title: Male mus musculus transcriptomes from whole liver tissue

city: Durham

first: Vincent

middle: Michael

last: Perez

state: NC

address: 25 Alexandria Wy

department: Translational reasearch

institute: Tempus AI

summary: The ketogenic diet has been successful in promoting weight loss among patients that have struggled with weight gain. This is due to the cellular switch in metabolism that utilizes liver-derived ketone bodies for the primary energy source rather than glucose. Fatty acid transport protein 2 (FATP2) is highly expressed in liver, small intestine, and kidney where it functions in both the transport of exogenous long chain fatty acids (LCFA) and in the activation to CoA thioesters of very long chain fatty acids (VLCFA). We have completed a multi-omic study of FATP2-null (Fatp2-/-) mice maintained on a ketogenic diet (KD) or paired control diet (CD), with and without a 24-hour fast (KD-fasted and CD-fasted) to address the impact of deleting FATP2 under high-stress conditions. Control (wt/wt) and Fatp2-/- mice were maintained on their respective diets for 4-weeks. Afterwards, half the population was sacrificed while the remaining were fasted for 24-hours prior to sacrifice. We then performed paired-end RNA-sequencing on the whole liver tissue to investigate differential gene expression. The differentially expressed genes mapped to ontologies such as the metabolism of amino acids and derivatives, fatty acid metabolism, protein localization, and components of the immune system’s complement cascade, and were supported by the proteome and histological staining.

overall_design: For RNA-sequencing, we used 4 animals for each experimental group, and we had 8 experimental groups, all of which were male mice. The groups were: [1] wildtype mice on a control-ketogenic diet (CD) fasted for 4 hours, [2] wildtype mice on a ketogenic diet (KD) fasted for 4 hours, [3] wildtype mice on a control-ketogenic diet (CD) fasted for 24 hours, [4] wildtype mice on a ketogenic diet (KD) fasted for 24 hours, [5] Fatp2-/- mice on a control-ketogenic diet (CD) fasted for 4 hours, [6] Fatp2-/- mice on a ketogenic diet (KD) fasted for 4 hours, [7] Fatp2-/- mice on a control-ketogenic diet (CD) fasted for 24 hours,  and [8] Fatp2-/- mice on a ketogenic diet (KD) fasted for 24 hours,

first: Jeff

last: Gabell

first: Nishi

last: Wase

first: Mark

middle: R

last: Behrens

first: Concetta

last: DiRusso

first: Paul

last: Black


title: Splicing Inhibition Reveals Novel Roles for SF3B1 in Transcription Dynamics and R-Loop Metabolism

status: Public on Jun 10 2020

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

country: USA

institute: UC Davis

type: Expression profiling by high throughput sequencing

summary: Efficient co-transcriptional splicing has been proposed to suppress the formation of genome-destabilizing R-loops upon interaction between nascent RNA and the DNA template. To test this, we inhibited the SF3B splicing complex using Pladienolide B (PladB) in human K562 cells and mapped R-loop genomic distributions. PladB caused widespread intron retention, as expected, and nearly 2,000 instances of R-loops gains. However, only minimal overlap existed between these two events, arguing that unspliced introns do not cause excessive R-loops. Instead, R-loop gains were driven by a loss of transcription termination over a specific subset of stress-response genes, defining a new class of “downstream of genes” (DoG) aberrant R-loops. Unexpectedly, the predominant response to splicing inhibition was a global R-loop loss over thousands of genes, resulting from a profound loss of transcription elongation. Thus, acute splicing inhibition triggered profound and contrasting alterations in transcriptional dynamics, which were reflected in the global R-loop landscape.

overall_design: RNA-seq, EU-seq, DRIP-seq, and sDRIP-seq were performed on control or treated K562 cells to characterize their polyA RNA, nascent RNA, and R-loop profiles. Specifically, K562 cells were subjected to either nothing, DMSO, or Pladienolide B; each for 2 hours and 4 hours. Each experiment was performed with at least 2 biological replicates.

first: Daisy

last: Castillo-Guzman

first: Stella

last: Hartono

first: Lionel

middle: A

last: Sanz


title: E.coli toxin-antitoxin systems

status: Public on Jun 11 2020

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

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

overall_design: Refer to individual Series


title: Analysis of differential expression profiles of Long noncoding RNA in peripheral blood of patients with active rheumatoid arthritis

city: Nanjing

first: Ming

last: Li

address: NO.138Xianlin Road

country: China

institute: Nanjing University of Chinese Medicine

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

summary: we studied the expression profile of lncRNA in peripheral blood of patients with active RA LncRNA and mRNA expression in peripheral blood from two activity RA patients and two healthy donors were analyzed with microarray profiling. peripheral blood of five active RA patients and five healthy control members were collected. Quantitative real-time PCR was further used to screen and verify the expression of lncRNA to verify the expression of the selected lncRNA; perform bioinformatics analysis to study the potential function of the differentially expressed genes, construct a receiver operating characteristic (ROC) curve to evaluate the clinical diagnostic value of the identified lncRNA, and use correlation analysis to explore the relationship between aberrantly expressed lncRNA that may have diagnostic value and clinical indicators.

overall_design: Two RA patients were used as the RA group, and two healthy people were used as the control group, and 6 ml of peripheral blood were collected respectively.,then perform LncRNAs chips by Arraystar Human LncRNAs chip (Arraystar)

first: Kexun

last: Ma


title: Conditional expression of PfAP2-G for controlled massive sexual conversion in Plasmodium falciparum

city: Barcelona

first: Oriol

last: Llorà-Batlle

address: Carrer Rosselló 153, 1st floor

country: Spain

institute: ISGlobal

type: Genome binding/occupancy profiling by high throughput sequencing


title: Conditional expression of PfAP2-G for controlled massive sexual conversion in Plasmodium falciparum. [ChIP-Seq]

summary: Malaria transmission requires the conversion of some asexual parasites into sexual forms termed gametocytes. The initial stages of sexual development, including sexually-committed schizonts and sexual rings, remain poorly characterized, in part because only a subset of parasites undergo sexual development and they are morphologically identical to their asexual counterparts. Here we present a system based on conditional expression of PfAP2-G, the master regulator of sexual conversion, for controlled sexual induction. Induction resulted in ~90% sexual conversion, which enables the characterization of early sexual stages without further purification. Transcriptomic analysis identified the alterations that follow pfap2-g activation, including identification of genes that are down-regulated. We also show that the inducible system enables the characterization of committed stages at the phenotypic level. Altogether, the inducible lines will facilitate the study of the initial stages of sexual development, which is important for the development of new strategies to stop malaria transmission.

overall_design: Samples from E5ind and 1.2Bind in non-inducing conditions; together with E5ind+Rapa_prol and 1.2Bind+Rapa_prol cultures, were processed to perform a ChIP-Seq experiment against H3K9me3.

first: Lucas

last: Michel-Todó

first: Alfred

last: Cortés


title: Myocardial Infarction accelerates breast cancer via innate immune reprogramming (RNA-seq)

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

summary: Disruptions of systemic homeostasis have emerged as critical regulators of cancer. Recent studies indicate that chronic or acute host stressors (e.g., obesity1, surgery2) alter cancer pathogenesis. Many cancer patients, particularly those with breast cancer, are at increased risk for cardiovascular disease due to treatment toxicity and resulting changes in lifestyle behaviors3-5. While elevated risk and incidence of cardiovascular events in breast cancer is well-established, whether such events impact cancer pathogenesis is not known. Herein, we show that an incident myocardial infarction (MI or heart attack) accelerates breast cancer outgrowth and cancer-specific mortality in mice and humans. In mouse models of breast cancer, MI epigenetically reprogrammed Ly6Chigh monocytes in the bone marrow reservoir to an immunosuppressive phenotype that was maintained at the transcriptional level in monocytes in the circulation and tumor.  In parallel, MI increased circulating Ly6Chigh monocyte levels and recruitment to tumors, and depletion of these cells abrogated MI-induced tumor growth.  Furthermore, evaluation of the relationship between a new onset post-diagnosis cardiovascular event and cancer outcomes in early-stage breast cancer patients revealed increased risk of recurrence and cancer-specific death, highlighting the clinical relevance of our findings. Collectively, our results demonstrate that MI induces alterations to systemic homeostasis, triggering cross-disease communication that accelerates breast cancer.

overall_design: Bulk RNA sequencing

first: Graeme

middle: J

last: Koelwyn

first: Emma

middle: M

last: Corr

first: Coen

last: van Solingen

first: Kathleen

middle: B

last: Albers

first: Milessa

middle: S

last: Afonso

first: P

last: Schlegel

first: Monika

last: Sharma

first: Lianne

middle: C

last: Shanley

first: Tessa

last: Barrett

first: Karishma

last: Rahman

first: Valeria

last: Mezzano

first: Edward

last: Fisher

first: Jonathan

middle: D

last: Newman

first: Daniela

middle: F

last: Quail

first: Erik

last: Nelson

first: Bette

last: Caan

first: Lee

middle: W

last: Jones

first: Kathryn

last: Moore


title: MAU2 and NIPBL variants in Cornelia de Lange syndrome reveal MAU2-independent loading of cohesin and uncover protective mechanisms against early truncating mutations in NIPBL

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

summary: For its association with chromatin, the cohesin complex depends on a heterodimer formed by NIPBL and MAU2. Variants in NIPBL are the main cause of CdLS and result in NIPBL haploinsufficiency. Using CRISPR, we generated cells homozygous for an out-of-frame duplication in NIPBL. Remarkably, alternative translation initiation rescued NIPBL expression in these cells and produced an N-terminally truncated NIPBL that lacks MAU2-interaction domain, causing a dramatic reduction of MAU2 protein levels while a lot of NIPBL functions remain intact.

overall_design: ChIP sequencing of SMC3, NIPBL wild type (WT) vs CRISPR edited cell HEK293T lines using HiSeq2500 sequencer. In total 9 samples are analysed. Smc3: WT vs CRISPR edited, 4 samples in total including input. NIPBL: WT vs CRISPR edited, 5 samples in total, including input.

first: Ilaria

last: Parenti

first: Erwan

last: Watrin

first: Frank

last: Kaiser

first: Kerstin

last: Wendt


title: Genome-wide maps of SWI/SNF complexes binding in WT and ARID1-less H2.35 cells

city: DALLAS

first: Zixi

last: Wang

state: TX

address: 5323 HARRY HINES BLVD

department: CRI

institute: UT SOUTHWESTERN MEDICAL CENTER

summary: Globally, the three categories of intact SWI/SNF complexes in control cells have shared and unique binding peaks, with cBAF showing the most abundant binding sites followed by ncBAF and pBAF. In control cells, within cBAF, ARID1B bound to only a subset of ARID1A peaks. In control cells, the binding pattern of BAF45d corresponded to ARID1A patterns, but binding was virtually eliminated in ARID1-less cells. In ARID1-less cells, ARID2 binding was essentially eliminated whereas Brd9 binding was unaltered.

