title: Vp1524, a Vibrio parahaemolyticus NAD+ dependent deacetylase, regulates host response during infection by induction of histone deacetylation

status: Public on Sep 22 2021

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

institute: Theomics International Private Limited

summary: Here we report V. parahaemolyticus (serotype O3:K6) infection induced histone deacetylation in intestinal epithelial cells, wherein we have shown deacetylation of H3K9, H3K56, H3K18 and H4K16 residues. Interestingly we observed concomitant downregulation of host deacetylases.

overall_design: Response to Infection at two different bacterial loads

first: Pragyan

last: Mishra

first: Shibangini

last: Beura

first: Sweta

last: Sikder

first: Madavan

last: Vasudevan

first: Manjima

last: Roy

first: Joydeep

last: Rakshit

first: Tapas

last: Kundu

first: Rahul

last: Modak


title: Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress

status: Public on Sep 08 2021

city: La Jolla

first: Ukrae

last: Cho

state: CA

address: 10010 N Torrey Pines Rd

department: Molecular and Cell Biology

country: USA

institute: Salk Institute for Biological Studies

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Dynamic CD4 T cell heterogeneity defines subset-specific suppression and PDL1-blockade driven functional restoration in chronic infection [Bulk-seq]

status: Public on Sep 20 2021

city: Toronto

first: Ramanandan

last: Prabhakaran

state: Ontario

address: 610 University Avenue

country: Canada

institute: University Health Network-Princess Margaret Cancer Center

summary: Inhibiting PD1:PDL1 signaling has transformed therapeutic immune restoration. CD4 T cells are critical to sustain immunity in chronic infections and cancer, yet little is known about how PD1/L1 modulates CD4 T helper (Th) responses or the ability to restore CD4 Th-mediated immunity by inhibiting PD1/L1 signaling. We demonstrate that PD1/L1 specifically suppresses CD4 Th1 cell amplification, prevents CD4 Th1 cytokine production, and abolishes CD4 CTL killing capacity during chronic infection. Inhibiting PDL1 during chronic infection rapidly restored these functions, while simultaneously enhancing Th1-like Treg amplification and activation, indicating a system-wide CD4-Th1 recalibration. Paradoxically, PDL1-blockade decreased TCR signaling, while re-directing intrinsically-suppressive type I interferon networks towards dominant IFNγ-mediated responses. Mechanistically, PDL1-blockade specifically targeted defined populations with pre-established, but actively-suppressed proliferative potential, with limited impact on minimally-cycling TCF1+ Tfh, despite high PD1 expression. Thus, CD4 T cells require unique differentiation and functional states to be targets of PDL1-directed suppression and therapeutic restoration.

overall_design: RNA-seq on Th1 and Tfh virus-specific CD4 SMARTA T cells at Day 7 LCMV-Armstrong

first: Brooks

last: David


title: The NSL complex is required for telomere maintenance and primary piRNA biogenesis from telomeric clusters

status: Public on Aug 26 2021

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

type: Non-coding RNA profiling by high throughput sequencing

summary: Telomeres cap and protect chromosome ends. Drosophila telomeres consist of repetitive sequences dominated by retrotransposons. Telomeric sequences are transcribed and participate in a negative feedback loop in which they are processed into self-targeting piRNA on the one hand and are serve as the sole source of the transposase responsible for telomere maintenance on the other hand. We show that the tight regulation of the expression of telomeric sequences in the germline is regulated by the NSL complex. As a consequence, both primary biogenesis from telomeric piRNA clusters as well as telomere stability are impaired in cells following NSL complex depletion.

overall_design:
The study characterizes the role of a transcriptional regulatory complex in the germline of D. melanogaster in regulating the piRNA pathway.

Please note that [1] the input samples do not have a corresponding processed file because the processed file is the INPUT-Normalized bigwig file.
[2] The diffexpr-resultsNSL*vsWhite.csv cwere generated from the whiteRNAi_*ovary_RNAseq and NSL*RNAi_ovary_RNAseq samples and is linked to the corresponding NSL*RNAi_ovary_RNAseq sample records.

first: Shantanu

middle: S

last: Iyer

first: Maria

last: Shvedunova

first: Georgiev

last: Plamen


title: Exposure to lipopolysaccharide induces sexually dimorphic placental adaptation by modifying placental efficiency, morphogenesis, and gene expression

city: Seoul

first: Da Som

last: Jeong

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Embryology

country: South Korea

institute: Yonsei University

summary: Sexual dimorphism in placental physiology during development affects the functionality of placental adaptation during adverse pregnancy, affecting fetal growth, development, and eventually fetal programming, which have long-term effects on the offspring’s adult life. However, studies focusing on the phenomenon and relationship between sex-specific placental adaptation and consequent altered fetal development are still elusive. Here, we established a prenatal maternal stress model by administering lipopolysaccharide (LPS) to pregnant ICR mice at the mid-gestational stage. To verify the appropriateness of the animal model to study sex differences in the sub-optimal uterus milieu, pregnancy complications were examined. To elucidate global transcriptomic changes occurring in the placenta, total RNA sequencing was performed in female and male placentas. LPS exposure at the mid-gestational stage induced placental inflammation in both sexes. In utero inflammatory conditions resulted in intrauterine fetal growth restriction and impaired placental development in a sex-specific manner depending on the dose of LPS. Sex-biased placental pathology was observed in the junctional zone and the labyrinth layer. Placental transcriptome analysis revealed widespread disparity in protein-coding and long non-coding genes between female and male placentas, presenting the relationship between morphology and function in a sex-specific IUGR model.

overall_design: Female and male placentas were isolated from pregnant ICR mice treated with 200 ml of PBS or LPS (400 mg/kg) at gestational day 15.5 for 48 hrs. For individual sample, we pooled 6-8 placentas from 3 different pregnant mice. For each group we have 2 biological replicates in PBS and 3 biological replicates in LPS. The total number of samples is 10.

first: Da-Som

first: Ji-Hoon

last: Oh

first: Ji-Yeon

last: Lee

first: Myoung-Hee

last: Kim


title: DNA methylation profiles for the SIOP Ependymoma I Study

status: Public on Aug 25 2021

city: Nottingham

first: Timothy

middle: A

last: Ritzmann

address: Coates Road

department: Children's Brain Tumour Research Centre

country: United Kingdom

institute: University of Nottingham

type: Methylation profiling by genome tiling array

summary:
DNA methylation profiles were generated for cases in the SIOP ependymoma I study. Samples were analysed using the Illumina 450k BeadChip and processed using the Heidelberg classifier (v11.2b).
The aim of the biological studies aspect of the trial was to perform a retrospective analysis of the methylation profiles of the participants in the trial.

overall_design: 35 samples were analysed and found to be consistent with ependymoma (74 participants in the study but the remainder did not have tissue available for analysis).

first: Rebecca

middle: J

last: Chapman

first: John

middle: P

last: Kilday

first: Nicola

last: Thorp

first: Piergiorgio

last: Modena

first: Robert

last: Dineen

first: Donald

last: Macarthur

first: Conor

last: Mallucci

last: Jaspan

first: Kristian

middle: W

last: Pajtler

first: Marzia

last: Giagnacovo

first: Thomas

last: Jacques

first: Simon

middle: M

last: Paine

first: David

last: Ellison

first: Eric

last: Bouffet

first: Richard

middle: G

last: Grundy


title: mRNA-sequencing of C2C12 myoblasts, myotubes, and reserve cells

first: Ukrae

last: Cho

summary: The transcriptome of C2C12 myoblasts, myotubes, and reserve cells were assessed by mRNA-sequencing. Our data reveals the difference in the transcriptional profiles of three different types of muscle cells.

overall_design: C2C12 myoblasts were harvested at ~95% confluency. After 7 days of myogenic differentiation in low serum medium, C2C12 myotubes and reserve cells were seperated by mild trypsinization. mRNA-sequencing was performed in paired-end 150 base pair mode on the Illumina NovaSeq 6000 platform. Paired-end fragments were mapped to mm10, filtered, and assembled into transcripts using HISAT2 , SAMtools , and StringTie . Differential expression was evaluated using DESeq2. Two biological replicates per sample.

first: Cho

last: Ukrae

first: Hetzer

last: Martin


title: Myokine irisin is a critical regulator of cognitive function III

status: Public on Aug 11 2021

city: Charlestown

first: Christiane

last: Wrann

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Identifying secreted mediators driving the cognitive benefits of exercise holds great promise for the treatment of cognitive decline in aging or Alzheimer’s disease (AD). Here, we show that irisin, the cleaved and circulating form of the exercise-induced membrane protein FNDC5, is sufficient to confer the exercise benefits on cognitive function. Genetic deletion of FNDC5/irisin (global F5KO mice) impairs cognitive function in exercise, aging, and AD. Diminished pattern separation in F5KOs can be rescued by delivering irisin directly into the dentate gyrus, suggesting that irisin is the active moiety. In F5KOs, adult-born neurons in the dentate gyrus are morphologically, transcriptionally, and functionally abnormal. Importantly, elevation of circulating irisin levels by peripheral administration, resulting in enrichment of central irisin, was sufficient to improve both the cognitive deficit and neuropathology in AD mouse models. Irisin is a crucial regulator of cognitive benefits of exercise and potential therapeutic for treating cognitive disorders including AD.

overall_design: Bulk RNA-seq of dentate gyrus of 10-week-old male F5KO and WT mice

middle: D

first: Sophia

last: Valaris

first: Renhao

last: Luo


title: Myokine irisin is a critical regulator of cognitive function


title: A Critical Role of Hepatic GABA in The Metabolic Dysfunction and Hyperphagia of Obesity

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

country: Japan

institute: Faculty of Medicine, Shimane University

summary: Hepatic lipid accumulation is a hallmark of type 2 diabetes (T2D) and associated with hyperinsulinemia, insulin resistance, and hyperphagia. Hepatic synthesis of GABA, catalyzed by GABA-transaminase (GABA-T), is upregulated in obese mice. To assess the role of hepatic GABA production in obesity-induced metabolic and energy dysregulation, we treated mice with two pharmacologic GABA-T inhibitors and also knocked down hepatic GABA-T expression using an antisense oligonucleotide. Hepatic GABA-T inhibition and knockdown decreased basal hyperinsulinemia and hyperglycemia, and improved glucose intolerance.  GABA-T knockdown improved insulin sensitivity assessed by hyperinsulinemic-euglycemic clamps in obese mice. Hepatic GABA-T knockdown also decreased food intake and induced weight loss without altering energy expenditure in obese mice.  Data from obese humans support that hepatic GABA production and transport are associated with serum insulin, HOMA-IR, T2D, and BMI. These results support a key role for hepatocyte GABA production in the dysfunctional glucoregulation and feeding behavior associated with obesity.

overall_design: We evaluated the relationship between gene expression of proteins involved in GABA production and transport and key metabolic parameters, such as hepatic triglyceride content, insulin, and muscle insulin sensitivity, in people with obesity (BMI >= 30).

