title: Loss of androgen signaling in mesenchymal SHH responsive cells diminishes prostate development, growth, and regeneration

status: Public on Jan 03 2020

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

summary: Prostate embryonic development, pubertal and adult growth, maintenance, and regeneration are regulated through androgen signaling-mediated mesenchymal epithelial interactions. Specifically, the essential role of mesenchymal androgen signaling in the development of prostate epithelium has been observed for over 30 years. However, the identity of the mesenchymal cells responsible for this paracrine regulation and related mechanisms are still unknown. Here, we provide the first demonstration of an indispensable role of the androgen receptor (AR) in sonic hedgehog (SHH) responsive Gli1-expressing cells, in regulating prostate development, growth, and regeneration. Selective deletion of AR expression in Gli1-expressing cells during embryogenesis disrupts prostatic budding and impairs prostate development and formation. Tissue recombination assays showed that urogenital mesenchyme (UGM) containing AR-deficient mesenchymal Gli1-expressing cells combined with wildtype urogenital epithelium (UGE) failed to develop normal prostate tissue in the presence of androgens, revealing the decisive role of AR in mesenchymal SHH responsive cells in prostate development. Prepubescent deletion of AR expression in Gli1 expressing cells resulted in severe impairment of androgen-induced prostate growth and regeneration. RNA-sequencing analysis showed significant alterations in signaling pathways related to prostate development, stem cells, organ morphogenesis appeared showed significant changes in AR-deficient Gli1-expressing cells. The transforming growth factor β (TGFβ) pathway was up-regulated in AR-deficient Gli1-expressing cells. We further demonstrated the activation of TGF- b signaling in AR deleted prostatic Gli1-expressing cells, which inhibits prostate epithelium growth through paracrine regulation. These data demonstrate a novel role of the AR in the Gli1-expressing cellular niche for regulating prostatic cell fate, morphogenesis, and renewal, and elucidate the mechanism by which mesenchymal androgen-signaling through SHH-responsive cells elicits the growth and regeneration of prostate epithelium.

overall_design: GFP+ cells were sorted from each prostate sample for sequencing. Two biological replicates were used for each condition each of which had two technical replicates for a total of 8 samples

first: Sun

last: Zijie


title: Characterization of tumor initiating cells from human glioblastoma multiforms by scRNA seq

city: New York

first: Viviane

last: Tabar

state: New York

address: 1275 York Avenue

country: USA

institute: Memorial Sloan Kettering Cancer Centre

type: Expression profiling by high throughput sequencing

summary: Radial Glia (RG) cells are the first neural stem cells to appear during embryonic development. Human embryonic RG cells demonstrates a specific set of gene expression compared to other type of progenitor cells. The goal of this study is to characterize  the potential origine of tumor initiating cells of human glioblastoma multiforms by single cell RNASeq analyses of freshly sorted glioblastoma cells. The objectives are: 1)idetify RG-like cells in adult brain tumor; 2) reveal transcriptionally dynamic clusters of RG-like cells, that share the profiles of normal human fetal radial glia and that reside in quiescent and cycling states; 3) signaling pathways that mediate the transition among the different stages of RG-like cells; 4)genomic aberation analyses to reveal the potential hierarchical tree of RG-like cells.

overall_design: scRNA seq of freshly sorted cells from specimen of 3 patients

first: Rong

last: Wang

first: Roshan

last: Sharma

first: Ashley

middle: M

last: Laughney

first: Ignas

last: Masilionis

first: Dana

last: Pe'er


title: Real-time quantitative PCR analysis of cortisol-indeced sex change in epinephelus coioides

status: Public on Jan 02 2020

city: Guangzhou

first: Jiaxing

last: Chen

state: Guangdong

address: Xingang Road No. 135, Haizhu District, Guangzhou

country: China

institute: Sun Yat-Sen University

summary: Cortisol was injected into the protogynous epinephelus coioides to investigate the role of this hormone on sex change. Following injection, we evaluated sex-related gene expression during the processes of cortisol-induced sex change in epinephelus coioides.

overall_design: qPCR gene expression profiling. Gonadal tissues were collected from the fish in each group at 24 hours after cortisol treatment (hat), 96 hat, 7 days after treatment (dat), 15 dat, 30 dat and 60 dat for gene expression analysis.

first: Yong

last: Zhang


title: Robust and persistent SIV and HIV reactivation under ART by N-803 and CD8 depletion

status: Public on Jan 06 2020

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
Impact of CD8 depletion on peripheral CD4+ T cells transcriptome during ART-treated SIV infection of rhesus macaques.
Analysis of CD8+ T cells, CD4+ T cells, and NK cell transcriptomes following administration of HIV/SIV latency reversing agent IL-15 superagonist N-803 in ART-suppressed SIV infected rhesus macaques.
Methods: RNA-Seq of sorted CD4+ T cells from SIV-infected, ART-suppressed rhesus macaques before intervention with the anti-CD8a depleting antibody MT807R1 and then again on day 3, week 2, and week 4 following the start of intervention. Some animals also had an intervention that includes four weekly administrations of the IL-15 superagonist complex N-803 initiated at the time of CD8 depletion.
Methods: RNA-Seq of sorted CD4+ T cells, CD8+ T cells, and NK cells from SIV-infected, ART-suppressed rhesus macaques before intervention with four weekly administrations of the IL-15 superagonist complex N-803, then again on day 3, week 2, and week 4 following the start of intervention.
Methods: RNA from sorted cells was collected and extracted and DNA was digested. Libraries were prepared and normalized, pooled, and clustered on a flow cells for sequencing. RNAseq data were aligned to the MacaM v7.8 assembly of the Indian rhesus macaque genome. To identify pathways differentially modulated, Gene Set Enrichment Analysis (GSEA)34 was performed on the ranked transcript lists using 1000 phenotype permutations and random seeding. Gene sets used included the MSigDB H (hallmark) gene sets

overall_design: Seven animals from each of the three groups were used (N-803 alone, CD8 depletion alone, CD8 depletion with N-803). Only CD4+ T cells were sorted and analyzed from the two groups receiving CD8 depletion. CD4+ T cells, CD8+ T cells, and NK cells were sorted and analyzed from the group receiving N-803 alone. Cells from four time points (pre-intervention, day 3, week 2, and week 4) were collected across groups and cell types.

first: Julia

middle: B

last: McBrien

first: Guido

last: Silvestri


title: Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation

city: Mainz

first: Annabelle

last: Dold

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, IMB

summary: Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning but the mechanism remained unsolved. Here, we show that Mkrn1 is essential for axis specification and pole plasm assembly by translational activation of oskar (osk). We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds specifically to osk 3’ UTR in regions overlapping with Bruno1 (Bru1) responsive elements (BREs) that regulate osk translation. We observe increased association of the translational repressor Bru1 with osk mRNA upon depletion of Mkrn1, indicating that both proteins compete for osk binding. Consistently, reducing Bru1 dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation, most likely by competing with Bru1 to bind to osk 3’ UTR.

overall_design: iCLIP analysis of Mkrn1 in S2R+ cells

first: Andrea

last: Hildebrandt

first: Anke

last: Busch

first: Mirko

last: Brüggemann

first: Kathi

last: Zarnack

first: Julian

last: König

first: Jean-Yves

last: Roignant


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

city: Boston

first: Shobha

last: Vasudevan

state: Massachusetts

address: 185 Cambridge Street, Simches Building

department: Cancer Center

institute: MGH

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 differentially expressed genes in quiescent cancer cells, we profiled quiescent and proliferating cells induced by serum starvation or AraC treatment at the transcriptome and translatome levels.

first: Sooncheol

last: Lee

first: Douglas

last: Micalizzi

first: Samuel

middle: S

last: Truesdell

first: Syed

middle: I

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

middle: T

last: Nicholson

first: David

last: Myers

first: Dongjun

first: Maria

middle: A

last: Mazzola

first: Radhika

last: Raheja

first: Adam

last: Langenbucher

first: Nicholas

middle: J

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: Genome-wide maps of chromatin state and gene expression in mouse liver.

city: Berkeley

first: Jose

last: Viscarra

state: Ca

address: 220 Morgan Hall

department: NST

institute: UC Berkeley

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using high throughput sequencing we report chromatin accessibility, H3K9 methylation status, and gene expression in mouse liver upon fasting/refeeding a high carb diet in wild-type and JMJD1C KO mice.

overall_design: Examination of chromatin accessibility, H3K9me2 methylation, and gene expression in mouse liver

first: Hei

last: Sul


title: Hap2-Ino80 mediated transcription facilitates de novo establishment of CENP-A chromatin

status: Public on Jan 05 2020

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

country: United Kingdom

institute: The University of Edinburgh

summary: Analysis of CENP-ACnp1 ChIP-Nexus from fission yeast

overall_design: Detection of  non-centromeric regions of the genome where islands of CENP-ACnp1 are retained at low levels

first: Puneet

last: Singh

first: Manu

last: Shukla

first: Pin

last: Tong


title: Effect of hMLL1 on EB-derived hematopoietic progenitors [scRNA-seq]

status: Public on Jan 01 2020

city: Aurora

first: Patricia

last: Ernst

state: CO

department: Pediatrics

institute: University of Colorado

summary: We determined the effect of expressing human MLL1 on differentiating hematopoietic progenitors from murine embryoid bodies

overall_design: ES cells in which a doxycycline-inducible MLL1 transgene was induced from day 4-6 were harvested at day 6 and c-Kit+/CD41+ hematopoietic progenitors were sorted

first: Weiwei

last: Yang

first: Kenneth

middle: L

last: Jones

first: G

middle: D

last: Trahan


title: CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention [ChIP-seq & RNA-seq]

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

summary: The DNA-binding protein CTCF and the cohesin complex function together to shape chromatin architecture in mammalian cells, but the molecular details of this process remain unclear. We demonstrate that a 79 amino acid region within the CTCF N-terminal domain but not the C-terminus is necessary for cohesin positioning at CTCF binding sites and chromatin loop formation. However, the N-terminus of CTCF, when fused to artificial zinc fingers that do not bind to CTCF DNA binding sites was not sufficient to redirect cohesin to different genomic locations, indicating that cohesin positioning by CTCF does not involve direct protein-protein interactions with cohesin subunits. BORIS (CTCFL), a germlinespecific paralog of CTCF was unable to anchor cohesin to CTCF DNA binding sites. Furthermore, CTCF-BORIS Chimeric constructs provided evidence that both the first two CTCF zinc fingers and, likely, the 3D geometry of CTCF-DNA complexes are involved in cohesin retention. Moreover, we were able to convert BORIS into CTCF with respect to cohesin positioning, thus providing additional molecular details of the cohesin retention function of CTCF. Our data suggest that the N-terminus of CTCF and the 3D spatial conformation of the CTCF-DNA complex act as a roadblock to constrain cohesin movement along DNA.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Genome-wide mapping of CTCF, RAD21, BORIS and Chimeric proteins occupancy in wild type and mutant CH12 cells.
Expression profiling by high throughput sequencing (RNA-seq) of wild type and mutant CH12 cells.


title: RNA-seq analysis of freshly isolated germinal center B cells

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary:
Purpose: The goal of this study is to complare the transcitpional profiles of freshly isolated, splenic, murin GCBC and other activated and naive non-germinal center B cell populations.