overall_design:
ChIP-Seq of SWI/SNF subunits in WT and ARID1-less H2.35 cells.
The ChIPs were all performed using a Ty1 antibody (https://www.diagenode.com/en/p/ty1-monoclonal-antibody-classic-50-ug-25-ul). Different proteins indicated in each file name were cloned with a 3xTy1 tag at the C-terminal and expressed in WT and ARID1-less (ARID1A inducible-KD and ARID1B KO) H2.35 cells, followed by ChIP using Ty1 antibody.

first: Wang

last: Zixi

first: Chen

last: Kenian

first: Zhu

last: Hao


title: Transcriptomic analysis of bone and fibrous tissue morphogenesis during digit tip regeneration in the adult mouse

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

summary:
Purpose: Investigate the transcriptomic landscape throughout the time course of murine digit regeneration after level-dependent amputation.
Methods: The terminal phalanx bone of hind limb digits was subjected to either a distal amputation (25% bone length loss) or proximal amputation (65% bone length loss). Total RNA was isolated from bone and fibrous tissues distal to the distal interphalangeal joint at 12, 14, and 21 days post-amputation (DPA). mRNA library was sequenced using Illumina HiSeq 3000. Trimmed reads were aligned to the mouse genome mm10 and batch-corrected.
Results: A limb-specific developmental signaling pathway is transiently upregulated at 14 DPA after distal amputation, corresponding with regeneration of digit tip tissues. Absence of a limb-specific pathway after proximal amputation corresponded with minimal regeneration and fibrotic scarring.
Conclusions: Digit regeneration is a level-dependent and spatiotemporally controlled process, with distal and proximal amputations showing significant differences in gene expression and tissue regrowth over time.

overall_design: mRNA profiles of the murine digit tip at various time points after distal amputation or proximal amputation were generated using high throughput sequencing.

first: Feini

last: Qu

first: Ilan

last: Palte

first: Paul

last: Gontarz

first: Farshid

last: Guilak


title: Myocardial Infarction accelerates breast cancer via innate immune reprogramming (ATAC-seq)

first: Emily

last: Brown

summary: Disruptions of systemic homeostasis have emerged as critical regulators of cancer. Recent studies indicate that chronic or acute host stressors (e.g., obesity1, surgery2) alter cancer pathogenesis. Many cancer patients, particularly those with breast cancer, are at increased risk for cardiovascular disease due to treatment toxicity and resulting changes in lifestyle behaviors3-5. While elevated risk and incidence of cardiovascular events in breast cancer is well-established, whether such events impact cancer pathogenesis is not known. Herein, we show that an incident myocardial infarction (MI or heart attack) accelerates breast cancer outgrowth and cancer-specific mortality in mice and humans. In mouse models of breast cancer, MI epigenetically reprogrammed Ly6Chigh monocytes in the bone marrow reservoir to an immunosuppressive phenotype that was maintained at the transcriptional level in monocytes in the circulation and tumor.  In parallel, MI increased circulating Ly6Chigh monocyte levels and recruitment to tumors, and depletion of these cells abrogated MI-induced tumor growth.  Furthermore, evaluation of the relationship between a new onset post-diagnosis cardiovascular event and cancer outcomes in early-stage breast cancer patients revealed increased risk of recurrence and cancer-specific death, highlighting the clinical relevance of our findings. Collectively, our results demonstrate that MI induces alterations to systemic homeostasis, triggering cross-disease communication Disruptions of systemic homeostasis have emerged as critical regulators of cancer. Recent studies indicate that chronic or acute host stressors (e.g., obesity1, surgery2) alter cancer pathogenesis. Many cancer patients, particularly those with breast cancer, are at increased risk for cardiovascular disease due to treatment toxicity and resulting changes in lifestyle behaviors3-5. While elevated risk and incidence of cardiovascular events in breast cancer is well-established, whether such events impact cancer pathogenesis is not known. Herein, we show that an incident myocardial infarction (MI or heart attack) accelerates breast cancer outgrowth and cancer-specific mortality in mice and humans. In mouse models of breast cancer, MI epigenetically reprogrammed Ly6Chigh monocytes in the bone marrow reservoir to an immunosuppressive phenotype that was maintained at the transcriptional level in monocytes in the circulation and tumor.  In parallel, MI increased circulating Ly6Chigh monocyte levels and recruitment to tumors, and depletion of these cells abrogated MI-induced tumor growth.  Furthermore, evaluation of the relationship between a new onset post-diagnosis cardiovascular event and cancer outcomes in early-stage breast cancer patients revealed increased risk of recurrence and cancer-specific death, highlighting the clinical relevance of our findings. Collectively, our results demonstrate that MI induces alterations to systemic homeostasis, triggering cross-disease communication that accelerates breast cancer.

overall_design: ATAC sequencing

first: Graeme

last: Koelwyn

first: Emma

last: Corr

first: Coen

last: van Solingen

first: Kathleen

last: Albers

first: Milessa

last: Afonso

first: P

last: Schlegel

first: Monika

last: Sharma

first: Lianne

last: Shanley

first: Tessa

last: Barrett

first: Karishma

last: Rahman

first: Valeria

last: Mezzano

first: Edward

last: Fisher

first: Jonathan

last: Newman

first: Daniela

last: Quail

first: Erik

last: Nelson

first: Bette

last: Caan


title: Conditional expression of PfAP2-G for controlled massive sexual conversion in Plasmodium falciparum [array]

first: Oriol

last: Llorà-Batlle

overall_design: Time-course transcriptomic analysis was performed using tightly synchronized E5ind cultures (0-5 h) induced with 10 nM rapamycin (Rapa) for 1 h at 25-30 hpi or with DMSO as control (Dmso). Samples for transcriptomic analysis were collected 15 h (T1), 28 h (T2) and 38 h (T3) after induction  (corresponding to 40-45 hpi schizonts of the first cycle, and 5-10 or 15-20 hpi rings of the next cycle, respectively). The reference pool consited of RNA from E5 wild-type cultures and E5ind cultures, in non-inducing conditions, throughout the asexual blood cycle. The analysis was performed with the results obtained from two independent biological replicates. A total of 12 individual microarray samples were processed. For the first replicate we used a microarray design AMADID-084561, which was later modified to include a small number of new probes and used for the second replicate (AMADID-085763).

first: Lucas

last: Michel-Todó

first: Alfred

last: Cortés


title: The p53-dependent role of JAB1 in OS pathogenesis

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: JAB1 is a regulator of ubiquitin mediated protein degradation upstream of the 26S proteasome. JAB1 regulates the ubiquitin proteasome system through controlling the activity of the largest family of E3 ubiquitin ligases, the Cullin-RING Ligases.  JAB1 is also a transcriptional co-factor contolling the expression of numerous genes and regulates musculoskeletal development in vivo. It is reported that JAB1 is overexpressed in many cancers, making it a potential oncogene. Thus, JAB1 has a highly spatiotemporal specific role in development and cancer pathogenesis. This study aims to determine the JAB1-mediated transcriptome that exists in osteosarcoma cells.

overall_design: Lentiviral shRNA silencing of JAB1 was performed in the metastatic osteosarcoma cell line 143B. 3 independent scrambled controls and 3 independent shRNA knockdown samples using 2 different shRNAs were submitted for standard RNA-sequencing protocol.

first: William

middle: E

last: Samsa

first: Alex

last: Miron

first: Ricky

first: Guang

last: Zhou


title: Epidermal basal cell-specific in vivo ribosome profiling to describe the translation landscape of HrasG12V and Eif2b5

city: Seattle

first: Elise

middle: Y

last: Cai

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: eIF2B5 is necessary for HrasG12V hyperplastic growth.  Ribosome profiling was used to describe HrasG12V and WT dependence on eIF2B5-mediated translation.

overall_design: E9.5 HrasG12V and WT mouse epidermis was transduced by in utero injection with shScrambled control or shEif2b5. E18.5 epidermal basal cells were enriched for ribosome profiling and RNAseq.

first: Slobodan

last: Beronja


title: Fli1 downregulation in scleroderma myeloid cells has profibrotic and proinflammatory effects

status: Public on Jun 09 2020

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Scleroderma is an autoimmune connective tissue disease characterized by immune dysregulation, vasculopathy and fibrosis. We have previously demonstrated that low Fli1 expression in scleroderma fibroblasts and endothelial cells plays an important role in SSc pathogenesis. Cells of myeloid and lymphoid origin also express Fli1 and are dysregulated in patients with SSc, playing key roles in disease pathogenesis However,  a role for immune Fli1 in SSc has not yet been described. Our aim was to elucidate whether Fli1 contributes to the immune dysregulation seen in scleroderma. Comparison of the expression of Fli1 in monocytes, B- and T-cell fractions of PBMCs isolated from scleroderma patients and healthy controls, showed an increase in Fli1 levels in monocytes. We used siRNA transfected human myeloid cells and mouse peritoneal macrophages obtained from Fli1flox/floxLysMCre+/+ mice, and found that markers of alternative macrophage activation were increased with Fli1 deletion. Coculture of Fli1-deficient myeloid cells and primary human or mouse fibroblasts resulted in a potent induction of collagen type I, independent of TGFβ upregulation.  We next analyzed global gene expression profile in response to Fli1 downregulation, to gain further insight into the molecular mechanisms of this process and to identify differentially expressed genes in myeloid cells. Of relevance to SSc, the top most upregulated pathways were hallmark IFN-ɣ and IFN-α response. Additionally, several genes previously linked to SSc pathogenesis and fibrosis in general were also induced, including MCP-1, MCP-3, MMP12, and CXCL10. ANKRD1, a profibrotic transcription co-regulator was the top upregulated gene in our array. Our results show that Fli1-deficient myeloid cells share key features with cells from SSc patients, with higher expression of profibrotic markers and activation of interferon responsive genes, thus suggesting that low Fli1 may contribute to SSc pathogenesis.

overall_design: THP-1 cells were treated with scrambled or Fli1 siRNA and gene expression was profiled.

first: Andreea

last: Bujor

first: Fatima

last: El Adili

first: Arshi

last: Parvez

first: Grace

last: Malden

first: Maria

last: Trojanowska


title: Differential expression of exosomal miRNAs between medulloblastoma patients and healthy controls

city: Shanghai

first: Ping

last: Xue

address: Rd Wanyuan

institute: Children's Hospital of Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: We characterized circulating exosomal miRNA profiles by miRNA-seq to identify those differentially expressed in children with MB relative to heathy controls

overall_design: Plasma samples from 4 medulloblastoma patients and 4 healthy controls were enrolled in the experiment. Exosomes were extracted, total RNA were isolated from the identified exosomes.miRNA profilings were performed.

first: Yufeng


title: Genomic binding profiles for ZNF165, ZNF446, and SMAD3 in triple-negative breast cancer

city: Dallas

first: Angelique

last: Whitehurst

address: 6001 Forest Park Rd

institute: University of Texas Southwestern Medical Center

summary: The testis protein ZNF165 is aberrantly expressed in triple-negative breast cancer (TNBC), where it modulates TGFβ signaling to promote tumor growth and survival. To investigate whether ZNF165 functions in this capacity via cooperation with SMAD3, a canonical TGFβ-induced transcription factor, we performed ChIP-seq for both factors in TNBC cell lines (WHIM12 and SUM159). Additionally, we established genomic binding profiles for ZNF446, a previously uncharacterized transcription factor that we have identified as a member of a ZNF165-SMAD3 complex.

