title: Epigenomic and transcriptomic differences between low-grade and acute inflammation in LPS-induced murine immune cells

status: Public on Mar 18 2021

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Chronic, low-grade inflammation has a widespread and significant impact on health, especially in Western-society. While inflammation is beneficial for the removal of microbes, low-grade inflammation never resolves and can cause or worsen other diseases. However, the process by which low-grade inflammation occurs is poorly understood. As lipopolysaccharide (LPS) is associated with chronic inflammatory diseases, we exposed murine bone-marrow derived monocytes to chronic LPS-stimulation at Low-dose (100pg/mL) or High-dose (1 µg/mL), as well as a PBS control. The cells were profiled for H3K27ac expression and gene expression. The gene expression of TRAM-deficient and IRAK-M-deficient mice with LPS exposure was also analyzed for mechanistic insight. We determined that many of the differences between the Low-dose and High-dose conditions are related to the TRIF-dependent pathway of TLR4 signaling. Furthermore, these changes are also seen in the epigenome, suggesting the epigenome may be what leads to the differential response. These findings further characterize the different means utilized in low-grade conditions, and how it might lead to a damaging, non-resolving state. Moreover, our data provide potential targets for future mechanistic or therapeutic studies.

overall_design:
H3K27ac was profiled in WT murine bone-marrow derived monocytes (BMDMs) treated with PBS, Low-dose LPS (100 pg/mL), or High-dose LPS (1 µg/mL). RNA-seq was also performed using BMDMs isolated from WT mice (PBS, Low, High), TRAM-KO mice (PBS, Low, High), and IRAK-M-KO mice (PBS, High) treated with different levels of LPS. Two replicates were generated per LPS dosage level and genotype.

Please note that the records have been updated with the additional samples (GSM5676885 - GSM5676904) on Nov 5, 2021.

first: Lynette

last: Naler


title: Analysis of diversity in barcoded virus library

status: Public on Apr 22 2021

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

country: USA

institute: Brigham and Women's Hospital

summary: Validating viral barcode diversity

overall_design: RNA extraction, reverse transcription, amplification and sequencing of barcodes

middle: A

first: Iain

middle: C

last: Clark

first: Zhaorong

last: Li

first: Francisco

middle: J

last: Quintana


title: Phosphorylation of Cajal body protein coilin activated by UHMK1 influences the sensitivity of colon cancer cells to 5-FU

status: Public on Mar 15 2021

city: Beijing

first: niu

last: huan

address: fengtai district of beijing

department: hereditary system

country: China

institute: Capital Medical University

type: Expression profiling by high throughput sequencing

summary: Drug resistance to 5-fluorouracil (5-FU) and recurrence after chemotherapy in colorectal cancer remain a challenge to be resolved for the improvement of patient outcomes. In the present study, we found that the application of conditioned medium (CM) derived from 5-FU-resistant colon cancer cells HCT-8/FU reduced the chemosensitivity of native HCT-8 to 5-FU, which was accompanied with the significant changes at number counts and morphology of Cajal bodys (CBs), a spherical nuclear body, dynamic exchanging constituent macromolecules (i.e., body-specific proteins and RNAs) with the nucleoplasmic space.It was shown that the disassembly and reassembly of CBs regulated by the phosphorylation of coilin, which was significantly activated by UHMK1. These led to a large number of variations of RNA alternative splicing in cells, which could contribute to the cell survival through remodeling of intracellular phenotype and transmitting preadaptive signal to adjacent cells in tumor microenvironment.

overall_design: Two paired 5-FU-resistant and -sensitive colon cancer cell lines,HCT-8/FU and HCT-8, HCT-8 cultured in CM from HCT-8/FU and HCT-8 cultured in CM from HCT-8,were used in the experiments to investigate the mechanism of cell response to environmental stimulation and the cell sensitivity to 5-FU.

first: Huan

last: Niu

first: Jing

last: Huang

first: Shan

last: Cheng

first: Wei

last: Ding


title: Analysis of diversity in barcoded plasmid library

summary: Validating plasmid barcode diversity

overall_design: Amplification and sequencing of barcodes


title: Heterogeneity of the human glial progenitor cells

status: Public on Mar 03 2021

first: Yuanyuan

last: Fu

address: 5 Yiheyuan Road

institute: BIOPIC, Peking University

summary: Glial cells distribute extensively in the brain and execute important functions. However, their developmental process and molecular features are still not fully explored in human, especially for fetal astrocytes. It is known that EGFR is involved in glial development and we found that the emergence of EGFR+ cells are near the start of gliogenesis and majority of those co-expressed SOX2 during human cerebral cortex development at midgestation. We performed single-cell RNA sequencing of thousands of EGFR+ cells in the human fetal brain cortex from GW21 to GW26. Compared with other published brain sequencing data, our dataset highly enriched the progenitor cells and glial cells. Multiple molecularly specific populations were identified.

overall_design:
We performed single-cell RNA sequencing on EGFR+ cells isolated from the frontal lobe of the human cerebral cortex from GW21 to GW26 to investigate the molecular features of progenitors, especially for glial cells.

*Raw data are not provided due to China's regulations on the management of human genetic resources.*


title: Single-cell RNAseq analysis of CaCl2-induced mouse abdominal aortic aneurysm (AAA) samples

city: Madison

first: Bo

last: Liu

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

summary: We performed single-cell RNA sequencing (scRNA-seq) on infrarenal abdominal aortas from C57BL/6J mice after perivascular CaCl2 treatment. Infrarenal abdominal aortas were collected four days after AAA induction and processed for sequencing. These data provide high-resolution insight into the complexity and heterogeneity of mouse AAA.

overall_design: AAA was induced in 12-week-old male C57BL/6J mice. Infrarenal abdominal aortas were perivascularly treated with 0.5 M CaCl2 for 10 minutes followed by PBS for 5 minutes. Mice in the sham group received 0.5 M NaCl treatment for 10 minutes followed by PBS for 5 minutes. Aortas were collected four days after AAA induction. Single-cell suspensions from four aortas were pooled as one sample.

last: Yang

first: Ting

last: Zhou

first: Amelia

last: Stranz

first: Elise

last: DeRoo


title: Single cell RNA-seq analysis of bronchial epithelium in patients with severe SARS-CoV-2 pneumonia

status: Public on Mar 05 2021

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

summary: To test whether airway epithelial and immune cells in patients with severe SARS-CoV-2 pneumonia exhibit specific gene expression signatures (namely interferon-response signature) we have performed bronchoscopy on intubated patients with severe SARS-CoV-2 pneumonia and obtained bronchial brushings.

overall_design:
Bronchial brushings from 4 patients with COVID-19 were obtained at Northwestern Memorial ICU. Single-cell libraries were prepared with 10x 5' V1 gene expression kit. Libraries were sequenced on Illumina NovaSeq 6000 and MiniSeq. Gene expression matrices were generated with 10x cellranger v3.1.0 software.
***RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns***

first: Ziyan

last: Lu

first: Nikolay

last: Markov

first: Richard

last: Wunderink


title: HIF-1 Recruits TRIM28 and DNA-PK to Release Paused RNA Polymerase II and Activate Target Gene Transcription in Response to Hypoxia

status: Public on Mar 02 2021

city: Baltimore

first: Gregg

middle: Leonard

last: Semenza

state: Maryland

address: 733 North Broadway

institute: Johns Hopkins University

summary: Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that acts as a master regulator of O2 homeostasis in metazoan species by binding to hypoxia response elements (HREs) and activating the transcription of hundreds of genes in response to reduced O2 availability. RNA polymerase II (Pol II) initiates transcription of many HIF target genes under non-hypoxic conditions, but pauses after 20-100 nucleotides and requires HIF-1 binding for release.  Here we report that in hypoxic breast cancer cells, HIF-1 recruits TRIM28 and DNA-dependent protein kinase (DNA-PK) to HREs to release paused Pol II. We show that HIF-1 and TRIM28 assemble the catalytically-active DNA-PK heterotrimer, which phosphorylates TRIM28 at serine-824, enabling recruitment of CDK9, which phosphorylates serine-2 of the Pol II large subunit C-terminal domain and the negative elongation factor to release paused Pol II, thereby stimulating productive transcriptional elongation. Our studies have revealed a critical molecular mechanism by which HIF-1 stimulates gene transcription and reveal that the anticancer effects of drugs targeting DNA-PK in breast cancer may be due in part to their inhibition of HIF-dependent transcription.

overall_design: Total 24 samples. SUM159 subclones (shNTC. shDKD, shDNA-PKcs and shTRIM28) were seeded into 6-well plates in three biological replicates and exposed to 20% or 1% O2 for 24 hours. Total RNA was isolated using TRIzol (Invitrogen) and treated with DNase (Qiagen). Library preparation and sequencing using the Illumina NovaSeq 6000 were performed by Johns Hopkins Genetics Resources Core Facility High-Throughput Sequencing Center. The Fastq files were subjected to quality check and analyzed by Genialis (https://www.genialis.com/). Differential expression results with FDR < 0.05 and mRNA fold change > 1.5 were used as a cutoff for further downstream analysis.

middle: L

first: Yongkang


title: Reveal seasonal climatic variations affect terpenes, norisoprenoids, and green leaf volatiles accumulation in four grape varieties under a double cropping system

status: Public on Mar 13 2021

first: Lu

last: Haocheng

address: No. 17 Tsinghua East Road, Beijing, 100083, China.

institute: China Agricultural University

summary: We determined the RNA sequence of V. vinifera cv. Victoria and V. vinifera cv. Muscat Hamburg grapes to reveal the transcriptomics variations between summer and winter berries under a double cropping system.  Transcriptomics analysis showed that the upregulated VviDXSs, VviPSYs, and VviCCDs expressions might contribute to accumulations of terpenes or norisoprenoids in winter berries.

overall_design: Total RNA obtained from deseed grape berries of of V. vinifera cv. Victoria and V. vinifera cv. Muscat Hamburg at three developmental stages (E-L 35, 36 and 38) in winter cropping compared to summer control crops.

first: Hao-Cheng

first: Wei-Kai

last: Chen

first: Chang-Qing

last: Duan

first: Jun

last: Wang


title: Dataset for Placental Genomic and Epigenomic Signatures in Infants Borns at Extremely Low Gestational Age [DNA methylation]

status: Public on Mar 01 2021

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

summary: These analyses set out to evaluate placental genomic and epigenomic signatures in newborns from the Extremely Low Gestational Age Newborns (ELGAN) cohort. Genome-wide mRNA, microRNA, and DNA methylation profiles were obtained from placenta samples collected at birth. Analyses were conducted to better understand placental molecular signatures and relate these to placental, maternal, infant, and later-in-life health indices.

