepared.

overall_design: Two biological replicates of each NAI-N3 and DMSO (mock) treated samples

first: Hiromi

last: Nishiyori

first: Hazuki

last: Takahashi

first: Piero

last: Carninci


title: Spatial transcriptomics of autoimmune alopecia

status: Public on Sep 25 2023

first: Jarish

last: Cohen

address: 513 Parnassus Ave, HSW12 Room 1201B

department: Dermatology

summary: Autoimmune alopecia is a prevalent, highly morbid disease. The inflammatory pathways causing hair loss are not well characterized. We profiled two tissue microarrays comparing healthy skin to scarring alopecia and alopecia areata via spatial transcriptomics to analyze the genes and pathways dysregulated in autoimmune alopecia in direct proximity to the hair follicle.

overall_design: Spatial transcriptomics with two transverse FFPE scalp sections from healthy donors placed alongside two transverse scalp sections from either scarring alopecia or alopecia areata

first: Michael

last: Rosenblum


title: Effects of the onecut family on herpes simplex virus 1 and host chromatin accessibility in Neuro-2a cells

status: Public on Sep 18 2023

city: Hangzhou

first: Xiang

last: Yuhang

address: Yuhang Tang street

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This is a part of the study that shows that a host gene,ONECUT2( OC2), promotes herpes simplex virus 1 (HSV-1) genome accessibility. These ATAC analyses are for viral and host genome accessibility in Neuro-2a cells. Neuro-2a cells were transfected with pOC2△HOX2 and pcDNA plasmids for 42 hours then infected with herpes simple virus1 for 2 hours.

overall_design: Comparison of cells overexpressing OC2△HOX2 with control cells. Infect the cells for viral and host genome accessibility identification

first: Dongli

last: Pan

first: Yuqi

last: Lin


title: RNA-seq for MV4-11 cell line in either the absence or presence of ANP32B

status: Public on Sep 12 2023

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for MV4-11 cell line in either the absence or presence of ANP32B

overall_design: 2 MV4-11 samples with no treatment and 2 MV4-11 samples with ANP32B knockdown

first: Pan

last: Jian

first: Wan

last: Xiaomei


title: RNA-seq for Kasumi-1 cell line in either the absence or presence of ANP32B

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for Kasumi-1 cell line in either the absence or presence of ANP32B

overall_design: 2 Kasumi-1 samples with no treatment and 2 Kasumi-1 samples with ANP32B knockdown


title: Genes expression files at single cell level on mouse embryonic cells treated with low dose ER stressor Thapsigargin

city: IOWA CITY

first: Thomas

last: rutkowski

state: Iowa

address: 51 newton Rd

department: Anatomy and Cell Biology

institute: uiowa

summary: GFP and Flpo MEFs are mixed at 1:1 ratio and cultured on the same dish. Cells are treated with 10nM Thapsigargin for 16hr. Cells were then trypsinized and sent for scRNA sequencing.

overall_design: CHOP FLuL/FLuL primary MEFs are infected with Ad-GFP or Ad-Flpo-GFP and GFP positive cells were sorted out by FACS and expanded. GFP cells do not express CHOP but express nanoluciferase instea whereas FLpo cells express CHOP but not nanoluciferase. GFP and FLpo cells were mixed at 1:1 ratio and plated in the same culture dish. Cells were then treated with 10 nM ER stressor thapsigargin for 16 hrs and collected for scRNA-seq.

first: Kaihua

last: Liu

last: Rutkowski

first: Chaoxian

last: Zhao


title: Evaluation of coloncyte genes in TNBS-induced colitis mice treated with I3C

status: Public on Sep 16 2023

city: Columbia

first: Philip

middle: Brandon

last: Busbee

state: SC

address: 6439 Garners Ferry Road

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

summary:
Transcriptome analysis was performed on enriched colon-dervied epithelial cells from non-colitis and TNBS-induced female Balb/cJ mice untreated or treated with indole-3-carbinol (I3C).
We used microarrays to detail the global programme of gene expression to identify distinct classes of upregulated and downregulated genes among experimental groups.

overall_design: A total of four samples were assessed with the following experimental groups: 1) Vehicle control, 2.) I3C treated, 3.) TNBS+Vehicle, 4.) TNBS+I3C. Samples were collected at experimental endpoint of the TNBS colitis model (Day 5). Colon-derived epithelial cells were enriched using PE-selection ket (Qiagen) from experimental mice.

first: Mitzi

last: Nagarkatti


title: RNA-seq identification of herpes simplex virus type 1 transcription in Neuro-2a cells overexpressing ONECUT2

summary: This is a part of the study that shows that a host gene,ONECUT2 (OC2), promote herpes simplex virus 1 (HSV-1) transcription. These RNA-seq analyses viral genes transcription in Neuro-2a cells. Neuro-2a cells were transfected with pOC2△HOX2 and pcDNA plasmids for 42 hours then infected with herpes simple virus1 for 5 hours.

overall_design: Comparison of cells overexpressing OC2△HOX2 with control cells. Infect the cells for viral  genes transcriptional identification


title: Dynamic enhancer landscapes in human craniofacial development [scATAC-seq]

status: Public on Sep 11 2023

city: Berkeley

first: Laura

middle: E

last: Cook

state: California

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

summary: The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. To annotate the cell type specificity of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating across these data sets, we identify major cell populations of the developing face and annotate over 16,000 candidate enhancers by their cell type-specific epigenomic profile. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we show the value of these data for the prediction of in vivo cell type specificity. Taken together, our data provide a critical resource for genetic and developmental studies of human craniofacial development.

overall_design: We combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution.

first: Sudha

last: Rajderkar

first: Kitt

last: Paraiso

first: Maria

middle: L

last: Amaral

last: Kosicki

first: Fabrice

last: Darbellay

first: Cailyn

last: Spurrell

first: Marco

last: Osterwalder

first: Yiwen

last: Zhu

first: Han

last: Wu

first: Sarah

last: Afzal

first: Matthew

last: Blow

first: Guy

last: Kelman

first: Iros

last: Barozzi

first: Yoko

last: Fukuda-Yuzawa

first: Jennifer

last: Akiyama

first: Veena

first: Stella

last: Tran

first: Ingrid

last: Plajzer-Frick

first: Catherine

last: Novak

first: Momoe

last: Kato

first: Riana

last: Hunter

first: Kianna

last: von Maydell

first: Allen

last: Wang

first: Lin

first: Sebastian

last: Preissl

first: Steven

last: Lisgo

first: Bing

last: Ren

first: Diane

last: Dickel

first: Len

last: Pennacchio

first: Axel

last: Visel


title: Dynamic enhancer landscapes in human craniofacial development [mouse ChIP]