overall_design: ChIP-seq for ZNF165, ZNF446, and SMAD3 in WHIM12 and/or SUM159 cells

first: Zane

last: Gibbs


title: CD73 Immune Checkpoint Defines Inducible Regulatory NK cells in the Tumor Microenvironment

city: Solna

first: Andreas

last: Lundqvist

address: Solnavägen 30, J6:20

country: Sweden

institute: Karolinska Institutet

summary: High levels of ecto-5'-nucleotidase (CD73) have been implicated in immune suppression and tumor progression. Elevated levels of CD73 has also been observed in patients who progress on anti–PD-1 immunotherapy. While regulatory T cells can express CD73 and inhibit T cell responses via the production of adenosine, less is known if conventional T cells and natural killer (NK) cells can express CD73. We found that the expression of CD73 is restricted to tumor-infiltrating NK cells and the frequency of these cells correlate with larger tumor size in patients with breast cancer. In addition, the expression of other immune checkpoint receptors including LAG-3 and VISTA was significantly higher in CD73 positive NK cells than on CD73 negative NK cells. Furthermore, the prognostic value of CD73 gene expression was influenced by NK cell signature expressed in patients with breast cancer and sarcoma. Mechanistically, upon engagement of 4-1BBL on tumor cells, NK cells transport CD73 in intracellular vesicles to the cell surface and extracellular space via actin polymerization-dependent exocytosis. These CD73 positive NK cells undergo transcriptional reprogramming and upregulate IL10 production via STAT3 transcriptional activity and suppress CD4 T cell activity. Altogether, our results support that tumors can hijack NK cells as a means to escape immunity and that CD73 expression defines an inducible population of NK cells with immune regulatory properties within the tumor microenvironment.

overall_design: NK cell populations from 5 healthy human donor peripherial blood mononuclear cells (PBMCs) were FAC-sorted based on CD73 surface expression 4 hours post tumor co-culture and transcriptional profiles were generated by high-throughput sequencing, in replicate, using the Illumina NextSeq 500 platform.

first: Emily

last: Blake

first: Marissa

last: Brooks

first: Shiyong

last: Neo


title: Transcriptome study of Acinobacter baumannii ddrR mutants in the presence or absence of mitomycin C

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: All RNA samples were isolated from the ddrR mutant strain of Acinobacter baumannii. The triplicates labeled “plus” have been subjected to mitomycin C (MMC) exposure (treated) and the triplicates labeled “minus” were not exposed to MMC (control). A comparison between treated and control samples to determine differential gene expression was performed.

overall_design: mRNA profiles of ddrR mutants in the presence of MMC (treated) and absence of MMC (control) were performed in triplicate.

first: Janelle

last: Hare

first: Sabine

last: Waigel

first: Juw

last: Park


title: RNA-Seq transcriptome profiling of embryonic age 17.5 or E17.5 ventricles of cardiac specific-estrogen-related receptor alpha and gamma (ERRa/g) knock out (KO) mouse generated by Nkx2.5-Cre driver and its control wild type.

city: Philadelphia

first: Tomoya

last: Sakamoto

state: PA

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

department: Cardiovascular Institute

institute: University of Pennsylvania

summary: Transcriptional regulatory circuits that drive cardiomyocyte maturation during the developmental process are poorly understood. Estrogen-related receptor alpha and gamma (ERRa/g) have been shown to be involved in all aspects of mitochondrial energy production. However, the function of ERR during the cardiac developmental process is not understood well. To examine the role of (ERRa/g), we generated cardiac-specific ERRa/g knockout (KO) mice and found that the KO mice died within 24 hours post-birth. At embryonic age 17.5, a number of genes involved in oxidative mitochondrial metabolism including OXPHOS, TCA cycle, and fatty acid oxidation were dramatically downregulated. Also, the mutant hearts exhibited a significant downregulation of adult cardiac contractile protein, ion channel and Ca2+ handling genes. In contrast, fetal cardiac genes and non-cardiac genes that express in fibroblast or endothelial cells were ectopically induced in the KO hearts. These results suggest that ERRa/g are essential factors for the broad cardiomyocyte maturation program.

overall_design: Examination of how gene expression levels are changed by KO ERRa/g in the embryonic hearts (E17.5) in triplicates. Two hearts were pooled for each replicate.

first: Feng

last: Qi

first: Daniel

middle: P

last: Kelly


title: Genome-wide estrogen-related receptor gamma (ERRg) occupancy in human iPS cell-derived cardiomyocytes (hiPSC-CMs)

summary: Estrogen-related receptor gamma (ERRg) has been shown to control gene expression involved in a broad range of mitochondrial energy metabolism including oxidative phosphorylation, TCA cycle, and fatty acid oxidation. However, ERRg direct targets were not identified in cardiomyocytes. With ERRg ChIP-seq, we found ERRg peaks on the promoter regions of mitochondrial energy metabolic genes as expected. Besides, ERRg extensively distributed the promoter regions of cardiac contractile, ion channels and Ca2+ handling protein genes. Surprisingly, the peaks also were found on non-cardiomyocyte genes and genes expressed in early-stage cardiomyocytes.

overall_design: With ChIP-seq, examination of ERRg occupancy on the human genome in wild type hiPSC-CMs and ERRg KO hiPSC-CMs.

first: Junil

last: Kim

first: Kyoung

last: Won


title: RNA-sequencing of fetal thymic epithelial cells (TECs), in control, loss-of-function and gain-of-function Notch mutants

city: Duarte

first: Anastasia

middle: I

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

summary: We have shown that Notch signalling pathway is a potent regulator of thymic epithelial progenitor cell differentiation. Here we generated RNA-sequencing profile of early fetal TECs expressing low, normal or high levels of Notch. We found that loss of Notch function has no significant effects on the E12.5 TEC transcriptome. In contrast, loss and gain-of-function of Notch result in considerable changes in the E14.5 TEC transcriptome. This study uncovered a role of Notch in regulating cell state in TEC differentiation, as well as target genes and pathways regulated by Notch in this context.

overall_design: Assay the transcriptomes of E12.5 control and Rbpj conditional knockout TECs and E14.5 control, Rbpj knockout and Rosa26NICD TECs. 100 cells per sample.

first: Dong

last: Liu

first: Simon

last: Tomlinson

first: C

last: Blackburn


title: Inducible heart specific MPC1 knockdown in adult mice

city: Salt Lake City

first: Jordan

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

summary: We report that knocking down the Mitochondrial Pruvate Carrier 1 (MPC1) in the hearts of adult mice is sufficient to induce hypertrophy and heart failure.

overall_design: Ventricular mRNA profiles of  both WT and MPC1CKO mice at 8 weeks and 16 weeks post KO induction.

first: Shannon

last: Schlater

first: Christopher

last: Stubben

first: Sutip

last: Navankasattusas

first: Rachit

last: Badolia

first: Ahmad

last: Cluntun

first: Stavros

last: Drakos


title: Quality control measures for placental sample purity in DNA methylation array analyses

city: Adelaide

first: Claire

last: Roberts

state: SA

address: AHMS building

department: Adelaide Medical School

country: Australia

institute: The University of Adelaide

type: Methylation profiling by genome tiling array

summary: The purity of tissue samples can affect the accuracy and utility of DNA methylation array analyses. This is particularly important for the placenta which is hypomethylated. Placental villous tissue from early pregnancy terminations can be difficult to separate from the non-villous tissue, resulting in potentially inaccurate results. We used several methods to identify mixed placental samples using DNA methylation array datasets from our laboratory and those contained in the NCBI GEO database, highlighting the importance of determining sample purity during quality control processes.

overall_design: Placental samples from 10 first trimester placentas (chorionic villi) were profiled using the Infinium HumanMethylation850 BeadChip.

first: Qianhui

last: Wan

middle: T


title: Transcriptomic Analysis of the Regulation of Cancer Stemness in Breast Ductal Carcinoma In Situ by Vitamin D Compounds

city: Piscataway

first: Nanjoo

last: Suh

state: NJ

address: 164 Frelinghuysen Road

department: Chemical Biology

institute: Rutgers, The State University of New Jersey

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptomic Analysis of the Regulation of Cancer Stemness in Breast Ductal Carcinoma In Situ by Vitamin D Compounds [Bisulfite-seq]

summary: A global profiling of changes in the gene signature of DCIS regulated by vitamin D compounds was examined in MCF10DCIS mammospheres.

overall_design: DNA CpG methylation profiles of MCF10DCIS mammospheres treated with two different vitamin D compounds for 5 days

first: Naing

middle: L

last: Shan

first: Audrey

last: Minden

first: Philip

last: Furmanski

first: Min

last: Bak

first: Li

last: Cai

first: Roman

last: Wernyj

first: David

last: Sargsyan

last: Cheng

first: Renyi

last: Wu

first: Hsiao-Chen

last: Kuo

first: Shanyi

last: Li

first: Mingzhu

last: Fang

first: Hubert

last: Maehr

first: Ah-Ng

last: Kong


title: New, Forgotten, and Savings Memory for Long-Term Sensitization in Aplysia Pleural Ganglia

city: River Forest

first: Robert

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

summary: We used a custom-designed microarray to characterize the transcriptional response that accompanies longt-term sensitization training in the marine mollusk Aplysia californica.  We characterized transcription for a new memory (1 day after training), a forgotten memory (8 days after training) and for a long-term savings memory (8 days after training but 1 day after a reminder that re-instates the sensitization memory).  All animals received a 1-day unilateral LTS training protocol (4 rounds of noxious shock at 30 min intervals, each shock 10s of 1/2s off 1/2on 90mA 60-hz biphasic square-wave shock).  This produced robust sensitization in all animals (measured as an increase in T-SWR response from baseline to 24h after training).  In the forgetting condition, animals received training on day 1, and post-tests on days 7 and 8 showed little-to-no evidence of recall (T-SWR responses on the trained side returned to close to baseline).  In the savings condition, animals received training on day 1 that produced strong sensitization, showed forgetting on day 7, and then received a weak bilateral shock as a reminder (day 7), producing a long-term savings memory on day 8 (a re-instatement of the behavioral expression of sensitization on the previously trained side).  In the new memory condition, animals received sham training on day 1, then real training on day 7, producing robust sensitization measured on day 8.  Pleural ganglia were harvested on day 8.  Samples from a left-trained and right-trained animal were combined to smooth out lateralized gene expression.  The pleural ganglia contains the VC nociceptors, which are thought to play a primary role in expressing LTS memory.

overall_design: This is a 3 (Phase of Memory: New, Forgotten, Savings) x 2 (Sensitization: Trained vs. Untrained) mixed design.  Each array is a two-color approach hybridized to a matched trained and untrained set of samples (with each sample containing tissue from a left- and right-trained animal).  There are 8 biological replicates for each of the 3 phases of memory (New, Forgotten, Savings), yielding 24 arrays run on 3 plates.  Dye swaps were used for 1/2 the samples in each condition, and both condition and dye swap was balanced across plates.

