title: RNA-seq analysis of callus of Arabidopsis WT and plt1 plt2

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.

overall_design: Arabidospsis Col-0 (wt) and plt1 plt2 double mutant (dm) hypocotyls were cultured on CIM (callus induction medium) for 5-6 d. About 100 calli were used for RNA extraction. Each genotype had 2 replicates.

last: Xu

first: Ning

last: Zhai


title: RNA-seq of astrocytes isolated from parental isolated mice

status: Public on Sep 08 2021

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

department: Research center

country: China

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary: To understand the transcriptome change in astrocytes after parental isolation

overall_design: Mice were subjected to parental isolation for 8 hours a day (9am~5pm) from postnatal day 2. Specifically, mice were divided into 2 groups: Father-only, control group that stay with their fathers. Isolated: experimental group that were separated from their parents. On postnatal day 7, mice were sacrificed to isolate astrocyte by ITGP5 immunopanning.

first: Jianqin

last: Niu

first: Yuxin

last: Wang


title: Thermal stress induces tissue damage and a broad shift in regenerative signaling pathways in the honey bee intestine

city: New York

first: Jonathan

middle: W.

last: Snow

state: New York

address: 3009 Broadway

department: Biology

country: USA

institute: Barnard College

summary: Honey bee colonies in the United States have suffered from a higher than usual rate of die-off in the last few years with a complex set of interacting stresses playing a key role. With changing climate, an increase in the frequency of severe weather events, such as heat waves, is anticipated and understanding how these changes may contribute to stress in the bee is of crucial. Individual honey bees appear to have a high capacity to endure thermal stress. One reason for this high-level endurance is likely their robust HSR which contributes to thermotolerance at the cellular level. To elucidate other determinants of this resilience, we used thermal stress coupled with RNAseq and identified broad transcriptional remodeling of a number of key signaling pathways in the honey bee in response to tissue damage, including those pathways known to be involved in digestive tract regeneration in the fruit fly such as the Hippo and JAK-STAT pathways. We also observe cell death and shedding of epithelial cells, which likely leads to induction of this regenerative program. We found that thermal stress affects many of these pathways in other tissues, suggesting a shared program of damage response. In addition to allowing for important foundational characterization of damage response program in this key pollinating species, this study suggest that a robust regeneration program may also be a critical contributor to thermotolerance at the tissue level.

overall_design:
Honey bees were fed sucose solution Containing 0.5% DMSO) at either 35°C  or 45°C  for 4 hours.

Please note that the control samples in GSE139368 were re-analyzed in the current study.

middle: W

first: Dunay

last: Bach

first: Miriam

last: Holzman

first: Jennifer

last: Mansfield


title: Single-cell RNA-seq analysis of Arabidopsis hypocotyl callus

city: Shanghai

overall_design: Arabidospsis Col-0 hypocotyls were cultured on CIM (callus induction medium) for 6 d. About 150 calli were used for protoplast isolation and single cell RNA-seq.


title: RNA-seq analysis of callus of Arabidopsis WT and wox5-1 wox7-1

overall_design: Arabidospsis Col-0 (wt) and wox5-1 wox7-1 double mutant (dm) hypocotyls were cultured on CIM (callus induction medium) for 5-6 d. About 100 calli were used for RNA extraction. Each genotype had 2 replicates.


title: Release of Notch signaling coordinated by inflammation confers cross-compartment differentiation plasticity during alveolar regeneration.

city: Austin

first: Yu Jin

last: Jang

state: Texas

address: 2506 Speedway, NMS 4.246

department: Molecular Biosciences

institute: University of Texas at Austin

summary: While the acquisition of cellular plasticity in adult stem cells is essential for rapid restoration after tissue injury, little is known about the underlying molecular mechanisms governing this process. Here, we reveal that Notch signaling is a pivotal determinant conferring cross-compartment differentiation plasticity of airway secretory cells. Temporal Notch inhibition in secretory cells is required for alveolar differentiation upon injury, which is mediated by IL-1β-dependent modulation of Jag1/2 expression in ciliated cells. We also identify Fosl2/Fra2 as an essential transcription factor responsible for the regeneration of secretory cell-derived alveolar type 2 (sAT2) cells retaining distinct genetic/epigenetic signatures. We furthermore reveal that KDR/FLK-1+ human secretory cells display a conserved capacity to generate AT2 cells via Notch inhibition. Our results demonstrate that Notch signaling acts as a functional rheostat for fate decision of secretory cells during injury repair, proposing a new potential therapeutic target for human lung alveolar regeneration.

overall_design: For lineage-labeled cells from Red2-NotchN1ICD mice, YFP+CD45-CD31-EpCAM+ or RFP+CD45-CD31-EpCAM+ cells were sorted at day 28 post bleomycin injury (4 mice were pooled for each experiment). For non-lineage-labeled cells isolated from Red2-NotchN1ICD mice in parallel with experiment of lineage-labeled cells, we combined the cells of EpCAM+RFP-RFP- and EpCAM- population with a ratio of 1:1, respectively. The resulting cell suspension (~110,000 cells each) were submitted as separate samples to be barcoded for the droplet-encapsulation single-cell RNA-seq experiments using the Chromium Controller (10X Genomics). Single cell cDNA synthesis, amplification, and sequencing libraries preparation were performed using the Single Cell 3' Reagent Kit as per the 10x Genomics protocol. Libraries were multiplexed so that 2 libraries were sequenced per single lane of HiSeq 4000 using the following parameters: Read1: 27 cycles, i7: 9 cycles, i5: 0 cycles; Read2: 100 cycles to generate 150bp paired end reads.

first: Jinwook

last: Choi

first: Catherine

last: Dabrowska

first: Elhadi

last: Iich

first: Kelly

middle: V

last: Evans

first: Benjamin

middle: D

last: Simons

first: Bon-Kyoung

last: Koo

first: Jonghwan

last: Kim

first: Joo-Hyeon

last: Lee


title: Release of Notch signaling coordinated by inflammation confers cross-compartment differentiation plasticity during alveolar regeneration

type: Genome binding/occupancy profiling by high throughput sequencing

summary: While the acquisition of cellular plasticity in adult stem cells is essential for rapid restoration after tissue injury, little is known about the underlying molecular mechanisms governing this process. Here, we reveal that Notch signaling is a pivotal determinant conferring cross-compartment differentiation plasticity of airway secretory cells. Temporal Notch inhibition in secretory cells is required for alveolar differentiation upon injury, which is mediated by IL-1β-dependent modulation of Jag1/2 expression in ciliated cells. We also identify Fosl2/Fra2 as an essential transcription factor responsible for the regeneration of secretory cell-derived alveolar type 2 (sAT2) cells retaining distinct genetic/epigenetic features. We furthermore reveal that KDR/FLK-1+ human secretory cells display a conserved capacity to generate AT2 cells via Notch inhibition. Our results demonstrate that Notch signaling acts as a functional rheostat for fate decision of secretory cells during injury repair, proposing a new potential therapeutic target for human lung alveolar regeneration.

overall_design: ATAC-seq was performed for secretory cells, AT2 cells derived from seceretory cells, and resident AT2 cells isolated from Scgb1a1-CreTM;R26RfGFP;Sftpc-dsRedIRES-DTR mice. RNA-seq was performed with samples from feeder free-cultured organoids of secretory cells with or without DAPT treatment, and AT2 cells.


title: RNA-seq of ER-targeted and cytosolic mRNAs with control or CNOT1-targeting siRNA treatment in HEK293 cells

status: Public on Sep 07 2021

city: Glasgow

first: Sarah

middle: Louise

last: Gillen

address: Beatson Institute, Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: Beatson Institute for Cancer Research

summary: Determination of mRNA localisation in HEK293 cells with and without the depletion of CNOT1

overall_design: HEK293 cells were treated with control or CNOT1-targeting siRNA for 48hrs. Cell lysates were then separated into cytosolic and ER fractions. The RNA in each fraction was sequenced.

first: Sara

middle: L


title: Gene expression of spheres made from mammary tumors of FRS2b hetero mice and knock-out mice

city: Nagoya

first: Nishimura

last: Tatsunori

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

country: Japan

institute: Nagoya University

summary: Precancerous tissue microenvironment is thought to be important for tumorigenesis when cancer stem-like cells (CSCs) begin to grow, though underlying mechanisms remain unclear. Here, we uncovered critical roles of luminal progenitor cells expressing FRS2β, an inhibitory adaptor for ErbB signaling, to create the cytokines-rich CSC niche in mammary tissues. Deficiency of FRS2β greatly decreased mammary tumorigenesis with decreased tumor stroma in mouse mammary tumor virus (MMTV)-ErbB2 mice. Moreover, FRS2β-deficient precancerous mammary tissues did not allow tumorigenesis derived from xenografted wild type FRS2β tumor cells. Insulin-like growth factor (IGF) 1 and CXC chemokine ligand (CXCL) 12, stemness- and stroma-inducing cytokines, respectively, were expressed at low levels in FRS2β-deficient precancerous mammary cells. Treatment with inhibitors against these cytokines in precancerous mice greatly decreased tumorigenic potential. In addition, human breast cancer tissues in which FRS2β is highly expressed in tumor cells harbor more stroma, and are associated with poor prognosis. Thus, cytokines-rich CSC niche and tumor microenvironment induced by FRS2β expressed in luminal progenitor cells and tumor cells play important roles for tumorigenesis.

overall_design: Comparison of expression between spheres made from mammary tumors of FRS2beta hetero and knock-out mice. We conducted three replicates.

first: Takahiko

last: Murayama

first: Natsuko

last: Kimura

first: Yukino

last: Machida

first: Daisuke

last: Iejima

first: Reiko

last: Sakamoto

first: Tatsunori

last: Nishimura

first: Mizuki

last: Yamamoto

first: Nobutaka

last: Kobayashi

first: Naoki

last: Itano

first: Yusuke

last: Inoue

first: Akihiko

last: Umezawa

first: Masataka

last: Ito

first: Nobuaki

last: Yoshida

first: Jun-ichiro

first: Kouichi

last: Akashi

first: Hideyuki

last: Saya

first: Masahiko

last: Kuroda

first: Issay

last: Kitabayashi

first: Arinobu

last: Tojo

first: Noriko

last: Gotoh


title: Arabidopsis callus

first: Lin

last: XU

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

overall_design: Refer to individual Series


title: DMC1 and H3K4me3 ChIP-seq from testes of B6xSPRETUS and B6xSTUS mice with genetically modified PRDM9 binding properties

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

institute: Oxford University

summary: Male offspring resulting from interbreeding of genetically diverged populations are frequently infertile or subfertile due to failures in chromosome pairing. The resulting reproductive isolation of the two populations represents an early step in speciation. In inter-subspecific mouse hybrids, the binding of the histone methyltransferase PRDM9 to both chromosome homologues at matching positions is important for successful chromosome pairing. This mechanistic property underpins Prdm9’s role as an important speciation gene, the only one yet identified in vertebrates. Here we show that this behaviour holds true for more distant evolutionary relationships across the species barrier. By altering PRDM9’s binding pattern, we restore fertility in hybrids of distinct species.