first: Laura

last: Cook

first: Sudha

last: Rajderkar

first: Kitt

last: Paraiso

first: Maria

last: Amaral

first: Michael

last: Kosicki

first: Fabrice

last: Darbellay

first: Cailyn

last: Spurrell

first: Marco

last: Osterwalder

first: Yiwen

last: Zhu

first: Han

last: Wu

first: Sarah

last: Afzal

first: Matthew

last: Blow

first: Guy

last: Kelman

first: Iros

first: Yoko

last: Lin


title: Dynamic enhancer landscapes in human craniofacial development [mouse RNA]

last: Barozzi

last: Fukuda-Yuzawa

first: Jennifer

last: Akiyama

first: Veena

first: Stella

last: Tran

first: Ingrid

last: Plajzer-Frick

first: Catherine

last: Novak

first: Momoe

last: Kato

first: Riana

last: Hunter

first: Kianna

last: von Maydell

first: Allen

last: Wang

first: Lin

first: Sebastian

last: Preissl

first: Steven

last: Lisgo

first: Bing

last: Ren

first: Diane

last: Dickel

first: Len


title: Dynamic enhancer landscapes in human craniofacial development [mouse ATAC]

first: Laura

last: Cook

first: Sudha

last: Rajderkar

first: Kitt

last: Paraiso

first: Maria

last: Amaral

first: Michael

last: Kosicki

first: Fabrice

last: Darbellay

first: Cailyn

last: Spurrell

first: Marco

last: Osterwalder

first: Yiwen

last: Zhu

first: Han

last: Wu

first: Sarah

last: Afzal

first: Matthew

last: Blow

first: Guy

first: Iros

last: Pennacchio

first: Axel

last: Visel


title: Cell lines with either no treatment or ANP32B knockdown

first: Fang

last: Fang

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

overall_design: Refer to individual Series


title: Identification of the binding DNA of ONECUT2 by ChIP in Neuro-2a cells

first: Xiang

last: Yuhang

summary: These ChIP-seq analyses identified binding DNAs of ONEUCT2 in Neuro-2a (mouse neuroblastoma)cells. We overexpressed  OC2ΔHOX (a gain-of-function mutant)  in Neuro-2a cells, and infected the cells with HSV-1 at 40 hours post transfection.  Samples infected for 5 hours were sequenced by ChIP for binding DNAs of  the OC2 mutant in  Neuro-2a cells.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChlP-seq) for OC2ΔHOX (a gain-of-function mutant) in Neuro-2a cells.

first: Yue

last: Deng

first: Yuqi

last: Lin

first: Yuhang

last: Xiang


title: CUT-TAG for AML cell lines with either no treatment or ANP32B knockdown

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results for H3K27ac in AML cell lines.

overall_design: 1 Kasumi-1 sample with no treatment and 1 Kasumi-1 sample with ANP32B knockdown, 1 MV4-11 sample with no treatment and 1 MV4-11 sample with ANP32B knockdown

first: Pan

last: Jian

first: Wan

last: Xiaomei


title: Dynamic enhancer landscapes in human craniofacial development [scRNA-seq]

first: Laura

last: Cook

first: Sudha

last: Rajderkar

first: Kitt

last: Paraiso

first: Maria

last: Amaral

first: Michael

last: Kosicki

first: Fabrice

last: Kelman

last: Barozzi

first: Yoko

last: Fukuda-Yuzawa

first: Jennifer

last: Akiyama

first: Veena

first: Stella

last: Tran

first: Ingrid

last: Plajzer-Frick

first: Catherine

last: Novak

first: Momoe

last: Kato

first: Riana

last: Hunter

first: Kianna

last: von Maydell

first: Allen

last: Wang

first: Lin

first: Sebastian

last: Preissl

first: Steven

last: Lisgo

first: Bing

last: Ren

first: Diane

last: Dickel

first: Len


title: Virus-specific TRM cells of both donor and recipient origin reside in human kidney transplants

city: Rotterdam

first: Hector

last: Tejeda Mora

address: Doctor Molewaterplein 40

department: Developmental Biology

institute: Erasmus MC

summary: Tissue-resident lymphocytes (TRLs) are critical for local protection against viral pathogens in peripheral tissue. However, it is unclear if TRLs perform a similar role in transplanted organs under chronic immunosuppressed conditions. The present study aimed to characterize the TRL compartment in human kidney transplant nephrectomies and examine its potential role in antiviral immunity. Paired single-cell transcriptome and T-cell receptor (TCR) sequencing showed that donor and recipient tissue-resident memory T (TRM) cells exhibit striking similarities in their transcriptomic profiles and share numerous TCR clonotypes predicted to target viral pathogens.

overall_design: Lymphocytes from kidney transprant nephrectomy specimens were obtained through mechanical and enzymatic (colleganase IV) digestion and the mononuclear cells were harvested through Ficoll density gradient centrifugation. Next, CD4+ and CD8+ tissue-resident memory T (TRM) cells were sorted from these mononuclear cell samples (n=4) using fluorescent-activated cell sorting (FACS). Residency of TRM cells was defined as the co-expression of CD69 plus CD103 and/or CD49a. Sorted TRM cells of the four samples were used for paired single-cell RNA and TCR sequencing using the 10x genomics platform.

first: Eric

last: Bindels

first: Daphne

last: Hullegie-Peelen


title: KSHV Terminal Repeat Regulates Inducible Lytic Gene Promoters

status: Public on Sep 08 2023

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: The Kaposi's sarcoma-associated herpesvirus (KSHV) genome consists of an approximately 140 kb unique coding region flanked by 30-40 copies of 0.8 kb terminal repeat (TR) sequence. KSHV genomes persist in latently infected cells as episomes via tethering to the host cell chromosomes, and KSHV latency associated nuclear antigen (LANA) plays a crucial role in latent episomal DNA replication and segregation during host cell mitosis by binding to TR. While TR's function in plasmid maintenance is well-established, TR’s transcription regulatory roles as gene enhancer has not been fully explored. Gene enhancer harbors transcription enzymes via arrays of transcription factors bindings and often forms phase separate nuclear body in part through recruitment of BRD4 and MED1 that contain intrinsically disordered domain. Here we show KSHV TR possesses transcription regulatory function with LANA. A series of Cleavage Under Targets & Release Using Nuclease (CUT&RUN) demonstrated that TR fragments are occupied by histone modifying enzymes that are known to interact with LANA in naturally infected cells, and the TR possessed characteristic enhancer histone modifications. The H3K4me3 and H3K27Ac modification were also conserved in unique region of the KSHV genome among three PEL cells, and the KSHV Origin of lytic replication (Ori-Lyt) showed similar protein and histone modification occupancies with TR's. In the Ori-Lyt region, the LANA protein complex colocalizes with H3K27Ac-modified nucleosome along with paused RNA polymerase II, and the nucleosome is franked by two K-Rta recruitment sites. The isolated reporter assays demonstrated that neighboring TR fragments enhanced viral lytic gene promoter activity independent of orientation in KSHV-infected and non-infected 293FT cells. K-Rta transactivation function was drastically enhanced with TR, while LANA acquired promoter repression function when the reporter was ligated with TR. The deletion of LANA acidic repeat sequence, a highly-disordered protein domain, further increased gene repression functions. Combined, the TR region is (i) an epigenetically active DNA element that is stitched within 12.5 kb (20-40 copies), (ii) has an array of transcription factor (LANA) binding sites, (iii) recruited by transcription related enzymes including BRD4 (bromodomain containing 4), (iv) decorated by histone H3K27Ac marks, and (v) possesses orientation-independent transcription activation function. KSHV TR is therefore an enhancer domain for KSHV inducible genes. However, in contrast to cellular enhancers that are bound by multiple transcription factors, perhaps KSHV enhancer is predominantly regulated by the LANA nuclear body on the TR. We suggest that KSHV evolved a clever mechanism to tightly control the latency-lytic switch with the TR/LANA complex.