overall_design: This study involves the evaluation of patients from the ELGAN cohort, comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation. Subjects were recruited from 2002 to 2004, and consisted of pregnant women scheduled to give birth at one of 14 participating institutions. Study procedures were approved by the Institutional Review Board at each of the 14 participating ELGAN sites, and consent was provided prior to hospital admission or soon after delivery. At or prior to delivery, maternal and demographic and clinical assessments were completed. A trained research nurse measured demographic and pregnancy variables after delivery using a structured questionnaire. Each infant’s anthropometric measures were recorded throughout hospitalization and at follow-up. Women participating in the ELGAN study also agreed to the collection of placenta samples. Immediately after delivery, placental tissue samples were collected and flash frozen in liquid nitrogen and stored at -80°C until processed. Placental tissue (~0.2g) was cut from the frozen biopsy sample and rinsed with sterile 1 X PBS to remove residual blood. Samples were then homogenized in Buffer RLT with β-mercaptoethanol (Qiagen, Valencia CA). An AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia CA) was used to extract DNA and RNA. Illumina HiSeq 2500 was used to determine genome-wide mRNA expression profiles. The HTG EdgeSeq miRNA Whole Transcriptome Assay (HTG Molecular Diagnostics, Tucson, AZ) was used to evaluate genome-wide microRNA expression profiles. Extracted DNA samples were bisulfate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) and associated methylation levels quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA).

first: Rebecca

last: Fry

middle: E

first: Hudson

last: Santos

first: Kyle

last: Roell


title: Single-cell RNA-Seq of TauP301L, PS2APP/TauP301L, and PS2APP/TauP301L/TREM2KO mouse hippocampi, 19-22 months old

status: Public on Feb 24 2021

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

summary: Loss-of-function mutations in TREM2 (triggering receptor expressed on myeloid cells 2) strongly increase Alzheimer’s disease (AD) risk. Preclinical models using Trem2 deletion or overexpression have revealed a protective Trem2 function related to β-amyloid accumulation, a process that is most prominent during the pre-diagnosis stages of AD. The role of TREM2 in later AD stages characterized by tau-mediated neurodegeneration is less clear. To understand Trem2 function in the context of both β-amyloid and tau pathologies, we examined Trem2-deficient mice expressing mutant tau alone (pR5-183 model) or in the TauPS2APP model, in which β-amyloid pathology exacerbates tau pathology and neurodegeneration. Single-cell RNA-sequencing in these models revealed robust disease-associated microglia (DAM) activation in TauPS2APP mice that was both amyloid-dependent and Trem2-dependent. In the presence of β-amyloid pathology, Trem2 deletion further exacerbated tau accumulation and spreading and promoted brain atrophy. Without β-amyloid pathology, Trem2 deletion did not affect these processes. Therefore, TREM2 may slow AD progression and reduce tau-driven neurodegeneration by restricting the degree to which β-amyloid facilitates the spreading of pathogenic tau

overall_design: RNA isolated from sorted hippocampi from male non-transgenic (n=2), Trem2ko (n=1), P301Lhomo (n=3), TauPS2APP (n=3), and TauPS2APP;Trem2ko (n=3) mice. All mice were 19-22 months at the time of perfusion. Following the manuscript, the one Trem2ko mouse was analyzed as a control, as indicated in the "genotype group" sample characteristic.

first: Seung-Hye

last: Lee

first: William

last: Meilandt

first: Brad

last: Friedman

first: Christopher

last: Bohlen

first: David

last: Hansen


title: Barcoded viral tracing of single-cell interactions in CNS inflammation

first: Michael

last: Wheeler

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

sample_organism:
Mus musculus
Suid alphaherpesvirus 1
unidentified plasmid

overall_design: Refer to individual Series


title: Systematic comparative analysis of strand-specific, cost-effective, RNA-seq library preparation methods for low input samples

status: Public on Feb 23 2021

first: Rajat

last: Bhatnagar

address: Two Tower Place, Suite 940

institute: Verge Genomics

summary: Despite the precipitous decline in the cost of genome sequencing over the last few years, library preparation for RNA-seq is still laborious and expensive for high throughput screening for drug discovery. Limited availability of RNA generated by some experimental workflows poses an additional challenge and typically adds to the cost of RNA library preparation. In a search for low cost, automation-compatible RNA library preparation kits that also maintain strand specificity and are amenable to low input RNA quantities, we systematically tested two recent commercial technologies – Swift and Swift Rapid – using the Illumina TruSeq stranded mRNA, the de facto standard workflow for bulk transcriptomics, as our reference. We used the Universal Human Reference RNA (UHRR) (composed of equal quantities of total RNA from 10 human cancer cell lines) to benchmark differential gene expression in these kits, at input quantities ranging between 10 ng to 500 ng. Read quality and alignment metrics revealed high mapping efficiency and uniform read coverage through genes for all samples across all three kits. Normalized read counts between all treatment groups were in high agreement, with pairwise Pearson correlation coefficients >0.97. Compared to the Illumina TruSeq stranded mRNA kit, both Swift RNA library kits are cost effective and offer shorter workflow times enabled by their patented Adaptase technology. Furthermore, the Swift RNA kit allows for a relatively broader (and lower) input range, producing consistent results across diverse samples. The Swift Rapid RNA method is the fastest and most cost effective NGS workflow that is best suited for higher RNA yields, with the exact same RNA input range as the Illumina TruSeq kit. We also found the Swift RNA kit to produce the fewest number of differentially expressed genes and pathways attributable to input mRNA concentration.

overall_design: Comparison of mRNA samples prepared with 3 different library preparation methods (Illumina TruSeq, Swift, Swift Rapid) at multiple input mRNA concentrations

first: Swati

last: Naphade


title: Transcriptome analysis of conventional dendritic cells (cDCs) introduced into the thymic microenvironment of re-aggregated thymic organ cultures (RTOCs)

city: Braunschweig

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

summary:
cDCs home from the periphery into the thymus. In order to determine the phenotypic and functional changes introduced by the thymic microenvironment to these thymus-homing cDCs, RNA-based next generation sequencing (RNAseq) was performed with splenic (sp-DC) and thymic conventional DCs (t-DCs) re-isolated from RTOCs after two days of culture.
Methods: RTOCs were generated from single-cell suspensions of thymi isolated from E14.5 to E16.5 fetuses of Foxp3hCD2 reporter mice (BALB/c background), and sp‑DCs or t‑DCs sorted from 4-8 weeks old female CD45.1xBALB/c mice were introduced. After two days of culture, 1‑2x103 cDCs were re-isolated from RTOCs as CD45.1+Lin-CD11chi by FACS, and total RNA for transcriptional profiling by low-input RNAseq was isolated. Total RNA from sp-DC and t-DCs isolated ex vivo from 4-8 weeks old female CD45.1xBALB/c mice was used as control. RNAseq was performed on an Illumina HiSeq2500 system. Differential gene expression between the four different conditions was computed from the read counts.
Results: The number of differentially expressed genes between ex vivo isolated sp-DC and t-DC was drastically reduced comparing sp-DCs and t-DCs re-isolated from RTOCs. This finding implies that the thymic microenvironment within an RTOC modulates the gene expression in sp‑DCs, conferring a transcriptomic profile that more closely resembled the one from t‑DCs.
Conclusion: The thymic microenvironment modulates the transcriptome of thymus-homing peripheral cDCs.

overall_design: RNAseq of sp-DC and t-DCs re-isolated from RTOCs two days after introduction, comparison to ex vivo isolated sp-DC and t-DC

first: Susanne

last: Herppich

first: Jochen

last: Huehn


title: Molecular alterations in the motor and somatosensory areas of the juvenile NeuroD2 deficient mouse

status: Public on Feb 09 2021

city: Marseille

first: Antoine

last: de Chevigny

address: Campus de Luminy

country: France

institute: INMED INSERM U1249

summary: We found morphofunctional alterations in the neocortex of NeuroD2 deficient mice that were  associated with autism/schizophrenia-like behaviors. Thus we asked what are the NeuroD2 target genes that are modified in NeuroD2 deficient mice. In particular it was interesting to determine which genes could be related with morphofunctional alterations and autism/schizophrenia

overall_design: In P28 mice we micro-dissected motor plus somatosensory areas, the regions where we found morphofunctional alterations, and performed RNA purification, library preparation and RNA sequencing

first: Leonard

last: Herault


title: MCF7_Hongjingtian Injection_gene expression

status: Public on Feb 18 2021

city: Hangzhou

first: shujing

last: zhang

address: Xihu district

department: College of Pharmaceutical Sciences

institute: Zhejiang University

summary:
This study compared the gene expression change of MCF7 cells before and after Hongjingtian Injection(HJT) treatment
We used microarrays to detail the global programme of gene expression before and after HJT treatment. We identified the differentially expressed genes during this process and looked for possible targets of HJT.

overall_design: MCF7 cells were treated with HJT(dilution ratio=1/10) for 6h compared with control

first: Shujing

last: Zhang


title: Next Generation Sequencing of bacterial surface-displayed ENAH EVH1 ligand peptides after a FACS titration sort (MassTitr)

city: Cambridge

first: Theresa

last: Hwang

address: 77 Massachusetts Ave

institute: MIT

summary: We used bacterial surface display and FACS to sort peptide binders to a tetramerized ENAH EVH1 domain at multiple concentrations of ENAH into 4 gates. This experiment was repeated three times. By calculating the distribution of each clone across gates at multiple concentrations, we are able to assess whether a clone exhibited concentration-dependent binding to ENAH EVH1 domain, allowing us to distinguish binders from nonbinders.

overall_design: A multiplexed, barcoded dataset with three replicate sorts of four bins at eight receptor concentrations

first: Amy

last: Keating


title: Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression (ATAC-Seq)

status: Public on Feb 04 2021

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: gRNA screening for HbF+ and HbF- samples were performed to identify candidate cis-regulatory elements.