overall_design: Examination of DMC1 and H3K4me3 binding in the testes of B6xSPRETUS and B6xSTUS F1 mice with wild-type and genetically modified Prdm9 alleles

first: Peter

last: Donnelly


title: Gene expression of S100A10 knocked down human breast cancer cells

first: Nishimura

last: Tatsunori

summary: The expression level of S100A10 was much higher in the CD44+ cancer cells metastasized to the liver than those at the primary site in the breast cancer patient-derived tumor xenograft mice. Expression level of S100A10 increased by the oncoprotein, PML/RARα and RAS, and its higher expression is linked to worse outcome in a number of cancer types including breast cancers

overall_design: Human breast cancer MDA-MB-231 cells were infected with lentivirus encoding shRNA sequences against S100A10.  Two different shRNA sequences (shS100A10-1, shS100A10-5) that effectively knockdown S100A10 were used. Analyses were duplicated.

first: Yohei

last: Shimono

first: Tatsunori

last: Nishimura


title: Circadian rhythms of ribosome binding for Drosophila astrocyte RNAs

status: Public on Sep 06 2021

city: Boston

first: Rob

last: Jackson

state: Massachusetts

address: 136 Harrison Ave.

department: Neuroscience

institute: Tufts University

summary: Raw RNAseq data (fastq) files that were analyzed for circadian changes in RNA ribosome binding. The numbers in the file names (00 - 44) represent circadian time (0 to 44 hours in constant dark and constant temperature). Two separate sets of samples (independent biological replicates) were collected over a 44-hour period of time.

overall_design: Translating ribosome affinity purification (TRAP) methods were employed to purify ribosomes and their RNA cargoes from Drosophila astrocytes. The Gal/UAS procedure was used to express a tagged ribosome (EGFP-L10a) in fly astrocytes in order to conduct TRAP. Four independent sets of timepoints (00-44 hours in constant conditions at 4 hour intervals) were sequenced in the study. These timepoints represent 2 biological replicates (2 technical replicates for each). Sets 1 and 2 below represent one biological replicate while sets 3 and 4 represent the other.

first: F

middle: R


title: DDR1 plays a distinctive role in mammary tumour growth

city: Washington DC

first: Xiujie

last: Sun

state: DC

address: 2300 I ST NW, Room 433

institute: The George Washington University

summary:
Purpose: The goals of this study are to compare mammary tumor transcriptome profiling with or without DDR1 in immunocompetent mice in an unbiased way.

Methods:
In vitro samples: DDR1 WT or KO in vitro cultured E0771 cells were sequenced. Rag1-/- samples:  DDR1 WT or KO E0771 cells were injected in Rag1-/- mice, and tumors were harvested and sequenced.
C57BL/6 samples:  DDR1 WT or KO E0771 cells were firstly inoculated into Rag1-/- mice. When tumor volume reached approximately 200~300 mm3 (usually 20 days after inoculation), 60 mg of tumor organoid were transplanted to WT C57BL/6 mice. Tumor samples were collected on day 4 after transplantation for RNA-seq.
Antibody treatment samples: DDR1 KO E0771 cells were reconstituted with human DDR1, then injected into C57BL/6 mice. Isotype control IgG or anti-hDDR1 ECD antibody treatment (10mg/kg intrutumural) started when tumor volume reached approximately 100 mm3. Tumor samples were collected on day 6 after treatment for RNA-seq.

Results: Approximately 50 million sequence reads were obtained per sample and identified more than 20,000 transcript isoforms.

Conclusions: The RNA-seq results represents the detailed analysis of DDR1 WT/KO mammary tumor transcriptomes in immunocompetent mice C57BL/6.

overall_design: RNA-seq of DDR1 WT or KO E0771 cells in vitro, in Rag1-/- hosts, and transplanted from Rag1-/- to C57BL/6 hosts. RNA-seq of E0771 tumors treated with DDR1 antibody.

first: Zhao

last: Lai

first: Rong

last: Li


title: Using Systems Biology Approaches to Identify  Signaling Pathways Activated During Chronic Wound Initiation

status: Public on Sep 05 2021

city: Riverside

first: Dr Manuela

last: Martins-Green

state: California

address: 900 University Ave

department: Molecular Cell and Systems Biology

institute: University of California

summary: Chronic wounds are a significant health problem worldwide. However, nothing is known about how chronic wounds initiate and develop. Here we use a chronic wound model in diabetic mice and a Systems Biology Approach using nanoString nCounter® technology and Weighted Gene Correlation Network Analysis (WGCNA), with tissues collected at 6, 12, 24 and 48 hr post-wounding, to identify metabolic signaling pathways involved in initiation of chronicity.  Normalized counts obtained from the nanoString nCounter® Mouse Metabolic Panel, were used for the WGCNA which groups genes into co-expression modules to visualize correlation network. Genes with significant Module Membership and Gene Trait Significance (p<0.05) were used to identify signaling pathways that are important for the development of chronicity. The pathway analysis using the Reactome database showed stabilization of PTEN which downregulates PI3K/AKT1, which in turn downregulates Nrf2, as shown by ELISA, thus disabling antioxidant production resulting in high oxidative stress levels. We find that pathways involved in inflammation, including those that generate pro-inflammatory lipids derived from arachidonic acid metabolism, IFNγ and catecholamines, occur.  Moreover, HIF3α is over-expressed, potentially blocking Hif1α and preventing activation of growth factors and cytokines that promote granulation tissue formation. We also find that FGF1 is under-expressed, while thrombospondin-1 is over-expressed, resulting in decreased angiogenesis, a process that is critical for healing. Finally, enzymes involved in glycolysis are downregulated resulting in decreased production of pyruvate, a molecule critical for ATP production, leading to extensive cell death and wound paralysis.  These findings offer new avenues of study that may lead to the development of novel treatments of CW to be administered right after debridement.

overall_design: For this study, we used a systems biology approach to identify metabolic signaling pathways important in initiation of wound chronicity.  We chose to focus our observations on four major processes involved in wound healing: Response to Injury, Inflammation, Hypoxia and Repair Response.  The window of 48hr post-wounding represents the initial stages of wound healing.  Therefore, the idea of identifying the signaling pathways contributing to initiation of chronicity was what drove us to obtain the data presented in this manuscript. In addition, because patients who suffer from CW have underlying conditions such as diabetes, cardiovascular diseases etc. treatment of CW can be fine-tuned if the disrupted pathways, and thereby candidate biomarkers and therapeutic targets, can be identified. This is the gap in literature that we intend to fill with a WGCNA of chronic wound initiation.  WGCNA helps identify modules significantly correlated to chronicity which puts the differentially expressed gene in the context of co-expressed and correlated genes thereby giving an insight into how the genes are regulated.

first: Manuela

first: Proma

last: Basu


title: ADAM10 shapes myeloid antigen-presenting cell homeostasis in the splenic marginal zone

city: Mainz

first: Ronald

last: Backer

address: Obere Zahlbacher Str. 67

department: Institute for Molecular Medicine

country: Germany

institute: University Medical Center of the Johannes Gutenberg-University Mainz

summary: The spleen contains phenotypically and functionally distinct cDC1 and cDC2 subpopulations, which each can be divided into several smaller and less-well characterized subsets. Despite advances in understanding the complexity of DC ontogeny and function by transcriptional programming, the significance of post-translational modifications in controlling tissue-specific cDC (subset) immunobiology remains elusive. Here, we identified the cell surface-expressed A-disintegrin-and-metalloproteinase 10 (ADAM10) as an essential regulator of cDC1 and cDC2 homeostasis in the splenic marginal zone (MZ). Mice with a CD11c-specific deletion of ADAM10 (ADAM10ΔCD11c) exhibited a complete loss of splenic ESAMhi cDC2A, because ADAM10 controlled their commitment, differentiation, survival, and EBI2-mediated localization within the MZ. Moreover, we discovered that ADAM10 is a molecular switch regulating cDC2 subset heterogeneity in the spleen, as this unbalanced cDC2A homeostasis in the absence of ADAM10 was compensated for by the emergence of a novel Clec12a+ cDC2B subset, closely resembling cDC2 generally found in peripheral lymph nodes. Moreover, in ADAM10ΔCD11c mice terminal differentiation of cDC1 was abrogated, resulting in reduced numbers of Langerin+ cDC1.

overall_design: Transcriptome analysis of WT and ADAM10-deficient splenic CD4+, CD8+ and CD4-CD8- conventional dendritic cells subsets

middle: A

first: Jean-Fred

last: Fontaine

first: Matthias

last: Klein

first: Tobias

last: Bopp

first: Björn

middle: E

last: Clausen


title: mRNA-seq in VDR knockout and control THP-1 cells

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

summary: The vitamin D receptor (VDR) has been knocked out in monocytic THP-1 cells after stimulation of ko and control cells with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), quadruplicate mRNA-seq has been performed

overall_design: The knockout has been performed by lentiviral CRISPR/Cas9 gene editing using a guideRNA (gRNA) directed against the VDR gene. The control cells have been created using a non-targeting gRNA (NTC). Prior to MRNA-seq, the cells were treated for 24 h with 100 nM 1,25(OH)2D3 or the solvent control (EtOH).

first: Sabine

last: Seuter

first: Marcel

middle: H

last: Schulz

first: Ralf

middle: P

last: Brandes


title: Circular RNA Expression and Regulation Profiling in Testicular Tissues of Immature and Mature Wandong Cattle (Bos taurus)

city: Hefei

first: Ibrar

middle: Muhammad

last: Khan

address: 1Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, Collage of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China, 230036

department: Animal Science

institute: Anhui Agricultural University

summary:
Wandong cattle are an autochthonous Chinese breed used extensively for beef production. The breed tolerates extreme weather conditions and raw feed and are resistant to tick-borne diseases. However, the genetic basis of testis development and sperm production as well as breeding management is not well established in local cattle.
In this study, we performed total RNA-Seq and comprehensively analyzed the circ-RNA expression profiling of the testes samples of six bulls at 3 years and 3 months of developmental age. In total, 17 013 circ-RNAs were identified, of which 681 circRNAs (P-adjust < 0.05) were differentially expressed (DE). Among these DE circ-RNAs, 579 were upregulated and 103 were downregulated in calf and bull testes. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the identified target genes were classified into three broad functional categories, including biological process, cellular component, and molecular function, and were enriched in the lysine degradation, cell cycle, and cell adhesion molecule pathways.

overall_design: Circular RNA experession and regulation in immature and mature local cattle bulls.

