title: MCM complexes are barriers that restrict loops and TADs

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Eukaryotic genomes are compacted into loops and topologically associating domains (TADs), which contribute to transcription, recombination and genomic stability. Cohesin extrudes DNA into loops that are thought to lengthen until it encounters CTCF boundaries. Little is known whether loop extrusion is impeded by macromolecular machines. We demonstrate that the replicative helicase MCM is a barrier that restricts loops and TADs in G1 phase. Single-nucleus Hi-C of one-cell embryos revealed that MCM loading reduces CTCF-anchored loops and increases TAD boundary insulation, suggesting loop extrusion is impeded before reaching CTCF. Single-molecule imaging provides evidence that MCM are physical barriers that constrain cohesin translocation in vitro. Simulations are consistent with MCM as abundant, random barriers with low permeability. We conclude that distinct loop extrusion barriers contribute to shaping 3D genomes.

overall_design: in situ Hi-C and micro-C from HCT116 MCM2-AID cells, treated with DMSO or Auxin, and with or without triptolide treatment

first: Bart

last: Dequeker

first: Johanna

last: Gassler

first: Sean

last: Powell

first: Imre

last: Gaspar

first: Kikuë

last: Tachibana


title: Expression data from isolated perivascular cells from tumor tissues

status: Public on Mar 03 2022

city: STOCKHOLM

first: Kayoko

last: Hosaka

state: Solna

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska institutet

summary: Tumor tissues contain various cell types and we focus on the stromal cell component in the tumor microenvironment to study their role and interaction. We isolated perivascular cells from two different fibrosarcoma tumor types and compared gene expression patterns.

overall_design: We isolated perivascular cells using NG2 markers and each group have three biological samples. For the FGF group, we established human FGF overexpressing cell lines and inject them into mice. For the control group,  the tumor cells did not express human FGF and were also injected into mice. The tumor size at the isolation time is similar.

first: Yunlong

last: Yang


title: Distinct contributions of ventral CA1/amygdala co-activation to the induction and maintenance of synaptic plasticity

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

type: Expression profiling by high throughput sequencing

summary: The amygdala is known to modulate hippocampal synaptic plasticity. One role could be an immediate effect of basolateral amygdala (BLA) in priming synaptic plasticity in the hippocampus. Another role could be through associative synaptic co-operation and competition that triggers events involved in the maintenance of synaptic potentiation. We present evidence that the timing and activity level of BLA stimulation are important factors for the induction and maintenance of long-term potentiation (LTP) in ventral hippocampal area CA1. A 100 Hz BLA co-stimulation facilitated the induction of LTP, whereas 200 Hz co-stimulation attenuated induction. A 100 Hz BLA co-stimulation also caused enhanced persistence, sufficient to prevent synaptic competition. This maintenance effect is likely through translational mechanisms, as mRNA expression of primary response genes was unaffected, whereas protein level of plasticity-related products was increased. Further understanding of the neural mechanisms of amygdala modulation on hippocampus could provide insights into the mechanisms of emotional disorders.

overall_design: Gene expression in microdissected vCA1 acute slices 30 min following L-LTP induction with strong tetanization (STET) accompanied by 100Hz (S100) or 200Hz (S200) basolateral amygdala stimulation. (Conditions: Control [basal], LTP [STET], STET + S100, STET + S200; N=3)

first: Yee

middle: S

last: Chong

first: Yan

middle: J

last: Lee

first: Toh

middle: H

last: Ch'ng

first: Sreedharan

last: Sajikumar


title: ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis

city: Oxford

first: Aleksandr

last: Fedorov

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A disappointingly small proportion (10-30%) of patients with cancer show lasting responses to immune checkpoint blockade (ICB)-based monotherapies. The RNA-editing enzyme ADAR1 is an emerging determinant of resistance to ICB therapy, and prevents ICB responsiveness by repressing immunogenic double-stranded (ds)RNAs, such as those arising from the dysregulated expression of endogenous retroelements (EREs). These dsRNAs trigger an interferon (IFN)-dependent antitumor response by activating the A-form dsRNA (A-RNA) sensing proteins MDA-5, PKR, and OAS1. Here, we show that ADAR1 also prevents accrual of endogenous Z-form dsRNA elements (Z-RNAs) which were enriched in the 3’UTRs of IFN-stimulated mRNAs. Depleting ADAR1 resulted in Z-RNA accumulation and activation of the Z-RNA sensor ZBP1, culminating in RIPK3-mediated necroptosis. As no clinically viable ADAR1 inhibitors currently exist, we searched for a compound that can override the requirement for ADAR1 inhibition and directly activate ZBP1. We identified a small molecule, the curaxin CBL0137, which potently activates ZBP1 by triggering Z-DNA formation in cells. CBL0137 induced ZBP1-dependent necroptosis in cancer-associated fibroblasts and strongly reversed ICB unresponsiveness in mouse models of melanoma. Collectively, these results demonstrate that ADAR1 represses endogenous Z-RNAs and identifies ZBP1-mediated necroptosis as a new determinant of tumor immunogenicity masked by ADAR1. Therapeutic activation of ZBP1-induced necroptosis provides a readily-translatable avenue for rekindling immune responsiveness of ICB-resistant human cancers.

overall_design: ChIP-seq of mouse embryonic fibroblasts(MEFs) with FLAG-tagged ZBP1 for two conditions: untreated cells (FLAG, IgG antibodies), cells treated with CBL0137 for 14 hours(FLAG, IgG, Z22 antibodies).

first: Ting

last: Zhang

first: Chaoran

last: Yin

first: Alan

last: Herbert

first: Siddharth

last: Balachandran

first: Vasily

last: Studitsky


title: Single-nuclei RNA sequencing analysis of myocardial infarction in WT and PDGFRb EC-specific KO mouse

status: Public on Mar 02 2022

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

country: USA

institute: University of Pennsylvania

summary: To investigate the transcriptome change in myocardial infarction (MI)-associated cells, we prepared single nuclei derived from mouse injured infarcted heart tissues and performed RNA sequencing analysis. Considering that adult cardiomyocytes are limited for 10XGenomics scRNA-seq due to large size not compatible with microfluidic channels, we prepared nuclei from the tissues. Particularly, cardiac nuclei were harvested from PDGFRb fl/fl control or Cdh5-Cre; PDGFRb fl/fl KO mouse.

overall_design: Myocardial infarction (MI) was induced in WT or PDGFRb EC-specific KO mice by ligation of left coronary artery. 2 weeks or 4 weeks after the surgery, infarcted tissues were harvested. Single-nuclei was prepared for RNA sequencing.

first: Menggui

last: Huang

first: Duo


title: RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [mRNA_seq libraries]

status: Public on Mar 04 2022

city: Cambridge

first: Satyaki

last: PRV

state: MA

address: 455 Main street, Room number 549

institute: Whitehead Institute for Biomedical Research

summary: Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to  offspring – is under complex epigenetic control. We show here that plant-specific RNA  Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. thaliana endosperm from reciprocal heterozygotes produced by crossing wild-type plants to Pol IV mutants. We find that maternally and paternally acting Pol IV have divergent effects on endosperm. Losses of maternal and paternal Pol IV impact sRNAs and DNA methylation at distinct genomic sites. Strikingly, maternally and paternally-acting Pol IV have antagonistic impacts on gene expression at some  loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of origin effects have only rarely been described and are consistent with a gene regulatory system  evolving under parental conflict

overall_design: Sequencing of three replicates of F1 seed endosperm mRNA from mat nrpd1+/- (Ler nrpd1-/- x  Col-0 F1), pat nrpd1+/- (Ler x Col nrpd1-/- F1), nrpd1-/- (Ler nrpd1-/- x Col-0 nrpd1-/- F1) and two replicates of wild-type (Ler x Col-0 F1).

first: Mary

last: Gehring

first: PRV

last: Satyaki


title: Chikungunya Virus Time Course Infection of Human Macrophages

city: Provo

first: Brett

middle: E

last: Pickett

state: UT

department: Microbiology and Molecular Biology

institute: Brigham Young University

summary: Human monocyte-derived macrophage cells were infected with Chikungunya virus (CHIKV) to identify and quantify intracellular transcriptional changes that contribute to the host response to infection with CHIKV. RNA was collected from these cells at 8 and 24 hours post-infection (hpi) and were compared to mock-infected cells. The RNAseq data was then analyzed to determine the genes, functions, and signaling pathways that were significantly affected in an effort to predict existing drugs that could be repurposed as potential therapeutics for CHIKV.

overall_design: mRNA profiles of human monocyte-derived macrophages at 8hpi and 24hpi with Chikungunya virus (CHIKV)

first: Madison

last: Gray

first: Israel

last: Guerrero-Arguero

first: Antonio

last: Solis-Leal

first: Richard

middle: A

last: Robison

first: Bradford

middle: K

last: Berges


title: Direct cellular reprogramming facilitates development of viral T antigen-driven Merkel cell carcinoma in mice

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Co-expression of MCPyV TAgs and the Merkel cell lineage determinant ATOH1, in p53-deficient keratinocytes and their neuroendocrine progeny, yields tumors closely mimicking human MCC. Direct cellular reprogramming in vivo may provide a novel approach to generate tumors for which the cell of origin is uncertain.

overall_design: Characterization of skin tumors arising in transgene-inducible mice expressing Merkel cell polyomavirus T antigens, plus or minus the lineage reprogramming transcription factor ATOH1, plus or minus Trp53 deletion.

first: Monique

last: Verhaegen

middle: C

first: Andrzej

last: Dlugosz


title: RNA-sequencing of bovine fetal ovaries throughout gestation

city: Adelaide

first: Katja

last: Hummitzsch

state: SA

address: Level 5, North Tce/George Street

department: Obstetrics& Gynaecology

country: Australia

institute: The University of Adelaide

summary: Understanding the developmental origins of reproductive disorders cannot be achieved without understanding normal development and the connected transcriptomics of the fetal ovary. To better understand this, we profiled and analysed RNA from fetal ovaries across gestation (62-276 days, n=19). The platform used detected 25,133 genes for each sample across gestation. Principal Component analysis of the data clustered the samples in three stages of development [early I (up to 98 days), early II (98-135 days) and late (> 135 days)]. Differential expression of genes between the three stages will then be used to delineate the pathways which are up-/down-regulated during these developmental stages.

overall_design: Bovine fetal ovary mRNA profiles from two gestational stages, early  (≤ 135 days, n=9) and late (> 136 days, n=10)

first: Rafiatu

last: Azumah

first: Raymond

last: Rodgers

last: Anderson

first: Justin


first: Aleksandr

last: Fedorov

overall_design: Strand-specific total RNA-seq of IFNb-treated mouse embryonic fibroblasts (Zbp1-/-, Adar1-/-  MEFs) at three time points: 0h(untreated), 24h, 48h. Each experiment includes four biological replicas.

first: Ting

last: Zhang

first: Chaoran

last: Yin

first: Alan

last: Herbert

first: Siddharth

last: Balachandran

first: Vasily

last: Studitsky


title: Regulation of Chromatin Accessibility by hypoxia and HIF_2

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

institute: University of Liverool

summary: ATAC-seq was performed to investigate changes in chromatin accessibility in repsonse to HIF stabilisation via VH298

overall_design: HIF 1/2-α stabilisation was induced independent of dioxygenase inhibition by treating HeLa cells with 100 µM VH298 for 24 hs. DMSO treated cells were used as control. ATAC-seq was used to determine chromatin accessibility changes.

first: Michael

last: Batie


title: Sotos syndrome and healthy control subjects

status: Public on Mar 01 2022

city: Manchester

first: Caroline

last: Dive

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road

institute: Cancer Research UK Manchester Institute

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

overall_design: Refer to individual Series


title: Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation.

