title: Gene expression in Tudor-SN knockdown Drosophila in normoxic and hypoxic conditions

city: Helsinki

first: Juha

middle: Mikael

last: Saarikettu

address: Viikinkari 1

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: The RNA-binding protein Snd1/Tudor-SN can regulate gene expression through various mechanisms and is suggested to function in stress responses. Here we have analyzed mRNA expression in Tudor-SN knockdown and control flies in hypoxic and normoxic conditions.

overall_design: Total RNA was obtained from adult flies.  The Drosophila UAS-GAL4 system was used for knockdown with Daughterless-GAL4 (Da-GAL4) for ubiquitous gene silencing.  The UAS-Tudor-SN RNAi line was from Bloomington Drosophila Stock Center, Indiana University (Stock number 34865). The experimental setting included biological triplicate samples (3 controls +  3 knockdowns) each containing 10 flies in conditions of hypoxia, either 2% or 6% oxygen for 6 hours, or at normal atmospheric oxygen.


title: SRCAP ChIP-sequencing of mouse intestinal stem cells (ISCs)

status: Public on Jan 28 2020

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

country: China

institute: Institute of Biophysics, CAS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We previously demonstrated that SRCAP regulates the self-renewal of ESCs and modulates lymphoid lineage commitment. We further validated that SRCAP was mainly distributed in liver, spleen and intestine by Northern blot. SRCAP was also highly expressed in Lgr5+ ISCs. We then sought to explore the physiological role of SRCAP in the regulation of self-renewal maintenance of ISCs.We identified that Srcap deficiency impairs the self-renewal of ISCs and intestinal epithelial regeneration. Through SRCAP ChIP-sequencing, we sough to identify the key gene regulated by SRCAP in ISC self-renewal.

overall_design: Primary Lgr5+ ISCs were isolated from tamoxifen treated Srcapflox/flox; Lgr5-Cre+ mice (Srcap KO) and Srcap+/+; Lgr5-Cre+ mice (Srcap WT). No in vitro culture were done. Crypts were isolated from Lgr5GFP mice.For ISC isolation, the crypts were dissociated into individual cells with 1x TrypLE express supplemented with 0.8 kU/ml DNaseI (Roche) followed by sorting according to GFP intensity. Sheared chromatin (sonicated to 200–500 bp) from ISCs (5×105) fixed in 1% formaldehyde was incubated with 4 μg antibody overnight at 4℃ followed by immunoprecipitation with salmon sperm DNA/protein agarose beads. After washing, elution and cross-link reversal, DNA from each ChIP sample and corresponding input sample were purified and prepared followed by library construction and sequenced on  BGISEQ-500 platform (BGI America Co., Cambridge, MA).

first: Buqing

last: Ye


title: Thymic resilience and T cell output require Liver X Receptors

status: Public on Jan 29 2020

city: Boston

first: Christopher

last: Chan

address: 185 Cambridge St

country: USA

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: The thymus is a primary lymphoid organ necessary for optimal T cell development. Here we show that liver X receptors, which are a class of nuclear receptors and transcription factors with diverse functions in metabolism and immunity, critically contribute to thymic integrity and function. LXRαβ-deficient mice develop a fatty, rapidly-involuting thymus, and acquire a shrunken and prematurely senescent peripheral T cell repertoire. The functions of LXRαβ are cell specific and the resulting phenotypes mutually independent. Whereas macrophages require LXRαβ for reverse cholesterol transport and lipid removal, thymic epithelial cells (TEC) and thymocytes respectively utilize LXRαβ for self-renewal and negative selection. Consequently, TEC-derived LXRαβ protect against premature involution in homeostasis and orchestrate thymic regeneration following stress, while thymocyte-derived LXRαβ limit cell disposal during negative selection and confer heightened sensitivity to experimental autoimmune encephalomyelitis. These results identify three distinct but complementary mechanisms by which LXRαβ govern T lymphocyte education.

overall_design: Cortical and medullary thymic epithelial cells sorted from LXRalpha-flox LXRbeta-flox control versus FoxN1-Cre LXRalpha-flox LXRbeta-flox (4 total groups)

middle: T

first: Filip

middle: K

last: Swirski


title: A SPEN Complex Serves as a Scaffold to Coordinate Multiple Epigenetic Regulatory Mechanisms in Breast Cancer Stem Cells

status: Public on Jan 25 2020

city: Ann Arbor

first: Michael

middle: Dale

last: Brooks

state: Michigan

address: 2800 Plymouth Rd Building 26 Rm 329S

department: Internal Medicine

institute: University of Michigan

summary: There is substantial evidence that many cancers, including human breast cancer are hierarchically organized and driven by a cellular population that displays stem cell properties. These stem-like cells (CSC’s) mediate tumor metastasis and by virtue of their relative therapeutic resistance mediate tumor recurrence. Both normal and malignant stem cells are regulated through epigenetic mechanisms which involve DNA and histone modifications as well as noncoding RNAs. However, the mechanisms responsible for coordinating these multiple levels of epigenetic regulation in CSC’s remain elusive. Here, we identify a SPEN-Xist complex in breast CSC’s cells which, by virtue of inclusion of multiple epigenetic regulatory proteins, provides a scaffold for coordinating multiple levels of epigenetic regulation in these cells. Genetic knockdown of SPEN or XIST significantly reduces the CSC population as accessed by ALDH expression, sphere formation or tumor initiating capacity in xerograph models. Gene expression analysts suggests that the SPEN- XIST complex modulates multiple CSC regulatory pathways via the coordination of epigenetic modulatory proteins.    This work has fundamental implications for understanding the epigenetic regulation of cancer stem cells as well as for developing strategies to target these cells

overall_design: Two control samples compared to two SHARP knockdown samples

first: Brooks

middle: D

last: Michael

first: Zhu

last: Yongyou


title: PAF1 Drives Pancreatic Cancer Oncogenesis by Promoting Stemness via PHF5A/DDX3 Sub-complex (ChIP-seq)

city: Omaha

first: Saswati

last: Karmakar

state: NE

address: 42nd st & Emile

institute: UNMC

summary: In this study, we established that PAF1 is critical for pancreatic tumorigenesis, and CSC-driven tumor maintenance because depletion of PAF1 resulted in significantly less tumor burden and reduction in CSC populations.

overall_design: Chromatin immunoprecipitation was performed using PAF1 and PHF5A antibodies; and IgG antibody was used as control

first: Surinder

last: Batra


title: Effect of total-body Irradiation on gene expression in mouse whole blood

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

summary: For victims of radiological accidents, rapid dose estimation and damage prediction are essential. Administering the gold-standard biodosimetry chromosome aberration assay requires highly skilled individuals and several days of labor; consequently, rapid turnaround is an important concern. Identification of new dose estimation markers and damage-predicting in vivo molecules to replace the chromosome aberration assay is crucial to improving the delivery time of medical treatment. Here, we investigated the applicability of mRNA levels using a mouse model. Female C57BL/6J mice were X-ray irradiated at various doses, and a DNA microarray was then performed to identify differentially expressed mRNAs in whole blood. The microarray analysis identified 14 radioresponsive mRNAs with more than fourfold differences by pattern matching in the expression at 24 h postirradiation. In particular, mRNA expression of Slfn4, Itgb5, Smim3, Tmem40, Litaf, Gp1bb and Cxx1c was significantly increased in a radiation-dose-dependent manner, as validated by reverse transcription quantitative polymerase chain reaction. We also performed an analysis using the cBioPortal for Cancer Genomics and found that the overall survival of ovarian adenocarcinoma patients with alterations in Smim3 and that of thymoma patients with alterations in Cxx1c had a worse prognosis than patients without these alterations. These findings suggest that the expression of several genes in whole blood was a sensitive and specific biomarker of radiation exposure and can be used as a rapid and reliable prospective molecular biomarker in radiological emergencies.

overall_design: Seven-week-old female C57BL/6JJcl mice were delivered from the breeding facilities of Clea Japan (Tokyo, Japan). Eight-week-old mice were randomly divided into 4 groups and subjected to varying TBI doses of 0, 0.5, 1 or 3 Gy of X-rays (150 kVp, 20 mA, 0.5-mm aluminum and 0.3-mm copper filters) at a dose rate of 1.0 Gy/min using an MBR-1520R X-ray generator (Hitachi Medical, Tokyo, Japan). All mice were housed in standard cages in a conventional clean room under a 12-h light/dark cycle. The mice had ad libitum access to sterilized standard laboratory mouse chow diet and drinking water. In the present study, the selection criteria applied prior to sacrifice were >20% loss of body weight and respiratory distress. After 24-h, mice treated with TBI only (TBI mice) and those that did not receive TBI (control mice) were anaesthetized with isoflurane (Powerful Isoful®; Zoetis, London, UK) and sacrificed for collection of whole blood.

first: Masaru

last: Yamaguchi

first: Teruki

last: Nishida

first: Yoshiaki

last: Sato

first: Ikuo

last: Kashiwakura


title: Triangular Correlation (TrC) between cancer aggressiveness, cell uptake capability and cell deformability

status: Public on Jan 24 2020

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: The malignancy potential is correlated with mechanical deformability of the cancer cells. Therefore, mechanical properties of individual patient cells can contribute essential knowledge in cancer diagnostics and in precision therapies. However, clinical applications are limited by lack of current knowledge and of reliable and robust cell mechanical tests. In a comprehensive study, we found a Triangular Correlation (TrC) between cell deformability, phagocytic like capacity, and cancer aggressiveness. A significant application of the TrC is that phagocytic measurements can be a surrogate marker for detecting malignancy of cancer cells based on mechanical properties. We found that the uptake of inert sub-micron and micro-beads was massively higher in cancer cells compared with non-cancerous cells. Moreover, cells with a higher malignancy potential had greater uptake capacity. Importantly, in a reciprocal approach, we sorted either human bladder cancer cells or melanoma cells into subpopulations, solely based on their phagocytic capacity. The more phagocytic subpopulations showed elevated phenotypes of cancer aggressiveness ex vivo and in vivo. The uptake potential was found to be an imprinted feature preserved genetically and enriched over the sorting cycles. A gene expression profile revealed differences in gene sets associated with regulation of cell-cell and extracellular matrix adhesions and epithelial-to-mesenchymal transition. Chromatin immunoprecipitation sequencing showed that differences in gene expression were reflected also at the chromatin level. Importantly, in all cases studied here, enhanced phagocytic ability and elevated aggressiveness phenotypes were correlated with greater cell deformability, providing the mechanical link of the TrC. A computational model supported the notion that the uptake capacity can be a marker for malignancy mediated by cell mechanics. Our multidisciplinary approach, which involved complementary directions of study in several types of cancer cells, provides the proof of concept that phagocytic measurements can be applied for cancer diagnostics and precision medicine.