middle: M


title: Inhibition of granuloma triglyceride synthesis imparts control of Mycobacterium tuberculosis through curtailed inflammatory responses

status: Public on Sep 04 2021

city: New Delhi

first: Sheetal

last: Gandotra

address: Sukhdev Vihar, Mathura Road

department: Chemical and System Biology

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

summary: We report the impact of granuloma triglyceride lowering on progression of infection in the C3HeB/FeJ mouse model.

overall_design: Triglyceride lowering was acheived by intravenous administration of the DGAT1 (diacylglycerol O-acyltransferase 1) inhibitor T863.  C3HeB/FeJ mice were infected at high dose (500 cfu) with Mycobacterium tuberculosis Erdman strain, and then treated either with T863 or vehicle control from d8 to d28. T863 treated mice exhibited a heterogenous response to treatment in terms of bacterial control. A "High cfu"group exhibited no difference in CFU compared to vehicle treated mice (control) while a "low cfu"group exhibited 97-25% reduction in CFU compared to control mice. RNA-seq was performed on lung tissue from these mice.

first: Stanzin

last: Dawa

first: Prabhakar

last: Arumugam


title: Determination of the effects of endurance exercise training on the human skeletal muscle miRNAome by miRNA sequencing

city: Copenhagen

first: Christian

last: Garde

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

type: Non-coding RNA profiling by high throughput sequencing

summary: Short RNA sequncing was performed to determine the effects of endurance exercise training on miRNA expression in human skeletal muscle.

overall_design: Human skeletal muscle biopsies from male volunteers were collected prior to and after a 14 consecutive day exercise training program consisting of 1 hour/day endurance exercise. Exercise was performed at ~80% peak oxygen uptake during each session (for more details see PMID: 21360670). The biopsies collected after completion of the exercise training program were collected 16 hours after the 14th training session. In total 6 biopsies were sequenced representing biopsies collected before or after the exercise program from three human volunteers.

first: Brendan

last: Egan

first: Anna

last: Krook


title: Transcriptome profile of papaya ripening

city: São Paulo

first: Caroline

middle: Giacomelli

last: Soares

state: SP

address: Av. Lineu Prestes 580, Bloco 14

department: Department of Food Science and Experimental Nutrition

country: Brazil

institute: School of Pharmaceutical Sciences, University of São Paulo

summary: We report the application of NGS-derived transcriptome profile to elucidate a temporal line of both control and ethylene-induced ripening process of papaya fruit focusing on ripening-induced transcripts that act directly on plant cell wall disassembling

overall_design: Fruits were collected at 3 different times of the year (biological triplicate) and treated with 100-ppm ethylene for 12 hours and then let to ripe for 12 hours more. In this way, it was created five groups of analyses: control 0hrs, 12hs and 24hs and ethylene-treated fruits 12hs and 24hs.

middle: G

first: Samira

middle: B

last: Prado

first: João

last: Fabi

first: Sónia

middle: C

last: Andrade


title: RNA-sequencing the gene expression profiles of RA PBMCs treatment with B. longum RAPO

status: Public on Sep 03 2021

city: Seoul

first: Mi-La

last: Cho

address: 222,Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of Korea

summary: PBMCs were isolated from RA patients and subjected to T-cell activation conditions with B. longum RAPO or vehicle.

overall_design: mRNA expression profiles of the  'RA patients PBMC'  by NovaSeq 6000

first: Jhun

middle: J

last: Yeon

first: Lee

middle: S

last: Yoon


title: Regulation of PGC-1alpha function by its C-terminal domain [RNA-seq]

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: PGC-1alpha has been proposed to couple gene transcription and RNA processing via SR-rich domains and an RNA recognition motif located at the C-terminal domain (CTD). However, the full extent by which the CTD of PGC-1alpha regulates its function in gene expression and RNA processing remains largely unknown. Here, we used RNA-seq to evaluate the effects of CTD deletion (dCTD) on PGC-1alpha function. We found that deletion of the CTD of PGC-1alpha virtually abolished its effects on transcriptome remodeling and the resulting increase in oxidative capacity in skeletal muscle cells. Moreover, we implemented in vitro affinity purification followed by sequencing (in vitro AP-seq), which revealed more than 700 RNAs bound to the CTD of PGC-1alpha. The majority of these RNAs were transcribed at DNA regulatory elements such as promoters and distal intergenic regions. These results demonstrate that PGC-1alpha function is highly modulated at the CTD via multivalent protein-RNA interactions.

overall_design: Differentiated C2C12 muscle cells were transduced with an adenovirus to overexpress LacZ (control condition), PGC-1alpha full length (FL) or PGC-1alpha delta CTD (dCTD) for 48 h. Next, RNA was extracted for RNA-seq. For in vitro AP-seq, RNA from PGC-1alpha FL overexpressing cell was extracted and, then, incubated with a recombinant protein consisting of the CTD of PGC-1alpha. Next, RNA bound to the CTD of PGC-1alpha was purified for sequencing. RNA-seq and in vitro AP-seq were performed with 3 and 2 biological replicates, respectively.

first: Christoph

last: Handschin


title: ATAC-seq and multi-omics analysis of human liver highlight a hepatocyte-specific enhancer for ACOT1 regulating the balance of acyl-CoA and free fatty acids in type 2 diabetes.

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

summary: ATAC-seq (assay for transposase-accessible chromatin followed by sequencing) is widely used to decode chromatin accessibility. Here we performed high-sensitive ATAC-seq in 9 human liver samples from normal and T2D donors, and identified a set of differentially accessible regions (DARs). DARs were overlapped with publicly available CREs databases and integrated with multi-omics data to identify candidates for further experimental validations. We identified 7 DARs that mark putative regulatory elements including a candidate enhancer for the ACOT1 gene that regulates the balance of acyl-CoA and free fatty acids in the cytoplasm. The relevance of ACOT1 regulation in T2D was supported by the analysis of transcriptomics and proteomics data in liver tissue.  Conclusions: Our strategy that integrates chromatin accessibility with DNA binding and other types of omics provides novel insights towards the role of genetic regulation in complex multifactorial diseases such as T2D.

overall_design: ATAC-seq perfomed on 11 liver samples, 3 samples (L9, L10 and L11) were harvested from donor diagnosed with T2D, 8 from control donors characterized by normoglycemia, and each sample has two replicates

first: Xingqi

last: Chen

first: Yonglong

last: Dang


title: Regulation of PGC-1alpha function by its C-terminal domain [in vitro AP-seq]


title: Liver RNA-seq and T cell repertoire of mice with cholangitis

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology


title: Fibroblast pyruvate carboxylase is required for collagen production in the tumor microenvironment

city: Chicago

first: Simon

last: Schwoerer

address: 900 E 57th St

institute: University of Chicago

summary: The aberrant production of collagen by fibroblasts is a hallmark of many solid tumors and can influence cancer progression. How fibroblasts produce collagen within tumor microenvironments which are nutrient-poor is not understood. Here, we show that pyruvate carboxylase (PC) activity increases in fibroblasts cultured in a low glutamine environment, and that PC is required for collagen production by tumor-associated fibroblasts in vivo.

overall_design: RNA-sequencing of NIH-3T3 cells expressing a control sgRNA (R26 sg1), PC sg2 or PC sg5, cultured for 48h in DMEM containing 0.2 mM L-glutamine

last: Schwörer

first: Craig

last: Thompson


title: A Cell Type-Specific Atlas of the Inner Ear Transcriptional Response to Acoustic Trauma

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Using the RiboTag approach, we profiled the cell type-specific molecular landscape of the outer hair cells and supporting cells as well as the whole cochlea, both before and after noise trauma (6h and 24h) that induces a permanent hearing loss.

overall_design: 10-week-old PrestinCreERT2;RiboTag;CBA and Sox2CreERT2;RiboTag;CBA mice were subjected to a 105dB SPL noise for 2h. Control animals from both strains were not subjected to noise. For the noise group, mice were euthanized and the cochlear tissue dissected 6 hours or 24 hours following noise exposure. Tissue was homogenized, an aliquot was processed for RNA extraction (input sample representing the whole cochlea) and the rest of the homogenized tissue was processed for RiboTag immunoprecipitation using an HA antibody (IP samples). Both input and IP samples were sequenced.

first: Ronna

last: Hertzano

first: Ran

last: Elkon

first: Beatrice

last: Milon

first: Yang

last: Song


title: T cell repertoire in cholangiocarcinoma lesion and liver of a mouse affected with primary biliary cholangitis

summary: We report in this study the expansion of T cell clonotypes inflitrating both ectopic cholangiocarcinoma (CCA) and liver tissues in a mouse suffering from primary biliary cholangitis (PBC) (Paillet et al, J Exp Med, 2021).   We wondered whether the specificity of T cells found in PBC livers and tumors developing post-PBC might be shared to some extent, comparing them to circulating T cells from the blood (Paillet et al, J Exp Med, 2021). Single-cell TCR sequencing coupled to single-cell RNA sequencing (scTCR/RNA-seq) led to the identification of 8112 distinct clonotypes with a hierarchy of clonotypes enrichment that was significantly higher in PBC livers than in peripheral blood, as well as in CCA compared to blood and liver. Indeed, 12 distinct clonotypes accounted for ~20% of the tumor T cell infiltrate. The overlap of clonotypes between liver and tumor was superior to the overlap between blood and liver, or blood and tumor. Among the 128 clonotypes enriched (i.e. accounting for > 0.1% of total T cells infiltrating the tissue) in the tumor, 25 were also detected and enriched in the liver. Two clonotypes (#2 and #13) were particularly expanded, each representing over 0.5% of the total T cell population in both liver and tumor post-PBC (Paillet et al, J Exp Med, 2021).   Bioinformatic analysis of the scRNA-seq data of total T cells isolated from the liver and tumor of a PBC mouse revealed a net distinction between the transcriptome of T lymphocytes located in the two organs. Only one phenotypic cluster (h) was observed in both liver and tumor. The 25 liver/tumor dual-enriched (>0.1%) clonotypes were spread across few clusters (mostly c, j, k in the tumor; b and i in the liver). Among these clusters, three corresponded to CD8+ T cells (c, i, k) and two corresponded to CD4+ T cells (b, j). They exhibited a preponderant Tc1/Th1 polarization as illustrated by the expression of the enhancers Tbx21 and/or Eomes, and of effector molecules, namely IFNγ for Th1 (b, j), or the cytotoxic markers granzymes B and K for Tc1 (c, i, k) (Paillet et al, J Exp Med, 2021). Interestingly, the two clusters containing most of the enriched CD4+ T cell clonotypes presented a multifunctional signature characterized by the co-expression of IFNγ along with either IL4 (cluster b in the liver) or GzmB and KLRG1 (cluster j in the tumor). Clearly, the two most enriched clonotypes shared between CCA tumor and PBC liver belonged to the category of CD8+ cytotoxic T lymphocytes (clusters c + k in tumor, and cluster i in the liver). Moreover, they showed signs of prolonged activation/exhaustion with the expression of Pdcd1 (encoding PD-1), Lag3, Harvc2/Tim3 and Tigit, yet in a lesser extent than another cluster of CD8+ T cells (tumor cluster f) that contains only little shared clonotypes (Paillet et al, J Exp Med, 2021).

