title: Maturation and circuit integration of transplanted human cortical organoids

status: Public on Jul 23 2022

city: Stanford

first: Kevin

last: Kelley

state: CA

address: 318 Campus Drive, W200

institute: Stanford University

summary: We show that human stem cell-derived cortical organoids transplanted into the somatosensory cortex of newborn athymic rats develop mature cell types that integrate into sensory and motivation-related circuits. Magnetic resonance imaging allows monitoring of post-transplantation organoid growth across multiple stem cell lines and animals, while single nucleus profiling reveals high cell diversity and progression of corticogenesis, as well as the emergence of an activity-dependent transcriptional program in neurons.

overall_design: single nucleus RNA-sequencing of transplanted human cortical organoid and age matched cortical organoid

first: Omer

last: Revah

first: Felicity

last: Gore

middle: W

first: Jimena

last: Andersen

first: Noriaki

last: Sakai

first: Xiaoyu

last: Chen

first: Min-Yin

last: Li

first: Fikri

last: Birey

first: Xiao

last: Yang

first: Nay

last: Saw

first: Samuel

last: Baker

first: Neal

middle: D

last: Amin

first: Shravanti

last: Kulkarni

first: Rachana

last: Mudipalli

first: Bianxiao

last: Cui

first: Seiji

last: Nishino

first: Gerald

last: Grant

first: Juliet

middle: K

last: Knowles

first: Mehrdad

last: Shamloo

first: John

last: Huguenard

first: Karl

last: Deisseroth

first: Sergiu

middle: P

last: Pașca


title: Single cell RNA-seq of human ABCB5-positive limbal stem cells

status: Public on Aug 09 2022

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

country: USA

institute: Brigham and Women's Hospital

type: Expression profiling by high throughput sequencing

summary: We performed single cell RNA-seq of human ABCB5-positive limbal stem cells (LSCs) to examine their homogeneity.

overall_design:
ABCB5-positive LSC mRNA profiles of 3 human donor at single cell level.

UPDATE: [Feb-12-2026] The barcodes.tsv, genes.tsv, and matrix.mtx files were replaced with DEGs.csv.

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Raw files for human/patient samples are not available due to concerns about personally identifiable sequence data being available for open access.
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first: Yuzuru

last: Sasamoto

first: Catherine

middle: A

last: Lee

middle: Y


title: Effect of SOX9 dosage changes on gene expression in hESC-derived cranial neural crest cells [RNA-seq]

status: Public on Jul 04 2022

first: Sahin

last: Naqvi

state: CA California

address: 265 Campus Drive, Lokey Stem Cell Research Building/SIM1

summary: To assess the effects of quantitative SOX9 dosage changes on gene expression in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of differing concentrations of the degrader molecule dTAGV-1 results in different SOX9 concentrations, as measured by flow cytometry. We then profiled gene expression profiling in each of these SOX9 concentrations

overall_design: Genome-wide gene expression profiling (RNA-Seq) of WT and SOX9-tagged H9 hESC-dervied cranial neural crest cells (CNCCs)


title: Effect of SOX9 depletion on transcription mRNA in hESC-derived cranial neural crest cells [SLAM-seq]

summary: To assess the effects of SOX9 depletion on transcription in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of the degrader molecule dTAGV-1 results in SOX9 depletion. We then profiled transcription by metabolic labeling of RNA (SLAM-Seq) in undepleted CNCCs or CNCCs in which SOX9 was depleted for 3h or 24h

overall_design: Genome-wide transcription profiling (SLAM-Seq) of WT and SOX9-tagged H9 hESC-dervied cranial neural crest cells (CNCCs)


title: Effect of SOX9 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To assess the effects of quantitative SOX9 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of differing concentrations of the degrader molecule dTAGV-1 results in different SOX9 concentrations, as measured by flow cytometry. We then profiled chromatin accessibility in each of these SOX9 concentrations

overall_design: Genome-wide chromatin accessibility profiling (ATAC-Seq) of WT and SOX9-tagged H9 hESC-derivied cranial neural crest cells (CNCCs)


title: Effect of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells [ChIP-seq]

summary: To assess the effects of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of the degrader molecule dTAGV-1 results in SOX9 depletion. We then profiled the active chromatin mark H3K27ac by ChIP-Seq in undepleted CNCCs or CNCCs in which SOX9 was depleted for 3h or 24h. We also titrated SOX9 to four distinct levels with dTAGV-1 and assessed SOX9 binding by V5 ChIP-seq, as well as TWIST1 and TFAP2A binding by ChIP-seq.

overall_design: Genome-wide chromatin mark and TF binding profiling (H3K27ac, V5, TWIST1, TFAP2A ChIP-seq) of WT and SOX9-tagged H9 hESC-derived cranial neural crest cells (CNCCs)


title: PRC1-mediated epigenetic programming is required to generate the ovarian reserve

status: Public on Jun 26 2022

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

institute: UC Davis

summary: The ovarian reserve defines the female reproductive lifespan, which in humans spans decades due to robust maintenance of meiotic arrest in oocytes residing in primordial follicles. Epigenetic reprogramming, including DNA demethylation, accompanies meiotic entry, but the chromatin changes that underpin the generation and preservation of ovarian reserves are poorly defined. We report that the Polycomb Repressive Complex 1 (PRC1) establishes repressive chromatin states in perinatal mouse oocytes that directly suppress the gene expression program of meiotic prophase-I and thereby enable the transition to dictyate arrest. PRC1 dysfuction causes depletion of the ovarian reserve and leads to premature ovarian failure. Our study demonstrates a fundamental role for PRC1-mediated gene silencing in female reproductive lifespan, and reveals a critical window of epigenetic programming required to establish ovarian reserve.

overall_design: RNA-seq analysis using PRC1ctrl and PRC1cKO P1 or P5 non-growing oocytes; Cut&Run analysis using PRC1ctrl and PRC1cKO P1 non-growing oocytes or wildtype (stella-GFP) P1 non-growing oocytes

first: Mengwen

last: Hu

middle: H


title: Precise modulation of transcription factor levels reveals drivers of dosage sensitivity

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

overall_design: Refer to individual Series


title: Analysis of time series gene expression and DNA methylation reveals the molecular features of myocardial infarction progression (RNA-Seq)

status: Public on Jun 23 2022

city: Shanghai

first: Han

last: Yuru

state: Shanghai

address: 279 Zhouzhu Rd. Pudong New District, Shanghai

country: China

institute: Shanghai University of Medicine and Health Sciences

summary: Myocardial infarction (MI) is one of the deadliest diseases in the world, and the changes at the molecular level after MI and the DNA methylation features are not clear. Understanding the molecular characteristics of the early stages of MI is of significance for the treatment of the disease. In this study, RNA-seq and MeDIP-seq were performed on heart tissue from mouse models at multiple time points (0 h, 10 min,1 h, 6 h, 24 h and 72 h) to explore genetic and epigenetic features that influence MI progression. Analysis based on a single point in time, the number of differentially expressed genes (DEGs)and differentially methylated regions (DMRs)increased with the time of myocardial infarction, using 0 h as a control group. Moreover, within 10 minutes of MI onset, the cells are mainly in immune response, and as the duration of MI increases, apoptosis begins to occur. Analysis based on time series data, the expression of 1012 genes was specifically downregulated, and these genes were associated with energy metabolism. The expression of 5806 genes was specifically upregulated, and these genes were associated with immune regulation, inflammation and apoptosis. 14 transcription factors were identified in the genes involved in apoptosis and inflammation, which may be potential drug targets. Analysis based on MeDIP-seq combined with RNA-seq methodology, focused on methylation at the promoter region. GO revealed that the downregulated genes with hypermethylation at 72 h were enriched in biological processes such as cardiac muscle contraction. In addition, the upregulated genes with hypomethylation at 72 h were enriched in biological processes, such as cell-cell adhesion, regulation of the apoptotic signalling pathway and regulation of angiogenesis. Among these genes, the Tnni3 gene was also present in the downregulated model. Hypermethylation of Tnni3 at 72 hours after MI may be an important cause of exacerbation of MI.

overall_design: Eighteen 12-week-old male C57BL/6JR mice were included in the experiment. The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (50 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately. The mice in the control group received the same operation, sutured through the inferior artery, but not ligated. Complete anaesthesia of mice with 1-3% isoflurane after specific time of MI, followed by euthanasia by cervical dislocation. Total RNA was isolated from myocardial region of infarcted left ventricle.

first: Yanfei

last: Li


title: Bulk RNAseq analysis of hypertrophic cardiomyopathy (HCM) hiPSC-derived cardiomyocytes (hiPSC-CMs) and the isogenic control

status: Public on Jul 06 2022

city: Minneapolis

first: Brenda

last: Ogle

state: MN

address: 7-130 Hasselmo Hall 312 Church St. SE

department: Biomedical Engineering

institute: University of Minnesota

summary: To investigate HCM mutation-associated molecular details at the early stage of disease development, we performed bulk RNA-seq analysis at Day 15 of differentiation using RNA isolated from the isogenic control and mutant hiPSC-CMs. We performed pair-end sequencing with >30 million reads per sample with clean read counts of more than 96% for each sample.

overall_design: mRNA profiles of Day15 MYH7 R723C with MYH6 R725C mutant hiPSC-CMs and isogenic control

middle: M

first: Jeanne

last: Hsieh

first: Bhairab

middle: N

last: Singh


title: RNA sequencing of wild-type and mutant KRAS human lung cancer cell lines with of without FASN inhibition.

status: Public on Jun 29 2022

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: The goal of this study is to compare the RNA-seq derived transcriptome of mutant KRAS and wild-type KRAS lung cancer cell lines under fatty acid synthase (FASN) inhibition. We extracted total RNA with TRIzol from cells treated with 0.2 μM TVB-3664 (FASN inhibitor) or 0.2% DMSO for 4 days. One µg of total DNAse-treated RNA was used for library. cDNA was ligated to adapters and PCR amplified. Before being normalized and pooled, samples were quantified by Qubit then run on the Illumina NextSeq 500. Reads were aligned to the human hg38 reference genome. Only uniquely mapped reads were retained for further analyses. Gencode annotation for human (version v37) was used as reference alignment annotation and downstream quantification. Gene level expression was calculated using featureCount (v2.0.1) using intersection-strict mode by exon. Counts were calculated based on protein-coding genes from the annotation file. Low expressed genes were filtered using a per time-point approach with RPKM >= 0.5 in all samples in one or the other group.

overall_design: We extracted total RNA from 2 mutant KRAS (H460 and A549) and 2 wild-type KRAS (H522 and H661) human lung cancer cell lines treated with 0.2 μM TVB-3664 or 0.2% DMSO for 4 days

first: Cristina

last: Andreani

first: Caterina

last: Bartolacci

first: Pier

last: Scaglioni


title: Restoring a homeostatic microglia state by combination antiretroviral therapy in SIV-infected rhesus macaques

status: Public on Jun 22 2022

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

summary: Although modern therapies like cART have transformed HIV from a lethal disease to a manageable condition, associated neurocognitive consequences remain a concern. Paradoxically, microglia and macrophages, which comprise the innate defense system in the brain and are crucial for CNS homeostasis, are targets for HIV and key players in its neuropathogenesis. In addition, these infected cells can serve as viral reservoirs even in effectively treated infection. Here using an scRNA-seq approach in the SIV-NHP model, we demonstrate differential transcriptional programs in brain myeloid cells from monkeys under four conditions: uninfected, chronically SIV-infected, chronically SIV-infected treated with combination antiretroviral therapy (cART), and SIVE. Our study reveals alterations in composition (both lineage and gene expression profiles) of the cell populations between groups. Importantly, treatment with cART largely restored the homeostatic microglia profile present in uninfected animals that was disrupted in SIV-infected untreated animals

overall_design: Microglia/Macrophages were isolated and cryopreserved from the rhesus monkey brains of 3 saline-treated (control), 3 saline-treated SIV-infected, 3 saline-treated SIV-infected treated with cART and 1 saline-treated SIV-infected with encephalitis. They were subsequently thawed and immunomagnetically enriched for CD11b+ cells, and further purified by flow cytometry, sorted for CD11b positive, live events, and processed for scRNA by the 10xGenomics platform.

first: Howard

middle: S

last: Fox

first: Andrew

middle: J

last: Trease

last: Morsey


title: Analysis of time series gene expression and DNA methylation reveals the molecular features of myocardial infarction progression

type: Methylation profiling by high throughput sequencing


title: The application of LIMe-ID to study the impact of PRC2 perturbations on lamina assoication.

status: Public on Jun 17 2022

city: Cambridge

first: Brian

last: Liau

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

summary: We developed and performed LIMe-ID to simultaneously measure lamina association and DNA methylation in one experimental workflow. We then conducted LIMe-ID following perturbations of PRC2 to better understand the influence of H3K27me3 on lamina association.

overall_design: LIMe-ID experiments were performed in duplicate for either the M.CviPI-Lamin-B1 K562 cell line following inhibitor/vehicle treatments or the FLAG-NLS-M.CviPI-Lamin-B1 K562 EZH2 knock-in cell line following dTAG-13/vehicle treatment. EZH2 inihibtion, EED inhibition and vehicle (DMSO) treatment were each performed in duplicate for 72 hours with doxycycline added for the final 24 hours of the drug treatment for the inhibitor LIMe-ID. For the degradation LIMe-ID experiment, dTAG-13 and vehicle (DMSO) treatment were each performed in duplicate for 72 hours with doxycycline added for the final 24 hours of the drug treatment.

middle: B

first: Allison

last: Siegenfeld

first: Shelby

last: Roseman

first: Heejin

last: Roh


title: Comprehensive Benchmarking of CITE-seq versus DOGMA-seq Single Cell Multimodal Omics

status: Public on Jun 13 2022

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

summary: The recently developed transcription, epitopes, and chromatin accessibility by sequencing (TEA-seq) and similar DOGMA-seq single-cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent optimization, benchmarking and evaluation are lacking. We explored the utility, pros and cons of DOGMA-seq compared to the bimodal cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) assay in activated and stimulated human peripheral blood T cells. We identified an optimal incubation time and concentration of digitonin (DIG) for cell permeabilization and found that single-cell trimodal omics measurements after DIG permeabilization were generally better than after an alternative “low-loss lysis” (LLL) permeabilization condition. Next, we found that DOGMA-seq with optimized DIG permeabilization and its ATAC library provides more information, even though its mRNA and cell surface protein antibody-derived tag (ADT) libraries have slightly inferior quality, compared to CITE-seq. Finally, we recognized the additional value of DOGMA-seq for studying lineage-specific T helper cells.

overall_design:
For comparison between DIG and LLL conditions, eight aliquots of T cells were activated and stimulated separately. After labeled by hashtags, two groups of four aliquots of T cells were pooled together, stained by antibody cocktail, and permeabilized with DIG or LLL. For comparison between CITE-seq and DOGMA-seq, sixteen aliquots of T cells were activated and stimulated separately. After labeled by hashtags, two groups of eight aliquots of T cells were pooled together, stained by antibody cocktail, and subjected to CITE-seq or DOGMA-seq.

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Raw files for human/patient samples will be available in dbGaP (https://www.ncbi.nlm.nih.gov/gap) under phs004468.v1.p1 for controlled access to the personally identifiable sequence data.
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first: Zhongli

last: Xu

first: Elisa

last: Heidrich-O’Hare

first: Richard

last: Duerr


title: Telomerase-Dependent Ageing In The Zebrafish Brain

status: Public on Jun 09 2022

city: Sheffield

first: Catarina

middle: Martins

last: Henriques

address: Bateson Centre, Firth Court, The University of Sheffield, Western Bank

department: Oncology & Metabolism

country: United Kingdom

institute: The University of Sheffield

summary:
Decreased telomerase expression, telomere shortening, senescence-associated markers and inflammation have all been independently observed in the ageing brain and associated with disease. However, causality between limited telomerase expression and brain senescence and neuro-inflammation in the natural ageing setting is yet to be established. Here, we address these questions using the zebrafish as an ageing model which, akin to humans, displays premature ageing and death in the absence of telomerase and where telomere shortening is a driver of cellular senescence.
Our work shows for the first time that telomerase deficiency (tert-/-) accelerates key hallmarks of ageing identified in the Wild Type (WT) zebrafish brain at transcriptional, cellular, tissue and functional levels. We show that Tert-dependent transcriptomic changes associated with dysregulation of gene expression, stress response and dysregulation of immune genes are accompanied by accelerated accumulation of senescence-associated markers and inflammation in the aged brain. Importantly, In vivo, these changes correlate with increased blood-brain barrier permeability and altered cognitive behaviour. Of note, telomerase-dependent accumulation of senescence-associated markers in the brain occurs not only in the expected proliferative areas but also in non-proliferative ones, where it is unlikely due to telomere-dependent replicative exhaustion, suggesting that non-canonical roles of telomerase may be involved.
Together, our work suggests that telomerase has a protective role in the zebrafish brain against the accumulation of senescence and neuro-inflammation and is required for blood brain barrier integrity.

overall_design:
RNA-Sequencing of whole brain tissues, throughout the lifespan of WT and telomerase-deficient (tert-/-) fish. The data 4 age-groups of WT (2, 9, 22 and >30 months), corresponding to young, adult, median lifespan and old; and 3 age-groups of telomerase-deficient fish (2, 9, and 22 months), which correspond to young, medium lifespan and old. Each group has a sample size of 3 animals.
To identify signatures of ageing, WT brain samples were subjected separately to DESEq2 analysis, comparing the time points 9, 22 and >30 months with the time-point of 2 months. Then, tert-/- samples at 2, 9 and 22 months were compared with WT at 2 months, to identify telomerase-dependent ageing processes.

first: Raquel

middle: R

last: Martins

first: Savandara

last: Besse

first: Pam

last: Ellis

first: Naomi

last: Hartopp

first: Nadiyah

last: Mughal

first: Owain

last: Evans

first: Mina

last: Wahib

first: Zerkif

last: Yazigan

first: Heather

last: Mortiboys

first: Michael

last: Rera


title: The development and application of LIMe-Hi-C to simultanteously study lamina association, DNA methylation and chromosome conformation at baseline and upon EZH2 and DNMT1 inhibition

first: Brian

last: Liau

summary: We developed and performed LIMe-Hi-C in order to assess lamina association, DNA methylation, and chromosome conformation in one experimental workflow. We combined LIMe-Hi-C with chemcial inhibition of EZH2 and DNMT1 to better understand the influence of H3K27me3 and DNA methylation on 3D genome organization.

overall_design: LIMe-Hi-C experiments were performed in triplicate for FLAG-NLS-M.CviPI-Lamin-B1 K562 cells. A no doxycycline triplicate condition was included as a control to assess the specificity of the  lamina association signal. EZH2 inihibtion, DNMT1 inhibition and vehicle (DMSO) treatment were each performed in triplicate for 72 hours with doxycycline added for the final 24 hours of the drug treatment. The DMSO + doxyxline condition was utilized as a control. An in situ Hi-C experiment in singlicate for the DMSO + doxycyline condition was included as quality control for the bisulfite Hi-C workflow.

first: Allison

last: Siegenfeld

first: Shelby

last: Roseman


title: The estrogen receptor α cistrome of human endometrium and epithelial organoids and progesterone receptor cistrome in epithelial organoids

status: Public on May 26 2022

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: The ESR1 Cistrome in human endometrial biopsies was characterized and compared to gene regulations between the proliferative and mid-secretory pahses to infer estrogen target genes. ESR1 and PGR cistromes and 3D-cjromatin structures in cultured endometrial biopsies were characterized and compared to gene regulations induced by estrogen or progesterone in comparison to the whole endometrium.

overall_design: ESR1 ChIPseq of endometrial biopsies from proliferative or mid-secretory phases and ESR1 and PGR ChIPseq of human endometrial epithelial cells grown in culture organoid cultures and treated with estradiol and medroxyprogesterone acetate

first: Sylvia

middle: C

last: Hewitt

first: San-pin

last: Wu

first: Tianyuan

last: Wang

first: Mita

last: Ray

first: Marja

last: Brolinson

first: Steven

middle: L

last: Young

first: Thomas

middle: E

last: Spencer

first: Alan

last: DeCherney

first: Francesco

last: DeMayo


title: Single Cell transcriptomic atlas of mouse sex determination and gonadal differentiation

status: Public on May 27 2022

city: Geneve

first: Chloe

last: MAYERE

address: Michel Servet, 1

country: Switzerland

institute: UNIGE

summary:
Gonadal sex determination represents a unique model for studying cell fate decisions. However, a complete understanding of the different cell lineages forming the developing testis and ovary remains elusive. Here, we investigated the origin, specification, and subsequent sex-specific differentiation of a previously uncharacterized population of supporting-like cells (SLCs) in the developing mouse gonads. The SLC lineage is closely related to the coelomic epithelium and specified as early as E10.5, making it the first somatic lineage to be specified in the bipotential gonad. SLC progenitors are localized within the genital ridge at the interface with the mesonephros and initially coexpress Wnt4 and Sox9. SLCs become sexually dimorphic around E12.5, progressively acquire a more Sertoli- or pregranulosa-like identity and contribute to the formation of the rete testis and rete ovarii. Last, we found that WNT4 is a crucial regulator of the SLC lineage and is required for normal development of the rete testis.

In the present study, we built a transcriptomic atlas of the entire cell population of the developing female and male gonads during the process of mouse sex determination. We identified a previously uncharacterized population of supporting-like cells (SLC) and shed light on the origin and the developmental trajectory of this important cell lineage during the process of testis and ovary development.

overall_design: 20 10X single cell captures in duplicates at 5 stages (E10.5, E11.5, E12.5, E13.5 and E16.5) of gonadal ridges (E10.5, E11.5) and gonads in XX and XY CD1 mouse embryos

first: Chloé

last: Mayère

first: Violaine

last: Regard

first: Yasmine

last: Neirijnck

first: Pauline

last: Sararols

first: Isabelle

last: Stévant

first: Françoise

last: Kühne

first: Serge

last: Nef


title: Inhibition of EZH2 with GSK343 in the LIMe-Hi-C K562 clone

first: Brian

last: Liau

summary: We characterized the the effect of EZH2 inhibition on gene expression in the LIMe-Hi-C K562 clone

overall_design: For RNA-seq preparation, the M.CviPI-Lamin-B1 inducible K562 clone was treated in triplicate with either with vehicle (DMSO 0.1% v/v) or GSK343 (1µM) for 72 hours and induced with doxcycline (1µg/mL) for the final 24 hours of the drug treatments. Upon completion of the treatments, RNA was isolated and sequenced to assess changes in transcription.

first: Allison

last: Siegenfeld

first: Shelby

last: Roseman

first: Heejin

last: Roh


title: The application of quantitative ChIP-seq to study the impact of EZH2 inhibition on the facultative and constitutive heterochromatin landscape

summary: We conducted quantitative ChIP-seq following inhibition of EZH2 to better understand the influence of H3K27me3 on facultative and consitutive heterochromatin.

overall_design: Quantitative ChIP-seq was performed in duplicate for H3K27me3 and H3K9me3 following 72 hours of EZH2 inhibitor or vehicle treatment with doxycycline added for the final 24 hours of the drug treatment.


title: Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery


title: Heterologous ChAdOx1-BNT162b2 vaccination in Korean cohort induces robust immune and antibody responses that includes Omicron

status: Public on May 20 2022

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Heterologous ChAdOx1-BNT162b2 vaccination induces a stronger immune response than BNT162b2-BNT162b2. Here we investigated the molecular transcriptome, germline allelic variants of immunoglobulin loci, and anti-Omicron antibody levels in 46 office and lab workers from the Republic of Korea following ChAdOx1-BNT162b2 vaccination. Anti-spike-specific IgG antibody levels against the ancestral SARS-CoV-2 strain increased from 70 AU/ml to 14,000 AU/ml to 142,000 AU/ml one, three and seven days following the second vaccination. Titers against VOC, including Omicron, were two- to three-fold lower, yet higher than those measured following BNT162b2-BNT162b2 vaccination. RNA-seq of peripheral immune cells demonstrated activation of interferon pathways with increased IGHV clonal transcripts encoding neutralizing antibodies. scRNA-seq revealed enriched B cell and CD4+ T cell responses in both ChAdOx1-BNT162b2 and BNT162b2-BNT162b2 recipients, but a stronger clonal expansion of memory B cells with ChAdOx1-BNT162b2. In summary, heterologous ChAdOx1-BNT162b2 provides an innate and adaptive immune response that exceeds homologous BNT162b2 vaccination.


title: Genome-wide identification of codanin-1 binding sites in human K562 erythroleukemia cells with chromatin immunoprecipitation coupled with next-generation sequencing

status: Public on May 19 2022

city: New Haven

first: Gary

last: Kupfer

address: 333 Cedar St

institute: Yale

summary: Congenital dyserythropoietic anemia type I (CDA-I) is an autosomal recessive disorder marked by ineffective erythropoiesis, abnormal morphology of bone marrow erythroblasts, and iron overload. Most cases of CDA-I are caused by mutations in the CDAN1 gene, which encodes for a ubiquitous protein of unknown function, codanin-1. To study the function of codanin-1 in CDA-I erythroid pathophysiology several erythroid models were developed. Here we show that codanin-1 expression is required for erythroid progenitor development and normal erythroid cell differentiation. Erythroid cells lacking codanin-1 demonstrated morphologic changes similar to that observed in CDA-I. Global gene expression changes after codanin-1 knockdown revealed alterations in a set of key erythroid genes. In particular, the AHSP gene, which showed decreased mRNA expression after codanin-1 knockdown in CD34+ cells, also demonstrated increased codanin-1 occupancy at its gene regulatory region by chromatin immunoprecipitation coupled to high-throughput sequencing. Using cell models recapitulating many features of CDA-I, we have confirmed the importance of codanin-1 during erythroid differentiation and provide mechanistic insight into how loss of codanin-1 expression results in CDA-I.

overall_design: ChIP-Seq analysis of codanin-1 binding sites in human K562 erythroleukemia cells. ChIP assays were performed using anti-codanin-1 antibodies (Cod1, Cod2). Cod1 corresponds to homemade antibody raised against N-terminal fragment of codanin-1 (amino acids 123-142, ProteinTech). Cod2 corresponds to commercial antibody raised against C-terminal fragment of codanin-1 from Santa Cruz (sc-68404, Santa Cruz). As controls, anti-GATA1 antibody (N6) (sc-265X, Santa Cruz) and rabbit IgG (sc-2027, Santa Cruz) were used.

first: Linette

last: Bosques

first: Shilpa

last: Hattangadi

first: Caroline

last: Tang

first: Sameet

last: Mehta


title: Heterologous ChAdOx1-BNT162b2 vaccination in a Korean cohort induces a robust genetic immune and antibody response that includes Omicron [RNA_seq]

summary: Heterologous ChAdOx1-BNT162b2 vaccination induces a stronger immune response than two doses of BNT162b2. Yet, the molecular transcriptome, the germline allelic variants of immunoglobulin loci and anti-Omicron antibody levels induced by the heterologous vaccination have not been formally investigated. Moreover, there is a paucity of COVID-19 vaccine studies including diverse genetic populations. Here, we show a robust molecular immune transcriptome and antibody repertoire in 46 office and lab workers from the Republic of Korea after heterologous vaccination, ChAdOx1 followed by BNT162b2. Anti-spike-specific IgG antibody levels against the ancestral SARS-CoV-2 strain increased from 70 AU/ml immediately following the first vaccination to 14,000 U/ml within three days after the second vaccination and 142,000 AU/ml after seven days. Antibody titers against more recent variants, including Omicron, were two- to three-fold lower, yet higher than those obtained after the second dose of a BNT162b2-BNT162b2 homologous vaccination. RNA-seq conducted on peripheral immune cells demonstrated a strong activation of interferon-induced genetic programs in the heterologous cohort and an increase of specific IGHV clonal transcripts encoding neutralizing antibodies was detected. Enrichment of B cell and CD4+ T cell responses was observed following both ChAdOx1-BNT162b2 heterologous and BNT162b2-BNT162b2 homologous vaccination using scRNA-seq, but clonally expanded memory B cells were relatively stronger in the heterologous cohort. In summary, a heterologous vaccination with ChAdOx1 followed by BNT162b2 provides an innate and adaptive immune response exceeding that seen in homologous BNT162b2 vaccination.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from individuals who had received the ChAdOx1 or BNT162b2 mRNA vaccines.

first: Hye-Kyung


title: Human endometrium and epithelial organoids

first: Franco

last: Demayo


title: Codanin-1 binding sites in human K562 erythroleukemia cells; Global Gene expression changes in response codanin-1 knockdown in erythroid-committed cells


title: Progesterone signaling in endometrial epithelial organoids

summary: 3D chromatin structure of endometrial organoids and PRKO and Sox17cKO mouse uterus

overall_design: HiC of endometrial orgaoids treated with estrogen and progesterone and ovariectomized uterus from progesterone receptor-null (PRKO) and PR-CrexSox17-flox mice 1 hour after treatment with V or progesterone

first: Sylvia

last: Hewitt

first: San-pin

last: Wu

first: Sara

last: Grimm

first: Tianyuan

last: Wang

first: Artiom

last: Gruzdev

first: Mita

last: Ray

first: Marja

last: Brolinson

first: Steven

last: Young

first: Thomas

last: Spencer

first: Alan

last: DeCherney

first: Francesco

last: DeMayo


title: Type 2 cytokines in the thymus activate Sirpa+ dendritic cells to promote clonal deletion

status: Public on May 09 2022

first: Kristin

last: Hogquist

address: 2101 6th St SE

summary: The thymus contains a diversity of dendritic cells (DC) that exist in defined locations and have different antigen processing and presenting features. This suggests that they play non-redundant roles in mediating thymocyte selection. In an effort to eliminate SIRP+ cDC2, we discovered that a substantial proportion expresses the surface lectin, CD301b, in the thymus. These cells resemble the CD301b+ type 2 immune response promoting DC that are present in the skin draining lymph nodes. Transcriptional and phenotypic comparison to other DC subsets in the thymus revealed that thymic CD301b+ cDC represent an activated state that exhibits enhanced antigen processing and presentation. Furthermore, CD301b+ cDC2 demonstrated a type 2 cytokine signature and required steady state IL-4 receptor signaling. Selective ablation of CD301b+ cDC2 impaired clonal deletion without affecting regulatory T cells. TCR alpha repertoire sequencing confirmed that cDC2 promote deletion of conventional T cells with minimal effect on regulatory T cell selection. Together, these findings suggest that cytokine-induced activation of DC in the thymus substantially enforces central tolerance.

overall_design: CD11c and CD11b expressing cells were sorted from the thymus of 7-week-old wildtype (WT) and Mgl2DTR_eGFP treated with diptheria toxin for 48 hours and cells were submitted for scRNA sequencing

first: Elise

last: Breed

first: Matouš

last: Vobořil

first: Katharine

last: Ashby

first: Ryan

last: Martinez

first: Lily

last: Qian

first: Haiguang

first: Oscar

last: Salgado

first: Christine

last: O'Connor


title: Heterologous ChAdOx1-BNT162b2 vaccination in a Korean cohort induces a robust genetic immune and antibody response that includes Omicron [scRNA-seq]

first: Hye Kyung

last: Lee

overall_design: scRNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from individuals who had received the 2 doses of ChAdOx1 (N=2), 2 doses of BNT162b2 (N=2), and heterologous ChAdOx1 and BNT162b2 vaccination (N=2).

first: Hye-Kyung


title: Transcriptional profile of human endometrial epithelial cells grown as organoids and treated with hormones

first: Franco

last: Demayo

summary: Endometrial epithelial cells were cultured as organoids and transcriptional profiles of vehicle, E2 or E2+MPA treated cultures were compared.

overall_design: gene responses of organoids isolated from 2 donors were grown and treated with E2, E2+MPA and  or vehicle

first: Sylvia

last: Hewitt

first: San-pin

last: Wu

first: Sara

last: Grimm

first: Tianyuan

last: Wang

first: Artiom

first: Mita


title: RNA sequencing reveals global gene expression changes in response to codanin-1 knockdown in erythroid-committed cells

first: Gary

last: Kupfer

overall_design: RNA-Seq was used to analyze the effects of CDAN1 (codanin-1) knockdown in erythroid-induced human primary cells transduced with non-targeting shRNA (shControl) or shRNAs targeting different regions of CDAN1, the 3’UTR or the coding sequence.

first: Linette

last: Bosques

first: Caroline

last: Tang

first: Sameet

last: Mehta


title: Gene expression profiling of Tumor and liver infiltrating NK cells from patients with Hepatocellular Carcinoma

city: Parma

first: ALESSANDRA

last: ZECCA

state: Parma

address: Via gramsci, 14

country: Italy

institute: University of Parma

summary: Natural Killer (NK) cells play a central role in cell-mediated immune response to cancer. In previous studies number and function of NK-cells have been shown to be positively correlated with HCC outcome. In this study, we have performed a genetic expression analysis comparing mRNA expression by NK cells from tumor samples derived from HCC patients to NK cells infiltrating the liver counterpart and to NK cells in the normal liver as controls.  The bioinformatic analysis has been completed by an immunophenotypic study, functional analysis and metabolic assessment of the infiltrating NK cells. It is known that NK cells may present functional defects in HCC patients however previous studies have not systematically address the molecular mechanisms associated with these defects by an unbiased genetic expression study. We have identified altered cellular pathways and hypothesized possible mechanisms that could be targeted for restoring an immune-protective NK cell response.

overall_design: Liver and tumor-infiltrating lymphocytes from 11 patients with HCC arising in Hepatitis C virus (HCV) infection and 6 patients undergoing liver resection for colorectal metastasis as control were stained with appropriate fluorescent antibodies, in order to distinguish NK-cells. RNA was purified from sorted NK-cells and  amplified. cDNA was labeled and hybridized to Agilent microarrays.

first: Alessandra

last: Zecca

first: Valeria

last: Barili

first: Elisabetta

last: Cariani

first: Gabriele

last: Missale


title: Caterpillar-Induced Rice Volatile (E)-β-Farnesene Impairs the Development and Survival of Chilo suppressalis Larvae by Disrupting Insect Hormone Balance

status: Public on May 04 2022

city: nanjing

first: yang

last: niuzi

state: jiangsu

department: College of  Plant Protection

institute: jaas

summary: In this study, an artificial feeding study containing (E)-β-farnesene (0.8g/kg) with C. suppressalis larvae was conducted to investigate its physical performance, and results revealed that the average 2nd instar duration in C. suppressalis significantly increased from 4.78 days to 6.31 days after Eβf treatment (P<0.001), and in 3rd instar C. larvae also significantly increased from 5.70 days to 8.00 days (P<0.001). There were no significant differences in 4th and 5th C. suppressalis larval between Eβf treatment and control(P>0.05). The mortality rates of 2nd C. suppressalis larvae were increased by 21.00-fold, compared with control(P<0.001), 3rd C. suppressalis larval increased by 6.39-fold(P<0.001). Comparative transcriptome analysis also showed that multiple DEGs involved in insect hormone biosynthesis pathway, the results of hormone assay in 3rd instar larvae showed the balance between juvenile hormones and ecdysteroids was disrupted. Eβf treatment increased juvenile hormones titers, but not the ecdysteroids. The results of qPCR were consistent with RNA-seq. Taken together, Eβf impairs the development and survival of C. suppressalis larvae by disrupting insect hormone balance. Moreover, the altered pathways were associated with carbohydrates, xenobiotics and cofactors and vitamins in C. suppressalis larvae. Altogether, our findings identify Eβf impair the development and survival of C. suppressalis larvae. Additionally, our data also revealed a potential mechanism that Eβf impaired the development and survival of C. suppressalis larval by disrupting insect hormone balance. These findings may contribute to the integrated control of C. suppressalis.

overall_design: Examination of 2 different transcriptome in Chilo suppressalis.

first: Lei

last: Yang

first: Yang

last: Sun

first: Jichao

last: Fang


title: Multi-omics Analysis reveals novel therapeutic vulnerabilities in lung cancer

city: Houston

first: Randa

last: El-zein

address: 6670 Bertner Avenue

institute: Houston Methodist

summary: Non-small cell lung cancer (NSCLC) comprises the majority (~85%) of all lung tumors, with lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) being the most frequently diagnosed histological subtypes. Currently, multi-modal omics profiles had been carried out in NSCLC, but no studies reported yet a systems biology approach to provide a complete picture of molecular perturbations specifically for LUAD and LUSC.

overall_design: In this study, we integrated transcriptomics, metabolomics and adducteomics for the first time to analyze 30 paired human lung tumors and adjacent noncancerous tissues. We portrayed unique metabolite related gene signatures to distinguish LUAD from LUSC and several altered pathways aberrantly expressed at both transcriptional and metabolic levels. Additionally, the integration studies revealed a 28-metabolite gene signature in TCGA-LUAD cohort and demonstrated a significant association with survival, especially for 6 metabolite related genes as therapeutic targets. To further explore, we identified AZD-6482, a clinical trial drug from LINCS/connectivity map and found that it significantly inhibited 3 genes from the 28-gene signature. By integrating adducteomics, we found a differential expression of 307 genes correlated with 6 DNA adducts in LUSC although LUAD did not show much correlation. We found that γ-hydroxy-propanodeoxyguanosine (γ-OH-PdG) is the major DNA adduct formed in LUSC, but not in adjacent noncancerous tissue and significantly correlated with 295 modulated genes as well. We also have identified aberrant signaling pathways for each specific DNA adducts in LUSC compared to adjacent normal. Overall, we have provided a broad picture of integration of omics that can distinguish LUAD and LUSC, prediction of patient survival and identification of therapeutic targets and anticancer drugs. Ultimately, genes modulated by DNA adducts in LUSC could serve as biomarkers or therapeutic targets for cigarette smoke induced lung cancer.

first: Cristian

last: Coarfa

first: Jose

last: Thaiparambil

first: Dimuthu

last: Perera

first: Jianrong

last: Dong

first: Sandra


title: Characterisation of resident alveolar macrophages in bronchoalveolar lavage fluid (BALF) in non-fumer healthy, fumer and COPD patients

status: Public on May 23 2022

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

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

overall_design: Refer to individual Series


title: Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats

status: Public on Apr 25 2022

city: La Jolla

first: Daniel

last: Munro

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

summary: Elevated intraocular pressure (IOP) is influenced by environmental and genetic factors. It is associated with 23 multiple disease processes with primary open angle glaucoma (POAG) being the most prevalent. Due to its 24 complex, multifactorial nature, genetic predisposition is not completely understood thus, there is an urgent 25 need for additional investigations into the genetic regulation of IOP. Heterogenous stock (HS) outbred rats are 26 a multigenerational outbred population derived from eight inbred strains that have been fully sequenced. This 27 population is ideal for genome-wide association studies (GWAS) due to the accumulated recombinations 28 among well-defined haplotypes, the relatively high allele frequencies, access to a large collection of tissue 29 samples, and the large allelic effect size compared to human studies. The purpose of this study was to identify 30 genetic loci underlying elevated IOP using HS rats. Both male and female HS rats (N=1,812) were used in the 31 study. Genotyping-by-sequencing was used to obtain ~3.5M single nucleotide polymorphisms from each 32 individual. We performed a GWAS for the IOP phenotype using a linear mixed model and used permutation to 33 determine a genome-wide significance threshold. We also estimated SNP heritabilities. Our GWAS results 34 identified three genome-wide significant loci for elevated IOP on chromosomes 1, 5, and 16. These loci 35 contained 7 genes in total including Tyr, Grm5, Ctsc, Rab38, MGC94199, Plekhf2, and Csmd1. We also 36 mapped expression quantitative trait loci (eQTLs) in HS rat eye tissue and discovered a cis-eQTL for Ctsc 37 among our significant loci. Tyr is the only gene that has been previously associated with human IOP. This 38 study highlights the efficacy of HS rats for investigating the genetics of elevated IOP and identifying potential 39 candidate genes for future functional testing. In summary, GWAS using HS rats is a powerful method for 40 identifying genome regions that harbor variants responsible for the variation in quantitative traits, such as IOP. 41 Additional studies are ongoing to further narrow the list of candidate genes in these intervals.

overall_design: mRNA profiles from the eye tissue of 53 HS rats

first: Samuel

last: Fowler

first: Tengfei

last: Wang

first: Apurva

last: Chitre

first: T

last: Hollingsworth

first: Angel

last: Garcia Martinez

first: Celine

last: St. Pierre

first: Hannah

last: Bimschleger

first: Jianjun

last: Gao

first: Riyan

last: Cheng

first: Pejman

last: Mohammadi

first: Hao

last: Chen

first: Oksana

last: Polesskaya

first: Abraham

last: Palmer

first: Monica

last: Jablonski


title: Methylation profiling by array for Parkinson's disease using brain tissue

status: Public on Apr 20 2022

city: Royal Oak

first: Stewart

middle: F

last: Graham

state: Michigan

address: 3811 West 13 Mile Road, Suite 415

department: OBGYN

institute: Corewell Health - Research Institute

type: Methylation profiling by genome tiling array

summary:
Parkinson’s disease is second most prevalent neurodegenerative disorder. Parkinson’s disease is hypothesized to be caused by a multifaceted interplay between genetic and environmental factors. We profiled the DNA methylation using the frontal lobe from people who died from Parkinson’s disease and compared them with age-, and sex-matched controls. We hypothesized that the complex regulation of DNA methylation and metabolome leads to deficits that cause irregular motor function among Parkinson’s disease subjects and the metabolomic disparities may reflect the effect of these complex interactions. Herein, we aim to integrate quantitative metabolomics and DNA methylation of brain tissue from primary motor cortex (Brodmann area 4) from Parkinson’s disease sufferers to better understand the biochemistry associated with the onset of the disease.
Parkinson’s disease (PD) is second most prevalent neurodegenerative disorder following Alzheimer’s disease. Parkinson’s disease is hypothesized to be caused by a multifaceted interplay between genetic and environmental factors. Herein, and for the first time, we describe the integration of metabolomics and epigenetics (genome-wide DNA methylation; epimetabolomics) to profile the frontal lobe from people who died from PD and compared them with age-, and sex-matched controls. We identified 48 metabolites to be at significantly different concentrations (FDR q<0.05), 4,313 differentially methylated sites [5'-C-phosphate-G-3' (CpGs)] (FDR q<0.05) and increased DNA methylation age in the primary motor cortex of people who died from PD.  We identified Primary bile acid biosynthesis as the major biochemical pathway to be perturbed in the frontal lobe of PD sufferers, and the metabolite taurine (p-value = 5.91E-06) as being positively correlated with CpG cg14286187 (SLC25A27; CYP39A1) (FDR q = 0.002), highlighting previously unreported biochemical changes associated with PD pathogenesis. In this novel multi-omics study, we identify regulatory mechanisms which we believe warrant future translational investigation and central biomarkers of PD which require further validation in more accessible biomatrices.