overall_design:
The goal of these studies was to utilize CUT&RUN in order to determine the lanscape of histone-modifying enzymes that interact with LANA and occupy the KSHV Terminal Repeat fragents in naturally infected cells . For this CUT&RUN was performed for BRD4, ADNP, MLL1, SMC1, SMARCA5, CTCF, RNA polymerase II, and histone modification marks (H327Ac, H3K4me1, H3K4me2, H3K27me3 ).

Please note that the records have been updated with the additional *CPM_norm.bigWig files on Oct 19, 2023.

first: Yoshihiro

last: Izumiya

first: Kumar

last: Ashish

middle: G


title: Methylation data from human retina samples profiled with Infinium HumanMethylationEPIC BeadChip

city: Bethesda

first: Jayshree

last: Advani

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Age-related macular degeneration (AMD) is a complex multifactorial disease with at least 34 loci contributing to genetic susceptibility. To gain functional understanding of AMD genetics, we generated DNA methylation profiles of retina from 160 individuals including both controls and cases at distinct stages of AMD. With genotypes over 8 million common single nucleotide polymorphisms (SNPs) in cis, we identified 37,453 methylation quantitative trait loci (mQTL) and by integrating transcriptome of the same samples we identified 12,505 eQTLs and 13,747 DNAm sites that affect gene expression (eQTMs). We then integrated the AMD-genome-wide association studies (GWAS) data with mQTLs and eQTLs ascertained 87 target genes that may contribute to AMD risk. Our studies expand the methylation landscape of retina and AMD leading to direct targets for biological evaluation.

overall_design: Genome wide DNA methylation profiling of human retina tissue samples from post-mortem donors. The Infinium HumanMethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs sites from 160 tissue samples

first: Puja

last: Mehta

first: Andrew

last: Hamel

first: Sudeep

last: Mehrotra

first: Christina

last: Kiel

first: Tobias

last: Strunz

first: Ximena

last: Corso Diaz

first: Madeline

last: Kwicklis

first: Freekje

last: van Asten

first: Rinki

last: Ratnapriya

first: Dena

last: Hernandez

first: Sandra

last: Montezuma

first: Deborah

last: Ferrington

first: Bernhard

last: Weber

first: Ayellet

middle: V

last: Segrè

first: Anand

last: Swaroop


title: Two-motif model illuminates DICER's cleavage preferences [DICER]

status: Public on Sep 06 2023

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: DICER is a key regulator of gene expression in animals through its production of miRNAs and siRNAs by processing shRNA. To advance our understanding of this process, we employed high-throughput assays using various shRNA variants and both wild-type and mutant DICER (DICERΔdsRBD). Our analysis revealed that DICER predominantly cleaves shRNAs at two positions, specifically at 21 (DC21) and 22 (DC22) nucleotides from the 5'-end. Our investigation identified two independent motifs, mAHG and YSR, that determine whether DICER cleaves at DC21 or DC22, depending on their location in shRNA/pre-miRNAs. These motifs can work together or independently to determine the cleavage sites of DICER. Furthermore, our findings indicate that dsRBD enhances cleavage at DC21, and mAHG strengthens the interaction between dsRBD and RNA, leading to an even greater enhancement of DC21 cleavage. Conversely, YSR functions independently of dsRBD. Our study proposes a two-motif model that sheds light on the intricate regulatory mechanisms involved in gene expression by elucidating how DICER recognizes its substrate, providing valuable insights into this critical biological process.

overall_design: RNA sequencing

first: Cong-Truc

last: Le

first: Trung-Duc

last: Nguyen

first: Tuan-Anh


title: DNA methylation-environment interactions in the human genome

status: Public on Sep 07 2023

city: Durham

first: Rachel

middle: A

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

institute: Duke University

summary: This project uses the massively parallel reporter assay, mSTARR-seq (Lea et al., 2018) to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity across nearly the entire human genome. We assessed enhancer activity at almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. Experiments were performed in K562 and HepG2 cells.

overall_design: In this data set, 6 replicate flasks of K562 cells were treated for 6 hours with each of the following treatments: dexamethasone (1 uM), IFNA2b (2,000U/ml), or vehicle control (media). Cells were then collected for mRNA-Seq to assess the endogenous gene expression response of K562 cells to treatment.


title: Dynamic enhancer landscapes in human craniofacial development [human ChIP]

first: Laura

last: Cook

first: Sudha

last: Rajderkar

first: Kitt

last: Paraiso

first: Maria

last: Amaral

first: Michael

last: Kosicki

first: Fabrice

last: Darbellay

first: Cailyn

last: Spurrell

first: Marco

last: Osterwalder

first: Yiwen

last: Zhu

first: Han

last: Wu

first: Sarah

middle: Y

last: Afzal

first: Matthew

middle: J

last: Blow

first: Guy

last: Kelman

first: Iros

last: Barozzi

first: Yoko

last: Fukuda-Yuzawa

first: Jennifer

last: Akiyama

first: Veena

first: Stella

last: Tran

first: Ingrid

last: Plajzer-Frick

first: Catherine

middle: S

last: Novak

first: Momoe

last: Kato

first: Riana

last: Hunter

first: Kianna

last: von Maydell

first: Allen

last: Wang

first: Lin

last: Lin

first: Sebastian

last: Preissl

first: Steven

last: Lisgo

first: Bing

last: Ren

first: Diane

last: Dickel

first: Len

last: Pennacchio

first: Axel

last: Visel


title: Dynamic enhancer landscapes in human craniofacial development [human RNA]