overall_design: Autoimmune primary biliary cholangitis (PBC) was induced in a C57Bl/6 mice as described before: Chang et al., 2014; Wakabayashi et al., 2008. Briefly, mice were immunized with 100 µg of 2-octynoic acid BSA conjugate (2OA-BSA) intraperitoneally (i.p.) in a mix of PBS and complete Freund’s adjuvant (CFA, Sigma-Aldrich) at day 0 and were reboosted at days 14 and 28 with 2OA-BSA and incomplete Freund’s Adjuvant (IFA, Sigma Aldrich). Concomitantly with the two first injections of 2OA-BSA, mice were also injected intravenously (i.v.) with 2 μg of α-galactosylceramide (α-GalCer, Abcam) in PBS.   Thirty-five days after the beginning of cholangitis induction, 3x10^6 SB1-JP4 cells (murine cholangiocarcinoma cells) were resuspended in 100 µL of PBS and injected subcutaneously, under anesthesia with 2.5% isoflurane, in the right flank of C57Bl/6 mice.  For sinlge cell (sc)-RNA-seq and sc-TCR (T cell receptor)-seq, blood was drawn 7 days before and 34 days after PBC induction. One hundred five days after cholangitis induction (equivalent to 70 days after the engraftment of the CCA cells), blood, liver and the CCA tumor were collected from a PBC mouse (Paillet at al, J Exp Med, 2021).

first: Juliette

last: Paillet

first: Jonathan

last: Pol


title: Regulation of PGC-1alpha function by its C-terminal domain

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

overall_design: Refer to individual Series


title: The Xiaogu San Attenuates Pain and Cartilage Damage in Rats with Monosodium Iodoacetate Induced Osteoarthritis

status: Public on Sep 02 2021

city: Nanning

first: Rilan

address: Department of Acupuncture, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine Guangxi Zhuang Autonomous Region, China

department: Department of Acupuncture

summary: Methods: A total of 24 Sprague Dawley rats were evenly and randomly divided into three separate groups including the normal control (NC), OA and XGS groups. MIA (50 μL, 10 mg/mL) was injected into the left knee joints of the rats to induce OA. After 7 days, The rats of XGS group were given XGS (0.45 g) that was externally applied to the left knee joint, were fixed with gauze and continuously administered XGS for 28 days. Morphological changes in tissues and organs were examined using H&E staining. Biochemical indicators were measured using an automatic biochemical analyzer. Inflammatory cytokines were detected using ELISA kits and immunohistochemistry. RNA-based high-throughput sequencing (RNA-seq) was performed to detect differential expression of mRNAs in normal and MIA–induced OA rats.

overall_design: Detection of gene differential expression in cartilage tissues of normal mice and the monosodium iodoacetate induced osteoarthritis rat.

first: Xiaoyun

last: Zhang

first: Zilong

last: Liao

first: Ying

last: Zhu

first: Yueping

first: Jianhang

last: Liu

first: Xia


title: Microvessels support engraftment and functionality of human islets and hESC-derived pancreatic progenitors in diabetes models

city: Toronto

first: Yasaman

last: Aghazadeh

state: ON

address: 101, College St

country: Canada

institute: McEwen Stem Cell Institute

summary: Single nuclei sequencing of grafts developed 14 weeks post transplantation of human embryonic stem cell derived pancreatic progenitors alone (PP) or with rat adipose derived microvessels (PPMV) into the subcutaneous pocket of diabetic (STZ-induced) Scid-beige mice.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
- hESC H1 line was differentiated to stage 4 pancreatic progenitors and embedded in collagen hydrogels alone (PP) or with microvessel fragments (PPMV) freshly isolated from epididymal fat of Sprague-Dawley rats.
- The PP and PPMV containing hydrogels were transplanted subcutaneously into STZ-induced diabetic Scid-beige male mice.
- 14 weeks post-transplantation the grafts were retrieved from 3 mice,  transplanted with independent PP differentiations and 3 mice transplanted with matching PP and independent MV isolations.
- The 3 corresponding grafts were merged to generate 1 PP and 1 PPMV sample.
- The two samples were subjected to nuclei isolation and single nuclei sequencing.

first: Frankie

last: Poon

first: Farida

last: Sarangi

first: Frances

middle: T

last: Wong

first: Safwat

last: Khan

first: Xuetao

last: Sun

first: Rupal

last: Hatkar

first: Brian

last: Cox

first: Sara

last: Nunes

first: Maria

last: Nostro


title: Combinatorial effects of amyloid beta and cytokines on primary human astrocytes

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

institute: University of Colorado Boulder

summary: Natural functions of the amyloid beta (Aβ) peptide are incompletely understood. We studied the effects nanomolar concentrations of Aβ in combination with known pro-inflammatory cytokines on primary human astrocytes, a cell type increasingly implicated in neurodegeneration. RNA-seq was performed to profile changes in astrocyte transcriptomes in response to high and low concentration Aβ alone, as well as low concentration Aβ and/or the cytokines C1q, TNF-α and IL-1α. Experiments were performed in triplicate within cells from one donor/supplier, and in triplicate using cells from three different donors/suppliers (to identify conserved biological responses).

overall_design: PolyA RNA isolated and purified from flash-frozen primary human astrocytes treated with high (1 µM) or low (10 nM) dose Aβ and/or 10 nm cytokines C1q, TNF-α or IL-1α.


title: Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: We charted the global changes in the epigenetic landscape, including DNA methylation and chromatin accessibility, during neural crest differentiation into melanophores and iridophores in zebrafish to identify epigenetic determinants shaping cell type-specific gene expression. Motif enrichment in the epigenetically dynamic regions revealed putative transcription factors that might be responsible for driving pigment cell identity. Through this effort, in the relatively uncharacterized iridophores, we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway.

overall_design: ATAC-seq, RNA-Seq, WGBS were generated for 15 somite NCC, 24 hpf NCC, 4-5 dpf Melanophore, and 4-5 dpf Iridophore cells from zebrafish.

first: Hyo

last: Jang

first: Yujie

last: Chen

first: Ting

last: Wang


title: Transcriptomic and epigenetic analysis of adipose tissue in Cushing Syndrome [mouse]

city: Barcelona

first: Mar

last: Gonzalez-Ramirez

address: C/ Dr Aiguader 88

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Chronic glucocorticoids (GCs) exposure, resulting from endogenous Cushing Syndrome (CS) or prescribed GCs therapy, is associated with a high cardiometabolic burden. Moreover, previous studies have reported persistence of metabolic syndrome features after remission of hypercortisolism and in particular in visceral adipose tissue (VAT). Thus, in this study we want to analyze the transcriptomic alterations in VAT during active and cured CS and correlate these persistent gene expression changes with histone modifications induced by GCs.

overall_design: RNA-seq (20 samples) and ChIP-seq (26 samples) of mouse visceral adipose tissue. CORT_5w means mouse model of active Cushing's syndrome, CORT_15w means recovered mice and VEH means controls.

first: Guillermo

last: Garcia

first: Felicia

last: Hanzu

first: Pedro

last: Vizan


title: Transcriptomic and epigenetic analysis of adipose tissue in Cushing Syndrome [human]

summary: Chronic glucocorticoids (GCs) exposure, resulting from endogenous Cushing Syndrome (CS) or prescribed GCs therapy, is associated with a high cardiometabolic burden.  Moreover, previous studies have reported persistence of metabolic syndrome features after remission of hypercortisolism and in particular in visceral adipose tissue (VAT). Thus, in this study we want to analyze the transcriptomic alterations in VAT during active and cured CS and correlate these persistent gene expression changes with changes in histone modifications induced by GCs.

overall_design: RNA-seq (18 samples) and ChIP-seq (26 samples) of human visceral adipose tissue. CS means human patients of Cushing and CTL controls.


title: The potent and selective RIPK2 inhibitor BI 706039 improves intestinal   inflammation in the TRUC mouse model of Inflammatory Bowel   Disease

city: Ridgefield

first: Li

state: Connecticut

address: PO Box 368

institute: Boehringer Ingelheim Pharmaceuticals, Inc.

summary: Mouse distal colons were preserved snap frozen in RNAlater, homogenized in Trizol Reagent. A total of 100 ng of RNA per sample were used for   hybridization and run on the XT_PGX_MmV2_Inflammation_CSO 248 gene panel for multiplexed semi-quantitative analysis of colonic RNA markers of inflammation.

overall_design: Gene expression of TRUC mice treated with the anti-p40 monoclonal antibody and the BI 706039, and their relative controls, were analyzed from the customized 248 mouse gene Nanostring panel. The raw counts from Ncounter were normalized to housekeeping gene,   GAPDH, then log2 transformed, followed by non-parametric T-test with homes-Bonferroni  adjustment. T


title: Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (SNP array)

city: Memphis

first: Jared

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Dynamic changes to the epigenome are essential regulators of B cell differentiation and, when perturbed, can lead to cancer. We compared three types of mature B cell lymphoma/leukemia (BCL) and normal lymphocytes to identify common and distinct epigenetic perturbations that promote oncogenesis. Purified malignant B cells from 52 patients (18 Follicular, 11 Diffuse Large B Cell, 23 Chronic Lymphocytic Lymphomas) and normal B cell subsets from 28 donor tonsils were subjected to chromatin immunoprecipitation and sequencing (ChIP-seq) for H3K4me1, H3K9/14ac, and H3K27ac; FAIRE-seq for open chromatin; RNA-seq; and genome copy number arrays. We identified a novel super enhancer (SE) connected to the aberrant expression of FCMR and PIGR in multiple BCL subtypes, which may drive the tissue-specific expression of the two immunoglobulin receptor genes. These integrative studies also revealed that loss of normal B cell SEs in BCL was associated with significant reduction in linked gene expression, the greatest impact among regulatory elements. Downregulation of crucial B cell transcription factors (TF) and tumor suppressors was consistent across BCL subtypes and linked to significantly diminished or absent active chromatin marks in adjacent SEs. These BCL-repressed SEs are enriched in binding sites for the same suppressed TFs that they regulate, suggesting transcriptional regulatory feedback loops for these key B cell identity genes. In sum, this study defined common alterations in the regulomes of mature B cell leukemias and lymphomas and implicate SEs as important hubs of tumor suppressing transcriptional feedback loops that are perturbed in B cell cancer.

overall_design: Affymetrix Genome_Wide SNP6 arrays were performed according to the manufacturer's directions on DNA extracted from sorted B cells isolated from healthy tonsils, lymph nodes of follicular lymphoma or diffuse large B cell lymphoma patients, and peripheral blood of chronic lymphocytic leukemia patients.