Methods: Cells were freshly isolated, bead purified and FACS Ari sorted . Sorted cells (1.5-3x106 cells per sample) were washed twice in cold PBS and RNA was prepared using shredder-columns (Qiagen; QIAshredder 79656) and the RNeasy Plus Mini kit (Qiagen) following the manufacturer’s instructions. 3 independent RNA libraries per cell population were prepared using Illumina TruSeq Stranded mRNA sample preparation kit. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by using dUTP in the Second Strand Marking Mix, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The products are then purified and enriched with PCR to create the final cDNA library. The cDNA libraries are validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorometer. Quality is examined using Agilent Tapestation 2200.The cDNA libraries were pooled at a final concentration 1.8pM. Samples were sequenced using Illumina NextSeq 500 with 75bp paired-end reads and aligned to the mm10 genome using the STAR aligner. The number of uniquely aligned reads ranged from 31 to 77 million. Using an optimized data analysis workflow, Gene-level counts were determined using featureCounts and raw counts were analyzed for differential expression using the “voom” method in the “limma” R package.

Results: After determining genes that were differentially expressed between splenic GCBC and activated B cells, we performed gene set enrichment analysis (GSEA). Differentially expressed genes were compared to several previously defined hypoxic gene signatures.

overall_design: mRNA profiles of freshly isolated splenic murin germinal center B cells were generated using deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Florian

last: Weisel

first: Shuchi

last: Smita

first: Maria

last: Chikina


title: The structural basis for cohesin/CTCF anchored loops [ChIP-seq]

status: Public on Jan 07 2020

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: ChIP-Seq for CTCF and SCC1 was performed in control and mutant CTCF (Y226A, F228A) HAP1 cells.

first: Judith

middle: H

last: Haarhuis

last: Sedeño Cacciatore

first: Marjon

last: van Ruiten

first: Laureen

last: Willems

first: Elzo

last: de Wit

first: Benjamin

last: Rowland


title: Effect of hMLL1 overexpression on differentiating embyroid bodies [bulk RNA-seq]

summary: We determined the effect of overexpression of human MLL1 on differentiating murine embryoid bodies

overall_design: ES cells in which a doxycycline-inducible MLL1 transgene was induced from day 4-6 with 1µg/mL doxycycline were harvested at day 6 and c-Kit+/CD41+ hematopoietic progenitors were sorted


title: A transcriptomic study of selenium against liver injury by RNA-seq

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

department: School of life sciences

institute: Anhui University

summary: Evidence from biochemical indicators suggested that selenium could effectively repair the liver injury caused by beta-cypermethrin (β-CYP). However, the molecular mechanisms of selenium against liver injury induced by β-CYP remains unclear. In the present study, dynamic changes in gene expression profiles before and after the treatment of Na2SeO3 in liver injury mice were analyzed by using RNA sequencing. As a result, several essential genes and pathways were identified to be significantly associated with this process.

overall_design: The liver samples of mice are extracted from 3 groups, including the control group, the liver injury group with the treatment of 40mg/kg β-CYP, and the repair group with the treatment of 40mg/kg β-CYP and 50μg/kg Na2SeO3. RNA sequencing was performed by using the platform of Illumina HiSeq 3000. All experiments were performed in triplicates.

first: Qingyang

last: Tang

first: Mengting

last: Gong

first: Jian

last: Zhang

first: Bei

last: Huang


title: Gene Expression Profiles in Children with Suspected Sepsis in the Emergency Department

city: Philadelphia

first: Blanca

middle: E

last: Himes

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

summary:
Around 42,000 children suffer from severe sepsis each year in the US alone, resulting in significant morbidity, mortality and billion dollar expenditures in the US healthcare system. Sepsis recognition is a clinical challenge in children. Biomarkers are needed to tailor appropriate antimicrobial therapies and improve risk stratification.
The goal of this study was to determine if gene expression profiles from peripheral blood were associated with pathogen type and sepsis severity in children treated for suspected sepsis.

overall_design: Prospective cohort study in a tertiary pediatric emergency department. Participants were included if they were >56 days and <18 years of age, had suspected sepsis, and had not received broad spectrum antibiotics in the 4 hours prior to study eligibility. Control subjects (n=12) were patients in the same age range who had neither febrile illness nor treatment with antibiotics in the prior 14 days.

first: B

first: F

last: Balamuth


title: Physiological and transcriptomic responses to fishmeal-based diet and rapeseed meal-based diet in two strains of gibel carp (Carassius gibelio)

city: Wuhan

first: Wenjie

last: XU

address: No. 7 Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: This study was conducted to investigate the effects of the rapeseed meal (RM) on two strains of gibel carp (A strain and F strain) and to explore whether two strains show the different molecular mechanisms to the fishmeal (FM) and rapeseed meal (RM). Transcriptomic analysis showed that amino acid metabolism, lipid metabolism and digestive system were three main biological processes affected by RM diet in both strains. The differentially expressed genes between strains were involved in amino acid metabolism, immune responses and lipid metabolism.

overall_design: Liver of two strains of gibel carp at 8h after last feeding was used for transcriptome analysis.

last: Xu

first: Junyan

last: Jin


title: Transcriptional characterization of tissue-Tregs and whole tissues of skeletal muscles in muscle Treg TCR transgenic mice.

status: Public on Dec 31 2019

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Foxp3+CD4+ regulatory T cells (Tregs) play important roles in controlling both homeostatic processes and immune responses at the tissue and organismal levels. For example, Tregs promote muscle regeneration in acute or chronic injury models by direct effects on local muscle progenitor cells as well as on infiltrating inflammatory cells. Muscle Tregs have a transcriptome, a T cell receptor (TCR) repertoire and effector capabilities distinct from those of classical, lymphoid-organ Tregs, but it has proven difficult to study the provenance and functions of these unique features due to the rarity of muscle Tregs and their fragility upon isolation. Here, we attempted to side-step these hindrances by generating, characterizing and employing a line of mice carrying rearranged transgenes encoding the TCRα and TCRβ chains from a Treg clone rapidly and specifically expanded within acutely injured hindlimb muscle of young mice. Tregs displaying the transgene-encoded TCR preferentially accumulated in injured hindlimb muscle in a TCR-dependent manner both in the straight transgenic model and in adoptive-transfer systems; non-Treg CD4+ T cells expressing the same TCR did not specifically localize in injured muscle. The definitive muscle-Treg transcriptome was not established until the transgenic Tregs inhabited muscle. When crossed onto the mdx model of Duchenne muscular dystrophy, the muscle-Treg TCR transgenes drove enhanced accumulation of Tregs in hindlimb muscles and improved muscle regeneration. These findings invoke the possibility of harnessing muscle Tregs or their TCRs for treatment of skeletal muscle pathologies.

overall_design: For RNA-seq library construction of Tregs, Vβ8+ Tregs or total Tregs were double-sorted by Moflo from muscle and spleen of Tg+ or Tg-, respectively, Foxp3-GFP mice 3 days after Ctx-injury. 2x10^3 cells were lysed with TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma) and used for generating libraries. For whole-muscle RNA-seq library construction, muscles of Tg+ or Tg- mice were collected 8 days after Ctx-injury. Total RNAs were isolated using Trizol (Invitrogen) according to the manufacturer’s instructions. 5ng of RNA was used for generating each library, as above. Sequencing was performed on an Illumina NextSeq500 using the 2x25 base-pair read option.

first: Jun

last: Cho

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Flagellin adjuvanted F1/V subunit plague vaccine induces T cell and functional antibody responses with unique gene signatures

city: Rockville

first: Johannes

last: Goll

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

summary: Yersinia pestis, the cause of plague, could be weaponized. Unfortunately, development of new vaccines is limited by lack of correlates of protection. We used pre- and post-vaccination sera and peripheral blood mononuclear cells from a flagellin adjuvanted F1/V vaccine trial to evaluate potential gene expression markers that correlated with macrophage protection. Here, we report for the first time in humans that inverse caspase 3 levels which are measures of protective antibody significantly increased by 29% and 75% on day 14 and 28 post-second vaccination, respectively. In addition, there were significant increases in T cell responses on day 28 post-second vaccination. The strongest positive and negative correlations between protective antibody levels and gene expression signatures were identified for IFNG and ENSG00000225107 genes, respectively. Flagellin/F1/V subunit vaccine induced macrophage-protective antibody and significant CD4+ T cell responses. Several genes associated with macrophage-protective antibody were identified that could serve as potential correlates of protection.

overall_design:
Stored samples from a recently completed clinical trial (DMID 08-0066) were used. DMID 08-0066 was a phase I, randomized, double blind, placebo controlled, dose-escalation trial to evaluate flagellin/F1/V, a plague vaccine, in healthy adults. In the DMID 08-0066 clinical trial, volunteers were vaccinated with two doses of 1, 3, 6 or 10 µg flagellin-adjuvanted F1/V subunit plague vaccine 28 days apart. Sera and peripheral blood mononuclear cells (PBMC) collected at three time points (pre-vaccination, and days 14 and 28 post-second dose) from volunteers vaccinated with 6 μg and 10 μg of flagellin adjuvanted F1/V vaccine were used in this study. These two post vaccination time points from the high dose groups were selected because of higher antibody responses. Clinical samples from these two timepoints, sera stored at -80C and PBMC stored in liquid nitrogen, were used in this study. Supplementary Figure 1 summarizes the number of subjects by treatment group and assay type used in this study. As part of this study, DMID 15-0104, additional blood samples were collected from 7 volunteers who received 6 μg or 10 μg Flagellin/F1/V vaccine in the 08-0066 trial. Sera and PBMC from these additional blood samples were used to optimize immunological assays for this study. For transcriptomics, PBMCs were stimulated with F1/V vaccine antigen for 24 hours before RNA was extracted.