first: Laura

last: Cook

first: Sudha

last: Rajderkar

first: Kitt

last: Paraiso

first: Maria

last: Amaral

first: Michael

last: Kosicki

first: Fabrice

last: Darbellay

first: Cailyn

middle: H

last: Spurrell

first: Marco

last: Osterwalder

first: Yiwen

last: Zhu

first: Han

last: Wu

first: Sarah

last: Afzal

first: Matthew

last: Blow

first: Guy

last: Kelman

first: Iros

last: Barozzi

first: Yoko

middle: D


title: Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease

status: Public on Sep 03 2023

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Metastatic gastric carcinoma is a highly lethal cancer that responds poorly to conventional and molecularly targeted therapies. Despite its clinical relevance, the mechanisms underlying the behavior and therapeutic response of this disease are poorly understood owing, in part, to a paucity of tractable models that faithfully recapitulate different subtypes of the human disease. To close this gap, we developed methods to somatically introduce different oncogenic lesions directly into the stomach epithelium and show that genotypic configurations observed in patients produce metastatic gastric cancers that recapitulate the histological, molecular, and clinical features of all non-viral molecular subtypes of the human disease. Applying this platform to both wild-type and immune-deficient mice revealed previously unappreciated links between the genotype, organotropism and immune surveillance of metastatic cells that produced distinct patterns of metastasis that were mirrored in patients. Our results establish and credential a highly portable platform for producing autochthonous cancer models with flexible genotypes and host backgrounds, which can unravel mechanisms of gastric tumorigenesis or test new therapeutic concepts aimed at improving outcomes in gastric cancer patients.

overall_design: For RNA-seq analysis of the transcriptional profiles of MYC-p53, MYC-Apc and MYC-p53-Msh2 EPO-GEMM gastric tumors, as well as normal stomach of wild-type (WT) C57BL/6 mice, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Josef

last: Leibold

first: Corina

last: Amor

first: Kaloyan

middle: M

last: Tsanov

first: Francisco

last: Sánchez-Rivera

first: Judith

last: Feucht

first: Hsuan-An

last: Chen

first: Timour

last: Baslan

first: Sha

last: Tian

first: Janelle

last: Simon

first: Alexandra

last: Wuest

first: John

last: Wilkinson

first: Scott

middle: W

last: Lowe


title: Quantitative PCR (qRT-PCR) analysis of micro RNA expression in mouse cells

status: Public on Sep 04 2023

city: Seoul

first: Kinarm

last: Ko

address: 120, Neungdong-ro, Gwangjin-gu

summary: To comprehend the underlying mechanisms of NSC proliferation and differentiation, microRNA expression was investigated. Total RNA was extracted from NSCs, ESCs, and MEFs, and microRNA expression was examined using RT-PCR. This was accomplished utilizing the System Biosciences' Mouse miRNome Sanger miRVase microRNA Profiler Set.

overall_design: qPCR gene expression profiling. Equal amount total RNA from each cell was pooled prior to gene expression analysis.

first: Yukyeong

last: Lee


title: Synthetic Introns Identify GPATCH8 as Required for Mis-splicing by SF3B1 Mutations [RNA-seq]

status: Public on Sep 01 2023

first: Jahan

last: Rahman

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: Mutations in the RNA splicing factor SF3B1 are common across hematologic and solid cancers and result in widespread alterations in splicing but therapeutic means to correct this mis-splicing do not exist. Here we utilize synthetic introns uniquely responsive to mutant SF3B1 to identify trans factors required for aberrant mutant SF3B1 splicing activity. This revealed the G-patch domain containing protein GPATCH8 as required for mutant SF3B1-induced splicing alterations and impaired hematopoiesis. GPATCH8 is involved in quality control of branchpoint selection, interacts with the RNA helicase DHX15, and functionally opposes SUGP1, a G-patch protein recently implicated in SF3B1 mutant diseases. Silencing of GPATCH8 corrected one-third of mutant SF3B1 splicing defects and was sufficient to improve hematopoiesis in SF3B1 mutant mouse and human cells. These data identify GPATCH8 as a novel splicing factor required for mis-splicing by mutant SF3B1 and the therapeutic impact of correcting aberrant splicing in SF3B1 mutant cancers.

overall_design: We sought to determine the impact of GPATCH8 deletion on RNA splicing genome-wide. We therefore performed RNA-seq analyses of 293T cellsand AML (K562) cells1/with or without knockin of SF3B1K700E mutation,2/ with overexpression of SRSF2 WT or P95H mutant, 3/ with overexpression of U2AF1 WT or S34F mutant, in the presence or absence of GPATCH8 deletion.

first: Salima

last: Benbarche

first: Jose

last: Maria Bello Pineda

first: Laura

last: Baquero Galvis

first: Bo

last: Liu

first: Jeetayu

last: Biswas

first: Eric

last: Wang

first: Kadeen

last: Lyttle

first: Ariana

last: Dahi

first: Alexander

last: Lewis

first: Martina

last: Sarchi

first: Sanjoy

last: Mehta

first: Ralph

last: Garippa

first: Juliana

last: Ortiz-Pacheco

first: Zhuoning

last: Li

first: Mara

last: Monetti

first: Robert

last: Stanley

first: Sergei

last: Doulatov

middle: K

last: Bradley

first: Omar

last: Abdel-Wahab


title: Dynamic enhancer landscapes in human craniofacial development [human ATAC-seq]

last: Cook

first: Sudha

last: Rajderkar

first: Kitt

last: Paraiso

first: Maria

last: Amaral

first: Michael

last: Kosicki

first: Fabrice

last: Darbellay

first: Cailyn

last: Spurrell

first: Marco

last: Osterwalder

first: Yiwen

last: Zhu

first: Han

last: Wu

first: Sarah

last: Afzal

first: Matthew

last: Blow

first: Guy

last: Kelman

first: Iros

last: Barozzi

first: Yoko

last: Fukuda-Yuzawa

first: Jennifer

last: Akiyama

first: Veena

first: Stella

last: Tran

first: Ingrid

last: Plajzer-Frick

first: Catherine

last: SNovak

first: Momoe

last: Kato

first: Riana

last: Hunter

first: Kianna

last: von Maydell

first: Allen

first: Lin

last: Lin

first: Sebastian

last: Preissl

first: Steven

last: Lisgo

first: Bing

last: Ren

first: Diane

last: Dickel

first: Len

last: Pennacchio

first: Axel

last: Visel


title: Dynamic enhancer landscapes in human craniofacial development

first: Laura

last: Cook

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Actin associates with actively elongating genes