first: Irina


title: AMINO SUGARS RESHAPE INTERACTIONS BETWEEN STREPTOCOCCUS MUTANS AND STREPTOCOCCUS GORDONII

city: Gainesville

first: Lin

last: Zeng

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: Amino sugars, particularly glucosamine (GlcN) and N-acetylglucosamine (GlcNAc) are abundant carbon and nitrogen sources that are continually supplied in host secretions and the diet to biofilms colonizing the human mouth. Evidence is emerging that these amino sugars may provide an ecological advantage to beneficial commensals over oral pathobionts. Here we performed transcriptome analysis on Streptococcus mutans and Streptococcus gordonii growing in single-species or dual-species cultures with glucose, GlcN or GlcNAc as the primary carbohydrate source. Compared to glucose, GlcN caused drastic transcriptomic shifts in each bacterium when they were cultured alone. Likewise, co-cultivation in the presence of GlcN yielded transcriptomic profiles that were dramatically different than the single-species results from GlcN-grown cells. In contrast, GlcNAc elicited only minor changes in the transcriptome of either organism, in both single- and dual-species cultures. Interestingly, genes involved in pyruvate metabolism were among the most significantly affected by GlcN in both species, and these changes were consistent with measurements of pyruvate in culture supernates. Differing a previous report, growth of S. mutans alone with GlcN inhibited expression of multiple operons required for mutacin production. Co-cultivation with S. gordonii consistently increased the expression by S. mutans of two manganese transporter operons (slo and mntH) and decreased expression of mutacin genes. Conversely, S. gordonii appeared to be less affected by the presence of S. mutans, but did show increases in genes for biosynthetic processes in the co-cultures. In conclusion, amino sugars profoundly altered the interactions between the pathogen and the commensal, likely by reprogramming their central metabolism.

sample_organism:
Streptococcus gordonii
Streptococcus mutans

overall_design: mRNA profiling of Streptococcus mutans and Streptococcus gordonii, each grown to exponential phase in batch on a TV medium supplemented with glucose, GlcN, or GlcNAc, in the form of single-species and mixed-species cultures.

first: Lulu

last: Chen

first: Alejandro

last: Riveros Walker

last: Burne


title: Transcriptomic Analysis of the Regulation of Cancer Stemness in Breast Ductal Carcinoma In Situ by Vitamin D Compounds [RNA-Seq]

first: Nanjoo

last: Suh

overall_design: mRNA profiles of MCF10DCIS mammospheres treated with two different vitamin D compounds for 5 days

first: Naing

last: Shan

first: Audrey

last: Minden

last: Furmanski


title: CDCA2 inhibits apoptosis and promotes cell proliferation in prostate cancer and is directly regulated by HIF-1α pathway

city: Shenzhen

first: Yeqing

last: Yuan

address: Dongmen Road

institute: Shenzhen People's Hospital

summary: PURPOSE: In order to identify differential expression in Pca and test the gene expression profile in CDCA2 knockdown Du145 cell.

overall_design: RNA Sequencing was used to test the mRNA levels of PCa cell lines and normal prostate tissue. And RNA-sequencing  was used to determine expression profile in Du145 siControl and siCDCA2 samples.


title: Luminal Stem Cell Determinant SOX9 Controls Lineage Plasticity and Progression in Basal-Like Breast Cancer (ATAC-seq)

city: Bronx

first: John

middle: Robert

last: Christin

address: 1301 Morris Park Avenue, Room 108/114

institute: Albert Einstein College of Medicine

summary: Lineage plasticity plays an important role in the development of basal-like breast cancer (BLBC), an aggressive cancer subtype. Although studies suggest BLBC is likely to originate from luminal progenitor cells, it acquires substantial basal cell features and contains a heterogenous collection of cells exhibiting basal, luminal and bipotent phenotypes. Why luminal progenitors are prone to BLBC transformation and what drives luminal-to-basal/bipotent reprogramming remains unclear. Here we show that the transcription factor SOX9 acts as a determinant for ER– luminal stem/progenitor cells (LSPCs). SOX9 controls LSPC activity in part by activating both canonical and non-canonical NF-B signaling. Inactivation of p53 and Rb in a BLBC mouse tumor model leads to upregulation of SOX9, which drives luminal-to-bipotent reprogramming in vivo. SOX9 deletion inhibits the progression of benign, neoplastic lesions to invasive carcinoma. Furthermore, SOX9 is overexpressed and correlated with shorter relapse-free survival in human BLBC. These data show that ER– LSPC determinant SOX9 acts as a lineage-specific driver for BLBC transformation.

overall_design: Mammary glands from three Sox9-GFP; C3(1)/Tag animals were reduced to a single cell suspension. From this suspension luminal Sox9-GFP high and luminal Sox9-GFP low cells were FACS sorted and nuclei was isolated from these populations. The resulting nuclei were exposed to Tn5 and transpoase accesible DNA was sequenced to determine difference in genome accesibility.

middle: R

first: Wenjun

last: Guo


title: RNA-seq analysis of iPSC-derived brain microvascular endothelial cells following long-term cryopreservation

status: Public on Jun 08 2020

city: BALTIMORE

first: Peter

last: Searson

state: MD

address: 3400 North Charles Street

institute: Johns Hopkins University

summary: We report changes in gene expression from iPSC to iPSC-derived brain microvascular endothelial cells (dhBMECs) and from one-year cryopreservation of dhBMECs.

overall_design: 9 total samples collected; experiments were conducted using the BC1 iPSC line: iPSCs (n = 3), freshly differentiated dhBMECs (n = 3), one-year cryopreserved dhBMECs (n = 3)

first: Raleigh

last: Linville

last: Ye


title: Genome-wide maps of HHEX binding

city: Tokyo

first: Shuhei

last: Asada

address: 4-6-1 Shirokanedai, Minato-ku

department: Cellular Therapy

country: Japan

institute: Institute of Medical Science, The University of Tokyo

summary: The identification of the binding sites of HHEX.

overall_design: To identify the bona fide binding sites of HHEX, ChIP-seq analysis was performed on HEK293T cells transiently expressing HA-tagged HHEX along with the empty vector control.

first: Reina

last: Takeda

first: Sung-Joon

last: Park

first: Akihiko

last: Yokoyama

first: Akinori

last: Kanai

first: Kenta

last: Nakai

first: Toshiya

last: Inaba

first: Susumu

last: Goyama

first: Toshio

last: Kitamura


title: The effects of expression of mutant ASXL1 and HHEX on hematopoietic cells

summary: To identify target genes of mutant ASXL1 (ASXL1-MT) and HHEX in hematopoietic cells, we performed RNA-seq using RUNX1-ETO expressing cord blood cells transduced with vector or ASXL1-MT together with vector or HHEX.

overall_design:
Method:  RUNX1-ETO expressing cord blood cells were transduced with control vector, ASXL1-MT  (coexpressing GFP),  HHEX (coexpressing NGFR) or  ASXL1-MT+HHEX.  48hr after trunsduction,  GFP+/NGFR+ cells were sorted by FACS. Total RNA extracted from sorted GFP+/NGFR+ cells were then subjected to RNA-seq analysis.
Three biologically independent experiments were perfomed for each sample.

first: Akiko

last: Matsumoto

first: Satoshi

last: Yamasaki

first: Tatsuhiro

last: Shibata


title: Luminal Stem Cell Determinant SOX9 Controls Lineage Plasticity and Progression in Basal-Like Breast Cancer (Sox9-KO)

last: Christin

overall_design: Mammary glands from three Sox9Fl/Fl animals and thee MMTV-iCre; Sox9Fl/Fl animals, in diestrus, were reduced to a single cell suspension sperately. From the Sox9Fl/Fl animals ER-negative luminal cells (Lin-,EpcamHi,CD49fLo,Sca1-negative) were sorted into Trizol LS. From the MMTV-iCre;Sox9Fl/Fl animals the same gating scheme was used, with the addition of the cells being ECFP+, to sort Sox9-null ER-negative luminal cells into Trizol LS. The resulting RNA was analyzed for gene expression differences by microarray.


title: Transcriptome analysis using RNA sequencing of the hippocampus of aged LPAR2-/- versus wildtype control mice

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

country: Germany

institute: Goethe University Frankfurt

summary: We assessed the effect of a deletion of the lysophosphatidic acid receptor, LPAR2 in mice on gene regulation in the hippocampus of aged mice by comparing RNA-seq expression profiles. Presynaptic LPAR2 fortifies the release of glutamate, hence increases neuronal excitability and baseline activity. LPAR2 deficiency prevents an age-associated hyperexcitability and decline of hippocampal long-term-potentiation and improves repose and attention in behaving animals. RNAseq was performed to assess if these protective features manifested at the expressional level of pro-longevity or pro-aging genes. A total number of 18126 genes was reliably detected, and 16420 passed the filtering criteria of >3 valid samples per group. GSEA gene set enrichment analysis was used for gene ranking and identication of top up- and downregulated genes and evaluation of their functions based on P-value, Q-value, fold change and abundance. Among the top downregulated genes were several typical neuronal activity markers including Fos, Fosb, Egr2 suggesting that indeed neuronal baseline activity was lower in LPAR2-/- hippocampus.

overall_design: Hippocampal RNA from middle aged to aged mice was analyzed by RNA sequencing of 7 biological replicates using an Illumina HiSeq4000 system.

first: Johannes

last: Vogt

first: Susanne

last: Gerber


title: Role of HHEX in hematopoietic cells


title: Luminal Stem Cell Determinant SOX9 Controls Lineage Plasticity and Progression in Basal-Like Breast Cancer

first: John


title: Luminal Stem Cell Determinant SOX9 Controls Lineage Plasticity and Progression in Basal-Like Breast Cancer (Sox9-GFP)

summary: Lineage plasticity plays an important role in the development of basal-like breast cancer (BLBC), an aggressive cancer subtype. Although studies suggest BLBC is likely to originate from luminal progenitor cells, it acquires substantial basal cell features and contains a heterogenous collection of cells exhibiting basal, luminal and bipotent phenotypes. Why luminal progenitors are prone to BLBC transformation and what drives luminal-to-basal/bipotent reprogramming remains unclear. Here we show that the transcription factor SOX9 acts as a determinant for ER– luminal stem/progenitor cells (LSPCs). SOX9 controls LSPC activity in part by activating both canonical and non-canonical NF-KB signaling. Inactivation of p53 and Rb in a BLBC mouse tumor model leads to upregulation of SOX9, which drives luminal-to-bipotent reprogramming in vivo. SOX9 deletion inhibits the progression of benign, neoplastic lesions to invasive carcinoma. Furthermore, SOX9 is overexpressed and correlated with shorter relapse-free survival in human BLBC. These data show that ER– LSPC determinant SOX9 acts as a lineage-specific driver for BLBC transformation.

overall_design: Mammary glands from three Sox9-GFP; C3(1)/Tag animals were reduced to a single cell suspension. From this suspension luminal Sox9-GFP high and luminal Sox9-GFP low cells were FACS sorted and RNA was isolated from these populations. The resulting RNA was analyzed for gene expression differences by microarray.