***The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns.***

first: Fahreta

last: Hamzabegovic

first: William

middle: F

last: Hooper

first: Sharon

last: Frey

first: Casey

last: Gelber

first: Getahun

last: Abate


title: IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim Pharma

summary: Our understanding of signalling pathways that regulate human pluripotent epiblast cells is limited, despite their fundamental biological and clinical importance. In this study, we mined human embryo transcriptomics datasets, and identified expression of transcripts for the insulin and insulin growth factor 1 (IGF1) receptors, along with IGF1 ligand. Human embryos cultured in medium supplemented with IGF1 showed an increase in the proportion of NANOG-expressing pluripotent epiblast progenitor cells. Consequently, we generated a minimal chemically-defined culture medium informed by the signalling environment of the human embryo. We derived several human embryonic stem cell (hESC) lines and reprogrammed fibroblasts to induced pluripotent stem cells (iPSCs) in these conditions. Transcriptome and protein expression analyses confirmed that these hESCs and iPSCs expressed pluripotency-associated genes. Moreover, hESCs and iPSCs retained high viability, the ability to undergo spontaneous and directed differentiation, and a normal karyotype. By contrast, fibroblast growth factor 2 (FGF2) was detrimental to epiblast development and dispensable for hESC cultures maintained in exogenous insulin or IGF1. This is the first example of how integrating signalling insights from human blastocysts can be used to define hESC culture conditions that more closely recapitulate the embryonic niche.

overall_design: Single-cell RNA-seq

first: Sissy

last: Wamaitha

first: Kathy

last: Niakan


title: RNASeq of gene expressions in humanized APOE Male and Female aging Mice

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

summary: Late onset Alzheimer’s disease (LOAD) is a progressive neurodegenerative disease with four well-established risk factors: age, APOE4 genotype, female chromosomal sex, and maternal history of AD. Each risk factor impacts multiple systems, making LOAD a complex systems biology challenge. To investigate interactions between LOAD risk factors, we performed multiple scale analyses, including metabolomics, transcriptomics, brain magnetic resonance imaging (MRI), and beta-amyloid assessment, in 16 months old male and female mice with humanized human APOE3 (hAPOE3) or APOE4 (hAPOE4) genes. Metabolomic analyses indicated a sex difference in plasma profile whereas APOE genotype determined brain metabolic profile. Consistent with the brain metabolome, gene and pathway-based RNA-Seq analyses of the hippocampus indicated increased expression of fatty acid/lipid metabolism related genes and pathways in both hAPOE4 males and females. Further, female transcription of fatty acid and amino acids pathways were significantly different from males. MRI based imaging analyses indicated that in multiple white matter tracts, hAPOE4 males and females exhibited lower fractional anisotropy than their hAPOE3 counterparts, suggesting a lower level of white matter integrity in hAPOE4 mice. Consistent with the brain metabolomic and transcriptomic profile of hAPOE4 carriers, beta-amyloid generation was detectable in 16-month-old male and female brains. These data provide therapeutic targets based on chromosomal sex and APOE genotype.  Collectively, these data provide a framework for developing precision medicine interventions during the prodromal phase of LOAD, when the potential to reverse, prevent and delay LOAD progression is greatest.

overall_design: 5 animals/group. Female and male humanized APOE3 targeted replacement (hAPOE3) and APOE4 targeted replacement (hAPOE4) homozygous mice on a C57BL/6 background strain were obtained from Taconic Inc. Male hAPOE3 (M.APOE3), male hAPOE4 (M.APOE4), female hAPOE3 (F.APOE3) and female hAPOE4 (F.APOE4) animals were aged to 16 months.

first: Shang

last: Yuan

first: Mishra

last: Aarti

first: Wang

last: Tian

last: Yiwei

first: Desai

last: Maunil

first: Chen

last: Shuhua

first: Mao

last: Zisu


title: bulk RNA-seq of human nucleusus pulposus from scoliosis patients

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: Intervertebral disc degeneration (IDD) leads to low back pain and disability globally. Progressive loss of nucleus pulposus cells (NPCs) are associated with the onset of IDD. Cell-based therapy has been shown the promising for many diseases, including the IDD in preclinical studies. However, the limited availability of human NPCs has hurdled such application for IDD. This study aimed to define strategies to derive NPCs from human ESC/iPSC. Human ESC3, ESC9 and IMR-90-iPSC were used for a three-step protocol to direct differentiation toward mesodermal, subsequently notochordal and finally NPCs. Our results showed that notochordal-like cells (NCCs) were successfully derived from the first two-step of protocol confirmed by immunofluorescence staining of Noto, Brachyury (T) and Foxa2. RT-PCR results showed that the expression of Noto, T and Foxa2 was the highest at day 5 after differentiation. Furthermore, these NCCs can be differentiated into NPCs via the final step of the protocol. These NPCs expressed the tyrosine kinase receptor Tie2 (Tie2), disialoganglioside 2 (GD2), collagen II and aggrecan. Genome-wide transcriptomic analyses by sequencing (RNA-seq) further reveals the expression of a wide array of extra-cellular matrix (ECM) genes, up-stream regulators and pathways. Cross-comparison of our RNA-seq profiles with public NPC data confirms the differentiated products are much closer to NPCs than are ESC/iPSC. Co-culturing NPCs with Light2 cell line, a luciferase-based reporter responsive to sonic hedgehog (Shh) secreted protein, showed NPCs synthesized Shh. Transplantation of NPCs effectively attenuated the spinal injury in a puncture-induced disc degeneration (PDD) model in rat. Furthermore, we utilized CRISPR/Cas9 technology to seamlessly knock in an enhanced fluorescent protein (GFP) to the loci of the noto gene in ESC9. Our study demonstrates that NPCs could be induced from human ESC/iPSC. This study provides a cell source for the development of novel strategy for IDD diseases.

overall_design: We sequenced four NP from three scoliosis individuals

first: Tiffany

last: Au

first: Vivian

last: Tam

first: Kathryn

last: SE Cheah


title: Transcriptome analysis of pineal glands in a mouse model of Alzheimer’s disease

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

summary: The pineal gland maintains the circadian rhythm in the body by secreting the hormone melatonin. Alzheimer’s disease (AD) is the most common neurodegenerative disease. Pineal gland impairment in AD is widely observed, but no study to date has analyzed the transcriptome in the pineal glands of AD. To establish resources for the study on pineal gland dysfunction in AD, we performed a transcriptome analysis of the pineal glands of AD model mice and compared them to those of normal mice. There were diverse protein-coding RNAs, long noncoding RNAs and circular RNAs with global change in the pineal glands of AD mouse model. The analyzed data reported in this study will be an important resource for future studies to elucidate the altered physiology of the pineal gland in AD.

overall_design: Wild type pineal gland versus 5xFAD pineal gland (four biological replicates each)


title: CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

first: Elena

last: Pugacheva

summary: The DNA-binding protein CTCF and the cohesin complex function together to shape chromatin architecture in mammalian cells, but the molecular details of this process remain unclear. We demonstrate that a 79 amino acid region within the CTCF N-terminal domain but not the C-terminus is necessary for cohesin positioning at CTCF binding sites and chromatin loop formation. However, the N-terminus of CTCF, when fused to artificial zinc fingers that do not bind to CTCF DNA binding sites was not sufficient to redirect cohesin to different genomic locations, indicating that cohesin positioning by CTCF does not involve direct protein-protein interactions with cohesin subunits. BORIS (CTCFL), a germline-specific paralog of CTCF was unable to anchor cohesin to CTCF DNA binding sites. Furthermore, CTCF-BORIS Chimeric constructs provided evidence that both the first two CTCF zinc fingers and, likely, the 3D geometry of CTCF-DNA complexes are involved in cohesin retention. Moreover, we were able to convert BORIS into CTCF with respect to cohesin positioning, thus providing additional molecular details of the cohesin retention function of CTCF. Our data suggest that the N-terminus of CTCF and the 3D spatial conformation of the CTCF-DNA complex act as a roadblock to constrain cohesin movement along DNA.

overall_design: Genome-wide mapping of chromatin interactions in wild type and mutant CH12 cells by HiC-seq.

first: Naoki

last: Kubo


title: Stage-specific RNA-sequencing to identify genes differentially expressed between Toxoplasma gondii tachyzoites and bradyzoites

status: Public on Jan 16 2020

city: CAMBRIDGE

first: Benjamin

last: Waldman

address: 455 Main Street Rm. 555

department: Biology

institute: Whitehead Institute

summary: Using a differentiation reporter strain, unstressed parasites (tachyzoites) or stressed, reporter positive parasites (bradyzoites) were isolated by flow cytometry and analyzed for differential gene expression.