first: Jacqueline

last: Payton


title: Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (RNA array)

overall_design: Gene expression analysis was performed for chronic lymphocytic leukemia and tonsil-derived germinal center B cells using Affymetrix Human Gene 2.0 ST.


title: Defining the genetic and immune landscape of precursor myeloma progression with single-cell sequencing

first: Danielle

last: Croucher

state: Ontario

address: 101 College Street

department: Medical Biophysics

institute: University of Toronto

summary: Multiple Myeloma is universally preceded by a pre-malignant state, however, the genetic and immune mechanisms associated with transformation are incompletely understood thus hindering development of preventative treatment strategies. Using single-cell RNA sequencing, we profiled the transcriptomes of tumor and immune microenvironment cells derived from transgenic mice whose disease spanned the myeloma progression spectrum. This work in turn provides unique and previously unappreciated insight into the biology of precursor disease progression.

overall_design: BM were extracted from hind-leg bones of VkMYC/non-transgenic control mice, dissociated into a single cell suspension using mechanical disruption (syringe) and RBC's lysed. Single-cell RNA-sequencing libraries were then generated using the 10x Genomics Chromium Single Cell 3' Solution V2 protocol

first: Trevor

last: Pugh


title: Epithelial XBP1 coordinates TP53-driven DNA damage responses and suppression of intestinal carcinogenesis

status: Public on Sep 01 2021

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

summary: We assessed the impact of intestinal epithelial XBP1 in coordinating epithelial DNA damage responses. As our data revealed that low XBP1 activity in the context of chronic DNA damage is associated with both reduced p53 pathway activity and formation of tumors with metastaic potential in-vivo, we performed RNA sequencing of intestinal organoids (H2b/Xbp1fl/fl, H2bΔIEC, H2b/Xbp1ΔIEC, H2b/p53∆IEC) to identify a transcriptional program downstream of p53 that drives the tumorigenic in-vivo phenotype.

overall_design: Examination of Differentially Expressed Genes between small intestinal organoids derived from healthy tissue of 8-12 weeks old mice (n = 3) of indicated genotypes.

first: Lina

last: Welz

first: Konrad

last: Aden

first: Philip

last: Rosenstiel


title: The Enhancer Landscape during Early Neocortical Development

city: Stanford

first: Gill

last: Bejerano

address: 279 Campus Drive West (MC 5329)

department: Developmental Biology

institute: Stanford University

summary: Genetic studies have identified a core set of transcription factors and target genes that control the development of the neocortex, the region of the human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream and downstream genes, and the enhancers that mediate all these interactions remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate enhancers active in the dorsal cerebral wall of embryonic day 14.5 (E14.5) mice. Over 95% of the peaks we measure are conserved to human. Eight of ten (80%) candidates tested using mouse transgenesis drive activity in restricted laminar patterns within the neocortex. GREAT based computational analysis reveals highly significant correlation with genes expressed at E14.5 in key areas for neocortex development, and allows the grouping of enhancers by known biological functions and pathways for further studies. We find that multiple genes are flanked by dozens of candidate enhancers each, including well-known key neocortical genes as well as suspected and novel genes. Nearly a quarter of our candidate enhancers are conserved well beyond mammals. Human and zebrafish regions orthologous to our candidate enhancers are shown to most often function in other aspects of central nervous system development. Finally, we find strong evidence that specific interspersed repeat families have contributed potentially key developmental enhancers via co-option. Our analysis expands the methodologies available for extracting the richness of information found in genome-wide functional maps.

overall_design: Examination of enhancer-associated co-activator protein p300 in mouse E14.5 neocortex.

first: James

last: Notwell


title: Neoadjuvant talimogene laherparepvec plus surgery vs surgery alone for resectable stage IIIB-IVM1a melanoma

city: Thousand Oaks

first: Abraham

last: Anderson

address: 1 amgen center drive

institute: Amgen Inc.

summary:
This study was intended to describe transcriptional changes after TVEC treatment among immune related genes.
Tumor gene expression analysis (nanostring, pan cancer immmune profiling panel) was performed to evaluate tumor inflammation status at baseline (in TVEC and control arms) and after treatment with TVEC.  Objectives aimed to improve understanding of TVEC therapeutic mechanism of action, included assessment of baseline tumor inflammation status and assessment of change in tumor inflammation status.

overall_design: This data set consists of immune-related gene expression profiles of 135 melanoma biopsies, derived from 79 patients with resectable stage IIIB-IVM1a melanoma who were randomized to receive T-VEC followed by surgery (Arm 1) or surgery alone (Arm 2).  Two timepoints in Arm 1 (baseline and after T-VEC treatment) and one timepoint in Arm 2 (baseline) were assayed. RNA was extracted from melanoma tumor biopsies and resected tumor tissue for gene expression analysis. Formalin-fixed paraffin-embedded (FFPE) curls were deparaffinized using 100% xylene. Deparaffinized samples were washed with 100% ethanol and then dried at 37°C. RNA was extracted from tissues using the QIAgen RNeasy FFPE kit (QIAgen, catalog #73504) on the QIAcube robotic workstation. Nucleic acid concentrations were determined using the NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific). Relative gene expression was evaluated on the NanoString nCounter platform and the starting material was 300 ng of total RNA using the PanCancer Immune Profiling Panel.

first: Reinhard

last: Dummer

first: David

last: Gyorki

first: John

last: Hyngstrom

first: Adam

last: Berger

first: Robert

last: Conry

first: Lev

last: Demidov

first: Anjali

last: Sharma

first: Sheryl

last: Treichel

first: Kevin

last: Gorski

first: Edward

last: Chan

first: Mark

last: Faries

first: Merrick

middle: I

last: Ross


title: NanoString Analysis of Gene Expression in B16.F10 Tumors Treated with the cGAS Activator, NanoISD

city: Nashville

last: Wilson

state: TN

address: 2400 Highland Ave., 107 Olin Hall

institute: Vanderbilt University

summary: Characterization of the immune profile (i.e. tumor RNA) of a murine B16.F10 tumor 6 hours post a single 100 µL intratumoral injection of 2 µg NanoISD, Free D-PDB at an equivalent dose, or PBS.

overall_design: 12 biological samples are analyzed, comprising 3 treatment groups (i.e. PBS, D-PDB, and NanoISD), each with 4 biological replicates. PBS and D-PDB represent the negative control and vehicle control, respectively. Each biologial sample was evaluated for the mRNA expression of 43 myeloid-related genes along with 5 house-keeping genes (i.e. Gapdh, Gusb, Hdac3, Rpl19, and Tbp)

first: Kyle

last: Garland

first: Ann

last: Hanna

first: Justin

last: Balko


title: Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (RNA-seq)

first: Jared

last: Andrews

overall_design: 2x100 bp paired-end RNA-sequencing was performed on rRNA-depleted RNA libraries generated from sorted CD19+ B cells from primary peripherial blood or lymph node biopsies of chronic lymphocytic leukemia, follicular lymphoma, and diffuse large b cell patients or donor tonsils.

first: Jacqueline

last: Payton


title: Integrated Transcriptome and Multiple Activated Pathways in Endometrial Cancer

city: Jinan

first: Weidong

last: Zhao

address: Shandong University, Jinan, Shandong, 250012, China.

institute: Anhui Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong

summary: Because the incidence of endometrial cancer is notably increasing worldwide, it has become the leading gynecologic cancer in the United States. Standard treatment results in the loss of reproductive function in women of childbearing age. Furthermore, advanced cancer stages are associated with poor overall survival. The aim of this study was to explore the abnormal expression profile of genes during the development of endometrial cancer, which is essential to provide a better understanding of the mechanisms involved. Five pairs of endometrial cancer tissues and normal endometrial tissues were subjected to next-generation transcriptome sequencing technology. Quantitative real-time PCR (RT-qPCR) was performed to validate the expression profile of key differentially expressed genes (2.0-fold change, adj. p < 0.05) (DEGs) identified in the RNA-seq result. GO and KEGG pathways were used for bioinformatic analyses. The transcriptomic sequencing results showed 1153 DEGs, including 673 upregulated and 480 downregulated genes, in the EC specimens. Decreased expression of ID1, IGF1, GDF7, SMAD9, TGF-beta and WNT4, as well as GDF5, INHBA and ERBB4 overexpression, were confirmed in EC using RT-qPCR. Additionally, EC tissue exhibited marked enrichment in genes promoting cellular adhesion, proliferation, migration and plasma membrane. KEGG analysis revealed changes in various pathways, such as the TGF-beta, PI3K-Akt, Wnt, and estrogen pathways. Our data describe the molecular events involved in the pathogenesis of EC, which may be potential diagnostic markers and targets of therapeutic interventions.

overall_design: Total RNA from 5 pairs of cancerous and normal endometrial tissues pooled,  and reverse transcribed into cDNAs.

first: Qi

last: Jin

first: Xiaohua

last: Jiang

first: Bo

last: Xu


title: Loss of Endothelial HIF-Prolyl hydroxylase 2 (PHD2) Induces Cardiac Hypertrophy and Fibrosis

city: St. Louis

first: Zhiyu

last: Dai

address: 4960 Childrens Place

summary: Total RNA was isolated from left ventricular tissues from wild type, Egln1Tie2Cre, and Egln1/Hif2aTie2Cre mice for RNA-seq

overall_design: Left ventricular tissues from 3 wild type, 3 Egln1Tie2Cre, and 3 Egln1/Hif2aTie2Cre mice were isolated. A similar amount of RNA was pooled from each genotype strain.  RNA-seq was performed.

first: Youyang


title: Key Super Enhancers Drive Tumor-Suppressing Transcription Feedback Programs in Mature B Cell Cancers (ChIP-seq, FAIRE-seq)

overall_design: 42 or 50 bp single-end ChIP-sequencing was performed on DNA libraries generated from sorted CD19+ B cells from primary peripherial blood or lymph node biopsies of chronic lymphocytic leukemia, follicular lymphoma, and diffuse large B cell patients or donor tonsils.


title: Defining tumor-associated vascular heterogeneity in pediatric high-grade and diffuse midline gliomas

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

summary: The blood-brain barrier (BBB) plays important roles in brain tumor pathogenesis and treatment response, yet our understanding of its function and heterogeneity within or across brain tumor types remains poorly characterized. Here we analyze the neurovascular unit (NVU) of pediatric high-grade glioma (pHGG) and diffuse midline glioma (DMG) using patient derived xenografts and natively forming glioma mouse models. We show tumor-associated vascular differences between these glioma subtypes, and parallels between PDX and mouse model systems, with DMG models maintaining a more normal vascular architecture, BBB function and endothelial transcriptional program relative to pHGG models. Unlike prior work in angiogenic brain tumors, we find that expression of secreted Wnt antagonists do not alter the tumor-associated vascular phenotype in DMG tumor models. Together, these findings highlight vascular heterogeneity between pHGG and DMG and differences in their response to alterations in developmental BBB signals that may participate in driving these pathological differences.

overall_design: Three to four biological replicates were analyzed for each of 5 conditions (three normal brain conditions and two brain tumor conditions; three-four samples per condition).

first: Xin

last: Wei


title: Single cell RNA-seq of liver cells from B6J mice fed a chow or a high-fat-and-high-sucrose diet

city: Dallas

first: Simeng

last: Wang

address: 5323 Harry Hines

institute: UT Southwestern Medical Center

summary: Cannabinoid receptor-1 (CB-1) blockage in brain is responsible for weight loss, many of the metabolic benefits associated with CB-1 blockade have been attributed to inhibition of CB-1 signaling in the periphery. We produced mice that lacked CB-1 receptors in hepatocytes or stellate cells to determine if CB-1 signaling contributes to the development of NAFLD or liver fibrosis. Deletion of CB-1 receptors in hepatocytes did not alter the development of NAFLD in mice fed a high sucrose high fat diet (HSD) or high fat diet (HFD). Similarly, deletion of CB-1 deletion specifically in stellate cells also did not prevent the development of NAFLD in mice fed the HFD nor did it protect mice for carbon tetrachloride-induced fibrosis. To determine if a small population of cells in liver express CB-1 at high levels either before and/or after HSD feeding, here we performed single cell RNA-sequencing of livers from wild-type mice fed chow or a HSD for 17 weeks and analyzed CB-1 expression. Single-cell sequencing of hepatocytes and stellate cells reveals low Cnr1 expression in livers of mice fed a chow or HSD. Combined, these studies do not support a direct role for hepatocyte or stellate cell CB-1 signaling in the development of NAFLD or liver fibrosis.

overall_design: Two pairs of mice (one pair fed a chow, one pair fed a high-fat-and-high-sucrose diet for 17 weeks) were used for single cell sequencing. For each pair, one mouse was perfused for hepatocyte preparation, and the other for stellate cells preparation. All cells were collected as single cell suspension.

first: Jay

middle: D

last: Horton


title: Epithelial Wnt secretion drives the progression of inflammation-induced colon carcinoma

city: Ankara

first: Bahar

last: Degirmenci

address: Faculty of Science, B Building Room 241

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

summary: Colon cancer is initiated by stem cells that escape the strict control. In most colon tumors this process is driven through aberrant activation of Wnt signaling by mutations that occur in components acting downstream of the receptor complex and that unfetter tumor cells from the need for Wnt ligands. Here we describe a special type of colon cancer that does not depend on mutated core components of the Wnt pathway. Genetically blocking Wnt secretion from epithelial cells of such tumors results in apoptosis, reduced expression of colon cancer markers, followed by enhanced tumor differentiation. In contrast to the normal colonic epithelium, such tumor cells auto-secrete Wnt ligands to maintain their uncontrolled proliferative behavior. In humans, we determined certain cases of colon cancers in which the Wnt pathway is hyperactive, but not through mutations in its core components. Our findings illuminate the path in therapy to find further subtypes of Wnt- dependent colon cancer, that might be responsive to Wnt secretion inhibitors.

overall_design: Examination of gene expression of wild type (WT) and Villin-Wls cKO tumors.

first: Cansu

last: Dincer

first: H

last: Demirel

first: Linda

last: Berkova

first: Andreas

last: Moor

first: Abdullah

last: Kahraman

first: George

last: Hausmann

first: Michel

last: Aguet

first: Nurcan

last: Tuncbag

first: Tomas

last: Valenta

first: Konrad

last: Basler


title: Analysis of transriptomic dysregulation upon neonatal and adult downregulation of Taf1 isoforms in rodents

city: New York

first: Michelle

last: Ehrlich

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: We report the gene expression alterations observed in the striatum of 4 months old mice that received neonatal intracerebroventricular injection with specifically designed AAV1miRNA targeting nTaf1 and cnTaf or the scramble control

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Examination of gene expression alteration in the striatum of the mice injected with nTaf1, or cnTaf1 versus the scramble control

first: Maria-Daniela

last: Cirnaru

first: Jordi

last: Creus-Muncunill

first: Shareen

last: Nelson

first: Travis

last: Lewis

first: Jaime

last: Watson

first: Lisa

last: Ellerby

first: Pedro

last: Gonzalez-Alegre


title: 3D spheroid human placenta-derived mesenchymal stem cells enhances anti-inflammatory response and trophic-factors secretion

city: Beijing

first: Junhao

last: Deng

state: Beijing

address: Fuxing Road,  Beijing, 100853, People’s Republic of China.

institute: Chinese PLA General Hospital

summary: We found significant difference between the 3D-spheroid cultured- and conventionally cultured mesenchymal stem cells (3D MSCs and 2D MSCs) in terms of anti-inflammatory response and ability to secrete trophic factors, implying that 3D MSCs may better improve the tissue repair and promote functional recovery. Next-generation sequencing has revolutionized system-based analysis of cellular pathways. The aims of this study are to compare the transcriptome profile between the 3D-spheroid cultured- and conventionally cultured mesenchymal stem cells (3D MSCs and 2D MSCs).

overall_design: Human placenta derived MSCs (HuMSCs) were isolated and cultured for three passages. Then they were cultured as 3D MSCs and 2D MSCs, respectively. Two types of cells were collected and prepared for the RNA-sequencing.

first: Miao

last: Li

first: Ming

first: Zhirui

first: Licheng

last: Zhang

first: Peifu

last: Tang


title: Integration of transcriptomic and epigenomic analyses uncovered Lrrc15 as a potential contributing factor to cartilage damage in osteoarthritis

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

summary:
Objective: We used the destabilization of the medial meniscus (DMM) model to identify temporal changes in DNA methylation patterns associated with structural and transcriptomic changes in cartilage during osteoarthritis (OA) progression.
Methods: RNA sequencing (RNAseq) and Reduced Representation Oxidative Bisulfite Sequencing (RRoxBS) analyses were done in total RNA and DNA obtained from micro-dissected cartilage at 4 and 12 weeks after DMM surgery. Murine and human primary chondrocytes were used to evaluate the cytokine- and methylation-dependent changes in the expression of Lrrc15, and its contribution to IL-1beta-induced changes in chondrocytes.
Results: We identified time-dependent alterations in epigenomic patterns in cartilage after DMM, with significant changes in 5mC and 5hmC methylation comparing samples retrieved at 4 and 12 weeks after surgery. Integration of RNAseq and RRoxBS datasets identified Lrrc15 as a hypomethylated gene with  increased expression at 4 weeks after surgery. We confirmed LRRC15 immunostaining in OA cartilage, and experiments in human and murine primary chondrocytes showed that the expression of Lrrc15 is DNA methylation-dependent and induced by IL1beta and TNFalfa in vitro. Knockdown experiments showed that Lrrc15 contributes to the IL1beta-driven expression of catabolic genes relevant to OA, including Mmp13.
Significance:  Our integrative analyses showed that the structural progression of OA is accompanied by transcriptomic and dynamic epigenomic changes in articular cartilage. We found that Lrrc15 is differentially methylated and expressed in OA cartilage, and that it may contribute to the cytokine-driven responses of OA chondrocytes.  A better understanding of the role of Lrrc15 in cartilage homeostasis and osteoarthritis may help us uncover targets with therapeutic potential.

overall_design: Knee articular cartilage was harvested from DMM-operated and contralateral/non-operated legs at 4 and 12 weeks post-surgery. Cartilage samples were used for RNA  or DNA isolation. Total RNA was used for RNA-seq, and DNA was used for Reduced Representation Oxidative Bisulfite Sequencing (RRoxBS) at the Epigenomics Core at Weill Cornell Medical College.  CpG sites in the resulting RRoxBS data were interrogated for methylation patterns and differential methylation and hydroxymethylation using methylKit. The differential methylation data was queried for differentially methylated regions using eDMR. RNA-Seq reads passing Illumina’s purity filter were adapter trimmed using FLEXBAR barcode and adapter processing tool. The trimmed reads were aligned to the Gencode mm10/ GRC38.p3 build of the mouse genome using STAR aligner with default parameters. Read counts for RefSeq (NCBI) transcripts were then quantified from the alignments using the feature Counts software package. Significant differential expression (adjusted p-value < 0.05) was assessed between the read counts for the control and DMM sample groups using the DESeq2 R Bioconductor package. Gene Ontology (GO) enrichment analysis for Biological Processes and Molecular Functions was performed for differentially expressed genes and genes associated with differentially methylated regions using the clusterProfiler Biocondutor R package.

first: Purva

last: Singh

first: Mengying

last: Wang

first: Samantha

last: Lessard

first: Tania

last: Pannellini

first: Camila

last: Carballo

first: Scott

last: Rodeo

first: Mary

last: Goldring

first: Miguel

last: Otero


title: Genetic analysis argues for a coactivator function for the Saccharomyces cerevisiae Tup1 corepressor [ChIP-Seq]

city: Salt Lake City

first: David

last: Stillman

state: Utah

address: 15 N Medical Drive East, EEJMRB

department: Pathology

institute: University of Utah

summary: The Tup1-Cyc8 corepressor complex of Saccharomyces cerevisiae is recruited to promoters by DNA-binding proteins to repress transcription of genes, including the a-specific mating type genes. We report here a tup1(S649F) mutant that displays mating irregularities similar to a tup1 null and an a-predominant growth defect. RNA-Seq and ChIP-Seq were used to analyze gene expression and Tup1 binding changes in mutant vs. wild-type in both a and a cells. Increased Tup1(S649F) binding tended to occur upstream of upregulated genes, whereas locations with decreased binding usually did not show changes in gene expression, suggesting this mutant not only loses corepressor function but also behaves as a coactivator. Based upon studies demonstrating a dual role of Tup1 in both repression and activation, we postulate that the coactivator function of Tup1(S649F) results from diminished interaction with repressor proteins, including a2. We also found that large changes in mating type-specific gene expression between a and a or between mutant and wild-type were not easily explained by the range of Tup1 binding levels within their promoters, as predicted by the classic model of a-specific gene repression by Tup1. Most surprisingly, we observed Tup1 binding upstream of the a-specific gene MFA2 and the a-specific gene MF(ALPHA)1 in cells in which each gene was expressed rather than repressed. These results, combined with identification of additional mating related genes upregulated in the tup1(S649F) a strain, illustrate that the role of Tup1 in distinguishing mating types in yeast appears to be both more comprehensive and more nuanced than previously appreciated.

overall_design: Genomic localization of Tup1-V5 and Tup1(S649F)-V5 was determined by chromatin immunoprecipitation from cross-linked S. cerevisiae cells, followed by Illumina paired-end sequencing. Three replicate ChIPs and a single input control are included for each strain.