first: Caroline

middle: E

last: Geisler

first: Susma

last: Ghimire

first: Stephanie

last: Bruggink

first: Kendra

last: Miller

first: Savanna

middle: N

last: Weninger

first: Jason

last: Kronenfeld

first: Samuel

last: Klein

first: Frank

last: Duca

first: Benjamin

last: Renquist


title: Myokine irisin is a critical regulator of cognitive function I

overall_design: To evaluate the therapeutic potential of peripherally delivered irisin, 8-month-old male APP/PS1 mice received AAV8-irisin-FLAG or AAV8-GFP via tail vein injections to overexpress irisin in the liver and moderately increase circulating irisin levels. Two months later, the micro-dissected hippocampi were analyzed by RNA-seq.

first: Mohammad

middle: R

last: Islam

first: Robert

last: Kitchen


title: Transcriptomic effect of high-fat diet and PCN treatment on mouse liver

status: Public on Aug 06 2021

city: Oulu

first: Jukka

last: Hakkola

address: Aapistie 5

department: Research Unit of Biomedicine

country: Finland

institute: University of Oulu

summary: PCN, a selective murine PXR agonist, was administered to obese mice with the goal to investigate what transcriptional changes PXR activation cause in the livers of obese mice.

overall_design: n=3/group. Groups: Chow, high-fat diet, high-fat diet + vehicle, high-fat diet + PCN

first: Mikko

last: Karpale


title: Myokine irisin is a critical regulator of cognitive function II

first: Christiane

last: Wrann

overall_design: We have developed a novel approach to ascertain the transcriptional program of newborn neurons by selectively labeling the nuclei of newborn neurons using a GFP-reporter retrovirus driven by a synapsin-promotor (RV-SYN-GTRgp), followed by FACS-sorting isolated nuclei for next-gen RNA-sequencing (RNA-seq). This approach yielded 200-500 immature neuron nuclei per mouse. This novel approach was used to assess the transcriptome of newborn neurons from FNDC5 KO mice (F5KO) and wildtype littermates (WT). Mice were housed either with or without a running wheel. Therefore, we have four groups in this experiment: WT-sedentary, WT-running, F5KO-sedentary, and F5KO-running.


title: Early transcriptome response of Trichoderma virens to colonization of maize roots

status: Public on Aug 03 2021

city: College Station

first: James

last: Taylor

state: Texas

address: 2132 TAMU

department: Plant Pathology and Microbiology

institute: Texas A&M University

summary: In this study, we explored the genes involved with the host communication and colonization process through transcriptomic profiling of Trichoderma virens as it colonizes hydroponic maize roots, compared to the fungus without roots present.

overall_design: Comparison of gene expression from samples of fungus with or without maize roots present at 6, 12, 15, 24, and 36 hpi

first: Benny

last: Horwitz

first: Charles

last: Kenerley


title: Systems analysis of viral infection in the embryonic central nervous system (CNS)

status: Public on Aug 21 2021

city: Boston

first: Amanda

middle: J.

last: Guise

address: 3 Blackfan Circle

department: F.M. Kirby Center for Neurobiology

institute: Boston Children's Hospital & Harvard Medical School

summary: A new mouse model for congenital Zika infection in a wildtype, immunocompetent background employing intraplacental infection resulted in productive infection of embryonic brains and features of microcephaly during early development (E10.5-16.5). Gross morphological characterization showed translational relevance for understanding the viral neuropathogenesis and Zika-associated microcephaly in humans. Thus, an integrated, multi-omics (RNA-sequencing, proteomics) analysis of fetal brain tissues was performed to understand pathways perturbed by viral infection in developing brains. These analyses identified virus-induced defects in cell cycle progression and neurodevelopment, in S-phase DNA replication and NEUROD2/TBR2 transcription factor cascades, respectively. Among the most significant responses was induction of innate immune programs in ZIKV-infected brains, including immunoproteasome activation and MHC-I antigen display associated with immune cell infiltration and neuronal death during early development. Identification of specific components within major pathways contributing to viral infection-induced effects on neurodevelopment provides novel targets for therapeutic intervention against neurotropic infections and ZIKV-associated microcephaly specifically.

overall_design: Total RNA was extracted from whole E14.5 brains (3 ZIKV-infected (ZIKV) and 3 Mock-infected (CTRL) litter-matched embryos) following ZIKV-infection at E10.5 for RNAseq comparison.

first: Tojo

last: Nakayama

first: Kimino

last: Fujimura

first: Anaïs

last: Meziani

first: Dylan

last: Vaughan

first: Andrew

last: Kodani

first: Long

last: Cheng

first: Ann

middle: F

last: Durbin

first: Irene

last: Bosch

first: Lee

last: Gehrke

first: Hanno

last: Steen

first: Ganeshwaran

middle: H

last: Mochida

first: Judith


title: Single-cell transcriptomic analysis reveals unique cell types and patterns of gene expression in the frog corneal epithelium.

status: Public on Jul 21 2021

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

summary: Here, we use scRNA-seq to expand our understanding of the vertebrate corneal epithelium in an amphibian model, having undertaken a comprehensive characterization of cellular and transcriptional heterogeneity to identify novel corneal marker genes.

overall_design: Adult Xenopus laevis were obtained from Nasco (Fort Atkinson, WI). Fertilized eggs were collected, and larvae were raised to Stage 49-51 based on developmental staging by Nieuwkoop and Faber (1956). The corneal epithelial tissue was dissected using very fine microscissors (Henry et al., 2019), taking care not to include any surrounding skin. Corneal tissue was dissociated and processed through the 10X pipeline, and we identified 5173 cells using Cellranger.

first: Surabhi

last: Sonam

first: John

last: Henry


title: RNA Sequencing of Blood in Coronary Artery Disease; Involvement of Regulatory T Cell Imbalance

status: Public on Jul 16 2021

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University


title: RNA Sequencing of Blood in Coronary Artery Disease; Involvement of Regulatory T Cell Imbalance [Validation Cohort]

summary:
Background: Cardiovascular disease had a global prevalence of 523 million cases and 18.6 million deaths in 2019.  The current standard for diagnosing coronary artery disease (CAD) is coronary angiography.  Surprisingly, despite well-established clinical indications, up to 40% of the one million invasive cardiac catheterizations return a result of ‘no blockage’.  The present studies employed RNA sequencing of whole blood to identify an RNA signature in patients presenting with a clinical suspicion of CAD.
Methods: Whole blood RNA was depleted of ribosomal RNA (rRNA) and analyzed by single-molecule sequencing of RNA (RNAseq) to identify transcripts associated with CAD (TRACs) in a discovery group of 96 patients presenting for elective coronary catheterization.  The resulting transcript counts were compared between groups to identify differentially expressed genes (DEGs).  Results: Surprisingly, 98% of DEGs/TRACs were down-regulated ~1.7-fold in patients with mild to severe CAD (>20% stenosis).  The TRACs were independent of comorbid risk factors for CAD, such as gender, hypertension, and smoking.  Bioinformatic analysis identified an enrichment in transcripts such as FoxP1, ICOSLG, IKZF4/Eos, SMYD3, TRIM28, and TCF3/E2A that are likely markers of regulatory T cells (Treg), consistent with known reductions in Tregs in CAD.  A validation cohort of 80 patients confirmed the overall pattern (92% down-regulation) and supported many of the Treg-related changes. TRACs were enriched for transcripts associated with stress granules, which sequester RNAs, and ciliary and synaptic transcripts, possibly consistent with changes in the immune synapse of developing T cells.
Conclusions: These studies identify a novel mRNA signature of a Treg-like defect in CAD patients and provides a blueprint for a diagnostic test for CAD. The pattern of changes is consistent with stress-related changes in the maturation of T and Treg cells, possibly due to changes in the immune synapse.

overall_design:
Observational study; no intervention; CAD defined by Invasive Coronary Angiography; CAD defined as >20% stenosis
*** Raw data not submitted due to patient privacy concerns. Sequence files will be provided separately to users that can provide IRB and HIPPAA assurances. ***


title: RNA Sequencing of Blood in Coronary Artery Disease; Involvement of Regulatory T Cell Imbalance [Discovery Cohort]


title: Genome wide methylation of lung adenocarcinoma samples

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

summary: Genome wide DNA methylation profiling of  lung adenocarcinoma samples. Illumina Infinium 450K(n=61) and EPIC (n=27) arrays were used to obtain DNA methylation data.

overall_design: Bisulphite converted DNA from the 88 samples were hybridised to the Illumina Infinium 450K and EPIC Human Methylation Beadchip.

first: Kayla

last: Guidry

first: Kwok-Kin

last: Wong


title: Metformin preconditioning protects against myocardial stunning and preserves mitochondrial dynamics and protein translation in a mouse model of cardiac arrest

status: Public on Aug 01 2021

city: Cleveland

first: Cody

last: Rutledge

state: OH

address: 2103 Cornell Road

department: Medicine

institute: CWRU

summary: We compare microarray data from homogenized left ventricles of the heart at 24 hours after sham surgey vs 8-min potassium chloride induced sudden cardiac arrest and resuscitation

overall_design: 8 sham hearts vs 8 cardiac arrest taken 24 hours after cardiac arrest

first: Brett

last: Kaufman


title: MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection [MtrA_OE_pH]

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: The success of Mycobacterium tuberculosis (Mtb) is largely due to its ability to withstand numerous stresses imposed by host immunity. Here, we present a data-driven model that captures these adaptive mechanisms and reveals the dynamic interplay of host-derived stresses and genome-encoded regulatory programs in Mtb. The model captures the genome-wide distribution of cis-acting gene regulatory elements and the conditional influences of transcription factors at those elements to elicit environment-specific responses. Analysis of transcriptional responses that may be essential for Mtb’s survival in acidic conditions identified regulatory control by the MtrAB two-component signal system. Using genome-wide transcriptomics as well as imaging studies, we have characterized the MtrAB circuit by tunable CRISPRi knockdown in both Mtb and the non-pathogenic organism, M. smegmatis (Msm). These experiments validated the essentiality of MtrA in Mtb, but not Msm. We identified that MtrA regulates multiple enzymes that cleave cell wall peptidoglycan and is required for efficient cell division. Moreover, our results suggest that peptidoglycan cleavage, regulated by MtrA, is required for Mtb to survive intracellular stress. Further, we present MtrA as an attractive drug target, as even weak repression of mtrA results in loss of Mtb viability and completely clears the bacteria with low-dose isoniazid or rifampicin treatment.