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: Nuclear actin has been demonstrated to be essential for optimal transcription, but the molecular mechanisms and direct binding partner for actin in the RNA polymerase complex have remained unknown. By using purified proteins in several biochemical assays, we demonstrate a direct and specific interaction between monomeric actin and Cdk9, the kinase subunit of the positive transcription elongation factor b (P-TEFb) required for RNA polymerase II (Pol II) pause-release. This interaction is not dependent on kinase activity of Cdk9 and is not involved with releasing P-TEFb from its inhibitor 7SK snRNP complex. Supporting the specific role for actin in the elongation phase of transcription, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) reveals that actin interacts with genes only upon their active transcription elongation. This study therefore provides novel insights into the mechanisms by which actin facilitates the transcription process.

overall_design: chromatin immunoprecipitationfollowed by deep sequencing (ChIP-seq) of actin (AC-74) and Pol II phosphorylated at serine 5 (Pol II S5P) in S2R+  cells culture at room temperature (non-heat shock; NHS) or heat shocked for 20 min at 37°C (HS). Normal mouse IgG and input were used as negative controls

first: Bina

last: Prajapati

first: Salla

last: Kyheröinen


title: Analysis of breast cancer cells

city: SAN FRANCISCO

first: Alison

last: Parisian

address: 780 Brannan St

institute: Olema Pharmaceuticals


title: PRO-seq analysis of estradiol, OP-1250, fulvestrant and 4OH-tamoxifen treatments at multiple timepoints in breast cancer cells

summary: The estrogen receptor (ER) is a well-established target for the treatment of breast cancer, with the majority of patients presenting as ER-positive (ER+). Endocrine therapy is a mainstay of breast cancer treatment but the development of resistance mutations in response to aromatase inhibitors, poor pharmacokinetic properties of fulvestrant, agonist activity of tamoxifen, and limited benefit for elacestrant leave unmet needs for patients with or without resistance mutations in ESR1, the gene that encodes the ER protein. Here we describe OP-1250, a novel, orally bioavailable complete ER antagonist and selective ER degrader. OP-1250, like fulvestrant, has no agonist activity on the ER and completely blocks estrogen-induced transcriptional activity. In addition, OP-1250 demonstrates favorable biochemical binding affinity, ER degradation, and antiproliferative activity in ER+ breast cancer models that is comparable or superior to other agents of interest. OP-1250 has superior pharmacokinetic properties relative to fulvestrant, including oral bioavailability and brain penetrance, as well as superior performance in wild-type and ESR1-mutant breast cancer xenograft studies. OP-1250 combines well with cyclin-dependent kinase 4 and 6 inhibitors in xenograft studies of ER+ breast cancer models and effectively shrinks intracranially implanted tumors, resulting in prolonged animal survival. With demonstrated preclinical efficacy exceeding fulvestrant in wild-type models, elacestrant in ESR1-mutant models, and tamoxifen in intracranial xenografts, OP-1250 has the potential to benefit patients with ER+ breast cancer.

overall_design: MCF7 or CAMA1 cells were plated in estradiol-depleted charcoal dextran stripped serum-containing media for 24 hours prior to dosing with 316 nM compound or 100 pM 17-beta estradiol and harvested after 15 min, 1 hr, 6 hr or 24 hr treatment. For estradiol pretreated conditions, cells were treated for 24 hours with 17-beta estradiol prior to compound treatment and harvested after 15 min, 1 hr, 6 hr or 24 hr treatment. Harvested samples were processed for precision run-on sequencing.

first: Susanna

last: Barratt

first: Leslie

last: Hodges-Gallagher

first: Fabian

last: Ortega

first: Guadalupe

last: Peña

first: Judevin

last: Sapugay

first: Brandon

last: Robello

first: Richard

last: Sun

first: David

last: Kulp

first: Gopinath

last: Palanisamy

middle: C

last: Myles

first: Peter

last: Kushner

first: Cyrus

last: Harmon


title: Inflammatory markers and frailty in home-dwelling elderly, a cross-sectional study

city: Oslo

first: Kirsten

middle: B

last: Holven

address: Sognsvannsveien 9

department: Department of Nutrition

country: Norway

institute: University of Oslo

summary:
Low-grade, chronic inflammation during ageing  (“inflammageing”) is suggested to be involved in the development of frailty in older age. However, studies on the association between frailty, using the frailty index definition, and inflammatory markers are limited.
The aim of this study was to investigate the relationship between inflammatory markers and frailty index (FI) in older, home-dwelling adults. Home-dwelling men and women aged ≥ 70 years old, living in South-East Norway were recruited and included in a cross-sectional study. The FI used in the current study was developed according to Rockwood’s frailty index and included 38 variables, resulting in an FI score between 0 and 1 for each participant. Circulating inflammatory markers (IL-6, CRP, IGF-1, cystatin C, cathepsin S, and glycoprotein Acetyls) were analyzed from non-fasting blood samples using ELISA. Whole-genome PBMC transcriptomics was used to study the association between FI score and inflammation.
The present study was a cross-sectional study that included home-dwelling men and women aged ≥ 70 years old, living in the Skedsmo area, South-East Norway. The study was conducted in 2014/2015 and has been described previously [Ottestad I, Ulven SM, Øyri LKL, Sandvei KS, Gjevestad GO, Bye A, et al. Reduced plasma concentration of branched-chain amino acids in sarcopenic older subjects: a cross-sectional study. Br J Nutr. 2018;120(4):445-53]. The participants were recruited by the National Register and received an invitation letter by mail. Briefly, a total of 2820 subjects were invited, and 437 subjects participated in the study. The participants met for a single study visit, and data was collected on dietary intake, body weight and composition, physical performance, medical history, cognitive function, risk of malnutrition, anthropometric measurements, blood pressure, heart rate, and quality of life. Non-fasting blood samples were also collected.