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: We report the gene expression profile of two polypolid Saccharomyces pastorianus, lager yeast strains, the Group I strain CBS1538 and the Group II strain W34/70. Saccharomyces pastorianus is a hybrid of Saccharomuyces cerevisiaie and Saccharomyces eubayanus. We report that the gene expression patterns are correlated with the gene copy number of S. cerevisiae and S. eubayanus alleles.

overall_design: The strains were grown under fermentation conditions and samples were taken on Day 2 and Day 4 of the fermentation for RNAseq analysis. The strains were also grown in minimal medium without amino acids and with (NH4)2SO4 as a nitrogen source. The transcript patterns were compared in the three conditions.

first: Roberto

last: de la Cerda García-Caro

first: Ursula

last: Bond


title: Regulation of Chromatin Accessibility by hypoxia and HIF_1

summary: ATAC-seq was performed to investigate changes in chromatin accessibility in repsonse to hypoxia

overall_design: HeLa cells were grown at 21% oxygen, treated with control and HIF1B siRNA and exposed to 1% oxygen (hypoxia) for 0, 1 and 24 hs. HeLa cells were also grown at 21% oxygen, treated with control siRNA and exposed to 1% oxygen for 24 hs followed by reoxygenation  at 21% oxygen for 1 h. ATAC-seq was used to determine chromatin accessibility changes.


title: RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [sRNA_seq libraries]

first: Satyaki

last: PRV

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Sequencing of three replicates of sRNA from mat nrpd1+/- (Ler  nrpd1-/- x  Col-0 F1) and nrpd1-/- (Ler nrpd1-/-  x Col-0 nrpd1-/- F1) and two replicates from pat nrpd1+/- (Ler x Col  nrpd1-/- F1)

first: Mary

last: Gehring

first: PRV

last: Satyaki


title: The ParB clamp docks onto Smc for DNA loading via a joint-ParB interface

city: Lausanne

first: Anna

last: Anchimiuk

state: Vaud

address: UNIL-Sorge District

department: Department of Fundamental Microbiology

institute: University of Lausanne

summary: Chromosomes readily unlink from one another and segregate to daughter cells during cell division highlighting a remarkable ability of cells to organize long DNA molecules. SMC complexes mediate chromosome folding by DNA loop extrusion. In most bacteria, SMC complexes start loop extrusion at the ParB/parS partition complex formed near the replication origin. Whether they are recruited by recognizing a specific DNA structure in the partition complex or a protein component is unknown. By replacing genes in Bacillus subtilis with orthologous sequences from Streptococcus pneumoniae, we show that the three subunits of the bacterial Smc complex together with the ParB protein form a functional module that can organize and segregate chromosomes when transplanted into another organism. Using chimeric proteins and chemical cross-linking, we find that ParB binds to the Smc subunit directly. We map a binding interface to the Smc joint and the ParB CTP-binding domain. Structure prediction indicates how the ParB clamp presents DNA to the Smc complex to initiate DNA loop extrusion.

overall_design: Chromosome conformation capture of Bacillus subtilis carrying heterologous Smc-ScpAB and chimeric loader protein ParB

first: Florian

last: Bock

first: Stephan

last: Gruber


title: Gene Expression Profiling of Acute Pancreatitis

city: Vancouver

first: Robert

middle: E. W.

last: Hancock

state: British Columbia

address: 2259 - Lower Mall Research Station

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary: Peripheral blood was collected from 87 patients with acute pancreatitis (AP) of varying severity (Mild=57, Moderately-Severe=20, Severe=10) within 24 hours of presentation to the hospital and from 32 healthy controls. RNA-Seq was performed to identify changes in expression in severe AP cf. mild, moderately-severe, and healthy controls.

overall_design: RNA-Seq of blood collected from pancreatitis patients with varying levels of severity.

first: Bhavjinder

last: Dhillon

first: Maryam

last: Nasverdani

first: Tracy

last: Chew

first: Arjun

last: Baghela

first: Benjamin

last: Tang

first: Reza

last: Falsafi

first: Guy

last: Eslick

last: Cox


title: The role of the RNA chaperone protein ProQ in Pasteurella multocida

city: Melbourne

first: Deanna

last: Deveson Lucas

state: Victoria

address: 15 Innovation walk, Monash University, Clayton

institute: Monash University

summary: The Gram-negative pathogen Pasteurella multocida is responsible for many important animal diseases. While a number of P. multocida virulence factors have been identified, very little is known about how gene expression and protein production is regulated in this organism. One mechanism by which bacteria regulate transcript abundance and protein production is riboregulation, which involves the interaction of a small RNA (sRNA) with a target mRNA to alter transcript stability and/or translational efficiency. This interaction often requires stabilization by a ribosome binding protein such as ProQ or Hfq. In E. coli and other species, ProQ has been shown to play a critical role in stabilizing sRNA-mRNA interactions and preferentially binds to 3’ stem-loop regions of the mRNA transcripts, characteristic of intrinsic transcriptional terminators. The aim of this study was to determine the role of ProQ riboregulation in P. multocida and identify the RNA regions to which it binds. We assessed differentially expressed transcripts in a proQ mutant and identified sites of direct ProQ-RNA interaction using in vivo UV-crosslinking and analysis of cDNA (CRAC). These analyses demonstrated that ProQ binds to, and stabilises, ProQ-dependant sRNAs and transfer RNAs in P. multocida via adenosine enriched, highly structured sequences. The binding of ProQ to two RNA molecules was characterised and showed that ProQ bound within the coding sequence of the uncharacterized PmVP161_1121 and within the 3’ region of the sRNA Prrc13.

overall_design:
We report the transcriptional changes caused by the lack or overexpression of the ProQ protein
RNA-seq comparing wild-type, proQ mutant and complemented mutant strains of P. multocida

first: John

middle: D

last: Boyce

first: Emily

middle: L

last: Gulliver


title: RNA-seq analysis of control, NASH, and TH-treated NASH liver

first: Jin

last: Zhou

address: 8 College Road

department: CVMD

institute: Duke-NUS Medical School

summary: We performed RNA-seq analysis of pooled RNA extracted from liver of mice fed normal chow (control), WDF (NASH), and WDF+TH (TH-treated NASH).

overall_design: We compared the difference in NASH vs control, and TH-treated NASH vs NASH

first: Paul

middle: M

last: Yen


title: Gene expression signatures of splenic CD31+ACKR4+ and CD31+ACKR4- endothelial cells from Ackr4GFP/wt mice

city: Hannover

first: Berislav

last: Bosnjak

address: Carl-Neuberg Straße 1

department: Institute of Immunology

country: Germany

institute: Hannover Medical School

summary: The atypical chemokine receptor 4 (ACKR4)-expressing  spleen endothelial cells (ECs) form a three-dimensional sinusoidal network connected via shunts to the marginal sinus and tightly surrounds the outer perimeter of the marginal zone. To better define this new  vascular compartment within the red pulp of the spleen, were sorted CD31+ACKR4+ and CD31+ACKR4- EC populations, routinely yielding 92-98% cell purity and analyzed their transcriptional profiles.

overall_design: Samples of CD31+ACKR4+ and CD31+ACKR4- EC populations were obtained in two completely independent flow cytometric sorts from spleens of 2-3 Ackr4GFP/wt mice (Heinzel et al., 2007, Proc Natl Acad Sci U S A 104, 8421) for each sort.

first: Kathrin

last: Werth

first: Reinhold

last: Förster


title: RNA-sequencing of PRMT7 proficient and deficient B16.F10 melanoma cells: siLuciferase (control) and siPRMT7 transcriptomes in B16.F10

city: Montreal

first: Stephane

last: Richard

state: Quebec

address: 3755 Côte-Ste-Catherine Road

department: Departments of Oncology and Medicine

institute: Lady Davis Institute - JGH, McGill University

summary:
Purpose: RNA-sequencing analysis defined a novel role for PRMT7 in melanoma cancer immunotherapy.
Methods: PRMT7-deficient cells and control B16.F10 cells treated with mIFN-γ (100ng/ml) for 24 hours. B16.F10 melanoma cells mRNA profiles were generated by deep sequencing, in triplicate using TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, Hiseq4000, SR75 platform located at San Diego, CA; UCSD IGM Genomics Facility, La Jolla, CA). Resulting libraries were multiplexed and sequenced with 100 base pair (bp) to a depth of approximately 30 million reads per sample. The sequence reads that passed quality filters were trimmed with Trimmomatic v0.39. STAR v2.7.1a was then used to align the reads to the mouse genome (mm10/GRCm38). Gene expression was quantified across all samples with HOMER v4.11.1, and the normalization was carried out through the regularized logarithm (rlog) transformation of DESeq2 v1.26.0. Differential expression between PRMT7 WT and knockdown samples were calculated through DESeq2 v1.26.0, and the gene expression was considered significantly different if the absolute value of the log-fold-change (LFC) was higher than 2, the base means larger than 10 and the false discovery rate (FDR) less than 0.05.
Results: Differential expression analysis between the siLuc and siPRMT7 conditions yielded 185 and 251 genes with statistically significant differences and absolute fold change greater than 2 in the IFN– and IFN+ treatments respectively. Of these, 85% of genes are upregulated in the IFN– treatment, while 72% of genes are downregulated in the IFN+ treatment. Gene ontology analysis using the 185 and 251 lists of differentially expressed genes implies that the downregulated biological processes are enriched for the immune response pathways, while upregulated genes are more involved in the cell cycle process. Altered expression of some genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to better understand PRMT7 function in cancer immunotherapy.
Conclusions: Our study represents the first detailed analysis of B16.F10 melanoma transcriptomes without PRMT7 expression, with biologic replicates, generated by RNA-seq technology. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of PRMT7 biologic functions in modulating melanoma transcriptome.