overall_design: To investigate gene expression changes of mtrA overexpression, we used M. tuberculosis strain containing an ATc-inducible vector as described previously in Minch et al (PMID: 25581030). For each sample, cultures of M. tuberculosis were cultured in standard 7H9-rich media containing 50 μg/ml hygromycin B to mid-log phase, washed three times in 1x PBS and diluted back to OD600 = 0.05 into either neutral or acidic pH media with 50 μg/ml hygromycin B and the presence or absence of ATc inducer. Samples, in biological triplicate from two separate experiments, were collected after 18 hours of ATc induction, centrifuged at high speed for 5 min, supernatant was discarded and the cell pellet was immediately flash frozen in liquid nitrogen. Cell pellets were stored at -80° C until RNA extraction was performed. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.

first: Nitin

last: Baliga


title: The importance of adipose tissue NAD+ biology in regulating metabolic flexibility.

status: Public on Jul 01 2021

first: Jun

last: Yoshino

summary: Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme regulating cellular energy metabolism across all species. Recent studies have shown the pleiotropic roles of adipose tissue NAD+ biology in adipose tissue and whole-body metabolism. The major purpose of the present study was to test the hypothesis that adipose tissue NAD+ biosynthesis, mediated by nicotinamide phosphoribosyltransferase (NAMPT), is a physiological regulator of whole-body metabolic flexibility. To this end, we analyzed adipocyte-specific Nampt knockout (ANKO) mice and subcutaneous white adipose tissue (WAT) biopsy samples obtained from human subjects. We found ANKO mice preferably utilized glucose substrate during the light period or after prolonged fasting. In contrast, ANKO mice had marked decreases in stimulation of glucose oxidation and suppression of fat oxidation during the postprandial status despite hyperinsulinemia. Data obtained from RNA-sequencing of WAT suggest that loss of NAMPT causes inflammation, oxidative stress, defective fatty acid oxidation, and mitochondrial dysfunction in WAT, key features of obesity and metabolic inflexibility. We also found WAT NAD+ concentration was decreased in people with obesity and insulin resistance compared with those who were non-obese and insulin-sensitive. In addition, bariatric surgery-induced 20% weight loss increased WAT NAD+ concentration in people with obesity. Taken together, our results reveal the importance of adipose tissue NAMPT-mediated NAD+ biosynthesis in regulating whole-body metabolic flexibility. Our results also provide translational and clinical insight into adipose tissue NAD+ biology in obesity and whole-body metabolic health.

overall_design: We determined the effects of adipocyte-specific Nampt deletion on subcutaneous white adipose tissue gene expression profiling by analyzing control (flox/flox) and adipocyte-specific Nampt knockout (ANKO) mice (n=3 per group).

first: Michael

last: Franczyk


title: MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection [mtrA_knockdown]

sample_organism:
Mycolicibacterium smegmatis
Mycobacterium tuberculosis

overall_design: Cultures were grown to mid-log phase in 7H9-rich media with Kanamycin (50 μg/ml) and then diluted back in the presence or absence of ATc to induce CRISPRi-mediated mtrA knockdown. Knockdown was allowed to proceed for 14 hours (M. smegmatis) or 4 days (M. tuberculosis). Samples, in biological quadruplicate, were collected by centrifugation at high speed for 5 min, discarding supernatant and immediately flash freezing the cell pellet in liquid nitrogen. Cell pellets were stored at -80° C until RNA extraction was performed. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Expression data from imbibed wheat seeds developed at different temperatures

status: Public on Jun 30 2021

city: Winnipeg

first: Belay

middle: T.

last: Ayele

state: MB

address: 222 Agriculture Building

department: Plant Science

institute: University of Manitoba

summary:
Transcriptomic analysis of maintenance of dormancy induced by seed development temperature
We used Affymetrix GeneChip Wheat Genome Array to detail transcriptional programs underlying maintenance of dormancy induced by seed development tempearture in imbibing seeds of wheat

overall_design: Embryos of 48 h Imbibed seeds developed at different temperatures were used for RNA extraction and hybridization on Affymetrix GeneChip.

first: Ayele

middle: T

last: Belay

first: Jordan

middle: C

last: Mark

first: Pham

last: Tuan


title: MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection [pH]

summary: The success of Mycobacterium tuberculosis (Mtb) is largely due to its ability to withstand numerous stresses imposed by host immunity. Here, we present a data-driven model that captures these adaptive mechanisms and reveals the dynamic interplay of host-derived stresses and genome-encoded regulatory programs in Mtb. The model captures the genome-wide distribution of cis-acting gene regulatory elements and the conditional influences of transcription factors at those elements to elicit environment-specific responses. Analysis of transcriptional responses that may be essential for Mtb’s survival in acidic conditions identified regulatory control by the MtrAB two-component signal system. This data is a comparison of  transcriptional differences (RNA-seq) between low pH (pH 5.6) and neutral pH (pH7) of Mtb

overall_design: To investigate gene expression changes of M. tuberculosis at acidic pH, cultures of M. tuberculosis were cultured in standard 7H9-rich media to mid-log phase, washed three times in 1x PBS and diluted back to OD600 = 0.1 into either neutral or acidic pH media. Samples, in biological triplicate, were collected right after transfer and after 24 hours in neutral or acidic pH media. Samples were centrifuged at high speed for 5 min, supernatant was discarded and the cell pellet was immediately flash frozen in liquid nitrogen. Cell pellets were stored at -80° C until RNA extraction was performed. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.

middle: S


title: ALKBH5 K235 acetylation regulates the RNA m6A profiles

city: Guangzhou

first: Guang-Rong

last: Yan

state: Guangdong

address: 63 Duobao Road

country: China

institute: Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University

summary: We performed the transcripome-wild m6A-sequencing to compare the m6A profiles of negative control (NC) HeLa cells and ALKBH5 KO HeLa cells stably re-expressing wild type ALKBH5 (WT) or its mutant K235R (K235R)

overall_design: The m6A profiles and mRNA prolifes in negative control (NC) HeLa cells and ALKBH5 KO HeLa cells stably re-expressing wild type ALKBH5 (WT) or its mutant K235R (K235R) were generated by m6A-sequencing (m6A-seq)(IP) and RNA-sequencing (RNA-seq)(Input) using Illumina Novaseq6000.

first: Xiao-Lan

last: Zhang


title: Histone ChIP-seq from middle frontal area 46 (ENCSR927IOS)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: The developing mouse coronal suture at single-cell resolution

status: Public on Jun 17 2021

city: Oxford

first: Steve

last: Twigg

address: John Radcliffe Hospital

institute: University of Oxford

summary: Sutures separate the flat bones of the skull and enable coordinated growth of the brain and overlying cranium. In order to uncover the cellular diversity within sutures, we conducted single-cell transcriptomic and histological analyses of the embryonic murine coronal suture. We identify Erg and Pthlh as early markers of osteogenic progenitors in sutures, and distinct pre-osteoblast signatures between the bone fronts and periosteum. diverse mesenchymal layers at the coronal suture, including multiple distinct meningeal layers below the suture, and ligamentous, ectocranial, and hypodermal layers above the sutureIn the ectocranial layers above the suture, we observe a ligament-like population spanning the frontal and parietal bones and expressing genes implicated in mechanosensation. Mesenchyme in and around the coronal suture is asymmetrically distributed between the frontal and parietal bones, and we identify different states of osteogenic cells extending from the bone fronts into the more mature bone, and a potential signature for sutural stem cellsIn the meningeal layers, we detect a potential chondrogenic periosteal dura population that may be involved in endochondral ossification that closes sutures. Expression of genes mutated in craniosynostosis is spread across diverse cell types, suggesting multiple points at which homeostasis can fail. This single-cell atlas provides a resource to understand the development of the coronal suture, the suture most commonly fused in craniosynostosis.

first: D'Juan

last: Farmer


title: Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterations

status: Public on Jun 09 2021

city: Uppsala

first: Iliana

middle: Kyriaki

last: Kerzeli

state: Uppsala

address: Husargatan 3

country: Sweden

institute: Uppsala University

summary: Bladder cancer, one of the most prevalent malignancies worldwide, remains hard to classify due to a staggering molecular complexity. Despite a plethora of diagnostic tools and therapies, it is hard to outline the key steps leading up to the transition from high-risk non–muscle-invasive bladder cancer (NMIBC) to muscle-invasive bladder cancer (MIBC). Carcinogen-induced murine models can recapitulate urothelial carcinogenesis and natural anti-tumor immunity. Herein, we have developed and profiled a novel model of progressive NMIBC based on 10 weeks of OH-BBN exposure in hepatocyte growth factor/cyclin dependent kinase 4 (R24C) (Hgf-Cdk4R24C) mice. The profiling of the model was performed by histology grading, single cell transcriptomic and proteomic analysis, while the derivation of a tumorigenic cell line was validated and used to assess in vivo anti-tumor effects in response to immunotherapy.   Established NMIBC was present in females at 10 weeks post OH-BBN exposure while neoplasia was not as advanced in male mice, however all mice progressed to MIBC. Single cell RNA sequencing analysis revealed an intratumoral heterogeneity also described in the human disease trajectory. Moreover, although immune activation biomarkers were elevated in urine during carcinogen exposure, anti-programmed cell death protein 1 (anti-PD1) monotherapy did not prevent tumor progression. Furthermore, anti-PD1 immunotherapy did not control the growth of subcutaneous tumors formed by the newly derived urothelial cancer cell line. However, treatment with CpG-oligodeoxynucleotides (ODN) significantly decreased tumor volume, but only in females.   In conclusion, the molecular map of this novel preclinical model of bladder cancer provides an opportunity to further investigate pharmacological therapies ahead with regards to both targeted drugs and immunotherapies to improve the strategies of how we should tackle the heterogeneous tumor microenvironment in urothelial bladder cancer to improve responses rates in the clinic.

overall_design: Single cell analysis was performed for whole mouse bladders after a) 10 weeks of OH-BBN exposure and after b) progression to MIBC, as well as of c) healthy Hgf-Cdk4R24C bladders, d) orthotopic MB49 tumor bearing (C57BL/6) bladders and e) healthy C57BL/6 bladders. On the 10-week endpoint Hgf-Cdk4R24C tumors required pooling of samples due to low cell numbers per bladder (one pool of n= 4 females and one of n= 5 males). For the MIBC endpoint, one whole tumor bearing bladder per male and female were analyzed. Healthy Hgf-Cdk4R24C bladders were pooled together (n= 4 males and n= 4 females). A pool of day 5 orthotopic MB49 tumors (pool of n= 5) and a pool of 5 healthy C57BL/6 bladders as control were also analyzed.

first: Ramy

last: Elgendy

middle: K


title: Histone ChIP-seq from middle frontal area 46 (ENCSR461GYN)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: C/EBPδ drives key endocrine signals in human fetal membranes at parturition

status: Public on Jul 15 2021

city: Shanghai

first: Wangsheng

last: Wang

state: Please Select

address: 845 Lingshan Rd.