first: Wenjun

last: Guo


title: RRBS Profiling of Clonal Cell Lines with Different Circadian Period

first: Joseph

last: Takahashi

address: 5323 Harry Hines Blvd., NA4.118

department: HHMI, Neuroscience

summary: Composed of negative feedback loops, circadian oscillations are thought to be noise-resistant. Yet, individual cells in culture are remarkably heterogenous, oscillating independently and with different period lengths. To assess whether differential methylation contributes to heritable heterogeneity of circadian periods, we used reduced representation bisulfite sequencing (RRBS) to explore DNA methylation profiles and their correlation with the transcriptome in the 10 clonal cell lines.  To investigate the mechanisms underlying this heterogeneity, we generated and characterized hundreds of clonal cell lines from the same parent culture. By comparing clonal lines with different circadian periods, we identified a group of differentially methylated regions (DMRs).

overall_design: Divided 10 clonal cell lines into 2 groups based on circadian period length. Compare DNA methylation profiles from different groups to identify  differentially methylated regions (DMRs) potentially responsible for circadian periodicity determination.

first: Yan

last: Li


title: Wide-spread disruption of transcription termination in HSV-1 infection:  Next generation sequencing of total and newly transcribed (4sU-RNA) RNA from different virus strains and mutant viruses

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Primary human foreskin fibroblasts (HFF) were infected with the indicated HSV-1 strains and mutants thereof at a multiplicity of infection (MOI) of 10. Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. Newly transcribed RNA was purified following the protocol described in Raedle et al. JoVE 2013.

overall_design: Newly transcribed RNA was labelled for one hour at the indicated times of infection. Cells were harvested immediately thereafter using Trizol. Following isolation of total RNA and thiol-specific biotinylation, 4sU-RNA was purified and subjected to RNA-seq following rRNA depletion using Ribo-zero. Two independent biological replicates were analysed.

first: Lars

last: Dolken

first: Andrzej

last: Rutkowksi

first: Thomas

last: Hennig


title: Clonal Cell Lines with Different Circadian Period


title: Transcriptome profiling of Entamoeba histolytica in normal and stressed condition.

city: South Delhi

first: Sudha

last: Bhattacharya

state: Delhi

address: JNU Near Ber Sarai

department: School of Environmental Sciences

country: India

institute: Jawaharlal Nehru University

summary: Promoter motifs in Entamoeba histolytica were earlier analysed using microarray data with lower dynamic range of gene expression. Additionally, previous transcriptomic studies did not provide information on the nature of highly transcribed genes, and downstream promoter motifs important for gene expression. To address these issues we generated RNA-Seq data and identified the high and low expressing genes, especially with respect to virulence potential. We analysed sequences both upstream and downstream of start site for important motifs.

overall_design: We used RNA-Seq data to classify genes according to expression levels, which ranged six orders of magnitude. Data were validated by reporter gene expression. We looked for conserved motifs in sequences upstream and downstream of the initiation codon. Following enrichment by AME we found seven motifs significantly enriched in high expression- and three in low expression-classes. Two of these motifs (M4 and M6) were located downstream of AUG, were exclusively enriched in high expression class. We deleted these motifs to study the regulation of reporter gene expression. We also looked at gene expression changes in cells subjected to growth stress by serum starvation, and experimentally validated the data. (doi: 10.1186/s12864-019-5570-z)

first: Sarah

last: Naiyer

first: Devinder

last: Kaur

first: Jamalludin

last: Ahamad

first: Shashi

last: Singh

first: Yatendra

first: Vivek

last: Thakur

first: Alok


title: Bulk RNA-sequencing of microglia in 3XTg-AD mice treated with anti-Nk1.1 depleting antibodies or isotype control

city: New Brunswick, NJ 089

first: Qi

last: Yang

state: New Jersey

address: 89 French St

institute: Rutgers

summary: The goal of this experiment is to determine the effects of NK cells on microglia inflammation in 3XTg-AD mice.  We examined the transcriptomal changes of microglia in mice treated with anti-NK1.1 anitbodies and isotype controls by deep RNA-Seq.

overall_design: We depleted NK cells in 3XTg-AD mice using anti-NK1.1 depleting antibodies. We then sorted microglia  by flouorescence activated cell sorting. RNA-seq was performed with the bulk microglia populations.

first: Yuanyue

last: Zhang


title: Transcriptional Profiling of Clonal Cell Lines with Different Circadian Period

city: Dallas

institute: University of Texas Southwestern Medical Center

summary: Composed of negative feedback loops, circadian oscillations are thought to be noise-resistant. Yet, individual cells in culture are remarkably heterogenous, oscillating independently and with different period lengths. To investigate the mechanisms underlying this heterogeneity, we generated and characterized hundreds of clonal cell lines from the same parent culture as well as subclones from clonal lines. By comparing clonal lines with different circadian periods, we identified a pool of candidate genes that determine periodicity.

overall_design: Divided 10 clonal cell lines and 24 subclones into different groups based on circadian period length. Compare transcriptional profiles from different groups to identify candidate genes responsible for circadian periodicity determination.


title: An RNA Endonuclease-Kinase Complex Required for Spreading and Epigenetic Inheritance of Heterochromatin

city: Boston

first: Danesh

last: Moazed

state: MA

address: 240 Longwood Avenue, LHRRB 517

department: Cell Biology

institute: Harvard Medical School

summary: The highly conserved multienzyme Rix1-containing complex (hereafter referred to as the rixosome), is required for ribosomal RNA (rRNA) processing and also localizes to heterochromatin in fission yeast, but its role in heterochromatin formation is unknown. Here we report the isolation of separation of function mutations in subunits of the rixosome that abolish its physical association with Swi6/HP1 and localization to heterochromatin, but do not affect growth or rRNA processing. These mutations abolish the epigenetic inheritance of silencing and histone H3 lysine 9 methylation (H3K9me), accumulate heterochromatic RNAs, and cannot spread H3K9me and silencing away from nucleation sites into an inserted transgene. We further show that the rixosome acts upstream of the conserved 5’-3’ exoribonuclease Dhp1/XRN2 to promote heterochromatic RNA degradation. These findings reveal a new RNA degradation pathway that specifically localizes to heterochromatin to degrade nascent transcripts and enable heterochromatin spreading and inheritance.

overall_design: ChIP-seq analysis of histone modifications and chromatin associated proteins

first: Gergana

last: Shipkovenska


title: Single cell RNA-sequencing of NK cells from control wildtype and 3XTg-AD mice

summary: The goal of this study is to examine the single-cell transcriptomes of NK cells from the brains of 3XTg-AD and control wildtype mice. The data generated will elucidate the transcriptomal changes of NK cells in the pro-inflammatory microenvironment of mice with Alzheimer's disease pathologies.

overall_design: We examined the single-cell transcriptomes of NK cells isolated from  the brains of wildtype and 3XTg-AD mice by the 10Xgenomics chromium single-cell RNA-seq techniques.


title: Hepatocytic c-Jun N-terminal kinases (JNK)-1/2 function determines cell fate during carcinogenesis

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Aberrant biliary hyperproliferation resulting from lack of differentiating signals favoring the maintenance of an immature and proliferative phenotype by biliary epithelial cells are ultimately responsible for ducto/cystogenesis and intrahepatic cholangiocarcinoma (CCA) formation. Mitogen-activated protein kinase (MAPK) signaling is pivotal for CCA-related tumorigenesis. In particular, targeted inhibition of JNK signaling has shown therapeutic potential. However, the cell-type specific role and mechanisms triggered by JNK in liver parenchymal cells during CCA remains largely unknown. Here, we aimed to investigate the relevance of JNK function in hepatocytes in experimental carcinogenesis. JNK signaling in hepatocytes was inhibited by crossing AlbCre-JNK1LoxP/LoxP mice with JNK2-deficient mice to generate Jnk1LoxP/LoxP/Jnk2−/− (JNKΔhepa) mice. JNKΔhepa mice were further interbred with hepatocyte-specific Nemo-knockout mice (NEMOΔhepa), a model of chronic liver inflammation and spontaneous hepatocarcinogenesis, to generate NEMO/JNKΔhepa mice. The impact of JNK deletion on liver damage, cell death, compensatory proliferation, fibrogenesis, and tumor development in NEMOΔhepa mice was determined. Moreover, regulation of essential genes was assessed by RT-PCR, immunoblottings and immunostains. Additionally, JNK2 inhibition, specifically in hepatocytes of NEMOΔhepa/JNK1Δhepa mice, was performed using siRNA (siJnk2) nanodelivery. Finally, active signaling pathways were blocked using specific inhibitors. Compound deletion of JNK1 and JNK2 in hepatocytes diminished hepatocarcinogenesis in both the DEN model of hepatocarcinogenesis and in NEMOΔhepa mice, but, in contrast, caused massive proliferation of the biliary ducts. Indeed, JNK deficiency in hepatocytes of NEMOΔhepa (NEMOΔhepa/JNKΔhepa) animals caused elevated fibrosis, increased apoptosis, increased compensatory proliferation, and elevated inflammatory cytokines expression, but reduced hepatocarcinogenesis. Furthermore, siJnk2 treatment in NEMOΔhepa/JNK1Δhepa mice recapitulated the phenotype of NEMOΔhepa/JNKΔhepa mice. Next, we sought to investigate the impact of molecular pathways in response to compound JNK deficiency in NEMOΔhepa mice. We found that NEMOΔhepa/JNKΔhepa livers exhibited overexpression of the IL-6/Stat3 pathway in addition to EGFR-Raf-MEK-ERK cascade. The functional relevance was tested by administering lapatinib - a dual tyrosine kinase inhibitor (TKI) of ErbB2 and EGFR signaling - to NEMOΔhepa/JNKΔhepa mice. Lapatinib effectively inhibited cystogenesis, improved transaminases and effectively blocked EGFR-Raf-MEK-ERK signaling. Our study defines a novel function of JNK in cell fate as well as hepatocarcinogenesis and opens new therapeutic avenues devised to inhibit pathways of cholangiocarcinogenesis.

overall_design: Livers were isolated from control, NEMO (NEMOΔhepa) single-knockout, NEMO/JNK1Δhepa (NEMOΔhepa/JNK1Δhepa) double-knockout, JNKΔhepa (Jnk1Δhepa/Jnk2Δhepa) double-knockout, and NEMO/JNKΔhepa (NEMOΔhepa/Jnk1Δhepa/Jnk2Δhepa) triple-knockout mice, after some of which were bile duct ligated or treated with DEN, and subjected to gene expression profiling.

first: F

middle: J

last: Cubero

first: M

last: Mohamed

middle: V

last: Boekschoten

first: C

last: Trautwein


title: rBC2LCN lectin detects early-stage HER2-positive breast cancer

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: We found that MCF-7 and T-47D or MDA-MB-157 and MDA-MB-231 are rBC2LCN-positive or -negative breast cancer cell lines, respectively. To examine a global gene expression comparison between the rBC2LCN-positive and -negative breast cancer cell lines, DNA microarray analysis was performed.