overall_design:
Gene expression data from PBMCs isolated from non-fasting blood samples collected at a screening visit (Amarone cross-sectional) for a randomized trial (Amarone RCT):
Data at cross-sectional screening visit: n = 437
PBMC samples analyzed with microarray (females only): n = 96
PBMC samples analyzed with microarray (females only), excl. outliers: n = 95 (excl. sample 52 - only non-normalized data provided)
PBMC samples with available outcome data (i.e., the FI score): n = 88 (excl. samples 2, 8, 14, 15, 18, 21, and 28)

first: Pia

last: Bålsrud

first: Stine

last: Ulven

first: Jacob

last: Christensen

first: Inger

last: Ottestad


title: Single Cell Transcriptomics Identifies Distinct Choroid Cell Populations Involved in Visually Guided Eye Growth

status: Public on Sep 05 2023

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: Postnatal ocular growth is regulated by a vision-dependent mechanism, termed emmetropization, which acts to minimize refractive error through coordinated growth of the ocular tissues. Many studies suggest that the ocular choroid participates in the emmetropization process via the production of scleral growth regulators that control ocular elongation and refractive development.   To elucidate the role of the choroid in emmetropization, we used single-cell RNA sequencing (scRNA-seq) to characterize the cell populations in the chick choroid and compare gene expression changes in these cell populations during conditions in which the eye is undergoing emmetropization. UMAP clustering analysis identified 24 distinct cell clusters in all chick choroids. 7 clusters were identified as fibroblast subpopulations; 5 clusters represented different populations of endothelial cells; 4 clusters were CD45+ macrophages, T cells and B cells; 3 clusters were Schwann cell subpopulations; and 2 clusters were identified as melanocytes. Additionally, single populations of RBCs, plasma cells and neuronal cells were identified.  Significant changes in gene expression between control and treated choroids were identified in 17 cell clusters, representing 95% of total choroidal cells. The majority of significant gene expression changes were relatively small (< 2 fold). The highest changes in gene expression were identified in a rare cell population (0.11% - 0.49% of total choroidal cells). This cell population expressed high levels of neuron-specific genes as well as several opsin genes suggestive of a rare neuronal cell population that is potentially light sensitive. Our results, for the first time, provide a comprehensive profile of the major choroidal cell types and their gene expression changes during the process of emmetropization as well as insights into the canonical pathways and upstream regulators that coordinate postnatal ocular growth.

overall_design: To investigate the gene expression changes in choroidal cell populations during the process of emmetropization, we isolated cells from choroid tissue digests of choroids isolated from chick eyes recovering from form deprivation myopia and contralateral control eyes. Following FACS sorting of live cells, live cells were processed for sc-RNA sequencing.  Comparative gene expression profiling analyses were performed for three samples of choroidal cell populations from control eyes and three sets of choroidal cell populations from recovering eyes.

first: Jody

last: Summers


title: Identification of differentially expressed miRNAs associated with diamide detoxification pathways in Spodoptera frugiperda

city: Daejeon

first: Rashmi

middle: Manohar

last: Mahalle

address: Yuseong-gu

institute: Chungnam National Unversity

summary: The fall armyworm (FAW) Spodoptera frugiperda is one of the most severe economic pests of multiple crops globally. Control of this pest is often achieved using insecticides; however, over time, S. frugiperda has developed resistance to new mode of action compounds, including diamides. Previous studies have indicated diamide resistance is a complex developmental process involving multiple detoxification genes. Still, the mechanism underlying the possible involvement of microRNAs in post-transcriptional regulation of resistance has not yet been elucidated. In this study, a global screen of microRNAs (miRNAs) revealed 109 known and 63 novel miRNAs. Nine miRNAs (four known and five novel) were differentially expressed between insecticide-resistant and -susceptible strains. Gene Ontology analysis predicted putative target transcripts of the differentially expressed miRNAs encoding significant genes belonging to detoxification pathways. Additionally, miRNAs are involved in response to diamide exposure, indicating they are probably associated with the detoxification pathway. Thus, this study provides comprehensive evidence for the link between repressed miRNA expression and induced target transcripts that possibly mediate diamide resistance through post-transcriptional regulation. These findings highlight important clues for further research to unravel the roles and mechanisms of miRNAs in conferring diamide resistance.

overall_design: We investigated the differentially expressed between insecticide-resistant and -susceptible strains of Spodoptera frugiperda.

last: Manohar Mahalle

first: Keon

last: Seong


title: Brain hypothyroidism leads to immune tolerance in microglia in Alzheimer's disease

first: Jong-Il

last: Kim

address: Daehakro 103

institute: Seoul National University


title: Brain hypothyroidism leads to immune tolerance in microglia in Alzheimer's disease [RNA-seq]

summary: An imbalance in thyroid hormones (THs) is associated with reversible dementia and Alzheimer’s disease (AD) pathogenesis. Whether hypothyroidism occurs in AD brains and how it affects AD pathology remain largely unknown. Here, we find that reduced conversion of thyroxine (T4) to tri-iodothyronine (T3) in the brain by decreased iodothyronine deiodinase 2 (DIO2) leads to hippocampal hypothyroidism in early AD model mice prior to TH changes in the blood. A TH deficiency causes immune tolerance with decreased phagocytic activity in microglia, thereby aggravating AD pathology. We demonstrate that microglial ecto-5’-nucleotidase (CD73) is reduced in the hypothyroid state and that its inhibition contributes to immune tolerance in microglia. Thus, our data define a molecular mechanism through which decreased conversion of T4 to T3 in the early AD brain, and consequent brain hypothyroidism causes microglial dysfunction and exacerbates AD pathology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the mouse microglia with Liothyronine treatment or no treatment.

first: Dong

first: Hyunjung

last: Choi

first: Woochan

last: Lee

first: Hayoung

first: Seok

last: Hong

first: June

last: Jeong

first: Jihui

last: Han

first: Hoon

last: Ryu

first: Jong

middle: I

first: Inhee

last: Mook-Jung


title: Brain hypothyroidism leads to immune tolerance in microglia in Alzheimer's disease [scRNA-seq]

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data for the brains of wild-type mice and AD model mice fed with control or iodine deficient diet.


title: Regulation of CpG methylation by the Glucocorticoid Receptor in zebrafish

city: Sheffield

first: Vincent

middle: Trevor

last: Cunliffe

state: South Yorkshire

address: Western Bank

department: School of Biosciences

country: United Kingdom

institute: University of Sheffield

type: Methylation profiling by high throughput sequencing

summary: The methylomes of whole adult zebrafish brains was compared in gr s357 mutants and wild type siblings

overall_design: Differentially Methylated Regions were identified in adult zebrafish grs357 homozygous mutant versus wild type sibling brains using Whole Genome Bisulfite Sequencing. Homozygous mutant and wild type siblings were analysed in duplicate.

middle: T

first: Helen

middle: L

last: Eachus


title: SERBP1 deacetylation inhibits ferroptosis to promote KSHV-induced cellular transformation by decaying lipoyltransferase 2 mRNA

status: Public on Aug 22 2023

city: Nanjing

first: jing

last: zhou

address: longmian Street No.101

institute: Nanjing Medical University

summary: Ferroptosis, a defensive strategy employed by the host to restrict pathogenic infections, has been implicated in the development and therapeutic responses of various types of tumors. However, the role of ferroptosis in KSHV-induced malignant tumors remains elusive. A steadily growing number of non-histone proteins have been identified as acetylation targets, their functions have yet to be revealed. In this study, we obtained a marked disparity in the landscape of acetylation between MM and KSHV-transformed MM (KMM) cells. SERBP1 deacetylation was upregulated in KMM cells and contributed to KSHV-induced cellular transformation by inhibiting ferroptosis. Mechanistically, KSHV-encoded viral interleukin-6 (vIL-6) hijacks SIRT3, a mitochondrial NAD+-dependent deacetylase, to interact with SERBP1 leading to the deacetylation of SERBP1. Deacetylated SERBP1 exhibits reduced binding to Lipt2 mRNA, which promotes Lipt2 mRNA degradation, resulting in ferroptosis inhibition. Our findings unveil a novel role of SERBP1 deacetylation in regulating ferroptosis and KSHV-induced cellular transformation and identify potential new therapeutic targets for KSHV infection and KSHV-induced cancers.