institute: Shanghai Jiao Tong University

summary: Amnion-derived prostaglandin E2 (PGE2) and cortisol are key to labor onset. Identification of the common transcription factor driving the expression of both cyclooxygenase-2 (COX-2) and 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1), the key enzymes in their production, may hold the key to the treatment of pre- and post-term labor. Here, we have found that the CCAAT enhancer binding protein δ (C/EBPδ) is such a transcription factor which underlies the feed-forward induction of COX-2 and 11β-HSD1 expression by their own products PGE2 and cortisol in human amnion fibroblasts so that their production would be ensured in the amnion for the onset of labor. Moreover, the abundance of C/EBPδ in amnion increases along with COX-2 and 11β-HSD1 at term and further increases at parturition. Knockout of C/EBPδ in mice delays the onset of labor further supporting the concept. In conclusion, C/EBPδ may serve as a novel pharmaceutical target in the amnion for treatment of pre- and post-term labor.

overall_design: RNA sequencing of human amnion fibroblasts with or without cortisol treatment.

first: Wang-sheng


title: Histone ChIP-seq from middle frontal area 46 (ENCSR299EQJ)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR220TRW)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (89 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ASCL1 represses a latent osteogenic program in small cell lung cancer in multiple cells of origin

status: Public on May 22 2021

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

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

overall_design: Refer to individual Series


title: ASCL1 represses a SOX9+ neural-crest-stem-like state in small cell lung cancer

summary: ASCL1 is a neuroendocrine-lineage-specific oncogenic driver of small cell lung cancer (SCLC), highly expressed in a significant fraction of tumors. However, ~25% of human SCLC are ASCL1-low and associated with low-neuroendocrine fate and high MYC expression. Using genetically-engineered mouse models (GEMMs), we show that alterations in Rb1/Trp53/Myc in the mouse lung induce an ASCL1+ state of SCLC in multiple cells of origin. Genetic depletion of ASCL1 in MYC-driven SCLC dramatically inhibits tumor initiation and progression to the NEUROD1+ subtype of SCLC. Surprisingly, ASCL1 loss promotes a SOX9+ mesenchymal/neural-crest-stem-like state and the emergence of bone and more rarely, cartilaginous tumors. ASCL1 is critical for expression of key lineage-related transcription factors NKX2-1, FOXA2, and INSM1, and represses regulators of Hippo, Wnt and Notch developmental pathways in vivo. ASCL1 also represses SOX9 expression in human SCLC cells, suggesting a conserved function for ASCL1. Here, we utilize single-cell RNA sequencing to capture transcriptomic signatures of RPM (Rb1/Trp53/Myc), RPR2 (Rb1/Trp53/Rbl2), and RPMA (Rb1/Trp53/Myc/Ascl1) GEMM tumors to support our conclusion that in MYC-driven SCLC, ASCL1 promotes neuroendocrine fate and represses the emergence of SOX9+ non-endodermal stem-like or mesenchymal fates. These data were integrated with 4 additional invasive RPM tumors from NCBI GEO: GSE149180.

overall_design: Single-cell RNA-sequencing using 10X platform on 1 RPMA tumor initiated with CMV-Cre (general promoter), 1  RPMA tumor initiated with CGRP-Cre (neuroendocrine cell-specific promoter), 1 early RPM tumor initiated with CGRP-Cre, and 1 RPR2 tumor initiated with CGRP-Cre. Tumors were digested with an enzymatic cocktail into single cell suspension and subject to 10X Chromium library preparation and Illumina sequencing targeting ~200M reads per sample.

first: Abbie

last: Ireland

first: Rachelle

last: Olsen


title: Histone ChIP-seq from middle frontal area 46 (ENCSR830EXC)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ASCL1 represses a latent osteogenic program in small cell lung cancer in multiple cells of origin [ChIP-Seq]

summary: ASCL1 is a neuroendocrine-lineage-specific oncogenic driver of small cell lung cancer (SCLC), highly expressed in a significant fraction of tumors. However, ~25% of human SCLC are ASCL1-low and associated with low-neuroendocrine fate and high MYC expression. Using genetically-engineered mouse models (GEMMs), we show that alterations in Rb1/Trp53/Myc in the mouse lung induce an ASCL1+ state of SCLC in multiple cell types. Genetic depletion of ASCL1 in MYC-driven SCLC dramatically inhibits tumor initiation, but surprisingly converts tumors to a SOX9+ mesenchymal/neural-crest-stem-like state that has the capacity to differentiate into RUNX2+bone tumors. ASCL1 represses SOX9 expression, as well as WNT and NOTCH developmental pathways, consistent with human gene expression data. SCLC demonstrates remarkable cell fate plasticity with ASCL1 repressing the emergence of non-endodermal stem-like fates that have the capacity for bone differentiation. Here, we perform ChIP on RPM tumors against ASCL1, NEUROD1, and H3k27Ac to view binding profiles and identify target genes of ASCL1 and NEUROD1.

overall_design: Individual lung tumors from mice were micro-dissected, flash frozen and stored at -80°C until chromatin immunoprecipitation


title: Targeting pH-responsive Transcriptional Regulation of Peptidoglycan Cleavage Potentiates Fast Clearance of Mycobacterium tuberculosis with Frontline Antibiotics

first: Eliza

last: Peterson

platform_organism:
Mycolicibacterium smegmatis
Mycobacterium tuberculosis


title: Histone ChIP-seq from middle frontal area 46 (ENCSR011BHU)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Melanoma dedifferentiation induced by interferon-gamma epigenetic remodeling in response to anti-PD-1 therapy

status: Public on May 10 2021

city: Los Angeles

first: Katherine

last: Sheu

address: 611 Charles E Young Dr E

institute: UCLA

summary: Melanoma dedifferentiation has been reported as a state of cellular resistance to targeted therapies and immunotherapies as cancer cells revert to a more primitive cellular phenotype. Here we show that, counterintuitively, the biopsies of patient tumors that respond to anti-programmed cell death receptor 1 (PD-1) therapy decreased expression of melanocytic markers and increased neural crest markers, suggesting treatment-induced dedifferentiation. When modeling the effects in vitro, we documented that melanoma cell lines that were originally melanocytic differentiated underwent a process of neural crest dedifferentiation when continuously exposed to interferon gamma (IFNγ), through a global chromatin landscape changes leading to enrichment in specific hyperaccessible chromatin regions. The IFNγ-induced dedifferentiation signature corresponded with improved outcomes in patients with melanoma, challenging the notion that neural crest dedifferentiation is entirely an adverse phenotype.

overall_design: ATAC sequencing of eight different human melanoma cell lines at baseline, following three days of TNF exposure, or following 2-5 weeks of IFNg exposure.

first: Yeon

middle: J

last: Kim

first: Antoni

last: Ribas


title: Histone ChIP-seq from middle frontal area 46 (ENCSR344PHP)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (88 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Leaf excision evokes an ultradian gene expression rhythm to prime de novo root regeneration (eur1-11)

status: Public on May 01 2021

city: Daegu

first: Kitae

last: Song

state: jung-gu

address: DGIST, 333, Techno jungang-daero,, Hyeonpung-myeon

institute: Institute for Basic Science

summary: The eur1-11 which developed by EMS mutation has no ultradian rhythm in excised leaf. This data set was focused on how EUR and eur1-11 effect on de novo root regeneration.

overall_design: After the excision, excised leaves were incubated at 22 °C in continuous light condition and RNA were collected at 0, 24, 48, 72, 96 hour for transcriptome analysis through RNA-seq.

first: Quy

last: Vu

first: Sunghyun

last: Hong


title: TXN, a Xanthohumol Derivative, Significantly Attenuates High-Fat Diet Induced Hepatic Steatosis In Vivo by Antagonizing PPARγ

status: Public on May 18 2021

city: Corvallis

first: Adrian

last: Gombart

state: OR

address: Linus Pauling Science Center

department: Linus Pauling Institute/Biochemistry and Biophysics

institute: Oregon State University

summary: We performed unbiased transcriptional profiling of livers from mice to determine mechanisms by which xanthohumol and tetrahydroxanthohumol supplementation could ameliorate hepatosteatosis induced by a HFD at the transcriptional level. We conducted RNA-seq analysis of total RNA of livers obtained from mice after 16 weeks on the diet. Analysis revealed changes in gene expression that suggested these hop-derived compounds antagonize the nuclear receptor PPARγ.

overall_design: Liver RNA-seq profiling of livers from 26 week old wild type C57BL/6J male mice fed one of four diets for 16 weeks (from age 10 weeks to 26 weeks old): LFD (low fat diet, n = 10), HFD (high fat diet, n = 10), HFD+HXN (xanthohumol 60 mg/kg body weight, n = 10), HFD+TXN (tetrahydroxanthohumol 30 mg/kg body weight, n = 9).    HFD group is used as the control/reference group for all analyses.

first: Yang

last: Zhang


title: Nicotinamide mononucleotide increases muscle insulin sensitivity in women with prediabetes

city: Izumo

first: Jun

last: Yoshino

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary: Studies in rodents have shown obesity and aging impair tissue nicotinamide adenine dinucleotide (NAD+) biosynthesis, which contributes to metabolic dysfunction. The availability of nicotinamide mononucleotide (NMN) is an important rate-limiting factor in mammalian NAD+ biosynthesis. We conducted a 10-week, randomized, placebo-controlled, double-blind trial to evaluate the effect of NMN supplementation on metabolic function in 25 postmenopausal women with prediabetes who were overweight/obese. Insulin-stimulated glucose disposal, assessed by using the hyperinsulinemic-euglycemic-clamp procedure, increased by 25±7% (P<0.01) in the NMN group, which was accompanied by an increase in insulin-stimulated phosphorylation of muscle AKT (P<0.01), whereas neither outcome changed after placebo treatment. Body composition (fat mass, fat-free mass, intra-abdominal fat, intrahepatic triglyceride content) and muscle mitochondrial respiratory capacity did not change after treatment with placebo or NMN. These results demonstrate NMN improves muscle insulin sensitivity in women with prediabetes who are overweight/obese, independent of changes in body composition or mitochondrial function.

overall_design: We obtained skeletal muscle samples obtained during the basal period and during the hyperinsulinemic-euglycemic clamp procedure (insulin infusion) from women who prediabetes before and after placebo (n=12) or NMN treatment (n=11).

first: Mihoko

first: Gary

last: Patti

first: Michael

middle: P

last: Franczyk

first: Kathryn

last: Mills

first: Gordon

middle: I

last: Smith

first: Miriam

last: Sindelar

first: Bruce

middle: W

last: Patterson

first: Shin-ichiro

last: Imai

first: Samuel

last: Klein


title: Leaf excision evokes an ultradian gene expression rhythm to prime de novo root regeneration

summary: Ultradian rhythm of gene expression in excised leaf.

overall_design: After the synchronization treatment (dark and incubated under dark and 16 °C conditions for 24 h after excision), excised leaves were incubated at 22 °C in continuous light condition and were collected every 30 min with a total of 16 time points for transcriptome analysis through RNA-seq.

first: Song

last: Kitae

first: Vu

last: Quy Thi


title: Expression profile of localized primary prostate cancer samples and the matched normal tissues

city: Beijing

first: Yanyang

last: Zhao

state: Not required for this country

address: No.1, Dahua Road,Dongdan

institute: Genetics Medicine

summary: To identify new oncogenic drivers in prostate cancer, we performed transcriptome analysis of localized primary prostate cancer samples and the matched normal tissues.

overall_design: mRNA profiles of 10 pairs of localized primary prostate cancer samples and the matched normal tissues were generated by deep sequencing, using Illumina HiSeq 2000.

first: Xiaoquan

last: Zhu


title: Expression data from stromal cells derived from idiopathic pulmonary fibrosis, lung adenocarcinoma and normal lung.

status: Public on Apr 27 2021

city: Oulu

first: Mervi

last: Kreus

address: Aapistie 5A

institute: University of Oulu

summary:
Idiopathic pulmonary fibrosis (IPF) and lung cancer share common risk factors, epigenetic and genetic alterations, cellular and molecular aberrations, the activation of similar signaling pathways and poor survival.
The aim of this study was to examine the gene expression profiles of stromal cells from patients with IPF and lung adenocarcinoma (ADC) as well as from normal lung.

overall_design: Gene expression was evaluated in stromal cells cultured from tumor and corresponding tumor-free peripheral lung of the patients with ADC undergoing lung cancer-resection surgery (n=4), and from surgical lung biopsy samples of the patients with IPF (n=3). In addition, gene expression was evaluated in one IPF sample derived from peripheral lung outside the tumor from a patient operated for lung cancer (n=1).

first: Siri

last: Lehtonen

first: Sini

last: Skarp

first: Riitta

last: Kaarteenaho


title: Hltf-deletion from the TME in a CDX model of CRC reprogrammed the human transcriptome-S-nitroso-proteome to promote inflammation and redirect metastasis

status: Public on Apr 23 2021

city: Lubbock

first: Beverly

last: Chilton

state: TX

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

summary: Hypermethylation of helicase-like transcription factor (HLTF) in colorectal cancer (CRC) cells occurs more frequently in men than women. Progressive epigenetic silencing of HLTF in tumor cells is accompanied by negligible expression in the tumor microenvironment (TME). Cell line-derived xenografts were established in control (Hltf+/+) and Hltf-deleted male Rag2-/-IL2rg-/- mice by direct orthotopic microinjection of HLTF+/+HCT116 cells into the submucosa of the cecum. Combinatorial induction of IL6 and S100A8/A9 in the Hltf-deleted TME with ICAM-1 and IL8 in the primary tumor activated a positive feedback loop. The proinflammatory niche produced a major shift in CDX metastasis to peritoneal dissemination compared to controls. Inducible nitric oxide (iNOS) gene expression and transactivation of the iNOS-S100A8/A9 signaling complex in Hltf-deleted TME reprogrammed the human S-nitroso-proteome. S-nitroso (SNO) proteins POTEE, TRIM52 and UN45B are S-nitrosylated on the conserved I/L-X-C-X2-D/E motif indicative of iNOS-S100A8/A9-mediated S-nitrosylation. 2D-DIGE and protein identification by MALDI-TOF/TOF mass spectrometry authenticated S-nitrosylation of 53 individual cysteines in half-site motifs (I/L-X-C or C-X-X-D/E) in CDX tumors. POTEE-SNO in CDX tumors is both a general S-nitrosylation target and an iNOS-S100A8/A9 site-specific (Cys638) target in the Hltf-deleted TME. REL is an example of convergence of transcriptomic-S-nitroso-proteomic signaling. The gene is transcriptionally activated in CDX  tumors with an Hltf-deleted TME, and REL-SNO (Cys143) is found in primary CDX tumors and all metastatic sites. Primary CDX tumors from Hltf-deleted TME shared 60% of their S-nitroso-proteome with all metastatic sites. Forty percent of SNO-proteins from primary CDX tumors were variably expressed at metastatic sites. Global S-nitrosylation of proteins in pathways related to cytoskeleton and motility is strongly implicated in the metastatic dissemination of CDX tumors. Hltf-deletion from the TME plays a major role in the pathogenesis of inflammation and links protein S-nitrosylation in primary CDX tumors with spatiotemporal continuity in metastatic progression even when the tumor cells express HLTF.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HCT116 cells that express HLTF were paced in mice that either do (control) or do not (test) express the Hltf gene. Resultant, primary CDX tumors were excised, profiled with RNAseq, and subjected to species specific mapping, Comparisons of gene expresison profiles for tumors (human) and the tumor microenvironment (mouse) were generated.

first: Rebecca

middle: A

last: Helmer

first: Raul

last: Martinez-Zaguilan

first: Gurvinder

last: Kaur

first: Lisa

first: Jannette

middle: M

last: Dufour


title: DNA methylation in sarcoma patients

status: Public on Apr 21 2021

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: We retrospectively identified adult patients who had received anti-PD-1 ICI therapy for recurrent sarcoma and performed DNA methylation profiling using Infinium MethylationEPIC microarrays. Response to anti-PD-1 ICI therapy was correlated with DNA methylation profiles.

overall_design: 8 responders to ICI and 27 non-responders to ICI were compared

first: Angelika

last: Starzer


title: The GUL-1 protein binds multiple RNAs and regulates cell wall remodeling in concert with the MAK-1 pathway in Neurospora crassa

status: Public on Apr 14 2021

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary:
The Neurospora crassa GUL-1 is part of the COT-1 pathway, which plays key roles in regulating polar hyphal growth and cell wall remodeling. We show that GUL-1 is a bona fide mRNA binding protein (RBP) that can associate with 828 “core” mRNA species. When cell wall integrity (CWI) is challenged, the repertoire of associated RNA species increases up to 2628 mRNAs (including its own transcript). GUL-1 can bind mRNAs of genes related to translation, cell wall remodeling, circadian clock, endoplasmatic reticulum (ER), as well as CWI and osmoregulatory response MAPK pathway components. GUL-1 interacts with over 100 different proteins, including stress granule proteins, components of the translational and cell wall remodeling machinery, as well as ER components and those of the MAPK, COT-1 and STRIPAK complexes. Several additional RBPs were also shown to physically interact with GUL-1. We demonstrate that under stress conditions GUL-1 can localize to the ER and that GUL-1 affects the CWI pathway as is evident via altered phosphorylation levels of MAK-1, interaction with mak-1 transcript and involvement in the expression level of the transcription factor adv-1. Taken together, we suggest that the RBP GUL-1 functions in multiple cellular processes, including the regulation of cell wall remodeling. The latter is mechanistically concerted with the MAK-1 pathway in a stress-related manner.
Methods: In this study we show that GUL-1 is a bona fide mRNA binding protein (RBP) that associates with different mRNAs, including its own transcript, as determined by RNA antisense purification and RNA immunoprecipitation experiments.
Results: We demonstrate that GUL-1 may physically interact with multiple proteins included translation processes, cell wall remodeling and cell wall integrity (CWI). We show that GUL-1 affects the CWI pathway as is evident via altered phosphorylation levels of MAK-1, interaction with mak-1 transcript and involvement in the expression level of the transcription factor adv-1.
Conclusions:We suggest that the RBP GUL-1 functions in the regulation of cell wall remodeling in concert with the MAK-1 pathway in a stress-related manner.

overall_design: RNA immunoprecipitation analysis was performed on the basis of the protocol described by Niranjanakumari et al., 2002, with minor modifications.

first: Inbal

last: Herold

first: Marisela

last: Garduño-Rosales

first: Zheng

last: Wang

last: López-Giráldez

first: Yaron

last: Orenstein

first: Rosa

last: Mouriño-Pérez

first: Jeffrey

last: Townsend

first: Igor

last: Ulitsky

first: Oded

last: Yarden


title: RNA-seq of the liver tissue from female F1 generation with parternal exposure to arsenic in drinking water

city: Hefei

first: Yanfeng

last: Xue

state: Anhui

address: Changjiang Western Road 130

institute: Anhui Agricultural University

summary: We treated C56BL/6 male mice with 0.25 ppm iAs in drinking water before breeding with untreated females. GTT and other metabolic assaies were done on F1 offsprings. iAsF1-F showed significantly impared glucose intolerance than conF1-F. RNA-seq was thus applied to the liver samples of F1 generation to explore potential mechanism.

overall_design: Compare the differences in transcriptome profiles between the liver sample from iAsF1-F and conF1-F.

last: Sun


title: Cx43 in Cdh5+ cells maintains blood-brain barrier integrity by NAD+ during aging

first: Rui

last: Zhan

address: 38 Xueyuan Road, Haidian District

institute: Peking University

summary: Blood-brain barrier (BBB) function deteriorates during aging, contributing to cognitive impairment and neurodegeneration. It is unclear what drives BBB leakage in aging and how it can be prevented. Using single-nucleus transcriptomics, we identified decreased connexin 43 (CX43) expression in Cadherin-5+ (Cdh5+) cerebral vascular cells in naturally aging mice and confirmed it in human brain samples. Global or Cdh5+ cell-specific CX43 deletion in mice exacerbated BBB dysfunction during aging. The CX43-dependent effect was not due to its canonical gap junction function but was associated with reduced NAD+ levels and mitochondrial dysfunction through NAD+-dependent sirtuin 3. CX43 interacts with and negatively regulates poly (ADP-ribose) polymerase 1 (PARP1). Pharmacologic inhibition of PARP1 by olaparib or nicotinamide mononucleotide supplementation rescued NAD+ levels and alleviated aging-associated BBB leakage. These findings establish the endothelial CX43-PARP1-NAD+ pathway’s role in vascular aging and identify a potential therapeutic strategy to combat aging-associated BBB leakage with neuroprotective implications.

overall_design: To investigate BBB-related transcriptomic changes across different cell types during natural aging, we studied the cortex from young (2-3-month-old) and old (18-22-month-old) mice (n = 3 pooled per group) using snRNA-seq with the 10x Genomics Chromium platform(Hu et al., 2017).

first: Xia

last: Meng

first: Jie

last: Xu

first: Hongtu

last: Cui

first: Lemin

last: Zheng


title: Removal of visceral adipose tissue prevents obesity-induced multi-organ insulin resistance, dyslipidemia, and NAFLD in mice

status: Public on Apr 01 2021

first: Jun

last: Yoshino

state: Shimane

summary: Obesity is associated with insulin resistance, an important risk factor of type 2 diabetes, atherogenic dyslipidemia, nonalcoholic fatty liver disease (NAFLD), and cardiovascular disease. It has been postulated that accumulation of visceral adipose tissue (VAT) causes obesity-induced insulin resistance. The major purpose of this study was to test hypothesis that prophylactic VAT removal prevents the development of obesity-induced multi-organ (liver, skeletal muscle, adipose tissue) insulin resistance, dyslipidemia, and NAFLD. Accordingly, we surgically removed epididymal VAT from adult C57BL/6J mice and then evaluated in vivo and cellular metabolic pathways involved in glucose and lipid metabolism following feeding of chronic high-fat diet (HFD). We found that VAT removal prevented HFD-induced insulin resistance and markedly increased AKT-mediated insulin signaling in subcutaneous adipose tissue (SAT), liver, and skeletal muscle. VAT removal improved plasma lipid profiling and prevented obesity-induced NAFLD. In addition, VAT removal significantly increased circulating level of adiponectin, a key insulin-sensitizing adipokine, whereas it decreased interleukin-6, a pro-inflammatory adipokine. Data obtained from RNA-sequencing suggest that VAT removal prevents obesity-induced oxidative stress and inflammation in liver and SAT respectively. These findings demonstrate the causative role of VAT in the development of obesity and related systemic metabolic complications, such as insulin resistance, dyslipidemia, and NAFLD.