overall_design: Breast carcinoma cell lines, MCF7 (HTB-22), T-47D (HTB-133), MDA-MB-157 (HTB-24), and MDA-MB-231 (HTB-26) were obtained from ATCC and maintained according to the provider’s instructions. The total mRNAs were extracted using ISOGEN (NIPPON GENE). DNA microarray was performed by a SurePrint G3 Human GE Microarray Kit, 8 x 60 K Ver. 1 (Agilent, G4851A).

first: Shuuji

last: Mawaribuchi


title: Single cell RNA-sequencing of microglia in 3XTg-AD mice treated with anti-Nk1.1 depleting antibodies or isotype control

summary: This project aims to understand the effects of NK cell depletion in the single-cell gene expression of microglia in mice with Alzheimer's disease pathology. We used 10Xgenomics technique to examine the single-cell transcriptomes of microglia in mice treated with anti-NK1.1 depleting antibodies and isotype controls.

overall_design: We sorted microglia from 3XTg-AD mice treated with anti-Nk1.1 depleting antibodies or isotype controls. Single-cell RNA-seq was performed using 10X Genomics Chromium isingle-cell controller and 5' gene expression kit.


title: The novel long noncoding RNA Lnc19959.2 modulating triglyceride metabolism associated genes through interaction with Purb and hnRNPA2B1 [RNA-seq]

city: Shanghai

first: dongsheng

last: xiao

address: No.151 Libing Road, Zhangjiang Hi-Tech Park Pudong, Shanghai 201203, P.R. China

institute: Shanghai Biotechnology Corporation

summary: High triglycerides can lead to atherosclerotic cardiovascular disease. Long noncoding RNAs (lncRNAs) are currently consider to have vital and wide range of biological functions, but the molecular mechanism underlying TG metabolism remains poorly understood. To identify novel lncRNAs differentially expressed in rat liver with hypertriglyceridemia using transcriptome sequencing and elucidated the function role in TG metabolism. In our study, we identified a novel lncRNA, Lnc19959.2, which was highly expression in rat liver with hypertriglyceridemia. Knockdown of lnc19959.2 has profound TG lowering effects in vitro and vivo. Subsequently genome-wide analysis identified that knockdown of Lnc19959.2 caused deregulation of many genes during TG homeostasis. Further mechanism studies reveal that Lnc19959.2 specifically bound to Purb to up-regulate expression of Apoa4, while bound to hnRNPA2B1 to down-regulate the expression of Cpt1a, Tm7sf2 and Gpam, respectively. In the upstream pathway, palmitate acid up-regulated CCAAT/Enhancer-Binding Protein Beta (Cebpb) facilitates its binding to promoter region of Lnc19959.2, which resulted in significant promotion of lnc19959.2 transcriptional activity. Our findings provide novel insights into transcriptional regulation of TG homeostasis by a novel lncRNA. This newly identified lncRNA could be exploited as novel therapeutic targets for hypertriglyceridemia.

first: Jing

last: Wang

first: Dao

last: Xiang

first: Shuai

last: Mei

first: Yuanchao

last: Jing

first: Dating

last: Sun

first: Chen

last: Chen

first: Dong

last: Hu

first: Shiyang

last: Li

first: Huihui

first: Yan

first: Hu

last: Ding


title: The novel long noncoding RNA Lnc19959.2 modulating triglyceride metabolism associated genes through interaction with Purb and hnRNPA2B1

overall_design: To identify novel lncRNAs differentially expressed in rat liver with hypertriglyceridemia using transcriptome sequencing and elucidated the function role in TG metabolism.


title: Neurodevelopmental disorder risk gene DYRK1A is required for ciliogenesis and brain size in Xenopus embryos

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

state: CA

address: 675 Nelson Rising Lane, Mail Code 0518

department: Psychiatry

institute: UCSF

summary: DYRK1A (dual specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A) is a high confidence autism risk gene that encodes a conserved kinase. In addition to autism, patients with putative loss of function variants in DYRK1A exhibit microcephaly, intellectual disability, developmental delay, and congenital anomalies of the kidney and urinary tract. DYRK1A is also located within the critical region for Down syndrome; therefore, understanding the role of DYRK1A in brain development is crucial for understanding the pathobiology of multiple developmental disorders. To characterize the function of this gene, we leveraged the diploid frog, Xenopus tropicalis. We discover that Dyrk1a is expressed in ciliated tissues, localizes to ciliary axonemes and basal bodies, and is required for ciliogenesis. We also demonstrate that Dyrk1a localizes to mitotic spindles and that its inhibition leads to decreased forebrain size, abnormal cell cycle progression, and cell death during brain development. These findings provide hypotheses about potential mechanisms of pathobiology and underscore the utility of X. tropicalis as a model system for understanding neurodevelopmental disorders.

overall_design: 3 replicates each of 3 pooled dissected stage 46 X. tropicalis brains, either uninjected or bilaterally injected with CRISPR reagents targeting dyrk1a at the 2 cell stage. Trizol extracted RNA, low yield library preparation, and Illumina sequencing.

first: Helen

first: A


title: Age-related gene expression in tissues of the long-lived red sea urchin

city: Gloucester

first: Andrea

middle: G

last: Bodnar

address: 417 Main Street

institute: Gloucester Marine Genomics Institute, Inc.

summary: The red sea urchin, Mesocentrotus franciscanus, is one the earth’s longest-lived animals, reported to live more than 100 years with indeterminate growth, life-long reproduction and no increase in mortality rate with age. To explore the idea that transcriptional stability is a key determinant of longevity and negligible senescence, age-related gene expression was examined in three tissues of the red sea urchin (Aristotle’s lantern muscle, esophagus and radial nerve cord). Genome-wide transcriptional profiling using RNA-Seq revealed remarkable stability in muscle and esophagus with very few age-related changes in gene expression. In contrast, expression of more than 900 genes was significantly altered with age in radial nerve cord including genes involved in nerve function, signaling, metabolism, cytoskeleton, transcriptional regulation and chromatin modification. Notably, there was an upregulation in expression of genes involved in synaptogenesis and axonogenesis suggesting enhanced nervous system activity with age. Among the signaling pathways affected by age, there was a downregulation in expression of key components of the mTOR signaling pathway and an upregulation of negative regulators of this pathway. This was accompanied by a reduction in expression of genes involved in protein synthesis and mitochondrial function and an increase in expression of genes that promote autophagy. Downregulation of the mTOR pathway together with the other observed changes reveals a unique age-related gene expression profile in the red sea urchin nervous system that may contribute to mitigation of the detrimental effects of aging in this long-lived animal.

overall_design: 18 samples in total for RNA-Seq analysis. RNA from Aristotle’s lantern muscle (ALM), esophagus (ES), and radial nerve cord (RN) from sea urchins of two size categories (Small and Large) for sea urchin collections conducted in 2010, 2011 and 2013. RNA was pooled from individuals for each tissue type and size category (ALM-S, ALM-L, ES-S, ES-L, RN-S and RN-L) and samples from each of the three sampling years were treated as independent replicates.


title: Role of CD133 in human embryonic stem cell proliferation and teratoma formation

city: Tianjin

first: Jie

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

summary: We knocked out CD133 by CRISPR/Cas9 to analyze the role of CD133 in human embryonic stem cells.

overall_design: 2 repeats of WT and 2 repeats of  CD133-/-  in human embryonic stem cells.

first: H

first: P

last: Gong

first: J

first: Y

last: Fu

first: Z

last: Zhou

first: L

last: Liu


title: CD5 dynamically calibrates basal NF-KB signaling in T cells during thymic development and peripheral activation

city: Bethesda

first: Apratim

last: Mitra

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

summary: Immature T cells undergo a process of positive selection in the thymus when their new T cell receptor (TCR) engages and signals in response to self-peptides. As the T cell matures, a slew of negative regulatory molecules, including the inhibitory surface glycoprotein CD5, are upregulated in proportion to the strength of the self-peptide signal. Together these regulators dampen TCR-proximal signaling and help avoid any subsequent peripheral activation of T cells by self-peptides. Paradoxically, antigen-specific T cells initially expressing more CD5 (CD5hi) have been found to better persist as effector/memory cells after a peripheral challenge. The molecular mechanisms underlying such a duality in CD5 function is not clear. We find that CD5 alters the basal activity of the NF-kB signaling in resting peripheral T cells. When CD5 was conditionally ablated, T cells were unable to maintain higher expression of the cytoplasmic NFκB inhibitor IκBα. Consistent with this, resting CD5hi T cells expressed more of the NFκB p65 protein than CD5lo cells, without significant increases in transcript levels, in the absence of TCR signals. This post-translationally stabilized cellular NFkB depot potentially confers a survival advantage to CD5hi T cells over CD5lo ones. Taken together, these data suggest a two-step model whereby the strength of self-peptide induced TCR signals lead to the upregulation of CD5, which subsequently maintains a proportional reserve of NFκB in peripheral T cells poised for responding to agonistic antigen-driven T cell activation.

overall_design: 4 cell types (CD4+CD5lo, CD4+CD5hi, CD8+CD5lo, CD8+CD5hi) x 4 biological replicates = 16 samples x 2 technical replicates

first: Courtney

middle: A

last: Matson

first: Seeyoung

last: Choi

first: Bin

last: Zhao

first: Livak

last: Ferenc

middle: K

first: Paul

last: Love

first: Nevil

last: Singh


title: The Evolving Immune Microenvironment of B-cell Acute Lymphoblastic Leukemia [human peripheral blood dataset]

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Single-cell RNA-seq analysis of primary human peripheral blood mononuclear cells (PBMCs) from two independent B-ALL patients (Texas Children's Hospital) and healthy PBMC donor samples (STEMCELL Technologies).

overall_design: Single-cell RNA-sequencing libraries of primary human peripheral blood immune populations. B-ALL patient bone marrow samples were separated into CD19+ B cell and CD19-CD45+ non-B cell fractions by flow-based sorting and then mixed at a ratio of 1:5 CD19+:CD19-CD45+ followed by scRNA-Seq. Total CD45+ peripheral blood cells were sequenced from healthy donors.

first: Matthew

last: Witkowski

first: Aristotelis

last: Tsirigos

first: Iannis

last: Aifantis


title: Wisp inhibits chondrogenic differentiation in heterotopic ossification

city: Baltimore

first: Jiajia

last: Xu

address: 720 Rutland Avenue

department: Pathology-Surgical Pathology

institute: The Johns Hopkins University School of Medicine

summary: Heterotopic ossification (HO) is the formation of extra-skeletal bone in muscle and soft tissues.  Better characterization of the signaling pathways predisposing to HO is critical to identifying therapies directed against this common and potentially debilitating condition.  WISP-1 (WNT1-inducible-signaling pathway protein 1) is a CCN family member and is expressed in skeletal cells during bone development or repair. Here, we sought to comprehensively explore the significance of WISP-1 across mouse and human HO. Among CCN family members, local Wisp1 expression was most highly upregulated within experimental trauma-associated HO by RNA sequencing, and increased Wisp1 corresponded to gene markers of osteochondral differentiation.  WISP1 immunolocalization demonstrated conserved expression in osteochondral cells across mouse and human HO, including an FOP-like model, post-traumatic model, and human examples of non-genetic HO.  Transgenic Wisp1 global knockout demonstrated an increase in cartilage and bone in a trauma-induced HO model.  Microarray and in vitro culture of Wisp1 null cells suggested that WISP1 functions as a negative regulator of chondrogenic differentiation, and that Wisp1 deletion results in unrestrained endochondral HO formation.  siRNA mediated WISP1 knockdown in human progenitor cells confirmed this finding.  Overall, these findings suggest that endogenous WISP1 has pathophysiologic relevance in trauma-induced HO and functions as a negative regulator of ectopic chondrogenesis.