overall_design: CRISPR pooled gRNA screening, RNA-seq, ChIP-seq and ATAC-seq were performed

first: Li

first: Yichao

last: Li


title: The CovR environmental sensor orchestrates competence bimodality in salivarius streptococci

status: Public on Jan 31 2021

city: Louvain-La-Neuve

first: Adrien

last: Knoops

address: Croix du sud 4-5, bte L7.07.06

department: LIBST

country: Belgium

institute: UCLouvain

summary: In bacteria, phenotypic heterogeneity rescues the need for diversity in isogenic populations and allow concomitant multiple survival strategies when choosing only one is too risky. This powerful tactic is exploited for competence in streptococci and results in a bimodal activation, where only a subset of the community triggers the system. Deciphering the mechanisms underlying this puzzling behavior has remained challenging, especially since its study has been mainly achieved in S. mutans, where two different but interconnected regulation networks control competence. In this work, we sought to determine the origin of bimodality associated to the ComRS system thanks to the simplified S. salivarius model that harbors no supplemental signaling system. Using a single cell fluorescence reporter system together with the overexpression of the main actors of the regulation network, we showed that the ComR intracellular concentration is directly linked to the proportion of competent cells in the population. We report that this type of activation requires a functional positive feedback loop acting on comS through Opp and a putative ComS exporter, PptAB. To determine the origin of the heterogeneity amplified by the loop, we developed a mathematical model suggesting that either noise on ComS or ComR abundance could explain bimodality. Because ComR abundance is central for competence bimodal activation, we conducted an in silico identification and a systematic deletion of all the Two Component Systems (TCS) present in S. salivarius and identified CovRS, a well described virulence regulator in GAS and GBS, as a repressor of comR transcription.  In vitro direct binding of CovR with the promoter of comR and transcriptomics confirmed those data. As CovRS integrates environmental stimuli that control ComR intracellular concentration, it represents the missing puzzle piece bridging environmental conditions and competence (bimodal) activation in salivarius streptococci.

overall_design: Examination of mRNA transcriptional profiles in WT and 2 point mutations mutant strains

first: Florence

last: Vande Capelle

first: Marie

last: Verhaegen

first: Johann

last: Mignolet

first: Laetitia

last: Fontaine

first: Philippe

last: Goffin

first: Andrea

last: Sass

first: Tom

last: Coenye

first: FranK

last: Delvigne

first: Laura

last: Ledesma-Garcia

first: Pascal

last: Hols


title: RNA sequencing analysis of pig neonatal left ventricular tissues

status: Public on Feb 15 2021

city: Cinicnnati

first: Katherine

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

summary: The goal of this study is to examine transcriptomic changes in the left ventricles during the transition from a regenerative to a non-regenerative state in the pig neonatal heart. RNA was isolated from pig left ventricular tissue at postnatal day (P)0, P7, and P15, to compare the regeneration-capable P0 cardiac transcriptomic environment to the non-regenerative timepoints of P7 and P15, in pig hearts.

overall_design: Left-ventricular RNA from newborn, one-week, and two-week pig hearts in triplicate per group was analyzed by deep RNA sequencing.

first: Nivedhitha

last: Velayutham


title: Genome-Wide Mapping of Transcription-Replication Interactions Using Transcription-Replication Immunoprecipitation on Nascent DNA Followed by Next Generation Sequencing (TRIPn-Seq)

status: Public on Feb 12 2021

city: Davis

first: Commodore

middle: Perry

last: St. Germain

address: One Shields Avenue

department: Microbiology and Molecular Genetics

institute: University of California, Davis

summary:
Purpose: Transcription and replication are both essential processes that require the processive translocation of large protein complexes through a complex chromatin environment. Transcription-replication interactions (TRIs) arise when transcription and replication occur simultaneously on the same tract of DNA and have been hypothesized to lead to detrimental effects on genome stability. Much of the work analyzing TRIs in mammals has been performed using artificial DNA constructs, chemical agents, and in immortalized cell lines that have abnormal cellular processes that allows for indefinite cellular division.
Methods: To understand where TRIs naturally arise in primary B cells, we performed a sequential immunoprecipitation (IP) of RNA polymerase II phosphorylated at serine 5 followed by an IP of nascent DNA in a process we call Transcription-Replication IP on Nascent DNA coupled with high-throughput sequencing (TRIPn-Seq).
Results: TRIPn-Seq defined the locations of 1009 independent TRI loci in rapidly proliferating mouse primary B cells. TRIs are associated with flanking RNA polymerase peaks mapping primarily to transcription start sites, where they often colocalize with R-loop structures and have a high propensity for G quadruplex formation. TRIs are likely difficult to replicate areas at the interface between early replicating regions and nascent transcription. TRIs are also enriched for DNA double-strand breaks that appear during S phase, stalled replication forks, and accumulate mutations in mouse tumors. Genes associated with TRIs are enriched for essential genes involved in early development and post-translational modifications, aging, and cancer.
Conclusion: We propose that replication stress at TRIs induces mutations at transcription start sites that change expression levels which may contribute to age-related phenotypes and tumor formation in mice and humans.

overall_design: TRIPn-Seq was performed on stimulated WT mouse primary B cells to locate transcription-replication interactions (TRIs) genome-wide. Experimental samples were treated with BrdU for 30 minutes to label nascent DNA. RNAP2 ChIP-Seq and DRIP-Seq were also performed to charaterize RNAP2pSer5 and R-loop profiles at TRIs.

middle: P

first: Hongchang

last: Zhao

first: Vrishti

last: Sinha

first: Lionel

last: Sanz

first: Frédéric

middle: H

last: Chédin

first: Jacqueline

last: Barlow


title: Cytokine-like protein 1-induced survival of monocytes suggests a combined strategy targeting MCL1 and MAPK in CMML

status: Public on Jan 23 2021

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

type: Methylation profiling by high throughput sequencing


title: A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis [human]

status: Public on Mar 29 2021

city: Edinburgh

first: Nic

last: Robertson

address: Swann Building, Max Born Crescent

department: Tollervey Lab

country: United Kingdom

institute: University of Edinburgh

summary: Mutations in the human RMRP gene cause Cartilage Hair Hypoplasia (CHH), an autosomal recessive disorder characterized by skeletal abnormalities and impaired T-cell activation. RMRP encodes a non-coding RNA, which forms the core of the RNase MRP ribonucleoprotein complex. In budding yeast, RMRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Analysis of pre-rRNA processing in patient-derived human fibroblasts with CHH-linked mutations showed a similar pattern of processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy, and the first human disorder of rRNA processing to be described.

overall_design: Human K562 cells with FLAG-HIS-tagged protein components of the MRP/P complex were grown in normal media, and RNA:protein interactions stabilised with UVC irradiation. RNAs interacting with tagged proteins were purified by CRAC.

first: Vadim

last: Shchepachev

first: David

last: Wright

first: Tomasz

middle: W

last: Turowski

first: Christos

last: Spanos

first: Aleksandra

last: Helwak

first: Rose

last: Zamoyska

last: Tollervey


title: Cytokine-like protein 1-induced survival of monocytes suggests a combined strategy targeting MCL1 and MAPK in CMML [RNA-Seq]

summary: Mouse models of chronic myeloid malignancies suggest that targeting mature cells of the malignant clone disrupts feedback loops that promote disease expansion. Here, we show that, in chronic myelomonocytic leukemia (CMML), monocytes that accumulate in the peripheral blood show a decreased propensity to die by apoptosis. BH3 profiling demonstrates their addiction to MCL1 (myeloid cell leukemia-1), which can be targeted with the small molecule inhibitor S63845. RNA sequencing and DNA methylation pattern analysis both point also to the implication of the MAPK (mitogen-activated protein kinase) pathway in the resistance of CMML monocytes to death and reveal an autocrine pathway in which the secreted cytokine CYTL1 (Cytokine-like protein 1) promotes ERK (extracellular signal-regulated kinase) activation through CCR2 (C-C chemokine receptor type 2). Combined MAPK and MCL1 inhibition restores apoptosis of CMML patient monocytes and reduces the expansion of patient-derived xenografts in mice. These results designate the combined inhibition of MCL1 and MAPK as a promising approach to slow down CMML progression by inducing leukemic monocyte apoptosis.

overall_design: CMML defective  apoptosis monocytes versus non defective apoptosis monocytes

first: Miguel

last: Torres-Martin

first: Maria

last: Figueroa


title: Transcriptome analysis of a protein-truncating mutation in sortilin-related receptor 1 (sorl1) associated with early-onset familial Alzheimer's disease indicates effects on mitochondrial and ribosome function in young-adult zebrafish brains

status: Public on Jan 11 2021

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

summary: The early cellular stresses which eventually lead to Alzheimer’s disease (AD) remain poorly understood. This is because we cannot access living, asymptomatic human AD brains for detailed molecular analyses. Sortilin-related receptor 1 (SORL1) encodes a multi-domain receptor protein genetically associated with both rare, early-onset familial AD (EOfAD) and common, sporadic late-onset AD (LOAD). SORL1 has been shown to play a role in the trafficking of the amyloid β A4 precursor protein (APP) which is cleaved proteolytically to form one of the pathological hallmarks of AD, amyloid β (Aβ) peptide. However, the other functions of SORL1 are less well understood. Here, we employed a reverse genetics approach to characterise the effect of an EOfAD mutation in SORL1 using zebrafish as a model organism. We performed targeted mutagenesis to generate an EOfAD-like mutation in the zebrafish orthologue of SORL1, and performed RNA-sequencing on mRNA isolated from a family of fish either heterozygous for the EOfAD-like mutation or their wild type siblings and identified subtle effects on the expression of genes likely indicating changes in mitochondrial and ribosomal function.

overall_design: a total of 12 fish were used in this study: 6 wild-type samples and 6 sorl1 W1818*/+ samples (EOfAD-like). These fish arised from the same parents and were raised together in the same tank until 6 months of age.

first: Stephen

middle: M

last: Pederson

first: Morgan

last: Newman

first: Michael

last: Lardelli


title: Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression

first: Yong

last: Cheng


title: Transcriptome profiling of human glioma and normal brain tissues by rRNA-deleted total RNAseq

status: Public on Jan 26 2021

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

institute: Northwestern University Feinberg School of Medicine

summary:
Purpose: To compare the coding and non-coding transcriptomic changes in human gliomas compared with normal brain tissues.
Methods: Biopsies were collected from 85 adult glioblastomas, 18 lower grade gliomas, and 15 normal brain tissues. Total RNA was isolated using the Qiagen RNeasy Mini kit or Trizol reagent according to the manufacturer's instruction. Stranded, rRNA-deleted libraries were prepared using the Illumina stranded Total RNA TruSEQ kit according to the manufacturer's instruction. Sequencing was performed on Illumina HiSeq 4000 instrument according to the manufacturer instructions. Reads were aligned to the human genome GRCh38 using HISAT2 (Version 2.1.0). Read counts for each gene were quantified using HTSeq-count (Version 0.10.0) and then normalized by DESeq2 (r package, version 1.20.0).
Results: Approximately 20 million paired-end reads at the length of 50 bp were obtained from each sample. The genome mapping efficiency was 85% on average for all samples. Altered expression of 6,132 protein-coding genes and 1,270 lncRNAs were identified.
Conclusions:We report the coding and non-coding transcriptomic changes in human gliomas compared with normal brain tissues.

overall_design: 85 adult glioblastomas, 18 lower grade gliomas, and 15 normal brain tissues were characterised by rRNA-depleted total RNAseq.

