title: Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network [ATAC-Seq]

first: Mattias

last: Mannervik

first: George

last: Hunt

first: Roshan

last: Vaid

last: Pirogov

first: Alexander

last: Pfab

first: Christoph

last: Ziegenhain

first: Rickard

last: Sandberg

first: Johan

last: Reimegård


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV10]

status: Public on Nov 21 2023

city: New York

first: Ellie

last: Ivanova

state: NY

address: 550 First Ave

department: Pathology

country: USA

institute: NYU Langone

type: Expression profiling by high throughput sequencing

summary: SARS-CoV-2 infection and vaccination elicit potent immune responses. Our study presents a comprehensive multimodal single-cell dataset of peripheral blood of patients with acute COVID-19 and of healthy volunteers before and after receiving the SARS-CoV-2 mRNA vaccine and booster. We compared host immune responses to the virus and vaccine using transcriptional profiling, coupled with B/T cell receptor repertoire reconstruction. COVID-19 patients displayed an enhanced interferon signature and cytotoxic gene upregulation, absent in vaccine recipients. These findings were validated in an independent dataset. Analysis of B and T cell repertoires revealed that, while the majority of clonal lymphocytes in COVID-19 patients were effector cells, clonal expansion was more evident among circulating memory cells in vaccine recipients. Furthermore, while clonal αβ T cell responses were observed in both COVID-19 patients and vaccine recipients, dramatic expansion of clonal gdT cells was found only in infected individuals. Our dataset enables comparative analyses of immune responses to infection versus vaccination, including clonal B and T cell responses. Taken together, our comparative analysis shows that vaccination induces a robust adaptive immune response, including a durable clonal B and T cell response, without the severe inflammation associated with infection.

overall_design: We profiled crculating immune cells from five adults with acute COVID-19 infection and nine healthy adults, seven of whom received theBNT162b2 vaccine. For three of the vaccine recipients, samples were also collected before and after receiving a booster. Samples were taken at multiple time points, resulting in a total of 42 post-vaccination and 9 post-infection samples

middle: N

first: Jasmine

last: Shwetar

first: Joseph

middle: C

last: Devlin

first: Terkild

middle: B

last: Buus

first: Sophie

last: Gray-Gillard

first: Akiko

last: Koide

first: Amber

last: Cornelius

first: Marie

middle: I

last: Samanovic

first: Alberto

last: Herrera

first: Eleni

middle: P

last: Mimitou

first: Chenzhen

last: Zhang

first: Trishala

last: Karmacharya

first: Ludovic

last: Desvignes

first: Niels

last: Ødum

first: Peter

last: Smibert

first: Robert

middle: J

last: Ulrich

first: Mark

last: Mulligan

first: Shohei

first: Kelly

middle: V

last: Ruggles

first: Ramin

middle: S

last: Herati

first: Sergei

last: Koralov


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV9]

first: Ellie

last: Ivanova

first: Jasmine

last: Shwetar

first: Joseph

last: Devlin

first: Terkild

last: Buus

first: Sophie


title: H3K27 acetylation profiling of B cells from Mb1Cre and Mct1f/fMb1Cre mice

status: Public on Nov 22 2023

city: Beijing

first: Ligong

last: Chen

address: Shuangqing Road No.30

country: China

institute: tsinghua university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using ChIP-seq we identified H3K27 acetylation loci in B cells from Mb1Cre and Mct1f/fMb1Cre mice

overall_design: ChIP-seq was performed in B cells from Mb1Cre and Mct1f/fMb1Cre mice


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV7]

last: Gray-Gillard

first: Akiko

last: Koide

first: Amber

last: Cornelius

first: Marie

last: Samanovic

first: Alberto

last: Herrera

first: Eleni

first: Chenzhen


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV6]

last: Mimitou

last: Zhang

first: Trishala

last: Karmacharya

first: Ludovic

last: Desvignes

first: Niels

last: Ødum

first: Peter

first: Robert

first: Mark


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV5]

first: Ellie

first: Jasmine

last: Smibert

last: Ulrich

last: Mulligan

first: Shohei

first: Kelly

last: Ruggles

first: Ramin

last: Herati

first: Sergei


title: Calprotectin blockade inhibits long-term vascular pathology following peritoneal dialysis-associated bacterial infection.

city: Cardiff

first: Anne-Catherine

last: Raby

state: Cardiff

address: Heath Park, Academic Avenue

country: United Kingdom

institute: Cardiff University

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

overall_design: Refer to individual Series


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection

last: Ivanova

overall_design:
Refer to individual Series

Seurat object: cv19_combined_obj.rds. Contains processed data for all experiments in SuperSeries


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV4]

last: Shwetar

first: Joseph

last: Devlin

first: Terkild

last: Buus

first: Sophie

last: Gray-Gillard

first: Akiko

first: Amber

first: Marie

last: Koralov


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV2]

last: Koide

last: Cornelius

last: Samanovic

first: Alberto

last: Herrera

first: Eleni

last: Mimitou

first: Chenzhen

first: Trishala

first: Ludovic

first: Niels


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV1]

first: Ellie

first: Jasmine

last: Zhang

last: Karmacharya

last: Desvignes

last: Ødum

first: Peter

last: Smibert

first: Robert

first: Mark

first: Shohei


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV3]

first: Joseph

first: Terkild

last: Ulrich

last: Mulligan

first: Kelly

last: Ruggles

first: Ramin

last: Herati

first: Sergei


title: Genome-wide expression analysis in Control and Atg5-deficient eosinophils.

city: Bern

first: Aref

last: Hosseini

state: Switzerland

address: Inselspital, INO-F

country: Switzerland

institute: Institute of Pharmacology

summary: Depletion of autophagy-associated protein 5 (Atg5), specifically within the eosinophil lineage in mice, resulted in increased body weight, impaired glucose metabolism, and structural alterations in adipose tissue. Our findings highlight that Atg5 influences the functional activity of eosinophils within adipose tissue rather than their quantity. To gain a deeper understanding of the molecular mechanisms underlying ATG5's role in eosinophils, we conducted total RNA-seq analyses on control and Atg5-deficient eosinophils isolated from both bone marrow and blood of mice.

overall_design: RNA expression profiling of control and Atg5-deficient eosinophils isolated from bone marrow and blood of threeAtg5flox/floxeoCreIl5tg mice and three eoCreIl5tg mice as control.

first: Yousefi

last: Shida

first: Simon

last: Hans-Uwe


title: Deciphering the age-dependent changes of pulmonary fibroblasts in mice by single-cell transcriptomics

city: Xiamen

first: Lingjuan

address: Xiangan South Street

institute: Xiamen University

summary: In brief, lung resident cells were isolated from lung of mice and 10x Genomics single cell RNAseq was applied to identify distinct cell populations. Low quality cells and outliers were discarded, and only ～22,826 viable cells were used for downstream analysis. These included ~5,237 cells – NB(10days mice); ~4,804 cells – Adult-M(2months mice); ~6,561cells-SD-10M (10month mice) ; ~6,224cells-SD-1d5Y (18month mice). Unsupervised clustering and gene expression were visualized with the Seurat 2.0 on R studio, and assignment of cell clusters was based on expression of validated marker genes. Subsequent in-depth analysis was assisted by GENE DENOVO Inc (Guangzhou, China). Overall, we found that a specific lung fibroblast population, We present a single-cell transcriptomic atlas encompassing lung tissues derived from mice at various stages of aging, uncovering substantial shifts in fibroblast differentiation and immune regulation throughout the aging process.

overall_design: Lung biopsies were collected from 4 groups, including  – NB(10days mice); – Adult-M(2months mice); SD-10M (10month mice) ; SD-1d5Y (18month mice) C57BL/6 mice.

first: Rundong

last: Wu


title: Whole genome duplication in arachnids - what happened next?

city: Berlin

first: Lauren

last: Sumner-Rooney

address: Museum für Naturkunde, FB1, Invalidenstrasse 43

country: Germany

institute: Museum für Naturkunde

summary: About 430 million years ago spiders and scorpions evolved from a common ancestor that had experienced a whole genome duplication (WGD) The genetic remnants of this WGD event (genes called ohnologs) can still be found in the genome of the approximately 45,000 species of these animals alive today and these ohnologs may have contributed to their adaptation and diversification. Interestingly, the WGD in arachnids like scorpions and spiders was contemporary with independent WGDs in vertebrates. This presents an opportunity to compare these events to determine if there are general principals underlying the outcomes of WGDs and their contribution to animal diversification. Therefore, the aims of this project are to identify arachnid ohnologs, explore how they have contributed to the evolutionary success of these animals, and compare the outcomes of this event to WGD in vertebrates. This includes sequencing new genomes and transcriptomes of species occupying key phylogenetic positions.

overall_design: To provide a chromosome-level genome assembly for the key early-diverging clade Synspermiata, we generated RNA-Seq of a whole adult to assist in annotation

first: Daniel

last: Leite

first: Alistair

last: McGregor

first: Anna

last: Schoenauer

first: Luis

last: Baudouin Gonzalez


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV14]

first: Ellie

last: Ivanova

first: Jasmine

last: Shwetar

last: Devlin

last: Buus

first: Sophie

last: Gray-Gillard

first: Akiko

last: Koide

first: Amber

last: Cornelius

first: Marie

last: Samanovic

first: Alberto

last: Herrera

first: Eleni

last: Mimitou

first: Chenzhen

last: Zhang

first: Trishala

last: Karmacharya

first: Ludovic

first: Niels

first: Peter

first: Robert

first: Mark

last: Koralov


title: Modulation of miR-29 influences myocardial compliance likely through coordinated regulation of calcium handling and extracellular matrix

city: Iowa City

first: Ethan

middle: J.

last: Anderson

state: Iowa

address: 180 South Grand Ave, CPB 548

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

summary: MicroRNAs (miRs) control the expression of diverse subsets of target mRNAs, and studies have found miR dysregulation in failing hearts. Expression of miR-29 is abundant in heart, increased with aging, and altered in cardiomyopathies. Prior studies demonstrate that miR-29 reduction via genetic knockout or pharmacologic blockade can blunt cardiac hypertrophy and fibrosis in mice. Surprisingly, this depended on specifically blunting miR-29 actions in cardiomyocytes versus fibroblasts. To begin developing more translationally-relevant vectors, we generated a novel transgene-encoded miR-29 inhibitor (TuD-29) that can be incorporated into a viral-mediated gene therapy for cardioprotection. Herein, we corroborate that miR-29 expression and activity is higher in cardiomyocytes versus fibroblasts and demonstrate that TuD-29 effectively blunts hypertrophic responses in cultured cardiomyocytes and mouse hearts. Furthermore, we found that adeno-associated viral (AAV)-mediated miR-29 overexpression in mouse hearts induces early diastolic dysfunction, whereas AAV:TuD-29 treatment improves cardiac output by increasing end-diastolic and stroke volumes. Integration of RNA-seq and miR-target interactomes reveals that miR-29 regulates genes involved in calcium handling, cell stress and hypertrophy, metabolism, ion transport, and extracellular matrix remodeling. These investigations support a likely versatile role for miR-29 in influencing myocardial compliance and relaxation, potentially providing a unique therapeutic avenue to improve diastolic function in heart failure patients.