overall_design: compare WT and Wisp1 KO mice adipose derived stromal cell from inguinal fat pad, 1 sample of each class

first: Aaron

last: James

first: Ching

last: Hsu

first: Carolyn

last: Meyers


title: The Evolving Immune Microenvironment of B-cell Acute Lymphoblastic Leukemia [human bone marrow dataset]

summary: Single-cell RNA-seq analysis of primary human bone marrow immune populations isolated from B-ALL patient samples (matched diagnosis, remission and relapse), and healthy bone marrow donor samples.

overall_design: Single-cell RNA-sequencing libraries of primary human bone marrow immune populations. B-ALL patient bone marrow samples were separated into CD19+ B cell and CD19-CD45+ non-B cell fractions by flow-based sorting and then mixed at a ratio of 1:5 CD19+:CD19-CD45+ followed by scRNA-Seq. Total CD45+ bone marrow cells were sequenced from healthy donors.


title: Neural Progenitor Cell Gene Expression In Response To CBP(S436A) mutant

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

summary: The histone acetyltransferase, CREB binding protein (CBP), is important for appropriate differentiation of neural stem/progenitor cells (NPCs). The serine 436 phosphoryaltion in CBP responds to enviormental cues to promote neuronal differentiaiton of adult NPCs (Fatt, et al, Stem Cell Reports, 5:1-8, 2015; Gouveia, et al., Stem Cell Reports, 11: 719-734, 2016). Here, we have used a phospho-null CBPS436A knock-in (KI) mouse strain to isolate subventricular zone (SVZ) NPCs, which were further expanded and differentiated ex vivo for RNAseq analysis. This allowed us to study underlying molecular mechanisms that mediate CBP Ser436 phosphorylation to promote adult NPC differentiation.

overall_design: SVZ NPCs were isolated from 2-month-old CBPS436A-KI and their wild type littermates (n=2/genotype) and expanded ex vivo. At Passage 2 (P2), the NPCs were directed to differentiation medium in the presence of metformin for 6 days. Total RNA from the P2 differentiating NPCs were used for RNA-seq analysis.

first: Jing

last: Wang

first: F

last: Dilworth


title: The Evolving Immune Microenvironment of B-cell Acute Lymphoblastic Leukemia [murine dataset]

summary: Single-cell RNA-seq analysis of murine bone marrow and peripheral blood mononuclear cells (PBMCs) immune populations isolated from B-ALL recipient animals and two healthy littermate controls.

overall_design: scRNA-Seq: For healthy recipients, processed bone marrow or peripheral blood cells were separated into GFP-CD45+Ly-6G- non-granulocytic cells and GFP-CD45+Ly-6G- non-granulocytic cells, then mixed at a ratio of 8 parts GFP-CD45+Ly-6G- non-granulocytic cells and 1 part GFP-CD45+Ly-6G+ granulocytic cells. For B-ALL recipients, cells were sorted and mixed to give 1 part GFP+CD19+ B-ALL blasts, 8 parts GFP-CD45+Ly-6G- non-granulocytic cells, and 1 part GFP-CD45+Ly-6G+ granulocytic cells.


title: Notch signaling licenses allergic airway inflammation by promoting lymph node egress of Th2 cells

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

summary: Transcriptome analyses of wildtype and Notch-deficient Th2 cells from mouse models of allergic airway inflammation.

overall_design: biological replicate (n=2-4) RNA-Seq experiments

first: Rudi

last: Hendriks


title: Microarray of CD11b+CD11c–Ly6Chi inflammatory monocytes in tumor tissue and spleens from Th9 treated mice

city: Winston-Salem

first: Yong

last: Lu

address: 575 N. Patterson Ave

department: Dept of Microbiology and Immunology

institute: wake forest school of medicine

summary: We recently reported that tumor-specific Th9 cells are less susceptible to exhaustion, fully cytolytic to tumor cells, and possess long-term persistence capacity because of their unique hyperproliferative T cell feature. However, these observations only revealed how tumor-specific Th9 cells eradicate antigen-positive tumor cells. Given the unmet need to develop effective ACT strategies with tumor-specific Th9 cells for solid tumors with the heterogeneity in antigen expression, the CD11b+CD11c–Ly6Chi inflammatory monocytes were flow-sorted from Th9 treated mice, and been further analyzed for microarray.

overall_design: Mice were treated with Th9 cells, and 10 days after Th9 transfer, tumor tissue and spleens were harvested and dissociated for cell sorting. CD11b+CD11c–Ly6Chi inflammatory monocytes were flow-sorted. Total RNA was extracted with the RNeasy Mini kit (Qiagen)

first: Gang

last: Xue


title: Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [RNA-Seq, mouse]

first: Yohan

last: Suryo Rahmanto

address: CRB-2, Rm 376, 1550 Orleans St

department: Department of Pathology

institute: Johns Hopkins School of Medicine

summary: Somatic mutations in ARID1A, a SWI/SNF chromatin remodeling gene, are prevalent in human malignancies linked to endometriosis. Through comprehensive chromatin immunoprecipitation sequencing and transposase-accessible chromatin sequencing, we identified chromatin binding regions for ARID1A/BRG1-containing SWI/SNF remodeling complexes, which were enriched at enhancers and corresponded to a euchromatin state. ARID1A deletion caused global affinity reduction of BRG1-containing complexes in chromatin. Integrative analyses with transcriptome data obtained from endometrial epithelium and human endometrioid carcinomas identified high-confidence ARID1A-regulated genes that participate in tissue regeneration and tumorigenesis. Deletion of Arid1a was found to inactivate the TGF-β pathway and to accelerate tumor progression from pre-cancerous lesions to endometrioid carcinomas. Collectively, this study establishes functional roles of ARID1A mutation and loss in tumor progression.

overall_design: Transcriptome profiling of uterine tumor in iPAD, iPD, and iAD mice

first: Y

first: W

last: Shen

first: I-M

last: Shih

first: T-L


title: Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [RNA-Seq]

overall_design: Transcriptome profiling of isogenic ARID1A knockout pair of human endometrial epithelial cells


title: Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Identification and characterization analysis of the HCV-related microRNA using a deep sequencing approach

status: Public on Jun 07 2020

city: Shijiazhuang

first: Xuemin

last: Niu

address: 139 Ziqiang Road

institute: The Third Hospital of Hebei Medical University

summary: In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from serum sample of HCV-related fibrosis and control healthy. In total, 41 miRNAs were dysregulated (30 upregulated and 11 downregulated) in the patients with chronic HCV infection compared with the healthy controls. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by HCV-induced fibrosis miRNAs. In addition, miRNAs of HCV-related fibrosis and control healthy  were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of miRNA in the chronic HCV infection patients and control healthy groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of HCV-related fibrosis miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of HCV-related fibrosis.

overall_design: Aberrant microRNA (miRNA) expression plays a pivotal role in the development of liver fibrosis. However, the functional roles of miRNAs in hepatitis C virus (HCV)-related liver fibrosis remain largely unknown. In this study, we systematically analyzed the serum miRNAs of patients with HCV-induced hepatic fibrosis with a microarray.

first: Rongqi

first: Yuemin


title: Microbiota-driven arginase 1 expression impedes the resolution of intestinal inflammation

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary: Arginase 1 (Arg1), which converts L-arginine into ornithine and urea, exerts pleiotropic immunoregulatory effects. Patients with inflammatory bowel disease (IBD) show an enhanced expression and activity of Arg1 in the intestinal (sub-)mucosa, but the function of Arg1 in IBD remains poorly characterized. Here, we found that Arg1 expression correlates with the degree of inflammation in colitic tissues of IBD patients. In mice with - experimental colitis Arg1 was upregulated in an IL-4-/IL-13- and intestinal microbiota-dependent manner. Tie2-Cre+/-Arg1fl/fl mice lacking Arg1 in hematopoietic and endothelial cells recovered faster from  colitis than Arg1-expressing littermates. This correlated with decreased vessel density, compositional changes in the intestinal microbiota, diminished infiltration by myeloid cellsand an accumulation of intraluminal polyamines that are associated with epithelial healing. Dietary L-arginine restriction abolished the protective effect of Arg1-deletion, suggesting that protection is related to an increased availability of L-arginine. Fecal microbiota transfers from Tie2-Cre+/-Arg1fl/fl mice into wildtype recipients restored the protective, anti-inflammatory phenotype while transfers from wildtype littermates into Arg1-deficient mice prevented the accelerated recovery from colitis. Thus, altered intestinal microbiota and metabolic products in Tie2-Cre+/-Arg1fl/fl mice account for the accelerated resolution from colitis in the absence of Arg1. Subsequently, L-arginine serves as novel therapeutic and diagnostic target for clinical intervention in IBD patients.

overall_design: Total RNA from 8 mice (4 conditional Arg1-ko and 4 wildtype littermates) was analyzed by RNA-Seq to identify differences in gene expression between the two groups.

first: Julia

last: Baier

first: Jochen

last: Mattner

first: Soeren

last: Lukassen

first: Arif

middle: B

last: Ekici


title: Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [ChIP-Seq]

summary: For ATAC-seq data processing, we used the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). In detail, for each sample, ATAC-seq reads were first checked for adaptor contamination. Then, adaptor trimmed reads were aligned to hg19 using Bowtie2  under paired-end mode with parameter “-X2000”, which permits 2000 bp for the maximum allowable insert size between two paired ends of each read. Using the ENCODE ATAC-seq pipeline, duplicated reads were properly filtered out. ATAC-seq enriched peaks were called using MACS2 (Zhang et al., 2008) based on remaining unique reads with parameters “-f BAMPE -q 0.05 --nomodel”. In total, we collected 45,569 peaks for the ARID1AWT sample and 27,480 peaks for the ARID1AKO sample.

overall_design: ChIP-seq profiling of isogenic ARID1A knockout pair of human endometrial epithelial cells


title: Epigenome analyses of HCT116 cells stably expressing UHRF1 mutant  [Illumina EPIC]

status: Public on Jun 06 2020

city: Seoul

first: Ja Young

last: Hahm

address: 84, Heukseok-ro, Dongjak-gu

country: South Korea

institute: Chung-Ang University

summary: UHRF1 is a key regulator of DNA methylation maintenance. In this study, we investigated whether acetylation of UHRF1 affects its hemimethylated DNA binding affinity and alters genome-wide DNA methylation pattern.   We show that cells with mutation in K490 of UHRF1 have distinct methylation profile versus wildtype UHRF1 expressing cells.