first: Tianzhi

last: Huang

first: Xuechao

last: Wan

first: Chang

last: Zeng

first: Wei

last: Zhang

first: Bo

last: Hu

first: Shiyuan


title: RNA sequencing analysis of VCaP WT and VCaPrev cells

status: Public on Dec 31 2020

city: Göttingen

first: Oliver

last: Hahn

address: Robert-Koch-Str. 40

department: Department of Urology

institute: University Medical Center Göttingen

summary: Here, we analyze gene expression of prostate cancer cell line VCaP (VCaP WT) and VCaP after testosterone boost (VCaPrev) in order to investigate the impact of the androgen axis on susceptibility to PCA treatments which are not directly AR-directed.

overall_design: VCaP WT vs. VCaP cells after long time treatment with increasing concentrations of testosterone (up to 1 nM). Analysis done in 2 biological replicates

first: Paul

last: Thelen

first: Johanna

last: Becker


title: Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice

status: Public on Jan 04 2021

city: Worcester

first: Richard

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

summary: The outcome of an encounter with Mycobacterium tuberculosis (Mtb) depends on the pathogen’s ability to adapt to the heterogeneous immune response of the host. Understanding this interplay has proven difficult, largely because experimentally tractable small animal models do not recapitulate the heterogenous disease observed in natural infections. We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to associate bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection and represent reproducible models of qualitatively distinct immune states. Global analysis of Mtb mutant fitness across the CC panel revealed that a large fraction of the pathogen’s genome is necessary for adaptation to specific host microenvironments. Both immunological and bacterial traits were associated with genetic variants distributed across the mouse genome, elucidating the complex genetic landscape that underlies host-pathogen interactions in a diverse population.

overall_design: Subject mice (48 Collaborative Cross strains, 8 Collaborative Cross parents, 4 k/o strains) were infected via tail vein injection with a saturated M. tuberculosis himar1 transposon library. Animals were sacrificed after 4 weeks, or earlier if moribund, and Tn-Seq was performed after library recovery from harvested spleens. In the majority of cases, two replicates were obtained per mouse  strain, 6 replicates in the case of in vitro-grown libraries.

first: Clare

last: Smith

first: Megan

middle: K

last: Proulx

first: Bibhuti

middle: B

last: Mishra

first: Jarukit

last: Long

first: Sae

last: Park

first: Ha-Na

last: Lee

last: Kiritsy

first: Michelle

last: Bellerose

first: Andrew

last: Olive

first: Kenan

last: Murphy

first: Kadamba

last: Papavinasasundaram

first: Frederick

last: Boehm

first: Charlotte

last: Reames

first: Rachel

last: Meade

first: Brea

last: Hampton

first: Colton

last: Linnertz

first: Ginger

middle: D

last: Shaw

first: Pablo

last: Hock

first: Timothy

last: Bell

first: Sabine

last: Ehrt

first: Dirk

last: Schnappinger

first: Fernando

last: de Villena

first: Martin

middle: T

last: Ferris

first: Thomas

middle: R

last: Ioerger

first: Christopher

last: Sassetti


title: TrAEL-seq for CUP1 locus

status: Public on Jan 21 2021

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: 1) The Pgal-3HA cup1 yeast strain, in which all  CUP1 ORFs are replaced with 3HA and all CUP1 promoters are replaced by GAL1-10 promoters (PMID: 28654659, which carries ~17 tandem repeats of the modified Pgal-3HA cup1 repeat) undergoes extensive CNV when shifted to galactose. Here we use TrAEL-seq to look for replication fork stalling in this strain with and without induction.   2) We also profile the impact on replication of integrating an ARSH4 origin upstream of the RSC30 gene (so outside the CUP1 locus), using the 3xCUP1 strain which carries 3 repeats of CUP1 (PMID: 28654659). The origin was integrated with a URA3 marker, the control strain has the URA3 marker but no origin.

overall_design: 1) Cells were pre-grown on YPraffinose, then resuspended in fresh YP 2% raffinose supplemented with nothing, 0.02% galactose, 2% galactose or 2% glucose as specified. Cells were harvested after 5 hours by resuspension in 70% ethanol.  2) Cells were grown in SC glucose and harvested by re-suspension in 70% ethanol.

first: Alex

last: Whale

first: Michelle

last: King

first: Jonathan

last: Houseley


title: Differential expression of circular RNA in oral leukoplakia: novel potential biomarkers exploration for diagnosis and prognosis of precancer

status: Public on Dec 16 2020

city: Shanghai

first: Zhou

last: haiwen

address: 500 Qu-xi Road, Shanghai

department: Oral Mucosal Diseases

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

summary: 6 pairs of OLK tissues and normal oral mucusal (NOM) tissues were obtained to detect circRNAs expression.The profile data showed that 366 circRNAs were significantly dysregulated in the OLK tissues, including 65 upregulated and 301 downregulated circRNA transcripts.There are 28 circRNAs were discovered firstly. 7 out of 10 selected circRNAs were further validated using Qrt-PCR

overall_design: Examination of different circular RNA expression in 2 tissue types.  Control samples are identical to healthy oral mucosa samples in GSE131182.

last: Haiwen

first: Xu

last: Siming


title: Lap2α is required for MRTF-A-SRF transcriptional activity

status: Public on Dec 15 2020

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

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

overall_design: Refer to individual Series


title: Lap2α is required for MRTF-A-SRF transcriptional activity [RNA-seq]

summary: Myocardin-related transcription factor A (MRTF-A) in complex with the serum response factor (SRF) regulates the expression of cytoskeletal genes in response to cytoplasmic and nuclear actin dynamics. Different components of nucleoskeleton, besides nuclear actin, also regulate the activity of MRTF-A. Here we extend these studies by showing that lamina-associated polypeptide 2α (Lap2α), the nucleoplasmic isoform of Lap2, is a novel regulator, and a direct binding partner of MRTF-A. Lap2α is a nucleoplasmic protein that interacts with A-type lamins and the retinoblastoma protein (pRb) and contributes to chromatin organization. Unlike other known MRTF-A regulators, Lap2α is not required for MRTF-A nucleo-cytoplasmic shuttling; it functions within the nucleus where it binds MRTF-A directly via its unique C-terminal domain prior to MRTF-A forming the complex with chromatin and SRF. Such interaction affects MRTF-A transcriptional activity since genome-wide analysis revealed reduced binding of MRTF-A to SRF target genes in Lap2α  knockout cells compared to control cells that consequently led to impaired expression of target genes. Our studies therefore add another regulatory layer to the control MRTF-A-SRF-mediated gene expression, and broaden the role of Lap2α in transcriptional regulation.

overall_design: To investigate the effect of Lap2 knockdown on gene expression, we performed RNA sequencing (RNA-seq) analysis of control and Lap2-depleted cells cultivated in serum-starved (0.3% FBS) conditions and after 45 min of serum stimulation (15% FBS) in triplicates.

first: Ekaterina

last: Sidorenko


title: Lap2α is required for MRTF-A-SRF transcriptional activity [ChIP-seq]

overall_design: To study the role of Lap2α in the regulation of MRTF-A activity, we examined MRTF-A-chromatin interaction in Lap2α WT and KO MDFs. We performed chromatin immunoprecipitation (ChIP) followed by deep sequencing (ChIP-seq) of MRTF-A in MDFs under serum starved (0.3% FBS) condition and 45 min after serum stimulation (15% FBS). In addition, Pol II phosphorylated at serine 5 (Pol II S5P) was included to monitor transcription activation of serum-inducible genes.


title: BACH2 Establishes the Transcriptional and Epigenetic Programs of Stem-Like CD8 T cells

status: Public on Dec 14 2020

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: During chronic infection and cancer, a self-renewing CD8 T cell subset maintains long-term T-cell immunity and mediate the response induced by immunotherapy. These stem-like CD8 T cells diverge from other CD8 subsets early in the immune response and display distinct transcriptional and epigenetic signatures. Here, we show that locus encoding transcriptional factor BACH2 is transcriptionally and epigenetically active in stem-like CD8 T cells but not in terminally exhausted CD8 T cells. Overexpression of BACH2 enforces the stem-like cell fate, whereas Bach2 deficiency impairs stem-like CD8 T cell differentiation. Using single-cell transcriptomics and epigenomics approaches, we demonstrate BACH2 as a key regulator of the transcriptional and epigenetic programs of stem-like CD8 T cells. In addition, BACH2 suppresses genes and pathways that drive terminal exhaustion through transcriptional repression and epigenetic silencing. Thus, our study reveals a novel pathway responsible for establishing the unique transcriptional and epigenetic program of stem-like CD8 T cells.

overall_design: ATAC-Seq analysis of stem-like and terminally exhausted antigen-specific CD8 T cells after chronic viral infection. Single-cell RNA-Seq, RNA-Seq, and ATAC-Seq analysis of control, BACH2 over expression, and BACH2 deficient antigen specific CD8 T cells after chronic viral infection.

first: Y

last: Chen

first: H

first: T

middle: Q

last: Wu


title: RNA sequencing of tumors from PPM1D transgenic mouse model

city: Stockholm

first: Per

last: Kogner

address: Tomtebodavägen 18a

department: Dept of Women's and Children's Health

country: Sweden

institute: Karolinska institutet

summary: The majority of cancers harbor alterations of the tumor suppressor TP53. However, childhood cancers, including unfavorable neuroblastoma, often lack TP53 mutations despite frequent loss of p53 function, suggesting alternative p53 inactivating mechanisms. Our study show that frequent gain of the p53-regulating gene PPM1D at chromosome 17q22.3 is linked to aggressive tumors and poor prognosis in neuroblastoma. A PPM1D transgenic mouse model develops cancers phenotypically and genetically similar to tumors arising in mice with dysfunctional p53 when subjected to low-dose irradiation. Tumors include T-cell lymphomas harboring Notch1- and Pten-mutations, adenocarcinomas and PHOX2B-expressing neuroblastomas, therey establishing PPM1D as a bona fide oncogene in wtTP53 cancer and childhood neuroblastoma. Pharmacological inhibition of WIP1 suppressed the growth of neural tumors in nude mice, proposing WIP1 as a therapeutic target in neural childhood tumors.

overall_design: Transgenic mice overexpressing PPM1D were subject to low-dose radiation and subsequently developed thymic lymphomas. Bulk RNA sequencing was performed on a total of 24 samples from 24 mice: 14 thymic lymphomas and 10 controls (thymic tissue from healthy mice). Controls were divided into four groups based on irradiation status and genotype: wild-type non-irradiated (n = 3), PPM1D-transgenic non-irradiated (n = 3), wild-type irradiated (n = 2), PPM1D-transgenic irradiated (n = 2). mRNA libraries were generated using the TruSeq Stranded cDNA kit (Illumina) and sequenced on the HiSeq 2500 platform for paired-end reads with a length of 100-125 bp for all samples.