overall_design: We evaluated the effects of epididymal visceral adipose tissue (VAT) removal on liver and subcutaneous adipose tissue (SAT) gene expression profiling under a high-fat diet condition (n=5 per group).

first: Michael

last: Franczyk

first: Mai

last: He


title: ASCL1 represses a latent osteogenic program in small cell lung cancer in multiple cells of origin [RNA-Seq]

first: Trudy

last: Oliver

summary: ASCL1 is a neuroendocrine-lineage-specific oncogenic driver of small cell lung cancer (SCLC), highly expressed in a significant fraction of tumors. However, ~25% of human SCLC are ASCL1-low and associated with low-neuroendocrine fate and high MYC expression. Using genetically-engineered mouse models (GEMMs), we show that alterations in Rb1/Trp53/Myc in the mouse lung induce an ASCL1+ state of SCLC in multiple cell types. Genetic depletion of ASCL1 in MYC-driven SCLC dramatically inhibits tumor initiation, but surprisingly converts tumors to a SOX9+mesenchymal/neural-crest-stem-like state that has the capacity to differentiate into RUNX2+bone tumors. ASCL1 represses SOX9 expression, as well as WNT and NOTCH developmental pathways, consistent with human gene expression data. SCLC demonstrates remarkable cell fate plasticity with ASCL1 repressing the emergence of non-endodermal stem-like fates that have the capacity for bone differentiation. Here we perform bulk RNA sequencing on RPMA tumor samples to compare gene expression patterrns with RPM tumors with intact ASCL1.

overall_design: Bulk RNA-sequencing on 7 RPMA tumors from the RPMA GEMM.

first: Rachelle

last: Olsen

first: Abbie

last: Ireland

middle: G


title: Transcriptional profiling of mouse intestinal tissue, with or without antibiotic or sulindac treatment

city: Glasgow

first: Andrew

last: Campbell

address: Switchback Road

institute: CRUK Beatson Institute

summary: Loss of APC or activation of Braf V600E mutation in combination with Alk5 loss in the intestinal epithelium under the control of VilCreER, with or without antibiotic/sulindac treatment

overall_design: RNAseq Expression data from small intestine or proximal colon, comparing WT vs VilCreER activated gene changes in the presence or absence of drug treatment

first: Owen

last: Sansom

first: Joshua

last: Leach

first: Kathryn

last: Gilroy


title: A RALF-like peptide EaF82 derived from Epipremnum aureum inhibits pollen development in Arabidopsis and tobacco

status: Public on Apr 06 2021

first: Jiahua

last: Xie

address: 302 E. Lawson Street

department: Pharmaceutical Sciences

institute: North Carolina Central University

summary: To investigate the function of previously cloned novel cysteine-rich peptide EaF82 which biochemical properties are similar to the Rapid Alkalinization Factor (RALF), we overexpressed EaF82 gene in Arabidopsis and found defects only in the pollen development. To further determine the affected genes and biological pathways, we compared the transcriptome profilings of two independent Arabidopsis EaF82 overexpressing lines (TA and TB) with that of the vector control line (C). The RNAseq analysis results revealed decreased expressions of five endogenous clade IV AtRALFs and genes responsible for cell wall modifications and pollen maturation, supporting the observed pollen abortion.

overall_design: The clusters of unopened flower buds of two indepentdent transgenic lines overexpressing EaF82, named TA and TB, and one control line expressing vector contruct, named C,  were examined. Each line has three biological replicate samples randomly collected from 36 subline plants.

first: Chiu-Yueh

last: Hung


title: Slic-seq for A-to-I edited transcripts enrichment

status: Public on Mar 27 2021

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

summary: Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional processing event involved in diversifying the transcriptome responsible for various biological processes. In this context, we developed a new biochemical method that enriches the inosine-containing RNA. The objective is the accurate identification of A-to-I editing sites, eliminating false positives caused by RNA-DNA differences. This method was applied to three neurological diseases, demonstrating that A-to-I editing sites significantly decreased in neuronal activity genes.

overall_design: 51 samples are analyzed(cell line data is mainly used to verify the reliability of the method, mouse brain tissue and mouse brain tissue is mainly used to study disease models)

first: Q

last: Wei

first: S

last: Han

first: K

last: Yuan

first: Z

first: Y

last: Chen

first: X

last: Weng

last: Zhou


title: Transcriptomic response in the skin of gilthead sea bream (Sparus aurata) fed garlic, carvacrol and thymol essential oils (EOs) additive

status: Public on Mar 31 2021

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Explore the underlying mechanisms-of-action of the essential oils diet in the skin of gilthead seabream.

overall_design: Transcriptomic analysis was conducted in order to determine the differences on gene expression level between these two dietary strategies at skin-specific level. The experimental design included two conditions: (1) fish fed basal diet with no essential oils (EOs) added (control); (2) fish fed 0.5% inclusion of a microencapsulated additive composed of a blend of garlic, carvacrol, and thymol synthetic EOs. After 65 days of feeding trial, total RNA were extracted invidually from gilthead sea bream (S. aurata) skin fed basal diet or an experimental diet containing 0.5% inclusion. Total RNA samples were grouped into 3 pools (n= 4 fish for each condition). The transcriptomic analysis was done following a reference design using the control diet group as reference.

first: Joana

last: Firmino

first: Eva

last: Vallejos-Vidal

middle: E

first: Enric

last: Gisbert


title: Training-induced excitatory synaptogenesis in a prefrontal cortex circuit is required for effort/reward evaluation

status: Public on Mar 24 2021

first: Cagla

last: Eroglu

address: 333A Nanaline building, Durham, NC 27710

department: Cell Biology

summary: We report bulk RNAseq data obtained from the Anterior Cingulate Cortex (ACC) microdissected from Untrained (n=5) and Trained (n=6) wild-type mice for an instrumental task, the lever-press task for food reward.

overall_design: ACC mRNA profile from Trained and Untrained adult WT mice

first: Francesco Paolo

last: Ulloa Severino

first: Oluwadamilola

last: Lawal

first: Kristina

last: Sakers

first: Namsoo

last: Kim

first: Chaichontat

last: Sriworarat

first: Scott

last: Soderling

first: Il

middle: H

first: Henry

last: Yin


title: Methylation profiling of subependymoma of the posterior fossa and ependymoma evolving from subependymoma

status: Public on Mar 22 2021

city: Berlin

first: Felix

last: Thierfelder

address: Charitépl. 1

institute: Charite

summary: Methylation analysis of subepndymoma of the posterior fossa

overall_design: Bisulphite converted DNA from the 53 samples were hybridised to the Illumina Infinium Human Methylation EPIC BeadChip and one was hybridised to the Illumina HumanMethylation450 BeadChip

first: Christian

last: Thomas

first: Leonillle

last: Schweizer


title: Effect of high fat diet feeding on adipose tissue macrophages

status: Public on Mar 18 2021

city: Edinburgh

first: Cecile

last: Benezech

address: 47 Little france Crescent

department: Centre for Cardiovascular Sciences

institute: University of Edinburgh

summary: Dyslipidemia is a main driver of cardiovascular diseases. The ability of macrophages to scavenge excess lipids implicate them as mediators in this process and understanding the mechanisms underlying macrophage lipid metabolism is key to the development of new treatments. Here we investigated how adipose tissue macrophages (ATMs) regulate post-prandial cholesterol transport. Single-cell RNA sequencing demonstrated that ingestion of lipids led to specific transcriptional activation of a population of resident ATMs expressing Lyve1, Tim4 and ABCA1.

overall_design: C57/BL6 mice were kept on control diet (n=3) or fed a high fat diet overnight (n=3). We performed droplet-based scRNA-seq on cell-sorted CD45+Lin-Ly6Clow/-F4/80+ macrophages.

first: Jordan

last: Portman

first: Peter

last: Smith

first: Prakash

last: Ramachandran

first: Neil

last: Henderson

first: Cécile


title: The impact of late gestation circadian disruption, by two weeks of exposure to chronic light dark phase from 5 weeks before expected calving to 3 weeks expected calving, on dairy cattle hepatic and mammary transcriptomes.

status: Public on Mar 16 2021

city: West Lafayette

first: Theresa

last: Casey

state: Indiana

address: 270 S. Russell Street

department: Animal Sciences

institute: Purdue University

summary: Our previous studies found circadian disruption increased insulin resistance and decreased mammary development in late pregnant cows.  The effect of circadian disruption on liver and mammary transcriptomes was measured to understand how it impacted hepatic function and mammary development.  At 35 d before expected calving (BEC) multiparous Holstein cows were assigned to either control (CON) or phase-shifted treatments (PS).  CON was exposed to 16 h light to 8 h of dark, and PS treatment was exposed to 16 h light to 8 h dark, but the phase of the light-dark cycle was shifted 6 h every 3 d.  At 21 d BEC, liver and mammary were biopsied. RNA was isolated  (n=6 CON and n=6 PS per tissue), libraries prepared and sequenced using paired end reads.  Reads mapping to bovine genome averaged 27 M ± 2 M, and aligned to 14,222 protein coding genes in liver and 15,480 in mammary analysis.

overall_design: Milking was ceased in multiparous Holstein at 60 d before expected calving (BEC) to begin their non-lactating dry period.  At 35 d BEC, cows were moved to a tie-stall barn and assigned to one of two study treatments, control (CON; n=6) or phase shift (PS; n=6), by blocking for lactation number and previous lactation yield. All cows were housed in the same experimental barn.  To separate treatments, the barn was partitioned with floor to ceiling double draping of fire-retardant tarps. To block natural light, windows were covered with black plastic, and caulking was applied around doors. Bright white light-emitting diode (LED) lights were positioned for 150 lx of light at the eye level of cows. CON cows were exposed to consistent light-dark cycles of 16 h light to 8 h of dark, with the light phase exposure from 0500 to 2100. The PS treatment was exposed to 16 h light to 8 h dark, but the phase of the light-dark cycle was shifted forward by 6 h every 3 d. Tissue used for this study was obtained by biopsy of mammary and liver at 21 d BEC.  The PS cows had been exposed to 2 weeks of chronic light-dark phase shifts, and at least 5 shifts in the light-dark cycle at the time of tissue biopsies.