overall_design: To identify the target mRNAs of SERBP1 influenced by its acetylation state, RNA immunoprecipitation-coupled RNA sequencing (RIP-Seq) was performed on SERBP1 KO KMM cells overexpressing SERBP1-WT or SERBP1-K68R.

first: Jing

last: Zhou

first: Qin

last: Yan

first: Wan

last: Li

first: Shou-Jiang

last: Gao

first: Chun

last: Lu


title: Neuronal deletion of the circadian clock gene Bmal1 induces cell-autonomous dopaminergic neurodegeneration

status: Public on Aug 18 2023

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: Circadian rhythm dysfunction is a hallmark of Parkinson Disease (PD), and diminished expression of the core clock gene Bmal1 has been described in PD patients. BMAL1 is required for core circadian clock function, but also serves non-rhythmic functions. Germline Bmal1 deletion can cause brain oxidative stress and synapse loss in mice, and can exacerbate dopaminergic neurodegeneration in response to MPTP. Here we examined the impact of cell type-specific Bmal1 deletion on dopaminergic neuron viability in vivo. We observed that global, post-natal deletion of Bmal1 caused spontaneous loss of tyrosine hydroxylase-positive (TH+) dopaminergic neurons in the substantia nigra pars compacta (SNpc). This was not due to disruption of behavioral circadian rhythms, and was not induced by astrocyte- or microglia-specific Bmal1 deletion. However, either pan-neuronal or TH neuron-specific Bmal1 deletion caused cell-autonomous loss of TH+ neurons in the SNpc. Finally, global Bmal1 deletion exacerbated TH+ neuron loss following injection of alpha-synclein fibrils. Transcriptomic analysis of neuron-specific Bmal1 KO brain revealed dysregulation of pathways involved in oxidative phosphorylation and Parkinson Disease.

overall_design: Inducible global Bmal1 KO mice (CAG-CreERT2;Bmal1(fx/fx) and Cre-;Bmal1(fx/fx) littermate controls were treated with tamoxifen for 5 days. Sixty days later, mice were perfused with PBS+heparin, and the midbrain was dissected out, frozen. RNA was later extracted and bulk RNAseq performed. N= 4 Cre- and 3 Cre+ mice.

first: Erik

last: Musiek

first: Albert

last: Davis

first: Patrick

last: Sheehan

first: Michael

last: Kanan


title: Acantholytic skin diseases

status: Public on Aug 29 2023

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Darier, Hailey-Hailey, and Grover’s diseases are rare acantholytic skin diseases. While these diseases have different underlying causes, they share defects in cell-cell adhesion in the epidermis and desmosome organization.The transcriptomic profiles of Darier, Hailey-Hailey, and Grover’s disease were found to share a remarkable overlap, which did not extend to other common inflammatory skin diseases. Analysis of enriched pathways showed a shared increase in keratinocyte differentiation, and a decrease in cell adhesion and actin organization pathways in Darier, Hailey-Hailey, and Grover’s disease. Direct comparison to atopic dermatitis and psoriasis showed that the downregulation in actin organization pathways was a unique feature in the acantholytic skin diseases. Further, upstream regulator analysis suggested that a decrease in SRF/MRTF activity was responsible for the downregulation of actin organization pathways. These findings highlight the significant level of similarity in the transcriptome of Darier, Hailey-Hailey, and Grover’s disease, and identify decreases in actin organization pathways as a unique signature present in these conditions.

overall_design:
To better understand the underlying mechanisms leading to disease in these conditions we performed RNA-seq on lesional skin samples from patients.

**Samples GSM7400532, GSM7400547, and GSM7400549 were deleted because the submitter stated that these Samples had data quality issues**

first: Johann

middle: E

last: Gudjonsson

first: Quinn

middle: R

last: Roth-Carter

first: Kathleen

last: Green


title: Human saliva modifies growth, biofilm architecture and competitive behaviors of oral streptococci

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

institute: The Ohio State University

summary: Our group recently transcriptomically characterized coculture growth between Streptococcus mutans and several species of commensal streptococci (Rose et al, 2023). However, these experiments were carried out in our lab-based experimental medium, tryptone and yeast extract (TY-). To understand whether culturing these species within a medium that more closely mimics their natural environment alters the interaction, we evaluated both monoculture and coculture growth between the dental caries pathogen Streptococcus mutans and oral commensal species Streptococcus oralis in a half TY- / half human saliva mix that was optimally chosen based on our initial characterization of oral streptococci behaviors in medium mixes containing saliva. Our results surprising show that inclusion of saliva enhances the competition of Streptococcus mutans against commensal streptococci through upregulation of carbohydrate uptake and glycolytic pathways.

sample_organism:
Streptococcus oralis
Streptococcus mutans

overall_design:
Streptococcus mutans UA159 and Streptococcus oralis 34 were grown either as monocultures or cocultures, inoculated 1:1.
All samples were grown in either TY- (regular lab-based experimental medium) or TY-Saliva (half TY / half human saliva).
Resulting comparisions included differentially expressed genes (DEGs) between TY-Saliva and TY- conditions for each monoculture as well as cocultures.