overall_design: Comparison of sub populations of cancer cells that were sorted based on their phagocytic capacity

first: Ouri

last: Schwob

first: Dvir

last: Dror

first: Talya

last: Millo

first: Natalie

last: Orehov

first: Yifat

last: Brill-Karniely

first: Ofra

last: Benny


title: Differential Expression profiles  of tRNA-Derived Small RNAs in Rats After Traumatic Spinal Cord Injury

first: Chuan

last: Qin

address: No.95,yong an road.

department: Department of Urology

institute: Beijing Friendship Hospital, Capital Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: The goals of this study are to screen differential expression profiles  of tRNA-Derived small RNAs (tsRNAs) in rats after traumatic spinal cord injury (SCI) using next-generation sequencing and qRT-PCR.As a result, in rat spinal cord 1 day after contusion, totally 297 tsRNAs differentially expressed were identified. 155 tsRNAs were significantly differentially expressed: 91 were significantly up-regulated, while 64 were significantly down-regulated after SCI (folding change>1.5; P<0.05).Next, four tsRNAs were selected to be verified by qRT-PCR. Taken together,this study explored, for the first time, the significant alteration of tsRNA expression profiles after traumatic SCI in rats and offered deep insights into many possible treatment targets of SCI by regulating tsRNAs.

overall_design: Differential Expression profiles  of tRNA-Derived Small RNAs of male Sprague–Dawley rats (250–300 g)  were generated by deep sequencing, using NextSeq 500/550 V2 kit (#FC-404-2005, Illumina). twelve rats were randomly assigned to two groups using a computer-generated randomization schedule: rats in the sham control group (n = 6) were treated with laminectomy alone without contusion, and rats in the SCI group (n = 6) were subjected to laminectomy plus contusion.Cord tissue samples from rats in the SCI (n=6) and sham groups (n=6) including the collecting tissue for the Sequencing (n=4 in SCI and sham group respectively) and additional tissues (n=2 in SCI and sham group respectively) were used in the PCR experiment.

first: Jian-Jun

last: Li


title: Hi-CoP, a simple and robust assay for detecting interactions of regulatory regions

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

summary: First we developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of accessible regions by directly purifying fragmentized crosslinked chromatin with DNA purification column. The CoP chromatin regions by CoP-seq are consistent with the accessible regions detected by ATAC-seq and FARIE-seq. Then we integrated CoP-seq and Hi-C technique (Hi-CoP) for interactions of accessible chromatin regions which represent active cis-regulatory elements in cells. Our data showed that Hi-CoP assay can robustly detect interactions of regulatory regions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Open chromatin were isolated with DNA purification column in K562 cell line and 4-12 weeks C57BL/6 WT mice thymocytes integrated Hi-C technique (Hi-CoP)or not.

first: Yan

last: Zhang

first: Zhaoqiang

first: Zhao

last: Hao

first: Delong

last: Feng

first: Shasha

last: Bian

first: Yuhe

last: Hou

first: Yanhong

last: Chen


title: Genome-wide H3K4me2 distribution comparison between Positive and Negative A375 (Human skin melanoma cell line)

first: Gilgi

summary: Purpose: Characterizing the epigenetic differences between the positive and negative cells by using histone modification (h3k4me2- Active loci)

overall_design: four samples for two lines; A375 positive and negaative cells, two biological replicates

first: Mohammad

last: Jaber

first: Netanel

last: Loyfer


title: Angiogenin derived from ABCB5+ mesenchymal stem cells improves diabetic wound via enhancing angiogenesis

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

summary: Severe angiopathy has been postulated as a major driver for diabetes associated secondary complications. So far the knowledge on underlying mechanisms and thereon based therapeutic options to attenuate these pathologies are limited. Here we systematically administered ABCB5+ MSCs for the treatment of chronic non-healing diabetic wounds employing db/db mice, a type II diabetes model as their number markedly declined during diabetes. We found that administration of ABCB5+ MSCs markedly accelerates wound closure in diabetic db/db mice as opposed to the vehicle treated control group. Strikingly, administration of ABCB5+ MSCs at the edges of the diabetic wounds triggered considerable neoangiogenesis, most likely by the releasing a Ribonuclease angiogenin that was identified through secretome analysis of ABCB5+ MSCs. Interestingly, silencing of angiogenin in ABCB5+ MSCs significantly delayed wound closure in diabetic db/db mice indicating its key role in skin regeneration. Moreover, angiogenin also impacted the polarization of macrophages. The findings from this study will provide novel insight into the unique capacity of ABCB5+ MSCs to mount an adaptive response at the wound site with the delivery of angiogenic molecules holds significant promise for the therapy of non-healing diabetes foot ulcers, and other pathologies with impaired angiogenesis. The benefits for refined stem cell based therapies is virtually unlimited.

overall_design: Transcriptome profiling of HUVEC

first: Karin

last: Scharffetter-Kochanek


title: Evaluation of M2-like macrophage enrichment after diffuse traumatic brain injury through transient interleukin-4 expression from engineered mesenchymal stromal cells

city: Durham

first: Syed Faaiz

last: Enam

state: NC

address: 308 Research Dr, Rm C-141 LSRC

department: Biomedical Engineering

institute: Duke University

summary: We report the effects of acute M2-like macrophage enrichment in a mouse closed head injury model of diffuse traumatic brain injury. Enrichment is achieved by engineering mesenchymal stromal cells with synthetic interleukin-4 (IL-4) mRNA to transiently express IL-4. Through a transcriptomic analysis of treated brain tissue, we begin to understand the effects of acute IL-4 and M2-like macrophage enrichment.

overall_design: Left brain cortex from naïve mice (SHAM) and mice with closed head injury and left hemisphere treatment with either phosphate-buffered saline (PBS), naïve mesenchymal stromal cells (MSC), or interleukin-4 expressing MSCs (IL-4 MSC)

first: Syed

middle: F

first: Sajidur

middle: R

last: Kader

first: Nicholas

last: Bodkin

first: Johnathan

middle: G

last: Lyon

first: Mark

last: Calhoun

first: Cesar

last: Azrak

first: Pooja

last: Tiwari

first: Daryll

last: Vanover

first: Haichen

last: Wang

first: Philip

middle: J

last: Santangelo

first: Ravi

middle: V

last: Bellamkonda


title: Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells

city: Madison

first: Aleksandar

middle: K.

last: Stanic

state: WI

address: 202 S. Park St., Meriter Atrium B

department: Obstetrics and Gynecology

institute: University of Wisconsin - Madison

summary: A successful pregnancy requires many physiological adaptations from the mother, including the establishment of tolerance towards the semiallogeneic fetus. Innate lymphoid cells (ILCs) have arisen as important players in immune regulation and tissue homeostasis at mucosal and barrier surfaces. Dimensionality reduction and transcriptomic analysis revealed the presence of two novel CD56Bright decidual ILCs, C10 and C2, that express divergent levels of Eomes. We found that decidual C10, C2, and cNKs correlated highly with previously identified first trimester decidual dNKs (dNK1-3). Functional analysis revealed polyfunctional profiles that depend on the nature of the stimulus, with a preference for IFNgamma and VEGF production. Overall, our data suggests persistence of pregnancy-specific decidual innate lymphocytes across pregnancy.

overall_design: Cells of interest (C10 and C2) were isolated from 3 different decidua samples (biological replicates). As a reference, cNKs were also isolated from the same decidua samples, as they are well characterized in the literature.

first: Jessica

last: Vazquez

first: Deborah

middle: A

last: Chasman

first: Gladys

middle: E

last: Lopez

first: Chanel

last: Tyler

first: Irene

middle: M

last: Ong


title: RNA-Seq and ChIP-Seq: cell lines

first: Gilgi

last: Friedlander

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

overall_design: Refer to individual Series


title: Inhibition of Methyltransferase Activity of Enhancer of Zeste 2 Leads to Enhanced Lipid Accumulation and Altered Chromatin Status in Zebrafish

status: Public on Jan 22 2020

city: Oslo

first: Leif

middle: Christopher

last: Lindeman

state: Oslo

address: Ullevålsveien 72

country: Norway

institute: Norwegian University of Life Sciences

summary: Recent studies indicate that exposure to environmental chemicals may increase susceptibility to developing metabolic diseases. This susceptibility might in part be caused by changes to the epigenetic landscape which consequently affect gene expression and lead to changes in lipid metabolism. These changes might be mediated by epigenetic markers such as Enhancer of Zeste2 (Ezh2), a histone H3K27 methyltransferase that has been implicated to play a role in lipid metabolismand adipogenesis. In this study, we used the zebrafish (Danio rerio) to investigate the role of Ezh2 on lipid metabolism and chromatin status following developmental exposure to the Ezh1/2 inhibitor PF-06726304 acetate.

overall_design: ATAC-seq of Ezh2 inhibitied zebrafish embryos

first: M

last: den Broeder

first: J

last: Ballangby

first: L

last: Kamminga

first: P

last: Aleström

last: Legler

last: Kamstra


title: RNA immunoprecipitation (RIP) of KHSRP from pancreatic cancer cell extracts cultured on fibronectin

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu

institute: Kochi Medical School

summary: KHSRP-bound transcripts were identified by RNA immunoprecipitation and sequencing (RIP-Seq) and bioinformatics analysis. A pancreatic cancer cell line S2-013 was cultured on fibronectin. We performed RIP of KHSRP using anti-KHSRP antibody from the fibronectin-stimulated S2-013 extracts, and identified the associated RNAs using a next generation sequencer.

overall_design: S2-013 cells were seeded on fibronectin and incubated for 5.5 h. After washing twice with PBS, cells were lysed in NP2 buffer. Lysates were immunoprecipitated with anti-KHSRP antibody or with normal rabbit IgG and Dynabeads Protein G. The immunoprecipitation products were processed by Hokkaido System Science (Sapporo, Japan) using an Illumina/Solexa instrument following standard procedures.


title: Transcriptome of ROS-low LSCs isolated from phenotypically primitive and monocytic primary acute myeloid leukemia (AML) cells

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

summary: To identify biological differences between primitive and monocytic primary AML, we sorted ROS-low enriched LSC subfractions from phenotypically monocytic (CD45-bright/SSC-high/CD117-/CD11b+/CD68+/CD64+) and primitive AML  (CD45-medium/SSC-low/CD117+/CD11b-/CD68-/CD64-)  specimens and performed RNA-seq analysis.

overall_design: RNA was isolated from freshly sorted primary AML cells and subjected to RNA-seq analysis.

first: Mohammad

last: Minhajuddin

first: Craig

last: Jordan


title: Chromatin accessibility dynamics in a model of human forebrain development

status: Public on Jan 23 2020

city: Stanford

first: Nasa

last: Sinnott-Armstrong

state: California

address: 318 Campus Drive, Clark Center S240

department: Genetics

institute: Stanford University

summary: In this study, we used a forebrain 3D spheroid model to map chromatin accessibility and gene expression changes throughout a dense time course spanning 20 months of neuronal and glial maturation.

overall_design:
We generated more than 100 ATAC-seq libraries from iPSC to 20 months in culture.