first: Jelena

last: Milosevic

first: Thale

last: Olsen


title: Single-cell transcriptomic analysis of the adult mouse spinal cord reveals fundamental molecular diversity of autonomic and skeletal motor neurons

city: Stanford

first: Aaron

last: Gitler

state: California

address: Beckman Center

department: Genetics

institute: Stanford University

summary: To characterize the diversity of cholinergic neurons in the spinal cord, we performed single-nucleus RNA sequencing on cholinergic-enriched pools of nuclei from the adult mouse.

overall_design:
Enrichment: Nuclei were enriched by fluorescence-activated nuclei sorting (FANS) of GFP+ cholinergic nuclei from reporter mice.
Barcoding: Nuclei were loaded into a 10X Chromium device and barcoded via oligo-dT reverse transcription using the V3 chemistry. Library prep: Libraries were prepared by PCR and size-exclusion according to published 10X protocols. Sequencing: Libraries were sequenced using NextSeq 550 high-throughput, 150-cycle kits and NovaSeq 100-cycle kits.

first: Jacob

middle: A

last: Blum

first: Sandy

last: Klemm

first: Jennifer

last: Shadrach

first: Kevin

last: Guttenplan

first: Lisa

last: Nakayama

first: Arwa

last: Kathiria

first: Phuong

last: Hoang

first: Olivia

last: Gautier

first: Julia

last: Kaltschmidt

first: William

last: Greenleaf


title: Sodium arsenite exposure inhibits histone acetyltransferase p300 for attenuating H3K27ac at enhancers in mouse embryonic fibroblast cells

status: Public on Dec 10 2020

city: Boston

first: Yanqiang

last: Li

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary: Both epidemiological investigations and animal studies have linked arsenic-contaminated water to cancers, in- cluding skin, liver and lung cancers. Besides genotoxicity, arsenic exposure-related pathogenesis of disease is widely considered through epigenetic mechanisms; however, the underlying mechanism remains to be deter- mined. Herein we explore the initial epigenetic changes via acute sodium arsenite (As) exposures of mouse em- bryonic fibroblast (MEF) cells and histone H3K79 methyltransferase Dot1L knockout (Dot1L− /−) MEF cells. Our RNA-seq and Western blot data demonstrated that, in both cell lines, acute As exposure abolished histone acetyl- transferase p300 at the RNA level and subsequent protein level. Consequently, p300-specific main target histone H3K27ac, a marker separating active from poised enhancers, decreased dramatically as validated by both West- ern blot and ChIP-qPCR/seq analyses. Concomitantly, H3K4me1 as another well-known marker for enhancers also showed significant decreases, suggesting an underappreciated crosstalk between H3K4me1 and H3K27ac involved in As exposure. Significantly, As exposure-reduced H3K27ac and H3K4me1 inhibited the expression of genes including EP300 itself and Kruppel Like Factor 4(Klf4) that both are tumor suppressor genes. Collectively, our investigations identified p300 as an internal bridging factor within cells to sense external environmental As exposure to alter chromatin, thereby changing gene transcription for disease pathogenesis.

overall_design: RNA-seq were performed for the control and low dose As treated MEF cell and Dot1L mutant to explore the  whole genome wide transcriptional response to the low dose As. In addition, we also investigated changes in histone mark  H3K27ac occupancy at the MEF and As treated MEF cells to see the histone change at the enhancer or promoter reigions of the differentially expressed genes.

first: Zhibin

last: Wang


title: Molecular bases of strain-specific responses of Phaseolus vulgaris roots to symbiotic bacteria with different efficiency in nitrogen-fixing symbiosis

city: LAUSANNE

first: JOAQUIN

last: CLUA

address: BIOPHORE

department: DBMV

country: Switzerland

institute: UNIL

summary: Some legume plants can establish a nitrogen-fixing symbiosis with rhizobia. Compatibilty between rhizobia and legumes is determined at species-specific level, but there are variations on the efficiency of the process determined by the capacity of the plant to select specific strains that are better partners in terms of the biological outcome. In this work we used a model system based in the coevolution of two genetic pools of common bean (Phaseolus vulgaris) with strains of R. etli that establish a more efficient interaction to study the transcriptional changes occurring in roots at an early time of the interaction.

overall_design: Phaseolus vulgaris roots of NAG12 and ALUBIA accessions were inoculated with Yeast Extract Mannitol media as a control (CTL), or the following R. etli strains: SC15, CE3, 55N1 and 124N1. Root tissue samples were collected 24 hours post inoculation.

first: Joaquín

last: Clúa

first: Claudio

last: Rivero

first: Carla

last: Roda

first: Carolina

last: Giorgis

first: Soledad

last: Donna

first: María

last: Zanetti

first: Flavio

last: Blanco


title: PPAR[gamma]2 exerts a tumor suppressive effect in human prostate cancer

city: NanJing

first: Zhengdong

last: Zhang

address: 101 Longmian Avenue

department: Department of Environmental Genomics, School of Public Health

institute: Nanjing Medical University

summary: The nuclear receptor PPAR[gamma] is a master regulator controlling energy metabolism and cell fate in the prostate. One advanced human prostate cancer cell line PC3 was used to examine the effects of restoration of PPAR[gamma]2 action.  Restoration of PPAR[gamma]2 action in PC3 cells inhibited cell proliferation and migration. PC3-PPAR[gamma]2 cDNA recombinants showed necrosis in cancer region and lymphocyte infiltration in surrounding stroma by H&E staining. They expressed low microtubules associated protein 1 light chain 3 (LC3), and high mixed lineage kinase domain-like (MLKL), CD4 and CD8 protein expression levels compare to the control by IHC staining. Gain-of-function of PPAR[gamma]2 in PC3 cells resulted in reprogramming of lipid and energy metabolism-associated signaling pathways by microarray analysis. These data are consistent with the idea that PPAR[gamma] action specific to PPAR[gamma]2, exerts a crucial tumor suppressive role on triggering autophagy and necroptosis in human prostate cancer initiation and progression.

overall_design: The expression and functional profiles of genes were compared between PC3 cells expressing PPAR[gamma]2 cDNA and empty vector. There were 3 replicates in each group.

first: Yonghui

first: Fulu

last: Dong

first: Ming

last: Jiang


title: Array comparative genomic hybridization analysis of metastatic lung tumors

status: Public on Dec 04 2020

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary:
Comparative genomic hybridization analysis for detection of recurring gene copy number variation (CNV) among a set of lung cancer mestastatic brain tumors
DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled Agilent characterized normal human reference DNA

overall_design: Twenty-seven de-identified, fresh-frozen surgically resected lung metastatic brain tumors were analyzed. The work was approved by the Wayne State University Institutional Review Board. Genomic DNA was isolated using the EZ1 Advanced workstation and DNA Tissue Kit (Qiagen, Germantown, MD). A Trinean DropSense96 Spectrophotometer (PerkinElmer, Waltham, MA) and TapeStation (Agilent, Santa Clara, CA) were used to measure DNA quantity and quality. aCGH analysis employed the Agilent SureScan platform and SurePrint G3 Cancer CGH+SNP (4x180K) microarrays following manufacturer’s recommendations. Agilent’s characterized normal human DNA (male or female, used according to patient gender) was the reference sample. Tumor sample DNA was labeled with Cy5 and normal reference DNA was labeled with Cy3. Probe fluorescence intensity data was extracted from scanned microarray images using Agilent Cytogenomics software. GC Correction, Diploid Peak Centralization (normalization) and Aberration Detection Method 2 (quality control) algorithms were also applied using this software. Aggregate data (all 27 samples) were analyzed using Nexus Copy Number software (Biodiscovery, El Segundo, CA).


title: Opposing genetic and immune mechanisms shape oncogenic programs in synovial sarcoma

status: Public on Dec 08 2020

city: Cambridge

first: Livnat

last: Jerby

address: 415 Main street

institute: Broad Institute of MIT and Harvard

summary: Synovial sarcoma (SyS) is an aggressive neoplasm driven by the SS18-SSX fusion, and characterized by low T cell infiltration. Here, we studied the cancer-immune interplay in SyS using an integrative approach that combines single-cell RNA-seq (scRNA-seq), spatial profiling, genetic and pharmacological perturbations. scRNA-Seq of 16,872 cells from 12 human SyS tumors uncovered a malignant subpopulation that marks immune deprived niches in situ and marks tumors with poor clinical outcomes in three independent cohorts. Functional analyses revealed that this malignant cell state is controlled by the SS18-SSX fusion, repressed by cytokines secreted by macrophages and T cells, and can be synergistically targeted with a combination of HDAC and CDK4/6 inhibitors. This drug combination enhanced malignant cell immunogenicity in SyS models, leading to induced T cell reactivity and T-cell-mediated killing. Our study provides a blueprint for investigating heterogeneity in fusion-driven malignancies and demonstrates an interplay between immune evasion and oncogenic processes that can be co-targeted in SyS and potentially in other malignancies.

overall_design:
Individual cells were dissociated from fresh tumor resections and profiled with a modified full length SMART-Seq2 protocol and with a droplet-based (10x) approach.

Raw data is to be made available through DUOS (controlled access) due to patient privacy concerns.

first: Cyril

last: Neftl

first: Marni

last: Shore

first: Matthew

middle: J

last: McBride

first: Brian

last: Haas

first: Benjamin

last: Izar

first: Angela

last: Volorio

first: Gaylor

last: Boulay

first: Luisa

last: Cironi

first: Alyssa

last: Richman

first: Liliane

middle: C

last: Broye

first: Joseph

last: Gurski

first: Christina

last: Luo

first: Ravindra

last: Mylvaganam

first: Lan

last: Nguyen

first: Shaolin

last: Mei

first: Johannes

middle: c

last: Melms

first: Christophe

last: Georgescu

first: Ofir

last: Cohen

first: Jorge

last: Buendia

first: Michael

middle: S

last: Cuoco

first: G

last: Nielsen

first: Ivan

last: Chebib

first: Gregory

last: Cote

first: Edwin

last: Choy

first: Igor

last: Letovanec

first: Stéphane

last: Cherix

first: Nikhil

last: Wagle

first: Peter

last: Sorger

first: Alex

last: Haynes

first: John

last: Mullen

last: Stamenkovic

first: Miguel

middle: N

last: Rivera

first: Cigall

last: Kadoch

first: Orit

last: Rozenblatt-Rosen

first: Nicolo

last: Riggi

first: Mario

last: Suva

first: Aviv

last: Regev


title: Cytokine-like protein 1-induced survival of monocytes suggests a combined strategy targeting MCL1 and MAPK in CMML [Bisulfite-Seq]

first: Qin

last: Yang

address: 1501 NW 10th Avenue

institute: University of Miami Miller School of Medicine

summary: Mouse models of chronic myeloid malignancies suggest that targeting mature cells of the malignant clone disrupts feedback loops that promote disease expansion. Here, we show that, in chronic myelomonocytic leukemia (CMML), monocytes that accumulate in the peripheral blood show a decreased propensity to die by apoptosis. BH3 profiling demonstrates their addiction to MCL1 (myeloid cell leukemia-1), which can be targeted with the small molecule inhibitor S63845. RNA sequencing and DNA methylation pattern analysis both point also to the implication of the MAPK (mitogen-activated protein kinase) pathway in the resistance of CMML monocytes to death and reveal an autocrine pathway in which the secreted cytokine CYTL1 (Cytokine-like protein 1) promotes ERK (extracellular signal-regulated kinase) activation through CCR2 (C-C chemokine receptor type 2). Combined MAPK and MCL1 inhibition restores apoptosis of CMML patient monocytes and reduces the expansion of patient-derived xenografts in mice. These results designate the combined inhibition of MCL1 and MAPK as a promising approach to slow down CMML progression by inducing leukemic monocyte apoptosis.