first: Dan

last: Peters

first: Allen

last: Choi

first: Kevin

last: Dong


title: Synthetic Introns Identify GPATCH8 as Required for Mis-splicing by SF3B1 Mutations

status: Public on Aug 31 2023

first: Jahan

last: Rahman

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

overall_design: Refer to individual Series


title: Immune stress suppresses innate immune signaling in preleukemic precursor B cells to cause leukemia

status: Public on Aug 10 2023

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary:
We used microarrays to investigate gene expression changes in leukemic bone marrow from Pax5+/-;Myd88+/- mice compared with bone marrow precursor B cells from WT mice and to study the effect of Myd88 downregulation in healthy Pax5+/- proB cells.
The initial steps of B-cell acute lymphoblastic leukemia (B-ALL) development usually pass unnoticed in children; germline or somatic alterations affecting transcription factor genes cause the appearance of preleukemic cells still compatible with normal hematopoiesis, and preclinical studies have shown that immune stressors can trigger the malignant transformation of these otherwise silent preleukemic precursors to full-blown B-ALL. Understanding how exposure to immune stressors drives this conversion is a longstanding and unsolved challenge. Here we unveiled a specific “gene/environmental factor” interaction triggering B-ALL development. Our data show that B-ALL development falls into the category of cancers associated with dysregulation of innate immunity, which plays a driving role in the clonal evolution of pre-malignant B-cell precursors toward B-ALL following exposure to an immune stress. Transcriptional profiling of B-ALL allowed the identification of an inflammation-dependent role for Myd88 as a key player in this process. A preleukemic B-cell-autonomous role was evidenced by a significant increase in B-ALL incidence upon Myd88 dowregulation in the leukemia-prone Pax5+/- model. Likewise, early innate immune response induction by Toll-like receptor (TLR) ligation during the preleukemic phase in Pax5+/- mice resulted in a significant delay of B-ALL development. These findings identify a central role for innate immunity dysregulation in B-ALL, with important implications for the understanding and potential therapeutic targeting of the preleukemic state in children.

overall_design: Leukemic bone marrow cells from 6 Pax5+/-;Myd88+/-  mice. Healthy proB cells from 4 wild-type (WT) mice, 4 Pax5+/- mice, 4 Pax5+/-;Myd88+/- mice, and 4 Pax5+/-;Myd88-/-. Healthy Bone Marrow proB and preB cells from 4 healthy wild-type mice. Leukemic bone marrow cells from 6 Pax5+/- mice.

first: Marta

last: Isidro-Hernández

first: Ana

last: Casado-García

first: Ninad

last: Oak

first: Silvia

last: Alemán-Arteaga

first: Belén

last: Ruiz-Corzo

first: Jorge

last: Martínez-Cano

first: Andrea

last: Mayado

first: Elena

middle: G

last: Sánchez

first: Oscar

last: Blanco

first: M

last: Gaspar

first: Alberto

last: Orfao

first: Diego

last: Alonso-López

first: Javier

last: De Las Rivas

first: Susana

last: Riesco

first: Pablo

last: Prieto-Matos

first: África

last: González-Murillo

first: Francisco

middle: J

last: Criado

first: María

last: Cenador

first: Manuel

last: Ramírez-Orellana

first: Jun

last: Yang

last: de Andrés

first: Carolina

last: Vicente-Dueñas

first: César

last: Cobaleda

first: Kim

last: Nichols

last: Sánchez-García


title: Transcriptomic analysis of cortex tissue from neuron-specific Bmal1 KO mice

status: Public on Aug 23 2023

first: Eric

last: Tycksen

summary: The circadian clock protein Bmal1 is critical for maintain circadian transcriptional funciton and rhythms. Global deleiton of Bmal1 renders whole mice behaviorally arrhythmic. However, cell-specific deletion of Bmal1 can reveal specific transcripts regulated by Bmal1 in a cell-specific manner. Here we used a BAC-transgenic Camk2a-iCre line to delete Bmal1 in a pan-neuronal manner. This mouse has previously been shown to have widespread Bmal1 deletion in neurons and to be arrhythmic (PMID: 25525750).  We performed bulk RNAseq on cerebral cortex tissue from Camk2a-iCre+;Bmal1(fx/fx) and Cre- control littermates. Appropriate Bmal1 targets were disregulated as expetced in these mice. Pathways analysis revealed transcripts involved in Parkinson Disease and oxidative phosphorylation to be enriched.

overall_design: Camk2a-iCre+;Bmal1(fx/fx) and Cre-;Bmal1(fx/fx) control mice N=3/genotype, were kept under normal 12:12 light:dark conditions until 4 months of age, then anesthetized and perfused with PBS. Cerebral cortex tissue was dissected and frozen, then later subjected to bulk RNAseq analysis. These Camk2a-iCre mice are BAG transgenic as previously described (see Izuma et al PMID: 25525750), which have pan-neuronal Bmal1 deletion and circaidan disruption.

first: Erik

middle: S

last: Musiek

first: Joseph

last: Takahashi

first: Mariko

last: Izumo


title: Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis II

status: Public on Aug 11 2023

city: Berkeley

first: Benjamin

last: Cole

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

summary: The symbiotic interaction of plants with arbuscular mycorrhizal fungi (AM fungi) is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both M. truncatula and R. irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated spatially-registered single-cell maps of interacting cells revealed major infected and uninfected plant root cell types. We observed that cortical cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi, indicating dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. Our study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.

overall_design:
Tissue from R. irregularis - inoculated and non-inoculated M. truncatula root tissue was cryosectioned and prepared for and analyzed with the 10X Genomics Visium platform.
wt.integrated2.rds - Seurat Object with all seven medicago root spatial datasets generated for this study (9 inoculated, 8 not-inoculated)
myc.integrated.rds - Seurat Object with only spatial datasets from R. irregularis inoculated root tissue (9)
wt.integrated2.meta.cvs - metadata for 'wt.integrated2' Seurat Object
myc.integrated.meta.cvs - metadata for 'myc.integrated' Seurat Object

first: Karen

last: Serrano

first: Margot

last: Bezrutczyk

first: Thai

last: Dao

first: Danielle

last: Goudeau

first: Ronan

last: O'Malley

first: Rex

last: Malmstrom

first: Axel

last: Visel

first: Henrik

middle: V

last: Scheller


title: Whole transcriptome profiling of murine Hic-5 HET and KO Cancer Associated Fibroblasts (CAFs)

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: To investigate the role of the differential expression of Hydrogen peroxide-inducible clone 5 (Hic-5) gene on CAFs, primary tumor cells from MMTV-PyMT mice that were heterozygous (HET) or knockout (KO) for the Hic-5 gene were freshly isolated and grown in culture. RNA was isolated using Trizol reagent. Sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit RiboZero Gold (Illumina), using 1 microgram of total RNA as input. Libraries were pooled and sequenced on the NextSeq 500 instrument (Illumina), with a single end 1 x 75 bp reads using a High Output cycle reagent kit.  FASTQ files were processed to remove adapter sequences and aligned using Bowtie2 version 2.2.5 to the mouse mm10 genome and quantified to  Ensembl Transcripts release 86.  Data were normalized by RPKM. Differential gene expression analyses were performed in Partek Flow using Gene Specific Analysis (GSA) method.

overall_design: Differential expression of technical triplicates of cultured mouse CAFs with either Hic-5 heterozygous (HET) or Hic-5 knockout (KO) genotypes.

first: Weiyi

last: Xu

first: Gregory

last: Goreczny

first: Ian

last: Forsythe

first: Theresa

last: Stowell

first: Christopher

last: Turner


title: Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis