title: BioChIP-seq analysis of atrial and ventricular cardiomyocytes

first: Xiaoran

summary: Cardiac TF and P300 chromatin occupancy in atria and ventricles.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for cardiac TFs: Gata4, Mef2a, Mef2c, Tead1, Srf, Nkx2-5, Tbx3 and P300 in atrium and ventricle cardiomyocytes cells.

first: Yangpo

last: Cao

first: Brynn

last: Akerberg

first: William

last: Pu


title: Targeting tumor-stroma communication by blocking endothelin-1 receptor signaling sensitizes high-grade serous ovarian cancer to PARP inhibitor

status: Public on Jan 11 2023

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

country: Italy

institute: University of Turin

type: Expression profiling by high throughput sequencing

summary: High-grade serous ovarian cancer (HG-SOC), characterized  by very frequent mutations in TP53 gene, is a highly lethal cancer and is refractory to therapeutic strategies. In HG-SOC, the reciprocal signal exchange between tumor cells and various types of stromal elements from the tumor microenvironment (TME) shapes the malignant phenotype and limits drug efficacy, suggesting that blunting the HG-SOC/TME interplay may improve the anti-tumor therapy response rate. Here, we unveil how the endothelin-1 (ET-1)/ET-1 receptors (ET-1R) signaling, instructing the mutual inter-regulation between HG-SOC cells, endothelial cells (EC) and activated fibroblasts, regulates malignant progression and PARP inhibitor (PARPi) response. Mechanistically, ET-1 axis, mimicking hypoxia, enhances the mutant p53 (mutp53)/YAP/hypoxia inducible factor-1α (HIF-1α) transcriptional cooperation, that culminates with the release of diffusible mediators, as ET-1 and VEGF, that charting a bilateral HG-SOC/stroma signaling route, regulate the acquisition of pro-metastatic traits and PARPi response. Concurrently, our study establishes that ET-1 signaling its instrumental for the activation of p53/YAP/HIF-1α transcriptional machinery within the EC and the activated fibroblasts, shaping their behaviour and secretome. The dual ET-1R antagonist macitentan, dismantling the ET-1R-mediated mutp53/YAP/HIF-1α network, interferes with the ET-1-guided tumor/stroma communication. In vivo macitentan, sensitizing HG-SOC patient-derived xenografts (PDX) to the PARPi, Olaparib, reduces their metastatic potential. Clinically relevant, ETAR/YAP/HIF-1α gene signature correlates with a dismal prognosis in HG-SOC patients. Our findings recognize in the networking between ET-1R and YAP/mutp53/HIF-1α a tumor/TME shared escaping strategy from DNA damaging agents and support the use of ET-1R antagonists in combinatorial treatments with PARPi for HG-SOC patients.

overall_design: We monitored the global transcriptome in a preclinical relevant model of patient-derived primary cultures of HG-SOC cells (PMOV10), harboring TP53 mutation, isolated from ascitic fluid. PMOV10 cells were stimulated with endothelin-1 (ET-1, 100 nM), or with the ET-1R antagonist macitentan (MAC, 1µM), alone or in combination with ET-1, or with acetic acid (1% in H20), as vehicle (CTR) for 24 hours, by employing 4 biological replicates for each condition.

first: Piera

last: Tocci

first: Celia

last: Roman

first: Rosanna

last: Sestito

first: Valeriana

last: Di Castro

first: Andrea

last: Sacconi

first: Giovanni

last: Tonon

first: Francesca

last: Paolini

last: Blandino

first: Anna

last: Bagnato


title: Asynchronous transcription and translation of neurotrasmitter-related genes characterize the initial stages of neuronal maturation in Drosophila

status: Public on Apr 19 2023

city: Portugal

first: Catarina

middle: CF

last: Homem

address: Rua Campo Mártires da Pátria, 130

country: Portugal

institute: CEDOC - NMS

summary: Neuron specification and maturation are essential for proper central nervous system development. However, the precise mechanisms that govern neuronal maturation, essential to shape and maintain neuronal circuitry, remain poorly understood. Here, we analyse early-born secondary neurons in the Drosophila larval brain revealing that the early maturation of secondary neurons goes through three consecutive phases: 1) Immediately after birth, neurons express pan-neuronal markers but do not transcribe terminal differentiation genes; 2) Transcription of terminal differentiation genes, such as neurotransmitter-related genes VGlut, ChAT or Gad1, starts shortly after neuron birth, but these transcripts are however not translated; 3) Translation of neurotransmitter-related genes only begins several hours later in mid pupa stages in a coordinated manner with animal developmental stage, albeit in an ecdysone independent-manner. These results support a model where temporal regulation of transcription and translation of neurotransmitter-related genes is an important mechanism to coordinate neuron maturation with brain development.

overall_design: scRNA-Seq profile of neuronal lineages of central brain and ventral nerve cord collected at 105h after larval hatching (2 samples)

middle: C

first: Graça

middle: S

last: Marques


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [Cut & Run III]

status: Public on Dec 14 2022

city: Boston

first: Susu

last: Zhang

state: MA

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This study aim to in-depth understand the function of a transcription factor fusion protein that drives the development of a highly aggressive pediatric malignancy. After engineered the endogenous PAX3-FOXO1 locus, we use chemical genetics to rapidly degrade the protein. This comprehensive, detailed, and accurate study with deep genomic analyses and deep proteomics provide a detailed mechanism by which PAX3-FOXO1 maintains an oncogenic transcriptional regulatory network.

overall_design: Deep mechanistic analysis including proteomics and 15 parameter genomics.

first: Scott

middle: W

last: Hiebert

first: Kristy

middle: R

last: Stengel

first: Jing

last: Wang

first: Qi

last: Liu

first: Hayes

last: McDonald

first: Monica

middle: L

last: Bomber

first: Hillary

middle: M

last: Layden

first: Jacob

last: Ellis

last: Borinstein


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ChIP-Seq II]


title: Regulation of mouse chamber selective enhancers

status: Public on Jan 30 2023

city: Jamaica Plain

first: Xiaoran

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

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

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Comparative analysis of the DNA methylation landscape in CD4, CD8, and B memory lineages

status: Public on Dec 16 2022

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

type: Methylation profiling by genome tiling array

summary: There is considerable evidence that epigenetic mechanisms and DNA methylation are critical drivers of immune cell lineage differentiation and activation. However, there has been limited coordinated investigation of common pathways in distinct cell types for immunological processes such as immune activation.  Further, it remains unclear if the memory cell subtypes differentiate distinctly by cell lineages. We used the Illumina EPIC array to characterize the DNA methylation similarities and differences in B cell, CD4 T, and CD8 T naïve and memory cells states. Our data describe considerable overlap in CpG dinucleotides and genes with altered DNA methylation in the process of naïve to memory activation across the three lineages, clearly suggesting that common pathways exist for immune memory generation. Further, our analyses revealed specific CpG dinucleotides and genes in CD4 T and CD8 T central to effector memory differentiation. Finally, we identified unique DNA methylation patterns in TEMRA CD8 T cells compared to other CD8 T memory cell subtypes.

overall_design: Bisulphite converted, EPIC arrayed DNA from naïve and memory B and T lymphocytes:  B naïve (n=6), B memory (n=7), CD4 naïve (n=6), CD4 central memory (n=6), CD4 effector memory (n=6), CD8 naïve (n=12), CD8 central memory (n=5), CD8 effector memory (n=4), CD8 TEMRA (n=5).

first: Ze

first: Rondi

middle: A

last: Butler

first: Devin

last: Koestler

first: Shelby

last: Bell-Glenn

first: Gayathri

last: Warrier

first: Annette

last: Molinaro

first: Brock

last: Christensen

first: John

middle: K

last: Wiencke

first: Karl

middle: T

last: Kelsey


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [Cut & Run II]

first: Susu

last: Zhang

first: Scott

last: Hiebert

first: Kristy

last: Stengel

first: Jing


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ATAC-Seq II]

last: Wang

first: Qi

last: Liu

first: Hayes

last: McDonald

first: Monica

first: Hillary


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [PRO-Seq II]

last: Bomber

last: Layden

first: Jacob

last: Ellis


title: The role of aV Integrin in regulating macrophage phenotype and function during cardiac remodeling after myocardial infarction

status: Public on Dec 31 2022

city: Bronx

first: Silvia

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

summary: Macrophages infiltrate the infarcted heart and play a critical role in repair, remodeling and fibrosis. Macrophages sense changes in the extracellular matrix (ECM) environment through Integrins, thus activating signaling pathways that regulate their function. Our data show that av integrin is highly expressed in isolated bone marrow macrophages and is markedly upregulated in response to TGF-β, a growth factor known to be activated in the infarcted heart. Accordingly, we hypothesize that aV integrin induction in infarct macrophages may regulate macrophage phenotype, function and response to key macrophage-activating signals following MI.

overall_design: In order to study the role of integrin aV in mmacrophages in vitro, we isolated bone marrow macrophages from WT mice and grow them  in fibronectic coated and normal culture dishes, and treated them with a anti-integrin αV neutralizing antibody and its control (IgG).

first: Ruoshui

last: Li

first: Bijun

last: Chen

first: Anis

last: Hanna

first: Claudio

last: Humeres

first: Jun

first: Nikolaos

middle: G

last: Frangogiannis


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [Cut & Run]

last: Borinstein


title: Stress responses elicited by glucose withdrawal in Aspergillus fumigatus

status: Public on Dec 09 2022

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: Glucose is a widely used carbon source in laboratory practice to culture Aspergillus fumigatus, however, glucose availability is often low in its “natural habitats” including the human body. We used a physiological–transcriptomical approach to reveal differences between A. fumigatus Af293 cultures incubated on glucose, glucose and peptone, peptone (carbon limitation), or without any carbon source (carbon starvation). Autolytic cell wall degradation was upregulated by both carbon starvation and limitation. The importance of autolytic cell wall degradation in adaptation to carbon stress was also highlighted by approximately 12.4% of the A. fumigatus genomes harbor duplication of genes involved in N-acetyl glucosamine utilization. Glucose withdrawal increased redox imbalance, altered both the transcription of antioxidative enzyme genes and oxidative stress tolerance, downregulated iron acquisition, but upregulated heme protein genes. Transcriptional activity of the Gliotoxin cluster was low in all experiments, while the Fumagillin cluster showed substantial activity both on glucose and under carbon starvation, and the Hexadehydro-astechrome cluster only on glucose. We concluded that glucose withdrawal substantially modified the physiology of A. fumigatus including processes that contribute to virulence. This may explain the challenge of predicting the in vivo behavior of A. fumigatus based on data from glucose rich cultures.

overall_design: The Af293 reference strain was studied under four culturing conditions differing in the available carbon/energy source: cultures incubated in glucose rich or carbon source free media as well as cultures growing on casein peptone or glucose plus casein peptone.  Each culturing condition was examined with three biological replicates.

first: Tamás

first: Barnabas

last: Gila

first: Karoly

last: Antal

first: Andrea

middle: P

last: Jónás

first: Istvan

last: Pocsi


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [RNA-Seq]

first: Susu

last: Zhang

first: Scott

last: Hiebert

first: Kristy

last: Stengel

first: Jing

last: Wang

first: Qi

last: Liu

first: Hayes


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [PRO-Seq]

last: McDonald

first: Monica

last: Bomber

first: Hillary

last: Layden

first: Jacob

last: Ellis


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ChIP-Seq]


title: Reemergence of pathogenic, autoantibody-producing B-cell clones in myasthenia gravis following B-cell depletion therapy.

status: Public on Nov 07 2022

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: Myasthenia gravis (MG) is an autoantibody-mediated autoimmune disorder of the neuromuscular junction. Some patients with MG have pathogenic mAbs that recognize muscle-specific tyrosine kinase (MuSK). Patients respond well to CD20-mediated B-cell depletion therapy (BCDT); most achieve complete stable remission. However, relapse often occurs. To further understand the immunomechanisms underlying relapse we sought to study autoantibody-producing B-cells over the course of BCDT. We developed a monomeric fluorescently labelled antigen to enrich for MuSK-specific B-cells, which was validated with a novel Nalm6 cell line engineered to express a human MuSK autoantibody as B-cell receptor. We found that MuSK-specific B-cells are rare within the circulation (<3 per 10 million cells). From two MuSK-specific B-cells isolated from two distinct patients, we generated human recombinant MuSK mAbs. The autoantibodies originated from plasmablasts, used the IgG4 subclass, recognized the Ig1-like domain of MuSK and showed pathogenic capacity using an in vitro AChR clustering assay. Persistent clones of the mAbs were identified through B-cell repertoire tracing. Clonal variants of 2E6 were detected at several timepoints spanning more than five years months and reemerged after BCDT-mediated remission, appearing several months prior to relapse. These results indicate that a reservoir of rare pathogenic MuSK autoantibody-expressing B cell clones survive BCDT, then reemerge prior to manifestation of clinical relapse. This study provides both a mechanistic understanding of MuSK MG relapse and a valuable candidate biomarker for relapse prediction.

overall_design: Samples from eight subjects were studied. Four subjects had the MuSK subtype of myastenia gravis, four were healthy cotrols. Samples underwent bulk BCR sequencing, as well as scRNA-seq and scBCR sequencing.

first: Miriam

last: Fichtner

first: Kenneth

middle: B

last: Hoehn

first: Steven

middle: H

last: Kleinstein

first: Kevin

last: O'Connor


title: Rebalancing TGFβ1/BMP Signals Preserves Effector and Memory Programs in Terminally Dysfunctional CD8+ T Cells [RNA-Seq]

status: Public on Nov 03 2022

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: T cell dysfunctionality prevents clearance of chronic infections and cancer. Furthermore, epigenetic programming in dysfunctional CD8+ T cells limits durable responses to T cell-based immunotherapies, including immune checkpoint blockade (ICB). However, major gaps concern how upstream signals drive acquisition of dysfunctional epigenetic programs, and whether therapeutically targeting these signals can remodel terminally dysfunctional T cells to an ICB-responsive state. Here, we use an in vitro model of human T cell dysfunction and complementary in vivo mouse chronic virus infection and tumor models. We show that post-effector TGFβ1 signaling establishes terminal dysfunction in human CD8+ T cells through stable epigenetic changes. Importantly, we demonstrate that promoting BMP signaling while blocking TGFβ1 restored effector and memory programs in dysfunctional human CD8+ T cells, induced superior anti-tumor activity, and boosted ICB responses during mouse chronic virus infection. Thus, rebalancing TGFβ1/BMP-signals in dysfunctional CD8+ T cells provides an exciting new approach to enhance T cell immunotherapies.

overall_design: In vitro chronic TCR stimulation of cord-blood derived human CD8+ T cells

first: Hazem

middle: E

last: Ghoneim

first: Abbey

last: Saadey

first: Amir

last: Yousif

last: Webb


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ATAC-Seq]

first: Susu

last: Zhang

first: Scott

last: Hiebert

last: Stengel

last: Borinstein


title: Gramd2+ alveolar type I cells can give rise to Kras-induced lung adenocarcinoma

status: Public on Oct 19 2022

city: Glendale

first: Crystal

last: Marconett

state: CA

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

summary: Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer and arises in the distal lung. LUAD encompasses several pathologic subtypes, including solid, lepidic, papillary, micropapillary, acinar and mixed subtypes, each with differing clinical outcomes or biological behavior. Specifically, lepidic histology is associated with improved survival relative to other LUAD histologies. Yet, the molecular and cellular underpinnings of these subtypes are largely unknown. Understanding which cell populations in the distal lung contribute to LUAD could provide insights for the marked heterogeneity in LUAD pathologic features, clinical presentation and responses to therapy.Recent studies have seen tumor-derived epithelial cells with an AT1 transcriptomic cell signature, suggesting AT1 cells may contribute to a subset of LUAD cases. We tested the ability of AT1 cells to give rise to LUAD by inducing KrasG12D, a known oncogenic driver in human LUAD. Activation of KrasG12D in Gram-domain containing 2 (Gramd2)+ AT1 cells gave rise to multiple LUAD lesions, primarily of papillary histology. In contrast, activation of KrasG12D in Sftpc+ AT2 cells resulted in LUAD lesions of lepidic histology. Immunohistochemistry established Gramd2:KrasG12D lesions were of primary lung origin and not metastatic events. Spatial transcriptomic profiling revealed distinct pathway alterations occurring within Gramd2- and Sftpc-derived LUAD. Immunofluorescence confirmed differences observed in the Spatial transcriptomic analysis in expression patterns and distribution of cell-specific markers between cell of origin, while universal upregulation of the Krt8 intermediate cell state marker was observed. Our results are consistent with Gramd2+ AT1 cells serving as a putative cell of origin for LUAD and suggest that LUAD may be a collection of adenocarcinomas that share a common location within the distal lung, but which arise from different cells of origin.

overall_design: Spatial transcriptomic profiling was performed at the Molecular Genomics Core, a part of the Norris Comprehensive Cancer Center and under manufacturer’s instructions. Briefly, three biological replicates (one block per mouse) of Gramd2:KrasG12D and Sftpc:KrasG12D underwent initial 10μM sectioning at the Tissue Pathology Core, part of the Norris Comprehensive Cancer Center. Sections were H&E stained (as above) and underwent pathology review. Regions of Interest (ROIs) then underwent sample preparation including test slide sample sequencing using the Visium Tissue Section Test Slide (PN-2000460, 10X Genomics, Dublin, CA, USA). H&E overlapping spatial transcriptomic regions was generated as part of the Cytassist pipeline. RNA quality assessment of test slides was determined by first extracting RNA using the Qiagen RNeasy FFPE kit (#73504, Qiagen, Hilden, Germany) and measuring RNA concentration using a Qubit fluorometer (#Q33238, ThermoFisher Scientific, Waltham, MA, USA). To determine The percentage of total fragments >200nt in length was determined by running the samples using a 4200 Tapestation (#G2991AA, Agilent, Santa Clara, CA). Once samples were determined to be of high enough quality to continue, 5μM FFPE sections were then placed in a 42C water bath and once rehydrated adhered to the Visium Spatial Gene Expression Slide (PN-2000233, 10X Genomics). Subsequently, samples were dried at 42C for 3hrs in a desiccation chamber and underwent deparrafinization using Qiagen Deparaffinization Solution (Cat # 19093) at 60C for 2 hr. Subsequently H&E staining (#MHS16, #HT110116 Millipore Sigma, Burlington MA, USA) was performed according to Visium technical parameters (CG000409) and images were captured with a Zeiss Axioscan2 microscope using a 10x objective. Decrosslinking was performed according to 10X standard protocol (CG000407) and immediately hybridized to the Visium Mouse Transcriptome probe set V1.0, which contained 20,551 genes targeted by 20,873 probes. Post-probe extension, sequencing library construction was performed using unique sample indices using the Dual Index Kit TS, Set A (PN-1000251) for Illumina-compatible sequencing. Paired-end sequencing (2x100) was performed on an Illumina instrument. Sequencing data was pre-processed using the Space Ranger pipelines (10x Genomics, https://cloud.10xgenomics.com/cloud-analysis). BCL data was demultiplexed and converted to FASTQ format using the spaceranger mkfastq pipeline. The spaceranger count pipeline was then used for read alignment to mouse genome reference mm10, Unique Molecular Identifier (UMI) counting, and generation of feature-spot matrices corresponding to the microscopic tissue image. The pipeline also performs automatic tissue detection and fiducial alignment from the image.

first: Minxiao

last: Yang

first: Hua

last: Shen

first: Per

last: Flodby

first: Michael

middle: D

last: Koss

first: Rania

last: Bassiouni

first: Yixin

last: Liu

first: Tea

last: Jashashvili

first: Aaron

last: Neely

first: Ezuka

last: Ogbolu

first: Jonathan

last: Castillo

first: Theresa

last: Stueve

first: Daniel

middle: J

last: Mullen

last: Ryan

first: John

last: Carpten

first: Alessandra

last: Castaldi

first: W

last: Wallace

first: Beiyun

last: Zhou

first: Zea

last: Borok

middle: N


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets

first: Susu

last: Zhang

first: Scott

last: Hiebert

first: Kristy

last: Stengel

first: Jing

last: Wang

first: Qi

first: Hayes

last: McDonald

first: Monica

last: Bomber

first: Hillary

last: Layden

first: Jacob

last: Ellis

middle: C

last: Borinstein


title: snRNAseq of human vascular dementia white matter vs control

status: Public on Sep 28 2022

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Transcriptional profiling of cells in white matter of the brain from cases with vascular dementia vs control cases

overall_design: nuc-seq study of human vascular dementia from corpus callosum white matter above the frontal ventricle in patients and controls. Samples prepared with straight nuc seq protocol, and in parallel sample, first with FACS isolation of ERG+ nuclei to isolate endothelial and microglial poulations

first: Dainel

last: Mitroi

first: S

last: Carmichael

first: William

last: Lowry


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function[RNA-seq_CPC]

status: Public on Oct 11 2022

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Tight control of cell fate choices is crucial for normal development. Here we show that lamin A/C plays a key role in chromatin organization in embryonic stem cells (ESCs), which safeguards naïve pluripotency and ensures proper cell fate choices during cardiogenesis. We find major changes in chromatin compaction and localization of cardiac genes already in Lmna−/−ESCs resulting in precocious activation of a transcriptional program promoting cardiomyocyte versus endothelial cell fate, accompanied by premature cardiomyocyte differentiation, cell cycle withdrawal, and abnormal contractility. Gata4 is activated by lamin A/C loss and Gata4 silencing or haploinsufficiency rescues the aberrant cardiovascular cell fate choices induced by lamin A/C deficiency. Importantly, we observe divergent functions of lamin A/C in naïve pluripotent stem cells and cardiomyocytes, which has distinct contributions to the transcriptional alterations of patients with LMNA-associated cardiomyopathy. Thus, disruption of lamin A/C-dependent chromatin architecture in ESCs is a primary event in LMNA loss-of-function cardiomyopathy.

overall_design: Conrol and Lmna KO E14 Tg(Nkx2-5-EmGFP)  mESCs were differentiated by hanging drop method. Day6 cardiac progenitor cells (CPCs) were  FACS-sorted by Nkx2-5+ GFP expression and performed RNA-seq.

first: Yinuo

first: Julio

last: Cordero

first: Adel

last: Elsherbiny

first: Linda

last: Kessler


title: Transcriptome of skin biopsies from Hidradenitis Suppurativa (HS) patients with anti-TNFalpha therapy.

status: Public on Sep 25 2022

city: Dublin

first: Walter

last: Kolch

address: School of Medicine, University College Dublin, Belfield, Dublin 4.

country: Ireland

institute: Systems Biology Ireland

summary: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disorder with significant morbidity. The pathogenesis remains incompletely understood although immune dysregulation plays an important role. It is challenging to treat and approximately 50% of patients respond clinically to adalimumab, the only licensed treatment.

overall_design: We completed bulk RNA-sequencing on lesional and non-lesional skin samples of patients before and after 12-weeks treatment with adalimumab.

first: Róisín

last: Hambly

first: Solene

last: Gatault

first: Luis

middle: F

last: Iglesias-Martinez

first: Brian

last: Kirby


title: Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza

status: Public on Aug 24 2022

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here, we report that a monocot plant, Spirodela polyrhiza, has lost CG gene body methylation, genome-wide CHH methylation, and the presence or expression of several genes in the highly conserved RNA-directed DNA methylation (RdDM) pathway. It has also lost the CHH methyltransferase CHROMOMETHYLASE 2. Consequently, the transcriptome is depleted of 24-nucleotide, heterochromatic, small interfering RNAs that act as guides for the deposition of 5mC to RdDM-targeted loci in all other currently sampled angiosperm genomes. Although the genome displays low levels of genome-wide 5mC primarily at LTR retrotransposons, CG maintenance methylation is still functional. In contrast, CHG methylation is weakly maintained even though H3K9me2 is present at loci dispersed throughout the euchromatin and highly enriched at regions likely demarcating pericentromeric regions. Collectively, these results illustrate that S. polyrhiza is maintaining CG and CHG methylation mostly at repeats. S. polyrhiza reproduces rapidly through clonal propagation in aquatic environments, which we hypothesize may enable low levels of maintenance methylation to persist in large populations.

overall_design: We generated MethylC-seq and small RNA-seq for two lines of S. polyrhiza, Sp7498 and Sp9509. Additionally, we generated H3K9me2 ChIP-seq and input gDNA as a control for line 9509.

first: Adam

last: Bewick

first: Alex

last: Harkess

first: Zefu

last: Lu

first: Blake

last: Meyers

first: R


title: Multiple Nf1 Schwann cell populations reprogram the plexiform neurofibroma tumor microenvironment

status: Public on Nov 23 2022

city: Cincinnati

first: Nancy

last: Ratner

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: To define alterations early in tumor formation, we studied nerve tumors in neurofibromatosis 1 (NF1), a tumor predisposition syndrome in which affected individuals develop plexiform neurofibroma (PN). These benign tumors are driven by NF1 loss in Schwann cells (SC). By comparing normal nerve cells to PN cells using single cell and bulk RNA sequencing, we identified changes in five SC populations, including a de novo Schwann cell progenitor-like population. Long after Nf1 loss, SC populations developed PN-specific expression of Dcn, Postn, and CD74, and showed dramatic expansion of immune and stromal cell populations; in human PN, immune and stromal cells comprised 90% of cells. Label transfer enabled verification of each SC population and predicted tumor unique patterns of cell-cell communication in each SC population. We identified PROS-AXL, FGF-FGFR, and MIF-CD74 and its effector pathway NFkB as deregulated in NF1 SC populations, including SCP-like cells. Each receptor-ligand pair was predicted to influence surrounding cells in mouse and human. These findings highlight remarkable changes in all PN cells driven by loss of NF1 in multiple types of SCs and identify therapeutic targets for PN.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
[Mouse] single cell mRNA profiles of paraspinal tumors (2 or 7 mo. Dhh-Cre;Nf1fl/fl) (n=6), and age-matched wild type dorsal root ganglia (DRG) with nerve roots

[Human] single cell mRNA profiles of human plexiform neurofibromas (n=4)
>>> Submitter declares that the human raw data will be deposited in dbGAP due to patient privacy concerns. <<<

first: Leah

last: Kershner

first: Jianqiang

last: Wu

first: Xiyuan

last: Zhang

first: Melissa

last: Perrino

first: Kwangmin

last: Choi

first: Nathan

last: Salomonis

first: Jack

last: Shern


title: Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation

status: Public on Jul 19 2022

city: Philadelphia

first: Desi

last: Alexander

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Histone acetylation is a key component in the consolidation of long-term fear memories, which are models for highly resilient and durable memory. Histone acetylation is fueled by acetyl-CoA and recently, nuclear-localized metabolic enzymes that produce this metabolite have emerged as direct and local regulators of histone acetylation. In particular, Acetyl-coA synthetase 2 (ACSS2) mediates histone acetylation in the mouse hippocampus. However, whether ACSS2 regulates long-term fear memory remains to be determined. Here, we show that Acss2 knockout is well-tolerated in mice, yet the Acss2 null mouse exhibits reduced acquisition of long-term fear memory. Loss of Acss2 leads to reductions in both histone acetylation and expression of critical learning and memory-related genes in the dorsal hippocampus, specifically following fear conditioning. Further, systemic administration of blood-brain-barrier (BBB)-permeable Acss2 inhibitors during the consolidation window reduces fear memory formation in mice and rats, and reduces anxiety in a predator-scent-stress (PSS) paradigm. Our findings suggest that nuclear acetyl-CoA metabolism via ACSS2 plays a critical, previously unappreciated role in the formation of fear memories.

overall_design: Included are two separately analyzed experiments that used RNA-seq to examine the transcriptome in the hippocampus from mice on a C57BL6/J background harboring a deletion of the metabolic gene Acss2. Experiment 1 (6 samples) consists of whole hippocampi processed from 3 genotypes (Acss2 WT[reference], Acss2 Het, and Acss2 KO), with two replicates each. All samples were processed together. Experiment 2 (17 samples) consists of 2 genotypes (Acss2 WT, Acss2 KO), 2 conditions (homecage-housed[reference], and fear conditioned). Replicates included are: 5 replicates WT untreated, 3 replicates WT fear conditioned, 5 replicates ACSS2- untreated, 4 replicates ACSS2- fear conditioned.

first: Tanya

last: Corman

first: Mariel

last: Mendoza

first: Andrew

last: Glass

first: Tal

last: Belity

first: Ranran

first: Rianne

middle: R

last: Campbell

first: Joseph

last: Han

first: Ashley

last: Keiser

first: Jeffrey

last: Winkler

first: Marcelo

last: Wood

first: Thomas

last: Kim

first: Benjamin

last: Garcia

first: Hagit

last: Cohen

first: Philipp

last: Mews

first: Gabor

last: Egervari

first: Shelley

last: Berger


title: Single-cell sequencing data for circulating CAR T cells in lymphoma patients

status: Public on Jul 28 2022

city: Stanford

first: Zinaida

last: Good

state: California

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

summary:
Purpose: To compare cell states amoung three populations of interest among circulating CAR T cells in patients with lymphoma.
Methods: Nine patients with large B-cell lymphoma (LBCL) were treated with axicabtagene ciloleucel (axi-cel), a commercial CD19-targeted CAR T-cell therapy. On day 7, fresh peripheral blood mononuclear cells were stained with an antibody panel for fluorescence-activated cell sorting (FACS), a panel for cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), and a viability dye. Single live CAR+ T cells were sorted from each patient, counted, processed for 5' single-cell RNA-sequencing with feature barcoding and TCR clonotype analysis on the 10X Genomics platform, and sequenced by the Stanford Genomics Facility (HighSeq 4000) or Novogene (NovaSeq 6000).
Results: We found that circulating CD4+ and CD8+ CAR T cells that express CD57 and T-bet are clonally expanded and display features of effector T cells. In contrast, CD4+ CD57- CAR T cells that express Helios expand polyclonally and display features of T regulatory cells.
Conclusions: This study provides insights into cell states of circulating CAR T cells on day 7 that associate with clinical response or toxicity in LBCL patients treated with axi-cel.

overall_design:
CAR T cells were sorted from blood of nine LBCL patients on day 7 following axi-cel infusion. Three populations of interest were identified within each CAR T-cell sample.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Crystal

middle: L

last: Mackall


title: Dual T cell– and B cell–intrinsic deficiency in humans

first: Nico

last: Marr


title: Restrained Wnt signaling pathway by enhanced EsGSK3β phosphorylation activity facilitates the infection of intracellular bacterium Spiroplasma and leads to neuropathic diseases in crustaceans

status: Public on Jul 16 2022

city: Xinxiang

first: Libo

last: Hou

state: Henan

address: 110 Room, College of Fisheries, 46 Jianshe East Road

country: China

institute: Henan normal university

summary:
To determine how Wnt-β-catenin regulates the innate immune response in crab hemocytes, Esβ-catenin and EsGSK3β RNA interference de novo transcriptomic analysis was performed to identify the innate immune-related genes regulated by this pathway.
Venn analysis of differentially transcribed genes from Esβ-catenin-dsRNA vs. GFP-dsRNA (significantly downregulated) and EsGSK3β-dsRNA vs. GFP-dsRNA (significantly upregulated) of the screening generated 434 candidates. KEGG enrichment analysis of those candidate genes showed that many innate immune-related genes belonged to the Toll and IMD signaling pathways.

overall_design: Transcriptomic analysis was performed to identify the down-regulated genes after Esβ-catenin RNAi and up-regualted genes after EsGSK3β RNAi. Each experiment was repeated three times. Venn analysis of differentially transcribed genes from Esβ-catenin-dsRNA vs. GFP-dsRNA (significantly downregulated) and EsGSK3β-dsRNA vs. GFP-dsRNA (significantly upregulated) to identify the target innate immune-related genes whose transcription was induced by Esβ-catenin and whose transcription was suppressed by EsGSK3β.

first: Qingguo

last: Meng


title: Asymmetrical forward and reverse developmental trajectories determine molecular programs of B cell antigen receptor editing

status: Public on Jul 06 2022

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: During B lymphopoiesis, B cell progenitors progress through alternating and mutually exclusive stages of clonal expansion and immunoglobulin (Ig) gene rearrangements. Great diversity is generated through the stochastic recombination of Ig gene segments encoding heavy and light chain variable domains. However, this commonly generates autoreactivity. Receptor editing is the predominant tolerance mechanism for self-reactive B cells in the bone marrow (BM). B cell receptor editing rescues autoreactive B cells from negative selection through renewed light chain recombination first at Igκ then Igλ loci. Receptor editing depends upon BM microenvironment cues and key transcription factors such as Nuclear factor kappa B, Forkhead box protein O and Transcription Factor 3. The specific BM factor required for receptor editing is unknown. Furthermore, how transcription factors coordinate these developmental programs to promote usage of the λ-chain remain poorly defined. Therefore, we utilized two mouse models that recapitulate pathways by which Igλ light chain positive B cells develop. The first possess deleted J kappa (Jκ) genes and, as such, models Igκ expression resulting from failed Igκ recombination (Igκdel). The second models autoreactivity by ubiquitous expression of a single-chain chimeric anti-Igκ antibody (κ-mac). Here, we demonstrated that autoreactive B cells transit asymmetric forward and reverse developmental trajectories. This imparted a unique epigenetic landscape on small pre-B cells, which opened chromatin to transcription factors essential for Igλ recombination. The consequences of this asymmetric developmental path were both amplified and complemented by CXCR4 signaling. These findings reveal how intrinsic molecular programs integrate with extrinsic signals to drive receptor editing.

overall_design: 63 samples collectively from Kappa-macroself mice (B6.Cg-Pepcb Ptprca Tg(UBC-scFv)2Nemz/J JAX Stock No: 006259), IgK deleted mice (PMID: 8458340), WT (Littermate control from Kappa-macroself mice), Cxcr4fl/fl Mb1-cre+ Kappa-macroself (+) and Cxcr4fl/fl Mb1-cre+ Kappa-macroself (-) mice. Sorted small pre-B (B220+CD19+CD43-IgM-FSClo) and immature B cells (B220loCD19+CD43-IgM+) were subjected to ATAC-seq (20 samples) and RNA-seq (19 samples). Small pre-B cells (B220+CD19+CD43-IgM-FSClo) were sorted from Cxcr4fl/fl Mb1-cre+ Kappa-macroself (+) and Cxcr4fl/fl Mb1-cre+ Kappa-macroself (-) mice, expanded in culture in the presence or absence of IL-7 and CXCL12 then subjected to RNA-seq (24 samples). Sorted small pre-B (B220+CD19+CD43-IgM-FSClo), large pre-B (B220+CD19+CD43-IgM-FSChi), immature B (B220loCD19+CD43-IgM+) from CD45.1 and CD45.2 mice were subjected to RNA-seq(14 samples).

first: Michael

last: Okoreeh

first: Domenick

last: Kennedy

first: Akinola

middle: O

last: Emmanuel

first: Margaret

last: Veselits

first: Azam

last: Moshin

first: Robert

last: Ladd

first: Steven

last: Erickson

first: Kaitlin

last: McLean

first: David

last: Nemazee

first: Malay

last: Mandal

first: Marcus

last: Clark


title: Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks

status: Public on Jun 15 2022

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo


title: MeRIP-Seq reveals the genome-wide maps of m6A modification on mRNA and lncRNA in OSCC

city: Tianjin

first: Xi

last: Wang

address: Qixiangtai Road, No. 12

department: The School and Hospital of Stomatology

institute: Tianjin Medical University

summary: We report the application of Methylated RNA Immunoprecipitation with Next Generation Sequencing and R software package in SCC25 and HAEC. By analysis the m6A peak areas which decorated in the 3' untranslated regions of target functional mRNAs and the entire interval of lncRNA, after that use gene ontology enrichment analysis and pathway enrichment analysis to indicate the explicit correlation to transcription, DNA-templated and pathways, we detect a series of m6A modification in mRNAs and lncRNAs, and explore some key clues in pathways related to OSCC which can guide the further studies on OSCC tumorigenesis and potential targeting.

overall_design: Examination of m6A modification in human aortic endothelial cells and human tongue phosphorus carcinoma cells.

first: Wei

last: Zhao


title: Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks [Hi-C]

summary: Genome function depends on regulated chromosome folding, and loop extrusion by the protein complex cohesin is essential for this multilayered organization. The chromosomal positioning of cohesin is controlled by transcription, and the complex also localizes to stalled replication forks. However, the role of transcription and replication in chromosome looping remains unclear. Here, we show that reduction of chromosome-bound RNA polymerase weakens normal cohesin loop extrusion boundaries, allowing cohesin to form new long-range chromosome cis interactions. Stress response genes activated by transcription inhibition are also shown to act as new loop extrusion boundaries. Furthermore, cohesin loop extrusion during early S-phase is jointly controlled by transcription and replication units. Together, the results reveal that replication and transcription machineries are chromosome folding regulators that block the progression of loop-extruding cohesin, opening for new perspectives on cohesin’s roles in genome function and stability.

overall_design: Analysis of chromosome conformation by Hi-C in Saccharomyces cerevisiae cells.

first: Kristian

last: Jeppsson

first: Toyonori

last: Sakata

first: Stefina

last: Milanova

first: Katsuhiko

last: Shirahige

first: Camilla

last: Björkegren


title: Epigenetic inheritance mediates phenotypic evolution in natural populations

status: Public on Jun 30 2022

city: Norwich

first: Jaemyung

last: Choi

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

summary: Genetic variation is regarded as a prerequisite for evolution. Theoretical models suggest epigenetic information inherited independently of DNA sequence can also enable evolution. However, whether epigenetic inheritance mediates phenotypic evolution in natural populations is unknown. Here we show that natural epigenetic DNA methylation variation in gene bodies regulates genes expression, and thereby influences the natural variation of complex traits in Arabidopsis thaliana. Notably, the effects of methylation variation on phenotypic diversity and gene expression variance are comparable with those of DNA sequence polymorphism. We also identify methylation epialleles in numerous genes associated with environmental conditions in native habitats, suggesting that intragenic methylation facilitates adaptation to fluctuating environments. Our results demonstrate that methylation variation fundamentally shapes phenotypic diversity in natural populations and provides an epigenetic basis for adaptive Darwinian evolution independent of genetic polymorphism.

overall_design: Bisulfite and RNA sequencing was performed using one h1;met1+/- plant and six h1 plants segregated from h1;met1+/- (h1;met1+/+). For bisulfite sequencing, we constructed one bs-seq library per plant. To profile RNA expression, we constructed three RNA-seq libraries per h1;met1+/- plant (3 replicates), and one RNA-seq library for h1;met1+/-.

first: Zaigham

last: Shahzad

first: Jonathan

last: Moore


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

status: Public on Jun 13 2022

city: Pittsburgh

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.

***************************************************************
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.
***************************************************************

first: Zhongli

last: Xu

first: Elisa

last: Heidrich-O’Hare

first: Richard

last: Duerr


title: Placental transcriptome analysis of hypertensive pregnancies identifies distinct gene expression profiles of preeclampsia superimposed on chronic hypertension

status: Public on May 30 2022

city: Ann Arbor

first: Ashley

last: Hesson

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

summary: The pathogenesis of preeclampsia superimposed on chronic hypertension is poorly understood relative to preeclampsia occurring in pregnant people without chronic hypertension. Placental transcriptomes in pregnancies complicated by de novo preeclampsia and superimposed preeclampsia have not been previously compared.

overall_design:
The goal of this study is to investigate the transcriptomes of placentas from different types of hypertensive pregnancies.
We identified pregnant people in the University of Michigan Biorepository for Understanding Maternal and Pediatric Health with hypertensive disorders affecting singleton, euploid gestations (N=36) along with non-hypertensive control subjects (N=12). Subjects were grouped as: (1) normotensive (N=12), (2) chronic hypertensive (N=13), (3) preterm preeclampsia with severe features (N=5), (4) term preeclampsia with severe features (N=11), (5) preterm superimposed preeclampsia (N=3), or (6) term superimposed preeclampsia (N=4). Bulk RNA sequencing of paraffin-embedded placental tissue was performed.

first: Elizabeth

last: Langen

first: Plazyo

last: Olesya

first: Johann

last: Gudjonsson

first: Santhi

last: Ganesh


title: Next Generation Sequencing of mouse hematopoietic cells retrovirally transfected with MNX1 or empty vector (Ctr) from fetal liver or mouse bone marrow and treated with or without pan-inhibitor against SAM-dependent methyltransferases Sinefungin

status: Public on Jun 14 2022

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

summary: Acute myeloid leukemia (AML) results from aberrant hematopoietic processes and these changes are frequently initiated by chromosomal translocations. One particular subtype, AML with translocation t(7;12)(q36;p13), is found in children diagnosed before two years of age. The chromosomal breakage points of the t(7;12) have consistently been found to be located  after exon 1 in the Motor neuron and pancreas homeobox 1 (MNX1) gene in chromosome 7, and after exon 2 in the ETV6 gene in chromosome 12. The aim of this study is the investigation of the leukomogenic potenial of MNX1 overexpression and MNX1-ETV6 fusion using mouse models, in addition to the molecular pathway through which MNX1 is inducing leukemia.

overall_design:
Fetal liver hematopietic cells from C57BL/6 mice were retrovirally transfected with MNX1 or empty vector and transplanted into 10-12 weeks old NOD.Cg-KitW-41J Tyr + Prkdcscid Il2rgtm1Wjl/ThomJ (NBSGW) mice. After establishment of leukmeia in the NBSGW mice, cells were collected from the bone marrow for mRNA expression profile. Additional controls with fetal liver hematopietic cells from C57BL/6 mice  retrovirally transfected with empty vector were used.
For InVitro experiments, fetal liver hematopietic cells were retrovirally transfected with empty vector or MNX1 overexpression and treated with or without 5μM Sinefungin

first: Ahmed

last: Waraky


title: Metabolic engineering reveals the relative importance of different sugar catabolic pathways during growth of Aspergillus niger on plant biomass

status: Public on Aug 31 2022

city: Utrecht

first: Ronald

last: de vries

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: westerdijkinstitute

summary: To evaluate the relative contribution of individual sugar catabolic pathways to the overall physiology of A. niger during growth on plant biomass, the A. niger sugar catabolic pathways involved in converting the most common monomers of plant biomass polysaccharides were blocked, and the phenotype as well as the transcriptomic response of these single-pathway deletion mutants was analysed on two distinct plant biomass substrates: wheat bran (WB) and sugar beet pulp (SBP). Deletion of all the above catabolic pathways were also combined in a single strain (?all), to evaluate whether other compounds of plant biomass could still support growth of A. niger when utilization of the major sugar components is blocked. On both WB and SBP, the strongest affected single-pathway deletion mutants were the PCP and glycolysis deficient mutants, delta-xkiA and delta-hxkA/delta-glkA, respectively. Especially on WB, which is a particularly rich substrate in pentose sugars, blocking PCP caused a significant effect in delta-xkiA with respect to both growth and transcriptomic response. However, delta-hxkA/delta-glkA was shown to be the most critically affected strain. On both substrates, combined deletion of hxkA and glkA resulted in the strongest growth reduction of all the single-pathway mutants, very similar to the multi-pathway deletion mutant delta-all. This result clearly pointed to glycolysis as the most essential and indispensable pathway for the survival of A. niger on these substrates. Since cellulose is not a preferred carbon source for A. niger, it seems that the double deletion of hxkA and glkA mostly affected the utilization of starch. (Note: A portion of this research was performed on a project award (10.46936/expl.proj.2019.51072/60006675) from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830)

overall_design: mRNA profiling of five Aspergillus niger strains grown on wheat bran or sugar beet pulp at two time points.

first: Tania

last: Chroumpi

first: Mar

last: Cubertorer Navarro

first: Agata

last: Terebienic

first: Astrid

last: Mueller

first: Jiajia

last: Li

first: Mao

last: Peng

first: Meng

last: Markillie

first: Hugh

last: Mitchell

first: Carrie

last: Nicora

first: Chelsea

middle: M

last: Hutchinson

first: Vanessa

last: Paurus

first: Samuel

last: Purvine

first: Chaevien

middle: S

last: Clendinen

first: Galya

last: Orr

first: Scott

last: Baker

first: Miia

last: Makela

last: de Vries


title: Negative regulation of endothelial to haematopoietic transition by Nupr1

status: Public on Jun 10 2022

city: Beijing

first: Di

last: Liu

address: No. 45 West Street, Beijing

institute: Xuanwu Hospital, Capital Medical University

summary: we uncovered that nuclear protein 1 (Nupr1), a transcription regulatory gene preferentially expressed in HECs, was a negative regulator of EHT. Nupr1 deficiency resulted in plentiful emergence of HSC-competent cells in the AGM region, including HECs and HSPCs. Further single-cell transcriptome combined serial functional assay revealed that loss of Nupr1 prominently accelerate EHT process, also promote the specification of HECs and strengthen their subsequent hematopoietic differentiation potential towards HSPC. Interestingly, we found that numerous inflammatory signals were specifically upregulated in Nupr1-/- EHT relevant populations, as elevated inflammatory response signals have been proved to promote EHT and HSPCs generation.

overall_design: Cd31+, Cd44+ cells form VEC-Cre and Nupr1fl/fl mice were isolated by Fluorescence-activated cell sorting (FACS)  and analyzed using scRNAseq.

first: Haizhen

last: Wang

first: Jie

last: Zhou


title: Rebalancing TGFβ1/BMP Signals Preserves Effector and Memory Programs in Terminally Dysfunctional CD8+ T Cells

status: Public on Nov 03 2022

city: Columbus

first: Amy

last: Hite

address: 1800 Cannon Drive 250 Lincoln Tower

institute: The Ohio State University

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

overall_design: Refer to individual Series


title: Effect of cardiomyocyte-specific deletion of glucocorticoid receptor on gene expression of cultured neonatal cardiomyocytes

status: Public on May 16 2022

city: Bologna

first: Gabriele

last: D'Uva

address: via Massarenti 9

institute: University of Bologna

summary: To investigate the role of the glucocorticoid receptor (GR) in the regulation of cardiomyocyte maturation and proliferation, we established a cardiomyocyte-specific GR knock-out (GR-cKO) mouse model by Cre-Lox technology. We thus performed gene expression profiling analysis using data obtained from RNA-seq of cardiomyocytes isolated from GR-cKO and control mouse models at neonatal stage and cultured in vitro. Our analyses unveiled a role for GR in regulating gene networks related to the energetic metabolism, which in turn may impact on cardiomyocyte proliferative and regenerative ability.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of cardiomyocytes isolated from GR-cKO and control mouse models at postnatal-day-1 (P1) and cultured in vitro


title: Effect of cardiomyocyte-specific deletion of glucocorticoid receptor on gene expression of the cardiac tissue during early postnatal development

summary: To investigate the role of the glucocorticoid receptor (GR) in the regulation of cardiomyocyte maturation and proliferation, we established a cardiomyocyte-specific GR knock-out (GR-cKO) mouse model by Cre-Lox technology. We thus performed gene expression profiling analysis using data obtained from RNA-seq of the cardiac tissue of GR-cKO and control mouse models extracted during the early postnatal development. Our analyses unveiled a role for GR in regulating gene networks related to the energetic metabolism, which in turn may impact on cardiomyocyte proliferative and regenerative ability.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of cardiac tissue lysates from GR-cKO and control mouse models at postnatal-day-7 (P7).


title: Repeat Detector: accurate, efficient, and flexible sizing of expanded CAG/CTG repeats from targeted DNA sequencing

status: Public on Mar 22 2022

city: Cardiff

first: Vincent

last: Dion

address: Hadyn Ellis Building

department: Dementia Research Institute

institute: Cardiff University

summary: Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and pre-clinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. In addition, interruptions are sometimes present within repeats and can alter disease manifestation. Despite advances in methodologies, determining repeat size and identifying interruptions in targeted sequencing datasets remains a major challenge. This is because standard alignment tools are ill-suited for the repetitive nature of these sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington’s disease (HD) and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 HD blood-derived samples and did not require prior knowledge of the flanking sequences or their polymorphisms within the patient population. We demonstrate that RD can be used to identify individuals with repeat interruptions and may provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and the development of novel therapies.

overall_design: 22 DNA samples from Huntington's disease individuals obtained from Coriell.org. 4 Samples from HEK-derived GFP(CAG)x lines with different repeat sizes.

first: Alysha

last: Taylor


title: ACVR1-mutant posterior fossa ependymoma

status: Public on May 01 2022

city: Bethesda

first: Drew

last: Pratt

state: Maryland

address: 10 Center Drive, Building 10, Room 2S235

department: Laboratory of Pathology

institute: National Institutes of Health

summary: Genomewide DNA methylation array profiling of nine posterior fossa ependymomas harboring activating mutations in ACVR1. Two samples clustered with the PFA subtype and demonstrated H3K27me3 loss by immunohistochemistry, while the remaining 7 showed retained H3K27me3 and formed a methylation cluster distinct from other ependymal tumors. For these previsouly unpublished cases, the Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue.

overall_design: Bisulfite converted genomic DNA extracted from 7 tumor samples was hybridized to Illumina Infinium EPIC Human DNA Methylation Beadchips

first: D


title: I-SPY2-990 mRNA/RPPA Data Resource: mRNA component

status: Public on May 25 2022

city: San Francisco

first: Denise

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

summary: The I-SPY2-990 mRNA/RPPA Data Resource contains gene expression and clinical data for 987 patients from 10 arms of the neoadjuvant I-SPY2 TRIAL for aggressive early stage breast cancer [210 Control (Ctr); 71 veliparib/carboplatin (VC); 114 neratinib (N); 93 MK2206; 106 ganitumab; 93 ganetespib; 134 trebananib; 52 TDM1/pertuzumab(P); 44 H/P; 69 pembrolizumab (pembro)]. All 987 patients have pretreatment full transcriptome expression data on over ~19,000 genes assayed on Agilent 44K. Clinical data includes HR, HER2 and MP status, response (pCR or no pCR), and treatment arm. The ISPY2-990 mRNA/RPPA Data Resource also includes normalized pre-treatment LCM-RPPA data for 139 key signaling proteins/phosphoproteins in cancer for 736 patients (see companion GEO record GSE196093 for data and details).

overall_design:
Fresh-frozen pre-treatment breast cancer tumors (n=987) from 10 arms of the neoadjuvant ISPY2 trial for high risk, early-stage breast cancer were assayed using two Agilent 44K expression arrays: (1) Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] or (2) Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)]; and these data were combined into a single gene-level dataset after batch-adjusting using ComBat.

The sample characteristics and their values represent:
HER2: the status of the HER2 gene
1 = positive; 0 = negative.
HR: the status of hormone (estrogen and progesterone) receptors
1 = positive; 0 = negative.
pCR: the status of a pathological complete response (pCR)
1 = complete response; 0 = failed complete response
MP: MammaPrint status
0 = MammaPrint high risk 1 (MP1); 1 = MammaPrint (ultra) high risk 2 (MP2)
Arm: arm of the trial per patient:
Paclitaxil (Control arm: HER2- subset); Paclitaxil + Trastuzumab (Control arm: HER2+ subset); Paclitaxel + ABT-888 (veliparib) + Carboplatin; Paclitaxel + AMG-386 (AMG-386 arm: HER2- subset); Paclitaxel + AMG-386 + Trastuzumab (AMG-386 arm: HER2+ subset); Paclitaxel + MK-2206 (MK-2206 arm: HER2- subset); Paclitaxel + MK-2206 + Trastuzumab (MK-2206 arm: HER2+ subset); Paclitaxel + Neratinib; Paclitaxel + Ganetespib; Paclitaxel + Ganitumab; Paclitaxel + Pembrolizumab; Paclitaxel + Pertuzumab + Trastuzumab; or T-DM1 + Pertuzumab. All patients also received subsequent doxorubicin + cyclophosphamide.

A ComBat batch correction process was applied to the raw data on a group of patients (~800). Linear adjustment factors from this group were derived so they could be applied to the remaining group of ~100 patients. The ISPY2_LinearFit_forCombiningExp<GPLXXXXX> files contain linear adjustments to go from raw to batch corrected data.

For fully normalized and batch corrected data on the gene level, please use "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt", provided in the supplementary files. For biomarkers/signatures used in the manuscript, please see supplemental data file in the manuscript.

first: Christina

last: Yau

first: Laura

last: van 't Veer


title: I-SPY2-990 mRNA/RPPA Data Resource

type:
Expression profiling by array
Protein profiling by protein array

summary:
The I-SPY2-990 mRNA/RPPA data resource contains gene expression, protein/phosphoprotein and clinical data for ~990 patients from the first 10 completed arms of the I-SPY 2 platform trial for aggressive, early stage breast cancer.  Experimental treatments include pan-HER2 inhibitors and anti-HER2 agents, PARP inhibitor/DNA damaging agent combinations, an AKT inhibitor, immunotherapy, and ANG1/2, IGF1R and HSP90 inhibitors added to standard of care chemotherapy.  All patients have pretreatment full transcriptome expression data on over ~19,000 genes assayed on Agilent 44K. 736 patients (all arms except ganitumab and ganetespib) have normalized LCM-RPPA data for 139 key signaling proteins/phosphoproteins in cancer. Clinical data includes HR, HER2 and MP status, response (pCR or no pCR), and treatment arm.

This SuperSeries is composed of the mRNA and RPPA SubSeries listed below.

overall_design: For details, please see individual series GSE19404 (mRNA) and GSE196093 (RPPA)


title: The role of endogenous Smad7 in regulating macrophage phenotype following myocardial infarction [JunLi_MyS7KOinvivo]

status: Public on Apr 29 2022

city: Bronx

first: Silvia

last: Hernandez

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: Induction of the inhibitory Smad, Smad7 serves as a negative feedback mechanism that restrains TGF-b-mediated actions in injured tissues. In inflammatory cells, Smad7 has been suggested to exert both pro-inflammatory actions attributed to inhibition of TGF-b-induced suppression of inflammation, and anti-inflammatory effects due to disruption of the TAK-1/NF-kB system. Myocardial infarction triggers a macrophage-driven inflammatory response that plays a central role in cardiac repair, but also contributes to adverse remodeling and fibrosis. We hypothesized that Smad7 upregulation in infarct macrophages may play a modulatory role in cardiac repair, by restraining effects of TGF-b. To test the hypothesis, we investigated the response of Myeloid cell-specific Smad7 knockout mice (MyS7KO) following myocardial infarction protocols, and we examined the in vitro effects of Smad7 in isolated macrophages. Smad7 was upregulated in a subset of infarct macrophages, peaking 7 days after infarction. Myeloid cell-specific Smad7 loss did not affect baseline macrophage gene expression and had no significant effects on homeostatic functions. Although RNA-seq analysis predicted that, in the absence of Smad7, infarct macrophages may have attenuated activation of inflammatory pathways and suppressed TREM1 signaling, myeloid cell-specific Smad7 loss had no significant effects on ventricular dysfunction, adverse remodeling, scar remodeling and collagen deposition after myocardial infarction. In isolated macrophages, TGF-b attenuated pro-inflammatory cytokine and chemokine expression, modulated synthesis of matrix remodeling genes, and had profound effects on macrophage profile, inducing genes associated with activation of sphingosine-1 phosphate and integrin signaling pathways, and inhibiting cholesterol biosynthesis genes. However, RNA-seq and PCR array experiments showed that Smad7 loss has minimal effects on TGF-b-mediated macrophage responses, restraining synthesis of only a small fraction of TGF-b-induced genes, such as Itga5, Olfml3 and Fabp7. Smad7 absence did not affect the anti-inflammatory actions of TGF-b in TNF-stimulated cells. In conclusion, our findings suggest a limited role for macrophage Smad7 in regulation of post-infarction inflammation and repair, and demonstrate that the anti-inflammatory effects of TGF-b in macrophages are not restrained by endogenous Smad7 induction.

overall_design: In order to study the role of Smad7 in myeloid cells in vivo, we generated mice with myeloid specific loss of Smad7 in lysozyme M+ cells (MyS7KO). We used a transgenic mouse line in which Cre recombinase is driven by the LyzM promoter (Jackson Laboratory, stock No: 004781). LyzM-Cre mice were bred with Smad7fl/fl mice (Jackson Laboratory, stock No: 017008) to generate LyzM-Cre;Smad7fl/fl animals (MyS7KO) and corresponding Smad7fl/fl control littermates. A model of non-reperfused myocardial infarction was induced by permanent ligation of left anterior descending coronary artery and samples were collected for baseline mice, and 3 and 7 days after coronary occlusion.

first: Jun

last: Li

first: Ruoshui

first: Izabela

last: Tuleta

first: Claudio

last: Humeres

first: Anis

last: Hanna

first: Bijun

last: Chen

first: Nikolaos

last: Frangogiannis


title: Profiling axonal transcriptome of mouse hippocampal neurons in response to force

status: Public on Mar 07 2022

city: Pisa

first: Vittoria

last: Raffa

state: Please Select

address: S.S. 12 Abetone e Brennero, 4

department: Department of Biology

institute: Università di Pisa

summary: Magnetically-actuated iron oxide nanoparticles (MNP) have emerged as a technology to chronically expose axons of developing neurons to extremely low mechanical forces. This force was found to induce axon outgrowth. Axon-Seq has been performed to profile local gene expression in response to the stimulus.

overall_design: Mouse hippocampal neurons were incubated with a growth medium modified with MNPs. Two conditions were analysed (cell cultures treated with a magnetic field or a null magnetic field).

first: Alessandro

last: Falconieri

first: Ugo

last: Borello


title: INO80 chromatin binding profile in mouse zygotene-spermatocytes

status: Public on Dec 16 2021

city: oklahoma

first: roberto

middle: jose

last: pezza

state: OK

department: cell cycle and cancer biology

institute: oklahoma medical research foundation

summary: INO80 ChIP-seq from synchronized early-zygotene spermatocytes (first wave)

overall_design: First generation mice from DBA/2J x C57BL/6J mix were synchronized at 2 dpp with fertilysin/retinoic acid treatment, spermatocytes were collected at early zygotene (8 days after retinoic acid treatment), purified using Percoll gradient centrifugation and INO80 ChIP-seq was performed.

first: Agustin

last: Carbajal

first: Irma

last: Gryniuk

first: Rodrigo

last: Orlandini di Castro

first: Roberto

last: Pezza


title: The role of endogenous Smad7 in regulating macrophage phenotype following myocardial infarction

state: New York


title: I-SPY2-990 mRNA/RPPA Data Resource: RPPA component

first: Denise

last: Wolf

summary: The RPPA component of the I-SPY2-990 mRNA/RPPA Data Resource contains protein/phosphoprotein data from pre-treatment laser capture microdissected (LCM) tumor biopsies for 139 key signaling proteins/phosphoproteins in cancer for 736 patients from 8 arms of the neoadjuvant I-SPY2 TRIAL (NCT01042379) for aggressive early stage breast cancer [194 Control (Ctr); 63 veliparib/carboplatin (VC); 105 neratinib (N); 87 MK2206; 128 trebananib; 49 TDM1/pertuzumab(P); 43 H/P; and 67 pembrolizumab (pembro)].   This record also contains clinical data for these patients, including HR, HER2 and MP status, response (pCR or no pCR), and treatment arm. RPPA endpoints assayed are from hormone receptor (n=4), HER family (n=14), cell cycle/proliferation (n=20), immune (n=18), DNA repair deficiency (DDR; n=15), AKT/mTOR/PI3K (n=7), apoptosis/autophagy (n=10), IGF1R (n=6), TIE/ANG (n=4), growth/survival/metabolism (n=22) and RTK (n=19) pathways.  For gene expresson data for all 736 patients with RPPA data, plus an additional 150 patients for a total 987 patients from 10 arms of  I-SPY2 (mRNA component of the I-SPY2-990 Data Resource), see the companion GEO record/subseries GSE194040.

overall_design:
Reverse phase protein array (RPPA) array run on isolates from pre-treatment breast cancer biopsy samples that were first LCM-enriched for epithelial cells.
The sample characteristics and their values represent:
HER2: the status of the HER2 gene. 1 = positive; 0 = negative.
HR: the status of hormone (estrogen and progesterone) receptors.  1 = positive; 0 = negative.
pCR: the status of a pathological complete response (pCR).  1 = complete response; 0 = failed complete response
Arm: arm of the trial per patient, detailing treatment during taxol-phase of protocol:
Paclitaxil (Control arm: HER2- subset); Paclitaxil + Trastuzumab (Control arm: HER2+ subset); Paclitaxel + ABT-888 (veliparib) + Carboplatin; Paclitaxel + AMG-386 (AMG-386 arm: HER2- subset); Paclitaxel + AMG-386 + Trastuzumab (AMG-386 arm: HER2+ subset); Paclitaxel + MK-2206 (MK-2206 arm: HER2- subset); Paclitaxel + MK-2206 + Trastuzumab (MK-2206 arm: HER2+ subset); Paclitaxel + Neratinib;  Paclitaxel + Pembrolizumab; Paclitaxel + Pertuzumab + Trastuzumab; or T-DM1 + Pertuzumab.  All patients also received subsequent doxorubicin + cyclophosphamide.
Arm (short name): abbreviated name of treatment arm in the trial per patient (n=8 arms) - Control, VC, AMG-386, MK-2206, N, Pembro, Pertuzumab, TDM1/P
RPPA Array:  Platform Array version.  Key to convert from raw to normalized data.

first: Christina

last: Yau

first: Julia

last: Wulfkuhle

first: Emanuel

last: Petricoin III

first: Laura

last: van ‘t Veer


title: Transcriptional profiles of melanoma metastases from patients responsive or resistant to BRAF/MEK inhibitor

status: Public on Apr 12 2022

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Transcriptional profiles of formalin-fixed-paraffin-embedded melanoma metastases including pre-treatment (PRE) and post-treatment (POST) specimens from 50 patients treated with BRAF inhibitors or with BRAF and MEK inhibitors

overall_design: 91 samples from 50 patients showing a long-term response (LR) or a short-term response (SR) to treatment are included


title: Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity

status: Public on Oct 27 2021

city: Glendale

first: Crystal

last: Marconett

address: 1856 Kirkby Rd

institute: Keck School of Medicine

summary: Background: Disruption of alveolar epithelial cell (AEC) differentiation is implicated in implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that impact morbidity and mortality worldwide. Elucidating underlying disease pathogenesis requires a mechanistic molecular understanding of AEC differentiation. Previous studies have focused on changes of individual transcription factors, and to date no study has comprehensively characterized the dynamic, global epigenomic alterations that facilitate this critical differentiation process in humans. We comprehensively profiled the epigenomic states of human AECs during type 2 to type 1-like cell differentiation, including the methylome and chromatin functional domains, and integrated this with transcriptome-wide RNA expression data.  Enhancer regions were drastically altered during AEC differentiation. Transcription factor binding analysis within enhancer regions revealed diverse interactive networks with enrichment for many transcription factors, including NKX2-1 and FOXA family members, as well as transcription factors with less well characterized roles in AEC differentiation, such as members of the MEF2, TEAD, and AP1 families. Additionally, associations among transcription factors changed during differentiation, implicating a complex network of heterotrimeric complex switching in driving differentiation. Integration of AEC enhancer states with the catalog of enhancer elements in the Roadmap Epigenomics Mapping Consortium and Encyclopedia of DNA Elements (ENCODE) revealed that AECs have similar epigenomic structures to other profiled epithelial cell types, including human mammary epithelial cells (HMECs), with NKX2-1 serving as a distinguishing feature of distal lung differentiation. Enhancer regions are hotspots of epigenomic alteration that regulate AEC differentiation. Furthermore, the differentiation process is regulated by dynamic networks of transcription factors acting in concert, rather than individually. These findings provide a roadmap for understanding the relationship between disruption of the epigenetic state during AEC differentiation and development of lung diseases that may be therapeutically amenable.

overall_design: RNA was isolated from 1 million cells for each timepoint using the GE triplePrep kit. RiboZero depletion was used as well as DNaseI to ensure RNA quality prior to library preparation. Library preparation was performed at the USC Epigenome Core. Barcodes used for multiplexed sequencing are indicated in the filename for each sample. Reads underwent paired-end sequencing and were aligned back to the hg19 genome. DNA was isolated from the same cells as RNA using the GE triplePrep kit. DNA underwent bisulfite treatment and sequencing at the USC Epigenome Core. Reads were mapped back to the bisulfite hg19 genome. BisSNP was used for SNP calling and generation of methylation calls. MethylSeekR was used for methylation domain calling. Chromatin immunoprecipitation was performed using antibodies against H3K27ac (Cat # 39133, Active Motif, Carlsbad CA), H3K4me1 (pAb-037-050, Diagenode, Denville NJ), CTCF (Cat #2899, Cell Signaling, Danvers MA), H3K27me3 (#07-449) and H3K9/14Ac (#06-599) from Millipore (Burlington, MA) and the Imprint Ultra Chromatin Immunoprecipitation Kit (Sigma-Aldrich, St Louis MO). Enrichment was verified at the previously identified GRAMD2 enhancer region prior to Next-generation sequencing library construction. Human GRAMD2 enhancer primer sequence: Forward 5’-GGT CTC CTG ATT TCC TGA TG -3’, Reverse 5’-AGG CTG ACT TCT CAC TAT TC-3’. FAIRE libraries were generated from the histone-depleted supernatants. Free DNA was isolated using an established protocol. Samples underwent library preparation and single end (SE) 50-cycle DNA sequencing using an Illumina HiSeq2000 (Illumina, San Diego CA) at the USC Epigenome Center (USC, Los Angeles CA).

first: Beiyun

last: Zhou

first: Theresa

last: Stueve

first: Evan

last: Mihalakakous

first: Lin

last: Miao

first: Daniel

last: Mullen

first: Yinchong

last: Wang

first: Yixin

last: Liu

first: Jiao

last: Luo

first: Evelyn

last: Tran

first: Kimberly

last: Siegmund

first: Sean

middle: K

last: Lynch

first: Amy

last: Ryan

first: Ite

middle: A

last: Offringa

first: Zea

last: Borok


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [Amplicon III]

status: Public on Nov 25 2021

first: Alexander

last: Marson

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression within these networks is sufficiently perturbed it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map the connections between regulatory genes and their downstream targets. However, it has been challenging to identify the upstream regulators for genes of interest. Here we develop a system for systematic discovery of upstream regulators of critical immune factors – IL2RA, IL-2, and CTLA4 – in primary human T cells. Then, CRISPR perturbations coupled with RNA-Seq, and ATAC-Seq, allowed us to map the full network of these regulators’ target genes and enhancers. These regulators form highly interconnected networks with extensive feedback loops. Furthermore, this network is highly enriched for autoimmune-associated disease variants and genes. These results provide insight into how autoimmune associated disease genes are regulated in T cells as well as broader principles about the structure of human gene regulatory networks.

overall_design: Amplicon sequencing to detect insertion/deletions at CRISPR guide RNA target sites.

first: Jacob

middle: W

last: Freimer

first: Oren

last: Shaked

first: Sahin

last: Naqvi

first: Nasa

last: Sinnott-Armstrong

first: Arwa

last: Kathiria

last: Chen

first: Jessica

middle: T

last: Cortez

first: William

last: Greenleaf

first: Jonathan

last: Pritchard


title: Developmental regulation of neuronal gene expression by Elongator complex protein 1 dosage

status: Public on Oct 25 2021

city: Boston

first: Susan

last: Slaugenhaupt

state: Massachusetts

address: 185 Cambridge Street, CPZN-5254

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Elongator is a highly conserved protein complex required for transcriptional elongation, intracellular transport and translation. Elongator complex protein 1 (ELP1) is the scaffolding protein of Elongator and is essential for its assembly and stability. Familial dysautonomia (FD), a hereditary sensory and autonomic neuropathy, is caused by a mutation in ELP1 that lead to a tissue-specific reduction of ELP1 protein. Our work to generate a phenotypic mouse model for FD led to the discovery that homozygous deletion of the mouse Elp1 gene leads to embryonic lethality prior to mid-gestation. Given that FD is caused by a reduction, not loss, of ELP1, we generated two new mouse models by introducing different copy numbers of the human FD ELP1 transgene into the Elp1 knockout mouse (Elp1-/-) and observed that human ELP1 expression rescues embryonic development in a dose dependent manner. We then conducted a comprehensive transcriptome analysis in mouse embryos to identify genes and pathways whose expression correlates with the amount of ELP1.  We found that ELP1 is essential for the expression of genes responsible for the formation and development of the nervous system. Further, gene length analysis of the differentially expressed genes showed that the loss of Elp1 mainly impacts the expression of long genes and that by gradually restoring Elongator their expression is progressively rescued. Finally, through evaluation of co-expression modules, we identified gene sets with unique expression patterns that depended on ELP1 expression.  Overall, this study highlights the crucial role of ELP1 during early embryonic neuronal development and reveals gene networks and biological pathways that are regulated by Elongator.

overall_design: Paired-end RNASeq in Elp1 KO mouse embryos with different dosage of human ELP1 gene with FD mutation. Total 29 RNASeq libraries. This includes 8 WT mouse embryos, 8 embryos KO Elp1 embryos, 7 FD1/KO embryos  (KO for Elp1 endogenous gene with one copy of human FD ELP1 transgene), and 6 FD9/KO embryos (KO for Elp1 endogenous gene with nine copies of human FD ELP1 transgene ).

first: Dadi

last: Gao

first: Elisabetta

last: Morini


title: Hepatocyte-specific perturbation of the NAD+ biosynthetic pathways in mice promotes reversible NASH-like phenotypes

status: Public on Nov 03 2021

city: Copenhagen N

first: Morten

last: Dall

address: BLEGDAMSVEJ 3B, BLDG. 7.7

country: Denmark

institute: University of Copenhagen

summary: We report that the decreased expression of mitochondrial genes we observe in hepatocyte-specific Nampt knockout mice is normalized in primary hepatocytes, and that hepatocyte isolations causes major changes to the hepatocyte transcriptome for both knockouts and wildtype mice.

overall_design: We isolated primary hepatocytes from wildtype and hepatocyte-specific Nampt knockout mice, and sequenced RNA from 1. a liver biopsy following perfusion with saline (L), 2. from washed hepatocytes prior to seeding (CS) and 3. from primary hepatocytes following 24h of culturing (PH) for both genotypes and compared transcriptomes

first: Anna

last: Hassing

first: Jonas

last: Treebak


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [Amplicon II]

first: Amy


title: UVB drives transcriptomic and epigenetic reprogramming which can be protected by antioxidant sulforaphane in human skin keratinocytes [Methyl-seq]

status: Public on Oct 07 2021

city: Piscataway

first: Hsiao-Chen Dina

last: Kuo

address: 160 frelinghuysen road

department: Ernest Mario School of Pharmacy

institute: Rutgers University

summary: Continuous exposure to ultraviolet (UV) is one of the main factors contributing to skin carcinogenesis. Sulforaphane (SFN) is a potent antioxidative agent which has potential to prevent the UV-induced skin cell transformation. We characterized the transcriptome and CpG methylation profile of human keratinocytes (HaCaT cells) treated with UVB and/or SFN using RNA sequencing.

overall_design: Samples of HaCaT cells were used for extraction of DNA and RNA; DNA was enriched by Agilent SureSelect Kit then bisulfite converted methyl-seq was performed. RNA-seq was performed with routine. Strategy. This dataset contains data for the Methyl-seq only; Check the other SubSeries under this SuperSeries for RNA-seq data.

first: Hsiao-Chen

first: Shanyi

last: Li

first: Lujing

last: Wang

first: Renyi

last: Wu

first: Davit

last: Sargsyan

first: Ah-Ng

last: Kong


title: Human colorectal tumor tissue: Tumor vs. histologically normal tissue

status: Public on Sep 17 2021

first: Tianqi

last: Liu

address: Fucheng street

institute: Peking University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Transcriptional profiling of human colorectal cancer tissues comparing control from histologically normal tissue samples adjacent to the tumors. High throughput bioluminescence imaging, and PET were performed. The overall goal was to determine the differential expression of lncRNA and mRNA between tumor and match normal samples.

overall_design:
Two-condition experiment, Tumor vs. Normal Control. Biological replicates: 9 normal tissue control replicates, 9 colorectal tumor samples.
Please note that the experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as single channel. Thus each raw data file contains raw data for both tumor [C] and normal tissue [N] samples, and is linked to the corresponding tumor tissue sample records.


title: UVB drives transcriptomic and epigenetic reprogramming which can be protected by antioxidant sulforaphane in human skin keratinocytes

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

overall_design: Refer to individual Series


title: Genetic control of pluripotency epigenome informs differentiation bias in mouse embryonic stem cells

status: Public on Oct 05 2021

city: Bar Harbor

first: Christopher

last: Baker

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Genetically diverse pluripotent stem cells (PSCs) display varied, heritable responses to differentiation cues in the culture environment. By harnessing these disparities through derivation of embryonic stem cells (ESCs) from the BXD mouse genetic reference panel, along with C57BL/6J (B6) and DBA/2J (D2) parental strains, we demonstrate genetically determined biases in lineage commitment and identify major regulators of the pluripotency epigenome. Upon transition to formative pluripotency using epiblast-like cells (EpiLCs), B6 quickly dissolves naïve networks adopting gene expression modules indicative of neuroectoderm lineages; whereas D2 retains aspects of naïve pluripotency with little bias in differentiation. Genetic mapping identifies 6 major trans-acting loci co-regulating chromatin accessibility and gene expression in ESCs and EpiLCs, indicating a common regulatory system impacting cell state transition. These loci distally modulate occupancy of pluripotency factors, including TRIM28, P300, and POU5F1, at hundreds of regulatory elements. One trans-acting locus on Chr 12 primarily impacts chromatin accessibility in ESCs; while in EpiLCs the same locus subsequently influences gene expression, suggesting early chromatin priming. Consequently, the distal gene targets of this locus are enriched for neurogenesis genes and were more highly expressed when cells carried B6 haplotypes at this Chr 12 locus, supporting genetic regulation of biases in cell fate. Spontaneous formation of embryoid bodies validated this with B6 showing a propensity towards neuroectoderm differentiation and D2 towards definitive endoderm, confirming the fundamental importance of genetic variation influencing cell fate decisions.

overall_design: Bulk RNA-seq and ATAC-seq performed in ESCs and EpiLCs in biological replicates derived from C57BL/6J, DBA/2J and BXD mouse strains. ChIP-seq performed in biological replicate ESCs. Single cell RNA-seq performed in embryoid bodies.

first: Candice

last: Byers


title: UVB drives transcriptomic and epigenetic reprogramming which can be protected by antioxidant sulforaphane in human skin keratinocytes [RNA-seq]

overall_design: Samples of HaCaT cells were used for extraction of DNA and RNA; DNA was enriched by Agilent SureSelect Kit then bisulfite converted methyl-seq was performed. RNA-seq was performed with routine. Strategy. This dataset contains data for the RNA-seq only; Check the other SubSeries under this SuperSeries for Methyl-seq data.


title: Effects of the Combination Therapy of a CDK4/6 and a MEK inhibitor in a Mouse Model of Diffuse Midline Glioma

status: Public on Sep 28 2021

city: Chicago

first: Yusuke

last: Tomita

state: Illinois

address: 225 E Chicago Ave Box 18

department: Pediatrics

institute: Northwestern University

summary: Diffuse intrinsic pontine glioma (DIPG) arises in the brainstem of children, leading tumor-related death among children. A heterozygous histone H3.3K27M mutation has been shown to occur in ~80% of DIPGs, and results in brainstem gliomagenesis. There is no clinical trial for the patients with DIPG that proved to prolong survival time so far. Recently, CDK4/6 inhibitor showed feasibility and early therapeutic effect against DIPG. Also, recent research with human DIPG specimens have detected the MAPK pathway highly activated. Here, we evaluated a novel combination therapy with CDK4/6 inhibitor and MEK inhibitor to the mouse DIPG model.  In order to generate DIPG‐bearing mice, we are using the RCAS/Tv‐a system, with which we are able to target specific genetic alterations in RCAS viruses (avian retroviruses) to specific cells‐of‐origin using transgenic Tv‐a‐expressing mice (Tv‐a being the receptor for RCAS viruses). We injected P3‐P5 Nestin-Tv-a;p53fl/fl mice (C56Bl/6 background) with RCAS‐PDGF‐A + RCAS‐H3.3K27M, and RCAS-Cre. The mice are treated with vehicle (methylcellurose), ribociclib as monotherapy, trametinib as monotherapy, and ribociclib and combination as combination. For short-term use, tumor tissues treated with ribociclib showed cytostatic effect, and those treated with trametinib showed cytotoxic effect, and those with combination showed both. Long-term use showed that combination therapy modestly prolonged mice survival compared with vehicle. Therefore, we need to find how DIPG showed registence to the long-term chemotherapy.

overall_design: Examination of gene expression differences in mouse DIPGs treated with vehicle, ribociclib, trametinib, and ribociclib and trametinib as combination

first: Oren

last: Becher


title: Characterization of tumor associated macrophages (TAM) in the tumor microenvironment of human melanoma

status: Public on Aug 09 2021

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

country: Spain

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

summary: Tumor cells attract and dynamically interact with monocytes/macrophages to subvert their differentiation into tumor associated macrophages (TAMs), which mainly promote immunosuppression and neoplastic progression, but the pathways and microenvironmental cues governing their protumoral deviation are not completely understood. Thus, identifying molecular pathways responsible for TAM differentiation may provide new therapeutic targets to improve the efficacy of immunotherapy of cancer.

overall_design: mRNA profiles of TAM ex vivo and in vitro in human melanoma. Ex vivo TAM were isolated from human skin melanoma. Monocytes from patients with melanoma were also isolated. In vitro TAM were created by coculturing monocytes or macrophages (M-CSF or GM-CSF differentiated) with different melanoma cell lines (BLM, A375 and SKMEL103) for 24 hours. All samples have been processed in triplicates

first: Alba

last: Gutiérrez Seijo

last: Samaniego García

first: Paloma

last: Sánchez-Mateos

first: Celia

last: Barrio Alonso

first: Elena

last: García Martínez


title: Single-cell RNA sequencing of human osteosarcoma

status: Public on Aug 19 2021

city: Nanning

first: Wenyu

last: Feng

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: We performed the scRNA-seq analysis of 6 osteosarcoma tissues based on the 10X Genomics.

overall_design: Primary osteosarcoma tissues from 6 patients were used for single cell RNA sequencing by 10X Genomics

first: Yun

first: Yan

last: Dai

first: Mengying

last: Bao

first: Zhenchao

last: Yuan

first: Yu

last: Ye

first: Mingwei

last: He

first: Zhaojie

last: Qin

first: Shijie

last: Liao

first: Juliang

first: Qian

last: Huang

first: Zhenyuan

last: Yu

first: Yonghua

last: Jiang

first: Jinling

first: Jie

last: Ma

first: Zengnan

last: Mo

first: Qingjun

last: Wei


title: Profiles of mRNA and lncRNA expression in colorectal cancer

status: Public on Aug 01 2021

city: Dongguan

first: Guangxian

last: Xu

state: Guangdong

address: No.1 Xincheng Blvd, Songshan Lake National High-tech Industrial Development Zone

department: College of Medical Technology

institute: Guangdong Medical University

summary: Colorectal cancer (CRC) is one of the most malignant cancers with high morbidity and mortality. Genetic factors are involved in the carcinogenesis of CRC, which consists of a complex accumulation of mutations in key regulatory genes and epigenetic regulation.Here we report significantly up-regulated as well as down-regulated mRNAs and lncRNAs in CRC tissues compared with their matched non-tumoral tissues.

overall_design: Examination of  Differential Expression of mRNAs and lncRNAs between 3 pairs of colorectal tumor tissues and normal tissues

first: Dan


title: Single Cell Immunophenotyping of Lyme Erythema Migrans [Single-Cell TCR Repertoire Sequencing]

status: Public on Jun 07 2021

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: Erythema migrans (EM) is a skin lesion caused by the spirochete B. burgdorferi (Bb) and is a hallmark initial sign of Lyme disease. Previous studies have demonstrated that T cells and innate immune cells mediate local inflammatory cytokine production that promote the reaction. Despite the established importance of B cells and antibodies in preventing Bb infection and resolving disease, the role of B cells in the skin immune response to Bb is incompletely defined. In this study, we characterized the immunophenotype of EM lesions and used single cell RNA-Seq to investigate B cell receptor (BCR) and T cell receptor (TCR) repertoires in the EM skin lesions and peripheral blood of patients with Lyme disease. We hypothesized that B cells from the circulation, potentially primed by exposure to Bb antigens in regional draining lymph nodes, are recruited into EM lesions and play an active role in the local response to infection. We found that B cells are more abundant in the EM lesion in comparison to autologous uninvolved skin and possess distinct characteristics, including abundant expression of MHCII genes and preferential IgM isotype usage. A subset exhibited low levels of somatic hypermutation despite a gene expression profile more consistent with memory than naïve B cell subsets. Moreover, infiltrating B cells were clonally expanded and a large fraction could be directly traced to circulating relatives. By leveraging single cell gene expression with paired BCR and TCR repertoire sequencing, we demonstrate, for the first time, that B cells are recruited to the skin infection site in early Lyme disease and express a phenotype suggesting that they could play a role in local antigen presentation and antibody production.

overall_design: Six subjects were studied, all with confirmed cases of Lyme Disease. Five of six had samples from both EM rash and unaffected skin. One subject had sample only from EM rash. One subject had an additional PBMC sample. Sequencing of TCR was performed using the 10X Genomics platform.

first: Tony

last: Melillo

first: Ruoyi

first: Steven

middle: H

last: Kleinstein

first: Linda

last: Bockenstedt


title: Single Cell Immunophenotyping of Lyme Erythema Migrans (Bulk BCR Repertoire Sequencing)

overall_design: Bulk BCR sequencing was performed on PBMCs from six subjects, all with confirmed cases of Lyme disease.


title: Cohesin regulates homology search during recombinational DNA repair

status: Public on Jul 21 2021

city: PARIS

first: Helene

last: Bordelet

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [Amplicon]

status: Public on Apr 26 2021

first: Alexander

last: Marson

state: CA

first: Jacob

last: Freimer

first: Oren

last: Shaked

first: Sahin

last: Naqvi

first: Nasa

last: Sinnott-Armstrong

first: Arwa

last: Kathiria

first: Amy

last: Chen

first: Jessica

last: Cortez

first: William

last: Greenleaf

first: Jonathan

last: Pritchard


title: Single Cell Immunophenotyping of Lyme Erythema Migrans (Seq-Well Single-Cell Gene Expression)

overall_design: Four subjects were studied, all with confirmed cases of Lyme Disease. Two of the four had samples from both EM rash and unaffected skin, the other two EM rash only. One subject had an additional PBMC sample. Single-cell GEX was performed using the SeqWell platform.

last: Jiang