overall_design: A total of 78 brain tissue samples were acquired from the NIH NeuroBioBank (40 brain tissue samples were from PD cases and 38 were from cognitively healthy subjects). The frozen brain tissues were obtained from the primary motor cortex (Brodmann area 4) and processed using Infinium MethylationEPIC Array following the manufacturer’s instructions (Illumina Infinium HD Methylation Assay Experienced User Card, Automated Protocol 15019521 v01). Raw signal intensity data were preprocessed from raw *.idat files using minfi Bioconductor package. The samples were normalized using Noob normalization. Methylation beta values were extracted for the remaining probes. Sample position effect on the EPIC array was adjusted using empiricalBayesLM function from WGCNA package. The effect of sample position was modeled as polynomial of second degree. Proportion of neuronal cells in each sample was then estimated using flow sorted PFC samples and estimateCellCount function from minfi package.

first: Sangeetha

last: Vishweswaraiah

first: Sumeyya

last: Akyol

first: Ali

last: Yilmaz

first: Zafer

last: Ugur

first: Juozas

last: Gordevicius

first: Kyung

last: Oh

first: Patrik

last: Brundin

first: Uppala

last: Radhakrishna

first: Viviane

last: Labrie


title: Characterization of two lung alveolar macrophages in bronchoalveolar lavage fluid (BALF) cells in non-fumer healthy, fumer and COPD patients

first: Qiang

last: BAI

summary:
Rationale: Alveolar macrophages (AM) are functionally important innate cells involved in lung homeostasis and immunity. However, it remains unclear whether ontogenically and functionally distinct subpopulations of AM can be found in healthy human airways, and to what extent conditions like smoking or chronic obstructive pulmonary disease (COPD) trigger changes in the AM compartment.
Objective: To explore the phenotypical, ontological, transcriptional and functional diversity of human AM isolated from healthy non-smokers, healthy smokers and COPD patients.
Methods: We analyzed bronchoalveolar lavage fluid (BALF) cells by flow cytometry, bulk and single-cell(sc) RNA-sequencing (RNA-seq).
Main Results: We found that BALF CD206 + macrophage subpopulations could be distinguished based on their level of auto-fluorescence. CD206 + autofluorescent high (AF hi ) AM were identified as classical self-proliferative AM, while autofluorescent low (AF lo ) AM originated from monocytes and were expressing both monocyte- and classical AM-related genes. Of note, monocyte-derived AF lo AM were equally represented in each category of subjects and exhibited a functionally distinct immunoregulatory profile, including the ability to secrete the immunosuppressive cytokine interleukin-10 (IL-10). Finally, we provide evidence that the monocyte-associated marker CCR2 can be used by flow cytometry to distinguish AM according to their origin.

overall_design: Analysis of CD14+ blood monocytes, autofluorescence hi (alveolar macrophages) and autofluorescence lo (regulatory macrophages) CD45+ CD206+ macrophages in bronchoalveolar lavage fluids (BALF) from 3 groups of patients: healthy non-smokers, healthy smokers and COPD patients.

last: Bai

first: Maude

last: Liégeois

first: Laurence

last: Fievez

first: Dimitri

last: Pirottin

first: Thomas

last: Marichal

first: Fabrice

last: Bureau


title: DNA methylation analysis of glioblastomas harboring FGFR3-TACC3 fusions identifies a methylation subclass with better patient survival.

status: Public on May 16 2022

city: BETHESDA

first: Zhichao

last: Wu

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

institute: NIH/NCI

summary: Genomewide DNA methylation array profiling of 244 gliobastoma and ganglioglioma samples to study FGFR3-TACC3 gene fusions and resolved into a new entity, glioblastoma IDH-wildtype, FGFR3-TACC3 fusion postive methylation outlier group (GBM-F3T3-O). GBM-F3T3-O showed a unique methylation profile and better survival than other glioblastoma patients. The methylation idat profiles were provided here.

overall_design:
Bisulfite converted genomic DNA extracted from tumor samples was hybridized to Illumina Infinium EPIC Human DNA Methylation Beadchips
Please note that the processed data files contains total 276 data columns, including 32 samples (columns) whose the raw data was provided by authors of paper PMID: 33168106.

first: Kenneth

last: Aldape


title: Therapeutic Implications for Intrinsic Phenotype Classification of Metastatic Castration Resistant Prostate Cancer

status: Public on May 03 2022

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Metastatic prostate cancers are recognized to exhibit subtypes categorized by underlying genomic alterations and phenotypes largely partitioned by androgen receptor signaling and neuroendocrine activity. In the present study we evaluated a phenotypic classification approach originally developed for subtyping breast carcinomas using the PAM50 gene signature. PAM50 subtypes associated with specific genotypes such as RB1 loss and phenotypes such as small cell/neuroendocrine carcinoma as well as tumor histology including cribriform morphology. In the context of clinical translation, PAM50 classification segregated tumors into groups with distinct druggable targets such as cell surface proteins amenable to antibody-drug-conjugates (ADCs). Classification into Luminal A, Luminal B and Basal tumors associated with time on androgen receptor signaling inhibitors, and responses to taxane chemotherapy. These findings support further clinical investigation of PAM50-based classification for prostate cancer patient stratification in therapeutic studies.

overall_design: RNA sequencing of prostate tumor patient-derived xenograft (PDX) models using Illumina TruSeq Library prep and sequenced on Illumina NovaSeq 6000 or HiSeq 2500.

first: Navonil

last: De Sarkar

first: Colm

last: Morrissey

first: Li

last: Xin

first: Martine

last: Roudier

first: Erolcan

last: Sayar

first: Dapei

last: Li

first: Eva

last: Corey

first: Michael

last: Haffner

first: Peter

last: Nelson


title: Analysis of histone modification with the deletion of components of the NSL complex

status: Public on Mar 18 2022

city: Changchun

first: hong

middle: sen

last: liu

address: qianjin

institute: jilin university

summary: The human males absent on the first (MOF)-containing non-specific lethal (NSL) histone acetyltransferase complex consists of 9 subunits can acetylate histone H4K16, H4K5 and H4K8. It has been known that this complex shares WDR5 subunit with the MLL/SET histone methyltransferases, suggesting that NSL complex is essential for the multiple transcriptional regulation mechanisms. However, there are few reports on the function of NSL HAT in genome, It is necessary to clarify the details and specificity of histone H4 acetylation cooperates with H3K4 methylation to regulate gene transcription. In this work, Our results show that The NSL complex plays a critical role in regulating multiple histone modifications by using the CRISPR/Cas9 NSL3-KO 293T cell line and ChIP-Seq approach. The global levels of highly enriched H4K16ac, H4K5ac, H3K4me2 and H3K4me3 at TSSs (TSS ± 3 kb region) are inhibited by NSL3-KO. NSL3-KO seemed to have little effect on the enhancer mark H3K27ac and repressor mark H3K27me3, but H3K4me1 was greatly affected by NSL3-KO. Moreover, the NSL complex govern gene transcription and identified genes by a coordinative mode of H4K16ac and H3K4me2/me3. What’s more, De novo motif analysis of MOF and NSL3 targets indicated that the NSL complex forms a gene regulatory network with multiple transcription factors by regulating their genes expression or cooperating with some factors through binding to specific motif.

overall_design: ChIP analysis of different histone modifications, pol II and the NSL complex subunits in 293T WT and NSL3KO cell line.

first: Yong

last: Cai

first: Jingji

last: Jin

first: Hongsen

last: Liu


title: Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control

status: Public on Apr 07 2022

first: Constantine

middle: Nicholas

last: Tzouanas

address: 45 Carleton St

department: Harvard-MIT Health Sciences and Technology

institute: Massachusetts Institute of Technology

summary: We used longitudinal scRNA-seq, PET-CT, and bacterial burden assays to understand the cellular features underlying granuloma timing and burden/resolution.

overall_design: Granulomas in Cynomolgus macaque were dissociated for scRNA-seq

first: Travis

middle: K

last: Hughes

first: Alex

last: Shalek


title: mRNA vaccination in octogenarian nuns 15 and 20 months after recovery from COVID-19 elicits robust immune and antibody responses that include Omicron

status: Public on Mar 09 2022

first: Hye Kyung

last: Lee

summary: Knowledge about the impact of prior SARS-CoV-2 infection of the elderly on mRNA vaccination response is needed to appropriately address the demand for additional vaccinations in this vulnerable population. Here we show that octogenarians, a high-risk population, mount a sustained SARS-CoV-2 spike-specific IgG antibody response for 15 months following infection. This response boosts antibody levels 35-fold upon receiving a single dose of BNT162b2 mRNA vaccine 15 months after recovery from COVID-19.  In contrast, antibody responses in naïve individuals boost only 6-fold after a second vaccine. Spike-specific ACE2 antibody binding responses in the previously infected octogenarians following two vaccine doses exceed those found in a naïve cohort after two doses. RNA-seq demonstrates activation of interferon-induced genetic programs, which persist only in the previously infected. A preferential increase of specific IGHV clonal transcripts that are the basis of neutralizing antibodies is observed only in the previously infected nuns.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from recovered COVID-19 patients and naïve individuals who had received the BNT162b mRNA vaccine.

first: Hye

first: Ludwig

last: Knabl


title: The Regulatory Evolution of the Primate Fine-Motor System

status: Public on Mar 07 2022

first: Morgan

last: Wirthlin

state: Pennsylvania

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

summary: In mammals, fine motor control is essential for skilled behavior, and is subserved by specialized subdivisions of the primary motor cortex (M1) and other components of the brain’s motor circuitry. We profiled the epigenomic state of several components of the Rhesus macaque motor system, including subdivisions of M1 corresponding to hand and orofacial control. We compared this to open chromatin data from M1 in rat, mouse, and human. We found broad similarities as well as unique specializations in open chromatin regions (OCRs) between M1 subdivisions and other brain regions, as well as species- and lineage-specific differences reflecting their evolutionary histories. By distinguishing shared mammalian M1 OCRs from primate- and human-specific specializations, we highlight gene regulatory programs that could subserve the evolution of skilled motor behaviors such as speech and tool use. Further, in order to predict candidate enhancers in additional species for which primary data was not available, we developed machine learning models trained on genome sequence across species.

sample_organism:
Macaca mulatta
Mus musculus
Rattus norvegicus

overall_design: To supplement publicly available open chromatin datasets, we generated bulk tissue ATAC-seq data from fresh mouse liver tissue (one male and one female replicate), fresh rat tissues (two male and one female replicate), and fresh macaque tissue (one male and one female replicate).  Our data includes cortex, striatum, and liver from all three species, and the cortex and striatum data from macaque consists of multiple sub-regions of these brain regions.

first: Irene

last: Kaplow

first: Alyssa

last: Lawler

first: Ashley

last: Brown

first: Jing

last: He

last: Kleyman

first: BaDoi

last: Phan

first: William

last: Stauffer

first: Andreas

last: Pfenning


title: FSCN1 promotes esophageal carcinoma progression through downregulating PTK6 via its RNA-binding protein effect

status: Public on Mar 05 2022

city: jilin

first: Hongfei

last: cai

address: No.1 Xinmin Street, Chaoyang District, Changchun City, Jilin Province

department: Ddepartment of Thoracic Surgery

institute: The First Hospital of Jilin University

summary: To explore the downstream molecules of FSCN1, shRNA targeting FSCN1 was designed and transfected into the ESCC cell line, ECA-109. Whole-genome expression profiling was performed to screen for related molecules.  To investigate the RNA binding property of FSCN1 in ESCC, RNA immunoprecipitation (RIP) was performed using an FSCN1 monoclonal antibody in ECA-109 cell lysate, and the associated RNA was analyzed by RNA-seq.

last: Cai


title: the RNA binding property of FSCN1

summary: To investigate the RNA binding property of FSCN1 in ESCC, RNA immunoprecipitation (RIP) was performed using an FSCN1 monoclonal antibody in ECA-109 cell lysate


title: Transcriptome profile of LX-2 cells

status: Public on Feb 28 2022

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary: To analyse gene expression differences between treated and untreated cells with human recombinant TGF beta in presence and in absence of mimic miR34b/c.

overall_design: Total RNA was extracted from n=5  or n=4 samples for group

first: R


title: scRNAseq muscle stem cells

status: Public on Mar 14 2022

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 270 S. Russell Street

institute: Purdue University

summary: Single-cell RNA sequencing muscle stem cells from non-injured, 5, and 10 days post injury

overall_design: Muscle stem cells were isolated from non-injured, 5 and 10 day post injury skeleta tibalis anterios mucsle using fluroescence activated cell sorting. n=3 male mice combined per sample; Pax7GkCre;sfGFP mice

first: Stephanie

last: Oprescu

first: Feng

last: Yue


title: Changes in skeletal muscle PAK1 levels regulate tissue crosstalk to impact whole body glucose homeostasis

status: Public on Feb 08 2022

city: Duarte

first: Debbie

middle: C.

last: Thurmond

state: California

address: 1500 E Duarte Rd

institute: City of Hope

summary: We have used RNA-seq to identify transcripts expressed in mouse skeletal muscle inducible PAK1 overexpression/knock-out.

overall_design: 15 mice preparation examed under 5 condition, WT with doxycyclin, skeletal muscle specific over expressed PAK1  with Doxycyclin or without doxycyclon, and skeletal muscle specific knock out PAK1 with or without doxycyclin.

first: Miwon

last: Ahn


title: Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level

status: Public on Feb 10 2022

first: Yanxiang

last: Deng

state: CT

address: 55 Prospect Street

institute: Yale University

summary: Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing. Spatially resolved chromatin states in mouse embryos revealed tissue-type-specific epigenetic regulations in concordance with ENCODE references and provide spatial information at tissue scale. Spatial-CUT&Tag revealed epigenetic control of the cortical layer development and spatial patterning of cell types determined by histone modification in mouse brain. Single-cell epigenomes can be derived in situ by identifying 20-micrometer pixels containing only one nucleus using immunofluorescence imaging. Spatial chromatin modification profiling in tissue may offer new opportunities to study epigenetic regulation, cell function, and fate decision in normal physiology and pathogenesis.

overall_design:
Spatially resolved genome-wide profiling of histone modifications (e.g., H3K27me3, H3K4me3, and H3K27ac) in mouse embryos, olfactory bulbs, and mouse brains.

Please note that the *spatial.tar.gz files (containing images and coordinates needed for downstream analysis) were added on Feb 17, 2022.

first: Rong

last: Fan


title: Integrative functional transcriptomic analyses implicate shared molecular circuits in sensorineural hearing loss

status: Public on Feb 16 2022

city: Kunming

first: Junjun

last: Hao

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

summary: Aging, noise exposure, and ototoxic drugs represent the three main causes of SNHL, leading to substantial similarities in pathophysiological characteristics of cochlear degeneration.  Although the common molecular mechanisms are widely assumed to underlie these similarities, its validity lacks systematic examination.  To address this question, we generated three SNHL mouse models from aging, noise exposure, and cisplatin ototoxicity and constructed gene coexpression networks for the cochlear transcriptome data across different hearing-damaged stages.

overall_design: The cochleae were harvested from controls (2-month-old mice), aging-induced SNHL (8-month-old and 12-month-old mice), noise-induced SNHL (2-month-old female mice after being exposed to noise for one hour and 2-month-old mice after being exposed to noise for 24 hours), and cisplatin-induced SNHL (2-month-old mice after being injected with cisplatin for one day and 2-month-old mice after being injected with cisplatin for three days).  An individual’s bilateral cochleae were collected as a biological replicate.  To ensure the reliability and repeatability of our data, at least three replicates were required.

first: Peng

last: Chen


title: The onset of whole-body regeneration in Botryllus schlosseri: morphological and molecular characterization

status: Public on Jan 28 2022

city: Villefranche-sur-mer

first: Stefano

last: Tiozzo

address: 181 chemin du Lazaret

institute: CNRS - IMEV

summary: Colonial tunicates are the only chordates that regularly regenerate a fully functional whole body as part of their asexual life cycle, starting from specific epithelia and/or mesenchymal cells. In addition, in some species, whole-body regeneration (WBR) can also be triggered by extensive injuries, which deplete most of their tissues and organs and leave behind only small fragments of their body. In this study we characterized the onset of WBR in Botryllus schlosseri, one colonial tunicate long used as a laboratory model. We first analyzed the transcriptomic response to a WBR-triggering injury. Then, through morphological characterization, in vivo observations via time-lapse, vital dyes, and cell transplant assays, we started to reconstruct the dynamics of the cells triggering regeneration, highlighting an interplay between mesenchymal and epithelial cells. The dynamics described here suggest that WBR in B. schlosseri is initiated by extravascular tissue fragments derived from the injured individuals rather than particular populations of blood-borne cells, as has been described in closely related species. The morphological and molecular datasets here reported provide the background for future mechanistic studies of the WBR ontogenesis in B. schlosseri and allow to compare it with other regenerative processes occurring in other tunicate species and possibly independently evolved.

overall_design: Transcriptomic profile of whole-body regeneration of Botryllus schlosseri at 0, 6, 18 and 24 hours post-injury

first: Alexandre

last: Alié

first: Lorenzo

last: Ricci


title: Single-cell Transcriptome Analysis Revealed that EGFR Mutation Leads to a Suppressive Tumor Immune Microenvironment in Lung Adenocarcinoma

status: Public on Feb 09 2022

city: Guangzhou

first: Qing

last: Zhou

state: Guangdong

address: 106#，ZHONG SHAN ER ROAD

institute: Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China

summary: We analyzed 40,799 single cells from nine samples and found that in EGFR-mutant LUAD, tumor cells generated an immunosuppressive microenvironment by releasing cytokines to attract suppressive immune cells such as myeloid-derived suppressor cells (MDSCs) directly or indirectly by interacting with macrophages, dendritic cells, or other cell types. By contrast, EGFR wild-type LUAD had a greater ability to recruit immunocompetent T cells such as TRMs and Th1 cells, thus driving a proinflammatory microenvironment.

overall_design: To evaluate the cellular landscape of the TME of lung adenocarcinoma based on EGFR mutation status, we collected nine tumor samples from eight patients with treatment-naïve LUAD for scRNA-seq and bioinformatic analyses.

first: Lei

last: Yang


title: Single nuclei RNAseq of rat area postrema and nucleus tractus solitarius after GDF15 treatment

status: Public on Jan 05 2022

city: Philadelphia

first: Benjamin

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

summary: We performed single-nuclei RNAseq of Sprague Dawley rat area postrema and nucleus tractus solitarius brain samples from animals treated with GDF-15 to identify cellular subtype specific changes in the neural transcriptome.

overall_design: We performed the 10x Genomics 3' gene expression assay (v3.1) on nuclei isolated from frozen Sprague Dawley rat area postrema and nucleus tractus solitarius combined brain punches. At the onset of the dark cycle, rats (~400 g) were injected with GDF15 (100 μg/kg, n=4) (i.p.). After six hours, rats were deeply anesthetized with a triple cocktail of ketamine, xylazine and acepromazine (180 mg/kg, 5.4 mg/kg and 1.28 mg/kg, respectively; i.p.) in the middle of the dark phase. Brains were removed and snap-frozen in dry ice-cold hexane. Three adjacent micro-punch samples (each ~1 cubic mm) containing the AP and left and right NTS were collected from coronally-prepared brains on a cryostat, pooled together, and stored at -80°C until further processing. Nuclei were isolated by differential centrifugation and microfluidically captured using the 10x Genomics Chromium controller. Sequencing libraries were constructed and sequenced on an Illumina NovaSeq 6000.

first: Richard

last: Crist

first: Matthew

last: Hayes

first: Bart

last: De Jonghe

first: Tito

last: Borner


title: Extended data for pancreas single-cell patch-seq dataset in nondiabetic and T2D

status: Public on Jan 27 2022

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

summary: Combined single-cell RNAseq and electrophysiological profiling of human pancreatic islet cells (pancreas patch-seq).

overall_design: The dataset contains 640 pancreas patch-seq cells from human donors (nondiabetic and with T2D). Single-cell RNA libraries are done using SmartSeq2.

first: Xiaoqing

last: Dai

first: Seung

last: Kim

first: Patrick

last: MacDonald

first: Stephen

last: Quake


title: RBM20 mutations result in cardiac remodelling and pathogenesis in mice

status: Public on Jan 01 2022

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Genetic studies show that mutations in a gene named as RNA binding motif 20 (RBM20) are associated with dilated cardiomyopathy (DCM). We selected two mutations (S637A and S639G) located in arginine/serine-rich (RS) domain of RNA binding motif 20 (RBM20) and generated two knock-in mouse models (Rbm20S637A and Rbm20S639G) respectively. The heterozygous (HT) and homozygous (HM) in both mouse lines displayed DCM phenotype with enlarged left ventricular (LV) chamber, thinner ventricular walls and reduced ejection fraction. We also observed higher mortality rate in both HM mice, ~50% in Rbm20S639G and ~34% in Rbm20S637A at an early age (<100days). Differentially expressed and spliced genes from RNA-seq data were involved in arrhythmia, cardiomyopathy, and sudden death based on Human Phenotype Ontology enrichment analysis (FDR≤0.05) in both mouse lines. Immunofluorescent analysis in tissues and single cardiomyocytes respectively showed both mutations promote RBM20 nucleocytoplasmic trafficking and protein condensates, suggesting they are gain-of-function mutations, leading to high mortality rate at younger age. Together, we reported a new mechanism by which cardiac genetic mutations causes protein trafficking and RNA-protein aggregation in cardiac remodelling.

overall_design: Study the underlying mechanisms of two Rbm20 mutations in cardiac remodeling in mice.

first: Wei

last: Guo

first: Chunyan

last: Wang

first: Camila

middle: U

last: Braz

first: Yanghai

last: Zhang


title: Genome-wide association studies identify novel genetic loci for epigenetic age acceleration among survivors of childhood cancer [Metadata_SJLIFE1_2138]

city: Memphis

first: Zhaoming

state: TN

address: 262 Danny Thomas Place

department: Epidemiology & Cancer Control

institute: St. Jude Children's Research Hospital

summary: Background: Increased epigenetic age acceleration (EAA) in survivors of childhood cancer is associated with specific treatment exposures, unfavorable health behaviors, and presence of certain chronic health conditions. To better understand inter-individual variability, we investigated the genetic basis underlying EAA.  Methods: Genome-wide association studies of EAA based on multiple epigenetic clocks (Hannum, Horvath, PhenoAge, and GrimAge) were performed. MethylationEPIC BeadChip array and whole-genome sequencing data were generated with blood-derived DNA from participants in the St. Jude Lifetime Cohort Study (discovery: 2,138 pre-existing and 502 newly generated data, all survivors; exploratory: 282 community controls). Linear regression models were fit for each epigenetic age against allelic dose of each genetic variant, adjusting for age at sampling, sex, and cancer treatment exposures. Fixed-effects meta-analysis was used to combine summary statistics from two discovery data sets. LD (Linkage disequilibrium) score regression was used to estimate single-nucleotide polymorphism (SNP)-based heritability.  Results:  For EAA-Horvath, a genome-wide significant association was mapped to SELP gene with the strongest SNP rs732314 (meta-GWAS: β=0.57, P=3.30×10-11). Moreover, the stratified analysis of the association between rs732314 and EAA-Horvath showed substantial heterogeneity between children and adults (meta-GWAS: β=0.97 vs. 0.51, I2=73.1%) as well as between survivors with and without chest/abdominal/pelvic-RT exposure (β=0.64 vs. 0.31, I2=66.3%). For EAA-Hannum, an association was mapped to HLA locus with the strongest SNP rs28366133 (meta-GWAS: β=0.78, P=3.78×10-11). There was no genome-wide significant hit for EAA-PhenoAge or EAA-GrimAge. Interestingly, among community controls, rs732314 was associated with EAA-Horvath (β=1.09, P=5.43×10-5), whereas rs28366133 was not associated with EAA-Hannum (β=0.21, P=0.49). The estimated heritability was 0.33 (SE=0.20) for EAA-Horvath and 0.17 (SE=0.23) for EAA-Hannum, but close to zero for EAA-PhenoAge and EAA-GrimAge.  Conclusions: We identified novel genetic variants in SELP gene and HLA region associated with EAA-Horvath and EAA-Hannum, respectively, among survivors of childhood cancer. The new genetic variants in combination with other replicated known variants can facilitate identification of survivors at higher risk in developing accelerated aging, and potentially inform drug targets for future intervention strategies among vulnerable survivors.

overall_design: We included (1) SJLIFE1: 2,138 survivors (median age at DNA sampling 31.8 years); (2) SJLIFE2: 502 survivors (median age at DNA sampling 16.5 years); (3) SJLIFE_controls: 282 non-cancer controls (median age at DNA sampling 35.0 years of European ancestry from the St. Jude Lifetime Cohort Study, a retrospective hospital-based study with prospective clinical follow-up. Cumulative doses of chemotherapy and region-specific radiation were abstracted from medical records. DNAm profile was measured using MethylationEPIC BeadChip with blood-derived DNA.

first: Qian

last: Dong

last: Song

last: Qin

first: Cheng

last: Chen

first: Zhenghong

last: Li

first: Xiaojun

last: Sun

first: John

last: Easton

first: Heather

last: Mulder

first: Emily

last: Plyler

first: Geoffrey

last: Neale

last: Walker

first: Xiaotu

last: Ma

first: Xiang

first: I-Chan

last: Huang

first: Yutaka

last: Yasui

first: Kirsten

last: Ness

first: Jinghui

first: Melissa

last: Hudson

first: Leslie

last: Robison


title: Time series data of chromatin and transcription throughout the cell cycle

status: Public on Jan 06 2022

city: Durham

first: Yulong

address: 208 Research Dr

institute: Duke University

summary: The occupancy states of DNA-binding nucleosomes and subnucleosome-sized proteins (e.g.  transcription factors, replication proteins, etc.) determine the chromatin accessibility landscape and provide additional regulatory context for DNA-templated processes including transcription and DNA replication. Throughout the mitotic cell division cycles, the transcriptome undergoes periodic reprogramming along with replication- and mitosis-induced global chromatin reconfiguration; however, profiling of the cell cycle-specific chromatin dynamics and understandings of its regulatory mechanisms remain limited. Here we employed high-resolution MNase-seq to factor-agnostically map the genome-wide chromatin occupancy with synchronized Saccharomyces cerevisiae cell populations, in parallel with transcriptome profiling by RNA-seq. Throughout the cell cycles, the occupancy of gene-body nucleosomes and promoter subnucleosomes (presumably TFs and polymerase) exhibit both transcription- dependent and independent periodicity, suggesting a decoupling between transcription and chromatin occupancy dynamics. The “phased” positioning of nucleosomes within gene bodies, however, is pervasively disorganized by replication fork progression, and also regulated by the intensity and cell cycle phase of transcriptional activation. Finally, we profiled the chromatin organization around replication origins throughout the complete cell cycle and revealed the chromatin context for origin efficiency.

overall_design: Time course of yeast released from α-factor and collected every 10 min from T=0 min (prior to release) to 150 min (Replicate 1) or 140 min (Replicate 2) post release. Because the recovery time from α-factor arrest for Replicate 1 is about one time point longer than Replicate 2, T=10 min for Replicate 1 is discarded and all later time points are shifted one time point earlier when  aligning the cell cycle timeline with Replicate 2.  Two biological replicates are conducted which include 30 samples of MNase chromatin and 29 samples of RNA (T=110 min for Replicate 2 is of bad quality and discarded).

first: David

last: MacAlpine

first: Alexander

last: Hartemink


title: Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and subsequent weight regain

status: Public on Mar 04 2022

city: Nashville

first: Matthew

middle: A

last: Cottam

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

summary: Most individuals do not maintain weight loss, and weight regain increases cardio-metabolic risk beyond that of obesity. Adipose inflammation directly contributes to insulin resistance; however, immune-related changes that occur with weight loss and weight regain are not well understood. Single cell RNA-sequencing was completed with CITE-sequencing and biological replicates to profile changes in murine immune subpopulations following obesity, weight loss, and weight cycling. Weight loss normalized glucose tolerance, however, type 2 immune cells did not repopulate adipose following weight loss. Many inflammatory populations persisted with weight loss and increased further following weight regain. Obesity drove T cell exhaustion and broad increases in antigen presentation, lipid handing, and inflammation that persisted with weight loss and weight cycling. This work provides critical groundwork for understanding the immunological causes of weight cycling-accelerated metabolic disease.

overall_design:
Epididymal adipose tissue immune cells isolated from lean, obese, weight loss, and weight cycled mice and sorted for viable CD45+ cells.

Grant ID: 20POST35120547
Grant Title: The Influence of Trained Innate Immunity on Macrophages in Metabolic Disease
Funding Source: American Heart Association (Dallas)

last: Caslin

first: Nathan

last: Winn

first: Alyssa

middle: H

last: Hasty


title: Immune-related gene expression profiling of Epithelial Ovarian Cancer after Neoadjuvant chemotherapy

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

summary: We explore the potential of immune-associated expression profiles in a series of Epithelial Ovarian Cancer (EOC) patients undergoing neoadjuvant chemotherapy (NACT), comparing primary lesions before patients underwent carboplatin/paclitaxel-based NACT (so-called ´biopsy samples´) and interval debulking surgery (IDS) samples from residual lesions after treatment with chemotherapy (so-called ´surgery samples´).

overall_design: nCounter immune profiling was used to carry out an immune-related gene expression analysis in 27 patients with EOC, comparing biopsy and surgery samples. Biopsy samples were collected from primary lesions before EOC patients underwent carboplatin/paclitaxel-based neoadjuvant chemotherapy, according to availability. Surgery samples were extracted from residual lesions after treatment with chemotherapy, according to availability. We analyzed only biopsy samples from 8 patients, only surgery samples from 2 patient and paired biopsy-surgery samples from 17 patients. We also compared responder and non-responder patients using the chemotherapy response score (CRS). This score stratifies patients with no/minimal tumor response (CRS1), partial response (CRS2) and total/near-total tumor response (CRS3) to NACT.

first: Iris

last: Lodewijk

first: Alejandra

last: Bernardini

last: Suárez-Cabrera

first: Elsa

last: Bernal

first: Rodrigo

last: Sánchez

first: Juan

last: Garcia

first: Katerin

last: Rojas

first: Lucía

last: Morales

first: Sarah

last: Wang

first: Xinwei

last: Han

first: Marta

last: Dueñas

first: Jesús

middle: M

last: Paramio

first: Luis

last: Manso


title: Skin expression data from psoriasis patients treated with the HSP90 inhibitor RGRN-305

status: Public on Jan 10 2022

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

summary:
HSP90 is a downstream regulator of TNFα and IL-17A signaling and may therefore serve as a novel target in the treatment of psoriasis.
We assessed global gene expression by microarray analysis to explore the molecular transformation in skin samples from psoriatic patients during treatment with the HSP90 inhibitor RGRN-305.

overall_design: Skin punch biopsies were taken from nonlesional (NL) and lesional (LS) psoriatic skin of 13 psoriatic patients before treatment and from lesional psoriatic skin at 4, 8, and 12 weeks during HSP90 inhibitor treatment. RNA was extracted from the skin biopsies and used for microarray analysis.