>>>Submitter states that the raw data will be made available through dbGaP due to patient privacy concerns<<<<

first: Alexandro

last: Trevino

first: Jimena

last: Andersen

first: Se-Jin

last: Yoon

first: Nina

last: Huber

first: Howard

middle: Y

last: Chang

first: Jonathan

last: Pritchard

first: William

last: Greenleaf

first: Sergiu

middle: P

last: Pasca


title: Selective Inhibition of the Second Bromodomain of BET Family Maintains Anti-Tumor Efficacy and Improves Tolerability

city: North Chicago

first: Josh

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

institute: AbbVie Inc.

summary: Here we report the discovery of ABBV-744, a first in class, highly potent and selective inhibitor of BET family BD2 domains with drug like properties.  ChIP-seq analysis revealed that ABBV-744 displaced BRD4 from AR-containing super enhancers and elicited potent inhibition of AR-dependent transcription without causing broad transcription alterations associated with exposure to pan BET inhibitors.

overall_design: BRD4 ChIP-Seq under four different treatment conditions in two cell lines.  H3K27Ac ChIP-Seq from two cell lines, vehicle treatment only.  AR ChIP-Seq in one cell line (LNCaP) with three treatment conditions.  BRD4 and AR ChIP-Seq were all spike-in controlled.

first: Emily

last: Faivre

first: Joshua


title: Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells

city: Los Angeles

first: Zhifei

last: Luo

state: CA

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

summary: Aberrant expression of HOXC6 and HOXC4 is commonly detected in prostate cancer. The high expression of these transcription factors is associated with aggressive prostate cancer and can predict cancer recurrence after treatment. Thus, HOXC4 and HOXC6 are clinically relevant biomarkers of aggressive prostate cancer. However, the molecular mechanisms by which these HOXC genes contribute to prostate cancer is not yet understood. To begin to address the role of HOXC4 and HOXC6 in prostate cancer, we performed RNA-seq analyses before and after siRNA-mediated knockdown of HOXC4 and/or HOXC6 and also performed ChIP-seq to identify genomic binding sites for both of these transcription factors. Our studies demonstrate that HOXC4 and HOXC6 co-localize with HOXB13, FOXA1 and AR, three transcription factors previously shown to contribute to the development of prostate cancer. We suggest that the aberrantly upregulated HOXC4 and HOXC6 proteins may compete with HOXB13 for binding sites, thus altering the prostate transcriptome. This competition model may be applicable to many different human cancers that display increased expression of a HOX transcription factor.

overall_design: Examination of HOXC6 binding sites in human prostate cancer 22Rv1 cell line. HOXC4 and HOXC6 were knockdown by siRNA the transcriptomic changes were investigated by RNA_seq.

first: Peggy

last: Farnham


title: Mouse Homolog of a Human TP53 Germline Mutation Reveals a Lipolytic Activity of p53

status: Public on Jan 21 2020

city: Bethesda

first: Paul

middle: M.

last: Hwang

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

summary: The physiological effects of the many germline mutations of TP53, encoding the tumor suppressor protein p53, are poorly understood.  Here, we report generating a p53 R178C knockin mouse modeling the human TP53 R181C mutation that is notable for its prevalence and prior molecular characterization.  Consistent with its weak cancer penetrance in humans, homozygous p53178C/C mice showed a modest increase in tumorigenesis but, surprisingly, were lean with decreased body fat content.  They displayed evidence of increased lipolysis and upregulation of fatty acid metabolism in their inguinal white adipose tissue (iWAT).  Gene expression and chromatin immunoprecipitation sequencing (ChIP-Seq) analyses showed that the mutant p53 bound and transactivated Beta-3-Adrenergic Receptor (ADRB3), a gene that is known to promote lipolysis and is associated with obesity.  The current study reveals that a germline mutation of p53 can affect fat metabolism which can impact cancer development.

overall_design: RNA-seq data of white adipose tissue obtained from wild-type p53, homozygous p53 R178C knockin mutant, and homozygous p53 knockout mice.  p53 ChIP-seq data of adipocytes derived from the stromal vascular fraction of adipose tissue.

first: Ju-Gyeong

last: Kang

first: Ji-Eun

last: Lee

first: Kai

last: Ge


title: Profiling of tumor-associated macrophages (TAM) after anti-MerTK treatment

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

summary:
RNA was isolated from purified TAMs from MC-38 tumor-bearing mice after 24 hours of anti-MerTK single dose treatment at 30mg/kg body weight intravenously.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0014685

overall_design: Gene expression profiling of TAMs from MC-38 tumor-bearing mice after 24 hours of anti-MerTK treatment

first: Yi

last: Zhou

first: Minhong

last: Yan


title: A Regulatory microRNA Network Controls Endothelial Cell Phenotypic Switch During Sprouting Angiogenesis [shDICER]

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

summary: We exploited a three-dimensional model of sprouting angiogenesis in which the phenotypic switch from quiescent ECs to tip cells was triggered by VEGF-A. The information obtained about modulated miRNAs and their related protein-coding gene targets was used to generate a co-expression network encompassing gene modules that are post-transcriptionally regulated and whose activity is required for sprouting.

overall_design: Gene expression profile study of HUVEC transduced with a non-targeting shRNA (pLKO) or with a shRNA targeting DICER1 (shDICER). Cells were cultured in a 3D collagen matrix as quiescent not-stimulated spheroids (SPHC), and subsequently stimulated with VEGF-A. Two replicates for each experimental point are included.

first: Noghero

last: Alessio

first: Bussolino

last: Federico

first: Corà

last: Davide

first: Rosano

last: Stefania


title: A Regulatory microRNA Network Controls Endothelial Cell Phenotypic Switch During Sprouting Angiogenesis


title: A Regulatory microRNA Network Controls Endothelial Cell Phenotypic Switch During Sprouting Angiogenesis [miRNA-seq]

overall_design: Gene expression profile study of HUVEC cultured in 3D collagen matrix as quiescent, not-stimulated spheroids (SPHC), and VEGF-A-stimulated sprouted spheroids (SPHV).

first: Alessio

last: Noghero

first: Federico

last: Bussolino

last: Corà

first: Stefania

last: Rosano


title: A Regulatory microRNA Network Controls Endothelial Cell Phenotypic Switch During Sprouting Angiogenesis [RNA-Seq]


title: Differential gene expression analysis on 24 arrays derived from the human HAC15 cell line

status: Public on Jan 20 2020

city: Berlin

first: Eric

last: Seidel

state: Berlin

address: Augustenburger Platz 1

institute: Charite Berlin

summary: In order to investigate gene expression changes in a model of mitotane resistant adrenocortical carcinoma, we generated mitotane resistant clones from HAC15 bulk cells via long-term treatment followed by clonal selection.

overall_design: Gene expression changes were assessed in nonresistant and resistant clones treated with DMSO or 50 µM mitotane for 18 h.

first: Gudrun

last: Walenda

first: Ute

last: Scholl

first: Liz

last: Li


title: Comparing the transcriptome of naïve C57BL/6 CD44+/+ vs CD44-/- alveolar macrophages

status: Public on Jan 17 2020

city: Vancouver

first: Pauline

last: Johnson

state: BC

address: 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

summary:
Purpose: Determine if alveolar macrophage express different transcriptional programs when CD44 expression is lost.
Methods: Alveolar macrophages were isolated from the bronchoalveolar lavage of 6-10 week old CD44+/+ and CD44-/- female mice. RNA was isolated an  sequenced using Illumina NextSeq 500. RNA was sequenced by the UBC Biomedical Research Center. RNA quality, 18S and 28S ribosomal RNA with RIN = 9.6, was determined by Agilent 2100 Bioanalyzer following standard protocol for NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with paired end 42bp  42bp reads. De-multiplexed read sequences were then aligned to the Mus musculus (mm10) reference sequence using Spliced Transcripts Alignment to a Reference, STAR (https://www.ncbi.nlm.nih.gov/pubmed/23104886), aligners.
Results and conclusion: Multiple pathways were abnormal in CD44-/- alveolar macrophages, in particular those involved in lipid metabolism and immune signaling.

overall_design: mRNA libraries generated from alveolar macrophages isolated from bronchoalvoelar lavage of 6-10 week old CD44+/+ and CD44-/- female mice, in triplicates, using Illumina NextSeq 500

first: Yifei

last: Dong

first: Zongyi

last: Ha


title: Adipocyte serine uptake curbs ROS generation and visceral adiposity [Human]

status: Public on Jan 19 2020

city: Bergen

first: Laurence

middle: William-Joseph

last: Dyer

address: Haukelandsveien 22

department: Clinical Institute

institute: University of Bergen

summary: Obesity, and visceral adiposity in particular, increases the risk of common metabolic diseases, including type 2 diabetes, cardiovascular disease, and several forms of cancer. However, the molecular mechanisms responsible for regional fat storage remain poorly characterized, preventing therapeutic innovation. We here applied a systematic genome-wide screen and translational approach, where human primary preadipocytes were isolated from liposuction aspirate and differentiated. At day 7 of differentiation, cells were treated with BMS-466442 or vehicle (DMSO) for 24 hours. After incubation, cells were lysed, and RNA was purified, DNase treated, and the RNA integrity number was checked. Subsequently, cDNA libraries were generated via the TruSeq Stranded mRNA Library Prep kit and sequenced by Illumina Hiseq 4000.