overall_design: CMML defective  apoptosis monocytes versus non defective apoptosis monocytes

last: Torres-Martin

first: Maria

middle: E

last: Figueroa


title: Targeting p300/CBP axis in lethal prostate cancer

status: Public on Dec 03 2020

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

summary: Treating CRPC remains challenging due to persistent AR signaling. Inhibiting transcriptional AR co-activators is an attractive therapeutic strategy. CCS1477, an inhibitor of p300/CBP, alters the transcriptome of Prostate Cancer cell models

overall_design: Transcriptional Alterations in prostate cancer models after treatment with p300/CBP inhibitor, BET inhibitor, or control

first: Adam

last: Sharp


title: CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains [RNA-seq]

status: Public on Nov 25 2020

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

summary: Insulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that potent insulation is provided by multiple CTCF binding sites. Furthermore, CTCF-mediated insulation is dependent on DNA sequences adjacent to its core binding motifs, and CTCF binding sites from topologically associating domains (TAD) boundaries are more likely to function as insulators than those outside TAD boundaries independent of binding strength. Using chromosomal conformation capture assays and high resolution chromatin imaging techniques, we demonstrate that insulators reduce enhancer-promoter contacts by forming local chromatin domains. Taken together, our results provide strong genetic, molecular and imaging evidence connecting chromatin topology to action of insulators in the mammalian genome.

overall_design:
Chromosome coordinates of variants:
'4CBS' was inserted between chr3:34,726,762-34,727,258; mm10
'4CBS downstream' was inserted between chr3:34,794,087-34,794,154; mm10.
Examination of insulator activity of CTCF binding seqences and their effects on chromatin topology in mouse embryonic cells

first: Huang

last: Hui

first: Ren

last: Bing


title: Histone acetylation modification analysis in uveal melanoma cells and normal melanocytes.

first: AI

last: ZHUANG

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

summary: In order to study the histone modification differences in uveal melanoma cells and normal melanocytes.

overall_design: Examination of histone acetylation modifications in 2 cell types.

first: A

last: Zhuang

first: P

last: Chai

first: X

last: Fan


title: TET2 regulates tRNA fragment generation by RNA hydroxymethyl modification

status: Public on Nov 18 2020

first: Roberto

last: Bonasio

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

type: Non-coding RNA profiling by high throughput sequencing

summary: Using CLIP-seq, hm5C RIP-seq, and small RNA-seq, we show that TET2 binds to tRNAs in mouse embryonic stem cells at sites enriched for hm5C. Loss of TET2 causes decreased hm5C on tRNAs and abrogation of all TET activity led to changes in 5' and 3' tRNA fragments.

overall_design: This  series includes samples for three experiments: CLIP-seq (two biological replicates each for two independent His-HA-TET2 clones plus input controls); RIP-seq (two biological replicates each for hm5C RIP-seq and input controls); and small RNA-seq (three biological replicates each from WT, E14, and 2 independent sets of replicates for Tet2 KO).

first: Chongsheng

last: He

first: Andrea

last: Schorn


title: miRNA content from human and mouse epicardial extracellular vesicles

city: Madrid

first: Cristina

middle: Villa

last: del Campo

state: Madrid

address: Melchor Fernandez Almagro, 3 Pabellon 18, CNIC

country: Spain

institute: CNIC

summary: The goal of the present study is to determine the miRNA cargo present in epicardial extracellular vesicles. For that, epicardial cells and human primary epicardial cells were cultured. Conditioned media was isolated from mouse epicardial cells and human primary epicardial cells derived from right atrial appendages in two different states: “cobble” (inactive) cells and “spindle” (active) . RNA from EVs was isolated and sequenced to determine the miRNA content profile.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination on miRNA content in epicardial Evs

last: Villa del Campo

first: Norman

last: Liaw

first: Gabriela

last: Salinas

first: Wolfram

last: Zimmermann

first: Paul

last: Riley


title: A SMAD4-modulated gene profile predicts disease-free survival in stage II and III colorectal cancer

status: Public on Nov 11 2020

city: MIAMI

first: Xi

last: CHEN

address: 1120 NW 14th Street

institute: University of Miami

summary:
Loss of SMAD4 is associated with worse outcomes for colorectal cancer patients. We used gene ontology and data driven approach to identify a SMAD4-modulated profile and test its association with patient outcome.
Using a discovery dataset of 250 colorectal cancer patients, we analyzed expression of BMP/Wnt target genes for association with SMAD4 expression. Promoters of the BMP/Wnt genes were interrogated for SMAD-binding elements. 15 genes were implicated and three tested for modulation by SMAD4 in patient-derived colorectal cancer tumoroids. Expression of the 15 genes was used for unsupervised hierarchical clustering of a training dataset and two resulting clusters modeled in a centroid model.

overall_design: In a discovery set of tumors from 250 CRC patients from VUMC and Moffitt Cancer Center, SMAD4 expression levels  were obtained from the data generated by the Affymetrix U133 Plus 2.0 Array platform. We examined the correlation of expression levels of the genes in the BMP/Wnt combined list with SMAD4 expression levels to identify significant probes. Second, to identify BMP/Wnt target genes with SMAD4-binding sites in the promotor region, we used the ExPlain Analysis System (Biobase) to retrieve promoter sequences and examine them for SMAD-binding elements (SBEs). We then determined which probes and corresponding genes from the SBE analysis were correlated with SMAD4 expression. The probes and genes from these two approaches were combined and this was carried forward as the SMAD4-modulated profile

last: Chen

first: J

last: Smith


title: Single-cell analysis of accessible chromatin in human mammary epithelial cells using scATAC-seq [scATAC-seq]

status: Public on Nov 09 2020

city: San Antonio

first: Meena

last: Kusi

state: TX

address: 7703 Floyd Curl Dr

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: Epigenome delineates lineage-specific transcriptional programs and restricts cell plasticity to prevent non-physiological cell fate transitions. Although cell diversification fosters tumor evolution and therapy resistance, upstream mechanisms that regulate the stability and plasticity of cancer epigenome remain elusive. Here, we show that 2-hydroxyglutarate (2HG) not only suppresses DNA repair but also mediates high-plasticity chromatin landscape. A combination of single-cell epigenomic and multi-omic approaches demonstrates that 2HG disarranges otherwise well-preserved stable nucleosome positioning and promotes cell-to-cell variability. 2HG induces loss of motif accessibility to luminal-defining transcriptional factors FOXA1, FOXP1 and GATA3 and a shift from luminal to basal-like gene expression. Breast tumors with high 2HG exhibit enhanced heterogeneity with undifferentiated epigenomic signatures linked to adverse patient prognosis. Further, ascorbate-2-phosphate (A2P) eradicates heterogeneity and impairs growth of high 2HG-producing breast cancer cells. These findings suggest 2HG as a key determinant of cancer plasticity and provide a rational strategy to counteract tumor cell evolution.

overall_design: Profiles of single-cell epigenomes were assayed using scATAC-seq across 3 samples.

first: Kohzoh

last: Mitsuya

first: Tim

middle: H

last: Huang


title: Single-cell analysis of accessible chromatin using scATAC-seq and transcriptome analysis using RNA-seq in human mammary epithelial cells

status: Public on Nov 17 2020

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

overall_design: Refer to individual Series


title: Heritable Pattern of Oxidized DNA Base Repair Coincides with Pre-Targeting of Repair Complexes to Open Chromatin

status: Public on Nov 03 2020

city: Houston

first: Sankar

last: Mitra

state: Texas

address: 6445 Main Street

department: Houston Methodist Cancer Center

institute: Houston Methodist Resrarch Institute

summary: Human genome stability requires efficient repair of oxidized bases, which is initiated via damage recognition and excision by NEIL1 and other base excision repair (BER) pathway DNA glycosylases (DGs). However, the biological mechanisms underlying detection of damaged bases among the million-fold excess of undamaged bases remain enigmatic. Indeed, mutation rates vary greatly within individual genomes, and lesion recognition by purified DGs in the chromatin context is inefficient. Employing super-resolution microscopy and coimmunoprecipitation assays, we find that acetylated NEIL1 (AcNEIL1), but not its nonacetylated form, is predominantly localized in the nucleus in association with epigenetic marks of uncondensed chromatin. Furthermore, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) revealed non-random AcNEIL1 binding near transcription start sites of weakly transcribed genes and along highly transcribed chromatin domains. Bioinformatic analyses revealed a striking correspondence between AcNEIL1 occupancy along the genome and mutation rates, with AcNEIL1-occupied sites exhibiting reduced mutations compared to AcNEIL1-free domains, both in cancer genomes and in population variation. Intriguingly, from the evolutionarily-conserved unstructured domain that targets NEIL1 to open chromatin, its damage surveillance of highly oxidation-susceptible sites to preserve essential gene function and to limit instability and cancer likely originated ~500 million years ago during the buildup of free atmospheric oxygen.

overall_design: Mapping acetylated NEIL1 in HCT116 cells

first: Albino

last: Bacolla

first: Shiladitya

last: Sengupta

first: Zu

last: Ye

first: Chunying

last: Yang

first: Joy

first: Ruth

last: De-Paula

first: Muralidhar

middle: L

last: Hegde

first: Zamal

last: Ahmed

first: Matthew

last: Mort

first: David

last: Cooper

first: John

last: Tainer


title: Expression profile of circular RNAs in oral squamous cell carcinoma

status: Public on Oct 28 2020

first: Zhou

last: haiwen

address: 500 Qu-xi Road, Shanghai

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

summary: We analyzed the circRNA expression profile in 6 pairs of samples of OSCC and normal oral mucosa tissues. The results showed that among the 122 DE circRNAs, 109 circRNAs were up-regulated and 13 circRNAs were down-regulated. 8 out of 10 selected circRNAs were validated by qRT-PCR. GO and KEGG analysis indicated identified DE circRNAs might be involved in the progression of OSCC.