first: Emily

last: Parnell

first: Timothy


title: H3K27ac ChIP-seq on mouse adrenal gland at different ages and in both sexes

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

institute: IPMC

summary: This study was performed to identify active enhancers (as defined by H3K27ac enrichment) in the mouse adrenal gland according to age and sex (in an age-matched fashion)

overall_design: 7 pooled adrenal gland samples were analyzed: E18.5 (30 glands), P1 females (22 glands), P1 males (22 glands), P2 weeks females (12 glands), P2 weeks males (12 glands), P12 weeks females (6 glands), P12 weeks males (6 glands)

last: Lalli


title: Genetic analysis argues for a coactivator function for the Saccharomyces cerevisiae Tup1 corepressor

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

overall_design: Refer to individual Series


title: Induced neural cells from human dental pulp ameliorate functional recovery in a murine model of cerebral infarction

city: Tsukuba

first: Aiki

last: Marushima

state: Ibaraki

address: 1-1-1, Tennodai

department: Department of Neurosurgery

institute: University of Tsukuba

summary: Human mesenchymal stem cells are a promising cell source for the treatment of stroke. Their primary mechanism of action occurs via neuroprotective effects by trophic factors, anti-inflammatory effects, and immunomodulation. However, the regeneration of damaged neuronal networks by cell transplantation remains still challenging. We hypothesized that cells induced to neural lineages would fit the niche, replace the lesion, and be more effective in improving symptoms compared with stem cells themselves. We investigated the characteristics of induced neural cells from human dental pulp tissue and compared the transplantation effects between these induced neural cells and uninduced dental pulp stem cells. Induced neural cells or dental pulp stem cells were intracerebrally transplanted 5 days after cerebral infarction induced by permanent middle cerebral artery occlusion in immunodeficient mice. Effects on functional recovery were also assessed through behavior testing. We used immunohistochemistry and neuron tracing to analyze the differentiation, axonal extension, and connectivity of transplanted cells to the host’s neural circuit. Transplantation of induced neural cells from human dental pulp ameliorated functional recovery after cerebral infarction compared with dental pulp stem cells. The induced neural cells comprised both neurons and glia and expressed functional voltage, and they were more related to neurogenesis in terms of transcriptomics. Induced neural cells had a higher viability than did dental pulp stem cells in hypoxic culture. We showed that induced neural cells from dental pulp tissue offer a novel therapeutic approach for recovery after cerebral infarction.

overall_design: Expression profiling of dental pulp stem cells and induced neural cells derived from dental pulp.

first: Hideaki

last: Matsumura

first: Hiroshi

last: Ishikawa

first: Junko

last: Toyomura

first: Akihiro

last: Ohyama

first: Miho

last: Watanabe

first: Shohei

last: Takaoka

first: Hiroki

last: Bukawa

first: Akira

first: Yuji

last: Matsumaru

first: Eiichi


title: Cyclic di-GMP Regulates Shigella flexneri Pathogenesis

city: Kalamazoo

first: Ben

middle: James

last: Koestler

state: MI

address: 1903 West Michigan Avenue, 3119 Wood Hall

department: Biological Sciences

institute: Western Michigan University

summary: We compared the transcriptomes of S. flexneri strains expressing the diguanylate cyclase VCA0956 (derived from V. cholerae)

overall_design: S. flexneri 2457T containing the plasmid pVCA0956. Strains were grown with (induced) or without (uninduced) 100 µM IPTG.

first: Benjamin

first: Ruchi

last: Ojha


title: Targeting TREM2 on tumor associated macrophages enhances efficacious immunotherapy

city: South San Francisco

first: Venkataraman

last: Sriram

state: California

address: 2 Tower Place

institute: Pionyr Immunotherapeutics

summary: Singe-cell transcriptomic profiling of immune cells from human tumors and the CT26 murine syngeneic tumor model

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 10X Genomics single-cell RNA sequencing of CD45+ sorted immune cells from 10 human tumors and 1 murine syngenic model

first: Mikhail

last: Binnewies


title: Genetic analysis argues for a coactivator function for the Saccharomyces cerevisiae Tup1 corepressor [RNA-Seq]

first: David

last: Stillman

overall_design: Gene expression in wild-type and tup1(S649F) mutants of a and a mating types was determined by isolation of RNA from logarithmically growing S. cerevisiae cells, followed by Illumina paired-end sequencing. Three replicate RNA samples are included for each strain.

first: Emily

first: Timothy


title: RNA-seq on mouse adrenal gland at different ages and in both sexes

first: Enzo

summary: This study was performed to analyze differentai gene expression profiles in the mouse adrenal gland according to age and sex (in an age-matched fashion)

overall_design: 7 pooled adrenal gland samples were analyzed: E18.5 (40 glands), P1 males (16 glands), P1 females (22 glands), P2 weeks males (6 glands), P2 weeks females (6 glands), P12 weeks males (4 glands), P12 weeks females (4 glands)

first: Lalli

last: Enzo


title: Single cell RNA-sequencing of Bardet Biedl Syndrome iPSC-derived hypothalamic neurons

first: Liheng

last: Wang

address: 1150 Saint Nicholas Avenue, Room 234

department: Department of Medicine

institute: Columbia University Medical Center

summary: Bardet-Biedl Syndrome (BBS) is a rare autosomal recessive disorder caused by mutations in genes encoding components of the primary cilium and characterized by hyperphagic obesity. We developed a cellular model of BBS using induced pluripotent stem cell (iPSCs)-derived hypothalamic arcuate-like neurons. Single-cell RNA sequencing of iPSC-derived hypothalamic neurons from BBS1M390R and isogenic control identified affected cell subpopulations and several down-regulated pathways in BBS1 hypomorphic neurons, including axon guidance, insulin signaling and cAMP pathway.

overall_design: Day 32 iPSC-derived hypothalamic neurons from BBS1B (BBS1M390R) and its isogenic control line (c-BBS1B) were analyzed by scRNA-seq.

first: Yang

last: Liu

first: Deyou

last: Zheng

first: Rudolph

middle: L

last: Leibel


title: Nitrate regulates maize root transcriptome through nitric oxide dependent and independent mechanisms

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

summary: Maize root responds to nitrate by modulating its development thorough the coordinated action of many players, interacting one each other. Among them, nitric oxide is produced in primary root of previously deprived seedlings early after the nitrate provision, thus inducing root elongation. In this study, a molecular untargeted approach was applied to discriminate the signaling and physiological pathways regulated by nitrate through nitric oxide from those regulated by nitrate itself of by further downstream factors.  To this aim an RNA-sequencing approach was applied to discover the main molecular signatures distinguishing the response of maize root to nitrate according to their dependency, or independency on nitric oxide. A set of subsequent detailed functional annotation tools (Gene Ontology enrichment, MapMan, KEGG reconstruction pathway, transcription factors detection) were used to try to gain further information on the importance of this molecule in the regulation of the maize transcriptional response to nitrate. Besides, the lateral root density was measured both in the presence of nitrate and in the presence of nitrate plus cPTIO, a specific NO scavenger, and compared to that observed for N-depleted roots.   Our results led to identify six clusters of transcripts according to their responsiveness to nitric oxide and to their regulation by nitrate provision. In general, common and specific features for the six clusters were identified allowing to discompose the overall root response to nitrate according to its dependency on nitric oxide.

overall_design: Illumina RNA-Seq analysis of maize root apexes samples collected from seedlings grown for 24 h in nutrient solution supplied with 1mM NO3- or 1 mM NO3- plus 1 mM cPTIO, compared to negative controls grown in a N-deprived nutrient solution. 3 days old maize B73 inbreed seedlings were treated for 24 h prior to roots collection and RNA extraction.  3 biological replicates per condition were produced, each composed by 10-15 plants.

first: Laura

last: Ravazzolo

first: Sara

last: Trevisan

first: Silvia

last: Iori

first: Mario

last: Malagoli

last: Quaggiotti


title: FNDC-1-Mediated Mitophagy and ATFS-1 Coordinate to Protect Against Hypoxia-Reoxygenation

city: Rush

first: keith

last: nehrke

address: 1514 Rush Scottsville Rd

institute: University of Rochester Medical Center

summary: Mitochondrial Quality Control (MQC) balances organelle adaptation and elimination, and mechanistic crosstalk between the underlying molecular processes impacts subsequent stress outcomes. FUN14 Domain Containing 1 (FUNDC1) is a mammalian mitophagy receptor that responds to hypoxia-reoxygenation (HR) stress. Here, we provide evidence that FNDC-1 is the C. elegans ortholog of FUNDC1, and that its loss protects against injury in a worm model of HR. This protection depends upon ATFS-1, a transcription factor that is central to the mitochondrial unfolded protein response (UPRmt). Global mRNA and metabolite profiling suggest that atfs-1 dependent stress responses and metabolic remodeling occur in response to the loss of fndc-1. These data support a role for FNDC-1 in non-hypoxic MQC, and further suggest that these changes are prophylactic in relation to subsequent HR. Our results highlight functional coordination between mitochondrial adaptation and elimination that organizes stress responses and metabolic rewiring to protect against HR injury.

overall_design: 3 strains were profiled, wild type (N2), fndc-1(rny14) and atfs-1(tm4525);fndc-1(rny14), with 5 biological samples of each strain, for a total of 15 samples. Synchronized populations were grown to day 1 of adulthood, then harvested for RNA.

first: Keith

last: Nehrke

first: Yunki

last: Lim


title: Exercise plasma dampens brain inflammation via clusterin and boosts memory

city: Palo Alto

first: Nathalie

last: Khoury

state: CA California

address: 3801 Miranda Avenue Blvd. 100 VAPA D3-111 - Neurology

institute: Stanford University

summary: We discovered “runner” plasma, collected from voluntarily running mice, infused into sedentary mice recapitulates the cellular and functional benefits of exercise on the adult brain.  Importantly, runner plasma reduces baseline neuroinflammatory gene expression and experimentally induced brain inflammation. Plasma proteomic analysis revealed a striking increase in complement cascade inhibitors including clusterin (CLU), which is facilitating the anti-inflammatory effects of runner plasma. Intravenously injected CLU strongly binds to brain endothelial cells reducing their inflammatory gene expression in an acute model of brain inflammation and in Alzheimer’s disease model mice. These findings demonstrate the existence of anti-inflammatory “exercise factors” that are transferrable, target the cerebrovasculature and benefit the brain.

overall_design: Identifying transcriptomic changes induced by exogenous clusterin on brain endothelial cells in two mouse models of acute (LPS) or chronic (APP) inflammation

first: Zurine

last: De Miguel

first: Andrew

last: Yang

first: Ryan

last: Vest

first: Davis

last: Lee


title: Intratumoral plasmid IL-12 expands CD8+ T cells and induces a CXCR3 signature in triple-negative breast tumors that sensitizes patient to anti-PD-1 therapy

city: Durham

first: Erika

last: Crosby

state: NC

address: 203 Research Dr. MSRBI Room 407

institute: DUKE UNIVERSITY MEDICAL CENTER

summary: We show that plasmid IL-12 injected intratumorally followed by co-localized electroporation induces a CXCR3 gene signature with enhanced antigen presentation, expansion, and licensing of T cells systemically. We highlight a patient that was previously non-responsive to atezolizumab and nab-paclitaxel, who demonstrated significant clinical response to nivolumab following TAVOTM therapy.

overall_design: CD45+ cells were sorted from treated murine TNBC tumors following treatment with control or IL-12 plasmid. Cells from 3 mice were pooled from each treatment and scRNAseq was performed.  Gene expression and TCR libraries were created using 10x Genomics Chromium Single Cell 5’ Library Construction Kit (v1.1).

first: Takuya

last: Osada

first: Hiroshi

last: Nagata

first: Chaitanya

last: Acharya


title: Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

summary: Adaptation and survival in response to diverse stressors involve reprogramming of mRNA translation. Although the cellular response to mild stress has been intensively studied, the response to severe stress remains unclear. We show here that under severe stress conditions, cells induce transient hibernation-like mechanisms in anticipation of recovery, which we have termed the Adaptive Pausing Response (APR). The APR is a coordinated cellular response that limits ATP supply and consumption processes via severe mitochondrial fragmentation and inhibits mRNA translation initiation by induction of ribosome pausing at translation initiation codons, respectively. During recovery from severe stress, cells exhibited adaptive ISR signaling, which permitted cell cycle progression, resumption of growth, and reversal of mitochondria fragmentation. We propose that the APR preserves vital elements of cellular function in response to severe environmental stress, and likely plays a major role in homeostasis and pathogenesis.

overall_design: Cells were treated with the appropriate stressor. Ribo-seq and corresponding RNA-seq experiments were performed.

first: Raul

last: Jobava

first: Shu-Bing

last: Qian

first: Maria

last: Hatzoglou


title: Comparative polyA+ RNA sequencing of hematopoietic stem cells from adult Osmr gene knock-out and wild-type mice

city: Brisbane

first: Jean-Pierre

last: Levesque

state: Queensland

address: 37 Kent St

department: Mater Research Institute

country: Australia

institute: Mater Research Institute-University of Queensland

summary: Germinal deletion of the Osmr gene encoding the oncostatin M receptor alpha chain enhances the mobilization of hematopoietic stem cells in response to G-CSF and clinically relevant combinations of G-CSF with CXCR4 antagonist Plerixafor or cyclophosphamide. This effect is inderectly mediated by hematopoietic stem cell niches in the bone marrow because hematopoietic cells do not express the Osmr gene whereas bone marrow endothelial cells and mesenchymal cells forming niches do. We find tha tOsmr deletion in the niche increases hematopoietic stem cells chemotaxis to CXCL12 and quiescence while decreasing E-selectin expression on bone marrow endothelial cells.

overall_design: To gain further insights on how absence of OSMR signaling in niches modulate HSC function, we sorted 1,000 lineage-negative KIT+ SCA1+ FLT3- CD48- cells, which include long-term and short-term reconstituting hematopoietic stem cells, from the bone marrow of adult naïve Osmr-/- mice and wild-type C57BL/6 control mice. PolyA+ RNA was isolated and  sequenced. Each reaction is from  1,000 cells each from a different mouse (6 WT miCe and 5 Osmr-/- mice). Subsequent gene set enrichment analysis (GSEA) on Hallmark and Gene Ontology (GO) pathways were performed and genes of interest were validated using real time quantitative PCR.

first: Kavita

last: Bisht

first: Hsu-Wen

last: Tseng


title: Physiologically-relevant Bisphenol A levels alter the developmental trajectory of an in vitro model of mouse Primordial Germ Cells

city: Los Angeles

first: Steen

middle: Kian Thye

last: Ooi

state: CA

address: 621 Charles E. Young Drive S.

department: Institute for Society and Genetics

institute: UCLA

summary:
Background: Animal-based studies indicate that Bisphenol A (BPA) exposure is detrimental to reproductive health, but its impact on the earliest stages of germ cell development remain poorly defined.
Objective: Using a murine in vitro model of early germ cell specification and differentiation, we sought to assess whether exposure to low levels of BPA prior to Primordial Germ Cell (PGC) formation alters their differentiation trajectory and unique molecular program.
Methods: We used an established method of in vitro differentiation of mouse Embryonic Stem Cells (ESCs) into Epiblast-like Cells (EpiLCs) followed by PGC-Like Cells (PGCLCs) which together recapitulates defined stages of early germ cell development. Cellular consequences were determined using hemocytometer-based cell counting, fixation and intracellular staining followed by flow cytometry/FACS on cells exposed to increasing doses of BPA. We also generated RNA-seq libraries from RNA extracted from FACS-purified PGCLCs and performed transcriptome analysis using bioinformatics-based approaches, to interrogate and characterise gene expression changes resulting from BPA exposure.
Results: Exposure of EpiLCs to BPA resulted in a dose-dependent increase in cell number, associated with an increase proportion of cells in S-phase as well as a reduced proportion undergoing apoptosis. Exposure also resulted in a greater proportion of EpiLCs showing signs of DNA damage. Remarkably, EpiLC exposure did not negatively impact PGC specification and resulted in dose-dependent increase in PGCLC proliferation. However, PGCLC transcriptome analysis revealed an aberrant program with significant deregulation of X-linked genes and retrotransposon expression. Differential gene expression analysis also revealed the deregulation of genes associated with lipid metabolism as well as deregulated expression of genes associated with later stages of gametogenesis.
Conclusions: Our findings represent the first characterisation of the consequences of early BPA exposure on a model of PGC development, highlighting altered cell behaviour and underlying pathways and molecular processes.

overall_design: EpiLC and PGCLC mRNA profiles from untreated and 100nM BPA-exposed cells

middle: K

first: Patrick

last: Allard


title: Longitudinal analysis of personal cfDNA methylome patterns in metastatic prostate cancer [plasma]

city: Dublin

first: Antoinette

last: Perry

address: Science West, University College Dublin, Belfield, Dublin, Ireland

country: Ireland

institute: University College Dublin

summary: Disease progression and therapeutic resistance are hallmarks of advanced stage prostate cancer (PCa), which remains a major cause of cancer-related mortality around the world. Longitudinal studies, coupled with the use of liquid biopsies, offer a potentially new and minimally invasive platform to study the dynamics of tumour progression. Our study aimed to investigate the dynamics of personal methylomic profiles of metastatic PCa (mPCa) patients, during disease progression and therapy administration. 52 plasma samples from 9 patients with mPCa were collected, longitudinally, over 13-21 months. After cell-free DNA (cfDNA) isolation, DNA methylation was profiled using the Infinium MethylationEPIC BeadChip and analysed using the minfi software. The top 5% most variable probes across time, within each individual, were utilised to study dynamic methylation patterns during disease progression and therapeutic response. Statistical testing was carried out to identify and validate ctDNA differentially methylated genes (DMGs). Personal cfDNA global methylation patterns were temporally stable throughout disease course. A proportion of analysed CpG sites presented a dynamic temporal pattern that was consistent with clinical events, such as therapy administration, and were prominently associated with immune response pathways. Study of ctDNA identified >2,000 DMGs with dynamic methylation patterns. We concluded that longitudinal assessment of cfDNA methylation in mPCa patients unveiled dynamic patterns associated with the occurrence of specific clinical events, thus highlighting the potential of using liquid biopsies to study PCa progression.

overall_design: cfDNA samples were collected, longitudinally, from 9 mPCa patients. DNA was isolated and methylation was measured using the Illumina Infinium Human MethylationEPIC BeadChip. Normalized beta-values were used to compare methylation patterns, within each individual, during disease progression.

first: R

last: Silva

first: A


title: Transcriptomic analyses of high-grade neuroendocrine carcinoma of gynecologic origin

city: Cleveland

first: Ata

last: Abbas

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

country: USA

institute: Case Western Reserve University

summary: High-grade neuroendocrine carcinomas (NECs) of the cervix are rare, aggressive cancers accounting for about 1-1.5% of all cervical cancer. The 5-year survival is up to 36% for early-stage disease; however, the advanced-stage disease has <10% survival, with relapse rates exceeding 90%. These cancers are likely to have a vascular invasion and nodal or visceral metastasis. Unfortunately, NEC of the cervix affects young women with a median age of 37. High-grade NECs of other gynecologic origins are even rarer, share similar aggressive behavior and poor outcomes. We performed stranded paired-end RNA-seq of 13 samples, including 12 samples with matched whole exome sequencing (WES) data. Sites of origin for tumors in our cohort were the cervix (69%), ovary (19%), and endometrium (12%). The median number of prior lines of therapy was 1. Median PFS and OS were 1 and 12 months, respectively, indicating their highly lethal nature. Comparing transcriptomic profiles with TCGA cervical and ovarian cancers, chromatin assembly and nucleosome organization were the top GO functions for significantly over-expressed genes in our cohort. Remarkably, under-expressed genes in our cohort were enriched for protein modification and catabolic processes, and neutrophil-mediated immunity. Compared to small cell lung cancer (SCLC), our cohort showed highly distinct transcriptomic patterns, and represented the YAP1 high molecular subtype.

overall_design: We performed stranded paired-end RNA-seq of 13 FFPE tumor samples.

first: Haider

last: Mahdi


title: Dickkopf-2 regulates stemness and differentiation of colorectal cancer cells via c-Src and HNF4α1

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

institute: Korea University College of Medicine

summary: Metastasis is the leading cause of cancer-related mortality. Cancer stem cells contribute to metastasis in the murine colon cancer models, but the underlying mechanisms are unclear. Here we report a Wnt ligand, Dickkopf2 (DKK2) is essential for colorectal cancer stemness. Genetic depletion of Dkk2 in intestinal epithelial or stem cells reduced tumorigenesis as well as expression of the stem cell marker gene Lgr5 in a model of colitis-associated cancer. Mechanistically, DKK2 activates c-Src followed by increased LGR5 expressing stem cells in colorectal cancer through degradation of HNF4α1. Splenic injection of DKK2-deficient cancer organoids into C57BL/6 mice resulted in a significant reduction of liver metastases compared to the control cancer organoids in spite of the presence of oncogenic mutations in Apc, Kras and Tp53 genes. These findings suggest that DKK2 is required for stemness of colorectal cancer cells, which in turn contributes to metastasis.

overall_design: Single cell RNA sequencing analyses of liver metastasized colon tumor cells in mice in the presence or absence of DKK2

first: Jae

middle: H

last: Shin

first: Alfred

last: Bothwell