first: Luiz

last: Brito


title: Single-cell RNA sequencing on human osteoblasts

status: Public on Mar 01 2021

city: New Orleans

first: Hong-Wen

last: Deng

state: Louisiana

address: 1324 Tulane Ave

institute: Tulane

summary: Here, we used single-cell RNA sequencing (scRNA-seq) to provide a high-resolution cellular taxonomy of freshly isolated primary human osteoblasts. Based on the gene expression patterns and cell lineage reconstruction, we identified three distinct clusters including preosteoblasts, mature osteoblasts, and an undetermined rare osteoblast subpopulation. Trajectory inference analysis suggested that the undetermined cluster may include osteoblast precursor cells which regulate the osteoblastogenesis process by giving rise to pre and mature osteoblasts. Investigation of the biological processes and signaling pathways enriched in each subpopulation revealed that in addition to bone formation, pre and undetermined osteoblasts may regulate both angiogenesis and hemopoiesis.

overall_design: We applied a widely used protocol for human osteoblast isolation to obtain the alkaline phosphatase (ALPL)high/CD45low cells from the femur head of one human subject with osteoarthritis through FACS. In total, 9,801 single cells were  encapsulated for cDNA synthesis and barcoded using the 10x Genomics Chromium system, followed by library construction and sequencing. After the qua¬lity control, we obtained 8,557 ALPLhigh/CD45low cells, with an average of 1,503 genes detected per cell.

first: Gong

last: Yun

first: Wang

last: Zun

first: Deng

last: Hong-Wen


title: Effect of TEAD4 on gene transcriptional responsiveness to TGF - β in HCCLM3 cells

status: Public on Mar 09 2021

city: Nanchang

first: Xiaohua

last: Yan

address: No. 1299, Xuefu Avenue, Honggutan

institute: Nanchang University

summary: 100 pM of recombinant TGF-β1 protein was used to stimulate the TEAD4-expressing HCCLM3 stable cells or the vector-expressing control cells for different time periods (0 / 4 / 12 h). Then cells were harvested for total RNA extraction and RNA-Seq analysis. Genes whose transcriptional responsiveness to TGF-β1 was attenuated by TEAD4 were underscored.

overall_design: vector/TGF-β1 (0, 4, 12h, respectively) and TEAD4/TGF-β1 (0, 4, 12h, respectively), 6 samples altogether


title: NG-Capture C analysis of 35 gene loci regulated by Fra-1 in MDA-MB-231 cells

status: Public on Feb 23 2021

city: Montpellier

first: Isabelle

last: Jariel-Encontre

state: Montpellier Cedex5

address: 208 Avenue des Apothicaires

country: France

institute: IRCM-U1194- INSERM

summary: In the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we used NG Capture-C approach to identify regulatory elements interacting with the promoters of 35 Fra-1 regulated genes in the triple negative breast cancer cell line MDA-MB-231

overall_design:
Identification of chromatin interactions by NG Capture-C between distal regulatory elements and the promoters of 35 Fra-1 regulated genes in MDA-MB-231 cells in presence and absence of Fra-1 (siRNA approach)
The 35 assayed genes include:
ABTB2
ASB1
CD44
CDCP1
EDN1
EMP1
FNDC3B
FOSL1
GALNT2
HEG1
HES1
HK2
HMGA1
ID1
IL8
KRT80
LIPH
LRP10
MAP2K1
MXD1
MYO10
PDE2A
PITPNC1
RPSAP52
SMAD6
SOX9
SRGAP1
SSFA2
TCF7L2
TES
TGFB2
TMC6
TNS3
TSPAN2
ZNF114

first: Fabienne

last: Bejjani

first: Claire

last: Tolza

first: Damien

last: Downes

first: Jim

last: Hughes

first: Marc

last: Piechaczyk


title: RNA-sequencing of primary soft tissue sarcomas and cell lines with ATRX deletion

status: Public on Mar 06 2021

city: Durham

first: Warren

last: Floyd

state: North Carolina

address: 450 Research Drive, LSRC Bldg, Room B324

department: Pharmacology and Molecular Cancer Biology

institute: Duke University

summary: RNA sequencing of a primary tumors from a sarcoma genetically engineerted mouse model with activation of oncogenic Kras, deletion of p53 and deletion of Atrx, as compared to control sarcomas with identical genetic alterations but with wild-type Atrx. Tumors were either untreated or recieved 20 Gy of ionizing radiation and were harvested at 4 hrs, 3 day, or 6 day timepoints post treatment. For cell lines, isogenic ATRX wild-type (WT) and ATRX knockout (KO) paired isogenic cell lines treated with either 1.)interferon stimulatory DNA (ISD) and harvested 24 hours after treatment, 2)4 Gy ionizing radiation and harvested 36 hours after treatment, or 3) untreated control. These experiments help determine the differential impact of ATRX mutational status on cGAS-STING and type-I interferon signaling in soft tissue sarcoma.

overall_design: RNA Sequencing of ATRX WT and KO primary sarcomas and soft tissue sarcoma cell lines.


title: Transcriptional regulation by Fra-1 in triple negative breast cancers

summary:
This SuperSeries is composed of the SubSeries listed below.
All the data are described in the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al.

overall_design: Refer to individual Series


title: Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses

status: Public on Feb 18 2021

city: Los Angeles

first: Katherine

last: Sheu

state: CA

address: 611 Charles E Young Dr E

institute: UCLA

summary: Macrophages initiate inﬂammatory responses via the transcription factor NFκB. The temporal pattern of NFκB activity determines which genes are expressed and thus, the type of response that ensues. Here, we examined how information about the stimulus is encoded in the dynamics of NFκB activity. We generated an mVenus-RelA reporter mouse line to enable high-throughput live-cell analysis of primary macrophages responding to host- and pathogen-derived stimuli. An information-theoretic workﬂow identiﬁed six dynamical features—termed signaling codons—that convey stimulus information to the nucleus. In particular, oscillatory trajectories were a hallmark of responses to cytokine but not pathogen-derived stimuli. Single-cell imaging and RNA sequencing of macrophages from a mouse model of Sjögren’s syndrome revealed inappropriate responses to stimuli, suggestive of confusion of two NFκB signaling codons. Thus, the dynamics of NFκB signaling classify immune threats through six signaling codons, and signal confusion based on defective codon deployment may underlie the etiology of some inﬂammatory diseases.

overall_design: Single cell RNAseq from Wildtype and Sjögren’s Syndrome mouse BMDMs stimulated with 10ng/ml TNF, 100ng/ml  LPS, or 50ug/ml p(I:C) for 8hours.

first: Alexander

last: Hoffmann


title: Transcriptional profiling of SI adenomas in Apc floxed mice

status: Public on Feb 19 2021

first: Andrew

last: Campbell

summary: Small intestinal adenomas in mice with Apc deficiency following tamoxifen-induced genetic recombination.

overall_design: RNAseq expression data from WT whole intestine vs intestinal adenomas that developed in aged Apc/+ VilCreER mice.

first: Owen

last: Sansom

first: David

last: Vincent

first: Dustin

last: Flanagan

first: Kathryn

last: Gilroy


title: RNA-sequencing of Chronic Phase Shift Protocol on Murine Pancreas

status: Public on Jan 21 2021

city: Madison

first: Sean

last: Ronnekleiv-Kelly

state: Wisconsin

address: 1400 University Ave

department: Surgery

institute: University of Wisconsin

summary: The objective of this study was to understand the long-term effects of a chronic phase shift protocol on the pancreatic transcriptome. A total of 144 wild-type C57Bl/6J 4-6 week old mice were housed under normal circadian conditions or disrupted using a chronic phase shift protocol whereby the light-dark cycle is advanced 8 hour every 2-3 days for 4 weeks. 12 hours prior to sacrafice mice were normalized under normal circadian conditions. Starting at ZT 0, mice were serially sacraficed at 4-hour intervals for 48 hours and the pancreas extracted. Pancreatic RNA was isolated and subjected to RNA-seq.

overall_design: A total of 144 samples were collected. Males (n = 3) and females (n=3) from each timepoint were pooled prior to sequencing. A total of 6 mice were sacraficed for each condition (normal circadian and circadian disrupted) at each timepoint.

first: Patrick

middle: B

last: Schwartz

first: Mark

last: Berres

first: Morgan

last: Walcheck


title: Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

status: Public on Jan 30 2021

city: St. Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 4515 McKinley Ave, Campus Box 8510

department: Genetics

institute: Washington University School of Medicine

summary: Enhancers and silencers often depend on the same transcription factors (TFs) and are imperfectly distinguished from each other by genomic assays of TF binding or chromatin state. To identify sequence features that define enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF CRX and found instances of enhancer, silencer, or no activity. Both enhancers and silencers contain more TF motifs than inactive sequences, but enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. Our results indicate that enhancers contain motifs for a diverse but degenerate collection of TFs, while silencers depend on a smaller and less diverse collection of TFs.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: Massively Parallel Reporter Assays of CRX-targeted cis-regulatory sequences in mouse retinas. Each unique sequence is tagged with 3 unique 9 bp barcodes. Each library also includes a basal control (basal promoter only) tagged with 18 unique 9 bp barcodes. Libraries contain genomic sequences centered on CRX motifs and versions of the same sequences with all CRX motifs abolished by point mutation. Libraries were cloned upstream of the Rho promoter or a minimal Polylinker. Libraries were electroporated into retinas dissected from P0 CD-1 mice. Retinas were harvested at P8. Barcode cDNA and the original DNA plasmids were sequenced. Three replicates per experiment.

first: Ryan

middle: Z

last: Friedman

last: Granas

first: Connie

last: Myers

first: Joseph

last: Corbo

first: Barak

last: Cohen


title: Unbiased functional identification and therapeutic targeting of T cell neoantigens in a spontaneous murine squamous cell carcinoma

status: Public on Jan 15 2021

city: San Diego

middle: S

last: Dolina

address: 9420 Athena Cir

institute: La Jolla Institute of Immunology

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


title: Mapping of epigenetic marks (H3K4me1, H3K4me3, H3K27ac), p300/CBP, PolII and CTCF on MDA-MB-231 genome

first: Isabelle

last: Jariel-Encontre

summary: In the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we mapped epigenetic marks (H3K4me1, H3K4me3, H3K27ac), p300/CBP, PolII and CTCF to characterize the binding sites of Fra-1 and Fra-2 on MDA-MB-231 genome. Data for Fra-1 and Fra-2 ChIP-seq are available on GEO database, accession number GSE132098 (Tolza et al., 2019, MCR 17, 1999-2014)

overall_design: ChIP-seq were carried out on MDA-MB-231 cells using antibodies specific of epigenetic marks (H3K4me1, H3K4me3, H3K27ac), p300/CBP, PolII and CTCF

first: Fabienne

last: Bejjani

first: Claire

last: Tolza

first: Muhammad

last: Maqbool

first: Marc

last: Piechaczyk


title: Human Astrocytes Model Derived from Induced Pluripotent Stem Cells

status: Public on Dec 16 2020

city: Tokyo

first: Nicolas

last: Leventoux

state: Tokyo

address: 35, Shinanomachi

department: Physiology

institute: Keio University

summary: Protocol to differentiate iPSC control lines into astrocytes. We performed the RNA sequencing of cells at different time point: embryoid bodies ; neurospheres at passage 1 ; neurospheres at passage 2 and differentiated astrocytes (iPast) for the 201B7 iPSC and iPast stage for WD39.