overall_design: Examination of different circular RNA expression in 2 tissue types.

first: Xu

last: Siming


title: Small RNA libraries from epidermal stem cell (ESC) and fibroblast (Fb) derived exosomes

status: Public on Oct 29 2020

first: Aristidis

last: Veves

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

summary: We employed high-throughput sequencing to profile the non-coding RNA content of primary ESC and Fb derived exosomes. All 6 libraries were sequenced to a comparable depth (ESC1: 12.3M, ESC2: 14M, ESC3: 12.8M, FB1: 14.7M, FB2: 13.7M, FB3: 12.3M) and exhibited a very low proportion of adapter-only reads or fragments shorter than 17bp (4.4 ± 0.5% ), showing efficient fragment incorporation during library preparation. All libraries had high small RNA content (>50% successfully aligned and assigned to small RNAs). ESC libraries had significantly higher small RNA content (ESC: 84.5 ± 0.005% vs FB: 60.5 ± 0.05%, p<0.05, two-sided Welch’s t-test). ESC samples show remarkably higher proportions of miRNAs (~9-fold higher, p=3.6*10-5 ) and snRNAs (~12-fold higher, p=0.002) compared to Fb. Fibroblasts exhibited higher RPM of reads mapping on lncRNAs (4-fold, p=0.052)

overall_design: Non-coding RNA-seq was performed on three biological replicates each of mouse epidermal stem cell (ESC) and dermal fibroblast (Fb) derived exosomes

first: Georgios

last: Theocharidis

first: Ioannis

last: Vlachos


title: Myocardial adaptations in advanced kidney disease

status: Public on Oct 27 2020

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

summary: Molecular changes underlying the failing heart in chronic kidney disease (CKD) remains largely undefined. To date, a severe paucity of translational studies investigating these changes utilizing human heart tissues from kidney failure patients exists. Moreover, no studies have examined alterations of the cardiac cytoskeleton in CKD, despite its central role in regulating organelle function, bioenergetics and myocardial remodeling. In this 3-arm cross-sectional controlled cohort study, we compared donor heart tissues from dialysis patients, to patients with hypertension with relatively preserved GFR, and healthy controls. We present evidence for transcriptomic changes in the hearts of dialysis patients, involving cytoskeletal dysregulation and dysfunction of mitochondrial bioenergetics.

overall_design: We conducted a 3-arm observational cross-sectional controlled cohort study of explanted human heart tissues. 109 donor hearts were collected, 50 met eligibility criteria for inclusion from hemodialysis-dependent patients (HD), hypertension (HTN) with relatively preserved GFR and healthy controls. Left ventricular tissues were subjected to pathologic examination and RNA-sequencing.

first: Kenneth

last: Lim

first: Tzongshi

last: Lu


title: Characterization of Rare Spindle and Root Cell Transcriptional Profiles in the Stria Vascularis of the Adult Mouse Cochlea

first: Michael

last: Hoa

address: 35 Convent Dr, Rm 1F-226

institute: National Institutes on Deafness and Other Communication Disorders, NIH

summary: snRNA-Seq using sample preservation distinguishes rare spindle and root cell transcriptional profiles

overall_design:
2 samples, Stria vascularis dissected from adult CBA/J mice per experiment

Grant information: ZIA DC000088-05

first: Shoujun

last: Gu

first: Rafal

last: Olszewski

first: Ian

last: Taukulis

first: Zheng

last: Wei

first: Daniel

last: Martin

first: Robert

last: Morell


title: RNA expression profile of adult male and female blood brain barrier (BBB)  cells of Drosophila melangaster

status: Public on Oct 31 2020

city: Northbrook

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: The RNA profile of BBB cells of adult male and female Drosophila was determined to examine the molecular basis of BBB contribution to sex-specific behavior

overall_design: Subperineurial glial cells of the blood brain barrier were marked by expression of UAS-dsRed driven by SNG-Gal4. Marked cells were hand-dissected from matched adult 4d old males and females. RNA was extracted and analyzed.

first: Chamala

last: Lama

first: Brigitte

last: Dauwalder


title: The effects of H3.3K27M mutation on developing mouse brain and cooperation with Trp53 on enhancing tumorigenesis in the genetic model of H3.3K27M

city: Toronto

first: Cynthia

last: Hawkins

state: Ontario

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

type: Genome variation profiling by high throughput sequencing


title: The effects of H3.3K27M mutation on developing mouse brain and cooperation with Trp53 on enhancing tumorigenesis in the genetic model of H3.3K27M [RNA-Seq]

summary: Diffuse intrinsic pontine gliomas (DIPG) are devastating pediatric brain tumors for which there is no effective therapy. A lack of pre-clinical genetic models has affected efforts to develop therapies targeted to DIPG. Over 60% of DIPG patients carry a mutation in the histone H3F3A gene (H3.3K27M) that is often accompanied by a mutation in the TP53 gene.  Here we created a genetic model in which H3.3K27M is expressed under the mouse Fabp7 promoter. These mice have disrupted embryonic development and increased susceptibility to development of lymphomas. Crosses to Trp53 knockout mice further accelerated lymphomagenesis and led to brain tumour development. Some but not all tumours acquired additional oncogenic alterations. The brain tumours faithfully recapitulate the expression profiles of DIPG patients, and brain tumours and lymphomas share significant similarities in pathway alterations, pointing to a core H3.3K27M transcriptome. Overall, this mouse model provides key insights into how H3.3K27M mutations regulate DIPG at the cellular and tumour level.

overall_design: H3.3K27M mice were generated by microinjection. We performed genome-wide RNA-Seq on mid/hind-brains isolated from WT (n=3) and H3.3K27M (n=3) E14.5 embryos, on brains of adult H3.3K27M mice (n=3) and tumours isolated from H3.3K27M mice (brain tumours, n=2; lymphomas, n=3) for a total of 14 samples.

last: Siddaway

first: Sanja

last: Pajovic


title: Chronic Aryl Hydrocarbon Receptor Activity Causes Adverse Muscle Affect: Implications for Smoking-induced Muscle Impairment

status: Public on Oct 23 2020

city: Gainesville

first: VIJAYENDRAN

last: CHANDRAN

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

institute: University of Florida

summary:
Purpose: The goal of this study was to analyze the gene expression levels by RNA sequencing from the plantaris muscle of mice exposed to normal air or tobacco smoke for 16 weeks.
Methods: Plantaris muscles were removed, flash frozen, and RNA was harvested using the RNeasy Tissue Mini Kit (Qiagen), according to manufacturer’s instructions. RNA was reverse transcribed to complementary DNA (Lexogen QuantSeq 3′ FWD), and sequenced on a HiSeq 4000 instrument (Illumina).
Results: Gene clusters representing neurogenesis/axon development, neuronal projection/synapse, and myofibril/sarcomere/muscle differentiation were amongst the most affected by chronic tobacco smoke exposure. In addition, mitochondrial network genes and neuromuscular genes were down-regulated in smoke-exposed mice.
Conclusions: Chronic tobacco smoke exposure in mice reprograms the skeletal muscle transcriptome, with a reduction in mitochondrial and neuromuscular junction genes being consistent with mitochondrial respiratory impairment and neuromuscular junction degeneration observed at whole tissue level.

overall_design: Plantaris muscle mRNA profiles of wild type mice exposed to tobacco smoke for 16 weeks

first: Russell

last: Hepple

first: Vijayendran

last: Chandran


title: Role of PTEN in B-ALL

status: Public on Oct 13 2020

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

summary: To elucidate the dependence of B-ALL cells on PTEN we analysed the transcriptional changes upon inducible Pten KO in BCR-ABL1 transformed pre-B cells.

overall_design: Transciptome analysis of Pten+/+ and Pten-/- cells transduced with BCR-ABL1 oncogene.

first: Markus

last: Muschen

first: Gang

last: Xiao


title: Establishment of hTERT immortalized mouse cardiosphere derived cell line.

status: Public on Oct 20 2020

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

summary: The analysis showed differences of transcriptomes between 5-azacytidine induced CDCs and control CDCs. We identified 10uM 5-azacytidine treatment for 3 days, following with normal culture for 4 weeks,could induce hTERT immortlized CDCs cardiac differentiation. Differential gene expression cluster analysis indicated big difference after 5-aza treatment, which include cardiomyocyte specific genes,such as tnnt2,desmin,mef2a,etc.

overall_design: Control CDCs and 5-aza treated CDCs mRNA profiles were generated by deep sequencing, in triplicate, using novaSeq6000.

first: Zhenglong

last: Guo


title: Expression data from HCT116 cell transduced with lentivirus encoding HAUS6 shRNA (sh-HAUS6) or Control shRNA (sh-Ctrl)

status: Public on Oct 01 2020

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: To further explore the underlying mechanism of HAUS6 knockdown on suppression of CRC cell growth in vivo and in vitro, Affymetrix human GeneChip primeview arrays  were performed to determine the global gene expression in HCT116 cells after transduction lentivirus encoding HAUS6 shRNA (n=3) or control shRNA (n=3).

overall_design: HCT116 cells were transduced with lentivirus encoding HAUS6 shRNA (n=3) or Control shRNA (n=3) for 72 h, and the samples were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Aling

last: Shen


title: Transcriptional responses of Escherichia coli to ceragenins and antimicrobial peptides

status: Public on Oct 26 2020

city: Berkeley

first: Gabriel

last: Mitchell

address: 1951 Oxford Street

department: Department of Molecular and Cell Biology

institute: University of California, Berkeley

summary: Here we report the results of a study comparing the global transcriptional responses of Escherichia coli to two well-studied CAMPs, LL37 and colistin, and two ceragenins with related structures, CSA13 and CSA131. We found that E. coli responds similarly to both CAMPs and ceragenins by inducing a Cpx envelope stress response. However, whereas E. coli exposed to CAMPs increased expression of genes involved in colanic acid biosynthesis, bacteria exposed to ceragenins specifically modulated functions related to phosphate transport, indicating distinct mechanisms of action between these two classes of molecules. Overall, this study suggests that while some bacterial responses to ceragenins overlap with those induced by naturally-occurring CAMPs, these synthetic molecules target the bacterial envelope using a distinctive mode of action.

overall_design: E. coli bacteria were grown to log phase and treated with supra-MIC concentrations of antibiotics for one hour before being harvested for RNA extraction and sequencing. Data are from 3 independent experiments.