first: Claus

last: Johansen

first: Anne

last: Bregnehøj

last: Emmanuel

first: Lars

last: Iversen


title: Evolutionarily conserved bacterial effectors hijack abscisic acid signaling to induce an aqueous microenvironment in the apoplast

status: Public on Dec 10 2021

city: Sherbrooke

first: Peter

last: Moffett

state: Québec

address: 2500 boulevard de l'universite, Departement de Biologie

department: Biologie

country: Canada

institute: Universite de Sherbrooke

summary:
Purpose: The goal of this study is to compare NGS-derived Arabidopsis thaliana transcriptome profiling  (RNA-Seq) obtained from tissues infected with a variety of Pseudomonas syryingae effector mutants to better understand their impact on their host's transcriptional program.
We report the application of RNA-sequencing technology (Illumina Hi-Seq) for high-throughput profiling Arabidopsis thaliana transcriptomes upon infection with the model pathogen Pseudomonas syringae (wild-type and mutants).

overall_design: Examination of Arabidopsis thaliana ecotype Col-0 infected with Pseudomonas syringae pv. tomato DC3000 (wild-type, hopm1-, avre1- and hopm1-/avre1-).

first: Charles

last: Roussin-Léveillée


title: Effects of intermittent fasting on the cognitive impairment in Alzheimer's disease mice: the roles of the gut brain axis regulation mechanism

status: Public on Dec 31 2021

city: Shenzhen

first: Jin

last: Xin

address: Beishan road

institute: BGI

summary: We reported a 16-week intermittent fasting intervention alleviated cognitive impairment in Alzheimer's disease. Here we present transcriptomics data of mice hippocampus to further investigate how intermittent fasting regulates vital biological processes and pathways. After mapping clean RNA-seq reads of all mice against the Mus musculus genome, we detected 56,412 genes (including 12,527 new predicted genes) with fragments per kilobase of transcripts per million mapped reads (FPKM) value. Gene set enrichment analysis (GSEA) was used for pathway or functional analysis of RNA-seq data.

overall_design:
7 FAD mice,7 MAD mice,6 FAF mice, 7 MAF mice, 8 FWT mice, 7 MWT mice, 6 FWF mice, 7 MWF mice

Treatment Definitions:
FAD: female AD mice + standard feed
MAD: male AD mice + standard feed
FAF: female AD mice + intermittent fasting treatment
MAF: male AD mice + intermittent fasting treatment
FWT: female control mice + standard feed
MWT: male control mice + standard feed
FWF: female control mice + intermittent fasting treatment
MWF: male control mice + intermittent fasting treatment

first: Mengzhen

last: Jia

first: Xin

last: Jin


title: A glioma immune cell atlas identifies prognostic macrophage signatures and a novel immunotherapy target, S100A4

status: Public on Dec 15 2021

city: Farmington

first: Parveen

last: Kumar

state: Connecticut

address: 10 Farmington Drive

institute: Application Computational Scientist

summary: Here, we report defining molecular signatures of immune-suppressive and inflammatory immune cells in human gliomas. We identified nine robust macrophage subtypes with distinct molecular signatures, each of which predicted good or poor survival for glioma patients. Our analysis of signature genes associated with immune suppressive macrophages, underscored S100A4 as a strong candidate for in vivo validation.

overall_design: We performed multiregional sampling coupled with multidimensional analyses of 18 GBM patients.  Each patient tumor was sampled from one or multiple regions, and each region was analyzed separately using droplet-based single-cell capture and sequencing. We analyzed a total of 201,986 cells that passed all QC from the 44 samples

first: Nourhan

last: Abdelfattah

first: Kyuson

last: Yun


title: scRNA-seq reveals tumor microenvironment remodeling induced by local intervention-based immunotherapy

status: Public on Dec 29 2021

city: Norman

first: KAILI

last: LIU

state: Oklahoma

address: 173 Felgar St

institute: The University of Oklahoma

summary: Laser immunotherapy (LIT) combines local photothermal therapy (PTT), to disrupt tumor homeostasis and release tumor antigens, and an intratumorally administered immunostimulant, N-dihydrogalactochitosan (GC), to induce antitumor immune responses. We performed single-cell RNA sequencing on tumor-infiltrating leukocytes of MMTV-PyMT mouse mammary tumors to determine LIT-induced myeloid and lymphoid compartment remodeling.  Analysis of 49,380 single cell transcriptomes from different treatment groups revealed proinflammatory IFNa, IFNg, and TNFa cytokine signaling pathways were enriched in both lymphoid and myeloid cells isolated from LIT-treated tumors. Interestingly, the CD4+ and CD8+ T cells in LIT and GC treated tumors resided in an activated state while immune cells in untreated and PTT-treated tumors remained in a neutral/resting state. Additionally, monocytes recruited into the LIT-treated tumors were driven towards proinflammatory M1-like macrophage phenotypes or monocyte-derived dendritic cells. Our results reveal that LIT prompts immunological remodeling of the tumor microenvironment by initiating broad proinflammatory responses to drive antitumor immunity.

overall_design: transcriptional profiling of CTRL, PTT, GC, LIT treated CD45+ tumor infiltrating cells performed by single-cell RNA sequencing

first: Ashley

last: Hoover

first: Kaili

last: Liu

first: Christa

middle: I

last: DeVette

first: Jason

last: Krawic

first: Connor

last: West

first: Delaney

last: Medcalf

first: Alana

last: Welm

first: Xiao-Hong

last: Sun

first: William

last: Hildebrand

first: Wei

last: Chen


title: Characterization of molecular changes associated with aging in the mouse auditory nerve

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

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

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

first: Hainan

last: Lang

first: Clarisse

last: Paganiban

first: Kenyaria

last: Noble


title: Regulation of chromatin accessibility in early zebrafish embryos by Pou5f3 and Sox19b transcription factors.

status: Public on Jan 07 2022

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

country: Germany

institute: University of Freiburg

summary: Pou5f3 and Sox19b transcription factors promote chromatin accessibility and activate zygotic transcription in zebrafish embryos. It is poorly understood how two transcription factors act together on chromatin. To answer this question, we performed  Omni-ATAC-seq on the zebrafish embryos, single and double mutants by Pou5f3 and Sox19b, as well as the wild-type, at two blastula developmental stages, oblong and dome. We report, that chromatin accessibility on 48% of all putative enhancers depends on Pou5f3 and Sox19b.  Out of them, accessibility on 33% enhancers is reduced in the double mutant and of 15% is increased.  Enhancers with reduced and increased chromatin accessibility differ in GC content and  transcription factors binding motif frequency, and are linked to early and late developmental regulatory genes, respectively. Our results indicate that Pou5f3 and Sox19b  not only activate early zygotic genes, but also prevent premature activation of  late developmental enhancers.

overall_design: Omni-ATAC-seq on whole embryos

first: Aileen

last: Riesle


title: MEK inhibition overcomes chemoimmunotherapy resistance by inducing CXCL10 in cancer cells

status: Public on Dec 08 2021

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

institute: UMR INSERM 1231

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: MEK inhibition overcomes chemoimmunotherapy resistance by inducing CXCL10 in cancer cells [France4]

summary: Chemotherapy with anti PD-1/PD-L1 mAb has become the standard of care for patients with metastatic non-small cell lung cancer (NSCLC). Using lung tumor models, where pemetrexed-platinum chemotherapy (PEM/CDDP) remains unable to synergize with immune checkpoint inhibitors (ICI), we linked failure of this treatment with its inability to induce CXCL10 expression and CD8+ T cell recruitment. Using drug screening, we showed that combining a MEK inhibitor (MEKi) with PEM/CDDP triggers CXCL10 secretion by cancer cells and CD8+ T cell recruitment, and restores ICI efficacy. PEM/CDDP plus MEKi promotes optineurin (OPTN)-dependent mitophagy, resulting in CXCL10 production in a mitochondrial DNA and TLR9-dependent manner. TLR9 or autophagy/mitophagy processes genetic inactivation of abort the antitumor efficacy of PEM/CDDP plus MEKi/anti PD-L1 therapy. In human NSCLC, high OPTN, TLR9 and CXCL10 expression is associated with better response to ICI. Our results underline the role of TLR9 and OPTN-dependent mitophagy in enhancing chemoimmunotherapy efficacy.

overall_design: This advanced non-small cell lung cancer (NSCLC) cohort  comprises patients treated with anti-PD1 therapy in first or second line as monotherapy at the Centre Georges-François Leclerc in Dijon (France #4), and is composed of 71 patients. Tumors were collected at diagnosis, stored, and used with the written informed consent of the patients and RNAseq data was generated in our NGS core facility. Raw data were pseudo-aligned and gene counts were quantified using the kallisto software. Clinical data were collected by Prof. F. Ghiringhelli.

first: Emeric

last: Limagne

first: Lisa

last: Nuttin

first: Marion

last: Thibaudin

first: Elise

last: Jacquin

first: Romain

last: Aucagne

first: Marjorie

last: Bon

first: Solène

last: Revy

first: Robby

last: Barnestein

last: Ballot

first: Caroline

last: Truntzer

first: Valentin

last: Derangère

first: Jean-David

last: Fumet

first: Charlène

last: Latour

first: Cédric

last: Rébé

first: Pierre-Simon

last: Bellaye

first: Coureche-Guillaume

last: Kaderbhaï

first: Aodrenn

last: Spill

first: Bertrand

last: Collin

first: Mary

last: Callanan

first: Aurélie

last: Lagrange

first: Laure

last: Favier

first: Bruno

last: Coudert

first: Laurent

last: Arnould

first: Sylvain

last: Ladoire

last: Routy

first: Philippe

last: Joubert


title: Inhibition of Soluble Epoxide Hydrolase is Protective Against the Multiomic Effects of a High Glycemic Diet on Brain Microvascular Inflammation and Cognitive Dysfunction

status: Public on Dec 07 2021

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary:
Diet is a modifiable risk factor for cardiovascular disease (CVD) and dementia, yet relatively little is known about the effect of a high glycemic diet (HGD) on the brain microvasculature.  The objective of our study was to determine the molecular effects of a HGD on hippocampal microvessels and cognitive function, and to determine if a soluble epoxide hydrolase (sEH) inhibitor (sEHI), known to be vasculoprotective and anti-inflammatory, modulates these effects.
Global hippocampal microvascular gene expression was fundamentally different for mice fed the HGD vs the LGD.  The HGD response was characterized by differential expression of 608 genes involved in cell signaling, neurodegeneration, metabolism, and cell adhesion/inflammation/oxidation effects reversible by t-AUCB and hence sEH inhibitor correlated with protection against Alzheimer’s dementia.

overall_design: Wild type male mice were fed a low glycemic diet (LGD, 12% sucrose/weight) or a HGD (34% sucrose/weight) with/without the sEHI, trans-4-[4-(3-adamantan-1-yl-ureido)-cyclohexyloxy]-benzoic acid (t-AUCB), for 12 wks. Brain hippocampal microvascular gene expression was assessed by microarray and data analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, gene networks, functional pathways, and transcription factors.

first: Dragan

last: Milenkovic

first: Jennifer

last: Norman

first: John

last: Rutledge

first: Amparo

last: Villablanca