overall_design: Total RNA-Seq of Human adipose tissue were sequenced on the Illumina HiSeq4000 platform

first: Simon

last: Dankel

first: Regine

last: Asen

first: Divya

last: Priyanka


title: IL-1-conferred gene expression pattern in ERa+ BCa and AR+ PCa cells is intrinsic to ERa- BCa and AR- PCa cells and promotes cell survival

status: Public on Jan 18 2020

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

summary: Background: Breast (BCa) and prostate (PCa) cancers are hormone receptor (HR)-driven cancers. Estrogen receptor alpha (ERa) is overexpressed in 70% of diagnosed BCa patients and androgen receptor (AR) is overexpressed in 80-90% of diagnosed PCa patients.  Thus, BCa and PCa patients are given therapy that reduces hormone levels or directly blocks HR activity; but most patients eventually develop treatment resistance.  15-30% of BCa patients and ≥ 30% of PCa patients that acquire treatment resistance develop tumors enriched in cancer cells with low or no HR accumulation.  Furthermore, 15-20% of BCa patients and 10-20% of PCa patients are intrinsically HR-negative (HR-), and thus, have intrinsic resistance to therapy.  We have previously reported that interleukin-1 (IL-1) inflammatory cytokine downregulates ERa and AR mRNA in HR-positive (HR+) BCa and PCa cell lines.  Additionally, we had identified pro-survival proteins and processes upregulated by IL-1 in HR+ BCa and PCa cells, that are basally high in HR- BCa and PCa cells. Therefore, we hypothesize that IL-1 confers a conserved gene expression pattern in HR+ BCa and PCa cells that mimics conserved basal gene expression patterns in HR- BCa and PCa cells, to promote HR-independent survival and tumorigenicity.  Methods: To identify changes in global gene expression we performed RNA sequencing (RNA-seq) for HR+ BCa and PCa cell lines exposed to IL-1 and for untreated HR- BCa and PCa cell lines.  We confirmed expression patterns of select genes by RT-qPCR and used siRNA and/or drug inhibition to silence select genes in BCa and PCa cell lines.  We also compared our gene expression data with publicly available data sets from hormone receptor-independent sublines.  Finally, we performed Ingenuity Pathway Analysis (IPA) to identify signaling pathways encode by our RNA-seq data set.  Results: We identified 350 genes in common between BCa and PCa cells that are induced or repressed by IL-1 in HR+ cells that are, respectively, basally high or low in HR- cells.  Among these genes, we identified Sequestome-1 (SQSTM1/p62) and SRY (Sex-Determining Region Y)-Box 9 (SOX9) to be essential for survival of HR- BCa and PCa cell lines.  Analysis of publicly available data indicates that p62 and SOX9 expression are elevated in hormone receptor-independent BCa and PCa sublines generated in vitro, suggesting that p62 and SOX9 have a role in acquired treatment resistance.  We also assessed HR- cell line viability in response verteporfin, an FDA approved therapy for macular degeneration known to target p62, and we found that verteporfin is cytotoxic for HR- cells lines.    Conclusions:  Taken together, our 350 gene set can be used to identify novel therapeutic targets and/or biomarkers conserved among acquired (e.g. due to inflammation) or intrinsic hormone receptor-independent BCa and PCa.

overall_design: MCF7 breast cancer cell lines was treated with vehicle control, IL-1 alpha or IL-1 beta for 5 days.   MDA-MB-231 breast cancer cell lines was treated with vehicle control for 5 days.  At Day 5 RNA was ectracted for RNA-sequencing and other analysis was performed such as western blot and RT-qPCR.

first: Afshan

last: Nawas

first: Mohammed

last: Kanchwala

first: Shayna

last: Thomas-Jardin

first: Haley

last: Dahl

first: Kelly

last: Daescu

first: Monica

last: Bautista

first: Vanessa

last: Anunobi

first: Ally

last: Wong

first: Rachel

last: Meade

first: Ragini

last: Mistry

first: Nisha

last: Ghatwai

first: Felix

last: Bayerl

first: Chao

last: Xing


title: The RNA N6-methyladenosine regulates chromatin remodeling and transcription [mESC_seq_RNA_mNET]

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

summary: The N6-methyladenosine (m6A) has been shown to regulate stability and translation of messenger RNA (mRNA) in various biological processes. Here, we show that the knockout of the m6A writer Mettl3 or a nuclear reader Ythdc1 in mouse embryonic stem cells (mESCs) induces chromatin openness and transcription activation in an m6A-dependent manner. We identified extensive m6A modifications on caRNAs (chromosome-associated RNAs, including promoter-associated RNAs, enhancer RNAs and repeats) that are installed by METTL3. YTHDC1 can bind to a portion of these m6A-modified RNAs and facilitate their decay through the NEXT-mediated nuclear degradation. Therefore, the m6A methylation of these caRNAs reduces their abundances. The knockout of Mettl3 elevates levels of caRNAs and promote open chromatin state and downstream transcription. Collectively, our results reveal that m6A on caRNAs can globally tune chromatin state and transcription.

overall_design: Examine transcription rate in control and two knockout METTL3 mESCs

first: Jun

last: Liu

first: Chuan

last: He


title: The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_nuclearRNA]

overall_design: Examine nuclear non-ribosome RNA decay in ckoYTHDC1 and control mESCs, and gene expression in control and two knockout METTL3 mESCs


title: The RNA N6-methyladenosine regulates chromatin remodeling and transcription [mESC_seq_ChIP_tf]

overall_design: Examination role of YY1, EP300 and JARID2 in three cell types.


title: The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_mettl3ChIP]

overall_design: Examination of METTL3 DNA binding sites in mESCs.


title: The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_histoneChIP]

overall_design: Examination of H3K27ac and H3K4me3 modifications in three cell types.


title: The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_nascentRNA]


title: The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_m6ARIP]

overall_design: chromatin-associated RNA m6A profiles of Mettl3 or Ythdc1 knockout mESCs and their controls  were generated by deep sequencing, in diplicate, using Illumina NovaSeq 6000.


title: RNA-sequencing of parasites overexpressing conditionally stabilized BFD1 to identify genes regulated by BFD1

status: Public on Jan 16 2020

city: CAMBRIDGE

first: Benjamin

middle: S

last: Waldman

state: MA

address: 455 Main Street Rm. 555

department: Biology

institute: Whitehead Institute

summary: WT (ME49∆KU80), ∆BFD1, or ∆BFD1/DD-BFD1-Ty parasites were treated with the stabilizing ligand Shield-1 (all three) or vehicle alone (WT and ∆BFD1/DD-BFD1-Ty) to identify genes differentially regulated by overexpression of BFD1.

overall_design: Data from three biological replicates.

first: Dominic

last: Schwarz

first: Marc

middle: H

last: Wadsworth II

first: Jeroen

last: Saeij

first: Alex

middle: K

last: Shalek

first: Sebastian

last: Lourido


title: Tet3 ablation in adult brain neurons increases anxiety-like behavior and regulates cognitive function in mice

city: London

first: Miguel

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

summary: TET3 is a member of the Ten-eleven translocation (TET) family of enzymes which oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). Tet3 is highly expressed in the brain, where 5hmC levels are most abundant. In adult mice, we observed that TET3 is present in mature neurons and oligodendrocytes but is absent in astrocytes. To investigate the function of TET3 in adult post-mitotic neurons, we crossed Tet3 floxed mice with a neuronal Cre-expressing mouse line, Camk2a-CreERT2, obtaining a Tet3 conditional KO mouse line. Ablation of Tet3 in adult mature neurons resulted in increased anxiety-like behavior with concomitant hypercorticalism, and impaired hippocampal-dependent spatial orientation. Transcriptome and gene-specific expression analysis of the hippocampus showed dysregulation of genes involved in glucocorticoid signaling pathway (HPA axis) in the ventral hippocampus, whereas upregulation of immediate early genes (IEGs) was observed in both dorsal and ventral hippocampal areas. Additionally, Tet3 cKO mice exhibit increased dendritic spine maturation in the ventral CA1 hippocampal subregion. Based on these observations, we suggest that TET3 is involved in molecular alterations, that govern hippocampal-dependent functions. These results reveal a critical role for epigenetic modifications in modulating brain functions, opening new insights into the molecular basis of psychiatric disorders.

overall_design: Tet3 fl/fl mice on a C57BL/6N background were crossed with B6;129S6 mice (24 JAX stock #012362 – Camk2a-CreERT2) expressing a tamoxifen-inducible Cre recombinase under the control of the mouse Camk2a promoter region to generate mice heterozygous for the floxed Tet3 allele and Cre- recombinase. These mice were interbred with C57BL/6N mice homozygous for the floxed Tet3 allele to generate mice heterozygous for Cre-recombinase and homozygous for the floxed Tet3 allele, designated as Tet3 cKO mice. Mice homozygous for the Tet3 floxed allele, but not carrying Cre-recombinase, were used as controls. From both groups, dorsal and ventral hippocampal brain regions were macrodissected and the RNA extracted. RNA-seq libraries were generated as described below.

first: Claudia

last: Antunes

first: Jorge

middle: D

last: Da Silva

first: Sonia

last: Guerra-Gomes

first: Nuno

last: Alves

first: Fabio

last: Ferreira

first: Eduardo

last: Loureiro-Campos

last: Sousa

first: Wolf

last: Reik

first: Luisa

last: Pinto

first: C Joana

last: Marques


title: Replicational dilution of H3K27me3 in mammalian cells and the role of poised promoters

city: Boston

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Differential effect of PRC2 loss on gene repression in intestinal stem cells, transit amplifying cells, and differentiated villus cells in intestine is explained by disparity in the rate of cell division and resulting difference in H3K27me3 loss.

overall_design: We conducted RNA-seq, ChIP-seq, scRNA-seq experiments using purified intestinal epithleal cells from wild-type and mutant adult mice and human lymphoma cell line.

first: Unmesh

last: Jadhav

first: Elisa

last: Manieri

first: Kodandaramireddy

last: Nalapareddy

first: Shariq

last: Madha

first: Shaon

last: Chakrabarti

first: Kai

last: Wucherpfennig

first: Megan

last: Barefoot


title: A Regulatory microRNA Network Controls Endothelial Cell Phenotypic Switch During Sprouting Angiogenesis [2D]

first: Davide

last: Cora'

overall_design: Gene expression profile study of HUVEC cells in a 2D condition, with and without stimulation with VEGF-A. Two replicates for each experimental point are included.

first: Alessio

last: Noghero

first: Federico

last: Bussolino

last: Corà

first: Stefania

last: Rosano


title: EspM regulates gene expression in response to the ESX-1 system in Mycobacterium marinum

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Regulation of M. marinum gene expression in an espM deletion strain

overall_design: M Marinum M based strains (Wild type, epsM mutant and complemented overexpressor strain) were cultured in 5mL 7H9 and 0.1% Tween-80 for two days, then moved to 25mL 7H9 and 0.1% Tween-80 for two days. All strains were then subcultured in Sauton’s media 0.01% Tween-80 at an OD of 0.8  for 48 hours. The cultures were collected by centrifugation and stored at -80 for 24 hours. Cells were lysed using a bead beater. Total RNA was prepared from the pellets using the Qiagen RNeasy kit.

first: K

last: Sanchez

first: M

last: Ferrell

first: A

last: Chirakos

last: Nicholson

first: R

last: Champion

first: P


title: Ascl2-dependent cell differentiation drives regeneration of abated intestinal stem cells

first: Ramesh

last: Shivdasani

summary: Functions of Ascl2 in colonic stem cell maintenance and regeneration. We used RNA-sequencing to profile gene expression in regenerating crypt cells and Ascl2-deficient colonic stem cells, and ASCL2 ChIP-seq to identify transcriptional target genes.