overall_design: mRNA profiles of CTRL and PRMT7 depleted B16.F10 melanoma cells treated with IFN-γ for 24h.

first: Nivine

last: Srour

first: Oscar

last: Villarreal


title: Transcriptome analysis of JAK2V617F HSPC and endogenous HSPC from irradiated and non-irradiated legs of recipient mice transplanted with JAK2V617F hematopoietic cells

city: Fontenay aux Roses

first: Daniel

last: LEWANDOWSKI

state: Ile-de-France

address: 18 route du Panorama

department: IBFJ/iRCM

country: France

institute: CEA

summary: using transplantation of transgenic knock-in JAK2V617F hematopoietic cells into a single irradiated leg, we show development of Polycythemia Vera (PV) from a single anatomical site in immuno-competent mice. Mutant cells colonizing the non-irradiated leg efficiently induce PV. We compared transcriptomic profiles of sorted JAK2V617F HSPC and their reciprocal endogenous WT HSPC in the non-irradiated and irradiated legs from recipient mice transplanted with JAK2V617F hematopoietic cells.

overall_design: we assesed the differentially expressed genes between endogenous WT and JAK2V617F sorted HSPC from the non-irradiated leg in order to find new potential therapeutic target for suppression of PV syndrome in this pre-clinical model through specific targeting of JAK2V617F cells.

last: Lewandowski

first: Shohei

last: Murakami


title: Skeletal muscle transcriptome response to a bout of endurance exercise in physically active and sedentary older adults

city: Manhattan

first: Aliza

last: Rubenstein

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: Age-related declines in cardiorespiratory fitness and physical function are mitigated by regular endurance exercise in older adults. This may be due, in part, to changes in the transcriptional program of skeletal muscle following repeated bouts of exercise. However, the impact of chronic exercise training on the transcriptional response to an acute bout of endurance exercise has not been clearly determined. Here, we characterized baseline differences in muscle transcriptome and exercise-induced response in older adults who were active/endurance trained or sedentary. RNA-sequencing was performed on vastus lateralis biopsy specimens obtained before, immediately after, and 3 h following a bout of endurance exercise (40 min of cycling at 60%–70% of heart rate reserve). Using a recently developed bioinformatics approach, we found that transcript signatures related to type I myofibers, mitochondria, and endothelial cells were higher in active/endurance-trained adults and were associated with key phenotypic features including V̇o2peak, ATPmax, and muscle fiber proportion. Immune cell signatures were elevated in the sedentary group and linked to visceral and intermuscular adipose tissue mass. Following acute exercise, we observed distinct temporal transcriptional signatures that were largely similar among groups. Enrichment analysis revealed catabolic processes were uniquely enriched in the sedentary group at the 3-h postexercise timepoint. In summary, this study revealed key transcriptional signatures that distinguished active and sedentary adults, which were associated with difference in oxidative capacity and depot-specific adiposity. The acute response signatures were consistent with beneficial effects of endurance exercise to improve muscle health in older adults irrespective of exercise history and adiposity.

overall_design: 19 older individuals (both male and female with two cohorts: Active and Sedentary) underwent an acute bout of cycling exercise with deep phenotyping and muscle biopsies before, immediately after, and three hours after exercise. Muscle biopsies were subjected to RNA-sequencing.

middle: B

first: J

last: Hinkley

first: Venugopalan

last: Nair

first: German

last: Nudelman

first: Todd

last: Trappe

first: Marcas

last: Bamman

first: Scott

middle: W

first: Bret

last: Goodpaster

first: Rick

last: Vega

first: Stuart

last: Sealfon

first: Elena

last: Zaslavsky

last: Coen


title: Partial pluripotent reprogramming in C2C12 myoblasts

status: Public on Feb 28 2022

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

address: 1170 Veterans Blvd

department: Computing

institute: Calico Life Sciences, LLC

summary: Partial pluripotent reprogramming has been reported to reverse some features of aging in mammalian cells and tissues. However, the impact of partial reprogramming on somatic cell identity programs and the necessity of individual pluripotency factors remain unknown. Here, we mapped trajectories of partial reprogramming in young and aged cells from multiple murine cell types using single cell transcriptomics to address these questions. We found that partial reprogramming restored youthful gene expression in adipogenic cells and mesenchymal stem cells but also temporarily suppressed somatic cell identity programs. We further screened Yamanaka Factor subsets and found that many combinations had an impact on aging gene expression and suppressed somatic identity, but that these effects were not tightly entangled. We also found that a partial reprogramming approach inspired by amphibian regeneration restored youthful gene expression in aged myogenic cells. Our results suggest that partial pluripotent reprogramming poses a neoplastic risk, but that restoration of youthful gene expression can be achieved with alternative strategies.

overall_design: C2C12 myoblasts were transduced with lentiviral vectors harboring CMV>Tet3G-T2A-Hygro alleles and positive cells were selected by culture in hygromycin B. Selected clones were then transduced with lentiviral vectors harboring TRE>{Sox2,Oct4,Klf4,Myc}-EFS>eGFP alleles and selected by FACS for eGFP expression. Cells were cultured for eight days in three experimental groups. (1) Control cells were not treated with Dox, (2) partially reprogrammed cells were treated with Dox for the first three days, and (3) positive control cells were treated with Dox for all eight days. RNA was isolated from triplicate wells of each condition on days 1, 3, 4, 5, 6, and 8. Only partially reprogrammed cells were collected on days 4, 5, and positive controls were only collected on day 8.


title: Characterization of peripheral blood TCR in patients with Type 1 Diabetes Mellitus by BD Rhapsody™ VDJ CDR3 Assay

city: Kyoto

first: Takuro

last: Okamura

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: We used the latest technology, BD Rhapsody, to analyze the pairing of α and β chains that constitute the TCR of PBMCs from patients with type 1 diabetes at the single-cell level.

overall_design: We used single-cell VDJ sequencing using the latest technology, BD Rhapsody, to identify the TCR sequences of autoreactive T cells characteristic of Japanese type 1 diabetes mellitus (T1DM) and to clarify the pairing of TCR of peripheral blood mononuclear cells from four patients with T1DM at the single-cell level.


title: Targeted suppression of miRNA-33 using pH low-insertion peptides improves atherosclerosis regression

city: New Haven

first: Xinbo

last: Zhang

state: Connecticut

address: Rm320, 10 Amistad St

department: Comparative Medicine

institute: Yale University

summary: Rationale: miRNA therapeutics have gained attention during the past decade. These oligonucleotide treatments can modulate the expression of miRNAs in vivo and could be used to correct the imbalance of gene expression found in human diseases such as obesity, metabolic syndrome and atherosclerosis. The in vivo efficacy of current anti-miRNAs technologies hindered by physiological and cellular barriers to delivery into targeted cells and the nature of miRNAs that allows one to target an entire pathway that may lead to deleterious off-target effects. For these reasons, novel targeted delivery systems to inhibit miRNAs in specific tissues will be important for developing effective therapeutic strategies for numerous diseases including atherosclerosis.    Objective: To explore the application of anti-miR-33 (miR-33-5p) conjugated pH Low-Insertion Peptides (pHLIP) constructs for the specific targeting of macrophages located in vascular lesions in the regression of atherosclerosis.  Methods and Results: The anti-miR-33 conjugated pHLIP constructs are preferentially delivered to atherosclerotic plaques macrophages. The inhibition of miR-33 using pHLIP-directed macrophage targeting improves atherosclerosis regression by increasing collagen content and decreased lipid accumulation within vascular lesions. Single cell RNA sequencing analysis revealed higher expression of fibrotic genes (Col2a1, Col3a1, Col1a2, Fn1, etc) and tissue inhibitor of metalloproteinase 3 (Timp3), and downregulation of matrix metallopeptidase 12 (Mmp12) in macrophages from atherosclerotic lesions targeted by pHLIP- anti-miR-33.  Conclusions: This study provides proof of principle for the application of pHLIP for treating advanced atherosclerosis via pharmacological inhibition of miR-33 in macrophages that avoids the deleterious effects in other metabolic tissues. This may open new therapeutic opportunities for atherosclerosis-associated cardiovascular diseases via selective delivery of other protective miRNAs.

overall_design: scRNA-seq of whole cells from atherosclerotic plaques of Ldlr-/- mouse treated with anti-miR-33pHLIP or ScrpHLIP

first: Carlos

last: Fernández-Hernando


title: ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis

city: Oxford

first: Aleksandr

last: Fedorov

address: John Radcliffe Hospital/Headley Way

institute: University of Oxford


title: The Androgen Receptor: A Therapeutic Target In Desmoplastic Small Round Cell Sarcoma

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

summary: Desmoplastic small round cell tumor (DSRCT) is an aggressive, usually incurable sarcoma subtype that predominantly occurs in post-pubertal young males. Recent evidence suggests that the androgen receptor (AR) can promote tumor progression in DSRCTs. However, the mechanism of AR-induced oncogenic stimulation remains undetermined. Herein, we demonstrate that  AR-directed antisense oligonucleotides (AR-ASO) block 5-dihydrotestosterone (DHT)-induced DSRCT cell proliferation and reduced xenograft tumor burden. RPPA analysis was performed to elucidate how AR signaling regulates cellular programs. To gain a preliminary understanding of the short-term pharmacodynamic effects of AR suppression, a group of JN-DSRCT xenografts was collected 10 days into their AR-ASO treatment for analysis by RPPA to assess early compensatory pharmacodynamic changes. Its blockade has long been of interest in managing prostate cancer, where a compensatory increase in AKT signaling has been reported following AR inhibition. Therefore, these results collectively validate another proof of concept of AR-based antisense activity in DSRCT and suggest a clinical path forward since the AR-ASO (AZD5312) was safe, and often effective, in PC patients (NCT03300505). Our findings have immediate clinical implications given the widespread availability of FDA-approved androgen-targeted agents used for prostate cancer.

overall_design: DSRCT  xenograft or PDX animal tumors for RPPA analysis were snap-frozen. Next, protein extraction from xenograft/PDX tumors was performed by homogenizing approximately 10 mg of frozen tissue in 500 μL of the lysis buffer using an electric tissue homogenizer (PRO Scientific). The homogenized tumors were incubated at +4°C for 2 hours to complete their dissociation and lysis. Altogether, the total lysed proteins from tumors were collected after centrifugation, quantified using BCA protein assay kit (Thermo Fisher Scientific), and stored at -80°C until further analyses. Lysates were processed, spotted onto nitrocellulose-coated FAST slides, probed with 377 validated primary antibodies, and detected using a DakoCytomation-catalyzed system with secondary antibodies. MicroVigene software program (VigeneTech) was used for automated spot identification, background correction, and individual spot-intensity determination. Expression data as Log2 values was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested.

first: Salah-Eddine

last: Lamhamedi-Cherradi

first: Brian

last: Menegaz


title: Cardiac fibroblasts regulate the development of heart failure via Htra3-TGF-β-IGFBP7 axis

city: Tokyo

first: Seitaro

last: Nomura

state: Select a State or Province

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

summary: Tissue fibrosis and organ dysfunction are hallmarks of age-related diseases including heart failure, but it remains elusive whether there is a common pathway to induce both events. Through single-cell RNA-seq, spatial transcriptomics, and genetic perturbation, we elucidate that high-temperature requirement A serine peptidase 3 (Htra3) is a critical regulator of cardiac fibrosis and heart failure by maintaining the identity of quiescent cardiac fibroblasts through degrading transforming growth factor-β (TGF-β). Pressure overload downregulates expression of Htra3 in cardiac fibroblasts and activated TGF-β signaling, which induces not only cardiac fibrosis but also heart failure through DNA damage accumulation and secretory phenotype induction in failing cardiomyocytes. Overexpression of Htra3 in the heart inhibits TGF-β signaling and ameliorates cardiac dysfunction after pressure overload. Htra3-regulated induction of spatio-temporal cardiac fibrosis and cardiomyocyte secretory phenotype are observed specifically in infarct regions after myocardial infarction. Integrative analyses of single-cardiomyocyte transcriptome and plasma proteome in human reveal that IGFBP7, which is a cytokine downstream of TGF-β and secreted from failing cardiomyocytes, is the most predictable marker of advanced heart failure. These findings highlight the roles of cardiac fibroblasts in regulating cardiomyocyte homeostasis and cardiac fibrosis through the Htra3-TGF-β-IGFBP7 pathway, which would be a therapeutic target for heart failure.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Integrative analyses of single-cell RNA-seq of cardiomyocytes and non-myocytes (including cardiac fibroblasts) and spatial transcriptomics during heart failure progression in mouse and human

>>>Submitter states that raw data are not available for human samples due to patient privacy concerns<<<

first: Toshiyuki

last: Ko

first: Kanna

last: Fujita

first: Takanori

first: Shintaro

last: Yamada

first: Hiroyuki

last: Aburatani

first: Issei

last: Komuro


title: Whole blood RNA-Seq of individuals with Sotos syndrome and healthy control subjects

first: Caroline

last: Dive

summary: To understand how NSD1 inactivation deregulates transcription, and to explore how this transcriptional deregulation affect human development, we profiled transcription in Sotos syndrome patients and healthy control individuals.

overall_design: RNA-Sequencing (RNA-Seq) was applied to primary whole blood samples of individuals with Sotos syndrome (i.e., probands, n=10), and matched healthy control subjects (n=15). Ten individuals with clinical features suggestive of classic Sotos syndrome (SS) whose diagnoses were confirmed molecularly (i.e., with an NSD1 mutation or deletion) were enrolled in the study. Also enrolled were one or both (if available) parents of each SS patient (parent controls, n=16), as well as siblings of patients that were of the same sex and close to the same age of the proband (n=3). Research subjects were recruited during two separate phases, which we refer to as the ‘discovery’ and ‘validation’ phases, each including five sets of patients and matched controls. The discovery phase sample set included five SS patients that were recruited at a local child health institute. For each proband, the discovery study included one or both parents whose samples were collected and processed at the same time. For three of these probands, anonymous sex and age-matched control subjects (blood donors) were included. The validation set included five SS probands as well as a healthy control subject that was matched to the case subject by sex, ancestry (Self-declared), and age (within six years). For each proband, at least one healthy control subject was included whose sample was collected and underwent all steps of processing and analysis at the same time as the probands sample, thereby serving as technical controls. Where available, siblings were included to act as controls that were matched for demographic factors (sex, age, and ancestry), as well as family and technical factors. Where matched siblings were not available, blood samples were collected from unrelated individuals that were matched to the patient by age, sex, and self-declared ancestry (Healthy volunteer controls) (N=2). Healthy control volunteers’ blood samples were collected on the same date and in the same location as the matched patient’s sample. One of these healthy volunteer control subjects (ID: 5530-P) is the mother of a proband that is included in this study, whose unaffected sibling is also included. The other healthy volunteer control subject (ID: 7634-M) is the mother of a patient whose sample was not analyzed as part of this study. Where siblings or volunteer subjects were not available, blood samples of sex/age matched healthy blood donors were accessed from a local blood collection facility. Where blood donor control samples were used, a sample of a parent of the proband was also included to control for technical variables and ancestry, representing the sex-matched parent where possible (for two out of three cases). For two infant subjects, where age/sex matched siblings were not available, nor could age-matched blood donor samples be accessed (due to the patient’s age), samples of both parents were included in all analysis.  See the associated publication for details of the study design.

first: Kevin

last: Brennan

first: Olivier

last: Gevaert


summary: A disappointingly small proportion (10-30%) of patients with cancer show lasting responses to immune checkpoint blockade (ICB)-based monotherapies. The RNA-editing enzyme ADAR1 is an emerging determinant of resistance to ICB therapy, and prevents ICB responsiveness by repressing immunogenic double-stranded (ds)RNAs, such as those arising from the dysregulated expression of endogenous retroelements (EREs). These dsRNAs trigger an interferon (IFN)-dependent antitumor response by activating the A-form dsRNA (A-RNA) sensing proteins MDA-5, PKR, and OAS1. Here, we show that ADAR1 also prevents accrual of endogenous Z-form dsRNA elements (Z-RNAs) which were enriched in the 3’UTRs of IFN-stimulated mRNAs. Depleting ADAR1 resulted in Z-RNA accumulation and activation of the Z-RNA sensor ZBP1, culminating in RIPK3-mediated necroptosis. As no clinically viable ADAR1 inhibitors currently exist, we searched for a compound that can override the requirement for ADAR1 inhibition and directly activate ZBP1. We identified a small molecule, the curaxin CBL0137, which potently activates ZBP1 by triggering Z-DNA formation in cells. CBL0137 induced ZBP1-dependent necroptosis in cancer-associated fibroblasts and strongly reversed ICB unresponsiveness in mouse models of melanoma. Collectively, these results demonstrate that ADAR1 represses endogenous Z-RNAs and identifies ZBP1-mediated necroptosis as a new determinant of tumor immunogenicity masked by ADAR1. Therapeutic activation of ZBP1-induced necroptosis provides a readily-translatable avenue for rekindling immune responsiveness of ICB-resistant human cancers.

overall_design: RIP-seq with IgG and Z22 antibodies for mouse embryonic fibroblasts (MEFs) of several genotypes. Experiments were performed in duplicates for cells treated with IFNb at the following time points: 0h(untreated), 24h, 48h, or 72h.

first: Ting

first: Chaoran

last: Yin

first: Alan

last: Herbert

first: Siddharth

last: Balachandran

first: Vasily

last: Studitsky


title: Endometrial epithelial Arid1a is essential in early pregnancy

city: Research Triangle Park

first: Ryan

last: Marquardt

state: NC

address: 111 T.W. Alexander Dr, Bldg 101, Room C-416, Mail Drop C-401

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

summary: Endometrial epithelial Arid1a is necessary for normal gene expression and maintenance of a receptive endometrium at pre-implantation stage in mice. We used RNA-sequencing to determine the differences in uterine gene expression resulting from deletion of endometrial epithelial Arid1a.

overall_design: Uteri of adult Arid1a f/f and Ltf iCre/+ Arid1a f/f mice were collected at gestation day 3.5 for RNA extraction and sequencing.

first: Jae-Wook

last: Jeong


title: Combination treatment with BMI1 and MAPK/ERK inhibitors is effective in medulloblastoma

city: London

first: Silvia

last: Marino

address: 4, Newark St

institute: Queen Mary University of London

summary: Epigenetic changes play a key role in the pathogenesis of medulloblastoma (MB), the most common malignant pediatric brain tumor. Here we identify a synergic vulnerability of BMI1High;CHD7Low MB cells to a combination treatment with BMI1 and MAPK/ERK inhibitors and we elucidate the molecular mechanisms underpinning the CHD7-BMI1-MAPK regulatory axis which mediates the anti-tumor effect of these inhibitors in vitro and in vivo, in a pre-clinical mouse model. Enhanced ERK1 and ERK2 phosphorylation activity is found in BMI1High;CHD7Low G4 MB patients, raising the possibility that they could be amenable to a similar therapy.

overall_design: RNA-Seq of MB cells treated with BMI1 and MAPK/ERK inhibitors.

first: Sara

last: Badodi

first: Nicola

last: Pomella


title: mTOR activity is essential for retinal pigment epithelium regeneration in zebrafish

city: Pittsburgh

first: Jeffrey

last: Gross

department: Ophthalmology

institute: University of Pittsburgh School Of Medicine

summary: Zebrafish is capable of endogenously regenerating functional retina pigment epithelium (RPE) after widespread genetic ablation which involves a series of cellular and molecular events that remain to be defined. Here, using the RPE genetic ablation model in zebrafish, we observed that mTOR signaling was activated in the RPE cells post-ablation. Pharmacological and genetic inhibition of mTOR signaling impaired RPE regeneration, while activation of mTOR signaling benefited RPE recovery, suggesting mTOR signaling was required and sufficient for RPE regeneration post-ablation in zebrafish. We further identified an interesting crosstalk between mTOR signaling and microglia/macrophages during RPE regeneration that mTOR acts as an upstream regulator of microglia/macrophage infiltration to the injury site while microglia/macrophage, in turn,  rainenforce mTOR activity.

overall_design: RNA-seq of  FACS-purified retinal pigment epithelium from ablated and unbalted rapamycin or DMSO treated larval eyes at 2 and 4 days post injury(dpi). MTZ+ for ablated samples and MTZ- for unablated.

first: Fangfang

last: Lu


title: Genome-wide DNA methylation profiling identifies epigenetic changes in CD4+ and CD14+ cells of multiple sclerosis patients

city: Moscow

first: Ivan

last: Kiselev

address: Ostrovitianov st. 1

country: Russia

institute: Pirogov Russian National Research Medical Universitty

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

overall_design: Refer to individual Series


title: Interleukin-6 modifies the expression profile of microRNA in mouse 3T3-L1 adipocytes

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

summary:
In the present study we examined the expression profile of microRNA in mouse 3T3-L1 adipocytes treated with IL-6, a known inflammatory cytokine and an adipo-myokine. The miRNA microarray analysis revealed increased expression of 9 miRNA species in adipocytes exposed to IL-6 (1 ng/ml) for 8 days of differentiation. In order to verify the microarray data, qRT-PCR analysis was performed to quantify miRNA expression and we confirmed the increased expression of miR-146b-3p (fold change =1.49±0.17).
Using Target Scan database we found potential targets for these miRNAs with expression modified by IL-6 and focused our further interest on genes/proteins involved in cytoskeleton organization and vesicle transport regulation, that is: actin, dynein, myosin light chain kinase, Rab4a, and glucose transporter Glut4.

overall_design: We compared the miRNA expression profiles of 3T3-L1 adipocytes exposed to IL-6 (1 ng/ml) for 8 days of differentiation to control group (non treated samples). Four microarrays were done for control group (non treated samples) and two for cells exposed to IL-6.

first: Maciej

last: Błaszczyk

first: Małgorzata

last: Gajewska

first: Marta

last: Dymowska

first: Tomasz

last: Domoradzki

first: Adam

last: Prostek

first: Magdalena

last: Hulanicka

first: Katarzyna

last: Grzelkowska-Kowalczyk


title: BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes

city: Boston

first: Eva

middle: Johanna

last: Schaefer

state: MASSACHUSETTS

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: Polycomb repressive epigenetic complexes are recurrently dysregulated in cancer. Unlike polycomb repressive complex 2 (PRC2), the role of PRC1 in oncogenesis and therapy resistance is not well defined. Here, we demonstrate that highly recurrent mutations of the PRC1 subunits BCOR and BCORL1 in leukemia disrupt assembly of a non-canonical PRC1.1 complex, thereby selectively unlinking the RING-PCGF enzymatic core from the chromatin targeting auxiliary subcomplex. As a result, BCOR-mutated PRC1.1 is localized to chromatin but lacks repressive activity, leading to epigenetic reprogramming and transcriptional activation at target loci. We define a set of functional targets that drive aberrant oncogenic signaling programs in PRC1.1 mutated cells and primary patient samples. Activation of these PRC1.1 targets in BCOR-mutated cells confers acquired resistance to treatment while sensitizing to targeted kinase inhibition. Our study thus reveals a novel epigenetic mechanism that explains PRC1.1 tumor suppressive activity and identifies a therapeutic strategy in PRC1.1 mutated cancer.

overall_design: Transcriptomic and epigenetic analysis of PRC1.1 complex regulatory functions in leukemia cells using RNA-seq, ChIP-seq, ATAC-seq, and methylation profiling (mERRBS).

first: R

last: Lindsley


title: NEAT-seq: Simultaneous profiling of intra-nuclear proteins, chromatin accessibility, and gene expression in single cells

status: Public on Feb 27 2022

city: Stanford

first: Amy

last: Chen

address: 279 Campus Drive West

institute: Stanford University

summary: Oligo-conjugated antibodies have allowed for joint measurement of surface protein abundance and the transcriptome in single cells using high-throughput sequencing. Extending these measurements to gene regulatory proteins in the nucleus would provide a powerful means to link changes in abundance of trans-acting TFs to changes in activity of cis-acting elements and expression of genes regulated by these factors and elements. Here, we introduce Nuclear protein Epitope, chromatin Accessibility, and Transcriptome sequencing (NEAT-seq), a technique to simultaneously measure nuclear protein abundance, chromatin accessibility, and the transcriptome in single cells. We apply this technique to profile CD4 memory T cells using a panel of master transcription factors (TFs) that drive distinct helper T cell subsets and regulatory T cells (Tregs) and identify examples of TFs with regulatory activity gated by three distinct mechanisms: transcription, translation, and regulation of chromatin binding. We further identify regulatory elements and target genes associated with each TF, which we use to link a non-coding GWAS SNP within a GATA motif to both strong allele-specific chromatin accessibility in cells expressing high levels of GATA, and a putative target gene.

overall_design: Multiomic single cell profiling of mouse ESC and human K562 mixture, primary human CD4+CD45RO+ memory T cells

first: Ben

last: Parks


title: Urinary extracellular vesicles and micro-RNA as markers of acute kidney injury after cardiac surgery

status: Public on Feb 26 2022

city: Leicester

first: Marcin

last: Wozniak

address: Leicester

institute: University of Leicester

summary:
Objectives: Secretion of extracellular vesicles (EV) and associated micro-RNAs (miR) is altered during cellular stress and may serve as biomarkers of organ injury. We hypothesized that measuring changes in urinary levels of EV and miR will predict the onset of acute kidney injury in cardiac surgery patients.
Design: Predictive accuracy biomarker study performed in the cohort of the REVAKI-2 trial
Setting: Single center ICU between September 2015 and September 2018
Interventions: Intravenous sildenafil citrate 12.5 mg kg-1 over 150 min or dextrose 5% at the commencement of surgery.
Measurements and main results: Urine samples were collected before and 24 hours after the procedure from 93 cardiac surgery patients. Urine EV concentrations and size distribution were assessed using NanoSight. EV derivation and levels were measured using flow cytometry. Samples from 10 selected patients were sequenced to detect differentially expressed miR. Verification was performed with advanced TaqMan assays in samples from all patients. Urine EV concentrations significantly increased in patients with AKI after surgery, with the percentage of EV positive for aquaporin-2 and β1-integrin also increasing. Pre surgery podocalyxin-positive EV were significantly lower, and β1-integrin EV werehigher in patients with AKI. The levels of the former correlated with the severity of theinjury. miR-125a-5p was expressed at higher levels in urine from patients with AKI stage 2/3. Levels of miR-10a-5p decreased after surgery in AKI patients; its levels correlated with the severity of the injury. Preoperative levels of podocalyxin EVs and miR-125a-5p had moderate AKI predictive value and, in a logistic model together with ICU lactate levels, offered good (AUC = 80.9%) AKI prediction.
Conclusions: Lower levels of podocalyxin-positive EV at baseline predict the severity of post-surgery AKI. Urine EV concentrations and miR expression offer excellent predictive accuracy when combined with commonly measured biomarkers.

first: Wozniak

last: Marcin

first: Douglas

last: Miller

first: Murphy

last: Gavin


title: Methylation profiling of CNS hemangioblastomas

city: Münster

first: Christian

last: Thomas

address: Pottkamp 2

institute: Institute of Neuropathology Münster, Germany

type: Methylation profiling by genome tiling array

summary: Hemangioblastomas of the central nervous system are highly vascular neoplasms that occur sporadically or as a manifestation of von Hippel-Lindau (VHL) disease. Despite their benign nature, hemangioblastomas are clinically heterogeneous and might be associated with significant morbidity due to mass effects of peritumoral cysts or tumor progression. Underlying molecular factors involved in hemangioblastoma tumor biology remain elusive. We investigated genome-wide DNA methylation profiles and clinical and histopathological features in a series of 47 hemangioblastomas from 42 patients, including 28 individuals with VHL disease.

overall_design: Bisulphite converted DNA from the 47 samples were hybridised to the MethylationEPIC BeadChip array.

first: Anne

last: Albers


title: Profound effect of a small cysteine-free protein (Cfp1) on genomic expression of Metarhizium robertsii

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

country: China

institute: Wenzhou Medical University

summary:
Purpose: This transcriptomic analysis aims at unveiling all possible genes orchestrated by Cfp1, which is evidently required for insect pathogenicity and virulence-related cellular events of Metarhizium robertsii.
Methods: Total RNAs were extracted from three 3-day-old hyphal cultures (replicates) of cfp1 disruption and wild-type strains grown under normal culture conditionsand and subjected to deep sequencing on Illumina NovaseqTM 6000 platform. The sequence reads that passed quality filters were mapped to the genome of Metarhizium robertsii. All genes differentially expressed in the disruptant versus the wild-type strain were enriched to GO function classes and KEGG pathways.
Results: The resultant transcriptome comprises 10681 detected genes. Among those, 605 genes were dysregulated in the absence of cfp1, including 356 down-regulated and 249 up-regulated.
Conclusions: Cfp1 lacking any predictable function domain has profound impact on the genomic expression of Metarhizium robertsii.

overall_design: RNA profiles from 3-day-old hyphal cultures of cfp1 disruption and wild-type strains.

first: Ming-guang

last: Feng

first: Ya-ni


title: Differentially Expressed Circular RNAs and their Therapeutic Mechanism in Nonsegmental Vitiligo Patients Treated with Methylprednisolone

status: Public on Feb 25 2022

city: Changzhou

first: Jiaqi

last: Zhang

state: Jiangsu

address: No.68 lake Gehu Road, Wujin District, Changzhou City, Jiangsu Province, China

department: Department of Dermatology

institute: The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University

summary: We identified the differentially expressed circular RNAs in vitiligo patients before and after treatment of methylprednisolone. We have completed the Arraystar Human circRNA Array V2 analysis of the 8 peripheral blood specimens. Whole blood samples (3 mL each) were collected by venipuncture into heparinized vacutainers from a total of four patients diagnosed with nonsegmental vitiligo before and after systemic glucocorticoid therapy (oral methylprednisolone tablets, 12mg daily for eight weeks).

overall_design: Eight peripheral blood specimens were collected from a total of four patients diagnosed with nonsegmental vitiligo before and after systemic glucocorticoid therapy。

first: Yan

last: Cao


title: The effects of low-level Er:YAG laser irradiation on proliferation and calcification of primary osteoblast-like cells isolated from rat calvaria

first: Sayaka

last: Katagiri

institute: Tokyo Medical and Dental University

summary: A number of reports showed that photo-bio-modulation by various lasers has favorable biological effects on cells. However, the effects of low-level Er:YAG laser irradiation on osteoblasts remain unclear. The purpose of this study was to evaluate the effects on proliferation and osteogenic differentiation of primary osteoblast-like cells by low-level Er:YAG laser irradiation. Osteoblast-like cells isolated from the calvariae of 3–5-day-old Wistar rats were irradiated by Er:YAG laser at energy fluences of 2.2, 3.3, or 4.3 J/cm2, respectively. After irradiation, cell surface temperature was measured and cell proliferation was evaluated by flow cytometry. Calcification was evaluated by measuring the Alizarin red S staining area after 7-day-culture with osteoinductive medium. Gene expressions in non-irradiated and laser-irradiated cells were evaluated by qPCR at 3, 6, and 12 hours after irradiation. Microarray analysis was performed to comprehensively evaluate gene expressions of non-irradiated cells and irradiated cells at 3.3 J/cm2 at 6 hours after irradiation. No pronounced increase of cell surface temperature was induced by low-level Er:YAG laser irradiation, and the Er:YAG laser irradiation did not affect osteoblast-like cell proliferation. Osteoblast-like cell calcification was significantly increased 7 days after Er:YAG laser irradiation at 3.3 J/cm2. Bglap expression was significantly increased in cells irradiated at 3.3 J/cm2 at 6 hours post-irradiation. Microarray analysis showed that irradiation at 3.3 J/cm2 caused up-regulation of inflammation-related genes and down-regulation of Wisp2. Gene set enrichment analysis also clarified enrichment of inflammation-related gene sets and Notch signaling pathway. In conclusion, Low-level Er:YAG laser irradiation enhanced calcification of primary osteoblast-like cells via enhanced Bglap expression and enriched Notch signaling pathway.

overall_design: Osteoblast-like cells non-irradiated and irradiated by Er:YAG laser at 3.3 J/cm2 was measured at 6 hours after irradiation.

first: Akira

last: Aoki


title: Genome-wide DNA methylation profiling identifies epigenetic changes in CD4+ and CD14+ cells of multiple sclerosis patients [CD14]

first: Ivan

last: Kiselev

summary: Multiple sclerosis (MS) is a chronic autoimmune and degenerative disease of the central nervous system, which develops in genetically predisposed individuals upon exposure to environmental influences. Environmental triggers of MS, such as viral infections or smoking, were demonstrated to affect DNA methylation, and thus to involve this important epigenetic mechanism  in the development of pathological processes. To identify DNA methylation hallmarks, associated with MS, we performed genome-wide DNA methylation profiling of two cell populations (CD4+ T-lymphocytes and CD14+ monocytes), collected from the same individuals (relapsing-remitting MS patients and healthy subjects), using Illumina 450K methylation arrays. We revealed significant changes in DNA methylation for both cell populations of studied groups. In CD4+ cells the majority of differentially methylated positions (DMPs) were shown to be hypomethylated, while in CD14+ cells – hypermethylated in MS patients. Noteworthy, in CD4+, but not in CD14+ cells, we found differential methylation of HLA-DRB6 gene from HLA locus, which is known to have the strongest genetic association with MS. Besides, about 20% of DMPs identified in studied cells were identical; they all had the same direction of methylation changes in both cell populations and may be involved in basic epigenetic processes occuring in MS. These findings suggest that the epigenetic mechanism of DNA methylation in immune cells contributes to MS; further studies are now required to validate these results and understand their functional significance.

overall_design: We performed a genome-wide DNA methylation analysis in CD14+ monocytes of 6 treatment-naïve patients with relapsing-remitting multiple sclerosis in stable remission (MS) and 8 healthy controls (HC).

first: Ludmila

last: Danilova


title: Transcriptomic analysis of IAA treated 3 DAG WT and er erl2 seedlings.

city: Knoxville

first: Elena

last: Shpak

state: Tennessee

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

summary: Proper control of Auxin localization and accumulation are essential for leaf primordia initiation. Additionally, previous work has shown that the ERECTA family of genes also control leaf initiation. In this study we seek to understand the interaction between Auxin and the er erl2 double mutant in 3 days after germination (DAG) old seedlings. WT and mutant seedlings were either treated with IAA or mock treatments for 30 minutes. RNA was isolated and poly-A enriched strand specific libraries were constructed and paired end sequencing was carried out. The mutant showed mild, yet consistent enrichment of chloroplast and carbohydrate metabolism gene ontology terms in our mutant compared to WT. However, at 30 minutes post IAA treatment, the mutant and WT did not have significantly different responses to auxin. This indicates that the ERECTA family genes do not play a significant role in the immediate and direct response to auxin.

overall_design: 2x2 Factorial analysis of WT and er erl2 mutants in Arabidopsis thaliana under Mock or IAA treatment

first: Daniel

last: DeGennaro

first: Ricardo

last: Urquidi Camacho


title: Differential methylation in patients treated with clozapine

status: Public on Feb 24 2022

city: Mexico City

first: José Jaime

last: Martínez Magaña

state: Mexico City

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan,

country: Mexico

institute: Instituto Nacional de Medicina Genómica

summary: Genome-wide DNA methylation profile of peripheral blood leukocyte samples taken from patients under clozapine treatment. The Infinium MethylationEPIC BeadChip was analyzed to obtain DNA methylation profiles in samples from 31 patients with psychotic disorders under treatment with clozapine and 56 patients with psychiatric disorders naïve to psychopharmacological treatment

overall_design: 32 samples were included from patients under treatment with clozapine.

first: N

last: Monroy-Jaramillo

first: David

last: Dávila


title: Integrating RNA-seq and assay for transposase-accessible chromatin by sequencing (ATAC-seq) predicts functionally-relevant chromatin regions

status: Public on Feb 23 2022

city: Salt Lake City

first: Adrian

last: Rothenfluh

state: Utah

department: Psychiatry

institute: University of Utah

summary: Gene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. Studies investigating the epigenome have begun to uncover the complex mechanisms regulating transcription. Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is quickly becoming the assay of choice for epigenomic investigations. Integrating epigenomic and transcriptomic data has the potential to reveal the chromatin-mediated mechanisms regulating transcription. However, integrating these two data types remains challenging. We used the insulin signaling pathway as a model to investigate chromatin regions and gene expression changes using ATAC- and RNA-seq in insulin-treated Drosophila S2 cells. We show that insulin causes widespread changes in chromatin accessibility and gene expression. Then, we attempted to integrate ATAC- and RNA-seq data to predict functionally-relevant chromatin regions that control the transcriptional response to insulin. We show that using differential chromatin accessibility can predict functionally-relevant genome regions, but that stratifying differentially-accessible chromatin regions by annotated feature type provides a better prediction of whether a chromatin region regulates gene expression. In particular, our data demonstrate a strong correlation between chromatin regions annotated to distal promoters (1-2 kb from the transcription start site). To test this prediction, we cloned candidate distal promoter regions upstream of luciferase and validated the functional relevance of these chromatin regions. Our data show that distal promoter regions selected by correlations with RNA-seq are more likely to control gene expression. Thus, correlating ATAC- and RNA-seq data can home in on functionally-relevant chromatin regions

overall_design: ATAC-seq and mRNA profiles of insulin-treated Drosophila S2 cells

first: Collin

last: Merrill

first: Austin

last: Montgomery

first: Miguel

last: Pabon

first: Aylin

middle: R

last: Rodan


title: Expression of Human Lung by Donor Type and EVLP Type

city: Toronto

first: Mingyao

last: Liu

state: ON

address: 101 College Street

department: Latner Thoracic Resaerch Laboratories

institute: University Health Network

summary: Study on lung transplantation encompassing a comprehensive and detailed investigation of differences at transcription level between DBD and DCD donor lungs.

overall_design: Lung tissue samples were collected at the end of cold ischemia (CIT), at University Health Network in Toronto, Canada. Lungs were donated by brain-death donors (DBD) and cardiac-death donors (DCD). Selected lungs were placed on the Ex Vivo Lung Perfusion (EVLP) circuit for assesment and repair and all other lungs were directly transplanted (Non-EVLP).

first: Cristina

last: Baciu

first: Andrew

last: Sage

last: Zamel

first: Xiaohui

last: Bai

first: Jason

last: Shin

first: Jonathan

last: Yeung

first: Shaf

last: Keshavjee


title: Chromatin binding of ER/TEAD/YAP in MCF-7 Cells after MST inhibitor treatment

city: Dallas

first: Xu

last: Li

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary: We report YAP could repress ER positive breat cancer progression and MST inhibitor treat MCF-7 cells were used as the model.

overall_design: Examination of ERa, TEAD and YAP chromatine binding signal in MCF-7 cells bwtween DMSO or MST inhibitor treatment.


title: Ligand-mediated PAI-1 inhibition in a mouse model of peritoneal carcinomatosis

status: Public on Feb 22 2022

city: Singapore

first: Johnny

middle: Chin-Ann

last: Ong

state: Singapore

address: 11 Hospital Drive

department: Division of Surgical Oncology

institute: National Cancer Centre Singapore

type:
Expression profiling by array
Protein profiling by protein array


title: Transcription feedback dynamics in the wake of cytoplasmic degradation shutdown

status: Public on Feb 20 2022

city: Jerusalem

first: Alon

last: Chappleboim

address: Givat Ram

department: Biological chemistry

country: Israel

institute: Hebrew University of Jerusalem

summary:
Purpose: Studying the dynamics of the transcriptional response to acute depletion of various critical mRNA processing factors
Methods: We used 4tU labeling and high-throughput polyA RNA-seq in yeast following auxin inducible degradation of key proteins.
Results: We captured the detailed dynamics of cells’ adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in nascent transcription and a gradual return to baseline mRNA levels. We present evidence that this transcriptional response is linked to cell cycle progression, and that it is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3’ degradation pathway are perturbed.
Conclusions:  Our data suggest that the RNA feedback mechanism is cell-cycle-linked and monitors the accumulation of inputs to the 5’-3’ exonucleolytic pathway rather than its outputs.

overall_design: Most samples are 4tU-labeled RNA-seq following the depletion of a key protein from cells.

first: Chappleboim

last: Alon


title: RNA-Seq analysis of the flavonoid-deficient Arabidopsis line, tt4-11

city: Blacksburg

first: Brenda

last: Winkel

state: VA

address: 1015 Life Science Circle

department: Biological Sciences

institute: Virginia Tech

summary: This is the first analysis of an Arabidopsis flavonoid mutant line by RNA-Seq, specifically, the chalcone synthase-deficient line, tt4-11.  There is one other publically-available microarray dataset for a related allele, tt4-3 (Nakabayashi et al., Plant J. 2014).  The data provide evidence for alterations in circadian clock and clock-controlled gene expression in the absence of chalcone synthase protein and/or flavonoid endproducts.

overall_design: tt4-11 and Col-0 (WT) were grown under conditions that are known to promote flavonoid production

first: Sherry

last: Hildreth

middle: J

first: Megan

middle: F

last: Naff

first: Sai

last: Karyala

first: Robert

last: Settlage


title: Expression data of ascites treated peritoneal carcinomatosis human cell lines

summary:
Characterizations of ascites proteome from ovarian PC and gastric PC have demonstrated that ascites contains elevated pro-tumorigenic factors. Reasoning that the composition of ascitic fluid might offer insight into the memory of key biological events occurring intra-abdominally, we hypothesized that paracrine factors essential for survival and growth of peritoneal deposits are secreted into and circulate within ascitic fluid. Our data from cytokine array profile suggest that ascites contains biologically active ligands capable of supporting cellular functions of cancer cells.
To decipher downstream signalling pathways activated in cancer cells when exposed to ascites, we performed gene expression analysis of Colo-205 and SNU-C1 cells upon exposure to PC ascites.

overall_design: Ascites treated peritoneal carcinomatosis cell lines (SNUC1 and COLO205) were subjected to patient derived cell free ascites (CFA) of varying concentrations.

first: Josephine

last: Hendrikson

first: Ong

last: Johnny


title: Target-dependent siRNA suppression distinguishes self from non-self endogenous siRNAs in C. elegans germline

status: Public on Feb 19 2022

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: Despite their prominent role in transposon silencing, expression of endo-siRNAs is not limited to the “non-self” DNA elements. Transcripts of protein-coding genes (“self” DNA) in some cases also produce endo-siRNAs in yeast, plants, and animals [1]. How cells distinguish these two populations of siRNAs to prevent unwanted silencing of self-genes in animals is not well understood. To address this question, we examined the expression of ectopic siRNAs from an LTR retrotransposon in C. elegans germline. We found that the abundance of ectopic siRNAs was dependent on their homologous target genes: ectopic siRNAs against genes expressed only in somatic cells can be abundantly expressed. In contrast, ectopic siRNAs against germline-expressed genes are often suppressed. This phenomenon, which we termed “target-directed siRNA suppression”, is dependent on the target mRNA and requires germline P-granule components. We found that siRNA suppression can also occur to naturally produced endo-siRNAs.  We suggest that siRNA suppression plays an important role in regulating siRNA expression and preventing self-genes from aberrant epigenetic silencing.

overall_design: small RNA-seq analyses of  C. elegans strains that express ectopic siRNAs from the LTR retrotransposon Cer3 for siRNA suppression study

first: Zoran

last: Gajic

first: Diljeet

last: Kaur

first: Julie

last: Ni

first: Zhaorong

last: Zhu

first: Anna

last: Zhebrun

first: Maria

first: Matthew

last: Kim

first: Julia

last: Hong

first: Monika

last: Priyadarshini

first: Christian

last: Frøkjær-Jensen


title: Lockd promotes myoblast proliferation and skeletal muscle regeneration through binding with Dhx36 to facilitate unwinding of 5’UTR rG4 and translation of Anp32e mRNA

status: Public on Feb 14 2022

city: Hong Kong

first: Yuwei

last: ZHANG

state: Hong Kong

address: Rm503, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital, Shatin, NT, HK

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: polysome profiling in WT and Lockd KO myoblast cells

overall_design: 8 polysome profiling experiments performed.

first: Huating

last: Wang

first: Xiaona

last: Chen

last: Zhang


title: ALS-Associated KIF5A Mutations Abolish Autoinhibition Resulting in a Toxic Gain of Function [RIP-seq]

status: Public on Feb 17 2022

city: Worcester

first: John

last: Landers

state: MA

address: 55 N Lake Ave

institute: UMass Chan Medical School

summary:
Purpose: The goal of this study is to identify and compare the mRNA interactomes of WT and ALS-related mutant (d27) KIF5A
Methods: RNA samples were extracted and sequenced on an Illumina NovaSeq6000 instrument at the Yale Center for Genome Analysis. The sample sequence quality control check was performed using FastQc. The STAR aligner program was used for read mapping with reference file and HTSeq was used to count the reads for each transcript in strand specific mode. The Differential expression analysis was performed using the DESeq2 package to compare the gene expression profiles between wild type and mutant was performed using the Wald test to generate p-values and Log2 fold changes. The STAR aligned RNA Sequence sample bam files were used to detect differential alternative splicing events with the Multivariate Analysis of Transcript Splicing (MATS) method. Pathway analysis was performed with Metascape
Results: With the RNA RIP Sequence pipeline, we analyzed the RNA Sequence from SKNAS cells expressing WT KIF5A and cells epxressing the KIF5a ALS delta27 mutant. We identified 1,184 transcripts that displayed enriched binding to KIF5AΔExon27 and 303 that showed decreased binding to KIF5A ΔExon27. Pathway analysis revealed several categories related to ALS pathogenesis. KIF5AΔExon27 enriched pathways included NGF-stimulated transcription, which is related to neurite outgrowth. Pathways that were underrepresented in KIF5A ΔExon27 samples compared to KIF5AWT included interactions between L1 and Ankyrins, synapse assembly, and potassium channels. The results demonstrate that mutations in KIF5A can result in altered interaction with proteins and RNA associated with ALS-related pathways.
Conclusions: Our analysis demonstates that ALS-related mutant KIF5A (d27) has altered RNA interactions compared to the WT protein.

overall_design: mRNA interactomes for WT and Mutant (d27) KIF5A

first: Desiree

last: Baron

first: Shankaracharya

last: Shankaracharya


title: ALS-Associated KIF5A Mutations Abolish Autoinhibition Resulting in a Toxic Gain of Function [RNA-seq]

summary:
Purpose: The goal of this study was to identify gene expression changes in iMNs containing a patient KIF5a mutation compared to an isogenic control.  Further, splicing changes were evaluated in the mutant vs WT sample.
Methods: RNA samples were extracted and sequenced on an Illumina NovaSeq6000 instrument at the Yale Center for Genome Analysis. The sample sequence quality control check was performed using FastQc. The STAR aligner program was used for read mapping with reference file and HTSeq was used to count the reads for each transcript in strand specific mode. The Differential expression analysis was performed using the DESeq2 package to compare the gene expression profiles between wild type and mutant was performed using the Wald test to generate p-values and Log2 fold changes. The STAR aligned RNA Sequence sample bam files were used to detect differential alternative splicing events with the Multivariate Analysis of Transcript Splicing (MATS) method. Pathway analysis was performed with Metascape
Results: With the RNA Sequence pipeline, we analyzed the RNA Sequence from wild-type parental line (Iso Control) and the heterozygous mutant line (KIF5AR1007K). The RNA Sequence analysis of the iMNs revealed 57 genes displaying altered expression. Using the method, Multivariate Analysis of Transcript Splicing (MATS), we identified 1,919 transcripts with altered splicing compared to the isogenic control iMNs. Of these, 1,000 exons showed decreased skipping, while 919 showed increased skipping in KIF5AR1007K lines. Pathway analysis of each of these groups suggests that this group of altered genes, as a whole, represents cytoskeletal and transport defects in the cell, both of which are hallmarks of neurodegenerative disease.

overall_design: mRNA profiles of DIV15 iMNs harboring a KIF5AR1007K mutation and its isogenic control


title: ALS-Associated KIF5A Mutations Abolish Autoinhibition Resulting in a Toxic Gain of Function

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

overall_design: Refer to individual Series


title: The Xia-Gibbs Syndrome protein Gibbin regulates mesodermal DNA methylation to pattern epithelial development (scRNA-Seq)

status: Public on Feb 13 2022

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

summary: The goal of these scRNA-seq experiments was to determine the identity of cellular populations after 7 day in RA/BMP4 or 50 days in DKSFM.

overall_design: All samples were performed in biological duplicate.

first: Annie

last: Collier

first: Sadhana

last: Gaddam


title: The Xia-Gibbs Syndrome protein Gibbin regulates mesodermal DNA methylation to pattern epithelial development (HiChIP)

summary: The goal of these Hi-ChIP experiments was to determine changes in cohesin-mediated chromatin contacts caused by AHDC1/Gibbin knockout.

overall_design: All samples were performed in biological triplicate and pooled to achieve sufficient sequencing depth.


title: The Xia-Gibbs Syndrome protein Gibbin regulates mesodermal DNA methylation to pattern epithelial development (ChIP-Seq)

summary: The goal of these ChIP-seq experiments was to determine binding sites for AHDC1/Gibbin, GATA3, CTCF proteins or the H3K9me3 histone mark in cells treated with RA/BMP4.e


title: Single cell transcriptomic studies of mouse colonic lamina propria cells from wildtype or RORgtS182A mutant mice

status: Public on Feb 15 2022

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: The evolutionarily conserved serine 182 residue on RORγt is phosphorylated. Here, we report that this residue is dispensable for thymic T cell development, but essential for maintaining proper balance of Th17-Treg populations in the colon. Single-cell RNA-seq (scRNA-seq) revealed that serine 182 residue on RORγt is critical for restricting IL-1b-mediated Th17 activities and promoting anti-inflammation cytokine IL-10 production in Lymphoid tissue (LT)-like RORγt+Foxp3+ regulatory T cells in inflamed tissues.

overall_design: Two independent biological replicates in each condition were performed. In wildtype mice, results from DSS treated colon  were compared to no treatment conditions. Results from RORgtS182A mutant mice were compared to those from wildtype mice in no treatment and DSS treatment conditions seperately.

first: Shengyun

last: Ma

first: Shefali

last: Patel

middle: T

last: Chang


title: Gibbin drives epithelial development by toggling CTCF binding and DNA methylation

city: Stanford

summary: The goal of these ATAC-seq experiments was to determine changes in chromatin accesiblity caused by loss of Gibbin (AHDC1) or GATA3 in non-neural ectoderm.

overall_design: There were six ATAC-seq samples total including WT, GKO, and GATA3 KO. All samples were perfoemd in biological duplicate.

first: Ann


title: Gene expression profile of the capillaries with the surrounding cells from the ossification front of the juvenile and adult mouse femurs

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: We performed RNA-Seq and compared expression levels of genes of endothelialal cells together with the surrounding cells derived by laser microdissection (LMD) from 4- and 12-week old ossification fronts of Tg(TIE2GFP)287Sato/J (endothelial cell reporter) mice. The aim of the expriments was to dissect the age-related changes in vascular and perivascular microenvironments during active bone growth and maturation.

overall_design: We developed a protocol to cut single capillaries with perivascular cells from undecalcified and unfixed bones of endothelial cell-specific GFP-reporter mice with a high RNA preservation rate for futher NGS. This protocol allowed us to analyse purely unmanipulated snap-frozen trancriptome of cells of interest. We performed laser microdissection (LMD) of single capillary with associated surrounding cells in the ossification front (OF) of juvenile, actively growing (4-week-old) and adult, mature (12-week-old) mice, followed by transcriptome comparison.

first: Maria

last: Dzamukova

first: Tobias

last: Brunner

first: Jadwiga

last: Miotla-Zarebska

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi

first: Anjali

last: Kusumbe

first: Ralf

last: Kühn

first: Tonia

last: Vincent

first: Max

last: Löhning


title: Gibbin (AHDC1) mesodermal regulation controls epithelial patterning

first: Anthony

last: Oro

summary: The objective of this experiment was to determine the DNA methylation status of WT and GKO hESCs treated with or without RA/BMP4.

overall_design: Experiments were performed in biological duplicate.


title: The Xia-Gibbs Syndrome protein Gibbin regulates mesodermal DNA methylation to pattern epithelial development (scRNA-Seq 2)

summary: The goal of these scRNA-seq experiments was to determine the identity of cellular populations after 3 day in RA/BMP4 or 7 days in RA/BMP4 followed by 14 days in DKSFM

first: Annie

last: Collier


title: High-resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration

status: Public on Feb 09 2022

city: Kansas City

first: Tatjana

last: Piotrowski

state: MO

institute: Stowers Institute for Medical Research

summary: NOT PROVIDED; REQUESTED

overall_design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo, 0min post-neomycin, 30min 1hr, 3hr, 5hr, 10hr

first: Sungmin

last: Baek

first: Nhung

last: Tran

first: Daniel

last: Diaz

first: Ya-Yin

last: Tsai


title: Deacetylation of YAP1 promotes the resistance to chemo-and targeted therapy in FLT3-ITD + AML cells

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

summary: The FLT3-ITD mutation occurs in about 30% of acute myeloid leukemia (AML) and is associated with poor prognosis. However, FLT3 inhibitors are only partially effective and prone to acquired resistance. Here, we identified Yes-associated protein 1 (YAP1) as a tumor suppressor in FLT3-ITD+ AML. YAP1 inactivation conferred FLT3-ITD+ AML cells resistance to chemo- and targeted therapy. Mass spectrometric assay revealed DNA damage repair gene poly (ADP-ribose) polymerase 1 (PARP1) might be the downstream of YAP1, and the pro-proliferative effect by YAP1 knockdown were partly reversed via PARP1 inhibitor. Importantly, histone deacetylase 10 (HDAC10) contributed to decreased YAP1 acetylation levels through histone H3 lysine 27 (H3K27) acetylation, leading to the reduced nuclear accumulation of YAP1. Selective HDAC10 inhibitor chidamide or HDAC10 knockdown activated YAP1, enhanced DNA damage and significantly attenuated FLT3-ITD+ AML cells resistance. Additionally, combination chidamide with FLT3 inhibitors or chemotherapy agents synergistically inhibited growth and increased apoptosis of FLT3-ITD+AML cell lines and acquired resistant cells from the relapse FLT3-ITD+ AML patients. These findings demonstrate that the HDAC10-YAP1-PARP1 axis maintains FLT3-ITD+ AML cells and targeting this axis might improve clinical outcomes in FLT3-ITD+ AML patients._x001F__x001F__x001F__x001F_

overall_design: Gene expression analysis by RNA-seq of MV4-11 cells（existing FLT3-ITD mutation) treated with 10 nM sorafenib for 24 days.MV4-11 cells were collected in Trizol for RNA-Sequence at Day 0, Day 6,Day 12,Day 18,Day 24.

first: Panpan

last: Feng

first: Jingru

last: Zhang

first: Jingjing

last: Ye


title: RT-qPCR of metabolite and ICB exposed organoids

status: Public on Feb 08 2022

city: Winston-Salem

first: Ethan

last: Shelkey

address: 391 Technology Way NE

institute: Wake Forest Institute for Regenerative Medicine

summary:
Organoids containing 4T1 TNBC and matched splenocytes were exposed to the metabolites hippuric acid or pyocyanin and/or a-CTLA-4 and a-PD-1 for 5 days
run on RT² Profiler™ PCR Array Mouse Cancer Inflammation & Immunity Crosstalk [PMAM-181Z]

overall_design: organoids treated with a metabolite, ICB, or both had mRNA expression values compared agaist an untreated control


title: Peptide nano-blanket impedes fibroblasts activation and subsequent formation of pre-metastatic niche

city: Hangzhou

first: Yi

last: Zhou

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

summary: Here we report an enzyme-activatable assembled peptide FR17 that can serve as a “flame-retarding blanket” at pre-metastatic niche (PMN) specifically to extinguish the “fire” of tumor-supportive microenvironment adaption. Our experiment demonstrated that the assembled peptide successfully reversed extracellular matrix deposition, vascular leakage and angiogenesis through inhibition on fibroblasts activation in PMN, which suppressed the remodeling of metastasis-supportive host stromal, and further prevented the recruitment of myeloid cells to PMN and then recovered the immunosuppressive microenvironment. Cell transcriptomic analysis of the pulmonary recruited MDSC suggested that FR17 intervention could regulate immune response activation, immune cells chemotaxis and migration pathways. Consequently, FR17 administration effectively inhibited pulmonary PMN formation and postoperative metastasis of melanoma, with only 30% lung-metastasis occurrence was observed for FR17 treated group at the time point when 100% occurrence was observed for the control group and 80% occurrence for anti-PD1 treated group, offering a robust therapeutic strategy against PMN establishing to prevent metastasis.

overall_design: A total of 4 samples were analyzed, including control (Ctrl), TP5, sFD17 and FR17. RNA preparations were extracted from CD11b+Ly6g+ myeloid-derived supperssor cells (MDSCs) sorted from lungs pooled from 10-12 mice from each group per sample.

first: Peng

last: Ke


title: Loss of PRC2 or KMT2D-COMPASS Generates Two Quasi-Mesenchymal Cell States with Distinct Metastatic Abilities

status: Public on Feb 07 2022

city: Cambridge

first: Yun

email: zhangyunbio@gmail.com, barc@wi.mit.edu

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research


title: Radioresistant Cells in STING Gain-of-function Mice Initiate Lymphocyte-dependent Lung Inflammation and IFNγ-dependent Mortality

status: Public on Feb 11 2022

first: Katherine

middle: A

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Chan Medical

summary: Pediatric patients with constitutively active mutations in the cytosolic dsDNA sensing adaptor STING develop an autoinflammatory syndrome known as STING Associated Vasculopathy with onset in Infancy (SAVI). SAVI patients have elevated interferon stimulated gene expression and suffer from interstitial lung disease (ILD) with lymphocyte predominate bronchus associated lymphoid tissue (BALT). Mice harboring SAVI mutations (STING V154M or VM) that recapitulate human disease also develop lymphocyte rich BALT formation. Ablation of either T or B lymphocytes prolongs survival of SAVI mice, but lung immune aggregates persist, indicating that T cells and B cells can independently be recruited as BALT. VM T cells produced IFNγ and IFNγR deficiency prolonged the survival of SAVI mice; however, T cell dependent recruitment of infiltrating myeloid cells to the lung was independent of IFNγ. Lethally irradiated VM recipients fully reconstituted with WT BM-derived cells still developed ILD, pointing to a critical role for VM-expressing radioresistant parenchymal and/or stromal cells in the recruitment and activation of pathogenic lymphocytes. We identified lung endothelial cells as radioresistant cells which express STING. Transcriptional analysis of VM endothelial cells revealed upregulation of chemokines, pro-inflammatory cytokines, and genes associated with antigen presentation. Together, our data show that VM-expressing radioresistant cells play a key role in the initiation of lung disease in VM mice and provide new insights for the treatment of SAVI patients, with implications for ILD associated with other connective tissue disorders.

overall_design: 4 samples from individual WT B6 mouse controls, and 5 samples from individual STING V154M B6 litter mates.

first: Kevin

last: Gao

first: Ann

last: Marshak-Rothstein


title: Whole genome sequencing reveals that variants in the Interleukin 18 Receptor Accessory Protein 3′UTR protect against ALS

city: Rehovot

first: Eran

last: Hornstein

address: Hornstein lab, 1314 Mayer building, Dep. Molecular Genetics,

institute: Weizmann Institute of Science

summary: The non-coding genome is substantially larger than the protein-coding genome, but has been largely unexplored by genetic association studies. Here, we performed region-based rare-variant association analysis of >25,000 variants in untranslated regions of 6,139 amyotrophic lateral sclerosis (ALS) whole-genomes and those of 70,403 non-ALS controls. We identified Interleukin-18 Receptor Accessory Protein (IL18RAP) 3′UTR variants as significantly enriched in non-ALS genomes and associated with five-fold reduced risk of developing ALS, and this was replicated in an independent cohort. These variants in the IL18RAP 3′UTR reduce mRNA stability and the binding of double-stranded RNA-binding proteins. Finally, the variants of IL18RAP 3′UTR confer a survival advantage for motor neurons because they dampen neurotoxicity of human iPSC-derived microglia bearing an ALS-associated expansion in C9orf72, and this depends on NF-κB signaling. This study reveals genetic variants that protect against ALS by reducing neuroinflammation, and emphasizes the importance of non-coding genetic association studies.

overall_design: Transcriptomics comparison in isogenic ipMG harboring variant vs. canonical IL18RAP 3'UTR, following exposure to LPS (100ng/mL) + IL18 (100ng/mL) (n=4 per group).

first: Chen

last: Eitan

first: Aviad

last: Siany

last: Yanowski


title: RNA seq analysis of adult olfactory epithelium exposed to Phenyl ethyl ethanol during early development in zebrafish

status: Public on Feb 06 2022

city: Valparaiso

first: Kathleen

last: Whitlock

state: Valparaiso

address: Pasaje Harrington 269

department: Centro Interdisciplinario de Neurociencia de Valparaíso (CINV)

country: Chile

institute: Universidad de Valparaiso

summary: The early exposure to the artificial odorant phenyl ethyl alcohol (PEA) is correlated with odor memory formation and the changes in gene expression in olfactory epithelium of zebrafish. In this study we performed a transcriptomic analysis using RNA seq, in order to compare the gene expression in the olfactory epithelium of adult zebrafish between PEA exposed fish during the early development and non-exposed fish

overall_design: In order to measure differential gene expression in olfactory epithelium of adult zebrafish exposed to the odorant Phenyl ethyl alcohol (PEA) during early development, embryos were collected and separated into experimental (PEA exposed) and control groups. Fish were exposed every day for 3 weeks of development to PEA (odorant exposed group) or distilled water (control groups), after which the fish were transferred to a recirculating system until sacrificed at six months after. Olfactory epithelium were collected from ten fish each group and total RNA was isolated using TRIZOL reagent. RNA seq analysis was performed using Illumina Hiseq 2500 system and Differential gene expression was estimated using DESeq2 (v1.24) within SARTools R package (v1.6.9). For more details on the experimental design review Calfun et al 2016 (DOI: 10.1093/chemse/bjw002; PMID: 26892307)

middle: E

first: Cristian

last: Calfun

first: Gino

last: Nardocci

first: Martin

last: Montecino


title: Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4 (dataset II)

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

summary: Reprogramming somatic cells to pluripotency represents a paradigm for cell fate determination. A binary logic of closing and opening chromatin provides  a simple way to understand iPSC reprogramming driven by both Yamanaka factors or chemicals.  Here we apply this logic to the design a four  factor combination, Jdp2, Glis1, Essrb and Sall4 (4F), that reprogram MEFs to chimera competent iPSCs efficiently.  RNA- and ATAC-seq reveal differences between JGES and 7F induced pluripotency, 7IP and JGES IP, in transcriptomic and chromatin accessibility dynamics(CAD). Sall4 emerges as a dominant force that can close and open chromatin with the help of Jdp2 and Glis1 in resetting somatic chromatin to a pluripotent state. These results reveal a previously unknown path between somatic and pluripotent states, open a door for cell fate control.

overall_design: In total, we collected 10  cell samples in reprogramming D0, D1, D3,D5 and D7 from 2 independent expriments. mRNA Library sequencing done with NextSeq500.

first: Bo

last: Wang