overall_design: Data from three biological replicates. When possible, duplicate samples for each biological replicate and timepoint were taken, libraries prepared in parallel, and treated as technical replicates in downstream analysis

first: Dominic

last: Schwarz

first: Marc

last: Wadsworth II

first: Jeroen

middle: P

last: Saeij

first: Alex

last: Shalek

first: Sebastian

last: Lourido


title: Assessment of gene expression signatures for overexpression of miR-1285-5p in breast cancer

city: Tokyo

first: AI

last: Mitsuhashi

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

summary: For  deep understading of miR-1285-5p in breast cancer, we have employed whole genome microarray expression profilings as a discovery platform to identify target genes of miR-1285-5p. Using human breast cancer cell lines (MCF7, MDA-MB-231, HCC1937 and HCC1954), 31 down-down regulated genes were identified by overexpression of miR-1285-5p reagardless of tumor biology. Functional interaction of miR-1285-5p with two genes (TMEM194A and SLC30A9) from this gene sets was evaluated by r-rt-PCR, Western blot and luciferase transporter assay.

overall_design: Overexpression of miR-1285-5p induced gene expression was measured after two days transfectioin using human breast cancer cells (MCF-7, MDA-MB-231, HCC1937 and HCC1954). Two independent experiments were performed in each cell line.

first: Ai

last: Hironaka-Mitsuhashi

first: Nobuyoshi

last: Kosama

first: Yusuke

last: Yamamoto

first: Takahiro

last: Ochiya.


title: Allelic histone-to-DNA methylation switch establishes secondary DMR  to maintain noncanonical imprinting

status: Public on Dec 26 2019

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

type: Methylation profiling by high throughput sequencing

summary: Faithful maintenance of genomic imprinting is essential for mammalian development.  While germline DNA methylation-dependent (canonical) imprinting is relatively stable during development, the recently discovered oocyte-derived H3K27me3-mediated noncanonical imprinting is mostly transient in early embryos with only a few genes maintain imprinted expression in the extraembryonic lineage.  How these few noncanonical imprinted genes maintain their extraembryonic-specific imprinting is unknown. Here we report that maintenance of extraembryonic-specific noncanonical imprinting requires maternal allele-specific de novo DNA methylation (secondary differentially methylation regions; DMRs) at implantation. The secondary DMRs are located at the gene promoters with paternal allele-specific H3K4me3 preformed during preimplantation development. Importantly, genetic ablation of Eed and DNA methyltransferases revealed that both maternal H3K27me3 and zygotic Dnmt3a/3b are required for establishing secondary DMRs and for maintaining noncanonical imprinting.  Thus, our study not only reveals the mechanism underlying maintenance of noncanonical imprinting, but also sheds light on how histone modifications in oocytes and preimplantation embryos may shape the secondary DMRs in post-implantation embryos.

overall_design:
Two RNA-seq replicates were performed for Dnmt3l control (CTR) and maternal KO (matKO) morula samples;
One replicate of whole genome bisulfite sequencing (WGBS) was performed for Eed CTR and matKO E6.5 extraembryonic ectoderm (ExE);
Two and seven RNA-seq replicates were performed for WT and Dnmt3a/3b double KO (DKO) E6.5 ExE;
Three RRBS replicates were performed for WT and Dnmt3a/3b DKO E6.5 ExE;
Two H3K27me3 CUT&RUN replicates were performed for WT and Dnmt3a/3b DKO E6.5 ExE;
Two H3K4me3 CUT&RUN replicates were performed for Eed CTR and matKO morula;
One H3K4me3 CUT&RUN replicate was performed for Eed CTR and matKO trophectoderm (TE).

first: Qiangzong

last: Yin

first: Inoue

last: Azusa

first: Chunxia

last: Zhang

first: Yi


title: A combined small RNA and transcriptome sequencing analysis illuminates the response of resistance to brown planthopper in rice [miRNA-seq]

first: Bo

last: Du

state: Hubei

address: Luojiashan

institute: Wuhan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Here, a combined small RNA and transcriptome sequencing analysis was performed on the BPH6-transgenic and Nipponbare plants sheath samples at the different feeding stage by BPH, and differentially expressed microRNAs (DEMs) and genes (DEGs) were identified and further analyzed for a possible involvement in BPH6 mediated resistance mechanism. A total of 217 DEMs and 7,874 DEGs were identified in the BPH6-transgenic and Nipponbare plants after BPH feeding. At the miRNA level, 29 miRNAs, including the members of miR160, miR166, miR169, miR1861, miR319 and miR390 family and other miRNAs, appeared opposite expression at early or late feeding stages between the two varieties, and 9 miRNAs specially expressed in the BPH6-transgenic plans, suggesting these miRNAs might play an important role in BPH6-mediated resistance to BPH. For the transcriptome, 949 DEGs appeared opposite expression at early or late feeding stages of two rice genotypes were identified and enriched in metabolic process, cellular development, cell wall organization, cellular component movement and hormone transport, and in involved in certain kinds of primary and secondary metabolite synthesis by GO and KEGG enrichment analysis. 24 genes were further selected to be considered as BPH resistance related gene candidates. Finally, integrated analysis of DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were selected as BPH resistance related miRNA-mRNA interaction candidates.

overall_design: 18 libraries were constructed, amplified and sequenced with the BPH6-transgenic and Nipponbare sheath before and after BPH feeding.

first: Guangcun

last: He


title: A combined small RNA and transcriptome sequencing analysis illuminates the response of resistance to brown planthopper in rice [RNA-seq]

summary: Here, a combined small RNA and transcriptome sequencing analysis was performed on the BPH6-transgenic and Nipponbare plants sheath samples at the different feeding stage by BPH, and differentially expressed microRNAs (DEMs) and genes (DEGs) were identified and further analyzed for a possible involvement in BPH6 mediated resistance mechanism. A total of 217 DEMs and 7,874 DEGs were identified in the BPH6-transgenic and Nipponbare plants after BPH feeding. At the miRNA level, 29 miRNAs, including the members of miR160, miR166, miR169, miR1861, miR319 and miR390 family and other miRNAs, appeared opposite expression at early or late feeding stages between the two varieties, and 9 miRNAs specially expressed in the BPH6-transgenic plans, suggesting these miRNAs might play an important role in BPH6-mediated resistance to BPH. For the transcriptome, 949 DEGs appeared opposite expression at early or late feeding stages of two rice genotypes were identified and enriched in metabolic process, cellular development, cell wall organization, cellular component movement and hormone transport, and in involved in certain kinds of primary and secondary metabolite synthesis by GO and KEGG enrichment analysis. 24 genes were further selected to be considered as BPH resistance related gene candidates. Finally, integrated analysis of DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were selected as BPH resistance related miRNA-mRNA interaction candidates, 18 pairs of which were identified by qRT-PCR, two pairs of which were further confirmed by protoplast fluorescence micrographs and western blotting.


title: A combined small RNA and transcriptome sequencing analysis illuminates the response of resistance to brown planthopper in rice

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

overall_design: Refer to individual Series


title: Single-cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.

status: Public on Dec 24 2019

city: Utrecht

first: Hessel

last: Honkoop

state: Zuid-Holland

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: While the heart regenerates poorly in mammals, efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration, resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However, there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes, we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single-cell RNA-sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non-proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover, these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity, while glycolysis gene expression and glucose uptake are increased, indicative for metabolic reprogramming. Mechanistically, this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore, pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming, which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair.

overall_design: Tg(nppa:mCitrine)  positive cells  (n=576) were collected from 13 cryoinjured hearts. As an internal control, also nppa negative cells were sorted. (n=192). In addition Tg(myl7:GFP) positive cells (n=768) were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.

first: Dennis

last: de Bakker

first: Alla

last: Aharonov

first: Fabian

last: Kruse

first: Avraham

last: Shakked

first: Phong

last: Nguyen

first: Cecilia

last: de Heus

first: Laurence

last: Garric

first: Mauro

last: Muraro

first: Adam

last: Shoffner

first: Federico

last: Tessadori

first: Joshua

middle: C

last: Peterson

first: Wendy

last: Noort

first: Alberto

last: Bertozzi

first: Gilbert

last: Weidinger

first: George

last: Posthuma

first: Dominic

last: Grün

first: Willem

last: van der Laarse

first: Judith

last: Klumperman

first: Richard

last: Jaspers

first: Kenneth

last: Poss

first: Alexander

last: van Oudenaarden

first: Eldad

last: Tzahor

last: Bakkers


title: Microbial activities associated with human intestinal mucosal biofilms change mRNAs and microRNAs to promote carcinogenesis in mice [RNA]

status: Public on Dec 30 2019

city: Gainesville

first: Christian

last: Jobin

state: Florida

department: Medicine

institute: University of Florida

summary: Disrupted interactions between host and intestinal bacteria are implicated in the development of colorectal cancer (CRC).  However, the functional impacts of these inter-kingdom interactions remain poorly defined. To examine this interplay, we performed mouse and microbiota RNA-sequencing on colon tissue from germ-free (GF) and gnotobiotic ApcMin/+;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BT) and biofilm-negative healthy (BX) tissues. The bacteria in BT mice differentially expressed >2,900 genes related to bacterial secretion, virulence and biofilms, but only affected 62 host genes.  Importantly, the bacterial communities from BT mice were transmissible and carcinogenic when administered to a new GF ApcMin/+;Il10-/- cohort, maintaining a set of 13 bacterial genera. Our findings suggest complex interactions within bacterial communities affecting bacterial composition and CRC development.

first: Cynthia

last: Sears


title: Mitochondrial integrity regulated by FABP5 is a cell-intrinsic checkpoint for Treg suppressive function

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Regulatory T cells (Tregs) negatively regulate immune-mediated inflammation that is essential for preventing autoimmunity, but which can be detrimental in cancer. Central to Treg activation are changes in lipid metabolism to support their survival and function. Fatty acid binding proteins (FABPs) are a family of lipid chaperones required to facilitate the uptake and trafficking of intracellular lipids. One family member, FABP5, is expressed in certain T cell subsets, but its function remains elusive. We show here that in Tregs, FABP5 inhibition causes mitochondrial defects, underscored by decreased OXPHOS, lipid elongation and desaturation, and loss of cristae structure, which augment their suppressive function. Mitochondrial dysfunction after FABP5 inhibition results in mtDNA release and consequent cGAS/STING-dependent type I IFN signaling, which induces increased production of the regulatory cytokine IL-10, promoting Treg cell suppressive activity. Together these data reveal that FABP5 acts as a gatekeeper of mitochondrial health to control Treg cell function.

overall_design: RNA-seq was performed on in vitro differentiated T regulatory cells, isolated from the spleen, exposed to the FABP5 inhibitor BMS309403.

first: Cameron

last: Field

first: Fran

last: Biaxauli Celda

first: Ryan

last: Kyle

first: Alanna

last: M. Cameron

first: David

last: Sanin

first: Keli

last: Hippen

first: Michael

last: Loschi

first: Daniel

last: Puleston

first: Mauro

last: Corrado

first: Joy

last: Edwards-Hicks

first: Katarzyna

last: Grzes

first: Edward

last: Pearce

first: Bruce

middle: R

last: Blazar

first: Erika


title: RNA Sequencing  Analysis of Pam3CSK4-stimulated BMDMs with or without Dopamine (DA)

status: Public on Dec 22 2019

city: Nanjing

first: Yuqing

last: Wu

address: 101 Longmian Road

institute: Nanjing Medical University

summary: Mice Pam3CSK4-stimulated bone marrow derived macrophages with DA or not genome.Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the most prominent downregulated pathway upon DA treatment was NF-kappaB signaling pathway. Consistently, the heatmap analysis displayed significantly decreased expression in many genes associated with NF-kappaB signaling and inflammation, such as Il6, Tnf, Il12b, Il1b, and Ccl5

overall_design: Pam3CSK4-stimulated BMDMs with or without DA mRNA profiles were generated by deep sequencing, in triplicate, using BGISEQ-500

first: Shuo

last: Yang

first: Yingchao

last: Hu


title: Tumor initiation: oncogenes as mechanical signals

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: RNA-seq of human breast epithelial cells (MCF10A) seeded on substrates of different stiffness.

overall_design: MCF10-A cells transduced with Empty vector of HER2-CA were transfected with siRNAs and replated after 24 hr on plastic or 0.5 kPa PAAm hydrogles. Samples were harvested 24 hr later.

first: Mattia

last: Forcato

first: Tito

last: Panciera

first: Anna

last: Citron

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Gene expression identifies metabolic and functional differences between intramuscular and subcutaneous adipocytes in cattle

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

summary: To further our understanding of bovine fat depot biology we screened 5 discrete fat depots (IMF, intermuscular, omental, kidney and subcutaneous) for patterns of genome-wide gene expression

overall_design: Gene expression in bovine fat depots was measured in 26 m old bos taurus steers representing 3 genetic backgrounds after 259 d in a feedlot .  Twelve (3 genetic background x 4 individual replicates per background) independent replicates were used to characterise each depot.

first: Nicholas

last: Hudson

first: Antonio

last: Reverter


title: rG4-seq for  P. aeruginosa and  E. coli

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

institute: City University of Hong Kong

summary: Escherichia coli  is the most widely studied strains, which has irreplaceable position in medicine and biology research. Pseudomonas aeruginosa, an opportunistic human pathogen, tends to cause potentially lethal acute or chronic infections in patients with cystic fibrosis (CF), immunocompromised individuals and burn victims. However, it is little know about the effect of the special secondary structure rG4 (G-quadruplex) in the mRNA on virulence regulation.  Here, we aim to reveal the new and important post-transcriptional regulatory roles of rG4 in bacterial pathogenicity and metabolic pathways.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Four samples for P. aeruginosa, 4 samples for E.coli, 150 bp single-ended RNA-Seq libraries from bacterial cell extracts after performing RTS reaction in different buffers (Li and K rich buffer). Each of the 2 conditions has 2 libraries from independent biological replicates.

last: Deng


title: Analysis of Hap2-GFP and Arp5-3HA ChIP-Seq from fission yeast

city: Edinburgh

first: Marcel

last: Lafos

state: Scotland

address: Max Born Crescent

department: Institute of Cell Biology

institute: University of Edinburgh

summary: High coincidence was observed for Hap2 and Arp5 peaks

overall_design: ChIP and library preparation was performed essentially as described (Shukla et al. 2018).

first: Robin

last: Allshire

first: Puneet

last: Singh

first: Manu

last: Shukla

first: Pin

last: Tong


title: Generation of E9.0 mouse embryonic progenitors

status: Public on Dec 20 2019

city: Boston

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: Multipotent Nkx2-1-positive lung epithelial primordial progenitors of the foregut endoderm are thought to be the developmental precursors to all adult lung epithelial lineages. However, little is known about the global transcriptomic programs or gene networks that regulate these gateway progenitors in vivo due to their rarity and transient presence during a narrow developmental window, embryonic day E9.0 in mice. Here we describe the unique genetic program of in vivo lung primordial progenitors and computationally identify the signaling pathways that are involved in their cell-fate determination from pre-specified embryonic foregut. We integrate this information in computational models to generate in vitro engineered lung primordial progenitors from mouse pluripotent stem cells, improving the fidelity of the resulting cells through unbiased, easy-to-interpret similarity scores and modulation of cell culture conditions, including biomechanical cues. As the genetic characterization of early in vivo embryonic progenitors is rapidly expanding, the methodology proposed here can have wide applicability to the in vitro derivation of bona fide tissue progenitors of all germ layers.

overall_design: For E9.0 single cell RNA-Seq data, Nkx2-1GFP-expressing domains (forebrain, thyroid, and lung) were isolated from E9.0 embryos and monodispersed using the collagenase-dispase method with the purpose of assessing the resemblance of our PSC-derived lung progenitors to in vivo lung primordial progenitors

first: Laertis

last: Ikonomou


title: Transcriptome sequencing of the callus in subculture 21d of YIL25 versus Teqing, the complementary transgenic line (pCPL) versusTeqing , the overexpressiong transgenic line (pOE) versusTeqing .

city: Beijing

first: Kun

last: Zhang

address: Haidian district Yuanmingyuanxilu2

institute: Chins Agricultural University

summary: To analyze the molecular function of BROWNING of CALLUS1 (BOC1), we performed RNA-seq experiments using callus that had been subcultured for 21 days from Teqing and YIL25, Teqing and the complementation line pCPL-BOC1-Teqing (pCPL), and also Teqing and the overexpression line pOE-BOC1-Teqing (pOE).We identified a total of 700 differentially expressed genes (DEGs), containing 410 DEGs upregulated in the callus of YIL25 versus Teqing, pCPL versus Teqing and downregulated in pOE versus Teqing. Besides, 290 DEGs downregulated in the callus of YIL25 versus Teqing and pCPL versus Teqing and upregulated in pOE versus Teqing. A large number of DEGs associated with stress response and cell death were presented.

overall_design: Examination the differentially expressed genes in the callus of subcultured for 21d between Teqing and YIL25, Teqing and the complementation line pCPL-BOC1-Teqing (pCPL), and also Teqing and the overexpression line pOE-BOC1-Teqing (pOE).


title: Bulk RNA-seq of mouse embryonic progenitor cells

summary: Population RNA-Seq analysis shows distinct gene expression profiles in specification of Nkx2-1+ endodermal and ectodermal populations

overall_design: Breeding cages were set up with one male and three female mice and the morning of the day a vaginal plug was detected was defined as embryonic day E0.5. Foregut endoderm and ectoderm cells were isolated from E8.25 embryos, forebrain and lung cells were isolated from E9.0 embryos and thyroid cells were isolated from E13.5 embryos

first: Darrell

last: Kotton


title: Genome-wide CRISPR-Cas9 screen identifies druggable synthetic lethality between LSD1 and MTORC1 in MLL-translocated AML

status: Public on Dec 23 2019

city: Manchester

first: Tim

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

summary: Lysine Specific Demethylase 1 (LSD1 or KDM1A) is one of a number of epigenetic regulators which have recently emerged as candidate therapeutic targets in acute myeloid leukaemia (AML). Pharmacological inhibitors of LSD1 such as the tranylcypromine derivatives have already commenced evaluation in early phase clinical trials; however like all acute leukaemia therapies, it is unlikely that these inhibitors are effective as single agents. Therefore, there is a strong rationale to identify proteins that collaborate with LSD1 to maintain the leukemic phenotype and could be targeted in combination with LSD1 for enhanced therapeutic benefit. Using a genome-wide CRISPR-Cas9 dropout screen in human THP1 cells, we identified multiple regulatory components of the amino acid sensing arm of mTORC1 signalling - RRAGA, MLST8, and LAMTOR2 – as synthetic lethalities with LSD1 inhibition. Genetic and/or pharmacologic inhibition of selected genes in combination with LSD1 inhibition showed significant anti-leukemic activity by inducing a more extensive and wide-ranging myeloid differentiation program and reducing cell proliferation in THP1 and primary human AML cells in vitro and in vivo. In conclusion, we report that inhibition of mTORC1 sensitizes human MLL-translocated AML cells to LSD1 inhibitor-mediated differentiation therefore highlighting a novel combination approach for evaluation in clinical trials.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Transcriptional profiles were generated by deep sequencing using Illumina NextSeq 500.