overall_design: Genome-wide DNA methylation profiling of HCT116 cell line with wildtype or acetylation mutant UHRF1 (UHRF1 K490R, UHRF1 K490Q), in which exogenous UHRF1 was integrated into the genome and endogenous UHRF1   was knocked down with shRNA

first: Sang-Beom

last: Seo

first: Ja


title: Epigenome analysis of HDAC1 stably knocked down HCT116 cells and HCT116 cells stably expressing UHRF1 mutant


title: Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [ATAC-Seq]

overall_design: ATAC-seq profiling of chromatin structure in isogenic ARID1A knockout pair of human endometrial epithelial cells

last: Wang


title: RNA-seq of primary islets in WT and Brsk2 transgenic mice

city: Nanjing

first: Ru-feng

last: Xu

state: Jiangsu Province

address: Longmian Avenue 101 number

department: Nanjing Medical University

institute: Rufeng Xu

summary: We investigated the underlying molecular mechanism of Brsk2's effects by comparing gene expression of whole primary islets isolated from Brsk2 TG mice and their control littermates by RNA sequencing.We chosed a four-day Dox administration and studied gene-expression differences resulting in hyperglycemia. A total of 23318 gene transcripts was captured,and 1020 genes showed significant expression differences (p-value<0.05 and >2-fold change) between the two group.Gene set-enrichment ananlysis was performed using Kyoto Encyclopedia of Genomes algorithms and MSigDB software.The most enriched pathways were linked to pathyways associated with olfactory tranduction, ribosomes, and pancreatic secretion. We focused on olfactory transduction because 1122 dysregulated genes are involved in that process.

overall_design: Islets mRNA of WT and Brsk2 over-expression transgenic mice

first: Xiao

last: Han

first: Yunxia

last: Zhu

first: Rufeng

first: Jing

last: Pang


title: Potassium starvation induces autophagy in yeast

city: Chapel Hill

first: Henrik

last: Dohlman

state: NC

address: 120 Mason Farm Rd, 4th Floor

department: Pharmacology

institute: University of North Carolina at Chapel Hill

summary: Autophagy is a conserved process that recycles cellular contents to promote survival. Although nitrogen starvation is the canonical inducer of autophagy, recent studies have revealed several other nutrients important to this process. In this study, we used a quantitative, high-throughput assay to identify potassium starvation as a new and potent inducer of autophagy. We found that potassium-dependent autophagy requires the core pathway kinases Atg1, Atg5, Vps34, as well as other components of Phosphatidylinositol 3-kinase Complex I. Transmission electron microscopy revealed abundant autophagosome formation in response to both stimuli. RNA sequencing indicated distinct transcriptional responses – nitrogen affects transport of ions such as copper while potassium targets the organization of other cellular components. Thus, nitrogen and potassium share the ability to influence metabolic supply and demand but do so in different ways. Both inputs promote catabolism through bulk autophagy, but inhibit cellular anabolism through distinct mechanisms.

overall_design: examine nitrogen and potassium starvation with no-treatment as control in yeast, each treatment is repeated 2 times

first: Shuang

last: Li


title: Epigenome analysis of HDAC1 stably knocked down HCT116 cell  [Illumina EPIC]

summary: UHRF1 is a key regulator of DNA methylation maintenance. In this study, we investigated whether acetylation of UHRF1 affects its hemimethylated DNA binding affinity and alters genome-wide DNA methylation pattern.  We observed that acetylation of UHRF1 is regulated by HDAC1 and PCAF. We investigated DNA methylation profile of HDAC1 depleted HCT116 cell with control cell.

overall_design: Genome-wide DNA methylation profiling of HDAC1 KD and control HCT116 cell line.


title: A molecular mechanism to regulate neural-specific A-to-I editing during development

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

department: Biology

institute: Indiana University, Bloomington

summary: Using a combination of molecular and genomic approaches we uncover a molecular mechanism that regulates RNA editing in a neural- and development-specific manner. We de novo identified 570 A-to-i editing sites in adult neural RNA-seq data and 6202 sites from re-analyzing L1 neural RNA seq.Comparing editomes during development led to the identification of both neural transcripts that were edited only in one life-stage. The stage-specific editing is largely regulated by differential gene expression during neural development, and proper gene expression of nearly one-third of these differentially expressed genes is dependent on adr-2, the only known A-to-I editing enzyme in C. elegans. However, we also identified a subset of neural transcripts which are edited and expressed throughout development. Interestingly, despite a neural-specific downregulation of adr-2 during development, the majority of sites edited throughout development exhibit increased editing in adult neural cells. Biochemical data suggests that ADR-1, a deaminase deficient member of the Adenosine deaminase acting on RNA (ADAR) family is competing with ADR-2 for binding to specific transcripts early in development. Our data suggest a model where during neural development, ADR-2 levels overcome ADR-1 repression, resulting in increased ADR-2 binding and editing of specific transcripts. Together, our findings reveal tissue- and development-specific regulation of RNA editing and identify a molecular mechanism that regulates ADAR substrate recognition and editing efficiency.

overall_design: High throughput sequencing of adult neural RNA-seq libraries and identification of A-to-I editing sites using SAILOR software

first: Suba

last: Rajendren

first: Pranathi

last: Vadlamani


title: mRNA and lncRNA microarray of vCAF modulating intrahepatic cholangiocarcinoma progression

city: San Diego

first: Yajing

last: Hao

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

summary: We found that the isolated and expanded MCAM positive vCAF subpopulations significantly accelerated ICC growth. To further investigate the effect of vCAF on ICC cells (GFP-FRH or GFP-RBE), we co-cultured the vCAF with GFP ICC cells or ICC cells alone for seven days, then we sorted the GFP-FRH or GFP-RBE cells via FACS and conducted transcriptome microarray analysis of GFP ICC cells alone or vCAF co-cultured GFP-ICC cells.

overall_design: microarray experiments, GFP-FRH or GFP-RBE  cells alone or co-cultured with vCAFs for 7 days.Then GFP-FRH or GFP-RBE were sorted by FACS and Total RNA was extracted with Trizol and hybridized to custom lncRNA and mRNA microarray

first: Xinlong

last: Yan

first: Dongdong

last: Zhang


title: Next Generation Sequencing to analyse regulators of constitutive VWF secretion

city: London

first: Francesca

last: Patella

address: Gower St

department: LMCB

country: United Kingdom

institute: University College London

summary: Constitutive VWF secretion can be increased by a range of factors; changes in VWF expression, levels of TNF-alpha or other environmental cues. An RNAseq analysis revealed that expression of RGS4 (Regulator of G protein signalling 4) was reduced in endothelial cells (HUVECs) grown under these conditions. si-RGS4 treatment of HUVECs increased constitutive basolateral secretion of VWF, probably by affecting the anterograde secretory pathway. In a simple model of endothelial damage we show that RGS4-silenced cells increased platelet recruitment onto the subendothelial matrix under flow. These results show that changes in RGS4 expression alter levels of subendothelial VWF, affecting platelet recruitment. This introduces a novel control over VWF function.

overall_design: mRNA profiles of conditions (si-VWF, EBM2 medium, TNFalpha and their controls) known to increase VWF constitutive secretion in HUVECs

first: Dan

last: Cutler


title: CUT&RUN comparing the occupancy of MAX, MNT, MGA, MYC and RNA pol II Ser5 in a MAX null vs MAX reconstituted mouse SCLC line (mRPMaxKO)

city: Seattle

first: Arnaud

last: Augert

state: Washington

address: 100 Fairview Avenue N. Thomas Building Room D4

institute: Fred Hutchinson Cancer Research Center

summary: The goal of this study was to compare the genomic occupancy of MAX, MNT, MGA and RNA pol II Ser5 in MAX restored versus MAX null SCLC (mRPMaxKO)

overall_design: CUT&RUN analysis of a MAX null vs MAX restored SCLC line (mRPMaxKO)

first: David

last: MacPherson

first: Robert

middle: N

last: Eisenman


title: Dissecting the transcriptomic landscape of the human intrahepatic cholangiocarcinoma by single cell RNA-sequencing analysis.

city: Beijing

first: Min

state: Beijing

address: No. 8 East Road, Fengtai District

department: The Fifth Medical Center of Chinese PLA General Hospital

institute: Academy of Military Medical Sciences

summary:
Intrahepatic cholangiocarcinoma (ICC) is the second most common malignancy arising in the liver, featured with high tumor heterogeneity and dismal prognosis. The cellular disversity and molecular basis of tumor cells interacted with surrounding niche cells remains poorly understood, limiting the development of targeted anti-tumor therapies.
To investigate the molecular diversity of fibroblast population, 2 tumor samples: ICC32S and STROMA24T were recruited in our study to perform fibroblast enriched scRNA-seq

overall_design: To comprehensively elucidate the ICC heterogeneity, we employed single-cell RNA sequencing (scRNA-seq) to profile 31,302 cells of five ICC samples, as well as three paired adjacent non-tumor tissues. Our results identify 31 cell subtypes and the heterogeneous malignant subtype was highly patient-specific, which has differential proliferative, migratory and inflammation phenotype.

first: Bing

last: Liu


title: Transcriptional analyses of a RPMax-/- cell line upon Max restoration using an inducible lentiviral vector.

summary: We analyze transcritpional changes upon Max restoration in a RPMax-/- cell line.

overall_design: RNA seq analyses of 3 control and 3 Max restored conditions


title: Transcriptional analyses of MAX altered SCLCs (RNA-seq)


title: Genomic occupancy of MAX and members of the MYC network in MAX WT and MAX null preSCs (polyclonal population)

summary: Conventional crosslinked ChIP was performed on sgCtrl (control guide RNA) and sgMax (guide RNA against Max) transduced preSCs (early stage SCLC line). We find that loss of MAX leads to decreased MAX, MYC and MNT occupancy.

overall_design: sgCtrl vs sgMax preSCs. Antibodies used: IgG control rabbit, IgG control mouse, anti-MAX, anti-MYC, anti-MNT, anti-RNA polII

first: Haritha

last: Mathsyaraja


title: RNA-sequencing Reveals Altered Gene Expression in the Ventromedial Hypothalamus Following Predator Odor Exposure

city: Kent

first: Colleen

middle: M

last: Novak

state: Ohio

address: 222 Cunningham Hall, Biological Sciences, Kent State University

department: Biological Sciences

institute: Kent State University

summary: It is unknown how the VMH regulates skeletal muscle metabolism and predator threat responses, or potential interactions between these. Because skeletal muscle has a great capacity for increasing energy expenditure and is rapidly activated by PO, understanding how the VMH regulates this process could uncover novel targets for obesity treatments. Due to lack of investigation, we sought to provide a foundation for mechanistic exploration. We report transcriptome-wide alterations of the VMH following PO exposure. Our results uncovered novel functional relationships among genes that can now be probed to better understand the dual processing role of the VMH in skeletal muscle metabolism and predator-threat responses.

overall_design: We compared two conditions run in triplicate. Specifically, we compared the RNA-seq results of 3 Sprague Dawley rats exposed to predator odor to 3 Sprague Dawley rats exposed to control odor.

first: Ashley

last: Shemery

first: Megan

last: Gibson

first: Daniel

last: Diamond