overall_design: This experiment used RNA-seq to assess differential gene expression in mouse heart after acute miR-29 overexpression. C57BL6/J male mice aged 3-5 weeks old, were randomized and injected IV via jugular vein with cardiotropic AAV2/9 that co-expresses the primary miR-29a transcript and GFP or an AAV2/9:GFP control virus (n=4 each). After 3 weeks post-injection, mice were euthanized, hearts dissected, and snap frozen in liquid nitrogen. Total RNA was extracted using Trizol, DNAse digested, and libraries were prepared for RNA sequencing using Illumina TruSeq Stranded kit with 500 ng of input RNA. Libraries were multiplexed and sequenced on a NovaSeq 6000 with an entire SP flowcell at a read depth of 11M reads per sample (90% aligned). Pseudoalignments to mm10 (GRCm38) and quantification were performed using the Kallisto/Sleuth pipeline aggregating on Ensembl gene ID, and pairwise differential gene expressions were calculated between the AAV:GFP control samples and the AAV:miR29a samples.  Gene expression data are expressed as "scaled_reads_per_base" where the average number of reads mapping to each base across the whole gene, and beta values are natural log fold change.

first: Jared

last: McLendon

first: Ryan

last: Boudreau


title: Chemical induction of hepatocyte revitalization in mouse hepatocytes [RNA-seq 2]

first: pengyan

last: lin

state: Beijing

address: No.5 Yiheyuan Road Haidian

department: College of Future Technology,

institute: Peking university

summary:
We  examined how each chemical contributed to hepatocyte revitalization by removing each component of the 5C induction cocktail individually.
We then compared deach chemical contributed to hepatocyte revitalization by removing each component of the 5C induction cocktail individually

overall_design: Comparative gene expression profiling analysis of RNA-seq data for damaged hepatocytes treated by removing each component of the 5C induction cocktail individually

first: Pengyan

last: Lin

first: Yunfei

last: Bai

first: Xinxin

last: Nian

first: Jun

last: Chi

first: Tianzhe

last: Chen

first: Jing

first: Wenpeng

first: Bin

last: Zhou

first: Yang

last: Liu

last: Zhao


title: Chemical induction of hepatocyte revitalization in mouse hepatocytes [RNA-seq 1]

summary: We then compared whole transcriptome bulk RNA-seq data of dHeps isolated from CCl4-injured mice and treated with either 5C, 3C, or DMSO. The expression of hepatocyte-enriched TFs and hepatocyte functional genes  was upregulated in both the 5C and 3C groups, while mesenchymal markers (Acta2, Mmp3), inflammatory-related genes (Cxcl10, Ecm1, Ccl6, and Cd68), and oxidative stress-related genes (Ncf2 and Ncf1), were down-regulated compared with their expression in the DMSO control group

overall_design: Comparative gene expression profiling analysis of RNA-seq data for damaged hepatocytes treated by 5C cocktail (i.e., Salidroside 5 µM, CID755673 50 µM, Forskolin 2 µM, GSK429286A 2 µM, and ETC-1002 5 µM), a 3C cocktail (i.e., CID755673 50 µM, GSK429286A 2 µM, and ETC-1002 5 µM), or the solvent control (DMSO) at day16.


title: ATAC-seq data for damaged hepatocytes treated by a 3C cocktail [ATAC-seq]

summary:
To better understand the mechanism by which 3C induced revitalization, we next conducted epigenetic analysis to identify differences in transcriptional regulation.
ATAC-seq data revealed that hepatocyte-enriched TFs, such as Hnf4a, Hnf1b, Hhex, and Prox1, and genes associated with epithelial cell proliferation and liver development were located in loci with open chromatin, whereas markers associated with mesenchymal transition, cell cycle arrest, apoptosis and inflammation (e.g., Col1a1, Mmp2, Ccl28, CxCr4, Ncf2) were located in closed chromatin loci in the 3C group

overall_design: Comparative chromation states of ATAC-seq data for damaged hepatocytes treated by a 3C cocktail (i.e., CID755673 50 µM, GSK429286A 2 µM, and ETC-1002 5 µM), or the solvent control (DMSO) at day16.


title: Developmental Basis of SHH Medulloblastoma Heterogeneity

city: Cambridge

first: Maxwell

last: Gold

state: MA

address: 21 Ames St

institute: MIT

summary: Single-Nucleus RNA-Sequencing and Single-Cell RNA-Sequencing from SHH Medulloblastoma Tumors with MBEN histology

overall_design: snRNA-Seq and scRNA-Seq from SHH MB tumors across histological subtypes to characterize the cell types present in these tumors.

first: Michael

middle: D

last: Taylor

first: Ernest

last: Fraenkel

first: Olivier

last: Ayrault


title: Single-cell characterization of human glioblastoma reveals regional differences in tumor-infiltrating leukocyte activation

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: We performed scRNA-seq on patient-matched biopsies from the tumor center and the peripheral infiltration zone of five primary glioblastoma (GBM) patients. Additionally, peripheral blood mononuclear cells (PBMC) of the same patients were included in the scRNAseq analysis to explore the transcriptional changes occurring during tumor infiltration of circulating immune cells.

overall_design:
Single-cell suspensions were generated from sorted CD45 and/or CD11B positive cells originating from glioblastoma tumor tissue or blood from 5 patients, and were loaded on separate wells of a 10X Genomics Chromium Single Cell Controller.

>>>Submitter states that raw data are unavailable due to patient privacy concerns.<<<

first: Philip

last: Schmassmann

first: Gregor

last: Hutter

first: Julien

last: Roux


title: DDR2-regulated arginase activity in ovarian cancer-associated fibroblasts promotes collagen production and tumor progression

status: Public on Nov 20 2023

city: St. Louis

first: Katherine

last: Fuh

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

summary: DDR2 regulates collagen production by CAFs in the tumor microenvironment by controlling the transcription of arginase 1, and CAFs are a major source of arginase activity and L-arginine metabolites in ovarian cancer models.  We aimed to determine which cell populations are DDR2 and Arg1 positive in the ID8 p53-/- BRCA2-/- tumor model

overall_design: Omental tumors from WT C57bl6 female mice bearing  ID8 p53-/- BRCA2-/- tumors were collected and dissociated and single-cell RNA sequencing was performed on the samples.

first: Favour

last: Akinjiyan


title: Gene expression profile at single cell level of liver cells from healthy mice or CCl4-injured mice [scRNA-seq]

first: pengyan

last: lin

summary: We characterized the phenotypes of dHeps from CCl4-induced chronic liver injury model mice (C57BL/6 background).

overall_design: We sequenced the hepatocytes isolated from CCl4 model and healthy livers using a 10Χ Chromium workflow and performed unsupervised clustering,

first: Pengyan

last: Lin

first: Yunfei

last: Bai

first: Xinxin

last: Zhang


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV8]

first: Ellie

last: Ivanova

first: Jasmine

last: Shwetar

first: Joseph

last: Devlin

first: Terkild

last: Buus

first: Sophie

last: Gray-Gillard

first: Akiko

last: Koide

first: Amber

last: Cornelius

first: Marie

last: Samanovic

first: Alberto

last: Herrera

first: Eleni

last: Mimitou

first: Chenzhen

first: Trishala

last: Karmacharya

first: Ludovic

last: Desvignes

first: Niels

last: Ødum

first: Peter

last: Smibert

first: Robert

last: Ulrich

first: Mark

last: Mulligan

first: Shohei

first: Kelly

last: Ruggles

first: Ramin

last: Herati

first: Sergei

last: Koralov


title: The effector program of human CD8 T cells can promote both target cell killing and tissue remodeling (HaCaT)

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

summary: CD8 T lymphocytes are classically viewed as cytotoxic T cells. Whether human CD8 T cells can, in parallel, induce a regenerative program is not completely understood. Here, we have studied antigen-specific assay systems, which revealed that human CD8 T cells not only mediated cytotoxicity, but also promoted bystander fibroblast and epithelial cell activation, leading to the production of tissue regenerative factors such as Amphiregulin (Areg). Tissue remodeling could be inhibited by blocking the epidermal growth factor receptor or the effector cytokines IFN- and TNF. Using single-cell chromatin accessibility and gene expression analysis, we identified a tissue-resident CD8 T cell population in healthy donor skin and adipose tissue with an effector program promoting Areg, TNF and IFNg expression, and a TCR-linkage analysis demonstrated a strong clonal relation between tissue and blood PD1+TIGIT+TOX+ CD8 T cells with tissue remodeling abilities. This regenerative program was also present in anti-cancer associated CD8 populations including chimeric antigen receptor (CAR) CD8 T cells. Once activated, the tissue regenerative program of human CD8 T cells enhanced tumor spheroid, as well as primary liver/bile duct organoid growth. Our findings may help to understand the conflicting CD8 biology in the tumor micromilieu and become relevant for the design of CD8 T-cell therapies for solid tumors.

overall_design: Co-culture of epithelial cells (HaCaT) with cell-free supernatant of influenza-specific T cells cultured on fibroblasts pulsed with varying peptide concentrations (influenza peptide)

first: Michael

last: Delacher

first: Markus

last: Feuerer

first: Lisa

last: Schmidleithner

first: Agnes

last: Hotz-Wagenblatt

first: Nicholas

last: Strieder


title: Chemically induced revitalization of damaged hepatocytes for regenerative liver repair

first: pengyan

last: lin

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Chemical induction of hepatocyte revitalization in injured human hepatocytes [RNA-seq 3]

summary: 3C cocktail could revitalize human hepatocytes displaying apoptotic and EMT phenotypes induced by TGF-β, and promote hepatocyte proliferation and maintenance

overall_design: RNA-seq analysis in cells collected after 3 days of DMSO or 3C treatment revealed global transcriptomic changes under 3C treatment compared with that in control cells

first: Pengyan

last: Lin

first: Yunfei

last: Bai

first: Xinxin

last: Nian

first: Jun

last: Chi

first: Tianzhe

last: Chen

first: Jing

last: Zhang

first: Wenpeng

first: Bin

last: Zhou

first: Yang

last: Liu

last: Zhao


title: Effect of PTCHD1 SNV and truncating variants on gene expression during differentiation of iPSCs to neural progenitor cells

status: Public on Nov 19 2023

city: Nedlands

first: Kathryn

middle: Olivia

last: Farley

state: WA

address: 15 Hospital Avenue

department: Precision Health

country: Australia

institute: Telethon Kids Institute

summary:
To investigate whether a SNV in the gene PTCHD1 was disease causative, we introduced the variant to KOLF-2 iPSCs via CRISPR/Cas9 homology directed repair. Three experimentally matched SNV and WT clones and two clones with truncating mutations were generated, and neural induction was induced.
We then performed gene expression profiling analysis using data obtained from RNA-seq of these cells at two timepoints (day 0 and day 24 of neural induction).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PTCHD1_WT, SNV and trunc KOLF-2 iPSCs and their derived neural progenitor cells.

first: Farley

last: Kathryn

first: Forbes

last: Catherine

first: Shaw

last: Nicole

first: Kuzminski

last: Emma

first: Ward

last: Michelle

first: Baynam

last: Gareth

first: Fear

last: Vanessa

first: Lassmann

last: Timo


title: Effect of normal and COX6A2-deficient human pluripotent stem cells on gene expression during cardiomyocyte differentiation.

status: Public on Nov 18 2023

city: Yantai

first: Mengqi

last: Jiang

address: 346 Guanhai Road, Laishan District, Yantai City, Shandong Province, China

institute: Binzhou Medical University

summary: Cardiac remodeling is the initiating factor for the development of heart failure, which can result from various cardiomyopathies. Cytochrome c oxidase subunit 6A2 (COX6A2) is one of the components of cytochrome c oxidase that drives oxidative phosphorylation. We here report a COX6A2-deficient human cardiac myocyte (CM) model that mimicked the human COX6A2 homozygous mutation and determined the effects of COX6A2 dysfunction and its underlying mechanism.COX6A2 gene knockout did not affect the pluripotency and differentiation efficiency of hiPSCs.  Myocardial cells with a COX6A2 gene knockout showed abnormal energy metabolism, increased oxidative stress levels, abnormal calcium transport activity, and decreased contractility.  In addition, L-carnitine and trimetazidine significantly improved energy metabolism in the COX6A2-deficient human myocardial model. Taken together, our data provide a COX6A2-deficient human cardiomyocyte model that exhibits abnormal energy metabolism, this model represents an important tool to gain insight into the mechanism of action of energy metabolism disorders resulting in myocardial remodeling, elucidate the gene-phenotype relationship of COX6A2 deficiency, and facilitate drug screening.

overall_design: To investigate the function of COX6A2 in  the pathogenesis of myocardial remodeling, we established a COX6A2-deficient human cardiac myocyte (CM) model. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells at one time point. Comparative gene exprission profiling analysis of RNA-seq data for cells.

first: Yun

last: Bai


title: The effector program of human CD8 T cells can promote both target cell killing and tissue remodeling (MRC5)

first: LIT

last: NGS-Core

overall_design: Co-culture of fibroblast MRC5 with  influenza-specific T cells cultured on fibroblasts pulsed with varying peptide concentrations (influenza peptide)

first: Michael

last: Delacher

first: Markus

last: Feuerer

first: Lisa

last: Schmidleithner

first: Agnes

last: Hotz-Wagenblatt

first: Nicholas

last: Strieder


title: scRNA-seq analysis of CD11c+ cells from bronchoalveolar lavage fluid during the IAV (PR/8, H1N1) infection course

city: Giessen

first: Rolf

middle: David

last: Glaser

address: Aulweg 128

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-Universität Giessen

summary: CX3CR1pos monocytes are mobilized upon infection and undergo monocyte-to-macrophage transition in inflamed tissues. Using scRNA-seq of CD11c+ cells from bronchoalveolar lavage fluid (BALF) infected with IAV (PR/8, H1N1 ,we demonstrate that, during severe viral pneumonia, bone marrow-derived macrophages (BMDM) pass co-ordinated trajectories of pro-inflammatory-to-tissue-healing phenotypes, before differentiating into tissue-resident alveolar macrophages, that retain a long-term tissue-protective phenotype.

first: Susanne

last: Herold

first: Learta

last: Pervizaj-Oruqaj

first: Marek

last: Bartkuhn


title: Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

state: CA

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12. In eukaryotes and their viruses, TnpB homologs occur as two distinct types, Fanzor1 and Fanzor2. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, revealing that a clade of IS607 TnpBs with unusual active site arrangement found primarily in cyanobacteria likely gave rise to both types of Fanzors. The widespread nature of Fanzors imply that the properties of this particular group of IS607 TnpBs  were particularly suited to adaptation and evolution in eukaryotes and their viruses. Biochemical analysis of a prokaryotic IS607 TnpB and virally encoded Fanzor1s revealed features that may have fostered co-evolution between TnpBs/Fanzors and their cognate transposases. These results provide insight into the evolutionary origins of a ubiquitous family of RNA-guided proteins that shows remarkable conservation across the three domains of life.

sample_organism:
Escherichia coli
Spodoptera frugiperda

platform_organism:
Escherichia coli
Spodoptera frugiperda

overall_design: We performed small RNA-sequencing experiments to examine reRNA expression in vivo by infecting S. frugiperda larvae with SfAV. To do so, we pricked the S. frugiperda larvae with an SfAV contaminated needle to mimic oviposition of parasitoids, which effectively transmits the virus. As ascoviruses primarily replicate in the hemolymph, we isolated and sequenced small-RNAs from hemolymph samples from infected S. frugiperda larvae. Mapping of small-RNA reads to the SfAV genome revealed that the reRNA of the Fanzor was one of the most highly transcribed small RNAs in the SfAV genome (accession: AM398843). Consistent with previously reported kinetics of ascovirus infection, we found that reRNA abundance increased 5 days post infection (dpi) compared to 2 dpi, when infected larvae began to develop a cloudy hemolymph caused by budded viral vesicles. In both samples, we observed expression of an RNA that mapped to the right end (RE) of the transposons and extended further downstream into the flanking DNA sequence.

first: Peter

middle: H

last: Yoon

first: Petr

last: Skopintsev

first: Honglue

last: Shi

first: LinXing

last: Chen

first: Benjamin

middle: A

last: Adler

first: Muntathar

last: Al-Shimary

first: Rory

last: Craig

first: Kenneth

last: Loi

first: Evan

last: DeTurk

first: Zheng

last: Li

first: Jasmine

last: Amerasekara

first: Hunter

last: Nisonoff

first: Kai

first: Arushi

last: Lahiri

first: Ron

last: Boger

first: Steve

last: Jacobsen

first: Jillian

middle: F

last: Banfield

first: Jennifer

last: Doudna


title: Filamentation and Biofilm Formation are Regulated by the Phase-Separation Capacity of Network Transcription Factors in Candida albicans

city: Providence

first: Collin

last: Ganser

state: Rhode Island

address: 171 Meeting St. Room 571

department: Molecular Microbiology and Immunology

institute: Brown University

summary: The ability of the fungus Candida albicans to filament and form biofilms contributes to its burden as a leading cause of hospital-acquired infections.  Biofilm development involves an interconnected transcriptional regulatory network (TRN) consisting of nine transcription factors (TFs) that bind both to their own regulatory regions and to those of the other network TFs.  Here, we show that seven of the nine TFs in the C. albicans biofilm network contain prion-like domains (PrLDs) that have been linked to the ability to form phase-separated condensates.  Construction of PrLD mutants in four biofilm TFs reveals that these domains are essential for filamentation and biofilm formation in C. albicans.  Moreover, biofilm PrLDs promote the formation of phase-separated condensates in the nuclei of live cells, and PrLD mutations that abolish phase separation (such as the removal of aromatic residues) also prevent biofilm formation.  Biofilm TF condensates can selectively recruit other TFs through PrLD-PrLD interactions and can co-recruit RNA polymerase II, implicating condensate formation in the assembly of active transcriptional complexes.  Finally, we show that PrLD mutations that block the phase separation of biofilm TFs also prevent filamentation in an in vivo model of gastrointestinal colonization.  Together, these studies associate transcriptional condensates with the regulation of filamentation and biofilm formation in C. albicans, and highlight how targeting of PrLD-PrLD interactions could prevent pathogenesis by this species.

overall_design:
C. albicans biofilm TF PrLDs were removed or mutated to determine their contribution to biofilm formation, filamentation, and phase separation.
Efg1 and Brg1 WT and YF-to-S mutants were grown under filament-inducing conditions, Spider medium at 37°C for 6 h, and measured for yeast vs. hyphal cells and harvested for RNA. RNA sequencing was performed on all strains (in triplicate) to measure gene expression.

first: Mae

last: Staples

first: Maureen

last: Dowell

first: Corey

last: Frazer

first: Joseph

last: Dainis

first: Shabnam

last: Sircaik

first: Richard

last: Bennett


title: Co-adjuvanting DDA/TDB liposomes with a TLR7 agonist allows for IgG2a/c class-switching in the absence of Th1 cells

status: Public on Nov 17 2023

city: Copenhagen

first: Julie

last: Zimmermann

address: Artillerivej 5

country: Denmark

institute: Statens Serum Institut

summary: Class-switching to IgG2a/c in mice is a hallmark response to intracellular pathogens. T cells can promote class-switching and the predominant pathway for induction of IgG2a/c antibody responses has been suggested to be via stimulation from Th1 cells. We previously formulated CAF®01 (cationic liposomes containing dimethyldioctadecylammonium bromide (DDA) and Trehalose-6,6-dibehenate (TDB)) with the lipidated TLR7/8 agonist 3M-052 (DDA/TDB/3M-052), which promoted robust Th1 immunity in newborn mice. When testing this adjuvant in adult mice using the recombinant Chlamydia trachomatis (C.t.) vaccine antigen CTH522, it similarly enhanced IgG2a/c responses compared to DDA/TDB, but surprisingly reduced the magnitude of the IFN-g+ Th1 response in a TLR7 agonist dose-dependent manner. Single cell RNA-sequencing revealed that DDA/TDB/3M-052 liposomes initiated early transcription of class-switch regulating genes directly in pre-germinal center B cells. Mixed bone marrow chimeras further demonstrated that this adjuvant did not require Th1 cells for IgG2a/c switching, but rather facilitated TLR7-dependent T-bet programming directly in B cells. This study underlines that adjuvant-directed IgG2a/c class-switching in vivo can occur in the absence of T cell help, via direct activation of TLR7 on B cells and positions DDA/TDB/3M-052 as a powerful adjuvant capable of eliciting type I-like immunity in B cells without strong induction of Th1 responses.

overall_design: Mice were immunized on day 0 and day 42 subcutaneously (s.c.) at the base of the tail with 2 μg recombinant CTH522 antigen in a volume of 200 μl TRIS/trehalose buffer (isotonic, pH 7.4) per immunization. Adjuvant doses were as follows: DDA/TDB liposomes (dose 250 μg/50 μg (DDA/TDB)) and DDA/TDB/3M-052_M liposomes (dose of 250 μg/50 μg (DDA/TDB)) with incorporation of 3M-052 in doses of 2 μg. TRIS (Naive mice) received 200 μL TRIS buffer. The lymph node where investigated on day 44. For each vaccine group, cells from the Lymph node of three mice were pooled and run on the 10x Chromium (10x Genomics) following a library preparation with Chromium Next GEM Single cell 3’ Reagent Kit v.3.1 (10x Genomics). Libraries were sequenced on the NovaSeq 6000 with the NovaSeq 6000 SP reagent kit v1.5 (Illumina). BCL files were converted to FASTQ files with bcl2fastq (Illumina) and data were then processed through Cellranger (10x Genomics, v6.1.2) and aligned to the mm10 genome. The raw transcript count matrix generated from alignment was loaded into R (v4.3.0) using the Seurat (v.4.3.0) package. A Seurat object was created (min.cells=3, min.features=200). Data were filtered (nFeature_RNA > 300 & nFeature_RNA < 3000 & percent.mt < 5), normalized (NormalizeData function from Seurat) and variable features were identified (FindVariableFeatures, selection.method=vst). Doublets were filtered out using DoubletFinder (v2.0.3). The three samples were integrated (FindIntegrationAnchors, IntegrateData from Seurat), scaled (ScaleData) and dimension-reduced by PCA (RunPCA). The first 13 PCs were used to construct a SNN network and a graph-based clustering approach. Louvain algorithm, was applied to identify cell clusters with the resolution set to 0.7. UMAP was constructed (RunUMAP), and differentially expressed markers for each cluster were found (FindAllMarkers, min.pct=0.25, logfc.threshold=0.25, test.use = wilcox).  The three B cells clusters were subset and re-clustered (normalized, variable features was identified, integrated, scaled and PCA transformed). The first 13 PCs were used to construct the UMAP (resolution=0.5).


title: Expression data that were specifically regulated by GPR65 in livers of mice undergoing BDL-induced liver fibrosis

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

summary: GPCRs are the most productive drug targets and targeted by one third of the drugs in clinical use, however, few GPCRs are reported to participate in liver fibrosis. In this study, we have identified that KCs-enriched GPR65 is upregulated in both human and mouse fibrotic livers and KCs from fibrotic livers. To identify the roles of GPR65 in liver fibrosis, we performed RNA-seq to analyze the effect of Gpr65 deficiency on BDL-induced liver fibrosis. The mice were divided into four groups: sham operation- treated WT mice (n=3), bile duct ligation (BDL)- treated WT mice (n=3), sham operation- treated GPR65-KO mice (n=3) and BDL- treated GPR65-KO mice (n=3).

overall_design: WT and GPR65-KO mice were divided into four groups: sham operation- treated WT mice (n=3), bile duct ligation (BDL)- treated WT mice (n=3), sham operation- treated GPR65-KO mice (n=3) and BDL- treated GPR65-KO mice (n=3). After 21 days of BDL, RNA-seq were performed to analyze the effect of Gpr65 deficient on BDL-induced liver fibrosis.

first: Wei

last: Hong

first: Tao

last: Han


title: The effector program of human CD8 T cells can support tissue remodeling abilities.

first: LIT

last: NGS-Core

summary:
This SuperSeries is composed of the SubSeries listed below.
Abstract Paper: CD8 T lymphocytes are classically viewed as cytotoxic T cells. Whether human CD8 T cells can, in parallel, induce a tissue regeneration program is poorly understood. Here, antigen-specific assay systems revealed that human CD8 T cells not only mediated cytotoxicity, but also promoted tissue remodeling. Activated CD8 T cells could produce the epidermal growth factor receptor (EGFR)-ligand amphiregulin (AREG) and sensitize epithelial cells for enhanced regeneration potential. Blocking the EGFR or the effector cytokines IFN-γ and TNF could inhibit tissue remodeling. This regenerative program enhanced tumor spheroid and stem-cell-mediated organoid growth. Using single-cell gene expression analysis, we identified an AREG+, tissue-resident CD8 T-cell population in healthy donor skin and adipose tissue with a strong TCR clonal relation to blood PD1+TIGIT+ CD8 T cells with tissue remodeling abilities. These findings may help to understand the complex CD8 biology in tumors and could become relevant for the design of therapeutic T-cell products.

overall_design: Refer to individual Series


title: TDP-43 expression impairs sleep in Drosophila and is rescued by Ataxin-2 knockdown

city: Philadelphia

first: Alexandra

last: Perlegos

state: PA

address: 231 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

summary: Exploring the intricate link between sleep and brain degeneration holds great promise for the development of effective therapeutics. Here we provide novel insights into the role of TDP-43 and Atx2 in regulating sleep and neurodegeneration using Drosophila. We demonstrate that expression of TDP-43 severely disrupts sleep, resulting in reduced sleep duration of the affected animals.  Sleep disruption by TDP-43 is completely rescued by Atx2 knockdown. To unravel the underlying mechanism of TDP43 sleep disruption and Atx2-mediated rescue, we conducted brain RNA sequencing analysis from flies expressing TDP-43 with or without Atx2 knockdown. Among RNAseq changes, we observed upregulation of genes associated with small molecule metabolism with TDP-43 expression, followed by their subsequent downregulation upon Atx2 knockdown. Utilizing these Atx2-regulated genes, we conducted an RNAi screen to identify additional sleep modifiers that interact with TDP-43.

overall_design: Drosophila brain tissue RNA-sequencing used to investigate the underlying mechanism of TDP43 sleep disruption and Atx2-mediated rescue

middle: E

first: Nancy

middle: M

last: Bonini

first: Matthew

last: Kayser


title: Next-generation sequencing facilitates quantitative analysis of IL-17A and control mice PH+ B-ALL cells transcriptomes

city: Beijing

first: Yunxuan

last: Li

address: Nanwei road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyze the differential genes and pathways in PH+ B-ALL cells isolated from BCR-ABLtTA mice by using RNA-seq.

overall_design: IL-17A treated PH+ B-ALL and Control PH+B-ALL cells mRNA profiles were generated by deep sequencing using Illumina Novaseq 6000.

first: Bing

last: Cui

first: Ke

first: Erlie

last: Jiang

first: Feng

last: Wang

first: Zhaona

last: Yang


title: Single-cell transcriptional analysis of developmental maturation strategies for human pluripotent stem cell-derived heart organoids

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

summary: Human pluripotent stem cells possess the ability to recapitulate key events of mammalian organogenesis in vitro, including heart development. Previously-described human heart organoid protocols elicit early embryonic-like cardiac phenotypes and morphologies. We hypothesized that human heart organoids can be made significantly more complex and physiologically relevant through the implementation of in utero gestational biochemical phenomena. Here, we designed and applied multiple developmental maturation strategies on our human heart organoids for a period of 10 days. Our data reveals the emergence of atrial and ventricular cardiomyocyte populations, valvular cells, epicardial cells, proepicardial-derived cells, endothelial cells, stromal cells, conductance cells, and cardiac progenitors, all of them cell types present in the primitive heart tube.

overall_design: Single-cell RNA-sequencing of various developmentally maturated human heart organoids

first: Brett

last: Volmert

first: Ashlin

last: Riggs

first: Artem

last: Kiselev

first: Sangbum

last: Park


title: Cellular and transcriptional signatures unveiled by single cell RNA-Seq (scRNA-Seq) following ex vivo infection of murine splenocytes with Borrelia burgdorferi

city: San Antonio

first: Venkatesh

last: Kumaresan

state: TX

address: 3.230, BSE Building, One UTSA circle

institute: The University of Texas at San Antonio

summary: Splenocytes comprised a wide-range of immune cells responsible for the protection against infectious diseases. We exposed splenocytes to GFP+ Borrelia, sorted GFP+ and GFP- splenocytes and performed single-cell RNA seq to analyze the DEGs between infected and bystander population in different immune cell populations

overall_design: We used single-cell RNA-Seq to study the splenocytes from C3H/HeN mice exposed to GFP-tagged Borrelia, sorted GFP+ splenocytes and GFP- bystander cells to uncover novel molecular and cellular signatures that contribute to early stages of immune responses against Bb.

first: Taylor

last: MacMackin Ingle

first: Nathan

last: Kilgore

first: Guoquan

last: Zhang

first: Brian

last: Hermann

first: Janakiram

last: Seshu


title: Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [snATAC-seq]

first: Katalin

last: Susztak

address: 3400 Civic Center Blvd, SCTR

summary: Mineralocorticoids play a critical role in maintaining sodium and potassium homeostasis and pathophysiological processes including hypertrophy, inflammation and fibrosis. Mineralocorticoid antagonists (MRAs) have shown to protect from kidney and heart disease, however, their molecular mechanism of action is poorly understood. Here we performed single nuclei and bulk transcriptomics and chromatin accessibility analysis to characterize the mode of kidney protection by steroidal and non-steroidal MRA treatment in a rat model of mineralocorticoid-induced cardiorenal end-organ damage. We define mineralocorticoid sensitive cell types and gene network in the kidney. We show that in diseased kidneys specific proximal tubule cells develop an injured profibrotic phenotype expressing Spp1 and Il34. Nonsteroidal finerenone protects from profibrotic differentiation of proximal tubule cells. Profibrotic gene signature can classify human kidney tissue samples and predict prognosis. Our multi-omics approach elucidates target cell types and potential mechanisms of renal protection by finerenone.

overall_design: We provided three types of datasets of rat kidneys: (i) single nuclei RNA-seq as follows: 3 Control - 3 DOCA treated - 2 DOCA+Finerenone treated - 3 DOCA + Spironolactone treated, (ii) single nuclei ATAC-seq as follows: 1 Control - 1 DOCA treated - 1 DOCA+Finerenone treated - 1 DOCA + Spironolactone treated, and (iii) Bulk RNA-seq as follows: 4 Control - 4 DOCA treated - 4 DOCA+Finerenone treated - 4 DOCA + Spironolactone treated

first: Amin

last: Abedini

first: Junan

last: Wu

first: Ziyuan

last: Ma

first: Michael

last: Balzer

first: Julia

last: Frederick

first: Hana

last: Cernecka

first: Peter

last: Kolkhof


title: Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [snRNA-seq]


title: Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism

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


title: Acrolein-induced transcriptomic alterations in male Wistar-Kyoto rats

status: Public on Nov 16 2023

city: Research Triangle Park

first: Devin

middle: Issac

last: Alewel

state: NC

address: 109 TW Alexander Drive

department: CPHEA/PHITD/CIB

institute: U.S. EPA

summary: Acute acrolein inhalation in male rats resulted in multi-tissue transcriptomic alterations that were observed through Illumina mRNA sequencing. Specifically, site-specific respiratory expression profile differences were noted between air- and acrolein-exposed groups. Nasal epithelial tissue demonstrated 452 differentially expressed genes (DEGs) (310 up-regulated and 142 down-regulated)and lung tissue demonstrated 95 DEGs (80 up-regulated and 15 down-regulated). Notable transcriptomic alterations were also observed in liver tissue of acrolein-exposed rats, with 1699 identified DEGs (788 up-regulated and 911 down-regulated). A variety of mRNA expression profile differences resulting from acute acrolein inhalation was observed in other peripheral tissues, including adipose, muscle, adrenals, hippocamus, and hypothalamus. Gene changes were largely representative of oxidative and inflammatory response in the nose, as well as xenobiotic metabolism changes in the lung. Liver changes, which were most numerous, included alterated metabolic signaling (Sirtuin and FXR signaling), as well as alterated oxidoreductive, GPCR, and glucocorticoid pathways. Together, these data demonstrate acrolein, a well-characterized respiratory irritant, induces systemic neuroendocrine immunological and metabolic stress.

overall_design: Adult male Wistar-Kyoto rats were exposed to air (0ppm) or acrolein nose-only for 4hr total exposure duration. For the first 30 minutes of exposure, increasing half-log exposure concentrations were used at 0, 0.1, 0.316, and 1 ppm, such that each concentration was employed for 7.5 minutes, with this 30 minute window being followed by 3.5 hours at the highest concentration of acrolein of 3.16 ppm. Exposures were conducted ~0700-1100 AM and performed under general room temperature and humidity. Immediately after exposure, rats were necropsied, tissues collected and flash frozen in liquid nitrogen, and frozen for later analysis. Later, RNA was extracted and sequenced.

first: D

first: T

middle: W

last: Jackson

first: K

last: Rentschler

first: M

middle: C

last: Schladweiler

first: A

last: Astriab-Fisher

first: S

last: Gavett

first: P

last: Evansky

first: U

last: Kodavanti


title: The TroR transcription factor genome-wide binding analysis in the halophilic archaeon Haloferax volcanii [ChIP-Seq]

city: Durham

first: Amy

middle: K

last: Schmid

address: 125 Science Dr.

institute: Duke University

summary: Iron is essential for almost all organisms, but can be toxic in excess. Cells use regulatory mechanisms to control the iron uptake, iron utilization and iron release mechanisms to ensure the availability of enough iron to be used for biological processess but minimizing the oxidative stress caused by the oxidation of free molecules of iron. In this paper we show that TroR is a transcription factor from the conserved family of proteins DtxR that directly binds the promoter of a set of genes involved in iron homeostasis meanwhile SirR is not a major regulator of iron homeostasis in the halophilic archaeon Haloferax volcanii.

overall_design: We used chromatin immunoprecipitation coupled with DNA-sequencing to determine what sequences of the genome are directly bound by the :HA epitope tagged TF SirR and TroR transcription factors

first: Mar

last: Martinez Pastor


title: The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii [RNA-Seq]

summary: Iron is essential for almost all organisms, but can be toxic in excess. Cells use regulatory mechanisms to control the iron uptake, iron utilization and iron release mechanisms to ensure the availability of enough iron to be used for biological processess but minimizing the oxidative stress caused by the oxidation of free molecules of iron. In this paper we show that TroR is a transcription factor from the conserved family of proteins DtxR that works as the major regulator of iron homeostasis in the halophilic archaeon Haloferax volcanii.

overall_design:
Using RNA seq, we compared the trancriptome of cells from parental strain versus the troR knockout strain, growing in minimal media containing iron in excess to understand if the TF TroR was involved in those cellular mechanims that determine iron homeostasis.
RNA was checked for quality, and 300-500 micrograms of  total RNA were depleted using RIBOZERO to remove rRNA.Libraries were constructed using ~50 ng of mRNA using the Kapa Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems, Illumina).


title: The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe [RNA-seq]

city: Winston-Salem

first: Ke

last: Zhang Reid

address: 1834 Wake Forest Rd

institute: Wake Forest University

summary: Eukaryotic chromatin is organized into either silenced heterochromatin or relaxed euchromatin regions, which controls the accessibility of transcriptional machinery and thus regulates gene expression. In fission yeast, Schizosaccharomyces pombe, Set1 is the sole H3K4 methyltransferase and is mainly enriched at the promoters of actively transcribed genes. In contrast, Clr4 methyltransferase initiates H3K9 methylation, which has long been regarded as a hallmark of heterochromatic silencing. Lsd1 and Lsd2 are two highly conserved H3K4 and H3K9 demethylases. As these histone-modifying enzymes perform critical roles in maintaining histone methylation patterns and, consequently, gene expression profiles, cross-regulations among these enzymes are parts of the complex regulatory networks. Thus, elucidating the mechanisms that govern their signaling and mutual regulations remains crucial. Here, we demonstrated that C-terminal truncation mutants, lsd1-∆HMG and lsd2-∆C, do not compromise the integrity of the Lsd1/2 complex but impair their chromatin-binding capacity at the promoter region of target genomic loci. We identified the protein-protein interactions between Lsd1/2 and Raf2 or Swd2, which are the subunits of the Clr4 complex (CLRC) and Set1-associated complexes (COMPASS), respectively. We showed that Clr4 and Set1 modulate the protein levels of Lsd1 and Lsd2 in opposite ways through the ubiquitin-proteasome-dependent pathway. During heat stress, the protein levels of Lsd1 and Lsd2 are upregulated in a Set1-dependent manner. The increase in protein levels is crucial for differential gene expression under stressed conditions. Together, our results support a cross-regulatory model by which Set1 and Clr4 methyltransferases control the protein levels of Lsd1/2 demethylases to shape the dynamic chromatin landscape.

overall_design: RNA was isolated from S. pombe strains (each genotype represented by 2 independently derived biological replicates) using the Quick-RNA Miniprep Kit (Zymo Research, R1054) following manufacturer protocols. RNA was recovered in RNase-free water, frozen, and shipped to Novogene where Plant and Animal Eukaryotic Strand Specific mRNA (WOBI) sequencing was performed with standard bioinformatics service (HiSeq PE150; 150 bp paired-end with directional protocol; 9G raw data per sample).

first: Liu

last: Haoran

first: Fadi

last: Bahjat

first: David

last: de la Cerda

first: Brendan

last: Lemezis

first: Jieyu

last: Gao

first: Qianqian

last: Song

first: Minghan

last: Chen

middle: Z

last: Reid


title: The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii


title: The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe


title: scRNA-Seq of bovine fetal testes derived from NANOS3 knockout and wildtype embryos

status: Public on Nov 15 2023

city: Davis

first: Maci

last: Mueller

address: One Shields Ave

department: Animal Sciences

institute: University of California, Davis

summary: We performed single cell RNA-sequencing (scRNA-Seq) of testes from bovine fetuses derived from either CRISPR/Cas9 NANOS3 knockout (KO; NANOS3 -/-) or wildtype control (NANOS3 +/+) embryos. The scRNA-Seq analysis showed a complete loss of primordial germ cells (PGCs) and gonocytes in NANOS3 KO fetal testes, while maintaining the development of somatic support cells.

overall_design: Bovine fetal testes derived from NANOS3 knockout and wildtype embryos were collected and prepared for scRNA-Seq analysis. Libraries were prepared with the whole transcriptome 100K kit from Parse Biosciences, which involves barcoding and then pooling cells from all samples prior to the generation of eight sublibraries. Because of the kit's design, sequencing reads of all samples are distributed across all eight sublibraries. For further details see the attached `README.tsv` file.


title: ISGF3 and STAT2/IRF9 direct basal and IFN-induced transcription through genome-wide binding of phosphorylated and unphosphorylated complexes to commonly ISRE containing ISGs

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University


title: ISGF3 and STAT2/IRF9 direct basal and IFN-induced transcription through genome-wide binding of phosphorylated and unphosphorylated complexes to commonly ISRE containing ISGs  [RNA-Seq]

summary: To further understand the role of phosphorylation in ISGF3- and STAT2/IRF9-mediated constitutive and long-term IFN-I-stimulated transcriptional responses, we performed RNA-Seq and ChIP-Seq, in combination with phosphorylation inhibition and anti-viral experiments. First, we identified a group of ISRE-containing ISGs that were commonly regulated in IFNα treated WT and STAT1-KO cells. Thus, in 2fTGH and Huh7.5 WT cells IFNα-inducible transcription and anti-viral activity relied on the recruitment of the ISGF3 components STAT1, STAT2 and IRF9 in a phosphorylation- and time-dependent manner. Likewise, in ST2-U3C and Huh-STAT1KO cells lacking STAT1, ISG expression correlated with DNA-binding of phosphorylated STAT2/IRF9. This pointed to a dominant role of classical ISGF3 and STAT2/IRF9, and not U-ISGF3 or U-STAT2/IRF9, in the regulation of early and prolonged ISG expression and viral protection, in WT and STAT1-KO cells. In addition, comparative experiments in U3C (STAT1-KO) cells overexpressing all ISGF3 components (ST1-ST2-IRF9-U3C), revealed a threshold-dependent role of U-ISFG3, and potentially U-STAT2/IRF9, in the regulation of constitutive and possibly long-term IFNα-treated ISG expression and anti-viral activity.

overall_design: Gene expression profiling analysis for 2fTGH, ST2-U3C, Huh7.5, and Huh STAT1KO cells treated with IFN alpha and study of constitutive, IFNa-independent antiviral response in cells overexpressing ISGF3 components (ST1-ST2-IRF9-U3C) vs STAT1KO cells (U3C)

first: H

last: Nowicka


title: Hierarchy and interconnected networks in the WhiB7 mediated transcriptional response of Mycobacterium abscessus to ribosome targeting antibiotics

status: Public on Nov 14 2023

city: Albany

first: Pallavi

last: Ghosh

address: 150 New Scotland Ave

department: New York State Department of Health

institute: Wadsworth Center

summary: global changes in gene expression in wild-type M. abscessus, △MabwhiB7 and △MabsigH strains upon tetracycline exposure followed by deterination of direct binding sites of whiB7 using CHIP-Seq

overall_design: RNA-seq data for M. abscessus ATCC19977 , △MabwhiB7 and △MabsigH in the presence of Tet

first: Kelley

last: Hurst-Hess

first: Charity

last: McManaman

first: Yong

last: Yang

first: Shamba

last: Gupta


title: VDJ analysis of IL-10+ and IL-10- splenic B1a, MZ, and FO B cells from sIgM-/- mouse

first: Gudrun

middle: Fiona

last: Debes

address: 233 South 10th Street

department: Microbiology and Immunology

institute: Thomas Jefferson University

summary: We compared the clonotypes of IL-10+ and IL-10- B1a, marginal zone and follicular B cells from the spleen of sIgM-/-IL10GFP mouse using 10X single cell RNAseq to analyze potential differences in clonality between IL-10+ and IL-10- B cells.

overall_design: splenic B cells from sIgM-/-IL10GFP mice were stimulated for 4 hours with PMA/Ionomycin/LPS and processed for CD19 magnetic bead enrichment followed by FACS sorting for B1a, marginal zone, and follicular B cell populations.  IL-10+ and IL-10- B cells from each subset were sorted separately based on GFP expression or absence.

first: Shannon

last: McGettigan

first: Gaurav

last: Kumar


title: Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [bulk RNA-seq]

first: Katalin

last: Susztak

first: Amin

last: Abedini

first: Junan

last: Wu

first: Ziyuan

last: Ma

first: Michael

middle: S

last: Balzer

first: Julia

last: Frederick

first: Hana

last: Cernecka

first: Peter

last: Kolkhof


title: The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe [ChIP-seq]

first: Ke

last: Zhang Reid

overall_design: Chromatin immunoprecipitation DNA-Sequencing (ChIP-Seq) for histone variants H3 (di-methyl K9) were performed in FTP (Protein A-, TEV cleavage site, and Flag- double epitope-tag) backgrounds were modified in S. pombe cells.

first: Liu

last: Haoran

first: Fadi

last: Bahjat

first: David

last: de la Cerda

first: Brendan

last: Lemezis

first: Jieyu

last: Gao

first: Qianqian

last: Song

first: Minghan

last: Chen

last: Reid


title: A temporal extracellular transcriptome atlas of human preimplantation development

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

institute: UCSD

summary: We develop a non-invasive method for comprehensive characterization of the extracellular RNAs (exRNA) in a single droplet of spent media that was used to culture human in vitro fertilization (IVF) embryos. We generate and provide as a resource the temporal extracellular transcriptome atlas of human preimplantation development (TETA). TETA consists of 245 exRNA sequencing datasets, corresponding to 245 collections of spent media at five developmental stages.

overall_design:
The spent media in their original culture dishes were obtained immediately after embryo transfer to fresh media. The fertility center follows a 7-day standard procedure. A total of 261 spent media droplets were collected at four time points, 18h, 68h, 120h, and 160h. Additionally, a set of unfertilized oocytes were cultured for up to 68 hours. A total of 34 droplets of oocyte spent media were collected. The spent media were carefully aspirated out from the original culture dishes and centrifuged at 500 ×g for 3 min under 4°C. The supernatant was aspirated and centrifuged again. A 7 μL aliquot of the supernatant of the 2nd round of centrifugation was used as the input to SILVER-seq.
NOTE FROM SUBMITTER: Due to sensitivity of the raw data in our project, we've decided to upload only the processed data. We will  deposit the raw data to dbGaP.

first: Qiuyang

first: Zixu

last: Zhou


title: Hyperactive Rac stimulates cannibalism of living target cells and enhances CAR-M-mediated cancer cell killing (BMDM RNA-seq)

status: Public on Nov 13 2023

city: Santa Barbara

first: Denise

middle: J.

last: Montell

address: University of California Santa Barbara

department: Molecular Cellular and Developmental Biology

institute: University of California Santa Barbara

summary: The 21kD GTPase Rac is an evolutionarily ancient regulator of cell shape and behavior. Rac2 is predominantly expressed in hematopoietic cells where it is essential for survival and motility. The hyperactivating mutation Rac2E62K also causes human immunodeficiency, although the mechanism remains unexplained. Here we report that in Drosophila, hyperactivating Rac stimulates ovarian cells to cannibalize neighboring cells, destroying the tissue. We then show that hyperactive Rac2E62K stimulates human HL60-derived macrophage-like cells to engulf and kill living T cell leukemia cells. Primary mouse Rac2E62K/+ bone-marrow-derived macrophages also cannibalize primary Rac2E62K/+ T cells due to a combination of macrophage hyperactivity and T cell hypersensitivity to engulfment. Additionally, Rac2E62K/+ macrophages non-autonomously stimulate wild type macrophages to engulf T cells. Rac2E62K also enhances engulfment of target cancer cells by chimeric antigen receptor-expressing macrophages (CAR-M). We propose that Rac-mediated cell cannibalism may contribute to Rac2E62K/+ human immunodeficiency and enhance CAR-M cancer immunotherapy.

overall_design:
To investigate the differential gene expression and inflammatory  profiles of bone marrow derived macrophages (BMDM) from Rac2+/+ and Rac2E62K/+mice.
To investigate the differential gene expression of bone marrow derived macrophages (BMDM), BMDMs from Rac2+/+ and Rac2E62K/+mice, and BMDMs from Rac2+/+ mice either stimulated to a classic M1 state or to a classic M2 state were compared. Samples were run in triplicate.

first: Abhinava

last: Mishra

first: Melanie

last: Rodriguez

first: Alba

middle: Y

last: Torres

first: Morgan

last: Smith

first: Anthony

first: Annalise

last: Bond

first: Meghan

last: Morrissey

middle: J


title: Hyperactive Rac stimulates cannibalism of living target cells and enhances CAR-M-mediated cancer cell killing

overall_design: Refer to individual Series


title: Hyperactive Rac stimulates cannibalism of living target cells and enhances CAR-M-mediated cancer cell killing (HL60 RNA-seq)

overall_design:
To test whether Rac2E62K causes substantial changes in the transcriptome of macrophages, we compared RNAseq profiles for control and Rac2E62K expressing HL60-derived macrophage-like cells.
HL60 cells were differentiated into macrophages. HL60 cells carrying Lck-GFP sequence without dominant activating Rac2 mutations were used as a control. Differential gene expression was compared between control and HL60-Rac2E62K-LckGFP expressing HL60-derived macrophage-like cells. Samples were run in triplicate.


title: DeMixSC: a deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples

city: HOUSTON

first: Rui

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Bulk deconvolution with single-cell/nucleus RNA-seq data is critical for understanding heterogeneity in complex biological samples, yet the technological discrepancy across sequencing platforms limits deconvolution accuracy. To address this, we introduce an experimental design to match inter-platform biological signals, hence revealing the technological discrepancy, and then develop a deconvolution framework called DeMixSC using the better-matched, i.e., benchmark, data. Built upon a novel weighted nonnegative least-squares framework, DeMixSC identifies and adjusts genes with high technological discrepancy and aligns the benchmark data with large patient cohorts of matched-tissue-type for large-scale deconvolution. Our results using a benchmark dataset of healthy retinas suggest much-improved deconvolution accuracy. Further analysis of a cohort of 453 patients with age-related macular degeneration supports the broad applicability of DeMixSC. Our findings reveal the impact of technological discrepancy on deconvolution performance and underscore the importance of a well-matched dataset to resolve this challenge. The developed DeMixSC framework is generally applicable for deconvolving large cohorts of disease tissues, and potentially cancer.

overall_design: Macula retinal mRNA profiles of 24 normal human samples

first: Shuai

last: Guo

first: Xiaoqian

last: Liu

first: Xuesen

last: Cheng


title: Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase

status: Public on Nov 12 2023

city: Stanford

first: Neuza

last: Reis Matias

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University


title: Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase [RNA-seq]

summary: During meiosis, germ cell and stage-specific components impose additional layers of regulation on the core cell cycle machinery to set up an extended G2 period termed meiotic prophase. In Drosophila males, meiotic prophase lasts 3.5 days, during which spermatocytes upregulate over 1800 genes and grow 25-fold. Previous work has shown that the cell cycle regulator Cyclin B (CycB) is subject to translational repression in immature spermatocytes, mediated by the RNA-binding protein Rbp4 and its partner Fest. Here, we show that the spermatocyte-specific protein Lut is required for translational repression of cycB in an 8-h window just before spermatocytes are fully mature. In males mutant for rbp4 or lut, spermatocytes enter and exit meiotic division 6-8 h earlier than in wild type. In addition, spermatocyte-specific isoforms of Syncrip (Syp) are required for expression of CycB protein in mature spermatocytes and normal entry into the meiotic divisions. Lut and Syp interact with Fest independent of RNA. Thus a set of spermatocyte-specific regulators choreograph the timing of expression of CycB protein during male meiotic prophase.

overall_design: These RNAseq libraries were used as control for easyCLIP analysis. We used 150 pairs of testes from 0-2 day-old wild type male flies per replicate. We chose Bam>GAL4 flies as WT samples.

middle: R

last: Matias


title: Transcriptomic profiling of A549 cells in response to Dexamethasone, in the context of GR inhibition based on antagonists as well as a novel GR-PROTAC

city: Zürich

first: Katharina

last: Gapp

address: Winterthurerstrasse 190

department: Health Science and Technology

institute: Swiss Federal Institue of Technology

summary: Glucocorticoid receptors (GR) are important therapeutic targets due to regulation of stress hormones, glucocorticoids (GCs). GCs are altered in neuropsychiatric diseases, but also in cancers and autoimmunes. GR antagonists show some success in modulating GC levels. Yet, occupancy-driven mode of action of the available inhibitors, prevents full inhibition and requires high doses, causing risks in the long-term. To complement the existing tools, we present a highly potent novel catalytic-driven GR degrader, KH-103. We show highly efficient and rapid GR chemical knockdown at nanomolar concentrations. KH-103 is selective for GR, has almost no transcriptional side-effects, and shows higher efficiency in blocking ligand-induced genomic effects compared to other antagonists. Application in cortical cultures, revealed a GR-dependent GC-induced increase in calcium peak-intervals negatable by KH-103 pretreatment. Finally, an in-vivo proof-of-concept application of KH-103 is presented. KH-103 opens new opportunities for more lucid interpretation of GR-functions without disadvantages of genetic-interventions with clinically translatable potentials.

overall_design: We cultured A495 cells and exposed them to different treatment regimes including dexamethasone (100nM), mifepristone (1uM), CORT113176 (1uM) and  KH-103 (100nM) or a combination there-of with varying exposure time and order. For exact timescales see column "title"/"B", then harvested cells to extract RNA using Quick-RNA Microprep Kit (Zymoresearch, R1051).  RNA samples at 25 ng/ul concentration were processed at  Novogene, UK. Non-directional Poly-A library preparations were performed according to the manufacturer's recommendations (Next® Ultra RNA Library Prep Kit for Illumina®)

first: Mahshid

last: Gazorpak

first: Karina

last: Hugentobler

first: Johannes

last: Bohacek

first: Erick

last: Carreira


title: PIKfyve inhibition upregulates surface expression of MHC class I to enhance immune responses in cancer

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: Despite the remarkable clinical success of immunotherapies in a subset of cancer patients, many fail to respond to treatment and exhibit primary resistance. Here, we found thatgenetic or pharmacologic inhibitionof the lipid kinase PIKfyve, a regulator of autophagic flux and lysosomal biogenesis,upregulated surface expression of major histocompatibility complex class I (MHC-I) in cancer cells via impairing autophagic flux, resulting in enhanced cancer cell killing mediated by CD8+ T cells. Genetic depletion or pharmacologic inhibition of PIKfyve elevated tumor-specific MHC-I surface expression, reduced tumor proliferation, and increased intratumoral functional CD8+T cellsinsyngeneic mouse models. Importantly, enhanced antitumor responses by Pikfyve-depletion was CD8+T cell- and MHC-I-dependent,as CD8+ T cell depletion or B2m knockout rescued tumor growth. Furthermore, PIKfyve inhibition improved response to various immunotherapies, including immune checkpoint blockade (ICB), adoptive cell therapy, and therapeutic vaccines. High expression of PIKFYVE was also predictive of poor response to ICB and prognostic of poor survival in ICB-treated cohorts. Collectively, our findings show that targeting PIKfyve enhances immunotherapies by elevating surface expression of MHC-I in cancer cells, and PIKfyve inhibitors have potential as novel agents to increase immunotherapy response in cancer patients.

overall_design: To compare the transcriptomic changes in pancreatic tumors established by Pikfvye-null KPC1361 versus control KPC1361 in C57BL/6

first: Yi

last: Bao

first: Yuanyuan

last: Qiao

first: Jae

last: Choi

first: Fan

last: Yang

first: Gabriel

last: Cruz

first: Caleb

first: Yuping

last: Zhang

first: Rahul

last: Mannan

first: Jiali

last: Yu

first: Mahnoor

last: Gondal

first: Parth

last: Borker

first: Alyssa

last: Azani

first: Sara

last: Grove

first: Tongchen

last: He

first: Xuhong

last: Cao

first: Fengyun

last: Su

last: Wang

first: Yu

last: Chang

first: Yang

last: Zheng

first: Ilona

last: Kryczek

first: Marcin

last: Cieslik

first: Michael

middle: D

last: Green

first: Weiping

last: Zou


title: Ribosome protein RPSA promotes the expression of proinflammatory cytokines induced by HSV-1 infection

city: beijing

first: yan

last: jiang

state: beijing

address: 东单三条5号 中国医学科学院基础医学研究所

institute: PUMC

summary: After HSV-1 infection, ribosomal protein RPSA can recognize viral DNA. To further verify the biological function of RPSA, we constructed the RPSA-deficient RAW264.7 macrophage cell line with the inducible CRISPR-Cas9 system, then found that the deletion of RPSA could effectively reduce the expression of proinflammatory cytokines such as IL-1α, IL-1β, IL-6, IL-12 and TNFα induced by HSV-1 infection.

overall_design: We constructed Rpsa induced knockout RAW264.7 cell lines and performed RNA-seq for total RNA in RAW264.7 cells infected with or without HSV-1.

first: Yan

last: Jiang

first: Henan

last: Xu


title: ISGF3 and STAT2/IRF9 direct basal and IFN-induced transcription through genome-wide binding of phosphorylated and unphosphorylated complexes to commonly ISRE containing ISGs   [ChIP-Seq]

first: Hans

last: Bluyssen

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for 2fTGH, ST2-U3C, Huh7.5, and Huh STAT1KO cells treated with IFN alpha

first: H

middle: A

last: Nowicka


title: Deficiency of RPSA reduces binding of P65 to proinflammatory cytokines promoter regions in HSV-1 infection

address: 东单三条5号 中国医学科学院基础医学研究所

summary: After HSV-1 infection, ribosomal protein RPSA can recognize viral DNA and promotes the expression of proinflammatory cytokines. Through ChIP-seq, we found that the enrichment of P65 in proinflammatory cytokines(Il1b, Il6, Il12b, etc.) promoter regions was decreased due to Rpsa deficiency.

overall_design: We constructed Rpsa induced konckout RAW264.7 cell lines and performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for P65 in WT and Rpsa-iKO RAW264.7 cells infected with or without HSV-1.


title: Translation-coupled sensing and degradation of RNA-protein crosslinks [Ribo-Seq: dataset_2]

city: Baltimore

first: Allen

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Reactive aldehydes are abundant cytotoxic metabolites, which challenge homoeostasis by crosslinking cellular macromolecules. Aldehyde-induced DNA-DNA crosslinks cause cancer and bone marrow failure in Fanconi anemia, while covalent DNA-protein crosslinks require proteolytic repair to prevent liver tumours and premature ageing. Whether RNA damage contributes to the toxicity of aldehydes and whether cells possess mechanisms to resolve RNA-protein crosslinks (RPCs) in particular is unknown. Studying the specific consequences of aldehyde-induced RNA damage is challenging due to confounding induction of DNA damage. Here, we establish photoactivatable ribonucleosides as a tractable model system to study aldehyde-mimicking RNA damage in the absence of DNA damage. We find that RNA crosslinking damage causes translational stress by stalling elongating ribosomes, which causes cell death upon ZAKα-dependent activation of the ribotoxic stress response (RSR) and GCN2-dependent activation of the integrated stress response (ISR). Moreover, we discover the principles of a translation-coupled cellular quality control mechanism that targets RPCs. Collisions between translating ribosomes and crosslinked mRNA-binding proteins trigger their ubiquitylation and subsequent proteasomal degradation. Our findings reveal RNA damage and RPC formation as a central aspect of aldehyde-induced toxicity and establish a framework to study the cellular responses to these threats in mechanistic detail.

overall_design: Ribosome profiling of two biological replicates of HAP1 cells with and without RNF14 knockout, treated with 4SU and UV and recovered for 0 or 30 min.


title: ATAC-seq analysis in Rpsa-iKO RAW264.7 cells after HSV-1 infection

address: 东单三条5号 中国医学科学院基础医学研究所

summary: After HSV-1 infection, ribosomal protein RPSA can recognize viral DNA and promotes the expression of proinflammatory cytokines. Through ATAC-seq, we found that chromatin accessibility around transcription start sites (TSS) of proinflammatory cytokinse in HSV-1 infected Rpsa-iKO RAW264.7 was significantly reduced

overall_design: We constructed Rpsa induced konckout RAW264.7 cell lines and performed Assay for Transposase Accessible Chromatin with high throughput sequencing in WT and Rpsa-iKO RAW264.7 cells infected with or without HSV-1.


title: The Genetic and Epigenetic Features of Bilateral Wilms Tumor Predisposition [RNA-Seq]

status: Public on Nov 10 2023

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

summary: This study comprehensively evaluated the landscape of genetic and epigenetic events that predispose to synchronous bilateral Wilms tumor (BWT). We performed whole exome or whole genome sequencing, total-strand RNA-seq, and DNA methylation analysis using germline and/or tumor samples from 68 patients with BWT from St. Jude Children’s Research Hospital and the Children’s Oncology Group.

overall_design: Libraries were prepared from 250 ng to 1000 ng of total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina P/N 20020613)

first: Andrew

last: Murphy

first: Xiang

last: Chen


title: p53 suppresses MHC class II antigen presentation by the intestinal epithelium to protect intestinal stem cells upon radiation

city: NEW BRUNSWICK

first: Jianming

state: NJ

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

summary: To investigate the role of p53 in radiation-induced gastrointestinal syndrome, we performed gene expression profiling analysis using data obtained from RNA-seq of small intestine tissues from WT and p53-/- mice at 1 day post 12Gy total-body irradiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of small intestine tissues from WT and p53-/- mice at 1 day post 12Gy total-body irradiation.

first: Chun-Yuan

first: Xue

last: Yang

first: Fan

last: Zhou

first: Juan

last: Liu

first: Jill

last: Bargonetti

first: Lanjing

last: Zhang

first: Ping

last: Xie

first: Zhaohui

last: Feng

first: Wenwei

last: Hu


title: RPSA and proinflammatory cytokines after HSV-1 infection

first: yan

last: jiang

address: 东单三条5号 中国医学科学院基础医学研究所

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


title: PRMT1 methylation of WTAP promotes multiple myeloma tumorigenesis by activating oxidative phosphorylation via m6A modification of NDUFS6 [m6A-Seq]

city: Xi'an

first: Yachun

last: Jia

state: None Selected

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

institute: xian jiaotong university

summary: Epigenetic modifications play important roles during the pathogenesis of multiple myeloma (MM). Here, we found that protein arginine methyltransferase 1 (PRMT1) was highly expressed in MM patients and its expression level was positively correlated with MM stages. High PRMT1 expression were notably related to adverse prognosis in MM patients. We further showed that silencing PRMT1 inhibited MM proliferation and tumorigenesis in vitro and in vivo. Mechanistically, we revealed that knockdown of PRMT1 reduced the oxidative phosphorylation (OXPHOS) of MM cells through downregulation of NDUFS6. Meanwhile, we identified that WTAP, a key component of the m6A methyltransferase complex, was methylated by PRMT1 and NDUFS6 was identified as a bona fide m6A target of WTAP. Finally, we found that PRMT1 inhibitor and bortezomib combination synergistically inhibited MM progression. Collectively, our results demonstrate that PRMT1 plays a crucial role during MM tumorigenesis and suggest that PRMT1 could be a potential therapeutic target in MM.

overall_design: To identify the functional downstream target genes responsible for the observed phenotype, MM.1S cells knocked down for PRMT1 were used for m6A-Seq analyses.

first: Guangyao

last: Kong


title: FEZ1 participates in human embryonic brain development by modulating neuronal progenitor subpopulation specification and migration [scRNA-seq]

city: Singapore

first: John Chua

last: Jia En

address: 28 Medical Dr

department: Centre for Life Sciences

country: Singapore

institute: National University of Singapore

summary: Using bulk RNA-seq and scRNA-seq, we identifed gene expression changes between wildtype and FEZ1 knockout brain organoids.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype and FEZ1 knockout brain organoids derived from H1 human embryonic stem cells

first: Yinghua

last: Qu

first: Omer

last: An

first: Henry

first: Yi-Chin

last: Toh

first: John

last: Chua


title: Co-chaperone-mediated post-translational control of efflux pump induction underlies adaptive β-lactam resistance in Caulobacter crescentus. [ChIP-Seq 2]

status: Public on Nov 09 2023

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

institute: University of Geneva, Faculty of Medicine / CMU

summary: The acquisition of multi-drug resistance (MDR) determinants jeopardizes treatment of bacterial infections with antibiotics. The tripartite efflux pump AcrAB-NodT confers adaptive MDR in the non-pathogenic α-proteobacterium Caulobacter crescentus via transcriptional induction by first-generation quinolone antibiotics. We discovered that overexpression of AcrAB-NodT by mutation or exogenous inducers confers resistance to cephalosporin and penicillin (β-lactam) antibiotics. Combining two-step mutagenesis-sequencing (Mut-Seq) and cephalosporin-resistant point mutants, we dissected how TipR targets a common operator of divergent tipR and acrAB-nodT promoter in adaptive and/or potentiated AcrAB-NodT-directed efflux. Chemical screening identified compounds that either interfere with DNA-binding by TipR  or induce its ClpXP-dependent proteolytic turnover. We found that long-term induction of AcrAB-NodT disfigures the envelope and that homeostatic control by TipR includes co-induction of the DnaJ-like co-chaperone DjlA, to boost pump assembly and/or capacity in anticipation of envelope stress. Thus, the adaptive MDR regulatory circuitry reconciles drug efflux with co-chaperone function for trans-envelope assemblies and maintenance.

overall_design: Examination of DjlA-HA and others DnaJ-like co-chaperone proteins whole genome binding/occupancy (ChIP-Seq) in the model organism Caulobacter crescentus.

first: Jordan

last: Costafrolaz

first: Gaël

last: Panis

first: Bastien

last: Casu

first: Silvia

last: Ardissone

first: Laurence

last: Degeorges

first: Martin

last: Pilhofer

middle: H


title: Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase [easyCLIP]

first: Neuza

last: Reis Matias

overall_design: Libraries were made following the protocol: Ultraviolet (UV) cross-linked and immunoprecipitation (CLIP)-sequencing (easyCLIP, Porter et al., 2021). easyCLIP was performed on testes from eYFP-Syp males as well as wild-type testes with no epitope (w1118, negative control), and cDNA libraries were made from the recovered RNAs.

last: Matias

first: Douglas

middle: F

last: Porter


title: Deficiency of Rpsa results in reduced levels of H3K4me3 in inflammatory cytokines promoter regions

first: yan

last: jiang

address: 东单三条5号 中国医学科学院基础医学研究所

summary: After HSV-1 infection, ribosomal protein RPSA can recognize viral DNA and promotes the expression of proinflammatory cytokines. Through ChIP-seq, we found that the level of H3K4me3 in proinflammatory cytokines(Il1b, Il6, Il12b, etc.) promoter regions was decreased due to Rpsa deficiency.

overall_design: We constructed Rpsa induced konckout RAW264.7 cell lines and performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me3 in WT and Rpsa-iKO RAW264.7 cells infected with or without HSV-1.

first: Yan

last: Jiang

first: Henan

last: Xu


title: mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with siRNA-mediated knockdown of KMT2E-AS1 or KMT2E

city: Pittsburgh

first: Satoshi

last: Okawa

address: 200 Lothrop Street

institute: University of Pittsburgh

summary:
Purpose: In lung tissue of mice with experimental PH, we identified an upregulated lncRNA 5031425E22 which mapped to a human ortholog KMT2E-AS1. Across mammals, this lncRNA gene sits adjacent (head-to-head) to the chromosomal location of the histone lysine N-methyltransferase 2E gene (KMT2E), a member of a family of regulators controlling histone 3 lysine 4 trimethylation (H3K4Me3) and chromatin remodeling. We found that both mouse lncRNA E22 and human KMT2E-AS1 were increased in multiple in vivo rodent and human instances of PH. This study was designed to compare the RNA profile of human pulmonary arterial endothelial cells (HPAECs) treated with siRNA targeting KMT2E-AS1, KMT2E and negative control respectively.
Method: Primary HPAECs were grown in EBM-2 basal medium supplemented with EGM-2 MV BulletKit (Lonza). Experiments were performed at passages 5 to 8. Cultured HPAECs were transfected with siRNAs targeting either negative control, KMT2E-AS1 or KMT2E, then exposed to hypoxic stress (0.2% oxygen) for 24 hours. Cells were harvested for total RNA extraction, and total RNA samples received ribosomal depletion and directional (stranded) RNA library prep. mRNA and lncRNA profiles were generated by deep sequencing, using NextSeq P3 flow cell (2 x 101bp, 40M reads/sample). RNA-Seq reads were mapped against the human genome build hg19 using STAR aligner and the read counts for each gene were calculated using featureCounts. Gene expression was normalized by DESeq2 with variance-stabilizing transformation (VST) and the low expression genes with total counts across all samples less than 10 were excluded. The differential gene expression analysis was performed using DESeq2 with the adjusted p-value cutoff of 0.05. The Benjamini-Hochberg method was used for multiple test correction. GSEA was conducted on differentially expressed genes with the enrichR R package [4] using the "GO_Biological_Process_2021", "Reactome_2022", "KEGG_2021_Human" databases.

overall_design: Hypoxic HPAEC RNA profile with siRNA knockdown of either KMT2E-AS1 or KMT2E

first: Stephen

last: Chan

first: Yi-Yin

last: Tai


title: Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression (tumor)

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Immune escape is a prerequisite of tumor growth. We previously described a decline in intratumor activated GZMB+CD8+ T cells and T cell receptor (TCR) clonotype diversity in invasive compared to in situ (DCIS) breast carcinomas implying a role for decreasing TCR diversity in tumor progression. Here, we evaluated peripheral blood TCR clonotype diversity in breast cancer patients diagnosed with DCIS or de novo stage IV disease at different ages. We found that peripheral TCR diversity is associated with clinicopathologic, and peripheral immune status and it correlates with the frequency of CD8+ T cells in DCIS of young patients. These results provide new insights to the role of host immunity and breast cancer development in different aged women.

overall_design: To identify the immune repertoire of the Bulk FFPE RNA seq data of 16 patients we ran the fastq files through RIMA. Ran the Bayes Prism deconvolution method to identify the immune cell repertoire of the Bulk RNA seq data. Performed differential gene expression analysis and GSEA across Chao1 high and Low patients.

first: Jun

last: Nishida

first: Simona

last: Cristea

first: Franziska

last: Michor

first: Sudheshna

last: Bodapati


title: The Genetic and Epigenetic Features of Bilateral Wilms Tumor Predisposition [DNA methylation]

first: Changde

last: Cheng

overall_design: Genomic DNA (1 µg) from Wilms tumors was bisulfite converted using the EZ DNA Methylation kit (Zymo Research Corp, Irvine, CA) according to the manufacturer’s instructions. Converted samples were processed and hybridized to the Infinium MethylationEPIC BeadChip (850K) system (Illumina, San Diego, CA).

first: Andrew

last: Murphy

first: Xiang

last: Chen


title: Efficient derivation of transgene-free porcine induced pluripotent stem cells enables in  vitro modeling of species-specific developmental timing

city: Calgary

first: Li-Fang (Jack)

last: Chu

state: Alberta

address: 2500 University Drive NW

country: Canada

institute: University of Calgary

summary: Sus domesticus (pig) are an excellent large mammalian model for comparative studiesdue to their relatively comparable physiology and organ size to humans. The derivation of  transgene-free porcine pluripotent stem cells (PiPSCs) will therefore benefit the development of  porcine-specific models for regenerative biology and its medical applications. In the past, this  effort has been hampered by a lack of understanding of the signaling milieu that stabilizes the  porcine pluripotent state in vitro. Here, we report that transgene-free PiPSCs can be efficiently  derived from porcine fibroblasts by episomal vectors along with microRNA-302/367 using  optimized protocols tailored for this species. Established PiPSCs can robustly differentiate into  derivates representing the primary germ layers in vitro and in vivo. Furthermore, the transgene-  free PiPSCs preserve intrinsic species-specific developmental timing in culture. This capacity is  demonstrated by establishing a porcine in vitro segmentation clock model that, for the first time,  displays a specific periodicity at ~ 3.7 hours, a time scale recapitulating in vivo porcine  somitogenesis. We therefore propose that these transgene-free PiPSCs can serve as a powerful  tool for modeling development and disease, informing both conserved and unique features of  mammalian pluripotency and developmental timing mechanisms.

overall_design: A total of 36 bulk RNA-seq samples: (1) compare undifferentiated clonal PiPSC lines to fibroblasts. (2) PiPSC differentiation to various lineage-specific progenitors. (3) PiPSC differentiation to primitive streak, PSM and somite cell fates. To construct the RNA-seq library, total RNA from each sample (an input of ~100 ng total (RNA) was used following the LM-seq protocol

first: Li-Fang

first: J

middle: V

last: Conrad

first: Susanne

last: Meyer

first: Daniel

last: Mamott

first: Bret

last: Duffin

first: Pranav

last: Ramesh

first: Maggie

last: Rusteika

first: Jaime

last: Neira

first: Jue

last: Zhang

first: Emily

last: Hiles

first: Eve

last: Higgins

first: John

last: Steill

first: Ron

last: Stewart

first: James

last: Thomson

first: Monica

last: Bautista

first: Jack

last: Freeman

first: Zijian

last: Ni

first: Shiying

last: Liu

first: Mark

last: Ungrin

first: Derrick

last: Rancourt

first: Dennis

middle: O

last: Clegg


title: POTENT LATENCY REVERSAL BY TAT RNA ENABLES IN-DEPTH MULTI-OMIC ANALYSIS OF THE TRANSLATION-COMPETENT HIV RESERVOIR

city: Beerse

first: Filmon

last: Eyassu

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

summary: HIV infection remains incurable due to the long-term persistence of latently infected cells, capable of refueling viremia upon antiretroviral therapy interruption. Shock-and-kill strategies aim to purge this latent reservoir by inducing the expression of viral genes, making infected cells visible for cleanup by the immune system. Here, we present a Tat mRNA formulation that, when combined with panobinostat, enables latency reversal at levels >3-fold higher than those reached with the most potent mitogens. We demonstrate that this mRNA formulation does not alter the transcriptome or phenotype of CD4 T cells, enabling the ex vivo assessment of infected cells upon latency reversal in a near-native state. Taking advantage of this characteristic, we show transcriptomic and proteomic differences between infected cells upon latency reversal and non-infected cells, including the upregulation of the cytotoxic protein granzyme A and a novel long non-coding RNA. Overall, we demonstrate that a Tat mRNA formulation enables potent reactivation of latent HIV, presenting a valuable research tool for studying the inducible HIV reservoir, as well as paving the way to a more effective shock-and-kill functional cure.

overall_design: Sorted CD4 cells from 4 donors were treated with various stimuli at 2 time points. Comparison made for each treatment at each time point

first: Marion

last: Pardons

first: Basiel

last: Cole

first: Laurens

last: Lambrechts

first: Sofie

last: Rutsaert

first: Ytse

last: Noppe

first: Jerel

last: Vega

first: Erik

last: Nijs

first: Ellen

last: Van Gulck

first: Daniel

last: Boden

first: Linos

last: Vandekerckhove


title: Co-chaperone-mediated post-translational control of efflux pump induction underlies adaptive β-lactam resistance in Caulobacter crescentus [RNA-seq]

first: Patrick

last: Viollier

overall_design: Global transcriptome profiling (gene expression) by RNA-Seq in Caulobacter crescentus NA1000(WT) after Nalidixic acid treatment.

first: Jordan

last: Costafrolaz

first: Gaël

last: Panis

first: Bastien

last: Casu

first: Silvia

last: Ardissone

first: Laurence

last: Degeorges

first: Martin

last: Pilhofer


title: Co-chaperone-mediated post-translational control of efflux pump induction underlies adaptive β-lactam resistance in Caulobacter crescentus [ChIP-seq]

overall_design: Examination of TipR and DjlA-HA whole genome binding/occupancy (ChIP-Seq) in the model organism Caulobacter crescentus.


title: Co-chaperone-mediated post-translational control of efflux pump induction underlies adaptive β-lactam resistance in Caulobacter crescentus

overall_design: Refer to individual Series


title: Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression (blood)

first: Kornelia

last: Polyak

state: MA

overall_design: To identify the immune repertoire of the Bulk RNA seq data of 93 patients we ran the fastq files through RIMA that generates a raw counts and transcript per million file. Ran the Bayes Prism deconvolution method to identify the immune cell repertoire of the Bulk RNA seq data and performed clustering analysis, differential gene expression analysis and GSEA to identify the significant differences across the Chao1 high and Low patients and different age groups.

first: Jun

last: Nishida

first: Simona

last: Cristea

first: Franziska

last: Michor

first: Sudheshna

last: Bodapati


title: Translation-coupled sensing and degradation of RNA-protein crosslinks [Ribo-Seq: dataset_1]

first: Allen

last: Buskirk

overall_design: Ribosome profiling of three biological replicates of HAP1 cells with and without treatment with 4-thio-uridine and UV to induce protein-RNA crosslinks.


title: Genome-wide maps of H3K4Me3 histone modification in human pulmonary endothelial cells under hypoxia

first: Adam

last: Handen

state: Pennsylvania

department: Vascular Medicine Institute

summary: Purpose: In lung tissue of mice with experimental PH, we identified an upregulated lncRNA 5031425E22 which mapped to a human ortholog KMT2E-AS1. Across mammals, this lncRNA gene sits adjacent (head-to-head) to the chromosomal location of the histone lysine N-methyltransferase 2E gene (KMT2E), a member of a family of regulators controlling histone 3 lysine 4 trimethylation (H3K4Me3) and chromatin remodeling. We found that both mouse lncRNA E22 and human KMT2E-AS1 were increased in multiple in vivo rodent and human instances of PH. This ChIP-sequencing study was designed to compare the histone 3 lysine 4 methylated regions/gene profile of human pulmonary arterial endothelial cells (HPAECs) under hypoxia as compared to normoxia. Method: Primary HPAECs were grown in EBM-2 basal medium supplemented with EGM-2 MV BulletKit (Lonza). Experiments were performed at passages 5 to 8. Cultured HPAECs were either under normoxia or hypoxia (0.2% oxygen) for 24 hours. Cells were fixed, crosslinked, and sonicated to get soluble chromatin for immunoprecipitation. 10% input of crosslinked DNA was saved while the remining DNA was precipitated with histone 3 lysine 4 antibody (H3K4Me3, Abcam, ab8580) or non-immune rabbit IgG (Pierce magnetic ChIP kit). Chromatin/antibody complex was then pulled down using Protein A/G Magnetic Beads (Pierece).  DNA samples were proceeded with ChIP-sequencing (sequencing platform: DNBSeqTM, 20M reads).

overall_design: H3K4Me3 ChIP pulldown of HPAECs under hypoxia vs normoxia using 7 total samples: 1 control, 3 normoxia, and 3 hypoxia.

first: Stephen

last: Chan

first: Miranda

last: Tai