first: Michael

last: Marletta

first: Jeffery

last: Cox


title: An Ifitm3-dependent amplification loop enables antibody responses and oncogenic signaling in B-cells

summary: Ifitm3 (interferon-inducible transmembrane protein 3) was previously identified as an endosomal antiviral effector protein that blocks viral infection1-4. In analyses of gene expression data from patients with B-cell leukemia and lymphoma, we identified Ifitm3 as one of the strongest predictors of poor clinical outcome. In normal resting B-cells, Ifitm3 was minimally expressed and mainly localized in endosomes. However, engagement of the B-cell receptor (BCR) and PI3K-activation strongly induced expression of Ifitm3 and phosphorylation of its N-terminus at Y20, resulting in accumulation at the cell surface. In B-cell leukemia, oncogenic kinases induced phosphorylation at Y20, resulting in constitutive plasma membrane localization of Ifitm3. Ifitm3¯ / ¯ naïve B-cells developed at normal numbers, however, B-cell activation upon antigen encounter, germinal center formation and production of antigen-specific antibodies were compromised. Likewise, oncogenes that typically induce development of leukemia and lymphoma failed to transform Ifitm3¯ / ¯ B-cells. Conversely, a phosphomimetic mutation of Y20 induced oncogenic PI3K-signaling and initiated transformation of premalignant B-cells into overt leukemia. Functional experiments revealed a previously unrecognized function of Ifitm3 as PIP3-scaffold and central amplifier of PI3K signaling downstream of the BCR and adhesion receptors. PI3K signal-amplification depends on binding of Ifitm3 to PIP3 via two lysine residues (K83 and K104) in its conserved intracellular loop. In Ifitm3¯ / ¯ B-cells, lipid rafts were depleted of PIP3, resulting in defective expression of >60 lipid raft-associated surface receptors, which impaired BCR-signaling and cellular adhesion. We conclude that phosphorylation of IFITM3 upon Bcell antigen-encounter induces a dynamic switch from antiviral effector functions in endosomes to a PI3K-amplification loop at the cell surface. IFITM3-dependent amplification of PI3K-signaling downstream of the BCR and adhesion receptors is critical to enable rapid expansion of B-cells with high affinity to antigen. In addition, multiple oncogenes depend on IFITM3 to assemble PIP3- dependent signaling complexes and amplify PI3K-signaling for malignant transformation.

overall_design: Transciptome analysis of Ifitm3+/+ and Ifitm3-/- cells transduced with BCR-ABL1 or NRAS G12D oncogenes.

first: Jaewoong

last: Lee


title: Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s disease

status: Public on Oct 22 2020

city: Adelaide

first: Karissa

last: Barthelson

address: North Terrace Campus

institute: The University of Adelaide

summary: To prevent or delay the onset of Alzheimer’s disease (AD), we must understand its molecular basis. The great majority of AD cases arise sporadically with a late onset after 65 years of age (LOAD). However, rare familial cases of AD can occur due to dominant mutations in a small number of genes that cause an early onset prior to 65 years of age (EOfAD). As EOfAD and LOAD share similar pathologies and disease progression, analysis of EOfAD genetic models may give insight into both subtypes of AD. Sortilin-related receptor 1 (SORL1) is genetically associated with both EOfAD and LOAD and provides a unique opportunity to investigate the relationships between both forms of AD. Currently, the role of SORL1 mutations in AD pathogenesis is unclear. To understand the molecular consequences of SORL1 mutation, we performed targeted mutagenesis of the orthologous gene in zebrafish. We generated an EOfAD-like mutation, V1482Afs, and a putatively null mutation, to investigate whether EOfAD-like mutations in sorl1 display haploinsufficiency by acting through loss-of-function mechanisms. We performed mRNA-sequencing on whole brains, comparing wild type fish with their siblings heterozygous for EOfAD-like or putatively loss-of-function mutations in sorl1, or transheterozygous for these mutations. Differential gene expression analysis identified a small number of differentially expressed genes due to the sorl1 genotypes. We also performed enrichment analysis on all detectable genes to obtain a more complete view on changes to gene expression by performing three methods of gene set enrichment analysis, then calculated an overall significance value using the harmonic mean p-value. This identified subtle effects on expression of genes involved in energy production, mRNA translation and mTORC1 signalling in both the EOfAD-like and null mutant brains, implying that these effects are due to sorl1 haploinsufficiency. Surprisingly, we also observed changes to expression of genes occurring only in the EOfAD-mutation carrier brains, suggesting gain-of-function effects. Transheterozygosity for the EOfAD-like and null mutations (i.e. lacking wild type sorl1), caused apparent effects on iron homeostasis and other transcriptome changes distinct from the single-mutation heterozygous fish. Our results provide insight into the possible early brain molecular effects of an EOfAD mutation in human SORL1. Differential effects of heterozygosity and complete loss of normal SORL1 expression are revealed.

overall_design: a total of 24 fish were used in this study: 8 wild-type samples, 6 V1482Afs/+ samples (EOfAD-like), 4 null samples (R122Pfs/+) and 6 trans-heterozygous samples (V1482Afs/R122Pfs). These fish arised from the same parents and were raised over three tanks side-by-side in the same re-circulating water system until 6 months of age.

first: Stephen

middle: M

last: Pederson

last: Lardelli


title: Integrated Genomic Analysis Reveals Key Features of Long Undecoded Transcript Isoform (LUTI)-based Gene Repression

status: Public on Nov 01 2020

first: Amy

middle: Moreda

last: Tresenrider

state: CA

address: 628 Barker Hall

department: Molecular and Cell Biology

institute: UC Berkeley

summary: Long Undecoded Transcript Isoforms (LUTIs) represent a class of non-canonical mRNAs that downregulate gene expression through the combined act of transcriptional and translational repression. While single gene studies revealed some important aspects of LUTI-based repression, how these features impact gene regulation at a global scale is unknown. By using transcript leader and direct RNA sequencing, here we identify 74 LUTI candidates that are expressed specifically during meiotic prophase. Translational repression of these candidates is ubiquitous and dependent on upstream open reading frames. However, LUTI-based transcriptional repression is highly variable. In only 50% of the cases, LUTI transcription causes downregulation of the protein-coding transcript isoform. Higher LUTI expression, enrichment of histone 3 lysine 36 trimethylation, and changes in nucleosome position are the strongest predictors of LUTI-based transcriptional repression. We conclude that LUTIs downregulate gene expression in a manner that integrates translational repression, chromatin state changes, and the magnitude of LUTI expression.

overall_design: A combination of direct RNA, MNase-seq, ChIP-seq, RNA-seq, and TL-seq was collected from budding yeast cells undergoing synchronous meiosis. Samples were taken at a premeiotic stage (after 2 hours in sporulation media (SPO)) and during meiotic prophase (after 4 hours in SPO). Between 2-4 replicates were collected for each assay. For all ChIP experiments, IP samples were compared to input samples.

first: Victoria

last: Jorgensen

first: Minghao

last: Chia

first: Hanna

last: Liao

first: Folkert

last: van Weven

first: Elçin

last: Ünal


title: The effects of H3.3K27M mutation on developing mouse brain and cooperation with Trp53 on enhancing tumorigenesis in the genetic model of H3.3K27M [Exome-Seq]

first: Cynthia

last: Hawkins

overall_design: H3.3K27M mice were generated by microinjection. H3.3K27M mice were generated by microinjection. We performed whole exome sequencing on tumours (n=10) and normal controls (n=6) from H3.3K27M (n=2 mice), H3.3K27M/Trp53+/- (n=3 mice), H3.3K27M/Trp53-/- (n=3 mice) and reference CD1 mice (n=1 mouse) for a total of 16 samples.

first: Robert

last: Siddaway

first: Sanja

last: Pajovic


status: Public on Sep 13 2020

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: 1601 SW Jefferson Way

institute: Oregon State University

summary: Type 2 diabetes (T2D), the most common form of diabetes, is one of the leading causes of death in the USA. Diet, genetics, environment, and the gut microbes are important factors causing T2D. However, the exactmechanisms by which these factors induce the disease are still unclear. Western diet-induced obesity mimicked the conditions of metabolic  syndrome and T2D in mice. Concurrent changes in the bacterial abundance and composition in  ileum and stool of mice indicated that the metabolic alterations are associated  with microbes.Using a transkingdom network and causal inference analysis, we  identified candidate microbes that can potentially mediate changes in metabolic  health. In line with our predictions, supplementing mice with the beneficial microbial  candidates ameliorated diet induced diabetes in mice. Transcriptomic studies  showed that these microbes improved metabolic  parameters by regulating  mitochondrial processes in the liver. Using systems biology network analyses,  followed by experimental validation, we identified key microbes and pathways regulating glucose metabolism. This research aims to uncover the mechanisms of microbiota dependent glucose metabolism to advance treatment of T2D.

overall_design: RNA-seq from the liver and ileum of mice on ND, WD, and WD with either Lactobacillus gasseri or Lactobacillus johnsonii.

first: Natalia

last: Shulzhenko


title: Genome-wide DNA binding patterns of KLF4 WT and mutant during reprogramming

status: Public on Sep 11 2020

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

summary: On days 2 and 10 after transduction in an induction method, ChIP DNA samples were collected from reprogramming MEF transduced with SeVdp carrying a mutant or WT. ChIP-Seq was performed using an anti-human KLF4 antibody.

overall_design: ChIP-seq using Anti-KLF4 antibody


title: Transcriptome analysis of N140fs and T141_L142delinsMISLISV mutations in the zebrafish orthologue of the Alzheimer's disease gene PSEN2

status: Public on Sep 19 2020

first: Lachlan

last: Baer

address: North Terrace

summary: Alzheimer’s disease is the most common form of age-related dementia. At least 15 mutations in the human gene PRESENILIN 2 (PSEN2) have been found to cause familial Alzheimer’s disease (fAD). Zebrafish possess an orthologous gene, psen2, and present opportunities for investigation of PRESENILIN function related to Alzheimer’s disease. The most prevalent and best characterized fAD mutation in PSEN2 is N141I. The equivalent codon in zebrafish psen2 is N140. We used genome editing technology in zebrafish to target generation of mutations to the N140 codon. We isolated two mutations: psen2N140fs, causing truncation of the coding sequence, and psen2T141_L142delinsMISLISV, that deletes the two codons immediately downstream of N140 and replaces them with seven codons coding for amino acid residues MISLISV. Thus, like almost every fAD mutation in the PRESENILIN genes, this latter mutation does not truncate the gene’s open reading frame.

overall_design: Five whole-brain libraries from each of the genotypes: wild type (+/+), heterozygous mutant psen2 (N140fs/+) and heterozygous mutant psen2 (T141_L142delinsMISLISV/+). After sequencing, one sample was identified to be incorrectly genotyped and actually had genotype (N140fs/T141_L142delinsMISLISV). Brains were taken from the zebrafish at age 6 months. All the fish were siblings from mating of a N140fs/+ fish with a T141_L142delinsMISLISV/+ fish and were raised together in the same tank. Both females and male brain samples are included in this study.

first: Haowei

last: Jiang

first: Morgan

last: Newman

first: Michael