overall_design: RNA-seq and ASCL2 ChIP-seq analyses of isolated mouse colonic stem cells. RNA-seq analyses of Ascl2-deficient mouse colonic stem cells. Single Cell RNA-seq analysis of regenerating colonic crypt cells. Transcript dynamics of colonic epithelial development.

first: Kazutaka

last: Murata

first: Unmesh

last: Jadhav

first: Johan

last: van Es

first: Justin

last: Dean

first: Alesia

last: Cavazza

first: Franziska

last: Michor

first: Hans

last: Clevers


title: CUT&RUN profiling of genomic BFD1 binding sites

first: Benjamin

last: Waldman

summary: Using an epitope-tagged BFD1-complemented strain, the genomic binding of BFD1 was assessed in alkaline-stress induced bradyzoites.

overall_design: One experimental (anti-Ty) and one control (Isotype) sample

first: Dominic

last: Schwarz

first: Marc

last: Wadsworth II

first: Jeroen

last: Saeij

first: Alex

last: Shalek

first: Sebastian

last: Lourido


title: Transcriptional signature of murine nasal ChAT-eGFP+ cells identified by RNASeq

first: Lora

last: Bankova

address: 60 Fenwood Road

department: Medicine

institute: Brigham and Women's Hospital

summary:
Purpose: Choline acetyltransferase (ChAT)-expressing epithelial cells are found in the upper and lower airways. In the trachea, they are referred to as brush cells. In the mouse nose two distinct populations of ChAT-eGFP+ cells had been previously described: a population of rare solitary chemosensory cells (SCCs) in the respiratory mucosa and a more abundant population of microvillous cells (MVCs) in the olfactory epithelium. Besides ChAT expression, SCCs share the expression of bitter taste receptors and signaling machinery with tracheal brush cells as well as close association with CGPR+ nerve fibers and an elongated shape. MVCs do not express bitter taste receptors, are not clearly associated with nerves and are smaller in size than SCCs.  We have previously reported the transcriptional profile of tracheal ChAT-expressing brush cells but the transcriptional profile of nasal chemosensory ChAT+ epithelial cells has not been reported.
Methods: In this study, we isolated nasal ChAT-eGFP+ cells by FACS from naïve ChAT(BAC)-eGFP mice with knockin of eGFP within a BAC spanning the ChAT locus, marking brush cells in the epithelium and performed transcriptome profiling using low input RNA sequencing.  We sorted two distinct subsets of ChAT-eGFP+ epithelial cells from the nasal mucosa based on FACS ice and granularity characteristic: ChAT-eGFP+ EpCAM+ FSC/SSChigh (representing 5% of all ChAT-eGFP+ cells) and FSC/SSClow  (representing 95% of all ChAT-eGFP+ cells), respectively. We compared them to unfractionated ChAT-eGFP- EpCAM+ epithelial cells.
Results: Both nasal ChAT-eGFP subsets shared the core transcriptional profile of chemosensory cells from the intestine, trachea, gallbladder and thymus including the expression of Il25, Pou2f3, Trpm5, Avil, Plcb2 and transcripts of eicosanoid biosynthetic enzymes suggesting that most ChAT-eGFP+ cells in the nose belong to the chemosensory/tuft/brush cel family. The two subsets of nasal ChAT-eGFP+ cells differed in expression of taste receptors and taste receptor signaling machinery.
Conclusions: Our study represents the first detailed analysis of the transcriptome of nasal ChAT-eGFP+ cells (brush cells) and identifies two subsets of nasal brush cells that share a core transcriptional signature but differ in expression of bitter taste receptors.

overall_design: Examination of gene expression of nasal cholinergic EpCAM+ ChAT-eGFP+ FSC/SSClow, EpCAM+ ChAT-eGFP+ SSC/SSChigh compared to EpCAM+ ChAT-eGFP- (EpCAM) nasal epithelial cells in naïve ChAT(BAC)-eGFP mice.

middle: G

first: Nora

last: Barrett


title: The RNA N6-methyladenosine regulates chromatin remodeling and transcription

first: Xiaoyang

last: Dou

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

overall_design: Refer to individual Series


title: Identification of a master regulator of differentiation in Toxoplasma


title: Selective egg cell polyspermy bypasses the triploid block

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Polyploidization, the increase in genome copies, is considered a major driving force for speciation. We have recently provided the first direct in planta evidence for polyspermy induced polyploidization. Capitalizing on a novel sco1-based polyspermy assay, we here show that polyspermy can selectively polyploidize the egg cell, while rendering the genome size of the ploidy-sensitive central cell unaffected. This unprecedented result indicates that polyspermy can bypass the triploid block, which is an established postzygotic polyploidization barrier. In fact, we here show that most polyspermy-derived seeds are insensitive to the triploid block suppressor admetos. The robustness of polyspermy-derived plants is evidenced by the first transcript profiling of triparental plants and our observation that these idiosyncratic organisms segregate tetraploid offspring within a single generation. Polyspermy-derived triparental plants are thus comparable to triploids recovered from interploidy crosses. Our results expand current polyploidization concepts and have important implications for plant breeding.

overall_design:
The dataset contains samples from biparental diploid, biparental triploid, and triparental triploid polyspermy plants. Each sample Is represented by five biological replicates and each biological replicate is represented by four technical replicates.
Sequencing performed by: Bielefeld University, CeBiTec & Faculty of Biology

first: Yanbo

last: Mao

first: Thomas

last: Nakel

first: Prisca

last: Viehöver

last: Baum

first: Dawit

last: Tekleyohansm

first: Dieu

last: Vo

first: Ivo

last: Grosse

first: Rita

last: Groß-Hardt


title: Single-cell RNA-sequencing of wildtype (ME49∆KU80) or mutant (ME49∆KU80∆BFD1) parasites under unstressed or stressed conditions

first: Benjamin

last: Waldman

summary: To profile cell-cycle progression and the asynchronous process of differentiation, we performed single-cell RNA-sequencing (scRNA-Seq) of T. gondii using Seq-Well (Gierahn et al., 2017). Wild-type or ∆BFD1 parasites were grown under unstressed or stressed conditions (24, 48 or 72 h), mechanically released from host cells, and analyzed.

overall_design: A single Seq-Well array was used for all unstressed timepoints, and two arrays were used for the 24 and 72 hour stressed timepoints.

last: Schwarz


title: Incubation of Neisseria gonorrhoeae 1291 with human polymorphonuclear leukocyte cells

status: Public on Jan 14 2020

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

summary: These experiments examined the transcriptomic response of N. gonorrhoeae 1291 to incubation with human PMNs under three different timepoints, 10 minutes, 180 minutes and 360 minutes.

overall_design: Neisseria gonorrhoeae 1291 was incubated with human PMNs for 10 minutes, 180 minutes or 360 minutes.  The 10 minute timepoint was examined with two biological replicates while the 180 minute and 360 minute were examined with four biological replicates.  After each incubation RNA was collected and sequenced to determine the transcriptome of N. gonorrhoeae as it responds to incubations with PMNs.

first: William

last: Nauseef

first: Christine

last: Cho

first: Caroline

last: Genco

first: Michael

last: Apicella


title: CRISPR-Cas9 screens to identify regulators of differentiation in Toxoplasma gondii

summary: Targeted gRNA screen against putative nucleic-acid binding proteins in a differentiation reporter strain context. By looking for gRNAs enriched in parasites no longer able to activate reporter expression, we can identify genes essential for this process

overall_design: There are five gRNAs designed per gene in the library. gRNA libraries contain 10 known essential genes, 10 known dispensible genes, 10 non-targeting gRNAs, and 5 gRNAs against the reporter construct itself. The mean log2 fold-change for guides against each gene are referred to as a fitness or differentiation score, based on comparisons of input library to the unstressed or mNG+ stressed samples, respectively. Candidate genes should be depleted specifically in the mNG+ population (low differentiation score relative to their fitness score), as should gRNAs against the mNG reporter.

first: Dominic

first: Marc

last: Wadsworth II

first: Jeroen

last: Saeij

first: Alex

last: Shalek

first: Sebastian

last: Lourido


title: The Dynamic Transcriptional Cell Atlas of Testis Development During Human Puberty

status: Public on Jan 13 2020

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

summary: The human testis undergoes dramatic developmental and structural changes during puberty, including proliferation and maturation of niche/somatic cells, and the onset of spermatogenesis. Here, we profiled and analyzed single-cell transcriptomes of ~10,000 testicular cells from four boys spanning puberty, and compared to infants and adults. During puberty, undifferentiated spermatogonia first expand and then differentiate, prior to gametogenesis. Notably, we identify a common pre-pubertal progenitor for Leydig and myoid cells, and reveal candidate factors/pathways for pubertal differentiation. Furthermore, pre-pubertal Sertoli cells form two states that differ in mitochondrial/metabolic transcription, which converge to a single mature population during puberty. Roles for testosterone in Sertoli cell maturation, antimicrobial peptide secretion and spermatogonial differentiation are revealed through analyses of testosterone-suppressed transgender female testis and via in vitro seminiferous tubule culturing. Overall, our transcriptional atlas of the developing human testis provides major insights into developmental changes and key factors/pathways that accompany male puberty.

overall_design: Single-cell RNA-seq of testicular cells from different ages of boys in puberty.  Testosterone-suppressed transgender female testis samples are included.

first: Bradley

last: Cairns


title: Characterization of the Late Response of Neisseria gonorrhoeae F62 to Iron and Fur

summary: In this study wild-type, fur mutant, and complemented fur mutant strains of the human pathogen Neisseria gonorrhoeae F62 were grown under high (100 uM iron) or low (100 uM desferal) iron conditions to identify genes whose expression was regulated by iron and/or Fur.  This study looked at the response 3 hours after the addition of iron or desferal.

overall_design: Examination of each of three strains under two conditions by RNA-seq


title: Gene expression data from human breast cancer MDA-MB-231 cells treated with siRNA targeting NONO

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: To examine the role of NONO in estrogen-independent breast cancer,  MDA-MB-231 cells were treated with siRNA targeting NONO or control siRNA (siControl). Microarray analysis revealed NONO-regulated genes in MDA-MB-231 cells.

overall_design: MDA-MB-231 cells were treated with siRNA targeting NONO or control siRNA.

first: Yuichi

last: Mitobe

first: Kaori

last: Iino

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Reducing Aspergillus fumigatus virulence through targeted dysregulation of the conidiation pathway

status: Public on Jan 15 2020

city: Montreal

first: Donald

last: Sheppard

state: QC

address: 1001 Boulevard Decarie, Research Institute, E03.3126

institute: McGill University

summary: Inhalation of conidia of the opportunistic mold Aspergillus fumigatus by immunocompromised hosts can lead to invasive pulmonary disease. Inhaled conidia that escape immune defenses germinate to form filamentous hyphae that invade lung tissues. Conidiation rarely occurs during invasive infection of the human host, allowing the bulk of fungal energy to be directed towards vegetative growth. We hypothesized that forced induction of conidiation during infection can suppress A. fumigatus vegetative growth, impairing the ability of this organism to cause disease. To study the effects of conidiation pathway dysregulation on A. fumigatus virulence, a key transcriptional regulator of conidiation (brlA) was expressed under the control of a doxycycline-inducible promoter. Time- and dose-dependent brlA overexpression was observed in response to doxycycline both in vitro and in vivo. Exposure of the inducible brlA overexpression strain to low doses of doxycycline under vegetative growth conditions in vitro induced conidiation, while high doses arrested growth. Overexpression of brlA attenuated A. fumigatus virulence in both an invertebrate and mouse model of invasive aspergillosis. RNA sequencing studies and phenotypic analysis revealed that brlA-overexpression results in altered cell signaling, amino acid and carbohydrate metabolism, including a marked up-regulation of trehalose biosynthesis and a downregulation in the biosynthesis of the polysaccharide virulence factor galactosaminogalactan. This proof-of-concept study demonstrates that activation of the conidiation pathway in A. fumigatus can reduce virulence and suggests that brlA-inducing small molecules may hold promise as a new class of therapeutics for A. fumigatus infection.

overall_design: Examining the gene expression profiles of two A. fumigatus strains (Wild type parent and an inducible gene-overexpression mutant), in two conditions (absence and presence of the inducer molecule doxycycline), each in biological triplicate.

first: James

middle: I

last: Stewart

first: Vinicius

last: Fava

first: Joshua

last: Keraert

first: Adithya

last: Subramanian

first: Fabrice

middle: N

last: Gravelat

first: Melanie

last: Lehoux

first: P

middle: L

last: Howell

first: Robert

last: Cramer

middle: C


title: miR-221-3p drives the Shift of M2-Macrophage to a Pro-Inflammatory Function by Modulating JAK3/STAT3 Signaling and is Increased in Rheumatoid Arthritis

status: Public on Jan 12 2020

city: Basel

first: Diego

last: Kyburz

address: Petersplatz 4

department: Biomedicine

country: Switzerland

institute: University of Basel

summary: We performed a transcriptome analysis of M2 macrophages generated in vitro from monocytes isolated from peripheral blood of healthy donors, and studied the effect of miR-221-3p mimic transfection and stimulation with LPS.

overall_design: miR-221-3p mimic was added to cultured macrophages for 63.5 hours, prior to stimulation with 100 ng/ml LPS for 8.5 hours.

first: Lilian

last: Quero


title: Altered expression of long non-coding and messenger RNAs in diabetic nephropathy following treatment with rosiglitazone

first: Liwen

last: Zhang

address: 197 Ruijin Er Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Diabetic nephropathy (DN) is characterized by metabolic disorder and inflammation. However, the regulatory effects that long noncoding RNAs (lncRNAs) have on the pathogenesis of DN and on the efficacy of rosiglitazone treatment has yet to be clearly defined. Herein, we performed unbiased RNA sequencing to characterize the transcriptomic profiles in db/db diabetic mouse model with or without rosiglitazone treatment that served to improve the phenotypes of DN. Differential expression analysis revealed that those genes that had their expression restored following treatment with rosiglitazone are likely involved in protection against DN. Our data elucidate the novel renoprotective molecular mechanism of PPARγ agonists and propose lncRNA targets for diabetic nephropathy treatment.

overall_design: Diabetic (db/db) mice were randomly divided into two groups and treated with 20 mg/kg/day of rosiglitazone (dbR group) or with a vehicle (dbdb group) by gavage for 8 weeks (from 7-15 weeks of age), respectively. Db/m littermates (control group) were also treated with the vehicle. Total RNA from kidney cortex of each mouse was sequenced (3 replicates per group) on illumina HiSeq X Ten platform.

first: Weiming

last: Wang


title: Expression analysis of mouse embryonic fibroblasts (MEFs) and Thymidine treatment-induced MEFs (induced cells)

status: Public on Jan 11 2020

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: Investigation of differentially expressed genes in thymidine treatment-induced MEFs. Mouse embryonic fibroblasts (MEFs) were obtained at E14.5 embryos and supplied with Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) with 15% FBS, 100 μg/ml streptomycin and 100 U/ml penicillin. Potential hematopoietic progenitor cells (CD45+CD41+CD31+c-Kit+) were negatively selected with Biotin labeled anti-CD45, anti-CD31, anti-CD41 and anti-c-Kit antibodies by magnetic beads. Hereafter, treated MEFs are referred to as 4neg MEFs for initiation of induction. 4neg MEFs were seeded on mitomycin (MMC)-treated MEFs as feeder cells and cultured in DMEM with 15% FBS, 100  μg/ml streptomycin, 100 U/ml penicillin, 2 mM L-glutamine, 0.1 mM non-essential amino acids and 100 μM thymidine as induction medium for 6 days. Cells were then trypsinized and re-seeded to new feeder cells for another 6 days. Cells were positively selected with Biotin labeled anti-CD45 by magnetic beads followed with analysis.

overall_design: Gene expression profiling for 4neg MEFs and CD45+ cells induced by thymidine for 12 days. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA).

first: Buqing

last: Ye

first: Zusen

last: Fan


title: Systemic HIV/SIV latency reversal via non-canonical NF-κB signaling in vivo

city: Chapel Hill

first: Corbin

last: Jones

state: NC

address: 250 Bell Tower

institute: University of North Carolina

summary: Molecules mimicking the active N-terminal tetrapeptide of the second mitochondrial-derived activator of caspases (SMACm) potently reverse HIV latency in vitro and ex vivo without the pleotropic cellular effects seen with other LRAs. We verified that SMACm facilitate latency reversal through activation of the non-canonical NFκB pathway as exemplified by rapid degradation of cIAP1, followed by a slower conversion of inactive p100 into active p52. A potent representative of this class, AZD5582, increases cell-associated HIV gag RNA expression in resting CD4+ T cells from ART-suppressed, HIV-infected donors while altering the expression of a restricted number of human genes. These findings represent the first demonstration that SMACm have single agent latency reversal activity in patient-derived cells and support evaluation of SMACm in preclinical animal models.

overall_design: Differential Expression Analysis using RNA-seq time-series comparison of treatment vs control vs mock on primary T-cells

first: Richard

last: Dunham

first: Chahroudi

last: Ann

first: J

middle: V

last: Garcia

first: Angela

last: Wahl


title: RNA-seq of Laser Captured Microdissected high-grade serous ovarian tumors

status: Public on Jan 10 2020

city: Oxford

first: Zhiyuan

last: Hu

address: John Radcliffe Hospital/Headley Way

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: The inter-differentiation between cell states promotes cancer cell survival under stress and fosters non-genetic heterogeneity (NGH). NGH is, therefore, a surrogate of tumor resilience but its quantification is confounded by genetic heterogeneity. Here we show that NGH can be accurately measured when informed by the molecular signatures of the normal cells of origin. We surveyed the transcriptomes of ~ 4000 normal fallopian tube epithelial (FTE) cells, the cells of origin of serous ovarian cancer (SOC), and identified six FTE subtypes. We used subtype signatures to deconvolute SOC expression data and found substantial intra-tumor NGH that was previously unrecognized. Importantly, NGH-based stratification of ~1700 tumors robustly predicted survival. Our findings lay the foundation for accurate prognostic and therapeutic stratification of SOC.

overall_design: We performed RNA sequencing on 36 laser capture microdissected (LCM)  tumor samples collected from 15 patients with HGSOC and classified tumors based on the  deconvolution analysis

first: Mara

last: Artibani

first: Salma

last: El-Sahhar

first: Garry

last: Mallett

first: Christopher

last: Yau

first: Ahmed

middle: A

last: Ahmed


title: Epigenetic Regulation in Activated Macrophages

status: Public on Jan 09 2020

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

country: Thailand

institute: Chulalongkorn University

summary: In this study, we compared active histone marks (trimethylation on lysine 4 on histone 3 (H3K4me3)) in LPS-stimulated macrophages and LPS/IC-stimulated macrophages using bone marrow derived murine macrophages using ChIP-seq approach.

overall_design: BMDMs were stimulated with LPS or LPS/IC before ChIP using anti-H3K4me3 antibody. The ChIP-seq data were generated using 50 bp single-end sequencing reads by BGI (Beijing, China).

first: Vichaya

last: Ruenjaiman

first: Yu-Wei

last: Leu

first: Asada

last: Leelahavanichkul

first: Monnat

last: Pongpanich


title: Peripheral blood expression profiles of patients with epilepsy receiving and not receiving antiepileptic drug monotherapy and their differential response to the treatment.

status: Public on Jan 08 2020

city: New Delhi

first: Ritushree

last: Kukreti

state: Delhi

address: CSIR-IGIB, Mall road, Opp. Jubilee Hall, University of Delhi

department: Genomics and Molecular Medicine Unit

country: India

institute: CSIR-IGIB

summary: The aim here was to identify mRNA expression biomarkers associated with the disease epilepsy and the antiepileptic drug response. Gene expression profiles of drug-naïve patients with epilepsy were compared with that of healthy controls. The profiles were significantly different between the two groups as well as patients with different epilepsy types i.e. idiopathic, symptomatic and cryptogenic. Besides, patients showing differential response to antiepileptic monotherapies were also having differential blood gene expression profiles.

overall_design: Total RNA obtained from peripheral blood samples of 34 drug-naïve patients with epilepsy and 57 followed-up patients showing differential response to antiepileptic drug monotherapy along with 50 healthy subjects as control group.

first: Chitra

last: Rawat

first: Rintu

last: Kutum

first: Samiksha

last: Kukal

first: Ankit

last: Srivastava

first: Ujjwal

middle: R

last: Dahiya

first: Suman

last: Kushwaha

first: Sangeeta

last: Sharma

first: Debasis

last: Dash

first: Luciano

last: Saso

first: Achal


title: Abundant and diverse non-coding small RNAs identified in an extremophilic microbial community using metatranscriptomics

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

address: 910 Light Street, Apartment 2

institute: The Johns Hopkins Univeristy

summary: Regulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks) from the Atacama Desert, sampled over two years with different weather conditions, with SnapT – a new sRNA annotation pipeline – we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed.

overall_design: We sequenced metatranscriptomic libraries of halite nodules from the Atacama Desert over two sampling timepoints (2016 & 2017) to investigate the transcriptional response and sRNAs in the microbial community. Halite nodules were harvested in Salar Grande, an ancient evaporated lake in the Northern part of the Atacama Desert {Robinson, 2015 #6954} in February 2016 and 2017, 3 and 15 months after a major rain event (Uritskiy et al, 2019). All nodules were harvested within a 50m2 area as previously described {Robinson, 2015 #6954}. The colonization zone of each nodule was grounded into a powder, pooling from 1-3 nodules until sufficient material was collected, and stored in the dark in dry conditions until DNA extraction in the lab. Samples used for RNA were stored in RNAlater at 4°C until RNA extraction in the lab. Total RNA was extracted from the fixed samples by first isolating the cells through gradual dissolving of the salt particles as previously described {Crits-Christoph, 2016 #8776; Robinson, 2015 #6954} and lysing them through mechanical bead beating with the RNAeasy PowerSoil RNA extraction kit (QIAGEN). Total RNA was then extracted from the lysate with a Quick-RNA miniprep kit (Zymo Research). Total RNAseq libraries were prepared with the SMARTer Stranded RNA-seq kit (TaKaRa), using 25ng of RNA input and 12 cycles for library amplification. We sequenced 22 libraries from replicate samples from 2016 and 24 libraries from replicate samples from 2017.

first: Gherman

last: Uritskiy

first: Rahul

last: Reddy

first: Adam

last: Munn

first: Katie

last: Farney

first: Jocelyne

last: DiRuggiero


title: Transcriptomic profiling of LPS-induced adrenal inflammation in sorted adrenal endothelial cells from C576L6 mice

city: Dresden

first: Lan-Sun

last: Chen

address: Fetscherstraße 74

institute: TU Dresden

summary: Altogether, this is the first study presenting the global changes of the transcriptome in the adrenal microvascular cells. The results of RNA sequencing and subsequent bioinformatics analysis revealed that adrenal vascular endothelial cells are active players not only involved in maintenance of the adrenal gland microenvironment, but also they play a key role in pathogen recognition and initiation of inflammation. However, our results also strongly suggest that systemic administration of LPS, which recapitulates to some degree situation in people with meningococcal sepsis, may develop certain damage, including vascular inflammation, hypoxia, blood coagulation and leakage. That may contribute to the adrenal dysfunction.

overall_design: Examination of acute LPS-induced transcriptomic changes in sorted mouse adrenal endothelial cells

first: Waldemar

last: Kanczkowski


title: Human naive CD4 T cell subsets on young and old donors

city: Singapore

first: Hassen

last: Kared

address: 8A Biomedical Grove - Immunos Building - Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN) - A*STAR

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of naive CD4 T cells.  By sequencing this population in young and older donors, we describe the heterogeneity of Tscm CD4 cells based on differential engagement of Wnt pathways and inflammation.

overall_design: Examination of naïve CD4 T cells from 4 young (23-35 years old) and 4 older (65-78 years old) donors

first: Kared

last: Hassen

first: Larbi

last: Anis


title: Microarray of HEK293-PIGS-KO and HEK293-PIGS-UBE2J1-DKO cells.

city: Osaka

first: Taroh

last: Kinoshita

address: ３-3-1 Yamadaoka, Suita, Osaka

institute: Research Institute for Microbial Diseases

summary: Transcriptome analysis of total RNA samples from HEK293-PIGS-KO and HEK293-PIGS-UBE2J1-DKO cells. To check whether KO of UBE2J1 upregulates genes of GPI biosthesis pathway, we used microarrays to analyze gene expression change by KO of UBE2J1 and comfirmed that known GPI pathway genes are not changed by ERAD-deficiency.

overall_design: HEK293-PIGS-KO and HEK293-PIGS-UBE2J1-DKO cells were collected for total RNA extraction by RNeasy Mini Kit, and microarray analysis on the Clariom S Array, Human.

first: Yicheng

last: Wang


title: Activation of Myd88-dependent TLRs mediates local and systemic inflammation in a mouse model of primary Sjögren’s syndrome

city: Buffalo

first: Jill

last: Kramer

state: NY

address: 3435 Main Street

institute: State University of New York at Buffalo

summary: Toll-like receptors (TLRs) are important mediators of chronic inflammation in numerous autoimmune diseases, although the role of these receptors in primary Sjögren’s syndrome (pSS) remains incompletely understood. Previous studies in our laboratory established Myd88 as a crucial mediator of disease, although the upstream signaling events that culminate in Myd88 activation have yet to be identified. To objective of this study was to identify specific Myd88-dependent TLR-related pathways that are dysregulated both locally and systemically in a mouse model of pSS (NOD.B10Sn-H2b/J (NOD.B10)). We performed RNA-sequencing on spleens derived from NOD.B10 mice. We then harvested salivary tissue and spleens from Myd88-sufficient and deficient C57BL/10 (BL/10) and NOD.B10 mice and performed flow cytometry to determine expression of Myd88-dependent TLRs. We then cultured splenocytes with TLR2 and TLR4 agonists and measured IL-6 secretion by ELISA. Next, we evaluated spontaneous and TLR4-mediated inflammatory cytokine secretion in NOD.B10 salivary tissue. Finally, we assessed spontaneous Myd88-dependent cytokine secretion by NOD.B10 salivary cells. We identified dysregulation of numerous TLR-related networks in pSS splenocytes, particularly those employed by TLR2 and TLR4. We found upregulation of TLRs in both the splenic and salivary tissue from pSS mice. In NOD.B10 splenic tissue, B cell TLR1, TLR2, and TLR6 expression was reduced to levels of BL/10 controls in the absence of Myd88. Splenocytes from NOD.B10 mice were hyper-responsive to TLR2 ligation and the endogenous molecule decorin modulated inflammation via TLR4. Finally, we found spontaneous secretion of numerous inflammatory cytokines and this was enhanced following TLR4 ligation in female NOD.B10 salivary tissue as compared to males. Moreover, we found that spontaneous production of salivary IL-6, MCP-1 and TNFa requires Myd88 in pSS salivary tissue.  Thus, our data demonstrate that Myd88-dependent TLR pathways contribute to the inflammatory landscape in pSS, and inhibition of such will likely have therapeutic utility.

overall_design: Spleens were isolated from (NOD.B10Sn-H2b/J ) NOD.B10 females at 26 weeks of age and from age and gender-matched BL/10 controls. RNA was isolated according to standard protocols using a Qiagen RNeasy kit. RNA meeting quality standards (>8.0) were used as input for RNA-seq using Illumina’sTru-seq low-throughput multiplex protocol. Three biological replicates for each strain were sequenced in parallel using an Illumina HiSeq 2500, with 50 cycle single-end read reactions.

first: Jeremy

last: Kiripolsky

first: Rose-Anne

last: Romano

first: Eileen

middle: M

last: Kasperek

first: Guan

last: Yu


title: Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages

status: Public on Jan 07 2020

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: Inner ear cochlear spiral ganglion neurons (SGNs) transmit sound information to the brainstem. Recent single cell RNA-Seq studies have revealed heterogeneities within SGNs. Nonetheless, much remains unknown about the transcriptome of SGNs, especially which genes are specifically expressed in SGNs. To address these questions, we needed a deeper and broader gene coverage than that in previous studies. We performed bulk RNA-Seq on mouse SGNs at five ages, and on two reference cell types (hair cells and glia). Their transcriptome comparison identified genes previously unknown to be specifically expressed in SGNs. To validate our dataset and provide useful genetic tools for this research field, we generated two knockin mouse strains: Scrt2-P2A-tdTomato and Celf4-3xHA-P2A-iCreER-T2A-EGFP. Our comprehensive analysis confirmed the SGN-selective expression of the candidate genes, testifying to the quality of our transcriptome data. These two mouse strains can be used to temporally label SGNs or to sort them.

overall_design: Examination of single cell type at 5 different time points with additional 2 cell types at a single time point for comparison

first: Zhiyong

last: Liu

first: Chao

last: Li


title: Longissimus dorsi muscle transcriptome in pure (Iberian x Iberian) and crossbred (Iberian x Large White)  pig fetuses at gestation day 77

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

summary: Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity.  Interestingly, the results suggested an interaction genotype*weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.

overall_design: In total 32 longissimus dorsi samples were analyzed, 8 coming from males and 8 coming from females within each genotype

last: Óvilo


title: Single cell RNA sequencing of human naive CD4 T cells on young and old donors


title: Immunological History Governs Human Stem Cell Memory CD4 Heterogeneity Via The Wnt Signaling Pathway

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

overall_design: Refer to individual Series


title: The structural basis for cohesin/CTCF anchored loops [Hi-C]

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: Cohesin catalyses the folding of the genome into loops that are anchored by CTCF. The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2-SCC1 subunits of cohesin. A 2.6 Å crystal structure of SA2-SCC1 in complex with CTCF reveals the molecular basis of the interaction. We demonstrate that this interaction is specifically required for CTCF-anchored loops and contributes to the positioning of cohesin at CTCF-binding sites. A similar motif is present in a number of established and novel cohesin ligands, including the cohesin release factor WAPL. Our data suggest that CTCF enables chromatin loop formation by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables dynamic regulation of chromatin folding by cohesin and CTCF.

overall_design: Hi-C was performed in control and mutant CTCF (Y226A, F228A) HAP1 cells in duplicate.