CRISPR screen samples were generated using Illumina HiSeq 2500.


title: The effect of modulating substratum biochemical properties on lung epithelial specification in vitro

summary: Bulk RNA-Seq of all epithelial cell populations from both 2D-Gelatin and 3D-Matrigel conditions, namely 2D-Nkx2-1+EPCAM+ (lung epithelial progenitors derived on 2D gelatin), 3D-Nkx2-1+EPCAM+ (lung epithelial progenitors derived on 3D Matrigel), and 3D-Nkx2-1-EPCAM+ (non-lung epithelial progenitors derived on 3D Matrigel).

overall_design: Nkx2-1mCherry mouse ESCs were differentiated into definitive endoderm over the course of 5 days in serum-free cSFDM medium with 50 ng/ml Activin A (R&D Systems 338-AC) added from days 2.5 to 5. The resulting embryoid bodies were plated onto P100 petri dishes in cSFDM supplemented with 100 ng/ml rmNoggin (R&D Systems 1967-NG) and 10 μM SB431542 (Sigma S4317).

first: Michael

last: Herrigues

middle: N


title: Genome-wide methylation profiles in coeliac disease and healthy controls

city: Penrith

first: Christine

last: Chiu

state: NSW

address: Locked Bag 1797

institute: Western Sydney University

summary: Genome wide DNA methylation profiling in saliva samples from individuals with and without coeliac disease. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. The study investigated DNA methylation profiles  associated with CD.

overall_design: Bisulphite converted DNA from 59 individuals with and without coeliac disease were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. All individuals were non-smokers and caucasian.

first: Joanne

middle: M

last: Lind

first: Nerissa

last: Hearn


title: bulk RNA-seq of human nucleusus pulposus cell differentiations from embryonic stem cells and iPSCs

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

institute: The University of Hong Kong

summary: Progressive loss of nucleus pulposus cells (NPCs) is associated with the onset of intervertebral disc degeneration (IDD). Transplantation of NPCs, derived from human pluripotent stem cells including hESC/iPSCs, may offer a novel therapy for IDD. To date, effective in vitro differentiations of notochordal and NP cells remained to be demonstrated. Towards this end, we developed a three-step protocol to directly differentiate hESC/iPSC towards mesodermal, then notochordal and finally NPCs. Our results showed that notochordal-like cells (NCCs) were successfully derived from the first two-steps of the protocol. Furthermore, these cells could be differentiated into NPCs. These NPCs expressed the tyrosine kinase receptor Tie2 (Tie2), disialoganglioside 2 (GD2), collagen II and aggrecan. Genome-wide transcriptomic analyses by sequencing (RNA-seq) revealed the expression of a wide array of known NP markers, extracellular matrix (ECM) genes, up-stream regulators and pathways. Cross-comparison of in vitro RNA-seq profiles with in vivo human NP data confirmed the in vitro NPCs are significantly more similar to in vivo NP than hESC/iPSCs. Transplantation of NPCs effectively attenuated disc injury in a rat model of IDD. We utilized CRISPR/Cas9 to seamlessly knock in an enhanced green fluorescent protein (eGFP) to the loci of the Noto gene in ESCs for NCC generation. Our study achieved effective notochordal differentiation and provided transcriptomic insights into the use of human ESC/iPSCs.

overall_design: We sequenced three lines of stem cells, and their respective differentiation products (each has four replicates)

first: Yuelin

first: Zhao

first: Tiffany

last: Au

first: Kathryn

last: Cheah

first: Qizhou

last: Lian


title: Chronic acidosis-associated transcriptome changes in cancer cells

city: Brussels

first: Cyril

last: Corbet

state: Select State/Prov.

address: Avenue Hippocrate 57

department: Institut de Recherche Expérimentale et Clinique (IREC)

country: Belgium

institute: UCLouvain

summary: The goal of this study was to examine the effects of chronic acidosis (pH 6.5) on the transcriptome of several cancer cell lines.

overall_design: Examination of transcriptome changes in 3 couples of cancer cell lines (i.e. native vs acidosis-adapted cancer cells)

first: Olivier

last: Feron


title: The structural basis for cohesin/CTCF anchored loops [RNA-seq]

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

address: Plesmanlaan 121

department: Gene regulation

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: RNA-Seq was performed in control and mutant CTCF (Y226A, F228A) HAP1 cells in triplicate.

first: Judith

last: Haarhuis

last: Sedeño Cacciatore

first: Laureen

last: Willems

first: Elzo

last: de Wit

first: Benjamin

last: Rowland


title: Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

city: East lansing

first: Jiming

last: Jiang

state: Michigan

address: 612 Wilson Rd

institute: Michigan State University

summary: We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to “specific MHSs” (sMHSs). sMHSs tend to be located away from promoters and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains.

overall_design: Chromatin are lightly digested by MNase to identify open chromatin regions in Arabidopsis thaliana.

first: Wenli

last: Zhang

first: Hainan

last: Zhao

first: Tao


title: Microbial activities associated with human intestinal mucosal biofilms change mRNAs and microRNAs to promote carcinogenesis in mice

first: Christian

last: Jobin

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

overall_design: Refer to individual Series


title: Expression data from cultured mouse macrophages isolated from Hilpdaflox/flox (WT) and HilpdaΔMΦ (KO) mice treated with a mixture of fatty acids

status: Public on Dec 19 2019

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Obesity leads to a state of chronic low-grade inflammation that features accumulation of lipid-laden macrophages in adipose tissue. Here, we determined the role of macrophage lipid droplet accumulation in the development of obesity-induced adipose tissue inflammation, using mice with myeloid-specific deficiency of the lipid-inducible HILPDA protein. HILPDA deficiency markedly reduced intracellular lipid levels and accumulation of fluorescently-labeled fatty acids. Decreased lipid storage in HILPDA-deficient macrophages could be rescued by inhibition of adipose triglyceride lipase (ATGL) and was associated with increased oxidative metabolism. In diet-induced obese mice, HILPDA deficiency did not alter inflammatory and metabolic parameters, despite markedly reducing lipid accumulation in macrophages. Overall, we find that HILPDA is a lipid-induced physiological inhibitor of ATGL-mediated lipolysis in macrophages that uncouples lipid storage in adipose tissue macrophages from inflammation and metabolic dysregulation. Our data question the contribution of lipid droplet accumulation in adipose tissue macrophages in obesity-induced inflammation and metabolic dysregulation.

overall_design: Bone marrow-derived macrophages (BMDM) isolated from Hilpdaflox/flox (WT) and HilpdaΔMΦ (KO) mice were treated with fatty acids, followed  by comparison of the transcriptional profiles.   were compared. Microarray profiling was performed on total RNA isolated from mouse bone marrow-derived macrophages treated with 600uM oleate:palmitate mixture (in a ratio of 1:2 palmitate to oleate) for 12 or 24 hours.

first: Xanthe

last: van Dierendonck

first: Montserrat

last: de la Rosa Rodriguez

first: Rinke

last: Stienstra

first: Sander

last: Kersten


title: Genome-wide binding profiles of HP1a and Prospero in Drosophila central brain neural precursors and neurons

status: Public on Dec 21 2019

first: Yan

last: Song

state: 北京

address: No.5 Yiheyuan Road

institute: Peking University

summary: Compacted heterochromatin blocks are prevalent in differentiated cells and present a barrier to cellular reprogramming. It remains obscure how heterochromatin remodeling is orchestrated during cell differentiation. Here we find that the evolutionarily conserved homeodomain transcription factor Prospero (Pros)/Prox1 ensures neuronal differentiation by driving heterochromatin domain condensation and expansion. Intriguingly, in mitotically dividing Drosophila neural precursors, Pros is retained at H3K9me3+ pericentromeric heterochromatin regions of chromosomes via liquid-liquid phase separation (LLPS). During mitotic exit of neural precursors, mitotically retained Pros recruits and concentrates heterochromatin protein 1 (HP1) into phase-separated condensates and drives heterochromatin compaction. This establishes a transcriptionally repressive chromatin environment that guarantees cell-cycle exit and terminal neuronal differentiation. Importantly, mammalian Prox1 employs a similar “mitotic-implantation-ensured heterochromatin condensation” strategy to reinforce neuronal differentiation. Together, our results unveiled a new paradigm whereby mitotic implantation of a transcription factor via LLPS remodels H3K9me3+ heterochromatin and drives timely and irreversible terminal differentiation.

overall_design: Targeted DamID. 4 samples: Dam-Pros-FL, Dam-Pros-ΔN7, Dam-HP1a and Dam alone drove by GMR71C09-GAL4, Gal80ts. Three biological replicates for each sample.


title: Elucidating BT4338 binding in Bacteroides thetaiotaomicron following 10 minutes of carbon starvation.

city: HERSHEY

first: Guy

last: Townsend

address: 500 University Drive, BMR Rm. C6820

department: Biochemistry & Molecular Biology

institute: Penn State College of Medicine

summary: Use ChIPseq to elucidate BT4338 binding in Bacteroides thetaiotaomicron following 10 minutes of carbon starvation.

overall_design: ChIPseq was performed on a strain encoding an HA-tagged BT4338 after 10 minutes of carbon starvation.

first: Eduardo

last: Groisman


title: Elucidating the BT4338 regulon

summary: RNAseq to define BT4338-dependent gene expression changes in B. thetaiotaomicron

overall_design: Isogenic wild-type and ΔBT4338 strains were grown to mid-exponential phase in mimial media containing glucose as the sole carbon source (-5) and switched to media lacking a carbon source for 10 minutes (+10)


title: Wildtype or Hilpda KO Mouse macrophages treated with fatty acids


title: HIF1α Regulates Early Metabolic Changes Due to Activation of Innate Immunity in Nuclear Reprogramming

status: Public on Dec 18 2019

city: Palo Alto

first: Sayed

last: Nazish

state: CA

address: 300 Pasteur Dr

institute: stanford

summary: Innate immune signaling has recently been shown to play an important role in nuclear reprogramming, by altering the epigenetic landscape and thereby facilitating transcription. However, the mechanisms that link innate immune activation and metabolic regulation in pluripotent stem cells remain poorly defined, particularly with regards to key molecular components. In this study, we show that hypoxia-inducible factor one (HIF1α), a central regulator of adaptation to limiting oxygen tension, is an unexpected but crucial regulator of innate immune-mediated nuclear reprogramming. HIF1α is dramatically upregulated as a consequence of Toll-like receptor 3 (TLR3) signaling and is necessary for efficient induction of pluripotency and transdifferentiation. Bioenergetics studies reveal that HIF1α regulates the reconfiguration of innate immune-mediated reprogramming through its well-established role in throwing a glycolytic switch. We believe that results from these studies can help us better understand the influence of immune signaling in tissue regeneration and lead to new therapeutic strategies.

overall_design: Human fibroblast treated with 30 ng/ml Poly I:C in endothelial cell medium for 0 day, 2 days, 4 days, and 6 days

first: Hongyue

last: Ruan

first: Chun

last: Liu


title: Microbial activities associated with human intestinal mucosal biofilms change mRNAs and microRNAs to promote carcinogenesis in mice [miRNA]

city: Gainesville

institute: University of Florida

summary: Disrupted interactions between host and intestinal bacteria are implicated in the development of colorectal cancer (CRC).  However, the functional impacts of these inter-kingdom interactions remain poorly defined. To examine this interplay, we performed small RNA sequencing on the stool of from germ-free (GF) and gnotobiotic ApcMin/+;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BT) and biofilm-negative healthy (BX) tissues.   revealed a group of significant differentially expressed miRNAs specific to BT compared to BX associated ApcMin/+;Il10-/- mice and several miRNAs that correlated with bacterial genera abundances. Our findings suggest complex interactions within bacterial communities affecting host-derived miRNA and CRC development.

overall_design: Small RNA sequencing  on stool samples from germ-free (GF) and gnotobiotic ApcMin/+;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BT) and biofilm-negative healthy (BX) tissues.

first: Cynthia

last: Sears


title: Early lineage commitment defines alveolar epithelial ontogeny in the lung (E13.5, E15.5 and E17.5)

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Multipotent Nkx2-1-positive lung epithelial primordial progenitors of the foregut endoderm are thought to be the developmental precursors to all adult lung epithelial lineages. However, little is known about the global transcriptomic programs or gene networks that regulate these gateway progenitors in vivo due to their rarity and transient presence during a narrow developmental window, embryonic day E9.0 in mice. Here we describe the unique genetic program of in vivo lung primordial progenitors and computationally identify the signaling pathways that are involved in their cell-fate determination from pre-specified embryonic foregut. We integrate this information in computational models to generate in vitro engineered lung primordial progenitors from mouse pluripotent stem cells, improving the fidelity of the resulting cells through unbiased, easy-to-interpret similarity scores and modulation of cell culture conditions, including biomechanical cues. As the genetic characterization of early in vivo embryonic progenitors is rapidly expanding, the methodology proposed here can have wide applicability to the in vitro derivation of bona fide tissue progenitors of all germ layers.

overall_design: Lungs from Nkx2-1GFP embryos of the respective embryonic day (E13.5, E15.5 and E17.5) were harvested and processed into single cell suspensions using an enzyme solution containing dispase (Collaborative Biosciences), collagenase I (Life Technologies), and RNAse-free DNAse (Promega). Nkx2-1GFP positive cells stained with DAPI were sorted for GFP and also DAPI to exclude dead cells using a FACSJazz (BD Biosciences) flow cytometer using wild type embryonic lung single cells suspensions as a negative control. Cells were collected into FACS tubes containing cell growth media composed of 10% fetal bovine serum in DMEM/F12 media. Cells were loaded onto a GemCode instrument (10X Genomics) to produce single-cell bar-coded droplets using 10X Single Cell 3’ v2 chemistry. Libraries generated were sequenced across at least one lane on the Illumina HiSeq2500 instrument with the HiSeq Rapid SBS kit. The resulting reads were aligned and gene level unique molecular identifier (UMI) counts obtain using Cell Ranger version 2.0.1 (10x Genomics).

first: David

last: Frank

first: Edward

last: Morrisey


title: A tendon comparative transcriptional atlas

city: New York

first: Christopher

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain

city: Chengdu

first: keying

last: Lu

state: Sichuan

address: Wuhou

department: State Key Laboratory of Biotherapy

institute: Sichuan university

summary: Rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brain. We identify gene modules associated with specific brain regions like the cerebral cortex, pituitary, and thalamus. In addition, we discover 9703 novel intergenic transcripts, including 1701 coding transcripts and 2845 lncRNAs. Most of the novel transcripts are only expressed in specific brain regions or cortical regions of specific individuals. We further survey the open chromatin regions in the hippocampal CA1 and several cerebral cortical regions of the rhesus macaque brain using ATAC-seq, revealing CA1- and cortex-specific open chromatin regions. Our results add to the growing body of knowledge regarding the baseline transcriptomic and open chromatin profiles in the brain of rhesus macaque.

overall_design: we characterized the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brain

first: Senlin

last: Yin

first: Keying

first: Jie

last: Tang


title: Extracellular vesicles from hepatocytes are therapeutic for toxin-mediated fibrosis and gene expression in the liver

city: Columbus

last: Brigstock

state: OH

address: 700 Children's Drive

institute: Nationwide Children's Hospital

summary: Norm mouse hepatocyte-derived extracellular vesicles were used to treat CCl4-injured mice and the hepatic transcript changes were measured by RNA-seq.

overall_design: 5 groups of mice were treated with or without CCl4 three times per week for 5 weeks. Some mice received EV i.p. three times per week over the last 2 weeks of the experiment. Mice were sacrificed 36 h after the last CCl4 injection, and liver tissues were used for RNA extraction, followed by RNA-seq analysis.

first: Xinlei

last: Li

first: Ruju

last: Chen

first: Sherri

last: Kemper


title: MiRNA array of hepatic extracellular vesicles in Ggpps-LKO mice

city: Nanjing

first: YUE

last: ZHAO

state: Jiangsu

address: Rm 2113, MengMinWei Building, Gulou Campus

department: Medical School

institute: Nanjing University

summary: Lipid overload results in lipid redistribution among metabolic organs such as liver, adipose, and muscle; therefore, the interplay between liver and other organs is important to maintain lipid homeostasis. Here, we show that liver responds to lipid overload firstly and sends hepatocyte-derived extracellular vesicles (EVs) targeting adipocytes to regulate adipogenesis and lipogenesis. Geranylgeranyl diphosphate synthase (Ggpps) expression in liver is enhanced by lipid overload and regulates EV secretion through Rab27A geranylgeranylation. Consistently, liver-specific Ggpps deficiency mice have reduced fat adipose deposition. The levels of several EV-derived miRNAs in the plasma of nonalcoholic fatty liver disease (NAFLD) patients are positively correlated with body mass index (BMI), and these miRNAs enhance adipocyte lipid accumulation. Thus, we highlight an inter-organ mechanism whereby the liver senses different metabolic states and sends corresponding signals to remodel adipose tissue to adapt to metabolic changes in response to lipid overload.

overall_design: The miRNA components in primary hepatocyte-derived EVs from WT and liver Ggpps defficient mice fed a normal chow diet or a HFD were profiled. Each sample comprised a pool of EVs derived from the primary hepatocytes of four animals.

first: Yue

last: Zhao

first: Meng-Fei

first: Shan

last: Jiang

first: Jing

last: Wu

first: Jia

first: Xian-Wen

last: Yuan

first: Di

last: Shen

first: Jing-Zi

last: Zhang

last: Zhou

first: Jian

last: He

first: Lei

last: Fang

first: Xi-Tai

last: Sun

first: Bin

last: Xue

first: Chao-Jun


title: Transcriptional analysis of tendons from mice

first: Christopher

last: Mendias

summary: We report RNA sequencing data from the Achilles, patellar, supraspinatus, and forepaw flexor tendons of adult male mice in the C57Bl/6 background.

overall_design: Differential expression of mRNAs were evaluated between each of the 4 different tendons


title: Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair

city: Oxford

first: Thomas

last: Cahill

address: Sherrington Building, Sherrington Rd

department: Department of Physiology, Anatomy, & Genetics

institute: University of Oxford

summary: The adult mammalian heart heals after myocardial infarction (MI) by deposition of scar tissue, leading to downstream arrhythmia, remodelling and heart failure1. In contrast, adult zebrafish and neonatal mouse hearts are capable of regenerating after injury.  Macrophages are key mediators of tissue repair and appear to be required for both regeneration and healing by scar formation, but the mechanisms underlying these distinct roles are poorly understood2-4. Here we investigated how macrophages differentially influence the mode of repair by determining their responses in scar-free versus scar-induced healing, comparing ventricular resection with cryo-injured adult zebrafish hearts and neonatal versus adult mouse hearts after MI.  Unbiased transcriptomics revealed molecular programmes implicating macrophages in the initiation and resolution of inflammation to dictate the kinetics of scarring during zebrafish regeneration and the activation of direct and indirect pathways to drive fibrosis in the adult mouse heart.  Most notably we observed up-regulation of collagen isoforms in both zebrafish and mouse macrophages following injury. Adoptive transfer of macrophages, from resected zebrafish hearts into cryo-injured hosts and splenic monocyte-derived macrophages from adult mouse donors into neonatal hearts, enhanced scar formation and induced fibrosis, respectively, via cell autonomous production of collagen.  In zebrafish, macrophage-specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo-injured hosts, as further evidence of a direct macrophage contribution to collagen deposition and scar formation.  These findings contrast with the current model of scarring, whereby collagen is laid down exclusively by myofibroblasts, and implicate macrophages as critical regulators of heart repair.

overall_design: RNA sequencing of cardiac macrophages following myocardial infarction in the neonatal and adult mouse

first: Filipa

last: Simões

first: Amy

last: Kenyon

first: Daria

last: Gavriouchkina

first: Madeleine

last: Lemieux

first: Damien

last: Barnette

first: Mala

last: Rohling

first: Michael

last: Weinberger

first: Eva

last: Masmanian

first: Ruth

last: Williams

first: David

last: Greaves

first: Robin

last: Choudhury

first: Tatjana

last: Sauka-Spengler

first: Paul

last: Riley


title: A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism: RNA profiles of metabolically active tissues.