overall_design: 5 samples

first: Hideyuki

last: Okano

first: Satoru

last: Morimoto

first: Kent

last: Imaizumi


title: Decreased adipose tissue oxygenation is associated with insulin resistance in people with obesity

status: Public on Dec 07 2020

city: Izumo

first: Jun

last: Yoshino

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary: We evaluated the potential importance of adipose tissue (AT) oxygenation on AT biology and insulin sensitivity in people. AT oxygen partial pressure (pO2), branched chain amino acid (BCAA) catabolism and marker of inflammation were determined in three groups stratified by adiposity and insulin sensitivity: 1) metabolically-healthy lean (MHL); 2) metabolically-healthy obese (MHO); and 3) metabolically-unhealthy obese (MUO). AT pO2 progressively declined from the MHL to the MHO to the MUO group, and was positively associated with hepatic and whole-body insulin sensitivity. AT pO2 was positively associated with AT expression of genes involved in BCAA catabolism and negatively associated with plasma BCAA concentrations. Although AT pO2 was negatively associated with AT markers of inflammation, it was not associated with plasma adipokine concentrations. These results support the notion that reduced AT pO2 in people with obesity contributes to insulin resistance by decreasing AT BCAA catabolism and thereby increasing plasma BCAA concentrations.

overall_design: We obtained subcutaneous adipose tissue samples from people who were metabolically-healthy lean (MHL), metabolically-healthy obese (MHO), and metabolically-unhealthy obese (MUO) (n=45). We then identified genes that were significantly associated with AT oxygen content based on data obtained from RNA-seq.

first: Vincenza

last: Cifarelli

first: Scott

middle: C

last: Beeman

first: Gordon

last: Smith

first: Darya

last: Morozov

last: Beals

first: Brandon

middle: D

last: Kayser

first: Jeramie

last: Watrous

first: Mohit

last: Jain

first: Bruce

last: Patterson

first: Samuel

last: Klein


title: Unbiased functional identification and therapeutic targeting of T cell neoantigens in a spontaneous murine squamous cell carcinoma [Single cell]

first: Joseph

last: Dolina

summary: The comparative resistance of some cancers including head and neck squamous cell carcinoma to checkpoint blockade is speculated to derive from the low frequency of expressed somatic mutations targeted by T cells as neoantigens.  SCCVII, a spontaneously arising murine squamous carcinoma resembling human HNSCC in several key features, is likewise poorly immunogenic as irradiated tumor cells alone fail to induce protective immunity within syngeneic hosts.  Justifying use of this model to identify NeoAgs, we confirm activated CD4+ and CD8+ T cells are detectable and essential for vaccine efficacy of SCC VII and polyI:C co-administration.  Whole-exome sequencing tumor versus normal genome identified 39 nonsynonymous missense mutations that were synthesized into 81 representative 20-mers.  NeoAg-specific CD4+ T cell IFN-γ responses were found against mutations of Pik3ca, Ctnnd1, and Otud5 while both CD4+ and CD8+ T cells produced IFN-γ when stimulated by a single Cltc mutation during in vitro recall assays.  Prophylactic immunization with a mixture of all stimulatory peptides or the Cltc NeoAg alone protected hosts from subsequent tumor challenge.  Further, the Cltc NeoAg, eliciting both CD4+ and CD8+ T cell responses, was also therapeutically beneficial in vivo.  Anti-PD-1 combinatorial blockade resulted in synergistic tumor rejection via boosting Cltc-specific responses and increasing response diversification via epitope spreading.  These data show that a functional NeoAg identification platform can be used to select immunotherapeutically relevant targets and filtration of neoepitopes that co-prime both CD4+ and CD8+ T cell responses is superior for practical intervention of poorly immunogenic tumors.

overall_design: For identifcation of TCRs from cells responding to NeoAg in vitro, TCR clonality was assessed in IFN-γ-captured CD4+ and CD8+ T cells via analysis of single-cell RNA-Seq data.  FASTQ files were first generated using Bcl2fastq (v2.17.0).  Quality control reports that were generated by FastQC (v0.11.2) (14) showed Nextera contamination, therefore cutadapt (v1.13) (15) was run with an adapter mask of 35 to exclude the contaminated regions.  The FASTQ files were then edited by the Seqtk (v1.3) package to increase read quality.  The trimfq function within Seqtk was used with an error rate threshold of 0.01 to trim the ends of each read and increase the data quality.  The trimmed files were analyzed using TraCeR (v0.6.0) (16) and the reference genome GRCm38.  TCR α and β chains detected by TraCeR were completed to full-length sequences by adding corresponding leader peptide sequences retrieved from the international ImMunoGeneTics information system (IMGT).  Productive TCR α and β chains were considered if clonal, which was defined as α and β chains identified together in more than one cell.

first: Joey

last: Lee

first: Feei-Ran

last: Chou

first: Samantha

last: Hall

first: Rukman

first: Sara

last: McArdle

first: Angela

last: Frentzen

first: Manasa

last: Lanka

first: Ashmitaa

middle: L

last: Premlal

first: Jason

last: Greenbaum

first: Grégory

last: Seumois

first: Bjoern

last: Peters

first: Stephen

last: Schoenberger


title: Unbiased functional identification and therapeutic targeting of T cell neoantigens in a spontaneous murine squamous cell carcinoma [Bulk-seq]

overall_design: For identificaion of NeoAg variants, which is described herein, sequence reads from Exome-Seq of the tumor and normal tail samples were aligned to the mm10 reference genome using SpeedSeq Align (v0.0.3a). Exome variants were identified using SpeedSeq Somatic (v0.0.3a) and variants were annotated using SNPeff (v4.1).  Reads from RNA-Seq of the tumor were aligned using STAR aligner (v2.4.1c).  In order to confirm the expression of exome variants in the tumor, the aligned RNA data was compared with the reference genome to check the presence of exome variants using Freebayes software (v0.9.16).  Variants were considered for further analysis only if they met following criteria:  sequencing depth at position of variant ≥ 10 in normal exome as well as in tumor exome and transcriptome, variant allele observations in normal exome = 0, variant allele observations in tumor exome ≥ 10, variant allele frequency in tumor RNA ≥ 20%, somatic score from SpeedSeq ≥ 0, SNP quality score ≥ 20, and the variant was protein coding and protein changing.  For single nucleotide variants, two 20-mer peptides containing the mutation at positions 6 and 15 for each variant were generated using an in-house peptide generation pipeline.  When the variant was near the start or the end of the protein sequence the mutation position was adjusted in the 20-mer peptide due to insufficient flanking amino acids.  For frameshift variants, two long peptides each with mutated amino acid at positions 6 and 15 were generated in such a way that the peptide terminated at the first found stop codon in the mutated sequence.  These long peptides were then broken into 20-mers with overlapping amino acids.  Peptides used in experiments were synthesized by A & A Labs (DBA Synthetic Biomolecules, San Diego, CA).

middle: R

last: Thota

middle: P


title: Protein Kinase A (PKA) inhibition in Saccharomyces cerevisiae and Kluyveromyces lactis

status: Public on Dec 24 2020

city: San Francisco

first: Hana

last: El-Samad

address: 1700 4th Street, Box 2542

department: Biochemistry and Biophysics

institute: University of California San Franicisco

summary: The goal of the study was to compare the response to Protien Kinase A (PKA) inhibition between Saccharomyces cerevisiae and Kluyveromyces lactis.  The ancestor of K. lactis did not undergo the Whole Genome Duplication (or Whole Genome Hybridization) event that S. cerevisiae experienced.  We found that many paralog pairs in S. cerevisiae were differentially induced in response to PKA inhibition, and that the shared ortholog for these paralog paris in K. lactis was typically not induced.  To inhibit PKA, strains containing point mutations rendering PKA sensitive to inhibition by the ATP analog 1-NM-PP1 were generated.  The transcription factors Msn2/4 and Rph1/Gis1 in S. cerevisiae and their shared orthologs in K. lactis were deleted in both species to quantify and compare the effect of those transcription factors on the response to PKA inhibition in each species.

sample_organism:
Saccharomyces cerevisiae
Kluyveromyces lactis

overall_design: Experiments were conducted in S. cerevisiae and K. lactis yeast.  3uM 1-NM-PP1 and DMSO control samples were collected at 50min.  Strains contained either no deleted genes, deletions of Msn2 and Msn4 or their shared ortholog in K. lactis, deletions of Rph1 and Gis1 or their shared ortholog in K. lactis, or deletions of all four genes (or both genes in K. lactis).  In S. cerevisiae all experiments were performed in strains containing either the PKA analog sensitive mutations or WT PKA.  In K. lactis, all experiments were performed in strains containing the PKA analog sensitive strains, except the strain containing no transcription factor deletions, which was performed in both PKA Analog Sensitive and WT PKA strains.  There were 3-4 biological replicates for each species, transcription factor mutation, PKA background, treatment combination, and a few technical replicates were included to assess batch effects of library preparation.

first: Benjamin

last: Heineike

last: El-samad


title: Select hyperactivating NLRP3 ligands enhance the Th1/Th17-inducing potential of human type 2 conventional dendritic cells

status: Public on Dec 02 2020

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

summary:
Among human DCs, the cDC2 subset represents the major human DC subset that is transcriptionally and functionally licensed for inflammasome responses as well as inflammasome formation in the absence of pyroptosis.
These findings may allow for the development of new approaches in the field of adjuvant and vaccine development and define the human cDC2 subpopulation as a prime target for the treatment of inflammasome-dependent inflammatory diseases.

overall_design:
NANOSTRING
cDC1s isolated from PBMCs of a healthy individual, 3h control-treated (3 replicates)
cDC1s isolated from PBMCs of a healthy individual, 3h R848-treated (3 replicates)
cDC2s isolated from PBMCs of a healthy individual, 3h control-treated (3 replicates)
cDC2s isolated from PBMCs of a healthy individual, 3h R848-treated (3 replicates)

first: Lukas

last: Hatscher

first: Christian

last: Lehmann

first: Ariawan

last: Purbojo

first: Constantin

last: Onderka

first: Arndt

last: Hartmann

first: Robert

last: Cesnjevar

first: Olaf

last: Gross

first: Falk

last: Nimmerjahn

first: Ivana

last: Ivanović-Burmazović

first: Meik

last: Kunz

last: Heger

first: Diana

last: Dudziak