first: Judith

last: Haarhuis

last: Sedeño Cacciatore

first: Marjon

last: van Ruiten

first: Laureen

last: Willems

first: Hans

last: Teunissen

first: Elzo

last: de Wit

first: Benjamin

last: Rowland


title: Single eye mRNA-Seq Reveals Normalisation of the Retinal Microglial Transcriptome Following Acute Inflammation

city: Bristol

first: Oliver

last: Bell

state: Bristol

address: Office F38, Biomedical Sciences Building, University Walk

institute: University of Bristol

summary: Background: Whether retinal microglia can maintain or restore immune homeostasis during and after inflammation is unclear. We performed single-eye mRNA-sequencing on microglia at different timepoints following a single inflammatory stimulus to characterise their transcriptome during and after resolution of endotoxin-induced uveitis (EIU). Experimental Approach: Cx3cr1CreER:R26-tdTomato (C57BL/6) male heterozygotes were administered tamoxifen via different regimes at 4-5 weeks of age. Four weeks post-tamoxifen, mice were injected intravitreally with 10 ng lipopolysaccharide (endotoxin induced uveitis, EIU). Six-hundred retinal microglia were obtained by FACS from individual naïve retinas and at 4 hours, 18 hours, and 2 weeks following EIU induction. Samples were sequenced to a depth of up to 16.7 million reads using the SMART-Seq v4 Ultra Low Input RNA kit. The data was analysed using Partek software and Ingenuity Pathway Analysis. Genes were considered differentially-expressed (DEG) if the FDR step-up p value was ≤0.05 and the fold-change was ≥±2. Results: Flow cytometric analysis indicates that the Cx3cr1CreER:R26-tdTomato strain is both sensitive (>95% tagging) and specific (>95% specificity) for microglia when tamoxifen is administered topically to the eye for 3 days. During “early” activation, 613 DEGs were identified. In contrast, 537 DEGs were observed during peak cellular infiltrate and none at 2 weeks, compared to baseline controls (1,069 total unique DEGs). Key marker changes were validated by qPCR, flow cytometry, and fluorescence microscopy. C5AR1 was identified and validated as a robust marker of differentiating microglial subsets during an LPS response. Conclusion: Using EIU to provide a single defined inflammatory stimulus, mRNA-Seq identified acute transcriptional changes in retinal microglia which returned to their original transcriptome after 2 weeks. Yolk-sac derived microglia are capable of restoring their homeostatic state after acute inflammation.

overall_design: 28 Sample experiment. Live primary microglia isolated using Cx3cr1CreER:R26-tdTomato mouse line by FACS (tdTomatohi, DRAQ7-). Naïve controls compared to different time-points of endotoxin-induced uveitis (EIU) -- lipopolysaccharide (LPS) administration. n=10 naïve; n=6 EIU 4h; n=5 EIU 18h; n=7 EIU 2w.

first: David

last: Copland

first: Amy

last: Ward

first: Lindsay

middle: B

last: Nicholson

first: Clemens

last: Lange

first: Colin

middle: J

last: Chu

first: Andrew

last: Dick


title: Systemic HIV/SIV latency reversal via activation of the non-canonical NF-B signaling pathway in vivo

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Resting CD4+ T cells that are both persistent and latently infected with HIV represent the most important challenge to HIV eradication.  Estimates indicate the need for >70 years of continuous, fully suppressive, antiretroviral therapy (ART) to eliminate the HIV reservoir. Alternatively, induction of HIV from its latent state could accelerate the decline of the reservoir, thereby shortening the time to eradication.  Previous attempts to reactivate latent HIV in preclinical animal models and in clinical trials have measured HIV induction in peripheral blood with minimal focus on tissue reservoirs and had limited effect.  We found that activation of the non-canonical NF-B signaling pathway via AZD5582 results in induction of HIV- and SIV-RNA expression in the blood and tissues of ART-suppressed humanized mice and rhesus macaques.  Analysis of resting CD4+ T cells from tissues after AZD55852 treatment revealed increased SIV-RNA in lymph nodes in macaques and robust induction of HIV in virtually all tissues analyzed in humanized mice including lymph nodes, thymus, bone marrow, liver, and lung. This promising new approach to latency reversal, in combination with the appropriate tools for systemic clearance of persistent HIV infection, greatly increases opportunities for HIV eradication.

overall_design: AZD5582 was administered weekly to six SIV-infected, ART-suppressed RMs for either three or ten weeks. Peripheral blood or lymph node derived CD4+ T cells were sampled pre-treatment and after three or ten weeks on treatment.

first: Christopher

last: Nixon

first: Maud

last: Mavigner

first: Gavin

last: Sampey

first: Alyssa

last: Brooks

first: Rae

last: Spagnuolo

last: Irlbeck

first: Cameron

last: Mattingly

first: Phong

middle: T

last: Ho

first: Nils

last: Schoof

first: Corinne

last: Cammon

first: Greg

first: Matthew

last: Kanke

first: Zhang

last: Wang

first: Rachel

last: Cleary

first: Amit

last: Upadhyay

first: Chandrav

last: De

first: Saintedym

last: Wills

first: Shane

last: Falcinelli

first: Cristin

last: Galardi

first: Hasse

last: Walum

first: Nathaniel

last: Schramm

first: Jennifer

last: Deutsch

first: Jeffrey

last: Lifson

first: Christine

last: Fennessey

first: Brandon

middle: F

last: Keele

first: Sherrie

last: Jean

first: Sean

last: Maguire

first: Baolin

last: Liao

first: Edward

middle: P

last: Browne

first: Robert

last: Ferris

first: Jessica

last: Brehm

last: Favre

first: Thomas

last: Vanderford

first: Steven

middle: E

last: Bosinger

first: Corbin


title: Activin A and BMP4 Signaling Expands Potency of Mouse Embryonic Stem Cells in Serum Free Media

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

type: Methylation profiling by high throughput sequencing

summary: Inhibitors of Mek1/2 and Gsk3b, known as 2i, and together with leukemia inhibitory factor, enhance the derivation of embryonic stem cells (ESCs) and promote ground-state pluripotency (2i/L-ESCs). However, recent reports show prolonged Mek1/2 suppression impairs the developmental potential of ESCs, and is rescued by serum (S/L-ESCs). In spite of the unclear roles of growth factors in serum, the coculture system has remained the gold standard. Here we show that culturing ESCs in Activin A, BMP4 and in the absence of MEK1/2 inhibitor (ABC/L medium) establishes stable ESCs, named advanced pluripotent stem cells derived from ESCs (esASCs). We demonstrate that esASCs contributed to germline lineages, full term chimeras and generated esASCs-derived mice by tetraploid complementation. We show that in contrast to 2i/L-ESCs, these esASCs display distinct molecular signatures and stable hypermethylated epigenome which is reversible and similar to S/L-ESCs. Importantly, we also derived novel ASCs (blASCs) from blastocysts in ABC/L medium. These blASCs are persisting at an intermediate state between naïve and primed state of pluripotency and stable hypermethylated epigenome. Our results provide insights into the derivation of novel ESCs with DNA hypermethylation from blastocysts in a chemically defined medium.

overall_design: Replicate RNA-seq and DNA methylation-seq datasets from mouse ESCs and EpiSCs, maintained in different stem cells culture conditions.

first: Baojiang

last: Wu

first: Junpeng

last: Gao


title: A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells

status: Public on Jan 06 2020

city: Boston

first: Shobha

last: Vasudevan

state: Massachusetts

address: 185 Cambridge Street, Simches Building

department: Cancer Center

institute: MGH


title: A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells [BMDMs]

summary: Quiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. While G0 cells have been studied at the transcriptome level, how post-transcriptional regulation contributes to their chemoresistance remains unknown. We induced chemoresistant and quiescent (G0) leukemic cells by serum-starvation or chemotherapy treatment. To study post-transcriptional regulation in G0 leukemic cells, we systematically analyzed their transcriptome, translatome, and proteome. We find that our resistant G0 cells recapitulate gene expression profiles of in vivo chemoresistant leukemic and G0 models. In G0 cells, canonical translation initiation is inhibited; yet we find that inflammatory genes are highly translated, indicating alternative post-transcriptional regulation. Importantly, AU-rich elements (AREs) are significantly enriched in the up-regulated G0 translatome and transcriptome. Mechanistically, we find the stress-responsive p38 MAPK-MK2 signaling pathway stabilizes ARE mRNAs by phosphorylation and inactivation of mRNA decay factor, tristetraprolin (TTP) in G0. This permits expression of ARE mRNAs that promote chemoresistance. Conversely, inhibition of TTP phosphorylation by p38 MAPK inhibitors and non-phosphorylatable TTP mutant decreases ARE-bearing TNFα and DUSP1 mRNAs and sensitizes leukemic cells to chemotherapy. Furthermore, co-inhibiting p38 MAPK and TNFα—prior to or along with chemotherapy—substantially reduced chemoresistance in primary leukemic cells ex vivo and in vivo. These studies uncover post-transcriptional regulation underlying chemoresistance in leukemia. Our data reveal the p38 MAPK-MK2-TTP axis as a key regulator of expression of ARE bearing mRNAs that promote chemoresistance. By disrupting this pathway, we developed an effective combination therapy against chemosurvival.

overall_design: To identify genes regulated by TTP phosphorylation in chemo-surviving cells, TTP wild-type (WT) or TTP-AA phosphorylation mutant were expressed in TTP knockout macrophages treated with vehicle control or AraC chemotherapy. Total RNAs isolated from macrophages were analyzed on Affymetrix microarrays.

first: Sooncheol

last: Lee

first: Douglas

last: Micalizzi

first: Samuel

middle: S

last: Truesdell

first: Syed

last: Bukhari

first: Myriam

last: Boukhali

first: Jennifer

last: Lombardi-Story

first: Yasutaka

last: Kato

first: Min-Kyung

last: Choo

first: Ipsita

last: Dey-Guha

first: Fei

last: Ji

first: Benjamin

last: Nicholson

first: David

last: Myers

first: Dongjun

first: Maria

last: Mazzola

first: Radhika

last: Raheja

first: Adam

last: Langenbucher

first: Nicholas

last: Haradhvala

first: Michael

last: Lawrence

first: Roopali

last: Gandhi

first: Christopher

last: Tiedje

first: Manuel

last: Diaz-Munoz

last: Sweetser

first: Ruslan

last: Sadreyev

last: Sykes

first: Wilhelm

last: Haas

first: Daniel

last: Haber

first: Shyamala

last: Maheswaran


title: Single-cell RNA sequencing of human fallopian tubes

first: Zhiyuan

last: Hu

overall_design: Sequenced cells, mainly epithelial cells, from normal fallopian tubes of eleven cancer patients to study the cell populations in the human fallopian tube epithelium

last: Yau

first: Ahmed

last: Ahmed


title: Comparative transcriptome analysis between resistant and susceptible tomato lines uncovers the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: Leaf mold disease caused by Cladosporium fulvum is a major disease in cultivated tomato plants and affects global tomato production. Some Cf genes, of which Cf-16 is an effective gene for resisting tomato leaf mold, are associated with leaf mold resistance; however, the molecular mechanism is largely unknown. We used comparative transcriptome analysis of C. fulvum-resistant (cv. Ontario7816, including the Cf-16 gene) and C. fulvum-susceptible (cv. Moneymaker) tomato lines to identify differentially expressed genes (DEGs) at 4 and 8 days postinfection with C. fulvum. Our results provide new insights into the resistance response mechanism of Cf genes to C. fulvum, especially the unique characteristics of Cf-16 in response to C. fulvum infection.

overall_design: mRNA profiles of  C. fulvum-resistant (cv. Ontario7816, including the Cf-16 gene) and C. fulvum-susceptible (cv. Moneymaker) tomato lines were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript .

first: Dongye

last: Zhang

first: Xiangyang

last: Xu