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Obesity and type 2 diabetes mellitus are global emergencies and long noncoding RNAs (lncRNAs) are regulatory transcrips with elusive functions in metabolism. Here we report that an unexpectedly high fraction of lncRNAs, but not protein-coding mRNAs, is repressed during diet-induced obesity (DIO) and refeeding, whilst nutrient deprivation specifically induced lncRNAs in mouse liver. Similarly, lncRNAs were lost in diabetic humans. LncRNA promoter analyses, global cistrome and gain-of-function analyses confirmed that increased MAFG signaling during DIO curbs lncRNA expression. Silencing Mafg in primary hepatocytes and in vivo elicited a fasting-like expression profile, improved glucose metabolism, derepressed lncRNAs and prevented mammalian target of rapamycin (mTOR)-driven protein translation. We found that obesity-repressed lincIRS2 is controlled by MAFG and observed that genetic and RNAi-mediated lincIRS2 loss causes hyperglycemia, insulin resistance and aberrant glucose output in lean mice. Taken together, we identify a novel MAFG-lncRNA axis controlling hepatic glucose metabolism in health and metabolic disease.

overall_design: RNA profiles of different metabollicaly active tissues were generated by deep sequencing, on Illumins HiSeeq 2500, without replicates.

first: Marta

last: Pradas-Juni

first: Nils

last: Hansmeier

first: Jenny

last: Link

first: Elena

last: Schmidt

last: Klemm

first: Eduardo

last: Fernandez-Rebollo

first: Rute

last: Loureiro

first: Ines

last: Dhouadi

first: Christoph

last: Kiefer

first: Bjørk

last: Larsen

last: Schwarzer

first: Sajjad

last: Khani

first: Matteo

last: Oliverio

first: Hande

last: Topel

first: Motoharu

last: Awazawa

first: Peter

last: Frommolt

first: Jörg

last: Heeren

first: Ludger

last: Scheja

last: Dieterich

first: Hildegard

last: Büning

first: Ling

last: Yang

first: Haiming

last: Cao

first: Dario

last: De Jesus

first: Rohit

last: Kulkarni

first: Branko

last: Zevnik

first: Simon

last: Tröder

first: Uwe

last: Knippschild

last: Edwards

first: Richard

middle: G

last: Lee

first: Masayuki

last: Yamamoto

middle: Q

last: de Aguiar Vallim

first: Jan-Wilhelm


title: A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism: Liver RNA profiles of mice treated with  adenoviruses expressing either Mafg cDNA  or empty vector.

first: Jan

last: Kornfeld

overall_design: Liver RNA profiles of 10-week-old mice treated with  adenoviruses expressing either Mafg cDNA  or empty vector were generated by deep sequencing, in three replicates on Illumina HiSeq 4000

first: Marta

last: Pradas-Juni

first: Nils

last: Hansmeier

first: Jenny

last: Link

first: Elena

last: Schmidt

first: Paul

last: Klemm

first: Eduardo

last: Fernandez-Rebollo

first: Rute

last: Loureiro

first: Ines

last: Dhouadi

first: Christoph

last: Kiefer

first: Bjørk

last: Larsen

first: Robin

last: Schwarzer

first: Sajjad

last: Khani

first: Matteo

last: Oliverio

last: Topel

last: Awazawa

first: Thomas


title: A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism: Liver RNA profiles of obese and lean mice.

overall_design: Liver RNA profiles of 36-week old  wild type control mice and three obesity models (wild type kept on HFD for 30 weeks, db/db, misty) were generated by deep sequencing, in triplicate on Illumina HiSeq 2500

first: Hande

first: Motoharu

first: Peter

last: Frommolt

first: Jörg

last: Heeren

first: Ludger

last: Scheja

last: Dieterich

first: Hildegard

last: Büning

first: Ling

last: Yang

first: Haiming

last: Cao

first: Dario

last: De Jesus

first: Rohit

last: Kulkarni

first: Branko

last: Zevnik

first: Simon

last: Tröder

first: Uwe

last: Knippschild

last: Edwards

first: Richard

last: Lee

first: Masayuki

last: Yamamoto

last: de Aguiar Vallim


title: Mouse peritoneal macrophages treated with three different fatty acids

first: Guido

last: Hooiveld

overall_design: Microarray profiling was performed on total RNA isolated from primary mouse peritoneal macrophages treated with palmitic, oleic acid or linoleic acid, or control.

first: Anastasia

last: Georgiadi

first: Sander

last: Kersten


title: Rip-seq of MTR4 in PLC/PRF5

city: Guangzhou

first: Kaiyuan

last: Ji

address: No.9 Jinsui Road, Guangzhou, China

department: Guangzhou Women and Children’s Medical Center

institute: Guangzhou Medical University

summary: Metabolic switch from oxidative phosphorylation to glycolysis is required for tumorigenesis by providing cancer cells with energy and substrates of biosynthesis, and also plays a key role in inducing immune suppressive tumor microenvironment that inhibits tumor immunotherapy. Therefore, to develop more effective cancer therapy, it is important to elucidate mechanisms that control cancer metabolic switch. MTR4 is a RNA helicase associated with nuclear exosome that plays key roles in RNA processing and surveillance. We demonstrated that MTR4 is frequently overexpressed in hepatocellular carcinoma (HCC) and this predicts poor prognosis of HCC patients. MTR4 is required for HCC tumorigenesis by maintaining cancer metabolic switch. Mechanistically, MTR4 is required for the expression of critical glycolytic proteins such as GLUT1 and PKM2 by binding to their pre-mRNA and ensuring correct alternative splicing. c-Myc binds to the promoter of MTR4 gene and is required for MTR4 expression, indicating that MTR4 is a key mediator of c-Myc function in promoting cancer metabolism. These findings reveal an important pathway to drive cancer metabolic switch and present MTR4 as a promising therapeutic target for treating HCC.

overall_design: Analysis of RIP-seq RNA data enabled the identification of the MTR4 binding sites in the PLC/PRF5 cell transcriptome.

first: Lili

last: Yu

first: Yang

last: Xu


title: A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism: Liver RNA profiles of lean non-diabetic, obese non-diabetic as well as obese diabetic humans.

first: Jan

last: Kornfeld

overall_design: Liver RNA profiles of lean non-diabetic, obese non-diabetic as well as obese diabetic human individuals were generated by deep sequencing, on Illumina HiSeq 4000, in four replicates.

first: Marta

last: Pradas-Juni

first: Nils

last: Hansmeier

first: Jenny

last: Link

first: Elena

last: Schmidt

first: Paul

last: Klemm

first: Eduardo

last: Fernandez-Rebollo

first: Rute

last: Loureiro

first: Ines

last: Dhouadi

first: Christoph

last: Kiefer

first: Bjørk

last: Larsen

first: Robin

last: Schwarzer

first: Sajjad

last: Khani

first: Matteo

last: Oliverio

first: Hande

last: Topel

first: Motoharu

last: Awazawa

first: Peter

last: Frommolt

first: Jörg

last: Heeren

first: Ludger

last: Scheja

last: Dieterich

last: Büning

last: Yang

first: Thomas

first: Jan-Wilhelm


title: MTR4 drives tumorigenesis of hepatocellular carcinoma by controlling alternative splicing of metabolic genes through PTBP1 recruitment

status: Public on Dec 17 2019

city: Shenzhen

first: Lili

last: Yu

state: Guangdong

address: No. 3025 Shennan Middle Road, Shenzhen

department: The Eighth affiliated hospital

institute: Sun Yat-Sen University

summary: Aberrant alternative splicing (AS) is implicated in cancer metabolic reprogramming that supplies cancer cells with energy and substrates for biosynthesis. Therefore, the elucidation of the mechanism underlying aberrant AS in cancer cells is important for developing specific and effective therapy. We demonstrated that MTR4, a RNA helicase important for RNA quality surveillance, is frequently overexpressed in hepatocellular carcinoma (HCC) and is correlated with increased glycolysis and poor prognosis of HCC patients. MTR4 is required for tumorigenesis of HCC cells by promoting glycolysis and expression of glycolytic genes. MTR4 binds to specific motifs of pre-mRNAs, including those of the key glycolytic genes, and regulates their AS by recruiting PTBP1. We discovered that MTR4 is a direct transcriptional target of c-Myc, suggesting that MTR4 mediates the metabolic function of c-Myc in HCC. These findings reveal mechanisms driving cancer-specific AS profile and present MTR4 as a specific therapeutic target for treating HCC.

overall_design: RNA-sequencing of MTR4 knockdown PLC/PRF5 and wild Control PLC/PRF5.

first: Yang

last: Xu


title: Early dynamics of photosynthetic Lhcf2 and Lhcf15 transcription and mRNA stabilities in response to herbivory-related decadienal in Phaeodactylum tricornutum

city: Austin

first: Dennis

middle: Cates

last: Wylie

state: Texas

address: 102 East 24th Street

department: Center for Biomedical Research Support

institute: University of Texas at Austin

summary: During grazing, damaged cells of various diatom species release oxylipins whose functions include signaling to nearby undamaged cells. Our study focused on the effects of the oxylipin 2-trans, 4-trans-decadienal (DD) during the light cycle on photosynthetic light harvesting complex (LHC) mRNA regulation in Phaeodactylum tricornutum.  RNAseq data revealed extensive suppression of LHC mRNAs measured at 3 h while a smaller set of LHC mRNAs were up-regulated.  RNA metabolic labeling studies of divergently regulated Lhcf2 and Lhcf15  mRNAs documented dynamic shifts in their transcription and mRNA stabilities during the light cycle after DD treatment.  The RNAseq dataset offers an extensive resource for expression profiling in the early response period to DD treatment.

overall_design: mRNA profiles of Phaeodactylum tricornutum cells treated with 10 µM DD or DMSO solvent control for 3 and 6 h were generated from duplicate cell replicates by Illumina NextSeq platform (8 samples total).

first: Shahima

last: Islam

first: Tanya

last: Sabharwal

first: Mona

last: Mehdy